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dc.contributor.authorKanji, Akbar
dc.contributor.authorHasan, Zahra
dc.contributor.authorAli, Asho M.
dc.contributor.authorMcNerney, Ruth
dc.contributor.authorMallard, Kim E.
dc.contributor.authorColl, Francesc
dc.contributor.authorHill-Cawthorne, Grant A.
dc.contributor.authorPain, Arnab
dc.contributor.authorNair, Mridul
dc.contributor.authorClark, Taane G.
dc.contributor.authorZaver, Ambreen
dc.contributor.authorJafri, Sana M Wasim
dc.contributor.authorHasan, Rumina
dc.identifier.citationKanji, A., Hasan, Z., Ali, A., McNerney, R., Mallard, K., Coll, F., … Hasan, R. (2015). Characterization of genomic variations in SNPs of PE_PGRS genes reveals deletions and insertions in extensively drug resistant (XDR) M. tuberculosis strains from Pakistan. International Journal of Mycobacteriology, 4, 116. doi:10.1016/j.ijmyco.2014.10.051
dc.description.abstractBackground: Mycobacterium tuberculosis (MTB) PE_PGRS genes belong to the PE multi-gene family. Although the function of the members of the PE_PGRS multi-gene family is not yet known, it is hypothesized that the PE_PGRS genes may be associated with genetic variability. Material and methods: Whole genome sequencing analysis was performed on (n= 37) extensively drug resistant (XDR) MTB strains from Pakistan which included Central Asian (n= 23), East African Indian (n= 2), X3 (n= 1), T group (n= 3) and Orphan (n= 8) MTB strains. Results: By analyzing 42 PE_PGRS genes, 111 SNPs were identified, of which 13 were non-synonymous SNPs (nsSNPs). The nsSNPs identified in the PE_PGRS genes were as follows: 6, 9, 10 and 55 present in each of the CAS, EAI, Orphan, T1 and X3 XDR MTB strains studied. Deletions in PE_PGRS genes: 19, 21 and 23 were observed in 7 (35.0%) CAS1 and 3 (37.5%) in Orphan XDR MTB strains, while deletions in the PE_PGRS genes: 49 and 50 were observed in 36 (95.0%) CAS1 and all CAS, CAS2 and Orphan XDR MTB strains. An insertion in PE_PGRS6 gene was observed in all CAS, EAI3 and Orphan, while insertions in the PE_PGRS genes 19 and 33 were observed in 19 (95%) CAS1 and all CAS, CAS2, EAI3 and Orphan 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, Insertions and Deletions in the PE_PGRS genes of XDR-TB strains from Pakistan. It highlights common genetic variations which may contribute to persistence.
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.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Division
dc.contributor.departmentBioscience Program
dc.contributor.departmentComputational Bioscience Research Center (CBRC)
dc.contributor.departmentPathogen Genomics Laboratory
dc.identifier.journalInternational Journal of Mycobacteriology
dc.conference.nameThe 1st Asian-African Congress of International Journal of Mycobacteriology, Iran
dc.contributor.institutionAga Khan University, Karachi, Pakistan
dc.contributor.institutionLondon School of Hygiene & 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.personPain, Arnab
kaust.personNair, Mridul

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