Whole Genome Sequencing Based Characterization of Extensively Drug-Resistant Mycobacterium tuberculosis Isolates from Pakistan

Handle URI:
http://hdl.handle.net/10754/346687
Title:
Whole Genome Sequencing Based Characterization of Extensively Drug-Resistant Mycobacterium tuberculosis Isolates from Pakistan
Authors:
Ali, Asho; Hasan, Zahra; McNerney, Ruth; Mallard, Kim; Hill-Cawthorne, Grant A. ( 0000-0002-3828-5473 ) ; Coll, Francesc; Nair, Mridul; Pain, Arnab ( 0000-0002-1755-2819 ) ; Clark, Taane G.; Hasan, Rumina
Abstract:
Improved molecular diagnostic methods for detection drug resistance in Mycobacterium tuberculosis (MTB) strains are required. Resistance to first- and second- line anti-tuberculous drugs has been associated with single nucleotide polymorphisms (SNPs) in particular genes. However, these SNPs can vary between MTB lineages therefore local data is required to describe different strain populations. We used whole genome sequencing (WGS) to characterize 37 extensively drug-resistant (XDR) MTB isolates from Pakistan and investigated 40 genes associated with drug resistance. Rifampicin resistance was attributable to SNPs in the rpoB hot-spot region. Isoniazid resistance was most commonly associated with the katG codon 315 (92%) mutation followed by inhA S94A (8%) however, one strain did not have SNPs in katG, inhA or oxyR-ahpC. All strains were pyrazimamide resistant but only 43% had pncA SNPs. Ethambutol resistant strains predominantly had embB codon 306 (62%) mutations, but additional SNPs at embB codons 406, 378 and 328 were also present. Fluoroquinolone resistance was associated with gyrA 91-94 codons in 81% of strains; four strains had only gyr B mutations, while others did not have SNPs in either gyrA or gyrB. Streptomycin resistant strains had mutations in ribosomal RNA genes; rpsL codon 43 (42%); rrs 500 region (16%), and gidB (34%) while six strains did not have mutations in any of these genes. Amikacin/kanamycin/capreomycin resistance was associated with SNPs in rrs at nt1401 (78%) and nt1484 (3%), except in seven (19%) strains. We estimate that if only the common hot-spot region targets of current commercial assays were used, the concordance between phenotypic and genotypic testing for these XDR strains would vary between rifampicin (100%), isoniazid (92%), flouroquinolones (81%), aminoglycoside (78%) and ethambutol (62%); while pncA sequencing would provide genotypic resistance in less than half the isolates. This work highlights the importance of expanded targets for drug resistance detection in MTB isolates.
KAUST Department:
Pathogen Genomics Laboratory
Citation:
Whole Genome Sequencing Based Characterization of Extensively Drug-Resistant Mycobacterium tuberculosis Isolates from Pakistan 2015, 10 (2):e0117771 PLOS ONE
Publisher:
Public Library of Science
Journal:
PLOS ONE
Issue Date:
26-Feb-2015
DOI:
10.1371/journal.pone.0117771
PubMed ID:
25719196
PubMed Central ID:
PMC4342168
Type:
Article
ISSN:
1932-6203
Additional Links:
http://dx.plos.org/10.1371/journal.pone.0117771
Appears in Collections:
Articles

Full metadata record

DC FieldValue Language
dc.contributor.authorAli, Ashoen
dc.contributor.authorHasan, Zahraen
dc.contributor.authorMcNerney, Ruthen
dc.contributor.authorMallard, Kimen
dc.contributor.authorHill-Cawthorne, Grant A.en
dc.contributor.authorColl, Francescen
dc.contributor.authorNair, Mridulen
dc.contributor.authorPain, Arnaben
dc.contributor.authorClark, Taane G.en
dc.contributor.authorHasan, Ruminaen
dc.date.accessioned2015-03-16T05:58:26Zen
dc.date.available2015-03-16T05:58:26Zen
dc.date.issued2015-02-26en
dc.identifier.citationWhole Genome Sequencing Based Characterization of Extensively Drug-Resistant Mycobacterium tuberculosis Isolates from Pakistan 2015, 10 (2):e0117771 PLOS ONEen
dc.identifier.issn1932-6203en
dc.identifier.pmid25719196en
dc.identifier.doi10.1371/journal.pone.0117771en
dc.identifier.urihttp://hdl.handle.net/10754/346687en
dc.description.abstractImproved molecular diagnostic methods for detection drug resistance in Mycobacterium tuberculosis (MTB) strains are required. Resistance to first- and second- line anti-tuberculous drugs has been associated with single nucleotide polymorphisms (SNPs) in particular genes. However, these SNPs can vary between MTB lineages therefore local data is required to describe different strain populations. We used whole genome sequencing (WGS) to characterize 37 extensively drug-resistant (XDR) MTB isolates from Pakistan and investigated 40 genes associated with drug resistance. Rifampicin resistance was attributable to SNPs in the rpoB hot-spot region. Isoniazid resistance was most commonly associated with the katG codon 315 (92%) mutation followed by inhA S94A (8%) however, one strain did not have SNPs in katG, inhA or oxyR-ahpC. All strains were pyrazimamide resistant but only 43% had pncA SNPs. Ethambutol resistant strains predominantly had embB codon 306 (62%) mutations, but additional SNPs at embB codons 406, 378 and 328 were also present. Fluoroquinolone resistance was associated with gyrA 91-94 codons in 81% of strains; four strains had only gyr B mutations, while others did not have SNPs in either gyrA or gyrB. Streptomycin resistant strains had mutations in ribosomal RNA genes; rpsL codon 43 (42%); rrs 500 region (16%), and gidB (34%) while six strains did not have mutations in any of these genes. Amikacin/kanamycin/capreomycin resistance was associated with SNPs in rrs at nt1401 (78%) and nt1484 (3%), except in seven (19%) strains. We estimate that if only the common hot-spot region targets of current commercial assays were used, the concordance between phenotypic and genotypic testing for these XDR strains would vary between rifampicin (100%), isoniazid (92%), flouroquinolones (81%), aminoglycoside (78%) and ethambutol (62%); while pncA sequencing would provide genotypic resistance in less than half the isolates. This work highlights the importance of expanded targets for drug resistance detection in MTB isolates.en
dc.publisherPublic Library of Scienceen
dc.relation.urlhttp://dx.plos.org/10.1371/journal.pone.0117771en
dc.rightsThis is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.en
dc.titleWhole Genome Sequencing Based Characterization of Extensively Drug-Resistant Mycobacterium tuberculosis Isolates from Pakistanen
dc.typeArticleen
dc.contributor.departmentPathogen Genomics Laboratoryen
dc.identifier.journalPLOS ONEen
dc.identifier.pmcidPMC4342168en
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionDepartment of Pathology and Microbiology, Aga Khan University Hospitalen
dc.contributor.institutionSchool of Nursing and Midwifery, The Aga Khan University Hospitalen
dc.contributor.institutionFaculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicineen
dc.contributor.institutionSydney Emerging Infections and Biosecurity Institute and School of Public Health, Sydney Medical School, University of Sydneyen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorHill-Cawthorne, Grant A.en
kaust.authorNair, Mridulen
kaust.authorPain, Arnaben

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