Whole genome sequencing-based characterization of extensively drug resistant (XDR) strains of Mycobacterium tuberculosis from Pakistan

Handle URI:
http://hdl.handle.net/10754/348483
Title:
Whole genome sequencing-based characterization of extensively drug resistant (XDR) strains of Mycobacterium tuberculosis from Pakistan
Authors:
Hasan, Zahra; Ali, Asho; 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:
Objectives: The global increase in drug resistance in Mycobacterium tuberculosis (MTB) strains increases the focus on improved molecular diagnostics for MTB. Extensively drug-resistant (XDR) - TB is caused by MTB strains resistant to rifampicin, isoniazid, fluoroquinolone and aminoglycoside antibiotics. Resistance to anti-tuberculous drugs has been associated with single nucleotide polymorphisms (SNPs), in particular MTB genes. However, there is regional variation between MTB lineages and the SNPs associated with resistance. Therefore, there is a need to identify common resistance conferring SNPs so that effective molecular-based diagnostic tests for MTB can be developed. This study investigated used whole genome sequencing (WGS) to characterize 37 XDR MTB isolates from Pakistan and investigated SNPs related to drug resistance. Methods: XDR-TB strains were selected. DNA was extracted from MTB strains, and samples underwent WGS with 76-base-paired end fragment sizes using Illumina paired end HiSeq2000 technology. Raw sequence data were mapped uniquely to H37Rv reference genome. The mappings allowed SNPs and small indels to be called using SAMtools/BCFtools. Results: This study found that in all XDR strains, rifampicin resistance was attributable to SNPs in the rpoB RDR region. Isoniazid resistance-associated mutations were primarily related to katG codon 315 followed by inhA S94A. Fluoroquinolone resistance was attributable to gyrA 91-94 codons in most strains, while one did not have SNPs in either gyrA or gyrB. Aminoglycoside resistance was mostly associated with SNPs in rrs, except in 6 strains. Ethambutol resistant strains had embB codon 306 mutations, but many strains did not have this present. The SNPs were compared with those present in commercial assays such as LiPA Hain MDRTBsl, and the sensitivity of the assays for these strains was evaluated. Conclusions: If common drug resistance associated with SNPs evaluated the concordance between phenotypic and genotypic testing, the results would be rifampicin (100%), isoniazid (89%), fluoroquinolones (95%), aminoglycoside (81%) and ethambutol (61%). 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 (XDR) strains of Mycobacterium tuberculosis from Pakistan 2015, 4:11 International Journal of Mycobacteriology
Publisher:
Elsevier BV
Journal:
International Journal of Mycobacteriology
Issue Date:
Mar-2015
DOI:
10.1016/j.ijmyco.2014.10.050
Type:
Abstract
ISSN:
22125531
Additional Links:
http://linkinghub.elsevier.com/retrieve/pii/S2212553114001721
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Articles

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DC FieldValue Language
dc.contributor.authorHasan, Zahraen
dc.contributor.authorAli, Ashoen
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.accessioned2015-04-02T13:42:21Zen
dc.date.available2015-04-02T13:42:21Zen
dc.date.issued2015-03en
dc.identifier.citationWhole genome sequencing-based characterization of extensively drug resistant (XDR) strains of Mycobacterium tuberculosis from Pakistan 2015, 4:11 International Journal of Mycobacteriologyen
dc.identifier.issn22125531en
dc.identifier.doi10.1016/j.ijmyco.2014.10.050en
dc.identifier.urihttp://hdl.handle.net/10754/348483en
dc.description.abstractObjectives: The global increase in drug resistance in Mycobacterium tuberculosis (MTB) strains increases the focus on improved molecular diagnostics for MTB. Extensively drug-resistant (XDR) - TB is caused by MTB strains resistant to rifampicin, isoniazid, fluoroquinolone and aminoglycoside antibiotics. Resistance to anti-tuberculous drugs has been associated with single nucleotide polymorphisms (SNPs), in particular MTB genes. However, there is regional variation between MTB lineages and the SNPs associated with resistance. Therefore, there is a need to identify common resistance conferring SNPs so that effective molecular-based diagnostic tests for MTB can be developed. This study investigated used whole genome sequencing (WGS) to characterize 37 XDR MTB isolates from Pakistan and investigated SNPs related to drug resistance. Methods: XDR-TB strains were selected. DNA was extracted from MTB strains, and samples underwent WGS with 76-base-paired end fragment sizes using Illumina paired end HiSeq2000 technology. Raw sequence data were mapped uniquely to H37Rv reference genome. The mappings allowed SNPs and small indels to be called using SAMtools/BCFtools. Results: This study found that in all XDR strains, rifampicin resistance was attributable to SNPs in the rpoB RDR region. Isoniazid resistance-associated mutations were primarily related to katG codon 315 followed by inhA S94A. Fluoroquinolone resistance was attributable to gyrA 91-94 codons in most strains, while one did not have SNPs in either gyrA or gyrB. Aminoglycoside resistance was mostly associated with SNPs in rrs, except in 6 strains. Ethambutol resistant strains had embB codon 306 mutations, but many strains did not have this present. The SNPs were compared with those present in commercial assays such as LiPA Hain MDRTBsl, and the sensitivity of the assays for these strains was evaluated. Conclusions: If common drug resistance associated with SNPs evaluated the concordance between phenotypic and genotypic testing, the results would be rifampicin (100%), isoniazid (89%), fluoroquinolones (95%), aminoglycoside (81%) and ethambutol (61%). This work highlights the importance of expanded targets for drug resistance detection in MTB isolates.en
dc.publisherElsevier BVen
dc.relation.urlhttp://linkinghub.elsevier.com/retrieve/pii/S2212553114001721en
dc.rightsArchived with thanks to International Journal of Mycobacteriology. http://creativecommons.org/licenses/by-nc-nd/4.0/en
dc.titleWhole genome sequencing-based characterization of extensively drug resistant (XDR) strains of Mycobacterium tuberculosis from Pakistanen
dc.typeAbstracten
dc.contributor.departmentPathogen Genomics Laboratoryen
dc.identifier.journalInternational Journal of Mycobacteriologyen
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionDepartment of Pathology and Microbiology, The Aga Khan University, Karachi, Pakistanen
dc.contributor.institutionDepartment of Pathology and Microbiology, Aga Khan University Hospital, Karachi, Pakistanen
dc.contributor.institutionSchool of Nursing and Midwifery, Aga Khan University Hospital, Karachi, Pakistanen
dc.contributor.institutionFaculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, United Kingdomen
dc.contributor.institutionSydney Emerging Infections and Biosecurity Institute and School of Public Health, Sydney Medical School, University of Sydney, NSW 2006, Australiaen
kaust.authorHill-Cawthorne, Grant A.en
kaust.authorNair, Mridulen
kaust.authorPain, Arnaben
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