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Alioto TS, Gut M, Rodiño-Janeiro BK, Cruz F, Gómez-Garrido J, Vázquez-Ucha JC, Mata C, Antoni R, Briansó F, Dabad M, Casals E, Ingham M, Álvarez-Tejado M, Bou G, Gut IG. Development of a novel streamlined workflow (AACRE) and database (inCREDBle) for genomic analysis of carbapenem-resistant Enterobacterales. Microb Genom 2023; 9. [PMID: 38010338 DOI: 10.1099/mgen.0.001132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023] Open
Abstract
In response to the threat of increasing antimicrobial resistance, we must increase the amount of available high-quality genomic data gathered on antibiotic-resistant bacteria. To this end, we developed an integrated pipeline for high-throughput long-read sequencing, assembly, annotation and analysis of bacterial isolates and used it to generate a large genomic data set of carbapenemase-producing Enterobacterales (CPE) isolates collected in Spain. The set of 461 isolates were sequenced with a combination of both Illumina and Oxford Nanopore Technologies (ONT) DNA sequencing technologies in order to provide genomic context for chromosomal loci and, most importantly, structural resolution of plasmids, important determinants for transmission of antimicrobial resistance. We developed an informatics pipeline called Assembly and Annotation of Carbapenem-Resistant Enterobacteriaceae (AACRE) for the full assembly and annotation of the bacterial genomes and their complement of plasmids. To explore the resulting genomic data set, we developed a new database called inCREDBle that not only stores the genomic data, but provides unique ways to filter and compare data, enabling comparative genomic analyses at the level of chromosomes, plasmids and individual genes. We identified a new sequence type, ST5000, and discovered a genomic locus unique to ST15 that may be linked to its increased spread in the population. In addition to our major objective of generating a large regional data set, we took the opportunity to compare the effects of sample quality and sequencing methods, including R9 versus R10 nanopore chemistry, on genome assembly and annotation quality. We conclude that converting short-read and hybrid microbial sequencing and assembly workflows to the latest nanopore chemistry will further reduce processing time and cost, truly enabling the routine monitoring of resistance transmission patterns at the resolution of complete chromosomes and plasmids.
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Affiliation(s)
- Tyler S Alioto
- Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028 Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Marta Gut
- Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028 Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Bruno Kotska Rodiño-Janeiro
- Microbiology Department, Complejo Hospitalario Universitario A Coruña-Instituto Investigación Biomédica A Coruña (INIBIC), A Coruña, Spain
| | - Fernando Cruz
- Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028 Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Jèssica Gómez-Garrido
- Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028 Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Juan Carlos Vázquez-Ucha
- Microbiology Department, Complejo Hospitalario Universitario A Coruña-Instituto Investigación Biomédica A Coruña (INIBIC), A Coruña, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), ISCIII, Madrid, Spain
| | - Caterina Mata
- Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028 Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Regina Antoni
- Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028 Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Ferran Briansó
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona (UB), Barcelona, Spain
- Roche Diagnostics, Sant Cugat del Vallès, Barcelona, Spain
| | - Marc Dabad
- Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028 Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Eloi Casals
- Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028 Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Matthew Ingham
- Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028 Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | | | - Germán Bou
- Microbiology Department, Complejo Hospitalario Universitario A Coruña-Instituto Investigación Biomédica A Coruña (INIBIC), A Coruña, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), ISCIII, Madrid, Spain
| | - Ivo G Gut
- Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028 Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
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Arca-Suárez J, Rodiño-Janeiro BK, Pérez A, Guijarro-Sánchez P, Vázquez-Ucha JC, Cruz F, Gómez-Garrido J, Alioto TS, Álvarez-Tejado M, Gut M, Gut I, Oviaño M, Beceiro A, Bou G. Emergence of 16S rRNA methyltransferases among carbapenemase-producing Enterobacterales in Spain studied by whole-genome sequencing. Int J Antimicrob Agents 2021; 59:106456. [PMID: 34688835 DOI: 10.1016/j.ijantimicag.2021.106456] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/08/2021] [Accepted: 10/09/2021] [Indexed: 11/27/2022]
Abstract
The emergence of 16S rRNA methyltransferases (RMTs) in Gram-negative pathogens bearing other clinically relevant resistance mechanisms, such as carbapenemase-producing Enterobacterales (CPE), is becoming an alarming concern. We investigated the prevalence, antimicrobial susceptibility, resistance mechanisms, molecular epidemiology and genetic support of RMTs in CPE isolates from Spain. This study included a collection of 468 CPE isolates recovered during 2018 from 32 participating Spanish hospitals. MICs were determined using the broth microdilution method, the agar dilution method (fosfomycin) or MIC gradient strips (plazomicin). All isolates were subjected to hybrid whole-genome sequencing (WGS). Sequence types (STs), core genome phylogenetic relatedness, horizontally acquired resistance mechanisms, plasmid analysis and the genetic environment of RMTs were determined in silico from WGS data in all RMT-positive isolates. Among the 468 CPE isolates evaluated, 24 isolates (5.1%) recovered from nine different hospitals spanning five Spanish regions showed resistance to all aminoglycosides and were positive for an RMT (21 RmtF, 2 ArmA and 1 RmtC). All RMT-producers showed high-level resistance to all aminoglycosides, including plazomicin, and in most cases exhibited an extensively drug-resistant susceptibility profile. The RMT-positive isolates showed low genetic diversity and were global clones of Klebsiella pneumoniae (ST147, ST101, ST395) and Enterobacter cloacae (ST93) bearing blaOXA-48, blaNDM-1 or blaVIM-1 carbapenemase genes. RMTs were harboured in five different multidrug resistance plasmids and linked to efficient mobile genetic elements. Our findings highlight that RMTs are emerging among clinical CPE isolates from Spain and their spread should be monitored to preserve the future clinical utility of aminoglycosides and plazomicin.
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Affiliation(s)
- Jorge Arca-Suárez
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña (CHUAC), A Coruña, Spain
| | - Bruno K Rodiño-Janeiro
- Prof. Martin Polz Laboratory, University of Vienna, Department for Microbiology and Ecosystem Science, Division of Microbial Ecology, Vienna, Austria
| | - Astrid Pérez
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña (CHUAC), A Coruña, Spain
| | - Paula Guijarro-Sánchez
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña (CHUAC), A Coruña, Spain
| | - Juan C Vázquez-Ucha
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña (CHUAC), A Coruña, Spain
| | - Fernando Cruz
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Jèssica Gómez-Garrido
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Tyler S Alioto
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universistat Pompeu Fabra (UPF), Barcelona, Spain
| | | | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universistat Pompeu Fabra (UPF), Barcelona, Spain
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universistat Pompeu Fabra (UPF), Barcelona, Spain
| | - Marina Oviaño
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña (CHUAC), A Coruña, Spain
| | - Alejandro Beceiro
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña (CHUAC), A Coruña, Spain
| | - Germán Bou
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña (CHUAC), A Coruña, Spain.
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- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña (CHUAC), A Coruña, Spain
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Vázquez-Ucha JC, Seoane-Estévez A, Rodiño-Janeiro BK, González-Bardanca M, Conde-Pérez K, Martínez-Guitián M, Alvarez-Fraga L, Arca-Suárez J, Lasarte-Monterrubio C, Gut M, Gut I, Álvarez-Tejado M, Oviaño M, Beceiro A, Bou G. Activity of imipenem/relebactam against a Spanish nationwide collection of carbapenemase-producing Enterobacterales. J Antimicrob Chemother 2021; 76:1498-1510. [PMID: 33677560 DOI: 10.1093/jac/dkab043] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 01/27/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Imipenem/relebactam is a novel carbapenem/β-lactamase inhibitor combination, developed to act against carbapenemase-producing Enterobacterales (CPE). OBJECTIVES To assess the in vitro activity of imipenem/relebactam against a Spanish nationwide collection of CPE by testing the susceptibility of these isolates to 16 widely used antimicrobials and to determine the underlying β-lactam resistance mechanisms involved and the molecular epidemiology of carbapenemases in Spain. MATERIALS AND METHODS Clinical CPE isolates (n = 401) collected for 2 months from 24 hospitals in Spain were tested. MIC50, MIC90 and susceptibility/resistance rates were interpreted in accordance with the EUCAST guidelines. β-Lactam resistance mechanisms and molecular epidemiology were characterized by WGS. RESULTS For all isolates, high rates of susceptibility to colistin (86.5%; MIC50/90 = 0.12/8 mg/L), imipenem/relebactam (85.8%; MIC50/90 = 0.5/4 mg/L) and ceftazidime/avibactam (83.8%, MIC50/90 = 1/≥256 mg/L) were observed. The subgroups of isolates producing OXA-48-like (n = 305, 75.1%) and KPC-like enzymes (n = 44, 10.8%) were highly susceptible to ceftazidime/avibactam (97.7%, MIC50/90 = 1/2 mg/L) and imipenem/relebactam (100.0%, MIC50/90 = ≤0.25/1 mg/L), respectively.The most widely disseminated high-risk clones of carbapenemase-producing Klebsiella pneumoniae across Spain were found to be ST11, ST147, ST392 and ST15 (mostly associated with OXA-48) and ST258/512 (in all cases producing KPC). CONCLUSIONS Imipenem/relebactam, colistin and ceftazidime/avibactam were the most active antimicrobials against all CPEs. Imipenem/relebactam is a valuable addition to the antimicrobial arsenal used in the fight against CPE, particularly against KPC-producing isolates, which in all cases were susceptible to this combination.
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Affiliation(s)
- Juan Carlos Vázquez-Ucha
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (CICA-INIBIC), Complejo Hospitalario Universitario A Coruña, Spain
| | - Alejandro Seoane-Estévez
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (CICA-INIBIC), Complejo Hospitalario Universitario A Coruña, Spain
| | - Bruno Kotska Rodiño-Janeiro
- Prof. Martin Polz Laboratory, University of Vienna, Department for Microbiology and Ecosystem Science, Division of Microbial Ecology, Vienna, Austria
| | - Mónica González-Bardanca
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (CICA-INIBIC), Complejo Hospitalario Universitario A Coruña, Spain
| | - Kelly Conde-Pérez
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (CICA-INIBIC), Complejo Hospitalario Universitario A Coruña, Spain
| | - Marta Martínez-Guitián
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (CICA-INIBIC), Complejo Hospitalario Universitario A Coruña, Spain
| | - Laura Alvarez-Fraga
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (CICA-INIBIC), Complejo Hospitalario Universitario A Coruña, Spain
| | - Jorge Arca-Suárez
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (CICA-INIBIC), Complejo Hospitalario Universitario A Coruña, Spain
| | - Cristina Lasarte-Monterrubio
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (CICA-INIBIC), Complejo Hospitalario Universitario A Coruña, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | - Marina Oviaño
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (CICA-INIBIC), Complejo Hospitalario Universitario A Coruña, Spain
| | - Alejandro Beceiro
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (CICA-INIBIC), Complejo Hospitalario Universitario A Coruña, Spain
| | - Germán Bou
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (CICA-INIBIC), Complejo Hospitalario Universitario A Coruña, Spain
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Pou C, Noguera-Julian M, Pérez-Álvarez S, García F, Delgado R, Dalmau D, Álvarez-Tejado M, Gonzalez D, Sayada C, Chueca N, Pulido F, Ibáñez L, Rodríguez C, Casadellà M, Santos JR, Ruiz L, Clotet B, Paredes R. Improved prediction of salvage antiretroviral therapy outcomes using ultrasensitive HIV-1 drug resistance testing. Clin Infect Dis 2014; 59:578-88. [PMID: 24879788 DOI: 10.1093/cid/ciu287] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The clinical relevance of ultrasensitive human immunodeficiency virus type 1 (HIV-1) genotypic resistance testing in antiretroviral treatment (ART)-experienced individuals remains unknown. METHODS This was a retrospective, multicentre, cohort study in ART-experienced, HIV-1-infected adults who initiated salvage ART including, at least 1 ritonavir-boosted protease inhibitor, raltegravir or etravirine. Presalvage ART Sanger and 454 sequencing of plasma HIV-1 were used to generate separate genotypic sensitivity scores (GSS) using the HIVdb, ANRS, and REGA algorithms. Virological failure (VF) was defined as 2 consecutive HIV-1 RNA levels ≥200 copies/mL at least 12 weeks after salvage ART initiation, whereas subjects remained on the same ART. The ability of Sanger and 454-GSS to predict VF was assessed by receiver operating characteristic (ROC) curves and survival analyses. RESULTS The study included 132 evaluable subjects; 28 (21%) developed VF. Using HIVdb, 454 predicted VF better than Sanger sequencing in the ROC curve analysis (area under the curve: 0.69 vs 0.60, Delong test P = .029). Time to VF was shorter for subjects with 454-GSS < 3 vs 454-GSS ≥ 3 (Log-rank P = .003) but not significantly different between Sanger-GSS < 3 and ≥3. Factors independently associated with increased risk of VF in multivariate Cox regression were a 454-GSS < 3 (HR = 4.6, 95 CI, [1.5, 14.0], P = .007), and the number of previous antiretrovirals received (HR = 1.2 per additional drug, 95 CI, [1.1, 1.3], P = .001). Equivalent findings were obtained with the ANRS and REGA algorithms. CONCLUSIONS Ultrasensitive HIV-1 genotyping improves GSS-based predictions of virological outcomes of salvage ART relative to Sanger sequencing. This may improve the clinical management of ART-experienced subjects living with HIV-1. CLINICAL TRIALS REGISTRATION NCT01346878.
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Affiliation(s)
- Christian Pou
- IrsiCaixa AIDS Research Institute - HIVACAT, Hospital Universitari Germans Trias i Pujol, Badalona Universitat Autònoma de Barcelona, Cerdanyola del Vallès
| | - Marc Noguera-Julian
- IrsiCaixa AIDS Research Institute - HIVACAT, Hospital Universitari Germans Trias i Pujol, Badalona Universitat Autònoma de Barcelona, Cerdanyola del Vallès Universitat de Vic-Universitat Central de Catalunya, Vic
| | - Susana Pérez-Álvarez
- IrsiCaixa AIDS Research Institute - HIVACAT, Hospital Universitari Germans Trias i Pujol, Badalona Universitat Autònoma de Barcelona, Cerdanyola del Vallès
| | - Federico García
- Microbiology and Molecular Biology Department, Hospital Universitario San Cecilio, Granada
| | - Rafael Delgado
- Laboratory of Molecular Microbiology, Instituto de Investigación Biomedica Hospital 12 de Octubre (i + 12), Madrid
| | - David Dalmau
- HIV/AIDS Department, Hospital Universitari MútuaTerrassa Universitat de Barcelona, Terrassa
| | | | | | - Chalom Sayada
- ABL SA, Barcelona, Spain ABL SA, Luxembourg, Luxembourg
| | - Natalia Chueca
- Microbiology and Molecular Biology Department, Hospital Universitario San Cecilio, Granada
| | - Federico Pulido
- Laboratory of Molecular Microbiology, Instituto de Investigación Biomedica Hospital 12 de Octubre (i + 12), Madrid
| | - Laura Ibáñez
- HIV/AIDS Department, Hospital Universitari MútuaTerrassa
| | - Cristina Rodríguez
- IrsiCaixa AIDS Research Institute - HIVACAT, Hospital Universitari Germans Trias i Pujol, Badalona Universitat Autònoma de Barcelona, Cerdanyola del Vallès
| | - Maria Casadellà
- IrsiCaixa AIDS Research Institute - HIVACAT, Hospital Universitari Germans Trias i Pujol, Badalona Universitat Autònoma de Barcelona, Cerdanyola del Vallès
| | - José R Santos
- Universitat Autònoma de Barcelona, Cerdanyola del Vallès HIV Unit, Internal Medicine Department, Hospital Universitari Germans Trias i Pujol, Badalona, Catalonia, Spain
| | - Lidia Ruiz
- IrsiCaixa AIDS Research Institute - HIVACAT, Hospital Universitari Germans Trias i Pujol, Badalona Universitat Autònoma de Barcelona, Cerdanyola del Vallès
| | - Bonaventura Clotet
- IrsiCaixa AIDS Research Institute - HIVACAT, Hospital Universitari Germans Trias i Pujol, Badalona Universitat Autònoma de Barcelona, Cerdanyola del Vallès Universitat de Vic-Universitat Central de Catalunya, Vic HIV Unit, Internal Medicine Department, Hospital Universitari Germans Trias i Pujol, Badalona, Catalonia, Spain
| | - Roger Paredes
- IrsiCaixa AIDS Research Institute - HIVACAT, Hospital Universitari Germans Trias i Pujol, Badalona Universitat Autònoma de Barcelona, Cerdanyola del Vallès Universitat de Vic-Universitat Central de Catalunya, Vic HIV Unit, Internal Medicine Department, Hospital Universitari Germans Trias i Pujol, Badalona, Catalonia, Spain
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Ariño J, Casamayor A, Pérez JP, Pedrola L, Álvarez-Tejado M, Marbà M, Santoyo J, Dopazo J. Assessing differential expression measurements by highly parallel pyrosequencing and DNA microarrays: a comparative study. OMICS 2011; 17:53-9. [PMID: 21919703 DOI: 10.1089/omi.2011.0065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
To explore the feasibility of pyrosequencing for quantitative differential gene expression analysis we have performed a comparative study of the results of the sequencing experiments to those obtained by a conventional DNA microarray platform. A conclusion from our analysis is that, over a threshold of 35 normalized reads per gene, the measurements of gene expression display a good correlation with the references. The observed concordance between pyrosequencing and DNA microarray platforms beyond the threshold was of 0.8, measured as a Pearson's correlation coefficient. In differential gene expression the initial aim is the quantification the differences among transcripts when comparing experimental conditions. Thus, even in a scenario of low coverage the concordance in the measurements is quite acceptable. On the other hand, the comparatively longer read size obtained by pyrosequencing allows detecting unconventional splicing forms.
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Affiliation(s)
- Joaquín Ariño
- Departament de Bioquímica y Biología Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
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Codoñer FM, Pou C, Thielen A, García F, Delgado R, Dalmau D, Álvarez-Tejado M, Ruiz L, Clotet B, Paredes R. Added value of deep sequencing relative to population sequencing in heavily pre-treated HIV-1-infected subjects. PLoS One 2011; 6:e19461. [PMID: 21602929 PMCID: PMC3094345 DOI: 10.1371/journal.pone.0019461] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Accepted: 03/30/2011] [Indexed: 12/29/2022] Open
Abstract
OBJECTIVE To explore the potential of deep HIV-1 sequencing for adding clinically relevant information relative to viral population sequencing in heavily pre-treated HIV-1-infected subjects. METHODS In a proof-of-concept study, deep sequencing was compared to population sequencing in HIV-1-infected individuals with previous triple-class virological failure who also developed virologic failure to deep salvage therapy including, at least, darunavir, tipranavir, etravirine or raltegravir. Viral susceptibility was inferred before salvage therapy initiation and at virological failure using deep and population sequencing genotypes interpreted with the HIVdb, Rega and ANRS algorithms. The threshold level for mutant detection with deep sequencing was 1%. RESULTS 7 subjects with previous exposure to a median of 15 antiretrovirals during a median of 13 years were included. Deep salvage therapy included darunavir, tipranavir, etravirine or raltegravir in 4, 2, 2 and 5 subjects, respectively. Self-reported treatment adherence was adequate in 4 and partial in 2; one individual underwent treatment interruption during follow-up. Deep sequencing detected all mutations found by population sequencing and identified additional resistance mutations in all but one individual, predominantly after virological failure to deep salvage therapy. Additional genotypic information led to consistent decreases in predicted susceptibility to etravirine, efavirenz, nucleoside reverse transcriptase inhibitors and indinavir in 2, 1, 2 and 1 subject, respectively. Deep sequencing data did not consistently modify the susceptibility predictions achieved with population sequencing for darunavir, tipranavir or raltegravir. CONCLUSIONS In this subset of heavily pre-treated individuals, deep sequencing improved the assessment of genotypic resistance to etravirine, but did not consistently provide additional information on darunavir, tipranavir or raltegravir susceptibility. These data may inform the design of future studies addressing the clinical value of minority drug-resistant variants in treatment-experienced subjects.
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Affiliation(s)
- Francisco M. Codoñer
- Institut de Recerca de la SIDA irsiCaixa-HIVACAT, Badalona, Spain
- * E-mail: (FMC); (RP)
| | - Christian Pou
- Institut de Recerca de la SIDA irsiCaixa-HIVACAT, Badalona, Spain
| | | | | | | | - David Dalmau
- Hospital Universitari Mutua Terrassa, Terrassa, Spain
| | | | - Lidia Ruiz
- Institut de Recerca de la SIDA irsiCaixa-HIVACAT, Badalona, Spain
| | - Bonaventura Clotet
- Institut de Recerca de la SIDA irsiCaixa-HIVACAT, Badalona, Spain
- Unitat VIH, Hospital Universitari Germans Trias I Pujol, Badalona, Spain
| | - Roger Paredes
- Institut de Recerca de la SIDA irsiCaixa-HIVACAT, Badalona, Spain
- Unitat VIH, Hospital Universitari Germans Trias I Pujol, Badalona, Spain
- * E-mail: (FMC); (RP)
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