pubmed: gonzález-candelas f

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  • Identification of a large, fast-expanding HIV-1 subtype B transmission cluster among MSM in Valencia, Spain.
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    Identification of a large, fast-expanding HIV-1 subtype B transmission cluster among MSM in Valencia, Spain.

    PLoS One. 2017;12(2):e0171062

    Authors: Patiño-Galindo JÁ, Torres-Puente M, Bracho MA, Alastrué I, Juan A, Navarro D, Galindo MJ, Gimeno C, Ortega E, González-Candelas F

    Abstract
    We describe and characterize an exceptionally large HIV-1 subtype B transmission cluster occurring in the Comunidad Valenciana (CV, Spain). A total of 1806 HIV-1 protease-reverse transcriptase (PR/RT) sequences from different patients were obtained in the CV between 2004 and 2014. After subtyping and generating a phylogenetic tree with additional HIV-1 subtype B sequences, a very large transmission cluster which included almost exclusively sequences from the CV was detected (n = 143 patients). This cluster was then validated and characterized with further maximum-likelihood phylogenetic analyses and Bayesian coalescent reconstructions. With these analyses, the CV cluster was delimited to 113 patients, predominately men who have sex with men (MSM). Although it was significantly located in the city of Valencia (n = 105), phylogenetic analyses suggested this cluster derives from a larger HIV lineage affecting other Spanish localities (n = 194). Coalescent analyses estimated its expansion in Valencia to have started between 1998 and 2004. From 2004 to 2009, members of this cluster represented only 1.46% of the HIV-1 subtype B samples studied in Valencia (n = 5/143), whereas from 2010 onwards its prevalence raised to 12.64% (n = 100/791). In conclusion, we have detected a very large transmission cluster in the CV where it has experienced a very fast growth in the recent years in the city of Valencia, thus contributing significantly to the HIV epidemic in this locality. Its transmission efficiency evidences shortcomings in HIV control measures in Spain and particularly in Valencia.

    PMID: 28152089 [PubMed - in process]




  • Comparative analysis of variation and selection in the HCV genome.
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    Comparative analysis of variation and selection in the HCV genome.

    Infect Genet Evol. 2017 Jan 10;49:104-110

    Authors: Patiño-Galindo JÁ, González-Candelas F

    Abstract
    Genotype 1 of the hepatitis C virus (HCV) is the most prevalent of the variants of this virus. Its two main subtypes, HCV-1a and HCV-1b, are associated to differences in epidemic features and risk groups, despite sharing similar features in most biological properties. We have analyzed the impact of positive selection on the evolution of these variants using complete genome coding regions, and compared the levels of genetic variability and the distribution of positively selected sites. We have also compared the distributions of positively selected and conserved sites considering different factors such as RNA secondary structure, the presence of different epitopes (antibody, CD4 and CD8), and secondary protein structure. <10% of the genome was found to be under positive selection, and purifying selection was the main evolutionary process acting in both subtypes. We found differences in the number of positively selected sites between subtypes in several genes (Core, HVR2 in E2, P7, helicase in NS3 and NS4a). Heterozygosity values in positively selected sites and the rate of non-synonymous substitutions were significantly higher in subtype HCV-1b. Logistic regression analyses revealed that similar selective forces act at the genome level in both subtypes: RNA secondary structure and CD4 T-cell epitopes are associated with conserved sites, while CD8 T-cell epitopes are associated with positive selection in both subtypes. These results indicate that similar selective constraints are acting along HCV-1a and HCV-1 b genomes, despite some differences in the distribution of positively selected sites at independent genes.

    PMID: 28087495 [PubMed - as supplied by publisher]




  • EvalMSA: A Program to Evaluate Multiple Sequence Alignments and Detect Outliers.
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    EvalMSA: A Program to Evaluate Multiple Sequence Alignments and Detect Outliers.

    Evol Bioinform Online. 2016;12:277-284

    Authors: Chiner-Oms A, González-Candelas F

    Abstract
    We present EvalMSA, a software tool for evaluating and detecting outliers in multiple sequence alignments (MSAs). This tool allows the identification of divergent sequences in MSAs by scoring the contribution of each row in the alignment to its quality using a sum-of-pair-based method and additional analyses. Our main goal is to provide users with objective data in order to take informed decisions about the relevance and/or pertinence of including/retaining a particular sequence in an MSA. EvalMSA is written in standard Perl and also uses some routines from the statistical language R. Therefore, it is necessary to install the R-base package in order to get full functionality. Binary packages are freely available from http://sourceforge.net/projects/evalmsa/for Linux and Windows.

    PMID: 27920488 [PubMed - in process]




  • Origin of modern syphilis and emergence of a pandemic Treponema pallidum cluster.
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    Origin of modern syphilis and emergence of a pandemic Treponema pallidum cluster.

    Nat Microbiol. 2016 Dec 05;2:16245

    Authors: Arora N, Schuenemann VJ, Jäger G, Peltzer A, Seitz A, Herbig A, Strouhal M, Grillová L, Sánchez-Busó L, Kühnert D, Bos KI, Davis LR, Mikalová L, Bruisten S, Komericki P, French P, Grant PR, Pando MA, Vaulet LG, Fermepin MR, Martinez A, Centurion Lara A, Giacani L, Norris SJ, Šmajs D, Bosshard PP, González-Candelas F, Nieselt K, Krause J, Bagheri HC

    Abstract
    The abrupt onslaught of the syphilis pandemic that started in the late fifteenth century established this devastating infectious disease as one of the most feared in human history(1). Surprisingly, despite the availability of effective antibiotic treatment since the mid-twentieth century, this bacterial infection, which is caused by Treponema pallidum subsp. pallidum (TPA), has been re-emerging globally in the last few decades with an estimated 10.6 million cases in 2008 (ref. 2). Although resistance to penicillin has not yet been identified, an increasing number of strains fail to respond to the second-line antibiotic azithromycin(3). Little is known about the genetic patterns in current infections or the evolutionary origins of the disease due to the low quantities of treponemal DNA in clinical samples and difficulties in cultivating the pathogen(4). Here, we used DNA capture and whole-genome sequencing to successfully interrogate genome-wide variation from syphilis patient specimens, combined with laboratory samples of TPA and two other subspecies. Phylogenetic comparisons based on the sequenced genomes indicate that the TPA strains examined share a common ancestor after the fifteenth century, within the early modern era. Moreover, most contemporary strains are azithromycin-resistant and are members of a globally dominant cluster, named here as SS14-Ω. The cluster diversified from a common ancestor in the mid-twentieth century subsequent to the discovery of antibiotics. Its recent phylogenetic divergence and global presence point to the emergence of a pandemic strain cluster.

    PMID: 27918528 [PubMed - in process]




  • Effect of Occupational Exposure on A(H1N1)pdm09 Infection and Hospitalization.
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    Effect of Occupational Exposure on A(H1N1)pdm09 Infection and Hospitalization.

    Ann Occup Hyg. 2016 Oct;60(8):1009-19

    Authors: Pujol J, Godoy P, Soldevila N, Castilla J, González-Candelas F, Mayoral JM, Astray J, García S, Martín V, Tamames S, Delgado M, García ÁD, CIBERESP Cases and Controls in Pandemic Influenza Working Group

    Abstract
    OBJECTIVE: To analyze relationships between occupational exposure and influenza infection and hospitalization during the 2009-2010 pandemic wave and the 2010-2011 influenza seasonal epidemic in Spain.
    METHODS: Occupations were classified as high, medium, or low risk of influenza exposure. To assess the risk of infection, 588 outpatient cases of influenza confirmed by reverse-transcription polymerase-chain-reaction (RT-PCR) were compared with 588 outpatients without influenza symptoms. To assess the risk of hospitalization, 337 outpatient influenza cases were compared with 337 inpatient influenza cases.
    RESULTS: The high risk of occupational exposure group was composed only of health care workers. After adjustment for age, sex, vaccination status, and predictive variables of influenza infection, patients with a high risk of occupational exposure had an aOR of 2.14 (95%CI: 1.25-3.66) of being an outpatient influenza case and an aOR of 0.43 (95%CI: 0.20-0.95) of being an inpatient influenza case, compared with those with a low risk.
    CONCLUSIONS: A high risk of occupational exposure is a risk factor for influenza infection but not for hospitalization.

    PMID: 27432191 [PubMed - in process]




  • Smoking may increase the risk of hospitalization due to influenza.
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    Smoking may increase the risk of hospitalization due to influenza.

    Eur J Public Health. 2016 Oct;26(5):882-887

    Authors: Godoy P, Castilla J, Mayoral JM, Delgado-Rodríguez M, Martín V, Astray J, Soldevila N, González-Candelas F, Castro A, Baricot M, Tamames S, Alonso J, Galán JC, Quintana JM, Pumarola T, Domínguez A, and the CIBERESP Cases and Controls in Pandemic Influenza Working Group, Spain

    Abstract
    BACKGROUND: Smoking may facilitate influenza virus infections and their severity. The objective was to investigate the risk of hospitalization due to influenza in Spanish smokers and ex-smokers.
    METHODS: We carried out a multicentre, case-control study in 2011. Cases [patients ≥ 18 years hospitalized > 24 h with real time polymerase chain reaction (RT-PCR)-confirmed influenza] were selected from 29 Spanish hospitals. For each case, we selected an outpatient aged ≥ 18 years with RT-PCR-confirmed influenza matched by age (±5 years), date of hospitalization of the case (±10 days) and province of residence. We collected epidemiological variables, comorbidities and the smoking history. The risk of hospitalization due to smoking was determined by the adjusted odds ratio (aOR) using logistic regression.
    RESULTS: We studied 471 hospitalized cases and 476 outpatient cases. Hospitalized cases had a higher frequency of influenza risk factors compared with outpatient cases. Hospitalized cases had a higher frequency of smoking (30.9% vs. 17.1%) and being ex-smokers (29.3% vs. 25.3%). Current smoking (aOR = 2.18, 95% CI: 1.23-3.87) and being an ex-smoker (aOR = 1.73, 95% CI: 1.07-2.82) were associated with the risk of hospitalization.
    CONCLUSIONS: Smoking may increase the risk of hospitalization in smokers and ex-smokers when infected by the influenza virus. Smoking prevention could reduce hospitalizations. Influenza vaccination is recommended for smokers.

    PMID: 27085194 [PubMed - in process]




  • Transmission dynamics of HIV-1 subtype B in the Basque Country, Spain.
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    Transmission dynamics of HIV-1 subtype B in the Basque Country, Spain.

    Infect Genet Evol. 2016 Jun;40:91-7

    Authors: Patiño-Galindo JA, Thomson MM, Pérez-Álvarez L, Delgado E, Cuevas MT, Fernández-García A, Nájera R, Iribarren JA, Cilla G, López-Soria L, Lezaun MJ, Cisterna R, González-Candelas F, Group of HIV-1 Antiretroviral Resistance Studies in the Basque Country

    Abstract
    This work was aimed to study the HIV-1 subtype B epidemics in the Basque Country, Spain. 1727 HIV-1 subtype B sequences comprising protease and reverse transcriptase (PR/RT) coding regions, sampled between 2001 and 2008, were analyzed. 156 transmission clusters were detected by means of phylogenetic analyses. Most of them comprised less than 4 individuals and, in total, they included 441 patients. Six clusters comprised 10 or more patients and were further analyzed in order to study their origin and diversification. Four clusters included men who had unprotected homosexual sex (MSM), one group was formed by intravenous drug users (IDUs), and another included both IDUs and people infected through unprotected heterosexual sex (HTs). Most of these clusters originated from the mid-1980s to the mid-1990s. Only one cluster, formed by MSM, originated after 2000. The time between infections was significantly lower in MSM groups than in those containing IDUs (P-value <0.0001). Nucleoside RT and non-nucleoside RT inhibitor (NRTI and NNRTI)-resistance mutations to antiretroviral treatment were found in these six clusters except the most recent MSM group, but only the IDU clusters presented protease inhibitor (PI)-resistance mutations. The most prevalent mutations for each inhibitor class were PI L90M, NRTI T215D/Y/F, and NNRTI K103N, which were also among the most prevalent resistant variants in the whole dataset. In conclusion, while most infections occur as isolated introductions into the population, the number of infections found to be epidemiologically related within the Basque Country is significant. Public health control measures should be reinforced to prevent the further expansion of transmission clusters and resistant mutations occurring within them.

    PMID: 26921800 [PubMed - in process]




  • Comprehensive Screening for Naturally Occurring Hepatitis C Virus Resistance to Direct-Acting Antivirals in the NS3, NS5A, and NS5B Genes in Worldwide Isolates of Viral Genotypes 1 to 6.
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    Comprehensive Screening for Naturally Occurring Hepatitis C Virus Resistance to Direct-Acting Antivirals in the NS3, NS5A, and NS5B Genes in Worldwide Isolates of Viral Genotypes 1 to 6.

    Antimicrob Agents Chemother. 2016 Apr;60(4):2402-16

    Authors: Patiño-Galindo JÁ, Salvatierra K, González-Candelas F, López-Labrador FX

    Abstract
    There is no comprehensive study available on the natural hepatitis C virus (HCV) polymorphism in sites associated with resistance including all viral genotypes which may present variable susceptibilities to particular direct-acting antivirals (DAAs). This study aimed to analyze the frequencies, genetic barriers, and evolutionary histories of naturally occurring resistance-associated variants (RAVs) in the six main HCV genotypes. A comprehensive analysis of up to 103 RAVs was performed in 2,901, 2,216, and 1,344 HCV isolates for the NS3, NS5A, and NS5B genes, respectively. We report significant intergenotypic differences in the frequencies of natural RAVs for these three HCV genes. In addition, we found a low genetic barrier for the generation of new RAVs, irrespective of the viral genotype. Furthermore, in 1,126 HCV genomes, including sequences spanning the three genes, haplotype analysis revealed a remarkably high frequency of viruses carrying more than one natural RAV to DAAs (53% of HCV-1a, 28.5% of HCV-1b, 67.1% of HCV-6, and 100% of genotype 2, 3, 4, and 5 haplotypes). With the exception of HCV-1a, the most prevalent haplotypes showed RAVs in at least two different viral genes. Finally, evolutionary analyses revealed that, while most natural RAVs appeared recently, others have been efficiently transmitted over time and cluster in well-supported clades. In summary, and despite the observed high efficacy of DAA-based regimens, we show that naturally occurring RAVs are common in all HCV genotypes and that there is an overall low genetic barrier for the selection of resistance mutations. There is a need for natural DAA resistance profiling specific for each HCV genotype.

    PMID: 26856832 [PubMed - indexed for MEDLINE]




  • Genomic Investigation of a Legionellosis Outbreak in a Persistently Colonized Hotel.
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    Genomic Investigation of a Legionellosis Outbreak in a Persistently Colonized Hotel.

    Front Microbiol. 2015;6:1556

    Authors: Sánchez-Busó L, Guiral S, Crespi S, Moya V, Camaró ML, Olmos MP, Adrián F, Morera V, González-Morán F, Vanaclocha H, González-Candelas F

    Abstract
    OBJECTIVES: A long-lasting legionellosis outbreak was reported between November 2011 and July 2012 in a hotel in Calpe (Spain) affecting 44 patients including six deaths. Intensive epidemiological and microbiological investigations were performed in order to detect the reservoirs.
    METHODS: Clinical and environmental samples were tested for the presence and genetic characterization of Legionella pneumophila. Six of the isolates were subjected to whole-genome sequencing.
    RESULTS: Sequencing of 14 clinical and 260 environmental samples revealed sequence type (ST) 23 as the main responsible strain for the infections. This ST was found in the spa pool, from where it spread to other hotel public spaces, explaining the ST23 clinical cases, including guests who had not visited the spa. Uncultured clinical specimens showed profiles compatible with ST23, ST578, and mixed patterns. Profiles compatible with ST578 were obtained by direct sequencing from biofilm samples collected from the domestic water system, which provided evidence for the source of infection for non ST23 patients. Whole genome data from five ST23 strains and the identification of different STs and Legionella species showed that different hotel premises were likely colonized since the hotel opening thus explaining how different patients had been infected by distinct STs.
    CONCLUSIONS: Both epidemiological and molecular data are essential in the investigation of legionellosis outbreaks. Whole-genome sequencing data revealed significant intra-ST variability and allowed to make further inference on the short-term evolution of a local colonization of L. pneumophila.

    PMID: 26834713 [PubMed]




  • Comparison of body mass index (BMI) with the CUN-BAE body adiposity estimator in the prediction of hypertension and type 2 diabetes.
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    Comparison of body mass index (BMI) with the CUN-BAE body adiposity estimator in the prediction of hypertension and type 2 diabetes.

    BMC Public Health. 2016 Jan 27;16:82

    Authors: Martín V, Dávila-Batista V, Castilla J, Godoy P, Delgado-Rodríguez M, Soldevila N, Molina AJ, Fernandez-Villa T, Astray J, Castro A, González-Candelas F, Mayoral JM, Quintana JM, Domínguez A, CIBERESP Cases and Controls in Pandemic Influenza Working Group, Spain

    Abstract
    BACKGROUND: Obesity is a world-wide epidemic whose prevalence is underestimated by BMI measurements, but CUN-BAE (Clínica Universidad de Navarra - Body Adiposity Estimator) estimates the percentage of body fat (BF) while incorporating information on sex and age, thus giving a better match. Our aim is to compare the BMI and CUN-BAE in determining the population attributable fraction (AFp) for obesity as a cause of chronic diseases.
    METHODS: We calculated the Pearson correlation coefficient between BMI and CUN-BAE, the Kappa index and the internal validity of the BMI. The risks of arterial hypertension (AHT) and diabetes mellitus (DM) and the AFp for obesity were assessed using both the BMI and CUN-BAE.
    RESULTS: 3888 white subjects were investigated. The overall correlation between BMI and CUN-BAE was R(2) = 0.48, which improved when sex and age were taken into account (R(2) > 0.90). The Kappa coefficient for diagnosis of obesity was low (28.7 %). The AFp was 50 % higher for DM and double for AHT when CUN-BAE was used.
    CONCLUSIONS: The overall correlation between BMI and CUN-BAE was not good. The AFp of obesity for AHT and DM may be underestimated if assessed using the BMI, as may the prevalence of obesity when estimated from the percentage of BF.

    PMID: 26817835 [PubMed - indexed for MEDLINE]




  • High Body Mass Index as a Risk Factor for Hospitalization Due to Influenza: A Case-Control Study.
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    High Body Mass Index as a Risk Factor for Hospitalization Due to Influenza: A Case-Control Study.

    Arch Bronconeumol. 2016 Jun;52(6):299-307

    Authors: Martín V, Castilla J, Godoy P, Delgado-Rodríguez M, Soldevila N, Fernández-Villa T, Molina AJ, Astray J, Castro A, González-Candelas F, Mayoral JM, Quintana JM, Domínguez Á, Grupo de Trabajo del Proyecto CIBERESP de Casos y Controles sobre la Gripe Pandémica, España

    Abstract
    INTRODUCTION: Obesity has emerged as a significant independent predictor of severity in pandemic influenzaA (H1N1)pdm09. The aim of this study was to investigate the association between body mass index (BMI) and the risk of hospitalization due to influenza.
    METHODS: Hospitalized patients (n=755) with laboratory-confirmed influenza were individually matched by age, admission/visit date, and province with an outpatient (n=783) with laboratory-confirmed influenza and an outpatient control (n=950). We compared the BMI using conditional logistic regression adjusted for potential confounding factors (aOR). The population attributable fraction (PAF) was calculated.
    RESULTS: A higher BMI was associated with an increased risk of hospitalization compared to both outpatient cases (aOR=1.11; 95%CI: 1.07-1.16) and outpatient controls (aOR=1.04; 95%CI: 1.01-1.07). Compared with normal weight, obesity type I, obesity type II and obesity type III was associated with a greater likelihood of hospitalization compared with outpatient cases (aOR=1.85, 95%CI: 1.05-3.26; aOR=5.24, 95%CI: 1.94-14.15 and aOR=44.38, 95%CI: 4.47-440.5). Compared with normal weight, obesity type II and obesity type III was associated with a greater likelihood of hospitalization compared with outpatient controls (aOR=4.37, 95%CI: 1.79-10.69 and aOR=4.95, 95%CI: 1.45-16.87). In persons without influenza vaccination, all categories of BMI≥30kg/m(2) were associated with a greater likelihood of hospitalization compared with normal weight in both outpatient cases and outpatient controls. The PAF of hospitalization by influenza due to BMI ranged from 21.9% to 8.5%; in the case of unvaccinated against influenza between 20.5% to 16.9%.
    CONCLUSION: A high BMI is associated with an increased risk of hospitalization due to influenza. High percentage of hospital admissions are attributable to their BMI, especially in non vaccinated.

    PMID: 26809749 [PubMed - in process]




  • Transmission of human immunodeficiency virus Type-1 by fresh-frozen plasma treated with methylene blue and light.
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    Transmission of human immunodeficiency virus Type-1 by fresh-frozen plasma treated with methylene blue and light.

    Transfusion. 2016 Apr;56(4):831-6

    Authors: Álvarez M, Luis-Hidalgo M, Bracho MA, Blanquer A, Larrea L, Villalba J, Puig N, Planelles D, Montoro J, González-Candelas F, Roig R

    Abstract
    BACKGROUND: The risk of transfusion-transmitted infection (TTI) has been minimized by introduction of nucleic acid testing (NAT) and pathogen inactivation (PI). This case report describes transmission of human immunodeficiency virus Type 1 (HIV-1) to two recipients despite these measures.
    STUDY DESIGN AND METHODS: In March 2009 a possible TTI of HIV-1 was identified in a patient that had received pooled buffy coat platelet concentrate (BC-PLT) in November 2005. The subsequent lookback study found two more patients who had received methylene blue (MB)-treated fresh-frozen plasma (FFP) and red blood cells (RBCs) from the same donation. In November 2005 the donor had tested negative for both HIV antibodies and HIV-1 RNA by 44 minipool (44 MP) NAT. Repository samples of this donation and samples from the recipients were used for viral load (VL) and sequence analysis.
    RESULTS: HIV-1 RNA was detectable by individual donation (ID)-NAT in the repository sample from the 2005 window period donation and a VL of 135 copies/mL was measured. HIV-1 infection was confirmed in both recipients of both BC-PLT (65 mL of plasma) and MB-FFP (261 mL of plasma), but not in the patient that had received 4-week-old RBCs (20 mL of plasma). The sequence analysis revealed a close phylogenetic relationship between the virus strains isolated from the donor and recipients, compatible with TTI.
    CONCLUSIONS: Approximately 17,600 and 4400 virions in the MB-FFP and BC-PLT were infectious, but 1350 virions in the RBCs were not. ID-NAT would have prevented this transmission, but the combination of MP-NAT and MB-PI did not.

    PMID: 26585542 [PubMed - indexed for MEDLINE]




  • Correction: No Major Host Genetic Risk Factor Contributed to A(H1N1)2009 Influenza Severity.
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    Correction: No Major Host Genetic Risk Factor Contributed to A(H1N1)2009 Influenza Severity.

    PLoS One. 2015;10(10):e0141661

    Authors: Garcia-Etxebarria K, Bracho MA, Galán JC, Pumarola T, Castilla J, Ortiz de Lejarazu R, Rodríguez-Dominguez M, Quintela I, Bonet N, Garcia-Garcerà M, Domínguez A, González-Candelas F, Calafell F, CIBERESP Cases, Controls in Pandemic Influenza Working Group

    PMID: 26517267 [PubMed]




  • No Major Host Genetic Risk Factor Contributed to A(H1N1)2009 Influenza Severity.
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    No Major Host Genetic Risk Factor Contributed to A(H1N1)2009 Influenza Severity.

    PLoS One. 2015;10(9):e0135983

    Authors: Garcia-Etxebarria K, Bracho MA, Galán JC, Pumarola T, Castilla J, Ortiz de Lejarazu R, Rodríguez-Dominguez M, Quintela I, Bonet N, Garcia-Garcerà M, Domínguez A, González-Candelas F, Calafell F, CIBERESP Cases and Controls in Pandemic Influenza Working Group

    Abstract
    While most patients affected by the influenza A(H1N1) pandemic experienced mild symptoms, a small fraction required hospitalization, often without concomitant factors that could explain such a severe course. We hypothesize that host genetic factors could contribute to aggravate the disease. To test this hypothesis, we compared the allele frequencies of 547,296 genome-wide single nucleotide polymorphisms (SNPs) between 49 severe and 107 mild confirmed influenza A cases, as well as against a general population sample of 549 individuals. When comparing severe vs. mild influenza A cases, only one SNP was close to the conventional p = 5×10-8. This SNP, rs28454025, sits in an intron of the GSK233 gene, which is involved in a neural development, but seems not to have any connections with immunological or inflammatory functions. Indirectly, a previous association reported with CD55 was replicated. Although sample sizes are low, we show that the statistical power in our design was sufficient to detect highly-penetrant, quasi-Mendelian genetic factors. Hence, and assuming that rs28454025 is likely to be a false positive, no major genetic factor was detected that could explain poor influenza A course.

    PMID: 26379185 [PubMed - indexed for MEDLINE]




  • Social class based on occupation is associated with hospitalization for A(H1N1)pdm09 infection. Comparison between hospitalized and ambulatory cases.
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    Social class based on occupation is associated with hospitalization for A(H1N1)pdm09 infection. Comparison between hospitalized and ambulatory cases.

    Epidemiol Infect. 2016 Mar;144(4):732-40

    Authors: Pujol J, Godoy P, Soldevila N, Castilla J, González-Candelas F, Mayoral JM, Astray J, Garcia S, Martin V, Tamames S, Delgado M, Domínguez A, CIBERESP Cases and Controls in Pandemic Influenza Working Group

    Abstract
    This study aimed to analyse the existence of an association between social class (categorized by type of occupation) and the occurrence of A(H1N1)pmd09 infection and hospitalization for two seasons (2009-2010 and 2010-2011). This multicentre study compared ambulatory A(H1N1)pmd09 confirmed cases with ambulatory controls to measure risk of infection, and with hospitalized A(H1N1)pmd09 confirmed cases to asses hospitalization risk. Study variables were: age, marital status, tobacco and alcohol use, pregnancy, chronic obstructive pulmonary disease, chronic respiratory failure, cardiovascular disease, diabetes, chronic liver disease, body mass index >40, systemic corticosteroid treatment and influenza vaccination status. Occupation was registered literally and coded into manual and non-manual worker occupational social class groups. A conditional logistic regression analysis was performed. There were 720 hospitalized cases, 996 ambulatory cases and 1062 ambulatory controls included in the study. No relationship between occupational social class and A(H1N1)pmd09 infection was found [adjusted odds ratio (aOR) 0·97, 95% confidence interval (CI) 0·74-1·27], but an association (aOR 1·53, 95% CI 1·01-2·31) between occupational class and hospitalization for A(H1N1)pmd09 was observed. Influenza vaccination was a protective factor for A(H1N1)pmd09 infection (aOR 0·41, 95% CI 0·23-0·73) but not for hospitalization. We conclude that manual workers have the highest risk of hospitalization when infected by influenza than other occupations but they do not have a different probability of being infected by influenza.

    PMID: 26271901 [PubMed - indexed for MEDLINE]




  • Geographical and Temporal Structures of Legionella pneumophila Sequence Types in Comunitat Valenciana (Spain), 1998 to 2013.
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    Geographical and Temporal Structures of Legionella pneumophila Sequence Types in Comunitat Valenciana (Spain), 1998 to 2013.

    Appl Environ Microbiol. 2015 Oct;81(20):7106-13

    Authors: Sánchez-Busó L, Coscollà M, Palero F, Camaró ML, Gimeno A, Moreno P, Escribano I, López Perezagua MM, Colomina J, Vanaclocha H, González-Candelas F

    Abstract
    Legionella pneumophila is an accidental human pathogen associated with aerosol formation in water-related sources. High recombination rates make Legionella populations genetically diverse, and nearly 2,000 different sequence types (STs) have been described to date for this environmental pathogen. The spatial distribution of STs is extremely heterogeneous, with some variants being present worldwide and others being detected at only a local scale. Similarly, some STs have been associated with disease outbreaks, such as ST578 or ST23. Spain is among the European countries with the highest incidences of reported legionellosis cases, and specifically, Comunitat Valenciana (CV) is the second most affected area in the country. In this work, we aimed at studying the overall diversity of Legionella pneumophila populations found in the period from 1998 to 2013 in 79 localities encompassing 23 regions within CV. To do so, we performed sequence-based typing (SBT) on 1,088 L. pneumophila strains detected in the area from both environmental and clinical sources. A comparison with the genetic structuring detected in a global data set that included 20 European and 7 non-European countries was performed. Our results reveal a level of diversity in CV that can be considered representative of the diversity found in other countries worldwide.

    PMID: 26231651 [PubMed - indexed for MEDLINE]




  • Expansion of the CRF19_cpx Variant in Spain.
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    Expansion of the CRF19_cpx Variant in Spain.

    J Clin Virol. 2015 Aug;69:146-9

    Authors: Patiño Galindo JA, Torres-Puente M, Gimeno C, Ortega E, Navarro D, Galindo MJ, Navarro L, Navarro V, Juan A, Belda J, Bracho MA, González-Candelas F, CRIVIH

    Abstract
    BACKGROUND: HIV-1 CRF19_cpx, is a recombinant variant found almost exclusively in Cuba and recently associated to a faster AIDS onset. Infection with this variant leads to higher viral loads and levels of RANTES and CXCR4 co-receptor use.
    OBJECTIVES: The goal of this study was to assess the presence of CRF19_cpx in the Spanish province of Valencia, given its high pathogenicity.
    STUDY DESIGN: 1294 HIV-1 protease-reverse transcriptase (PR/RT) sequences were obtained in Valencia (Spain), between 2005 and 2014. After subtyping, the detected CRF19_cpx sequences were aligned with 201 CRF19_cpx and 66 subtype D sequences retrieved from LANL, and subjected to maximum-likelihood phylogenetic analyses and Bayesian coalescent reconstructions. The presence of resistance mutations in the PR/RT region of these sequences was also analyzed.
    RESULTS: Among the 9 CRF19_cpx sequences from different patients found (prevalence <0.1%), 7 grouped in two well-supported clades (groups A, n=4, and B, n=3), suggesting the existence of at least two independent introductions which subsequently started to expand in the studied Spanish region. Unprotected sex between men was the only known transmission route. Coalescent analyses suggested that the introductions in Valencia occurred between 2008 and 2010. Resistance mutations in the RT region were found in all sequences from group A (V139D) and in two sequences from group B (E138A).
    CONCLUSIONS: This study reports for the first time the recent expansion of CRF19_cpx outside Cuba. Our results suggest that CRF19_cpx might become an emerging HIV variant in Spain, affecting Spanish native MSM and not only Cuban migrants.

    PMID: 26209397 [PubMed - indexed for MEDLINE]




  • Influenza vaccination of primary healthcare physicians may be associated with vaccination in their patients: a vaccination coverage study.
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    Influenza vaccination of primary healthcare physicians may be associated with vaccination in their patients: a vaccination coverage study.

    BMC Fam Pract. 2015 Mar 31;16:44

    Authors: Godoy P, Castilla J, Mayoral JM, Martín V, Astray J, Torner N, Toledo D, Soldevila N, González-Candelas F, García S, Diaz-Borrego J, Tamames S, Domínguez A, Working Group for the Survey on Influenza Vaccination in Primary Health Care Professionals

    Abstract
    BACKGROUND: To assess the contribution of physician-related factors, especially their influenza vaccine status, in the vaccination coverage of their patients.
    METHODS: A study of vaccination coverage was carried out in Spain in 2011-12. The dependent variable (vaccination coverage in patients aged ≥ 65 years) was obtained from regional records. Information was gathered on the vaccination of physicians through an anonymous web survey. We compared the vaccination coverage of patients with the vaccination of their physicians using the Student t test. Associations were determined using a multilevel regression model.
    RESULTS: The coverage in patients aged ≥ 65 years was 56.3% and was higher (57.3%) in patients whose physician had been vaccinated than in those whose physician had not (55.2%) (p = 0.008). In the multilevel regression model, vaccination of the physician was associated (p = 0.049) with vaccination of their patients after controlling for the effects of age (p = 0.046), region (p = 0.089), and opinions on the effectiveness of the vaccine (p = 0.013).
    CONCLUSIONS: Vaccination of physicians together with their opinions on the effectiveness of the vaccine may be a predictor of vaccination coverage in their patients. Further studies are required to confirm this.

    PMID: 25880501 [PubMed - indexed for MEDLINE]




  • A novel approach to identify candidate prognostic factors for hepatitis C treatment response integrating clinical and viral genetic data.
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    A novel approach to identify candidate prognostic factors for hepatitis C treatment response integrating clinical and viral genetic data.

    Evol Bioinform Online. 2015;11:15-24

    Authors: Amadoz A, González-Candelas F

    Abstract
    The combined therapy of pegylated interferon (IFN) plus ribavirin (RBV) has been for a long time the standard treatment for patients infected with hepatitis C virus (HCV). In the case of genotype 1, only 38%-48% of patients have a positive response to the combined treatment. In previous studies, viral genetic information has been occasionally included as a predictor. Here, we consider viral genetic variation in addition to 11 clinical and 19 viral populations and evolutionary parameters to identify candidate baseline prognostic factors that could be involved in the treatment outcome. We obtained potential prognostic models for HCV subtypes la and lb in combination as well as separately. We also found that viral genetic information is relevant for the combined treatment assessment of patients, as the potential prognostic model of joint subtypes includes 9 viral-related variables out of 11. Our proposed methodology fully characterizes viral genetic information and finds a combination of positions that modulate inter-patient variability.

    PMID: 25780333 [PubMed]




  • Comparative genomic and phylogenetic analyses of Gammaproteobacterial glg genes traced the origin of the Escherichia coli glycogen glgBXCAP operon to the last common ancestor of the sister orders Enterobacteriales and Pasteurellales.
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    Comparative genomic and phylogenetic analyses of Gammaproteobacterial glg genes traced the origin of the Escherichia coli glycogen glgBXCAP operon to the last common ancestor of the sister orders Enterobacteriales and Pasteurellales.

    PLoS One. 2015;10(1):e0115516

    Authors: Almagro G, Viale AM, Montero M, Rahimpour M, Muñoz FJ, Baroja-Fernández E, Bahaji A, Zúñiga M, González-Candelas F, Pozueta-Romero J

    Abstract
    Production of branched α-glucan, glycogen-like polymers is widely spread in the Bacteria domain. The glycogen pathway of synthesis and degradation has been fairly well characterized in the model enterobacterial species Escherichia coli (order Enterobacteriales, class Gammaproteobacteria), in which the cognate genes (branching enzyme glgB, debranching enzyme glgX, ADP-glucose pyrophosphorylase glgC, glycogen synthase glgA, and glycogen phosphorylase glgP) are clustered in a glgBXCAP operon arrangement. However, the evolutionary origin of this particular arrangement and of its constituent genes is unknown. Here, by using 265 complete gammaproteobacterial genomes we have carried out a comparative analysis of the presence, copy number and arrangement of glg genes in all lineages of the Gammaproteobacteria. These analyses revealed large variations in glg gene presence, copy number and arrangements among different gammaproteobacterial lineages. However, the glgBXCAP arrangement was remarkably conserved in all glg-possessing species of the orders Enterobacteriales and Pasteurellales (the E/P group). Subsequent phylogenetic analyses of glg genes present in the Gammaproteobacteria and in other main bacterial groups indicated that glg genes have undergone a complex evolutionary history in which horizontal gene transfer may have played an important role. These analyses also revealed that the E/P glgBXCAP genes (a) share a common evolutionary origin, (b) were vertically transmitted within the E/P group, and (c) are closely related to glg genes of some phylogenetically distant betaproteobacterial species. The overall data allowed tracing the origin of the E. coli glgBXCAP operon to the last common ancestor of the E/P group, and also to uncover a likely glgBXCAP transfer event from the E/P group to particular lineages of the Betaproteobacteria.

    PMID: 25607991 [PubMed - indexed for MEDLINE]




  • Managing an online survey about influenza vaccination in primary healthcare workers.
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    Managing an online survey about influenza vaccination in primary healthcare workers.

    Int J Environ Res Public Health. 2015 Jan 09;12(1):541-53

    Authors: Toledo D, Aerny N, Soldevila N, Baricot M, Godoy P, Castilla J, García-Gutierrez S, Torner N, Astray J, Mayoral JM, Tamames S, González-Candelas F, Martín V, Díaz J, Domíguez A, CIBERESP Working Group for the Survey on Influenza Vaccination in Primary Health Care Workers

    Abstract
    Online surveys are increasingly used due to their speed and efficiency. The aim of this study was to analyze factors that may have contributed to the quality and speed of response of an online survey on influenza vaccination in primary healthcare workers. A multicenter study including family physicians, nurses and pediatricians from primary healthcare teams from seven Spanish Autonomous Communities was designed. The centers were selected by simple random sampling. The survey remained active and accessible for 56 days and four reminders were sent. The odds ratios (OR) and their 95% confidence intervals (CI) were calculated to assess the association of sociodemographic variables and responding to the survey before the second reminder. Complete, validated information was obtained from 1965 primary healthcare workers. The total response rate was 36.2%. More nurses (46.3%) responded before the second reminder and more family physicians (52.8%) after the second reminder. The adjusted OR shows that family physicians responded later (AOR 1.46, 95% CI 1.2-1.8) than nurses. The responses obtained in the first 24 h after the initial sending and the reminders accounted for 41.7% of the completed surveys, indicating the importance of reminders.

    PMID: 25584421 [PubMed - indexed for MEDLINE]




  • Recombination in viruses: mechanisms, methods of study, and evolutionary consequences.
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    Recombination in viruses: mechanisms, methods of study, and evolutionary consequences.

    Infect Genet Evol. 2015 Mar;30:296-307

    Authors: Pérez-Losada M, Arenas M, Galán JC, Palero F, González-Candelas F

    Abstract
    Recombination is a pervasive process generating diversity in most viruses. It joins variants that arise independently within the same molecule, creating new opportunities for viruses to overcome selective pressures and to adapt to new environments and hosts. Consequently, the analysis of viral recombination attracts the interest of clinicians, epidemiologists, molecular biologists and evolutionary biologists. In this review we present an overview of three major areas related to viral recombination: (i) the molecular mechanisms that underlie recombination in model viruses, including DNA-viruses (Herpesvirus) and RNA-viruses (Human Influenza Virus and Human Immunodeficiency Virus), (ii) the analytical procedures to detect recombination in viral sequences and to determine the recombination breakpoints, along with the conceptual and methodological tools currently used and a brief overview of the impact of new sequencing technologies on the detection of recombination, and (iii) the major areas in the evolutionary analysis of viral populations on which recombination has an impact. These include the evaluation of selective pressures acting on viral populations, the application of evolutionary reconstructions in the characterization of centralized genes for vaccine design, and the evaluation of linkage disequilibrium and population structure.

    PMID: 25541518 [PubMed - indexed for MEDLINE]




  • Visualizing knowledge and attitude factors related to influenza vaccination of physicians.
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    Visualizing knowledge and attitude factors related to influenza vaccination of physicians.

    Vaccine. 2015 Feb 11;33(7):885-91

    Authors: Antón-Ladislao A, García-Gutiérrez S, Soldevila N, González-Candelas F, Godoy P, Castilla J, Mayoral JM, Astray J, Martín V, Tamames S, Toledo D, Aguirre U, Domínguez A, CIBERESP Working Group for the Survey on Influenza Vaccination in Primary Health Care Workers

    Abstract
    PURPOSE: To characterize groups of primary healthcare physicians according to sociodemographic data, years of professional experience and knowledge of and attitudes to influenza, and to evaluate differences between groups with respect to influenza vaccination in the 2011-2012 season.
    METHODS: We carried out an anonymous web survey of Spanish primary healthcare physicians in 2012. Information on vaccination, and knowledge of and attitudes to influenza was collected. Multiple correspondence analysis and cluster analysis were used to define groups of physicians.
    RESULTS: We included 835 physicians and identified three types. Type B were physicians with low professional experience of influenza. Types A and C were physicians with high professional experience with influenza, type A also had a high awareness of influenza and seasonal vaccination. Types A and C were older and more often male than type B (p<0.0001). Knowledge of influenza was greatest in type A and lowest in type B. Awareness of influenza was greatest in type A and lowest in type C. In type A, 71.0% of physicians were vaccinated in the 2011-2012 season, compared with 48.1% and 33.6% from types B and C, respectively (p<0.001).
    CONCLUSIONS: Additional efforts should be made to increase interest and concerns about preventing the transmission of influenza in physicians who do not believe influenza is a severe disease and are not concerned about its transmission.

    PMID: 25529290 [PubMed - indexed for MEDLINE]




  • Phylogenetic analysis of environmental Legionella pneumophila isolates from an endemic area (Alcoy, Spain).
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    Phylogenetic analysis of environmental Legionella pneumophila isolates from an endemic area (Alcoy, Spain).

    Infect Genet Evol. 2015 Mar;30:45-54

    Authors: Sánchez-Busó L, Olmos MP, Camaró ML, Adrián F, Calafat JM, González-Candelas F

    Abstract
    Environmental surveillance of Legionella pneumophila is a key component of the control measures established in urban settlements to ensure water safety and quality, with the aim of minimizing and limiting opportunistic infections in humans. In this work, we present results on the detection and genetic characterization of these bacteria in the outbreak-recurrent region of Alcoy (Comunidad Valenciana, Spain) using water and biofilm samples. We were particularly interested in studying the presence and distribution of L. pneumophila in the absence of outbreak or sporadic cases of legionellosis and in comparing the efficacy of culturing from water samples with a biofilm-based detection procedure using molecular amplification. To this end, water samples were taken from 120 sites distributed all around the city and its surroundings, as well as 60 biofilm swabs from half of the sampling sites. L. pneumophila could be isolated from water in just 4 of the locations. Touchdown PCR was applied to DNA extracted from water and also biofilm swabs, as a rapid method for both routine and outbreak investigations. L. pneumophila was detected by this method in 14 of the sites in which both water and biofilms were taken, although 13 of them tested positive using only the biofilm samples. These results show a ten-fold increase in the success rate of Legionella detection over water samples. The application of this method to study the presence of L. pneumophila in the water-supply system and risk facilities of Alcoy revealed different strains distributed in different areas of the city. Sequence Type ST578, endemic in the area and responsible for most clinical cases, was detected in one of the sampling sites. The number of positive samples correlated with water temperature but not with chlorine levels. The direct analysis of biofilm swabs improves the detection rate and genetic characterization of L. pneumophila and can complement analyses based on bacterial culture.

    PMID: 25511251 [PubMed - indexed for MEDLINE]




  • Knowledge of and attitudes to influenza in unvaccinated primary care physicians and nurses.
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    Knowledge of and attitudes to influenza in unvaccinated primary care physicians and nurses.

    Hum Vaccin Immunother. 2014;10(8):2378-86

    Authors: Domínguez A, Godoy P, Castilla J, María Mayoral J, Soldevila N, Torner N, Toledo D, Astray J, Tamames S, García-Gutiérrez S, González-Candelas F, Martín V, Díaz J, CIBERES P Working Group for the Survey on Influenza Vaccination in Primary Health Care Workers

    Abstract
    Primary healthcare workers, especially nurses, are exposed to the vast majority of patients with influenza and play an important role in vaccinating patients. Healthcare workers' misconceptions about influenza and influenza vaccination have been reported as possible factors associated with lack of vaccination. The objective of this study was to compare the characteristics of unvaccinated physicians and unvaccinated nurses in the 2011-2012 influenza season. We performed an anonymous web survey of Spanish primary healthcare workers in 2012. Information was collected on vaccination and knowledge of and attitudes to the influenza vaccine. Multivariate analysis was performed using unconditional logistic regression. We included 461 unvaccinated physicians and 402 unvaccinated nurses. Compared with unvaccinated nurses, unvaccinated physicians had more frequently received seasonal influenza vaccination in the preceding seasons (aOR 1.58; 95% CI 1.11-2.25), and more frequently believed that vaccination of high risk individuals is effective in reducing complications (aOR 2.53; 95% CI 1.30-4.95) and that influenza can be a serious illness (aOR 1.65; 95% CI 1.17-2.32). In contrast, unvaccinated physicians were less concerned about infecting patients (aOR 0.62; 95% CI 0.40-0.96). Unvaccinated nurses had more misconceptions than physicians about influenza and the influenza vaccine and more doubts about the severity of annual influenza epidemics in patients with high risk conditions and the prevention of complications by means of the influenza vaccination. For unvaccinated physicians, strategies to improve vaccination coverage should stress the importance of physicians as a possible source of infection of their patients. The effectiveness of influenza vaccination of high risk persons should be emphasized in nurses.

    PMID: 25424945 [PubMed - indexed for MEDLINE]




  • [Molecular epidemiology studies on the immigrant population in Spain].
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    [Molecular epidemiology studies on the immigrant population in Spain].

    Rev Esp Salud Publica. 2014 Nov-Dec;88(6):819-28

    Authors: González-Candelas F, Alma Bracho M, Comas I, d'Auria G, D Unková M, García R, Gosalbes MJ, Isaac S, Latorre A, López-Labrador FX, Patiño Galindo JÁ, Palero F, Pérez-Brocal V, Pérez-Cobas AE, Sánchez-Busó L, Silva FJ, Vázquez-Castellanos JF, Moya A

    Abstract
    BACKGROUND: Molecular epidemiology is a new scientific discipline which allows to integrate information on the genetic variation of infectious pathogens with their diffusion in a population and its subgroups including, for instance, resistance mutations to antibiotics and antiretrovirals. We present the results of an analysis of scientific publications that analyze the health status of the immigrant population in Spain from a molecular epidemiology perspective.
    METHODS: We reviewed original articles published in 1998-2014 with the keywords "molecular epidemiology", "molecular typing", "sequencing", "immigrant", and "Spain".
    RESULTS: From a total of 267 articles identified initially, only 50 passed through the established filters. Most of them (36) analyzed infections by Mycobacterium tuberculosis (3) and HIV (3), followed at a large distance by Staphylococcus aureus and hepatitis B virus. The main goal of these works was the typing of the pathogen and to determine the frequency of resistance mutations.
    CONCLUSION: Is difficult to generalize the conclusions from the analyzed articles because most of them have a purely descriptive and quite restricted scope, considering the type and size of the samples studied. Several studies are focused on the most likely origin for the strains or variants of the pathogen but others also reveal transmissions from the local to the immigrant populations.

    PMID: 25418571 [PubMed - indexed for MEDLINE]




  • Relating the outcome of HCV infection and different host SNP polymorphisms in a Majorcan population coinfected with HCV-HIV and treated with pegIFN-RBV.
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    Relating the outcome of HCV infection and different host SNP polymorphisms in a Majorcan population coinfected with HCV-HIV and treated with pegIFN-RBV.

    Int Microbiol. 2014 Mar;17(1):11-20

    Authors: Matas M, Picornell A, Cifuentes C, Payeras A, Homar F, González-Candelas F, López-Labrador FX, Moya A, Ramon C, Castro JA

    Abstract
    Hepatitis C virus (HCV) is one of the major causes of chronic hepatitis, cirrhosis, and hepatocellular carcinoma, and the development of HCV-related disease is accelerated in individuals coinfected with human immunodeficiency-1 virus (HIV). In the present study, we correlated different host single-nucleotide polymorphisms (SNPs) in the IL28B, CTLA4, LDLr, and HFE genes and mitochondrial DNA (mtDNA) haplogroups with the outcome of HCV infection and the response to pegylated-interferon plus ribavirin (pegIFN-RBV) treatment. Our study population consisted of 63 Majorcan patients coinfected with HCV and HIV and 59 anonymous unrelated controls. Whereas the population frequency of IL28B alleles was similar to that found in a North-American cohort of European descent, the frequency of the rs12979860 C allele was lower than that determined in other cohorts from Spain. The frequencies of CTLA4 and LDLr polymorphisms were comparable to those reported in other populations. Significant differences between cases and control cohorts occurred only for the H63D mutation of the HFE gene. There were no other differences in the frequencies of other polymorphisms or mtDNA haplogroups. The IL28B rs12979860 CC genotype was shown to be associated with a rapid virological response, and the spontaneous viral clearance rate for HCV was higher in patients with the CTLA4+49 G allele. There was no relationship between SNPs in the LDLr and HFE genes and mtDNA haplogroups and the response to treatment. Our results suggest that the host genetic background plays a significant role in the pegIFN-RBV response of patients coinfected with HCV and HIV.

    PMID: 25296442 [PubMed - indexed for MEDLINE]




  • Recombination drives genome evolution in outbreak-related Legionella pneumophila isolates.
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    Recombination drives genome evolution in outbreak-related Legionella pneumophila isolates.

    Nat Genet. 2014 Nov;46(11):1205-11

    Authors: Sánchez-Busó L, Comas I, Jorques G, González-Candelas F

    Abstract
    Legionella pneumophila is a strictly environmental pathogen and the etiological agent of legionellosis. It is known that non-vertical processes have a major role in the short-term evolution of pathogens, but little is known about the relevance of these and other processes in environmental bacteria. We report the whole-genome sequencing of 69 L. pneumophila strains linked to recurrent outbreaks in a single location (Alcoy, Spain) over 11 years. We found some examples where the genome sequences of isolates of the same sequence type and outbreak did not cluster together and were more closely related to sequences from different outbreaks. Our analyses identify 16 recombination events responsible for almost 98% of the SNPs detected in the core genome and an apparent acceleration in the evolutionary rate. These results have profound implications for the understanding of microbial populations and for public health interventions in Legionella outbreak investigations.

    PMID: 25282102 [PubMed - indexed for MEDLINE]




  • Computational models of liver fibrosis progression for hepatitis C virus chronic infection.
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    Computational models of liver fibrosis progression for hepatitis C virus chronic infection.

    BMC Bioinformatics. 2014;15 Suppl 8:S5

    Authors: Lara J, López-Labrador F, González-Candelas F, Berenguer M, Khudyakov YE

    Abstract
    BACKGROUND: Chronic infection with hepatitis C virus (HCV) is a risk factor for liver diseases such as fibrosis, cirrhosis and hepatocellular carcinoma. HCV genetic heterogeneity was hypothesized to be associated with severity of liver disease. However, no reliable viral markers predicting disease severity have been identified. Here, we report the utility of sequences from 3 HCV 1b genomic regions, Core, NS3 and NS5b, to identify viral genetic markers associated with fast and slow rate of fibrosis progression (RFP) among patients with and without liver transplantation (n = 42).
    METHODS: A correlation-based feature selection (CFS) method was used to detect and identify RFP-relevant viral markers. Machine-learning techniques, linear projection (LP) and Bayesian Networks (BN), were used to assess and identify associations between the HCV sequences and RFP.
    RESULTS: Both clustering of HCV sequences in LP graphs using physicochemical properties of nucleotides and BN analysis using polymorphic sites showed similarities among HCV variants sampled from patients with a similar RFP, while distinct HCV genetic properties were found associated with fast or slow RFP. Several RFP-relevant HCV sites were identified. Computational models parameterized using the identified sites accurately associated HCV strains with RFP in 70/30 split cross-validation (90-95% accuracy) and in validation tests (85-90% accuracy). Validation tests of the models constructed for patients with or without liver transplantation suggest that the RFP-relevant genetic markers identified in the HCV Core, NS3 and NS5b genomic regions may be useful for the prediction of RFP regardless of transplant status of patients.
    CONCLUSIONS: The apparent strong genetic association to RFP suggests that HCV genetic heterogeneity has a quantifiable effect on severity of liver disease, thus presenting opportunity for developing genetic assays for measuring virulence of HCV strains in clinical and public health settings.

    PMID: 25081062 [PubMed - indexed for MEDLINE]




  • Pandemic influenza A (H1N1) infection in pregnant and nonpregnant women in Spain (2009-2010).
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    Pandemic influenza A (H1N1) infection in pregnant and nonpregnant women in Spain (2009-2010).

    Jpn J Infect Dis. 2014;67(3):163-71

    Authors: Suárez-Varela MM, González-Candelas F, Astray J, Alonso J, Garin O, Castro A, Galán JC, Baricot M, Castilla J, Godoy P, Delgado-Rodríguez M, Martin V, Mayoral JM, Pumarola T, Quintana JM, Tamames S, Llopis-González A, Dominguez A, CIBERESP Cases and Controls in Pandemic Influenza Working Group, Spain

    Abstract
    The present study aimed to compare the main features of infection with pandemic influenza A virus in pregnant and nonpregnant women admitted to hospitals in Spain during the first waves of the 2009-2010 influenza pandemic. This was a prospective (November 2009 to June 2010), multicenter observational study. All cases were women of reproductive age who had not been vaccinated against seasonal or pandemic influenza A. Influenza infection was confirmed by reverse transcription-polymerase chain reaction (RT-PCR). The sociodemographic and clinical data of all cases were reviewed. A total of 219 inpatients, including 49 pregnant women and 170 nonpregnant women, were enrolled in the study upon admission to participating hospitals. The most substantially different symptoms between the groups were respiratory distress and unilobar consolidation, both of which were more frequent among nonpregnant women. Antibiotics and systemic corticosteroids were more frequently used in nonpregnant women; however, there were no differences in the rates of treatment with antivirals. Our findings indicated that the compared with nonpregnant women, pregnant women in this study did not have significantly different symptoms and were not at increased risk of complications from pandemic influenza virus infection.

    PMID: 24858604 [PubMed - indexed for MEDLINE]




  • Mixed infection by Legionella pneumophila in outbreak patients.
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    Mixed infection by Legionella pneumophila in outbreak patients.

    Int J Med Microbiol. 2014 May;304(3-4):307-13

    Authors: Coscollá M, Fernández C, Colomina J, Sánchez-Busó L, González-Candelas F

    Abstract
    During the molecular epidemiological study of a legionellosis outbreak, we obtained sequence based typing (SBT) profiles from uncultured respiratory samples of 15 affected patients. We detected several distinct allelic profiles some of which were a mixture of alleles present in the more common profiles. Chromatograms from the sequences of one patient with mixed profile showed polymorphisms in several positions, which could result from the simultaneous presence of different Legionella variants in the sample. In order to test this possibility, we cloned PCR amplification products from six loci for two patients with a mixed profile and a patient with a pure profile. After obtaining around 20 sequences for each locus of three patients, we detected several variants in two of them and two variants in the third one. In summary, the three analyzed patients showed evidence of more than one Legionella variant during the acute infection. These results indicate that probably some patients were infected by more than one strain, which could be due to co-infection from the same environmental source or, alternatively, to independent infections in a very short period of time. Although our data cannot discriminate between these hypotheses, these results suggest that Legionella infection patterns can be more complex than previously assumed. None of the environmental samples analyzed during this outbreak was even similar to any of the clinical ones.

    PMID: 24309206 [PubMed - indexed for MEDLINE]




  • Knowledge of and attitudes to influenza vaccination in healthy primary healthcare workers in Spain, 2011-2012.
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    Knowledge of and attitudes to influenza vaccination in healthy primary healthcare workers in Spain, 2011-2012.

    PLoS One. 2013;8(11):e81200

    Authors: Domínguez A, Godoy P, Castilla J, Soldevila N, Toledo D, Astray J, Mayoral JM, Tamames S, García-Gutiérrez S, González-Candelas F, Martín V, Díaz J, Torner N, CIBERESP Working Group for the Survey on Influenza Vaccination in Primary Health Care Workers

    Abstract
    Annual influenza vaccination is recommended for healthcare workers, but many do not follow the recommendation. The objective of this study was to investigate the factors associated with seasonal influenza vaccination in the 2011-2012 season. We carried out an anonymous web survey of Spanish primary healthcare workers in 2012. Information on vaccination, and knowledge and attitudes about the influenza vaccine was collected. Workers with medical conditions that contraindicated vaccination and those with high risk conditions were excluded. Multivariate analysis was performed using unconditional logistic regression. We included 1,749 workers. The overall vaccination coverage was 50.7% and was higher in workers aged ≥ 55 years (55.7%), males (57.4%) and paediatricians (63.1%). Factors associated with vaccination were concern about infection at work (aOR 4.93; 95% CI 3.72-6.53), considering that vaccination of heathcare workers is important (aOR 2.62; 95%CI 1.83-3.75) and that vaccination is effective in preventing influenza and its complications (aOR 2.40; 95% CI 1.56-3.67). No association was found between vaccination and knowledge of influenza or the vaccine characteristics. Educational programs should aim to remove the misconceptions and attitudes that limit compliance with recommendations about influenza vaccination in primary healthcare workers rather than only increasing knowledge about influenza and the characteristics of the vaccine.

    PMID: 24260560 [PubMed - indexed for MEDLINE]




  • Pandemic influenza A (H1N1) in non-vaccinated, pregnant women in Spain (2009-2010).
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    Pandemic influenza A (H1N1) in non-vaccinated, pregnant women in Spain (2009-2010).

    Matern Child Health J. 2014 Aug;18(6):1454-61

    Authors: Morales-Suárez-Varela M, González-Candelas F, Astray J, Alonso J, Castro A, Cantón R, Galán JC, Garin O, Soldevila N, Baricot M, Castilla J, Godoy P, Delgado-Rodríguez M, Martín V, Mayoral JM, Pumarola T, Quintana JM, Tamames S, Llopis-González A, Domínguez A, CIBERESP Cases and Controls in Pandemic Influenza Working Group, Spain

    Abstract
    The aim of this study was to investigate the main characteristics of non-vaccinated pregnant women who were hospitalised for influenza A (H1N1) pdm09 pandemic versus pregnant women hospitalised for non-influenza-related reasons in Spain, and to characterise the clinical presentation of the disease in this population to facilitate early diagnosis and future action programmes. Understanding influenza infection during pregnancy is important as pregnant women are a high-risk population for increased morbidity from influenza infection. We investigated the socio-demographic and clinical features of 51 non-vaccinated, pregnant women infected with the pandemic influenza A (H1N1) virus in Spain (cases) and compared them to 114 controls (non-vaccinated and non-infected pregnant women) aged 15-44 years. Substantial and significant odd ratios (ORs) for pandemic influenza A (H1N1) were found for the pregnant women who were obese compared with controls (body mass index > 30) (OR 3.03; 95% confidence intervals 1.13-8.11). The more prevalent symptoms observed in pandemic influenza-infected pregnant women were high temperature, cough (82.4%), malaise (80.5%), myalgia (56.1%), and headaches (54.9%). Our results suggest that the initial symptoms and risk factors for infection of pregnant women with the influenza A (H1N1) pdm09 virus are similar to the symptoms and risk factors for seasonal influenza, which make early diagnosis difficult, and reinforces the need to identify and protect high-risk groups.

    PMID: 24162551 [PubMed - indexed for MEDLINE]




  • Emerging trends in CRF02_AG variants transmission among men who have sex with men in Spain.
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    Emerging trends in CRF02_AG variants transmission among men who have sex with men in Spain.

    J Acquir Immune Defic Syndr. 2014 Mar 01;65(3):e130-3

    Authors: Bracho MA, Sentandreu V, Alastrué I, Belda J, Juan A, Fernández-García E, Santos C, Zafra T, Tasa T, Colomina S, González-Candelas F

    PMID: 24091696 [PubMed - indexed for MEDLINE]




  • Whole genome sequencing analysis of intrapatient microevolution in Mycobacterium tuberculosis: potential impact on the inference of tuberculosis transmission.
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    Whole genome sequencing analysis of intrapatient microevolution in Mycobacterium tuberculosis: potential impact on the inference of tuberculosis transmission.

    J Infect Dis. 2014 Jan 01;209(1):98-108

    Authors: Pérez-Lago L, Comas I, Navarro Y, González-Candelas F, Herranz M, Bouza E, García-de-Viedma D

    Abstract
    BACKGROUND: It has been accepted that the infection by Mycobacterium tuberculosis (M. tuberculosis) can be more heterogeneous than considered. The emergence of clonal variants caused by microevolution events leading to population heterogeneity is a phenomenon largely unexplored. Until now, we could only superficially analyze this phenomenon by standard fingerprinting (RFLP and VNTR).
    METHODS: In this study we applied whole genome sequencing for a more in-depth analysis of the scale of microevolution both at the intrapatient and interpatient scenarios.
    RESULTS: We found that the amount of variation accumulated within a patient can be as high as that observed between patients along a chain of transmission. Intrapatient diversity was found both at the extrapulmonary and respiratory sites, meaning that this variability can be transmitted and impact on the inference of transmission events. One of the events studied allowed us to track for a single strain the complete process of (i) interpatient microevolution, (ii) intrapatient respiratory variation, and (iii) isolation of different variants at different infected sites of this patient.
    CONCLUSIONS: Our study adds new data to the understanding of variability in M. tuberculosis in a wide clinical scenario and alerts about the difficulties of establishing thresholds to differentiate relatedness in M. tuberculosis with epidemiological purposes.

    PMID: 23945373 [PubMed - indexed for MEDLINE]




  • Molecular evolution in court: analysis of a large hepatitis C virus outbreak from an evolving source.
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    Molecular evolution in court: analysis of a large hepatitis C virus outbreak from an evolving source.

    BMC Biol. 2013 Jul 19;11:76

    Authors: González-Candelas F, Bracho MA, Wróbel B, Moya A

    Abstract
    BACKGROUND: Molecular phylogenetic analyses are used increasingly in the epidemiological investigation of outbreaks and transmission cases involving rapidly evolving RNA viruses. Here, we present the results of such an analysis that contributed to the conviction of an anesthetist as being responsible for the infection of 275 of his patients with hepatitis C virus.
    RESULTS: We obtained sequences of the NS5B and E1-E2 regions in the viral genome for 322 patients suspected to have been infected by the doctor, and for 44 local, unrelated controls. The analysis of 4,184 cloned sequences of the E1-E2 region allowed us to exclude 47 patients from the outbreak. A subset of patients had known dates of infection. We used these data to calibrate a relaxed molecular clock and to determine a rough estimate of the time of infection for each patient. A similar analysis led to an estimate for the time of infection of the source. The date turned out to be 10 years before the detection of the outbreak. The number of patients infected was small at first, but it increased substantially in the months before the detection of the outbreak.
    CONCLUSIONS: We have developed a procedure to integrate molecular phylogenetic reconstructions of rapidly evolving viral populations into a forensic setting adequate for molecular epidemiological analysis of outbreaks and transmission events. We applied this procedure to a large outbreak of hepatitis C virus caused by a single source and the results obtained played a key role in the trial that led to the conviction of the suspected source.

    PMID: 23870105 [PubMed - indexed for MEDLINE]




  • Trends in influenza vaccine coverage among primary healthcare workers in Spain, 2008-2011.
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    Trends in influenza vaccine coverage among primary healthcare workers in Spain, 2008-2011.

    Prev Med. 2013 Sep;57(3):206-11

    Authors: Castilla J, Martínez-Baz I, Godoy P, Toledo D, Astray J, García S, Mayoral JM, Martín V, González-Candelas F, Guevara M, Diaz-Borrego J, Torner N, Baricot M, Tamames S, Domínguez A, CIBERESP Working Group for the Survey on Influenza Vaccination in Primary Healthcare Professionals

    Abstract
    OBJECTIVE: To evaluate trends in seasonal influenza vaccination coverage in primary healthcare workers (PHCWs) in Spain between 2008 and 2011.
    METHODS: We made an anonymous web survey of PHCWs in 2012. Information on attitudes towards and knowledge of influenza vaccine, and immunization in previous seasons was collected. Self-reported vaccination coverage and factors related to vaccination continuity were analysed.
    RESULTS: Of 5433 workers contacted, 2625 (48.3%) responded to the survey: 47.0% were general practitioners, 10.3% paediatricians and 42.7% nurses. Their reported vaccination rates from seasons 2008-2009 to 2011-2012 decreased over time: 58.4%, 57.4%, 53.2% and 49.3% (linear trend, p < 0.001). Among workers vaccinated in any previous season, 70.2% were vaccinated again in 2011-2012, compared with 5.2% among those not previously vaccinated (p < 0.001). Continuity of vaccination increased with age and with the worker or cohabitant having a major chronic condition. Vaccination was higher in workers who recognized vaccination as effective and those worried about being infected or infecting patients.
    CONCLUSION: Influenza vaccination coverage in PHCWs has declined, especially after the pandemic. Intensive interventions are needed to change this trend. Knowledge of vaccination should be reinforced by stressing the effectiveness of the vaccine and the risks of influenza for workers and patients.

    PMID: 23732251 [PubMed - indexed for MEDLINE]




  • Different prognosis in hospitalized patients with influenza one season after the pandemic H1N1 influenza of 2009-2010 in Spain.
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    Different prognosis in hospitalized patients with influenza one season after the pandemic H1N1 influenza of 2009-2010 in Spain.

    Influenza Other Respir Viruses. 2013 Nov;7(6):1336-42

    Authors: Delgado-Rodríguez M, Castilla J, Godoy P, Martín V, Soldevila N, Alonso J, Astray J, Baricot M, Galán JC, Castro A, Gónzález-Candelas F, Mayoral JM, Quintana JM, Pumarola T, Tamames S, Sáez M, Domínguez A, CIBERESP Cases and Controls in Pandemic Influenza Working Group, Spain

    Abstract
    BACKGROUND: The present report compares prognosis in hospitalized cases with the H1N1 pandemic virus in two seasons.
    METHODS: Two series of hospitalized patients with laboratory-confirmed H1N1 pandemic influenza have been compared: 813 in the season 2009-2010 and 707 in the season 2010-2011. A detailed history of variables preceding hospital admission and during hospitalization was obtained by interview and clinical charts. A combined endpoint of death admission to intensive care was used as outcome due to the low number of deaths. Logistic regression was applied in the analysis for adverse outcome.
    RESULTS: Patients of the second season had different characteristics than in the first one (older, more underlying conditions, more malfunctioning organs and more symptoms). Patients with H1N1 pandemic virus when hospitalized were more frequently directly admitted to ICU during the 2010-2011 season than in the previous season (RR=2·10; 95% confidence intervals CI, 1·55-2·85), as a consequence of a higher presence of sepsis and respiratory distress. These patients also showed during hospitalization a higher risk of ICU admission or death (RR=3·22, 95% CI, 2·15-4·83). After adjusting for the differences in risk factors of adverse outcome, patients in the second season showed a higher risk of ICU admission and/or in-hospital death odds ratio (OR=3·77, 95% CI, 2·30-6·18).
    CONCLUSION: Hospitalized patients with H1N1 pandemic influenza during the second season were more severely affected at hospital admission and showed a worse prognosis than in previous season, independently of the differences found at hospital admission.

    PMID: 23647645 [PubMed - indexed for MEDLINE]




  • Genetic Characterization of Legionella pneumophila Isolated from a Common Watershed in Comunidad Valenciana, Spain.
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    Genetic Characterization of Legionella pneumophila Isolated from a Common Watershed in Comunidad Valenciana, Spain.

    PLoS One. 2013;8(4):e61564

    Authors: Sánchez-Busó L, Coscollá M, Pinto-Carbó M, Catalán V, González-Candelas F

    Abstract
    Legionella pneumophila infects humans to produce legionellosis and Pontiac fever only from environmental sources. In order to establish control measures and study the sources of outbreaks it is essential to know extent and distribution of strain variants of this bacterium in the environment. Sporadic and outbreak-related cases of legionellosis have been historically frequent in the Comunidad Valenciana region (CV, Spain), with a high prevalence in its Southeastern-most part (BV). Environmental investigations for the detection of Legionella pneumophila are performed in this area routinely. We present a population genetics study of 87 L. pneumophila strains isolated in 13 different localities of the BV area irrigated from the same watershed and compare them to a dataset of 46 strains isolated in different points of the whole CV. Our goal was to compare environmental genetic variation at two different geographic scales, at county and regional levels. Genetic diversity, recombination and population structure were analyzed with Sequence-Based Typing data and three intergenic regions. The results obtained reveal a low, but detectable, level of genetic differentiation between both datasets, mainly, but not only, attributed to the occurrence of unusual variants of the neuA locus present in the BV populations. This differentiation is still detectable when the 10 loci considered are analyzed independently, despite the relatively high incidence of the most common genetic variant in this species, sequence type 1 (ST-1). However, when the genetic data are considered without their associated geographic information, four major groups could be inferred at the genetic level which did not show any correlation with sampling locations. The overall results indicate that the population structure of these environmental samples results from the joint action of a global, widespread ST-1 along with genetic differentiation at shorter geographic distances, which in this case are related to the common watershed for the BV localities.

    PMID: 23634210 [PubMed - indexed for MEDLINE]




  • Effectiveness of vaccination with 23-valent pneumococcal polysaccharide vaccine in preventing hospitalization with laboratory confirmed influenza during the 2009-2010 and 2010-2011 seasons.
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    Effectiveness of vaccination with 23-valent pneumococcal polysaccharide vaccine in preventing hospitalization with laboratory confirmed influenza during the 2009-2010 and 2010-2011 seasons.

    Hum Vaccin Immunother. 2013 Apr;9(4):865-73

    Authors: Domínguez A, Castilla J, Godoy P, Delgado-Rodríguez M, Saez M, Soldevila N, Astray J, Mayoral JM, Martín V, Quintana JM, González-Candelas F, Galán JC, Tamames S, Castro A, Baricot M, Garín O, Pumarola T, CIBERESP Cases and Controls in Pandemic Influenza Working Group (Spain)

    Abstract
    BACKGROUND: Since influenza predisposes to bacterial pneumonia caused by Streptococcus pneumoniae, studies have suggested that pneumococcal vaccination might reduce its occurrence during pandemics. We assessed the effectiveness of pneumococcal polysaccharide vaccination alone and in combination with influenza vaccination in preventing influenza hospitalization during the 2009-2010 pandemic wave and 2010-2011 influenza epidemic.
    RESULTS: 1187 cases and 2328 controls were included. The adjusted estimate of effectiveness of pneumococcal vaccination in preventing influenza hospitalization was 41% (95% CI 8-62) in all patients and 43% (95% CI 2-78) in patients aged ≥ 65 y. The adjusted effectiveness of dual PPV23 and influenza vaccination was 81% (95% CI 65-90) in all patients and 76% (95% CI 46-90) in patients aged ≥ 65 y. The adjusted effectiveness of influenza vaccination alone was 58% (95% CI 38-72).
    METHODS: We conducted a multicenter case-control study in 36 Spanish hospitals. We selected patients aged ≥ 18 y hospitalized with confirmed influenza and two hospitalized controls per case, matched according to age, date of hospitalization and province of residence. Multivariate analysis was performed using conditional logistic regression. Subjects were considered vaccinated if they had received the pneumococcal or seasonal influenza vaccine>14 d (or>7 d for pandemic influenza vaccine) before the onset of symptoms (cases) or the onset of symptoms in matched cases (controls).
    CONCLUSIONS: In elderly people and adults with chronic illness, pneumococcal vaccination may reduce hospitalizations during the influenza season. In people vaccinated with both the influenza and pneumococcal vaccines, the benefit in hospitalizations avoided was greater than in those vaccinated only against influenza.

    PMID: 23563516 [PubMed - indexed for MEDLINE]




  • Influenza vaccine effectiveness in preventing outpatient, inpatient, and severe cases of laboratory-confirmed influenza.
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    Influenza vaccine effectiveness in preventing outpatient, inpatient, and severe cases of laboratory-confirmed influenza.

    Clin Infect Dis. 2013 Jul;57(2):167-75

    Authors: Castilla J, Godoy P, Domínguez A, Martínez-Baz I, Astray J, Martín V, Delgado-Rodríguez M, Baricot M, Soldevila N, Mayoral JM, Quintana JM, Galán JC, Castro A, González-Candelas F, Garín O, Saez M, Tamames S, Pumarola T, CIBERESP Cases and Controls in Influenza Working Group Spain

    Abstract
    BACKGROUND: In most seasons, the influenza vaccine is effective in preventing influenza, but it is not clear whether it is equally effective in preventing mild and severe cases. We designed a case-control study to compare the effectiveness of the influenza vaccine in preventing outpatient, inpatient, and severe or fatal cases of laboratory-confirmed influenza.
    METHODS: Hospitalized patients (n = 691) with laboratory-confirmed influenza in the 2010-2011 season recruited in 29 Spanish hospitals were individually matched by age, admission/visit date, and province with an outpatient with laboratory-confirmed influenza and an outpatient control. Severe cases were considered those patients admitted to intensive care units or who died in the hospital (n = 177). We compared the influenza vaccine status of controls and outpatient cases, inpatient cases, and severe cases using conditional logistic regression adjusted for potential confounding factors. Severe and nonsevere inpatient influenza cases were compared using unconditional logistic regression. Vaccine effectiveness was (1 - odds ratio) × 100.
    RESULTS: Vaccine effectiveness was 75% (adjusted odds ratio [AOR], 0.25; 95% confidence interval [CI], .16-.39) in preventing influenza outpatient cases, 60% (AOR, 0.40; 95% CI, .25-.63) in preventing influenza-associated hospitalizations, and 89% (AOR, 0.11; 95% CI, .04-.37) in preventing severe cases. In inpatients, influenza vaccination was associated with a lower risk of severe influenza (AOR, 0.42; 95% CI, .22-.80).
    CONCLUSIONS: Influenza vaccination prevented influenza cases and hospitalizations and was associated with a better prognosis in inpatients with influenza. The combined effect of these 2 mechanisms would explain the high effectiveness of the vaccine in preventing severe cases due to influenza.

    PMID: 23532475 [PubMed - indexed for MEDLINE]




  • Predictive factors of severe multilobar pneumonia and shock in patients with influenza.
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    Predictive factors of severe multilobar pneumonia and shock in patients with influenza.

    Emerg Med J. 2014 Apr;31(4):301-7

    Authors: Garcia Gutierrez S, Quintana JM, Baricot M, Bilbao A, Capelastegui A, Cilla Eguiluz CG, Domínguez A, Castilla J, Godoy P, Delgado-Rodríguez M, Soldevila N, Astray J, Mayoral JM, Martín V, González-Candelas F, Galán JC, Tamames S, Castro-Acosta AA, Garín O, Pumarola T, CIBERESP Cases and Controls in Pandemic Influenza Working Group, Spain

    Abstract
    PURPOSE: To identify risk factors present at admission in adult patients hospitalised due to influenza virus infection during the 2009/10 and 2010/11 seasons--including whether infection was from pandemic or seasonal influenza A infections--that were associated with the likelihood of developing severe pneumonia with multilobar involvement and shock.
    METHODS: Prospective cohort study. Patients hospitalised due to influenza virus infection were recruited. We collected information on sociodemographic characteristics, pre-existing medical conditions, vaccinations, toxic habits, previous medications, exposure to social environments, and EuroQoL-5D (EQ-5D). Severe pneumonia with multilobar involvement and/or shock (SPAS) was the primary outcome of interest. We constructed two multivariate logistic regression models to explain the likelihood of developing SPAS and to create a clinical prediction rule for developing SPAS that includes clinically relevant variables.
    RESULTS: Laboratory-confirmed A(H1N1)pdm09, EQ-5D utility score 7 days before admission, more than one comorbidity, altered mental status, dyspnoea on arrival, days from onset of symptoms, and influenza season were associated with SPAS. In addition, not being vaccinated against seasonal influenza in the previous year, anaemia, altered mental status, fever and dyspnoea on arrival at hospital, difficulties in performing activities of daily living in the previous 7 days, and days from onset of symptoms to arrival at hospital were related to the likelihood of SPAS (area under the curve value of 0.75; Hosmer-Lemeshow p value of 0.84).
    CONCLUSIONS: These variables should be taken into account by physicians evaluating a patient affected by influenza as additional information to that provided by the usual risk scores.

    PMID: 23449891 [PubMed - indexed for MEDLINE]




  • Antibiotics as selectors and accelerators of diversity in the mechanisms of resistance: from the resistome to genetic plasticity in the β-lactamases world.
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    Antibiotics as selectors and accelerators of diversity in the mechanisms of resistance: from the resistome to genetic plasticity in the β-lactamases world.

    Front Microbiol. 2013;4:9

    Authors: Galán JC, González-Candelas F, Rolain JM, Cantón R

    Abstract
    Antibiotics and antibiotic resistance determinants, natural molecules closely related to bacterial physiology and consistent with an ancient origin, are not only present in antibiotic-producing bacteria. Throughput sequencing technologies have revealed an unexpected reservoir of antibiotic resistance in the environment. These data suggest that co-evolution between antibiotic and antibiotic resistance genes has occurred since the beginning of time. This evolutionary race has probably been slow because of highly regulated processes and low antibiotic concentrations. Therefore to understand this global problem, a new variable must be introduced, that the antibiotic resistance is a natural event, inherent to life. However, the industrial production of natural and synthetic antibiotics has dramatically accelerated this race, selecting some of the many resistance genes present in nature and contributing to their diversification. One of the best models available to understand the biological impact of selection and diversification are β-lactamases. They constitute the most widespread mechanism of resistance, at least among pathogenic bacteria, with more than 1000 enzymes identified in the literature. In the last years, there has been growing concern about the description, spread, and diversification of β-lactamases with carbapenemase activity and AmpC-type in plasmids. Phylogenies of these enzymes help the understanding of the evolutionary forces driving their selection. Moreover, understanding the adaptive potential of β-lactamases contribute to exploration the evolutionary antagonists trajectories through the design of more efficient synthetic molecules. In this review, we attempt to analyze the antibiotic resistance problem from intrinsic and environmental resistomes to the adaptive potential of resistance genes and the driving forces involved in their diversification, in order to provide a global perspective of the resistance problem.

    PMID: 23404545 [PubMed]




  • Social factors related to the clinical severity of influenza cases in Spain during the A (H1N1) 2009 virus pandemic.
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    Social factors related to the clinical severity of influenza cases in Spain during the A (H1N1) 2009 virus pandemic.

    BMC Public Health. 2013 Feb 07;13:118

    Authors: Mayoral JM, Alonso J, Garín O, Herrador Z, Astray J, Baricot M, Castilla J, Cantón R, Castro A, Delgado-Rodríguez M, Ferri A, Godoy P, Gónzález-Candelas F, Martín V, Pumarola T, Quintana JM, Soldevila N, Tamames S, Domínguez A, CIBERESP Cases and Controls in Pandemic Influenza Working Group, Spain

    Abstract
    BACKGROUND: During the 2009 influenza pandemic, a change in the type of patients most often affected by influenza was observed. The objective of this study was to assess the role of individual and social determinants in hospitalizations due to influenza A (H1N1) 2009 infection.
    METHODS: We studied hospitalized patients (cases) and outpatients (controls) with confirmed influenza A (H1N1) 2009 infection. A standardized questionnaire was used to collect data. Variables that might be related to the hospitalization of influenza cases were compared by estimation of the odds ratio (OR) and 95% confidence intervals (CI) and the variables entered into binomial logistic regression models.
    RESULTS: Hospitalization due to pandemic A (H1N1) 2009 influenza virus infections was associated with non-Caucasian ethnicity (OR: 2.18, 95% CI 1.17 - 4.08), overcrowding (OR: 2.84, 95% CI 1.20 - 6.72), comorbidity and the lack of previous preventive information (OR: 2.69, 95% CI: 1.50 - 4.83). Secondary or higher education was associated with a lower risk of hospitalization (OR 0.56, 95% CI: 0.36 - 0.87)
    CONCLUSIONS: In addition to individual factors such as comorbidity, other factors such as educational level, ethnicity or overcrowding were associated with hospitalization due to A (H1N1) 2009 influenza virus infections.

    PMID: 23391376 [PubMed - indexed for MEDLINE]




  • Benefit of conjugate pneumococcal vaccination in preventing influenza hospitalization in children: a case-control study.
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    Benefit of conjugate pneumococcal vaccination in preventing influenza hospitalization in children: a case-control study.

    Pediatr Infect Dis J. 2013 Apr;32(4):330-4

    Authors: Domínguez A, Castilla J, Godoy P, Delgado-Rodríguez M, Saez M, Soldevila N, Astray J, María Mayoral J, Martín V, María Quintana J, González-Candelas F, Galán JC, Tamames S, Acosta AC, Baricot M, Garín O, José García J, Moraga F, Pumarola T, CIBERESP Cases and Controls in Pandemic Influenza Working Group Spain

    Abstract
    BACKGROUND: The pneumococcal conjugate vaccine (PCV) might prevent hospitalizations in children because of the role of Streptococcus pneumoniae in the complications of influenza infection. We investigated the benefit of PCV vaccination in preventing influenza hospitalization in children <5 years of age during the 2009 to 2010 pandemic wave and the 2010 to 2011 influenza epidemic in Spain.
    METHODS: A multicenter matched case-control study was undertaken in 27 hospitals from 7 Spanish regions between July 2009 and April 2011. A case was defined as a hospitalized patient between 6 months and 5 years of age with influenza virus infection confirmed by real-time reverse-transcription polymerase chain reaction. We selected 2 matched controls for each case from patients with unplanned hospital admission for reasons other than acute respiratory infection or influenza-like illness. Cases and controls were matched according to age, date of hospitalization and province of residence. Crude and adjusted odds ratios were calculated for associations between influenza hospitalization and PCV vaccination.
    RESULTS: One hundred ninety-four cases and 342 controls were included in the study. In the 2009 to 2010 pandemic wave, the adjusted benefit in preventing hospitalization was 48% (95% confidence interval: 1 to 76) in fully vaccinated children compared with -79% (95% confidence interval: -341 to 27) in the 2010 to 2011 influenza season.
    CONCLUSIONS: The results obtained suggest that, in children <5 years of age, PCV vaccination reduced hospitalization during the 2009 to 2010 pandemic wave. By contrast, there was no observed benefit of vaccination in the 2010 to 2011 influenza season.

    PMID: 23337901 [PubMed - indexed for MEDLINE]




  • Generalized Linear Model (GLM) framework for the association of host variables and viral strains with liver fibrosis in HCV/HIV coinfected patients.
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    Generalized Linear Model (GLM) framework for the association of host variables and viral strains with liver fibrosis in HCV/HIV coinfected patients.

    Infect Genet Evol. 2013 Jan;13:284-91

    Authors: Matas M, Picornell A, Cifuentes C, Payeras A, Bassa A, Homar F, González-Candelas F, López-Labrador FX, Moya A, Ramon MM, Castro JA

    Abstract
    Chronic hepatitis C virus (HCV) infection is the main cause of advanced and end-stage liver disease world-wide, and an important factor of morbidity and mortality in Human Immunodeficiency virus-1 (HIV-1) co-infected individuals. Whereas the genetic variability of HCV has been studied extensively in monoinfected patients, comprehensive analyses of both patient and virus characteristics are still scarce in HCV/HIV co-infection. In order to find correlates for liver damage, we sought to analyze demographic, epidemiological and clinical features of HCV/HIV co-infected patients along with the genetic makeup of HCV (viral subtypes and lineage studied by nucleotide sequencing and phylogenetic analysis of the NS5B region). We used the Generalized Linear Model (GLM) methodology in order to integrate data from the virus and the infected host to find predictors for liver damage. The degree of liver disease was evaluated indirectly by means of two indexes (APRI and FIB-4) and accounting for the time since infection, to estimate fibrosis progression rates. Our analyses identified a reduced number of variables (both from the virus and the host) implicated in liver damage, which included the stage of HIV infection, levels of gamma-glutamil transferase and cholesterol, and some distinct HCV phylogenetic clades.

    PMID: 23174528 [PubMed - indexed for MEDLINE]




  • Evolutionary dynamics of the E1-E2 viral populations during combination therapy in non-responder patients chronically infected with hepatitis C virus subtype 1b.
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    Evolutionary dynamics of the E1-E2 viral populations during combination therapy in non-responder patients chronically infected with hepatitis C virus subtype 1b.

    Infect Genet Evol. 2013 Jan;13:1-10

    Authors: Saludes V, González-Candelas F, Planas R, Solà R, Ausina V, Martró E

    Abstract
    Half of the patients chronically infected with hepatitis C virus (HCV) genotype 1 fail to respond to pegylated interferon alpha (PEG-IFN) and ribavirin (RBV) therapy. This study assesses the effects of treatment on the evolution of the E1-E2 viral region in non-responder patients infected with HCV-1b. Twenty-three HCV-1b chronically infected patients were studied retrospectively, including 19 non-responders to PEG-IFN/RBV therapy (11 null-responders and 8 relapsers) in the study group, and 4 untreated patients in the control group. Genetic and phylogenetic analyses of the E1-E2 viral populations were performed at baseline and at the time of treatment failure to assess changes in genetic variability and evolutionary dynamics during treatment. Baseline virological characteristics were similar in null-responders, relapsers and controls. E1-E2 genetic variability decreased during treatment in non-responders, with a more pronounced decline in relapsers than in null-responders. A specific evolutionary pattern was not observed in null-responders, while a complete substitution of viral variants found at baseline characterised relapser patients. No specific E1-E2 amino acid substitution involved in treatment failure could be identified. In conclusion, although diverse evolutionary patterns with no apparent common adaptive changes were observed during therapy, treatment failure was characterised by a decline in genetic diversity.

    PMID: 23022712 [PubMed - indexed for MEDLINE]




  • Epidemiology and molecular investigation of hepatitis C infection following holiday haemodialysis.
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    Epidemiology and molecular investigation of hepatitis C infection following holiday haemodialysis.

    J Hosp Infect. 2012 Nov;82(3):158-63

    Authors: Roy KM, Galmés-Truyols A, Giménez-Duran J, Anderson E, Prempeh H, González-Candelas F, Bracho MA, Aitken C, Mactier R, Tejera E, Incident Groups in Scotland and Spain

    Abstract
    BACKGROUND: Hepatitis C virus infection (HCV) is not infrequent among haemodialysis patients. Most published reports suggest that patient-to-patient spread, either directly or indirectly, is the most common mode of transmission in renal units.
    AIM: To investigate the source of an outbreak, and the route of transmission, of acute HCV infection in two Scottish patients occurring within eight weeks of receiving haemodialysis in the same unit while on holiday in Majorca.
    METHODS: This was an international epidemiological and molecular investigation of HCV infection among a cohort of haemodialysis patients from nine countries.
    FINDINGS: No further HCV-positive infections were observed among residents and holidaymakers receiving haemodialysis at the unit in Majorca. Molecular investigations confirmed that a Spanish healthcare worker (HCW) was the source of infection for the two Scottish patients. The investigators were unable to determine the route of transmission.
    CONCLUSIONS: This outbreak is the first reported case of HCW-to-patient transmission of HCV in a renal unit, and the third reported case of transmission involving a HCW who had not performed invasive procedures. The issue of whether renal units are an exceptional case with regards to the risk of transmission associated with non-invasive procedures should be considered, in conjunction with the need to improve surveillance of blood-borne virus transmissions in renal units in the UK and abroad.

    PMID: 23022371 [PubMed - indexed for MEDLINE]




  • Effectiveness of pandemic and seasonal influenza vaccines in preventing pandemic influenza-associated hospitalization.
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    Effectiveness of pandemic and seasonal influenza vaccines in preventing pandemic influenza-associated hospitalization.

    Vaccine. 2012 Aug 17;30(38):5644-50

    Authors: Domínguez A, Castilla J, Godoy P, Delgado-Rodríguez M, Martín V, Saez M, Soldevila N, Quintana JM, Mayoral JM, Astray J, González-Candelas F, Cantón R, Tamames S, Castro A, Baricot M, Alonso J, Pumarola T, CIBERESP Cases and Controls in Pandemic Influenza Working Group Spain

    Abstract
    Vaccines are leading pharmacological measures for limiting the impact of pandemic influenza in the community. The objective of this study was to investigate the effectiveness of influenza (pandemic and seasonal) vaccines in preventing pandemic influenza-associated hospitalization. We conducted a multicenter matched case-control study in 36 Spanish hospitals. Patients hospitalized with confirmed pandemic influenza between November 2009 and February 2010 and two hospitalized controls per case, matched according to age, date of hospitalization and province of residence, were selected. Multivariate analysis was performed using conditional logistic regression. Subjects were considered vaccinated if they had received the vaccine >14 days (seasonal influenza vaccine) or >7 days (pandemic influenza vaccine) before the onset of symptoms (cases) or the onset of symptoms of the matched case (controls). For the pandemic influenza vaccine, vaccination effectiveness (VE) was estimated taking into account only patients recruited from November 23, 2009, seven days after the beginning of the pandemic influenza vaccination campaign. 638 cases and 1250 controls were included. The adjusted VE of the pandemic vaccine in the ≥18 years age group was 74.2% (95% CI, 29-90) and that of the influenza seasonal vaccine 15.0% (-34 to 43). The recommendation of influenza vaccination should be reinforced as a regular measure to reduce influenza-associated hospitalization during pandemics and seasonal epidemics.

    PMID: 22796136 [PubMed - indexed for MEDLINE]




  • Ultradeep sequencing analysis of population dynamics of virus escape mutants in RNAi-mediated resistant plants.
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    Ultradeep sequencing analysis of population dynamics of virus escape mutants in RNAi-mediated resistant plants.

    Mol Biol Evol. 2012 Nov;29(11):3297-307

    Authors: Martínez F, Lafforgue G, Morelli MJ, González-Candelas F, Chua NH, Daròs JA, Elena SF

    Abstract
    Plant artificial micro-RNAs (amiRs) have been engineered to target viral genomes and induce their degradation. However, the exceptional evolutionary plasticity of RNA viruses threatens the durability of the resistance conferred by these amiRs. It has recently been shown that viral populations not experiencing strong selective pressure from an antiviral amiR may already contain enough genetic variability in the target sequence to escape plant resistance in an almost deterministic manner. Furthermore, it has also been shown that viral populations exposed to subinhibitory concentrations of the antiviral amiR speed up this process. In this article, we have characterized the molecular evolutionary dynamics of an amiR target sequence in a viral genome under both conditions. The use of Illumina ultradeep sequencing has allowed us to identify virus sequence variants at frequencies as low as 2 × 10(-6) and to track their variation in time before and after the viral population was able of successfully infecting plants fully resistant to the ancestral virus. We found that every site in the amiR-target sequence of the viral genome presented variation and that the variant that eventually broke resistance was sampled among the many coexisting ones. In this system, viral evolution in fully susceptible plants results from an equilibrium between mutation and genetic drift, whereas evolution in partially resistant plants originates from more complex dynamics involving mutation, selection, and drift.

    PMID: 22593223 [PubMed - indexed for MEDLINE]




  • Effectiveness of hand hygiene and provision of information in preventing influenza cases requiring hospitalization.
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    Effectiveness of hand hygiene and provision of information in preventing influenza cases requiring hospitalization.

    Prev Med. 2012 Jun;54(6):434-9

    Authors: Godoy P, Castilla J, Delgado-Rodríguez M, Martín V, Soldevila N, Alonso J, Astray J, Baricot M, Cantón R, Castro A, González-Candelas F, Mayoral JM, Quintana JM, Pumarola T, Tamames S, Domínguez A, CIBERESP Cases and Controls in Pandemic Influenza Working Group, Spain

    Abstract
    BACKGROUND: The objective of the study was to investigate the effectiveness of non-pharmacological interventions in preventing cases of influenza requiring hospitalization.
    METHODS: We performed a multicenter case-control study in 36 hospitals, in 2010 in Spain. Hospitalized influenza cases confirmed by reverse-transcription polymerase chain reaction and three matched controls (two hospital and one community control) per case were selected. The use of non-pharmacological measures seven days before the onset of symptoms (frequency of hand washing, use of alcohol-based hand sanitizers and handwashing after touching contaminated surfaces) was collected.
    RESULTS: We studied 813 cases hospitalized for influenza and 2274 controls. The frequency of hand washing 5-10 times (adjusted odds ratio [aOR]=0.65) and >10 times (aOR=0.59) and handwashing after contact with contaminated surfaces (aOR=0.65) were protective factors and were dose-responsive (p<0.001). Alcohol-based hand sanitizers were associated with marginal benefits (aOR=0.82).
    CONCLUSIONS: Frequent handwashing should be recommended to prevent influenza cases requiring hospitalization.

    PMID: 22548868 [PubMed - indexed for MEDLINE]




  • Score to identify the severity of adult patients with influenza A (H1N1) 2009 virus infection at hospital admission.
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    Score to identify the severity of adult patients with influenza A (H1N1) 2009 virus infection at hospital admission.

    Eur J Clin Microbiol Infect Dis. 2012 Oct;31(10):2693-701

    Authors: Capelastegui A, Quintana JM, Bilbao A, España PP, Garin O, Alonso J, Astray J, Cantón R, Castilla J, Castro A, Delgado-Rodríguez M, Godoy P, Gónzález-Candelas F, Martín V, Mayoral JM, Pumarola T, Tamames S, Soldevila N, Baricot M, Domínguez A, CIBERESP Cases and Controls in Pandemic Influenza Working Group, Spain

    Abstract
    The objective of this paper was to develop a prognostic index for severe complications among hospitalized patients with influenza A (H1N1) 2009 virus infection. We conducted a prospective observational cohort study of 618 inpatients with 2009 H1N1 virus infection admitted to 36 Spanish hospitals between July 2009 and February 2010. Risk factors evaluated included host-related factors and clinical data at admission. We developed a composite index of severe in-hospital complications (SIHC), which included: mortality, mechanical ventilation, septic shock, acute respiratory distress syndrome, and requirement for resuscitation maneuvers. Six factors were independently associated with SIHC: age >45 years, male sex, number of comorbidities, pneumonia, dyspnea, and confusion. From the β parameter obtained in the multivariate model, a weight was assigned to each factor to compute the individual influenza risk score. The score shows an area under the receiver operating characteristic (ROC) curve of 0.77. The SIHC rate was 1.9 % in the low-risk group, 10.3 % in the intermediate-risk group, and 29.6 % in the high-risk group. The odds ratio for complications was 21.8 for the high-risk group compared with the low-risk group. This easy-to-score influenza A (H1N1) 2009 virus infection risk index accurately stratifies patients hospitalized for H1N1 virus infection into low-, intermediate-, and high-risk groups for SIHC.

    PMID: 22526871 [PubMed - indexed for MEDLINE]




  • Staphylococcus prevails in the skin microbiota of long-term immunodeficient mice.
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    Staphylococcus prevails in the skin microbiota of long-term immunodeficient mice.

    Environ Microbiol. 2012 Aug;14(8):2087-98

    Authors: Garcia-Garcerà M, Coscollà M, Garcia-Etxebarria K, Martín-Caballero J, González-Candelas F, Latorre A, Calafell F

    Abstract
    Host-commensal relationships in the skin are a complex system governed by variables related to the host, the bacteria and the environment. A disruption of this system may lead to new steady states, which, in turn, may lead to disease. We have studied one such disruption by characterizing the skin microbiota in healthy and immunodepressed (ID) mice. A detailed anatomopathological study failed to reveal any difference between the skin of healthy and ID mice. We sequenced the 16S rDNA V1-V2 gene region to saturation in 10 healthy and 10 ID 8 week-old mice, and found than all of the healthy and two of the ID mice had bacterial communities that were similar in composition to that of human skin, although, presumably because of the uniform raising conditions, less interindividual variation was found in mice. However, eight ID mice showed microbiota dominated by Staphylococcus epidermidis. Quantitative PCR amplification of 16S rDNA gene and of the Staphylococcus-specific TstaG region confirmed the previous results and indicated that the quantitative levels of Staphylococcus were similar in both groups while the total number of 16S copies was greater in the healthy mice. Thus, it is possible that, under long-term immunodeficiency, which removes the acquired but not the native immune system, S.epidermidis may inhibit the growth of other bacteria but does not cause a pathogenic state.

    PMID: 22524615 [PubMed - indexed for MEDLINE]




  • Prognosis of hospitalized patients with 2009 H1N1 influenza in Spain: influence of neuraminidase inhibitors.
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    Prognosis of hospitalized patients with 2009 H1N1 influenza in Spain: influence of neuraminidase inhibitors.

    J Antimicrob Chemother. 2012 Jul;67(7):1739-45

    Authors: Delgado-Rodríguez M, Castilla J, Godoy P, Martín V, Soldevila N, Alonso J, Astray J, Baricot M, Cantón R, Castro A, Gónzález-Candelas F, Mayoral JM, Quintana JM, Pumarola T, Tamames S, Sáez M, Domínguez A, CIBERESP Cases and Controls in Pandemic Influenza Working Group

    Abstract
    BACKGROUND: The H1N1 influenza pandemic strain has been associated with a poor prognosis in hospitalized patients. The present report evaluates the factors influencing prognosis.
    METHODS: A total of 813 patients hospitalized with H1N1 influenza in 36 hospitals (nationwide) in Spain were analysed. Detailed histories of variables preceding hospital admission were obtained by interview, validating data on medications and vaccine with their attending physicians. Data on treatment and complications during hospital stay were recorded. As definition of poor outcome, the endpoints of death and admission to intensive care were combined; and as a further outcome, length of stay was used.
    RESULTS: The mean age was 38.5 years (SD 22.8 years). There were 10 deaths and 79 admissions to intensive care (combined, 88). The use of neuraminidase inhibitors was reported by 495 patients (60.9%). The variables significantly associated with a poor outcome were diabetes (OR = 2.21, 95% CI = 1.21-4.02), corticosteroid therapy (OR = 3.37, 95% CI = 1.39-8.20) and use of histamine-2 receptor antagonists (OR = 2.68, 95% CI = 1.14-6.36), while the use of neuraminidase inhibitors (OR = 0.57, 95% CI = 0.34-0.94) was protective. Neuraminidase inhibitors within the first 2 days after the influenza onset reduced hospital stay by a mean of 1.9 days (95% CI = 4.7-6.6).
    CONCLUSIONS: The use of neuraminidase inhibitors decreases the length of hospital stay and admission to intensive care and/or death.

    PMID: 22467633 [PubMed - indexed for MEDLINE]




  • Risk factors and effectiveness of preventive measures against influenza in the community.
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    Risk factors and effectiveness of preventive measures against influenza in the community.

    Influenza Other Respir Viruses. 2013 Mar;7(2):177-83

    Authors: Castilla J, Godoy P, Domínguez Á, Martín V, Delgado-Rodríguez M, Martínez-Baz I, Baricot M, Soldevila N, Mayoral JM, Astray J, Quintana JM, Cantón R, Castro A, González-Candelas F, Alonso J, Saez M, Tamames S, Pumarola T, CIBERESP Cases and Controls in Influenza Working Group

    Abstract
    BACKGROUND: The role of different risk exposures and preventive measures against influenza has not been well established.
    OBJECTIVE: The aim of this study was to evaluate risk factors and measures to prevent influenza infection in the community.
    METHODS: We conducted a multicenter case-control study. Cases were 481 outpatients aged 18 years or older with laboratory-confirmed influenza A(H1N1)09 in the 2009-2010 season in Spain. A control was selected for each case from outpatients from the same area matched by age and date of consultation. Information on risk situations, preventive measures and other variables was obtained by interview and review of the medical record.
    RESULTS: In the multivariate conditional logistic regression analysis, the risk of a diagnosis of influenza increased with the number of cohabitants (compared with <3 cohabitants, three cohabitants had an OR= 1·80, 95% CI 1·12-2·89, and ≥5 cohabitants had an OR = 2·66, 95% CI 1·31-5·41) and for health care workers (OR = 2·94, 95% CI 1·53-5·66). The use of metropolitan public transport was associated with a lower frequency of a diagnosis of influenza (OR = 0·45, 95% CI 0·30-0·68) but not the use of taxis or long-distance transport. The influenza A(H1N1)09 vaccine had a protective effect (OR =0·13, 95% CI 0·04-0·48), unlike hand washing after touching contaminated surfaces or the use of alcohol-based hand sanitizers.
    CONCLUSION: The home environment appears to play an important role in the spread of influenza in adults, but not the use of public transport. Health care workers have a higher risk of contracting influenza. Vaccination was the most effective preventive measure.

    PMID: 22458533 [PubMed - indexed for MEDLINE]




  • Sociodemographic factors and clinical conditions associated to hospitalization in influenza A (H1N1) 2009 virus infected patients in Spain, 2009-2010.
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    Sociodemographic factors and clinical conditions associated to hospitalization in influenza A (H1N1) 2009 virus infected patients in Spain, 2009-2010.

    PLoS One. 2012;7(3):e33139

    Authors: González-Candelas F, Astray J, Alonso J, Castro A, Cantón R, Galán JC, Garin O, Sáez M, Soldevila N, Baricot M, Castilla J, Godoy P, Delgado-Rodríguez M, Martín V, Mayoral JM, Pumarola T, Quintana JM, Tamames S, Domínguez A, CIBERESP Cases and Controls in Pandemic Influenza Working Group

    Abstract
    The emergence and pandemic spread of a new strain of influenza A (H1N1) virus in 2009 resulted in a serious alarm in clinical and public health services all over the world. One distinguishing feature of this new influenza pandemic was the different profile of hospitalized patients compared to those from traditional seasonal influenza infections. Our goal was to analyze sociodemographic and clinical factors associated to hospitalization following infection by influenza A(H1N1) virus. We report the results of a Spanish nationwide study with laboratory confirmed infection by the new pandemic virus in a case-control design based on hospitalized patients. The main risk factors for hospitalization of influenza A (H1N1) 2009 were determined to be obesity (BMI≥40, with an odds-ratio [OR] 14.27), hematological neoplasia (OR 10.71), chronic heart disease, COPD (OR 5.16) and neurological disease, among the clinical conditions, whereas low education level and some ethnic backgrounds (Gypsies and Amerinds) were the sociodemographic variables found associated to hospitalization. The presence of any clinical condition of moderate risk almost triples the risk of hospitalization (OR 2.88) and high risk conditions raise this value markedly (OR 6.43). The risk of hospitalization increased proportionally when for two (OR 2.08) or for three or more (OR 4.86) risk factors were simultaneously present in the same patient. These findings should be considered when a new influenza virus appears in the human population.

    PMID: 22412995 [PubMed - indexed for MEDLINE]




  • Polyploid origin, genetic diversity and population structure in the tetraploid sea lavender Limonium narbonense Miller (Plumbaginaceae) from eastern Spain.
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    Polyploid origin, genetic diversity and population structure in the tetraploid sea lavender Limonium narbonense Miller (Plumbaginaceae) from eastern Spain.

    Genetica. 2011 Oct;139(10):1309-22

    Authors: Palop-Esteban M, Segarra-Moragues J, González-Candelas F

    Abstract
    Limonium narbonense Miller is a fertile tetraploid species with a sporophytic self-incompatibility system. This sea lavender is found in coastal salt marshes which have been under intense human pressure during the past decades resulting in significant habitat fragmentation. Eleven microsatellite loci specifically designed for this species were amplified in 135 individuals from five populations. These markers were used to investigate the polyploid nature, the levels of genetic diversity and population structure in this species. L. narbonense showed high levels of genetic diversity (A = 7.82, P = 100% H (T) = 0.446), consistent with its likely autotetraploid origin revealed in this study and obligate outcrossing breeding system. Inbreeding (F (IS)) values were low in the three southern populations (mean F (IS) = 0.062), and higher in the northern populations (mean F (IS) = 0.184). Bayesian analysis of population structure revealed that populations could be grouped into two genetic clusters, one including three southern populations and the other the two northernmost ones. Individuals from the two northernmost populations showed higher admixture of the two genetic clusters than individuals from the three southern ones. A thorough analysis of microsatellite electrophoretic patterns suggests an autotetraploid origin for L. narbonense. The genetic structure revealed in this study is attributed to a recent migration from the southern area. This result suggests a net gene flow from the south to the north, likely facilitated by migratory movements of birds visiting the temporary flooded ponds occupied by L. narbonense.

    PMID: 22297901 [PubMed - indexed for MEDLINE]




  • Enterovirus co-infections and onychomadesis after hand, foot, and mouth disease, Spain, 2008.
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    Enterovirus co-infections and onychomadesis after hand, foot, and mouth disease, Spain, 2008.

    Emerg Infect Dis. 2011 Dec;17(12):2223-31

    Authors: Bracho MA, González-Candelas F, Valero A, Córdoba J, Salazar A

    Abstract
    Hand, foot, and mouth disease (HFMD), a common disease caused by enteroviruses (EVs), usually affects children. Clustered and sporadic HFMD cases, followed by onychomadesis (nail shedding), occurred during summer and fall 2008 in Valencia, Spain. Fecal samples from onychomadesis patients, who did or did not have previous HFMD, and from healthy children exposed to onychomadesis patients tested positive for EV. The complete viral protein 1 capsid gene sequence was obtained for typing and phylogenetic analysis. Two EV serotypes, coxsackievirus A10 and coxsackievirus B1 (CVB1), were mainly detected as a monoinfection or co-infection in a childcare center where an onychomadesis outbreak occurred. On the basis of our results, and detection of CVB1 in 2 other contemporary onychomadesis outbreaks in childcare centers in Spain, we propose that mixed infection of an EV serotype that causes HFMD, plus the serotype CVB1, could explain the emergence after HFMD of onychomadesis, a rare and late complication.

    PMID: 22172227 [PubMed - indexed for MEDLINE]




  • Recombination in hepatitis C virus.
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    Recombination in hepatitis C virus.

    Viruses. 2011 Oct;3(10):2006-24

    Authors: González-Candelas F, López-Labrador FX, Bracho MA

    Abstract
    Hepatitis C virus (HCV) is a Flavivirus with a positive-sense, single-stranded RNA genome of about 9,600 nucleotides. It is a major cause of liver disease, infecting almost 200 million people all over the world. Similarly to most RNA viruses, HCV displays very high levels of genetic diversity which have been used to differentiate six major genotypes and about 80 subtypes. Although the different genotypes and subtypes share basic biological and pathogenic features they differ in clinical outcomes, response to treatment and epidemiology. The first HCV recombinant strain, in which different genome segments derived from parentals of different genotypes, was described in St. Petersburg (Russia) in 2002. Since then, there have been only a few more than a dozen reports including descriptions of HCV recombinants at all levels: between genotypes, between subtypes of the same genotype and even between strains of the same subtype. Here, we review the literature considering the reasons underlying the difficulties for unequivocally establishing recombination in this virus along with the analytical methods necessary to do it. Finally, we analyze the potential consequences, especially in clinical practice, of HCV recombination in light of the coming new therapeutic approaches against this virus.

    PMID: 22069526 [PubMed - indexed for MEDLINE]




  • Genotyping of a nosocomial outbreak of pandemic influenza A/H1N1 2009.
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    Genotyping of a nosocomial outbreak of pandemic influenza A/H1N1 2009.

    J Clin Virol. 2011 Oct;52(2):129-32

    Authors: Rodríguez-Sánchez B, Alonso M, Catalán P, Sánchez Conde M, González-Candelas F, Giannella M, Bouza E, García de Viedma D

    Abstract
    BACKGROUND: Epidemiological surveys have revealed outbreaks of pandemic influenza A (H1N1) 2009 in several different contexts. Molecular characterization of the influenza virus could help to provide a more accurate description of these outbreaks.
    OBJECTIVE: To genotype pandemic influenza A (H1N1) 2009 isolates from an epidemiologically defined nosocomial outbreak.
    STUDY DESIGN: We sequenced the neuraminidase (NA) and hemagglutinin (HA) influenza A (H1N1) 2009 genes from ten HIV-positive patients involved in an epidemiologically defined outbreak in the Clinical Microbiology and Infectious Diseases (CMID) Department. Sequences were aligned to search for specific genetic features of the involved strain. We also analyzed 37 unrelated influenza A (H1N1) 2009 cases from other hospital departments. All the sequences were used to obtain phylogenetic trees.
    RESULTS: Identical genotypic features were shared by nine of the 10 cases initially considered to be involved in the outbreak, but not by the remaining case. These features involved two silent mutations at N385 and V407 in the NA gene and three amino acid substitutions in the HA gene (D225E, A189T, and P300S). Searching for these substitutions in patients with influenza A (H1N1) 2009 hospitalized in other departments during the same period allowed us to identify an additional unsuspected immunocompetent case. The five outbreak-specific substitutions were absent in the remaining 36 unrelated controls. One of the substitutions (P300S) rendered detection of this variant by the CDC protocol inefficient. The other outbreak-specific substitutions (D225E and A189T) were identified at codons that have been analyzed in the context of virulence.
    CONCLUSIONS: Genotyping is essential to ensure a more accurate description of pandemic influenza A (H1N1) 2009 outbreaks.

    PMID: 21813318 [PubMed - indexed for MEDLINE]




  • Molecular surveillance of HIV-1 in Madrid, Spain: a phylogeographic analysis.
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    Molecular surveillance of HIV-1 in Madrid, Spain: a phylogeographic analysis.

    J Virol. 2011 Oct;85(20):10755-63

    Authors: González-Alba JM, Holguín A, Garcia R, García-Bujalance S, Alonso R, Suárez A, Delgado R, Cardeñoso L, González R, García-Bermejo I, Portero F, de Mendoza C, González-Candelas F, Galán JC

    Abstract
    The molecular epidemiology of HIV-1 is constantly changing, mainly as a result of human migratory flows and the high adaptive ability of the virus. In recent years, Spain has become one of Europe's main destinations for immigrants and one of the western European countries with the highest rates of HIV-positive patients. Using a phylogeographic approach, we have analyzed the relationship between HIV-1 variants detected in immigrant and native populations of the urban area of Madrid. Our project was based on two coincidental facts. First, resistance tests were extended to naïve and newly diagnosed patients, and second, the Spanish government legislated the provision of legal status to many immigrants. This allowed us to obtain a large data set (n = 2,792) from 11 Madrid hospitals of viral pol sequences from the two populations, and with this unique material, we explored the impact of immigration in the epidemiological trends of HIV-1 variants circulating in the largest Spanish city. The prevalence of infections by non-B HIV-1 variants in the studied cohort was 9%, rising to 25% among native Spanish patients. Multiple transmission events involving different lineages and subsubtypes were observed in all the subtypes and recombinant forms studied. Our results also revealed strong social clustering among the most recent immigrant groups, such as Russians and Romanians, but not in those groups who have lived in Madrid for many years. Additionally, we document for the first time the presence of CRF47_BF and CRF38_BF in Europe, and a new BG recombinant form found in Spaniards and Africans is tentatively proposed. These results suggest that the HIV-1 epidemic will evolve toward a more complex epidemiological landscape.

    PMID: 21795343 [PubMed - indexed for MEDLINE]




  • [Genetic factors in severe cases of (H1N1) 2009 influenza].
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    [Genetic factors in severe cases of (H1N1) 2009 influenza].

    Rev Esp Salud Publica. 2011 Jan-Feb;85(1):33-6

    Authors: Calafell i Majó F, González Candelas F

    Abstract
    The pandemic influenza (H1N1) 2009 raised a number of issues, of which we address the following: Why did between 25 and 30% of severe influenza cases show no obvious risk factor? We hypothesize that an element that can contribute to the answer are host genetic risk factors involved in poor disease progression. Several indications led us to this hypothesis: i) studies of familial aggregation in Iceland and Utah Mormons show some heritability of influenza mortality; ii) nearly 300 known human genes are necessary for the replication of the influenza virus, and iii) the most severe cases of influenza A (H1N1) 2009 showed a deregulation of the adaptive immune system. We are addressing this problem through a case-control design (hospitalized cases of influenza (H1N1) 2009 confirmed against outpatient cases, also confirmed for (H1N1) 2009), which will be genotyped for more than a million single nucleotide polymorphisms (SNPs) and copy number variations (CNVs).

    PMID: 21750840 [PubMed - indexed for MEDLINE]




  • [Risk factors of influenza (H1N1) 2009 hospitalization and effectiveness of pharmaceutical and nonpharmaceutical interventions in its prevention: a case-control study].
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    [Risk factors of influenza (H1N1) 2009 hospitalization and effectiveness of pharmaceutical and nonpharmaceutical interventions in its prevention: a case-control study].

    Rev Esp Salud Publica. 2011 Jan-Feb;85(1):3-15

    Authors: Domínguez A, Alonso J, Astray J, Baricot M, Cantón R, Castilla J, Castro A, Delgado M, Godoy P, González-Candelas F, Martín V, Mayoral JM, Quintana JM, Perea E, Pumarola T, Soldevila N, Tamames S, Grupo de Trabajo del Proyecto CIBERESP de Casos y Controles sobre la Gripe Pandémica

    Abstract
    Potentially useful pharmaceutical measures to limit the impact of pandemic influenza in the community include antiviral drugs (neuraminidase inhibitors) and the influenza and pneumococcal vaccines, as influenza predisposes to bacterial pneumonia caused by Streptococcus pneumoniae. Non-pharmaceutical measures include hand washing and respiratory hygiene. Due to the lack of knowledge of the effectiveness of these measures in a pandemic situation, in September 2009, CIBER de Epidemiología y Salud Pública presented a multicenter case-control study, with controls matched for age, hospital and date of hospitalization, to investigate these aspects in 37 hospitals in 7 Spanish autonomous communities, in response to the call for research projects by the Ministry of Science and Innovation Research Program on Influenza A (H1N1) in Spain. For each confirmed hospitalized case of pandemic influenza, 1 confirmed outpatient case and 3 controls (2 hospitalized and 1 outpatient) were selected. Demographic variables, underlying medical conditions, use of antiviral agents, vaccines received and hygiene habits were collected for all cases and controls. In hospitalized cases, information on antiviral therapy and disease progression was collected. A total of 3750 patients were recruited by October 2010. Data cleansing and the recovery of variables is now underway. The involvement of the Public Health Directorate has been instrumental in adapting the project to the evolution of the pandemic.

    PMID: 21750838 [PubMed - indexed for MEDLINE]




  • Hepatitis C virus sequences from different patients confirm the existence and transmissibility of subtype 2q, a rare subtype circulating in the metropolitan area of Barcelona, Spain.
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    Hepatitis C virus sequences from different patients confirm the existence and transmissibility of subtype 2q, a rare subtype circulating in the metropolitan area of Barcelona, Spain.

    J Med Virol. 2011 May;83(5):820-6

    Authors: Martró E, Valero A, Jordana-Lluch E, Saludes V, Planas R, González-Candelas F, Ausina V, Bracho MA

    Abstract
    The hepatitis C virus (HCV) has been classified into six genotypes and more than 70 subtypes with distinct geographical and epidemiological distributions. While 18 genotype 2 subtypes have been proposed, only 5 have had their complete sequence determined. The aim of this study was to characterize HCV isolates from three patients from the Barcelona metropolitan area of Spain for whom commercial genotyping methods provided discordant results. Full-length genome sequencing was carried out for 2 of the 3 patients; for the third patient only partial NS5B sequences could be obtained. The generated sequences were subjected to phylogenetic, recombination, and identity analyses. Sequences covering most of the HCV genome (9398 and 9566  nt in length) were obtained and showed a 90.3% identity to each other at the nucleotide level, while both sequences differed by 17.5-22.6% from the other fully sequenced genotype 2 subtypes. No evidence of recombination was found. The NS5B phylogenetic tree showed that sequences from the three patients cluster together with the only representative sequence of the provisionally designed 2q subtype, which also corresponds to a patient from Barcelona. Phylogenetic analysis of the full coding sequence showed that subtype 2q was more closely related to subtype 2k. The results obtained in this study suggest that subtype 2q now meets the requirements for confirmed designation status according to consensus criteria for HCV classification and nomenclature, and its epidemiological value is ensured as it has spread among several patients in the Barcelona metropolitan area.

    PMID: 21412791 [PubMed - indexed for MEDLINE]




  • Evolutionary history of the OmpR/IIIA family of signal transduction two component systems in Lactobacillaceae and Leuconostocaceae.
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    Evolutionary history of the OmpR/IIIA family of signal transduction two component systems in Lactobacillaceae and Leuconostocaceae.

    BMC Evol Biol. 2011 Feb 01;11:34

    Authors: Zúñiga M, Gómez-Escoín CL, González-Candelas F

    Abstract
    BACKGROUND: Two component systems (TCS) are signal transduction pathways which typically consist of a sensor histidine kinase (HK) and a response regulator (RR). In this study, we have analyzed the evolution of TCS of the OmpR/IIIA family in Lactobacillaceae and Leuconostocaceae, two families belonging to the group of lactic acid bacteria (LAB). LAB colonize nutrient-rich environments such as foodstuffs, plant materials and the gastrointestinal tract of animals thus driving the study of this group of both basic and applied interest.
    RESULTS: The genomes of 19 strains belonging to 16 different species have been analyzed. The number of TCS encoded by the strains considered in this study varied between 4 in Lactobacillus helveticus and 17 in Lactobacillus casei. The OmpR/IIIA family was the most prevalent in Lactobacillaceae accounting for 71% of the TCS present in this group. The phylogenetic analysis shows that no new TCS of this family has recently evolved in these Lactobacillaceae by either lineage-specific gene expansion or domain shuffling. Furthermore, no clear evidence of non-orthologous replacements of either RR or HK partners has been obtained, thus indicating that coevolution of cognate RR and HKs has been prevalent in Lactobacillaceae.
    CONCLUSIONS: The results obtained suggest that vertical inheritance of TCS present in the last common ancestor and lineage-specific gene losses appear as the main evolutionary forces involved in their evolution in Lactobacillaceae, although some HGT events cannot be ruled out. This would agree with the genomic analyses of Lactobacillales which show that gene losses have been a major trend in the evolution of this group.

    PMID: 21284862 [PubMed - indexed for MEDLINE]




  • Baseline prediction of combination therapy outcome in hepatitis C virus 1b infected patients by discriminant analysis using viral and host factors.
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    Baseline prediction of combination therapy outcome in hepatitis C virus 1b infected patients by discriminant analysis using viral and host factors.

    PLoS One. 2010 Nov 30;5(11):e14132

    Authors: Saludes V, Bracho MA, Valero O, Ardèvol M, Planas R, González-Candelas F, Ausina V, Martró E

    Abstract
    BACKGROUND: Current treatment of chronic hepatitis C virus (HCV) infection has limited efficacy -especially among genotype 1 infected patients-, is costly, and involves severe side effects. Thus, predicting non-response is of major interest for both patient wellbeing and health care expense. At present, treatment cannot be individualized on the basis of any baseline predictor of response. We aimed to identify pre-treatment clinical and virological parameters associated with treatment failure, as well as to assess whether therapy outcome could be predicted at baseline.
    METHODOLOGY: Forty-three HCV subtype 1b (HCV-1b) chronically infected patients treated with pegylated-interferon alpha plus ribavirin were retrospectively studied (21 responders and 22 non-responders). Host (gender, age, weight, transaminase levels, fibrosis stage, and source of infection) and viral-related factors (viral load, and genetic variability in the E1-E2 and Core regions) were assessed. Logistic regression and discriminant analyses were used to develop predictive models. A "leave-one-out" cross-validation method was used to assess the reliability of the discriminant models.
    PRINCIPAL FINDINGS: Lower alanine transaminase levels (ALT, p=0.009), a higher number of quasispecies variants in the E1-E2 region (number of haplotypes, nHap_E1-E2) (p=0.003), and the absence of both amino acid arginine at position 70 and leucine at position 91 in the Core region (p=0.039) were significantly associated with treatment failure. Therapy outcome was most accurately predicted by discriminant analysis (90.5% sensitivity and 95.5% specificity, 85.7% sensitivity and 81.8% specificity after cross-validation); the most significant variables included in the predictive model were the Core amino acid pattern, the nHap_E1-E2, and gamma-glutamyl transferase and ALT levels.
    CONCLUSIONS AND SIGNIFICANCE: Discriminant analysis has been shown as a useful tool to predict treatment outcome using baseline HCV genetic variability and host characteristics. The discriminant models obtained in this study led to accurate predictions in our population of Spanish HCV-1b treatment naïve patients.

    PMID: 21152430 [PubMed - indexed for MEDLINE]




  • MICROSATELIGHT--pipeline to expedite microsatellite analysis.
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    MICROSATELIGHT--pipeline to expedite microsatellite analysis.

    J Hered. 2011 Mar-Apr;102(2):247-9

    Authors: Palero F, González-Candelas F, Pascual M

    Abstract
    MICROSATELIGHT is a Perl/Tk pipeline with a graphical user interface that facilitates several tasks when scoring microsatellites. It implements new subroutines in R and PERL and takes advantage of features provided by previously developed freeware. MICROSATELIGHT takes raw genotype data and automates the peak identification through PeakScanner. The PeakSelect subroutine assigns peaks to different microsatellite markers according to their multiplex group, fluorochrome type, and size range. After peak selection, binning of alleles can be carried out 1) automatically through AlleloBin or 2) by manual bin definition through Binator. In both cases, several features for quality checking and further binning improvement are provided. The genotype table can then be converted into input files for several population genetics programs through CREATE. Finally, Hardy-Weinberg equilibrium tests and confidence intervals for null allele frequency can be obtained through GENEPOP. MICROSATELIGHT is the only freely available public-domain software that facilitates full multiplex microsatellite scoring, from electropherogram files to user-defined text files to be used with population genetics software. MICROSATELIGHT has been created for the Windows XP operating system and has been successfully tested under Windows 7. It is available at http://sourceforge.net/projects/microsatelight/.

    PMID: 21127193 [PubMed - indexed for MEDLINE]




  • Polyphyletic origin of Vibrio vulnificus biotype 2 as revealed by sequence-based analysis.
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    Polyphyletic origin of Vibrio vulnificus biotype 2 as revealed by sequence-based analysis.

    Appl Environ Microbiol. 2011 Jan;77(2):688-95

    Authors: Sanjuán E, González-Candelas F, Amaro C

    Abstract
    A sequence-based analysis of seven housekeeping and virulence-related genes shows that the species Vibrio vulnificus is subdivided into three phylogenetic lineages that do not correspond with the biotypes and that biotype 2 is polyphyletic. These results support the reclassification of biotype 2 as a pathovar that would group the strains with pathogenic potential to develop vibriosis in fish.

    PMID: 21097581 [PubMed - indexed for MEDLINE]




  • Domain organization and evolution of multifunctional autoprocessing repeats-in-toxin (MARTX) toxin in Vibrio vulnificus.
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    Domain organization and evolution of multifunctional autoprocessing repeats-in-toxin (MARTX) toxin in Vibrio vulnificus.

    Appl Environ Microbiol. 2011 Jan;77(2):657-68

    Authors: Roig FJ, González-Candelas F, Amaro C

    Abstract
    The objective of this study was to analyze multifunctional autoprocessing repeats-in-toxin (MARTX) toxin domain organization within the aquatic species Vibrio vulnificus as well as to study the evolution of the rtxA1 gene. The species is subdivided into three biotypes that differ in host range and geographical distribution. We have found three different types (I, II, and III) of V. vulnificus MARTX (MARTX(Vv)) toxins with common domains (an autocatalytic cysteine protease domain [CPD], an α/β-hydrolase domain, and a domain resembling that of the LifA protein of Escherichia coli O127:H6 E2348/69 [Efa/LifA]) and specific domains (a Rho-GTPase inactivation domain [RID], a domain of unknown function [DUF], a domain resembling that of the rtxA protein of Photorhabdus asymbiotica [rtxA(PA)], and an actin cross-linking domain [ACD]). Biotype 1 isolates harbor MARTX(Vv) toxin types I and II, biotype 2 isolates carry MARTX(Vv) toxin type III, and biotype 3 isolates have MARTX(Vv) toxin type II. The analyzed biotype 2 isolates harbor two identical copies of rtxA1, one chromosomal and the other plasmidic. The evolutionary history of the gene demonstrates that MARTX(Vv) toxins are mosaics, comprising pieces with different evolutionary histories, some of which have been acquired by intra- or interspecific horizontal gene transfer. Finally, we have found evidence that the evolutionary history of the rtxA1 gene for biotype 2 differs totally from the gene history of biotypes 1 and 3.

    PMID: 21075892 [PubMed - indexed for MEDLINE]




  • Quantifying nonvertical inheritance in the evolution of Legionella pneumophila.
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    Quantifying nonvertical inheritance in the evolution of Legionella pneumophila.

    Mol Biol Evol. 2011 Feb;28(2):985-1001

    Authors: Coscollá M, Comas I, González-Candelas F

    Abstract
    The exchange of genetic material among bacterial strains and species is recognized as an important factor determining their evolutionary, population genetic, and epidemiological features. We present a detailed analysis of nonvertical inheritance in Legionella pneumophila, a human pathogen and facultative intracellular parasite of amoebas. We have analyzed the exchange of L. pneumophila genetic material with other bacteria at three different levels: population genetics, population genomics, and phylogenomics. At the population genetics level, we have analyzed 89 clinical and environmental isolates after sequencing six coding loci and three intergenic regions for a total of 3,923 bp. In the population genomics analysis, we have studied the roles of recombination and mutation in the common portion of the genome sequence of four L. pneumophila strains. In the phylogenomic analysis, we have studied the phylogenetic origin of 1,700 genes in the L. pneumophila pangenome. For this, we have considered 12 possible phylogenetic alternatives, derived from a reference tree obtained from 104 genes from 41 species, which have been tested under a rigorous statistical framework. The results obtained agree in assigning an important role to nonvertical inheritance in shaping the composition of the L. pneumophila genome and of the genetic variation in its populations. We have found a negative correlation between phylogenetic distance and likelihood of horizontal gene transfer. Phylogenetic proximity and increased chances resulting from sharing the ecological niche provided by the amoeba host have likely had a major influence on the rate of gene exchange in Legionella.

    PMID: 20961962 [PubMed - indexed for MEDLINE]




  • Patient-to-patient transmission of hepatitis C virus (HCV) during colonoscopy diagnosis.
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    Patient-to-patient transmission of hepatitis C virus (HCV) during colonoscopy diagnosis.

    Virol J. 2010 Sep 08;7:217

    Authors: González-Candelas F, Guiral S, Carbó R, Valero A, Vanaclocha H, González F, Bracho MA

    Abstract
    BACKGROUND: No recognized risk factors can be identified in 10-40% of hepatitis C virus (HCV)-infected patients suggesting that the modes of transmission involved could be underestimated or unidentified. Invasive diagnostic procedures, such as endoscopy, have been considered as a potential HCV transmission route; although the actual extent of transmission in endoscopy procedures remains controversial. Most reported HCV outbreaks related to nosocomial acquisition have been attributed to unsafe injection practices and use of multi-dose vials. Only a few cases of likely patient-to-patient HCV transmission via a contaminated colonoscope have been reported to date. Nosocomial HCV infection may have important medical and legal implications and, therefore, possible transmission routes should be investigated. In this study, a case of nosocomial transmission of HCV from a common source to two patients who underwent colonoscopy in an endoscopy unit is reported.
    RESULTS: A retrospective epidemiological search after detection of index cases revealed several potentially infective procedures: sample blood collection, use of a peripheral catheter, anesthesia and colonoscopy procedures. The epidemiological investigation showed breaches in colonoscope reprocessing and deficiencies in the recording of valuable tracing data. Direct sequences from the NS5B region were obtained to determine the extent of the outbreak and cloned sequences from the E1-E2 region were used to establish the relationships among intrapatient viral populations. Phylogenetic analyses of individual sequences from viral populations infecting the three patients involved in the outbreak confirmed the patient pointed out by the epidemiological search as the source of the outbreak. Furthermore, the sequential order in which the patients underwent colonoscopy correlates with viral genetic variability estimates.
    CONCLUSIONS: Patient-to-patient transmission of HCV could be demonstrated although the precise route of transmission remained unclear. Viral genetic variability is proposed as a useful tool for tracing HCV transmission, especially in recent transmissions.

    PMID: 20825635 [PubMed - indexed for MEDLINE]




  • Legionellosis outbreak associated with asphalt paving machine, Spain, 2009.
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    Legionellosis outbreak associated with asphalt paving machine, Spain, 2009.

    Emerg Infect Dis. 2010 Sep;16(9):1381-7

    Authors: Coscollá M, Fenollar J, Escribano I, González-Candelas F

    Abstract
    From 1999 through 2005 in Alcoi, Spain, incidence of legionellosis was continually high. Over the next 4 years, incidence was lower, but an increase in July 2009 led health authorities to declare an epidemic outbreak. A molecular epidemiology investigation showed that the allelic profiles for all Legionella pneumophila samples from the 2009 outbreak patients were the same, thus pointing to a common genetic origin for their infections, and that they were identical to that of the organism that had caused the previous outbreaks. Spatial-temporal and sequence-based typing analyses indicated a milling machine used in street asphalt repaving and its water tank as the most likely sources. As opposed to other machines used for street cleaning, the responsible milling machine used water from a natural spring. When the operation of this machine was prohibited and cleaning measures were adopted, infections ceased.

    PMID: 20735921 [PubMed - indexed for MEDLINE]




  • Onychomadesis outbreak in Valencia, Spain associated with hand, foot, and mouth disease caused by enteroviruses.
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    Onychomadesis outbreak in Valencia, Spain associated with hand, foot, and mouth disease caused by enteroviruses.

    Pediatr Dermatol. 2011 Jan-Feb;28(1):1-5

    Authors: Davia JL, Bel PH, Ninet VZ, Bracho MA, González-Candelas F, Salazar A, Gobernado M, Bosch IF

    Abstract
    This report evaluates the June 2008 onychomadesis outbreak in Valencia, Spain. The study sample consisted of 221 onychomadesis cases and 77 nonaffected individuals who lived close to those affected. We collected data on dietary variables, hygiene products, and individual pathological histories. Feces and blood specimens were collected from 44 cases and 24 controls to evaluate exposure to infectious agents. Pathological background data revealed a high frequency (61%) of hand, foot, and mouth disease among the onychomadesis cases. Coxsackievirus A10 was the most commonly detected enterovirus in both case and control groups (49%). Other enteroviruses such as coxsackieviruses A5, A6, A16, B1, and B3; echoviruses 3, 4, and 9; and enterovirus 71 were present in low frequencies in the case and control groups (3-9%). The 2008 onychomadesis outbreak in the metropolitan area of Valencia was associated with an outbreak of hand, foot, and mouth disease primarily caused by coxsackievirus A10.

    PMID: 20553401 [PubMed - indexed for MEDLINE]




  • The USH2A c.2299delG mutation: dating its common origin in a Southern European population.
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    The USH2A c.2299delG mutation: dating its common origin in a Southern European population.

    Eur J Hum Genet. 2010 Jul;18(7):788-93

    Authors: Aller E, Larrieu L, Jaijo T, Baux D, Espinós C, González-Candelas F, Nájera C, Palau F, Claustres M, Roux AF, Millán JM

    Abstract
    Usher syndrome type II is the most common form of Usher syndrome. USH2A is the main responsible gene of the three known to be disease causing. It encodes two isoforms of the protein usherin. This protein is part of an interactome that has an essential role in the development and function of inner ear hair cells and photoreceptors. The gene contains 72 exons spanning over a region of 800 kb. Although numerous mutations have been described, the c.2299delG mutation is the most prevalent in several populations. Its ancestral origin was previously suggested after the identification of a common core haplotype restricted to 250 kb in the 5' region that encodes the short usherin isoform. By extending the haplotype analysis over the 800 kb region of the USH2A gene with a total of 14 intragenic single nucleotide polymorphisms, we have been able to define 10 different c.2299delG haplotypes, showing high variability but preserving the previously described core haplotype. An exhaustive c.2299delG/control haplotype study suggests that the major source of variability in the USH2A gene is recombination. Furthermore, we have evidenced twice the amount of recombination hotspots located in the 500 kb region that covers the 3' end of the gene, explaining the higher variability observed in this region when compared with the 250 kb of the 5' region. Our data confirm the common ancestral origin of the c.2299delG mutation.

    PMID: 20145675 [PubMed - indexed for MEDLINE]




  • Evolutionary trajectories of beta-lactamase CTX-M-1 cluster enzymes: predicting antibiotic resistance.
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    Evolutionary trajectories of beta-lactamase CTX-M-1 cluster enzymes: predicting antibiotic resistance.

    PLoS Pathog. 2010 Jan 22;6(1):e1000735

    Authors: Novais A, Comas I, Baquero F, Cantón R, Coque TM, Moya A, González-Candelas F, Galán JC

    Abstract
    Extended-spectrum beta-lactamases (ESBL) constitute a key antibiotic-resistance mechanism affecting Gram-negative bacteria, and also an excellent model for studying evolution in real time. A shift in the epidemiology of ESBLs is being observed, which is characterized by the explosive diversification and increase in frequency of the CTX-M-type beta-lactamases in different settings. This provides a unique opportunity for studying a protein evolutionary radiation by the sequential acquisition of specific mutations enhancing protein efficiency and fitness concomitantly. The existence of driver antibiotic molecules favoring protein divergence has been investigated by combining evolutionary analyses and experimental site-specific mutagenesis. Phylogenetic reconstruction with all the CTX-M variants described so far provided a hypothetical evolutionary scenario showing at least three diversification events. CTX-M-3 was likely the enzyme at the origin of the diversification in the CTX-M-1 cluster, which was coincident with positive selection acting on several amino acid positions. Sixty-three CTX-M-3 derivatives containing all combinations of mutations under positively selected positions were constructed, and their phenotypic efficiency was evaluated. The CTX-M-3 diversification process can only be explained in a complex selective landscape with at least two antibiotics (cefotaxime and ceftazidime), indicating the need to invoke mixtures of selective drivers in order to understand the final evolutionary outcome. Under this hypothesis, we found congruent results between the in silico and in vitro analyses of evolutionary trajectories. Three pathways driving the diversification of CTX-M-3 towards the most complex and efficient variants were identified. Whereas the P167S pathway has limited possibilities of further diversification, the D240G route shows a robust diversification network. In the third route, drift may have played a role in the early stages of CTX-M-3 evolution. Antimicrobial agents should not be considered only as selectors for efficient mechanisms of resistance but also as diversifying agents of the evolutionary trajectories. Different trajectories were identified using a combination of phylogenetic reconstructions and directed mutagenesis analyses, indicating that such an approach might be useful to fulfill the desirable goal of predicting evolutionary trajectories in antimicrobial resistance.

    PMID: 20107608 [PubMed - indexed for MEDLINE]




  • Bacterial and eukaryotic phosphoketolases: phylogeny, distribution and evolution.
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    Bacterial and eukaryotic phosphoketolases: phylogeny, distribution and evolution.

    J Mol Microbiol Biotechnol. 2010;18(1):37-51

    Authors: Sánchez B, Zúñiga M, González-Candelas F, de los Reyes-Gavilán CG, Margolles A

    Abstract
    Phosphoketolases (XFPs) are glycolytic enzymes present in several organisms belonging to the Eukarya and Bacteria domains. A total of 151 putative xfp genes were detected in 650 complete genomes available in public databases. Elimination of redundant sequences and pseudogenes rendered a final data set of 128 phosphoketolases, which was analyzed by phylogenetic methods. The distribution of xfp genes was uneven in most taxonomic groups, with the exception of the taxonomical division Lactobacillaceae, in which all the species studied harbored a putative xfp gene. Putative xfp genes were also present predominantly in Rhizobiales and Actinobacteria divisions, in which 23 out of 28 genomes and 23 out of 41 genomes contained at least one putative xfp homolog, respectively. Phylogenetic analyses showed clear discordance with the expected order of organismal descent even in groups where xfp is prevalent, such as Lactobacillaceae. The presence of putative paralogs in some organisms cannot account for these discrepancies; instead, these paralogs are most possibly xenologs. The results of the phylogenetic analyses, the distribution of xfp genes and the location of some xfp genes in plasmids are independent pieces of evidence that point to horizontal gene transfer as a major driving force in the evolution of phosphoketolases.

    PMID: 20068356 [PubMed - indexed for MEDLINE]




  • Direct sequencing of Legionella pneumophila from respiratory samples for sequence-based typing analysis.
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    Direct sequencing of Legionella pneumophila from respiratory samples for sequence-based typing analysis.

    J Clin Microbiol. 2009 Sep;47(9):2901-5

    Authors: Coscollá M, González-Candelas F

    Abstract
    We have developed a procedure to test the efficiency and reliability of sequencing of Legionella pneumophila genes directly from respiratory samples and have compared the results with those derived from cultured isolates. We tried to obtain the nucleotide sequences of six protein-coding loci included in the sequence-based typing scheme for Legionella pneumophila and three intergenic regions from 132 samples corresponding to 106 patients positive for urine antigen. A seminested PCR approach was used to amplify and sequence these nine loci directly from respiratory samples. Nucleotide sequences were directly obtained for 23 Legionella isolates and also for 66 respiratory secretions from a total of 69 patients. The efficiency of sequencing from respiratory secretions was higher than that of sequencing after the isolation of the Legionella isolates. Moreover, the perfect match between the sequences obtained by both approaches when respiratory samples and cultured isolates from the same patient were available corroborates the suitability of the direct sequencing approach for the identification of Legionella species and molecular epidemiology studies with Legionella species.

    PMID: 19605573 [PubMed - indexed for MEDLINE]




  • Unequal distribution of RT-PCR artifacts along the E1-E2 region of Hepatitis C virus.
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    Unequal distribution of RT-PCR artifacts along the E1-E2 region of Hepatitis C virus.

    J Virol Methods. 2009 Oct;161(1):136-40

    Authors: Domingo-Calap P, Sentandreu V, Bracho MA, González-Candelas F, Moya A, Sanjuán R

    Abstract
    Although viral variability studies have focused traditionally on consensus sequences, the relevance of molecular clone sequences for studying viral evolution at the intra-host level is being increasingly recognized. However, for this approach to be reliable, RT-PCR artifacts do not have to contribute excessively to the observed variability. Molecular clone sequences were obtained from an in vitro transcript to estimate the maximum error rate associated to RT-PCR for the Hepatitis C virus (HCV) E1-E2 region. On average, the frequency of RT-PCR errors was one order of magnitude lower than the level of intra-host genetic variability observed in samples from an HCV outbreak. However, RT-PCR errors were not distributed evenly along the E1-E2 region and were concentrated heavily in the hypervariable region 2 (HVR 2). Although it is concluded that RT-PCR molecular clone sequences are reliable, these results warn against extrapolation of RT-PCR error rates to different genome regions. The data suggest that the RNA sequence context or secondary structure can determine the fidelity of in vitro transcription or reverse transcription. Potentially, these factors might also modify the fidelity of the viral polymerase.

    PMID: 19523983 [PubMed - indexed for MEDLINE]




  • Comparison of clinical and environmental samples of Legionella pneumophila at the nucleotide sequence level.
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    Comparison of clinical and environmental samples of Legionella pneumophila at the nucleotide sequence level.

    Infect Genet Evol. 2009 Sep;9(5):882-8

    Authors: Coscollá M, González-Candelas F

    Abstract
    Legionella pneumophila serogroup 1 is the most common etiological agent of legionellosis. We have used clinical and environmental isolates from different sources to compare their genetic variability. We have obtained the nucleotide sequence for six protein-coding loci, included in the SBT scheme for L. pneumophila, and three intergenic regions from 127 samples, 47 of environmental origin and 80 from clinical samples. Levels of genetic variability were found to be higher in the environmental than in the clinical samples, but these did not represent a mere subset of the former. Not a single case of full identity between clinical and environmental isolates was found, which raises the possibility that only a specific subset of environmental isolates is actually capable of producing infection in humans. A phylogenetic analysis of the concatenate alignment of the nine loci sequences showed four main groups, each including clinical and environmental isolates, although their distribution was not uniform among them. The comparison of each individual gene tree with the others revealed several cases of incongruence involving samples from both origins, thus suggesting the presence of recombination in the two groups.

    PMID: 19465160 [PubMed - indexed for MEDLINE]




  • The role of positive selection in hepatitis C virus.
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    The role of positive selection in hepatitis C virus.

    Infect Genet Evol. 2009 Sep;9(5):860-6

    Authors: Cuevas JM, Gonzalez M, Torres-Puente M, Jiménez-Hernández N, Bracho MA, García-Robles I, González-Candelas F, Moya A

    Abstract
    Hepatitis C virus (HCV) is a major health problem worldwide, infecting an estimated 170 million people. In this study, we have employed a large data set of sequences (14,654 sequences from between 25 and 100 clone sequences per analyzed region and per patient) from 67 patients infected with HCV genotype 1 (23 subtype 1a and 44 subtype 1b). For all patients, a sample prior to combined therapy with alpha interferon plus ribavirin was available, whereas for some patients additional samples after 6 or 12 months of treatment were also available. Twenty-seven patients responded to treatment (12 subtype 1a and 15 subtype 1b) and forty patients did not respond to treatment (11 subtype 1a vs. 29 subtype 1b). Two regions of the HCV genome were analyzed, one compressing the hypervariable regions (HVR1, HVR2 and HVR3) of the envelope 2 glycoprotein and another one including the interferon sensitive determining region (ISDR) and the V3 domain of the NS5A protein. Previously (Cuevas, J.M., Torres-Puente, M., Jiménez-Hernández, N., Bracho, M.A., García-Robles, I., Wrobel, B., Carnicer, F., del Olmo, J., Ortega, E., Moya, A., González-Candelas, F., 2008b. Genetic variability of hepatitis C virus before and after combined therapy of interferon plus ribavirin. Plos One 3 (8), e3058), several amino acid positions in both regions analyzed were detected to be under positive selection. Here, we have compared the amino acid composition of each positively selected position between responder and non-responder patients for both subtypes. If we exclude some non-conclusive cases, no clear differences were detected in any case. In conclusion, identifying specific positions as completely discriminatory of treatment response seems to be a difficult task. Our results, in concordance with previous studies, suggest that HCV evasion strategies are more likely based on a global increased variability, which would yield combinations of mutations with an increased resistance, than on the fixation of specific amino acids conferring resistance to antiviral treatment or immune response. In this sense, the particular systemic response from each patient could play an essential role in determining the outcome of the antiviral treatment.

    PMID: 19463971 [PubMed - indexed for MEDLINE]




  • Molecular diversity and evolutionary processes of Alternaria solani in Brazil inferred using genealogical and coalescent approaches.
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    Molecular diversity and evolutionary processes of Alternaria solani in Brazil inferred using genealogical and coalescent approaches.

    Phytopathology. 2009 Jun;99(6):765-74

    Authors: Lourenço V, Moya A, González-Candelas F, Carbone I, Maffia LA, Mizubuti ES

    Abstract
    Alternaria spp. form a heterogeneous group of saprophytic and plant-pathogenic fungi widespread in temperate and tropical regions. However, the relationship between evolutionary processes and genetic diversity with epidemics is unknown for several plant-pathogenic Alternaria spp. The interaction of Alternaria solani populations with potato and tomato plants is an interesting case study for addressing questions related to molecular evolution of an asexual fungus. Gene genealogies based on the coalescent process were used to infer evolutionary processes that shape the A. solani population. Sequences of the rDNA internal transcribed spacer (ITS) region and the genes which encode the allergenic protein alt a 1 (Alt a 1) and glyceraldehyde-3-phosphate dehydrogenase (Gpd) were used to estimate haplotype and nucleotide diversity as well as for the coalescent analyses. The highest number of parsimony informative sites (n = 14), nucleotide diversity (0.007), and the average number of nucleotide differences (3.20) were obtained for Alt a 1. Although the highest number of haplotypes (n = 7) was generated for ITS, haplotype diversity was the lowest (0.148) for this region. Recombination was not detected. Subdivision was inferred from populations associated with hosts but there was no evidence of geographic subdivision, and gene flow is occurring among subpopulations. In the analysis of the Alt a 1, balancing selection and population expansion or purifying selection could have occurred in A. solani subpopulations associated with potato and tomato plants, respectively. There is strong evidence that the subpopulation of A. solani that causes early blight in potato is genetically distinct from the subpopulation that causes early blight in tomato. The population of A. solani is clonal, and gene flow and mutation are the main evolutionary processes shaping its genetic structure.

    PMID: 19453237 [PubMed - indexed for MEDLINE]




  • Effect of ribavirin on the mutation rate and spectrum of hepatitis C virus in vivo.
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    Effect of ribavirin on the mutation rate and spectrum of hepatitis C virus in vivo.

    J Virol. 2009 Jun;83(11):5760-4

    Authors: Cuevas JM, González-Candelas F, Moya A, Sanjuán R

    Abstract
    Their extremely error-prone replication makes RNA viruses targets for lethal mutagenesis. In the case of hepatitis C virus (HCV), the standard treatment includes ribavirin, a base analog with an in vitro mutagenic effect, but the in vivo mode of action of ribavirin remains poorly understood. Here, we test the mutagenic effects of ribavirin plus interferon treatment in vivo using a new method to estimate mutation rates based on the analysis of nonsense mutations. We apply this methodology to a large HCV sequence database containing over 15,000 reverse transcription-PCR molecular clone sequences from 74 patients infected with HCV. We obtained an estimate of the spontaneous mutation rate of ca. 10(-4) substitutions per site or lower, a value within the typically accepted range for RNA viruses. A roughly threefold increase in mutation rate and a significant shift in mutation spectrum were observed in samples from patients undergoing 6 months of interferon plus ribavirin treatment. This result is consistent with the known in vitro mutagenic effect of ribavirin and suggests that the antiviral effect of ribavirin plus interferon treatment is at least partly exerted through lethal mutagenesis.

    PMID: 19321623 [PubMed - indexed for MEDLINE]




  • Combined therapy of interferon plus ribavirin promotes multiple adaptive solutions in hepatitis C virus.
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    Combined therapy of interferon plus ribavirin promotes multiple adaptive solutions in hepatitis C virus.

    J Med Virol. 2009 Apr;81(4):650-6

    Authors: Cuevas JM, Torres-Puente M, Jiménez-Hernández N, Bracho MA, García-Robles I, Carnicer F, Olmo JD, Ortega E, González-Candelas F, Moya A

    Abstract
    Hepatitis C virus (HCV) presents several regions involved potentially in evading antiviral treatment and host immune system. Two regions, known as PKR-BD and V3 domains, have been proposed to be involved in resistance to interferon. Additionally, hypervariable regions in the envelope E2 glycoprotein are also good candidates to participate in evasion from the immune system. In this study, we have used a cohort of 22 non-responder patients to combined therapy (interferon alpha-2a plus ribavirin) for which samples obtained just before initiation of therapy and after 6 or/and 12 months of treatment were available. A range of 25-100 clones per patient, genome region and time sample were obtained. The predominant amino acid sequences for each time sample and patient were determined. Next, the sequences of the PKR-BD and V3 domains and the hypervariable regions from different time samples were compared for each patient. The highest levels of variability were detected at the three hypervariable regions of the E2 protein and, to a lower extent, at the V3 domain of the NS5A protein. However, no clear patterns of adaptation to the host immune system or to antiviral treatment were detected. In summary, although high levels of variability are correlated to viral adaptive response, antiviral treatment does not seem to promote convergent adaptive changes. Consequently, other regions must be involved in evasion strategies likely based on a combination of multiple mechanisms, in which pools of changes along the HCV genome could confer viruses the ability to overcome strong selective pressures.

    PMID: 19235859 [PubMed - indexed for MEDLINE]




  • Evidence of recombination in intrapatient populations of hepatitis C virus.
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    Evidence of recombination in intrapatient populations of hepatitis C virus.

    PLoS One. 2008 Sep 18;3(9):e3239

    Authors: Sentandreu V, Jiménez-Hernández N, Torres-Puente M, Bracho MA, Valero A, Gosalbes MJ, Ortega E, Moya A, González-Candelas F

    Abstract
    Hepatitis C virus (HCV) is a major cause of liver disease worldwide and a potential cause of substantial morbidity and mortality in the future. HCV is characterized by a high level of genetic heterogeneity. Although homologous recombination has been demonstrated in many members of the family Flaviviridae, to which HCV belongs, there are only a few studies reporting recombination on natural populations of HCV, suggesting that these events are rare in vivo. Furthermore, these few studies have focused on recombination between different HCV genotypes/subtypes but there are no reports on the extent of intra-genotype or intra-subtype recombination between viral strains infecting the same patient. Given the important implications of recombination for RNA virus evolution, our aim in this study has been to assess the existence and eventually the frequency of intragenic recombination on HCV. For this, we retrospectively have analyzed two regions of the HCV genome (NS5A and E1-E2) in samples from two different groups: (i) patients infected only with HCV (either treated with interferon plus ribavirin or treatment naïve), and (ii) HCV-HIV co-infected patients (with and without treatment against HIV). The complete data set comprised 17712 sequences from 136 serum samples derived from 111 patients. Recombination analyses were performed using 6 different methods implemented in the program RDP3. Recombination events were considered when detected by at least 3 of the 6 methods used and were identified in 10.7% of the amplified samples, distributed throughout all the groups described and the two genomic regions studied. The resulting recombination events were further verified by detailed phylogenetic analyses. The complete experimental procedure was applied to an artificial mixture of relatively closely viral populations and the ensuing analyses failed to reveal artifactual recombination. From these results we conclude that recombination should be considered as a potentially relevant mechanism generating genetic variation in HCV and with important implications for the treatment of this infection.

    PMID: 18800167 [PubMed - indexed for MEDLINE]




  • Genetic variability of hepatitis C virus before and after combined therapy of interferon plus ribavirin.
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    Genetic variability of hepatitis C virus before and after combined therapy of interferon plus ribavirin.

    PLoS One. 2008 Aug 26;3(8):e3058

    Authors: Cuevas JM, Torres-Puente M, Jiménez-Hernández N, Bracho MA, García-Robles I, Wrobel B, Carnicer F, del Olmo J, Ortega E, Moya A, González-Candelas F

    Abstract
    We present an analysis of the selective forces acting on two hepatitis C virus genome regions previously postulated to be involved in the viral response to combined antiviral therapy. One includes the three hypervariable regions in the envelope E2 glycoprotein, and the other encompasses the PKR binding domain and the V3 domain in the NS5A region. We used a cohort of 22 non-responder patients to combined therapy (interferon alpha-2a plus ribavirin) for which samples were obtained before initiation of therapy and after 6 or/and 12 months of treatment. A range of 25-100 clones per patient, genome region and time sample were sequenced. These were used to detect general patterns of adaptation, to identify particular adaptation mechanisms and to analyze the patterns of evolutionary change in both genome regions. These analyses failed to detect a common adaptive mechanism for the lack of response to antiviral treatment in these patients. On the contrary, a wide range of situations were observed, from patients showing no positively selected sites to others with many, and with completely different topologies in the reconstructed phylogenetic trees. Altogether, these results suggest that viral strategies to evade selection pressure from the immune system and antiviral therapies do not result from a single mechanism and they are likely based on a range of different alternatives, in which several different changes, or their combination, along the HCV genome confer viruses the ability to overcome strong selective pressures.

    PMID: 18725975 [PubMed - indexed for MEDLINE]




  • Evolution of snake venom disintegrins by positive Darwinian selection.
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    Evolution of snake venom disintegrins by positive Darwinian selection.

    Mol Biol Evol. 2008 Nov;25(11):2391-407

    Authors: Juárez P, Comas I, González-Candelas F, Calvete JJ

    Abstract
    PII-disintegrins, cysteine-rich polypeptides broadly distributed in the venoms of geographically diverse species of vipers and rattlesnakes, antagonize the adhesive functions of beta(1) and beta(3) integrin receptors. PII-disintegrins evolved in Viperidae by neofunctionalization of disintegrin-like domains of duplicated PIII-snake venom hemorrhagic metalloproteinase (SVMP) genes recruited into the venom proteome before the radiation of the advanced snakes. Minimization of the gene (loss of introns and coding regions) and the protein structures (successive loss of disulfide bonds) underpins the postduplication divergence of disintegrins. However, little is known about the underlying genetic mechanisms that have generated the structural and functional diversity among disintegrins. Phylogenetic inference and maximum likelihood-based codon substitution approaches were used to analyze the evolution of the disintegrin family. The topology of the phylogenetic tree does not parallel that of the species tree. This incongruence is consistent with that expected for a multigene family undergoing a birth-and-death process in which the appearance and disappearance of loci are being driven by selection. Cysteine and buried residues appear to be under strong purifying selection due to their role in maintaining the active conformation of disintegrins. Divergence of disintegrins is strongly influenced by positive Darwinian selection causing accelerated rate of substitution in a substantial proportion of surface-exposed disintegrin residues. Global and lineage-specific sites evolving under diversifying selection were identified. Several sites are located within the integrin-binding loop and the C-terminal tail, two regions that form a conformational functional epitope. Arginine-glycine-aspartic acid (RGD) was inferred to represent the ancestral integrin-recognition motif, which emerged from the subgroup of PIII-SVMPs bearing the RDECD sequence. The most parsimonious nucleotide substitution model required for the emergence of all known disintegrin's integrin inhibitory motifs from an ancestral RGD sequence involves a minimum of three mutations. The adaptive advantage of the emergence of motifs targeting beta(1) integrins and the role of positively selected sites located within nonfunctional disintegrin regions appear to be difficult to rationalize in the context of a predator-prey arms race. Perhaps, this represents a consequence of the neofunctionalization potential of the disintegrin domain, a feature that may underlie its recruitment into the venom proteome followed by its successful transformation into a toxin.

    PMID: 18701431 [PubMed - indexed for MEDLINE]




  • Mapping natural polymorphisms of hepatitis C virus NS3/4A protease and antiviral resistance to inhibitors in worldwide isolates.
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    Mapping natural polymorphisms of hepatitis C virus NS3/4A protease and antiviral resistance to inhibitors in worldwide isolates.

    Antivir Ther. 2008;13(4):481-94

    Authors: López-Labrador FX, Moya A, Gonzàlez-Candelas F

    Abstract
    BACKGROUND: Several inhibitors for the hepatitis C virus (HCV) NS3/4A protease are under development. Although previous studies identified viral resistance mutations, there is little information on the natural variability of proteases from the different viral subtypes. Here, we aimed to determine both the natural variability and presence of resistance or compensatory mutations to new protease inhibitors (PI) in NS3/4A proteases from worldwide HCV isolates.
    METHODS: A comprehensive analysis was performed in 380 HCV NS3 sequences (275 genotype 1; 105 other genotypes) from public HCV databases (EuHCVdb and Los Alamos). Amino acid polymorphism and signature patterns were deduced in the protease domain, including all sites associated with resistance to the PIs BILN-2061, Telaprevir (VX-950), Boceprevir (SCH-503034), SCH-6 and ITMN-191.
    RESULTS: Few of the residues in the catalytic triad or in substrate/metal-binding sites were polymorphic, and were identified in only 4/380 isolates. However, a relevant polymorphism was found in sites associated either with resistance to PI (V36, 1170 and D168) or with compensatory mutations (171, T72, Q86 and 1153). Furthermore, some unique genotype-specific signature patterns associated with resistance to PI were also identified.
    CONCLUSIONS: We describe for the first time the relevant natural polymorphisms of the HCV NS3/4A protease in worldwide isolates. Although the prevalence of major resistance mutations is very low, many compensatory sites are naturally polymorphic among proteases from several HCV subtypes. These data will help to determine whether HCV resistance is likely to be selected with new PIs and will aid the design of genotypic resistance testing.

    PMID: 18672527 [PubMed - indexed for MEDLINE]




  • Complete genome of a European hepatitis C virus subtype 1g isolate: phylogenetic and genetic analyses.
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    Complete genome of a European hepatitis C virus subtype 1g isolate: phylogenetic and genetic analyses.

    Virol J. 2008 Jun 05;5:72

    Authors: Bracho MA, Saludes V, Martró E, Bargalló A, González-Candelas F, Ausina V

    Abstract
    BACKGROUND: Hepatitis C virus isolates have been classified into six main genotypes and a variable number of subtypes within each genotype, mainly based on phylogenetic analysis. Analyses of the genetic relationship among genotypes and subtypes are more reliable when complete genome sequences (or at least the full coding region) are used; however, so far 31 of 80 confirmed or proposed subtypes have at least one complete genome available. Of these, 20 correspond to confirmed subtypes of epidemic interest.
    RESULTS: We present and analyse the first complete genome sequence of a HCV subtype 1g isolate. Phylogenetic and genetic distance analyses reveal that HCV-1g is the most divergent subtype among the HCV-1 confirmed subtypes. Potential genomic recombination events between genotypes or subtype 1 genomes were ruled out. We demonstrate phylogenetic congruence of previously deposited partial sequences of HCV-1g with respect to our sequence.
    CONCLUSION: In light of this, we propose changing the current status of its subtype-specific designation from provisional to confirmed.

    PMID: 18533988 [PubMed - indexed for MEDLINE]




  • Unraveling the evolutionary history of the phosphoryl-transfer chain of the phosphoenolpyruvate:phosphotransferase system through phylogenetic analyses and genome context.
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    Unraveling the evolutionary history of the phosphoryl-transfer chain of the phosphoenolpyruvate:phosphotransferase system through phylogenetic analyses and genome context.

    BMC Evol Biol. 2008 May 16;8:147

    Authors: Comas I, González-Candelas F, Zúñiga M

    Abstract
    BACKGROUND: The phosphoenolpyruvate phosphotransferase system (PTS) plays a major role in sugar transport and in the regulation of essential physiological processes in many bacteria. The PTS couples solute transport to its phosphorylation at the expense of phosphoenolpyruvate (PEP) and it consists of general cytoplasmic phosphoryl transfer proteins and specific enzyme II complexes which catalyze the uptake and phosphorylation of solutes. Previous studies have suggested that the evolution of the constituents of the enzyme II complexes has been driven largely by horizontal gene transfer whereas vertical inheritance has been prevalent in the general phosphoryl transfer proteins in some bacterial groups. The aim of this work is to test this hypothesis by studying the evolution of the phosphoryl transfer proteins of the PTS.
    RESULTS: We have analyzed the evolutionary history of the PTS phosphoryl transfer chain (PTS-ptc) components in 222 complete genomes by combining phylogenetic methods and analysis of genomic context. Phylogenetic analyses alone were not conclusive for the deepest nodes but when complemented with analyses of genomic context and functional information, the main evolutionary trends of this system could be depicted.
    CONCLUSION: The PTS-ptc evolved in bacteria after the divergence of early lineages such as Aquificales, Thermotogales and Thermus/Deinococcus. The subsequent evolutionary history of the PTS-ptc varied in different bacterial lineages: vertical inheritance and lineage-specific gene losses mainly explain the current situation in Actinobacteria and Firmicutes whereas horizontal gene transfer (HGT) also played a major role in Proteobacteria. Most remarkably, we have identified a HGT event from Firmicutes or Fusobacteria to the last common ancestor of the Enterobacteriaceae, Pasteurellaceae, Shewanellaceae and Vibrionaceae. This transfer led to extensive changes in the metabolic and regulatory networks of these bacteria including the development of a novel carbon catabolite repression system. Hence, this example illustrates that HGT can drive major physiological modifications in bacteria.

    PMID: 18485189 [PubMed - indexed for MEDLINE]




  • Refined analysis of genetic variability parameters in hepatitis C virus and the ability to predict antiviral treatment response.
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    Refined analysis of genetic variability parameters in hepatitis C virus and the ability to predict antiviral treatment response.

    J Viral Hepat. 2008 Aug;15(8):578-90

    Authors: Cuevas JM, Torres-Puente M, Jiménez-Hernández N, Bracho MA, García-Robles I, Carnicer F, Olmo JD, Ortega E, Moya A, González-Candelas F

    Abstract
    Hepatitis C virus (HCV) infects approximately 3% of the world population. The chronicity of hepatitis C seems to depend on the level of genetic variability. We have recently (Torres-Puente et al., J Viral Hepat, 2008; 15: 188) reported genetic variability estimates from a large-scale sequence analysis of 67 patients infected with HCV subtypes 1a (23 patients) and 1b (44 patients) and related them to response, or lack of, to alpha-interferon plus ribavirin treatment.. Two HCV genome regions were analysed in samples prior to antiviral therapy, one compressing the three hypervariable regions of the E2 glycoprotein and another one including the interferon sensitive determining region and the V3 domain of the NS5A protein. Haplotype and nucleotide diversity measures showed a clear tendency to higher genetic variability levels in nonresponder than in responder patients. Here, we have refined the analysis of genetic variability (haplotype and nucleotide diversity, number of haplotypes and mutations) by considering their distribution in each of the biologically meaningful subregions mentioned above, as well as in their surrounding and intervening regions. Variability levels are very heterogeneous among the different subregions, being higher for nonresponder patients. Interestingly, significant differences were detected in the biologically relevant regions, but also in the surrounding regions, suggesting that the level of variability of the whole HCV genome, rather than exclusively that from the hypervariable regions, is the main indicator of the treatment response. Finally, the number of haplotypes and mutations seem to be better discriminators than haplotype and nucleotide diversity, especially in the NS5A region.

    PMID: 18466261 [PubMed - indexed for MEDLINE]




  • Phylogeography and genetic variation of Triatoma dimidiata, the main Chagas disease vector in Central America, and its position within the genus Triatoma.
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    Phylogeography and genetic variation of Triatoma dimidiata, the main Chagas disease vector in Central America, and its position within the genus Triatoma.

    PLoS Negl Trop Dis. 2008 May 07;2(5):e233

    Authors: Bargues MD, Klisiowicz DR, Gonzalez-Candelas F, Ramsey JM, Monroy C, Ponce C, Salazar-Schettino PM, Panzera F, Abad-Franch F, Sousa OE, Schofield CJ, Dujardin JP, Guhl F, Mas-Coma S

    Abstract
    BACKGROUND: Among Chagas disease triatomine vectors, the largest genus, Triatoma, includes species of high public health interest. Triatoma dimidiata, the main vector throughout Central America and up to Ecuador, presents extensive phenotypic, genotypic, and behavioral diversity in sylvatic, peridomestic and domestic habitats, and non-domiciliated populations acting as reinfestation sources. DNA sequence analyses, phylogenetic reconstruction methods, and genetic variation approaches are combined to investigate the haplotype profiling, genetic polymorphism, phylogeography, and evolutionary trends of T. dimidiata and its closest relatives within Triatoma. This is the largest interpopulational analysis performed on a triatomine species so far.
    METHODOLOGY AND FINDINGS: Triatomines from Mexico, Guatemala, Honduras, Nicaragua, Panama, Cuba, Colombia, Ecuador, and Brazil were used. Triatoma dimidiata populations follow different evolutionary divergences in which geographical isolation appears to have had an important influence. A southern Mexican-northern Guatemalan ancestral form gave rise to two main clades. One clade remained confined to the Yucatan peninsula and northern parts of Chiapas State, Guatemala, and Honduras, with extant descendants deserving specific status. Within the second clade, extant subspecies diversity was shaped by adaptive radiation derived from Guatemalan ancestral populations. Central American populations correspond to subspecies T. d. dimidiata. A southern spread into Panama and Colombia gave the T. d. capitata forms, and a northwestern spread rising from Guatemala into Mexico gave the T. d. maculipennis forms. Triatoma hegneri appears as a subspecific insular form.
    CONCLUSIONS: The comparison with very numerous Triatoma species allows us to reach highly supported conclusions not only about T. dimidiata, but also on different, important Triatoma species groupings and their evolution. The very large intraspecific genetic variability found in T. dimidiata sensu lato has never been detected in a triatomine species before. The distinction between the five different taxa furnishes a new frame for future analyses of the different vector transmission capacities and epidemiological characteristics of Chagas disease. Results indicate that T. dimidiata will offer problems for control, although dwelling insecticide spraying might be successful against introduced populations in Ecuador.

    PMID: 18461141 [PubMed - indexed for MEDLINE]




  • Genetic variability in hepatitis C virus and its role in antiviral treatment response.
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    Genetic variability in hepatitis C virus and its role in antiviral treatment response.

    J Viral Hepat. 2008 Mar;15(3):188-99

    Authors: Torres-Puente M, Cuevas JM, Jiménez-Hernández N, Bracho MA, García-Robles I, Wrobel B, Carnicer F, Del Olmo J, Ortega E, Moya A, González-Candelas F

    Abstract
    Hepatitis C virus (HCV) is a major health problem worldwide, infecting an estimated 170 million people. The high genetic variability of HCV contributes to the chronicity of hepatitis C. Here, we report results from a large-scale sequence analysis of 67 patients infected with HCV genotype 1, 23 with subtype 1a and 44 with subtype 1b. Two regions of the HCV genome were analysed in samples prior to combined therapy with alpha interferon plus ribavirin, one compressing the hypervariable regions (HVR1, HVR2 and HVR3) of the E2 glycoprotein and another one including the interferon-sensitive determining region (ISDR) and the V3 domain of the NS5A protein. Genetic diversity measures showed a clear tendency to higher genetic variability levels in nonresponder patients to antiviral treatment than in responder patients, although highly disperse values were present within each response group for both subtypes. A more detailed analysis of amino acid composition revealed the presence of several subtype-specific variants in a few positions, but no discriminating positions between responder and nonresponder patients were detected. Our results also revealed that most amino acid positions were highly conserved, especially for subtype 1a. We conclude that the outcome of the antiviral treatment might depend not only on the nature of one or a few independent positions, but more likely on the combination of several positions along the HCV genome. Moreover, the own host's ability to generate an appropriate systemic response, in combination with the action of antivirals, is also likely to be essential for treatment outcome.

    PMID: 18233992 [PubMed - indexed for MEDLINE]




  • Hepatitis C virus and the controversial role of the interferon sensitivity determining region in the response to interferon treatment.
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    Hepatitis C virus and the controversial role of the interferon sensitivity determining region in the response to interferon treatment.

    J Med Virol. 2008 Feb;80(2):247-53

    Authors: Torres-Puente M, Cuevas JM, Jiménez-Hernández N, Bracho MA, García-Robles I, Carnicer F, del Olmo J, Ortega E, Moya A, González-Candelas F

    Abstract
    The degree of variability of the interferon sensitivity determining region (ISDR) in the hepatitis C virus (HCV) genome has been postulated to predict the response to interferon therapy, mainly in patients infected with subtype 1b, although this prediction has been the subject of a long controversy. This prediction has been tested by analyzing a cohort of 67 Spanish patients infected with HCV genotype 1, 23 of which were infected with subtype 1a and 44 with subtype 1b. A sample previous to therapy with alpha-interferon plus ribavirin was obtained and several clones (between 25 and 96) including the ISDR were sequenced from each patient. A significant correlation between mutations at the ISDR and response to treatment for subtype 1b patients, but not for those infected with subtype 1a, has been detected. Although the results suggest that the same relationship holds true for subtype 1a, lack of statistical power because of the small sample size of this subtype prevented firmer conclusions. However, identical ISDR sequences were found in responder and non-responder patients, suggesting that the stability of the ISDR sequence can occasionally help HCV to evade interferon therapy, although this is not a sufficient condition. More complex interactions, including the ISDR or not, are likely to exist and govern the HCV response to interferon treatment.

    PMID: 18098147 [PubMed - indexed for MEDLINE]




  • Using evolutionary tools to refine the new hypervariable region 3 within the envelope 2 protein of hepatitis C virus.
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    Using evolutionary tools to refine the new hypervariable region 3 within the envelope 2 protein of hepatitis C virus.

    Infect Genet Evol. 2008 Jan;8(1):74-82

    Authors: Torres-Puente M, Cuevas JM, Jiménez-Hernández N, Bracho MA, García-Robles I, Wrobel B, Carnicer F, del Olmo J, Ortega E, Moya A, González-Candelas F

    Abstract
    The envelope 2 protein of hepatitis C virus (HCV) presents three hypervariable regions, named HVR1, HVR2 and HVR3, in which the presence of antigenic sites has been described. Genetic variability in these regions may reflect the generation of escape mutants as a consequence of the immune response. Therefore, these regions would tend to accumulate amino acid changes along the infection process, an effect that could be accelerated by antiviral treatments. In this study, we have analyzed the E1-E2 region of 23 HCV patients non-responders to antiviral treatment, 7 of which were infected with subtype 1a, 15 with subtype 1b, and 1 with a new HCV-1 subtype, before and after 6 and/or 12 months of peg-interferon+ribavirin treatment. We have sequenced about 100 clones from each sample, analyzing a total of 4906 sequences. A detailed analysis of the evolutionary forces acting along the genome region studied confirmed the existence of the three hypervariable regions, characterized by significant changes in amino acid composition between samples taken at different times from the same patient and a high number of sites evolving under positive selection. Moreover, for the recently described HVR3, our results suggest that its location could be restricted to residues 434-450, instead of the originally postulated 431-466.

    PMID: 18063425 [PubMed - indexed for MEDLINE]




  • Effect of antiviral treatment and host susceptibility on positive selection in hepatitis C virus (HCV).
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    Effect of antiviral treatment and host susceptibility on positive selection in hepatitis C virus (HCV).

    Virus Res. 2008 Feb;131(2):224-32

    Authors: Jiménez-Hernández N, Sentandreu V, Castro JA, Torres-Puente M, Bracho A, García-Robles I, Ortega E, Del Olmo J, Carnicer F, González-Candelas F, Moya A

    Abstract
    We have conducted a large sequence study of the E1-E2 and NS5A regions of the HCV, subtypes 1a and b, both in patients previously treated with interferon, and untreated patients, who later responded, or not, to a combination therapy based on interferon plus ribavirin. We have examined the role played by the number of positively selected sites on disease progression and its relationship with several variables such as patients' age, sex and their risk of acquiring the disease. We have detected three groups of patients that respond or not to combination therapy: responders of intermediate age, older non-responders and young non-responders, they possess an increasing average number of positively selected sites in the E1-E2 region, respectively. We conclude that the host's genetic factors play an important role in whether the disease is contained or becomes chronic.

    PMID: 17980926 [PubMed - indexed for MEDLINE]




  • Common gene expression strategies revealed by genome-wide analysis in yeast.
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    Common gene expression strategies revealed by genome-wide analysis in yeast.

    Genome Biol. 2007;8(10):R222

    Authors: García-Martínez J, González-Candelas F, Pérez-Ortín JE

    Abstract
    BACKGROUND: Gene expression is a two-step synthesis process that ends with the necessary amount of each protein required to perform its function. Since the protein is the final product, the main focus of gene regulation should be centered on it. However, because mRNA is an intermediate step and the amounts of both mRNA and protein are controlled by their synthesis and degradation rates, the desired amount of protein can be achieved following different strategies.
    RESULTS: In this paper we present the first comprehensive analysis of the relationships among the six variables that characterize gene expression in a living organism: transcription and translation rates, mRNA and protein amounts, and mRNA and protein stabilities. We have used previously published data from exponentially growing Saccharomyces cerevisiae cells. We show that there is a general tendency to harmonize the levels of mRNA and protein by coordinating their synthesis rates and that functionally related genes tend to have similar values for the six variables.
    CONCLUSION: We propose that yeast cells use common expression strategies for genes acting in the same physiological pathways. This trend is more evident for genes coding for large and stable protein complexes, such as ribosomes or the proteasome. Hence, each functional group can be defined by a 'six variable profile' that illustrates the common strategy followed by the genes included in it. Genes encoding subunits of protein complexes show a tendency to have relatively unstable mRNAs and a less balanced profile for mRNA than for protein, suggesting a stronger regulation at the transcriptional level.

    PMID: 17945030 [PubMed - indexed for MEDLINE]




  • Historical and biological determinants of genetic diversity in the highly endemic triploid sea lavender Limonium dufourii (Plumbaginaceae).
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    Historical and biological determinants of genetic diversity in the highly endemic triploid sea lavender Limonium dufourii (Plumbaginaceae).

    Mol Ecol. 2007 Sep;16(18):3814-27

    Authors: Palop-Esteban M, Segarra-Moragues JG, González-Candelas F

    Abstract
    Microsatellite markers were used to evaluate the genetic diversity and population genetic structure in the critically endangered Limonium dufourii (Plumbaginaceae), a highly endemic triploid species from the coasts of eastern Spain. Sixty-five alleles from 13 microsatellite regions were amplified in a sample of 122 individuals collected from the six extant populations. Microsatellite patterns were consistent with the triploid nature of L. dufourii. Alleles were unambiguously assigned to two different parental subgenomes in this hybrid species and the greater contribution of the diploid parental subgenome was confirmed. Eleven, 25 and 26 multilocus genotypes were recorded from the haploid, diploid and from the combined information of both subgenomes, respectively. Genetic diversity was mostly distributed among populations (72.06% of the total genetic variation). Genotypes from Marjal del Moro populations grouped into two highly structured clusters (88.41% of the total variance). The observed patterns of distribution of genetic diversity are interpreted to result from multiple hybridization events and isolation between populations. Threats to this species are mainly anthropogenic (urbanization and tourism pressure), although stochastic risks cannot be ignored. Therefore, in order to preserve extant genetic variation of L. dufourii, in situ strategies such as the preservation of its habitat are a high priority. Several recommendations in order to assist ex situ measures to guarantee the success of conservation strategies and maintain the relationships between individuals and populations are proposed.

    PMID: 17850548 [PubMed - indexed for MEDLINE]




  • Contribution of insertions and deletions to the variability of hepatitis C virus populations.
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    Contribution of insertions and deletions to the variability of hepatitis C virus populations.

    J Gen Virol. 2007 Aug;88(Pt 8):2198-203

    Authors: Torres-Puente M, Cuevas JM, Jiménez-Hernández N, Bracho MA, García-Robles I, Carnicer F, del Olmo J, Ortega E, Moya A, González-Candelas F

    Abstract
    Little is known about the potential effects of insertions and deletions (indels) on the evolutionary dynamics of hepatitis C virus (HCV). In fact, the consequences of indels on antiviral treatment response are a field of investigation completely unexplored. Here, an extensive sequencing project was undertaken by cloning and sequencing serum samples from 25 patients infected with HCV subtype 1a and 48 patients with subtype 1b. For 23 patients, samples obtained after treatment with alpha interferon plus ribavirin were also available. Two genome fragments containing the hypervariable regions in the envelope 2 glycoprotein and the PKR-BD domain in NS5A were sequenced, yielding almost 16 000 sequences. Our results show that insertions are quite rare, but they are often present in biologically relevant domains of the HCV genome. Moreover, their frequency distributions between different time samples reflect the quasispecies dynamics of HCV populations. Deletions seem to be subject to negative selection.

    PMID: 17622623 [PubMed - indexed for MEDLINE]




  • epiPATH: an information system for the storage and management of molecular epidemiology data from infectious pathogens.
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    epiPATH: an information system for the storage and management of molecular epidemiology data from infectious pathogens.

    BMC Infect Dis. 2007 Apr 20;7:32

    Authors: Amadoz A, González-Candelas F

    Abstract
    BACKGROUND: Most research scientists working in the fields of molecular epidemiology, population and evolutionary genetics are confronted with the management of large volumes of data. Moreover, the data used in studies of infectious diseases are complex and usually derive from different institutions such as hospitals or laboratories. Since no public database scheme incorporating clinical and epidemiological information about patients and molecular information about pathogens is currently available, we have developed an information system, composed by a main database and a web-based interface, which integrates both types of data and satisfies requirements of good organization, simple accessibility, data security and multi-user support.
    RESULTS: From the moment a patient arrives to a hospital or health centre until the processing and analysis of molecular sequences obtained from infectious pathogens in the laboratory, lots of information is collected from different sources. We have divided the most relevant data into 12 conceptual modules around which we have organized the database schema. Our schema is very complete and it covers many aspects of sample sources, samples, laboratory processes, molecular sequences, phylogenetics results, clinical tests and results, clinical information, treatments, pathogens, transmissions, outbreaks and bibliographic information. Communication between end-users and the selected Relational Database Management System (RDMS) is carried out by default through a command-line window or through a user-friendly, web-based interface which provides access and management tools for the data.
    CONCLUSION: epiPATH is an information system for managing clinical and molecular information from infectious diseases. It facilitates daily work related to infectious pathogens and sequences obtained from them. This software is intended for local installation in order to safeguard private data and provides advanced SQL-users the flexibility to adapt it to their needs. The database schema, tool scripts and web-based interface are free software but data stored in our database server are not publicly available. epiPATH is distributed under the terms of GNU General Public License. More details about epiPATH can be found at http://genevo.uv.es/epipath.

    PMID: 17448245 [PubMed - indexed for MEDLINE]




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