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dc.contributor.authorKanji, Akbar
dc.contributor.authorHasan, Zahra
dc.contributor.authorAli, Asho
dc.contributor.authorMcNerney, Ruth
dc.contributor.authorMallard, Kim
dc.contributor.authorColl, Francesc
dc.contributor.authorHill-Cawthorne, Grant A.
dc.contributor.authorNair, Mridul
dc.contributor.authorClark, Taane G.
dc.contributor.authorZaver, Ambreen
dc.contributor.authorJafri, Sana
dc.contributor.authorHasan, Rumina
dc.date.accessioned2015-05-05T14:38:45Z
dc.date.available2015-05-05T14:38:45Z
dc.date.issued2015-01-21
dc.identifier.citationCharacterization of genomic variations in SNPs of PE_PGRS genes reveals deletions and insertions in extensively drug resistant (XDR) M. tuberculosis strains from Pakistan 2015, 4 (1):73 International Journal of Mycobacteriology
dc.identifier.issn22125531
dc.identifier.pmid26655202
dc.identifier.doi10.1016/j.ijmyco.2014.11.049
dc.identifier.urihttp://hdl.handle.net/10754/552321
dc.description.abstractBackground Mycobacterium tuberculosis (MTB) PE_PGRS genes belong to the PE multigene family. Although the function of PE_PGRS genes is unknown, it is hypothesized that the PE_PGRS genes may be associated with antigenic variability in MTB. Material and methods Whole genome sequencing analysis was performed on (n = 37) extensively drug-resistant (XDR) MTB strains from Pakistan, which included Lineage 1 (East African Indian, n = 2); Other lineage 1 (n = 3); Lineage 3 (Central Asian, n = 24); Other lineage 3 (n = 4); Lineage 4 (X3, n = 1) and T group (n = 3) MTB strains. Results There were 107 SNPs identified from the analysis of 42 PE_PGRS genes; of these, 13 were non-synonymous SNPs (nsSNPs). The nsSNPs identified in PE_PGRS genes – 6, 9 and 10 – were common in all EAI, CAS, Other lineages (1 and 3), T1 and X3. Deletions (DELs) in PE_PGRS genes – 3 and 19 – were observed in 17 (80.9%) CAS1 and 6 (85.7%) in Other lineages (1 and 3) XDR MTB strains, while DELs in the PE_PGRS49 were observed in all CAS1, CAS, CAS2 and Other lineages (1 and 3) XDR MTB strains. All CAS, EAI and Other lineages (1 and 3) strains showed insertions (INS) in PE_PGRS6 gene, while INS in the PE_PGRS genes 19 and 33 were observed in 20 (95.2%) CAS1, all CAS, CAS2, EAI and Other lineages (1 and 3) XDR MTB strains. Conclusion Genetic diversity in PE_PGRS genes contributes to antigenic variability and may result in increased immunogenicity of strains. This is the first study identifying variations in nsSNPs and INDELs in the PE_PGRS genes of XDR-TB strains from Pakistan. It highlights common genetic variations which may contribute to persistence.
dc.publisherMedknow
dc.relation.urlhttp://linkinghub.elsevier.com/retrieve/pii/S2212553115000126
dc.rightsArchived with thanks to International Journal of Mycobacteriology. http://creativecommons.org/licenses/by-nc-nd/4.0/
dc.subjectWhole genome sequencing
dc.subjectMycobacterium tuberculosis
dc.subjectPE_PGRS genes
dc.titleCharacterization of genomic variations in SNPs of PE_PGRS genes reveals deletions and insertions in extensively drug resistant (XDR) M. tuberculosis strains from Pakistan
dc.typeArticle
dc.contributor.departmentBioscience Program
dc.contributor.departmentComputational Bioscience Research Center (CBRC)
dc.contributor.departmentPathogen Genomics Laboratory
dc.identifier.journalInternational Journal of Mycobacteriology
dc.eprint.versionPublisher's Version/PDF
dc.contributor.institutionAga Khan University, Karachi, Pakistan
dc.contributor.institutionLondon School of Hygiene and Tropical Medicine (LSHTM), United Kingdom
dc.contributor.institutionSydney Emerging Infections and Biosecurity Institute and School of Public Health, Sydney Medical School, University of Sydney, NSW 2006, Australia
kaust.personHill-Cawthorne, Grant A.
kaust.personNair, Mridul
refterms.dateFOA2018-06-13T10:29:28Z
dc.date.published-online2015-01-21
dc.date.published-print2015-03


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