Characterization of genomic variations in SNPs of PE_PGRS genes reveals deletions and insertions in extensively drug resistant (XDR) M. tuberculosis strains from Pakistan

Handle URI:
http://hdl.handle.net/10754/566083
Title:
Characterization of genomic variations in SNPs of PE_PGRS genes reveals deletions and insertions in extensively drug resistant (XDR) M. tuberculosis strains from Pakistan
Authors:
Kanji, Akbar; Hasan, Zahra; Ali, Asho M.; McNerney, Ruth; Mallard, Kim E.; Coll, Francesc; Hill-Cawthorne, Grant A. ( 0000-0002-3828-5473 ) ; Pain, Arnab ( 0000-0002-1755-2819 ) ; Nair, Mridul; Clark, Taane G.; Zaver, Ambreen; Jafri, Sana M Wasim; Hasan, Rumina
Abstract:
Background: 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.
KAUST Department:
Pathogen Genomics Laboratory
Publisher:
Elsevier BV
Journal:
International Journal of Mycobacteriology
Conference/Event name:
The 1st Asian-African Congress of International Journal of Mycobacteriology, Iran
Issue Date:
Mar-2015
DOI:
10.1016/j.ijmyco.2014.10.051
Type:
Presentation
ISSN:
22125531
Appears in Collections:
Presentations

Full metadata record

DC FieldValue Language
dc.contributor.authorKanji, Akbaren
dc.contributor.authorHasan, Zahraen
dc.contributor.authorAli, Asho M.en
dc.contributor.authorMcNerney, Ruthen
dc.contributor.authorMallard, Kim E.en
dc.contributor.authorColl, Francescen
dc.contributor.authorHill-Cawthorne, Grant A.en
dc.contributor.authorPain, Arnaben
dc.contributor.authorNair, Mridulen
dc.contributor.authorClark, Taane G.en
dc.contributor.authorZaver, Ambreenen
dc.contributor.authorJafri, Sana M Wasimen
dc.contributor.authorHasan, Ruminaen
dc.date.accessioned2015-08-12T09:27:35Zen
dc.date.available2015-08-12T09:27:35Zen
dc.date.issued2015-03en
dc.identifier.issn22125531en
dc.identifier.doi10.1016/j.ijmyco.2014.10.051en
dc.identifier.urihttp://hdl.handle.net/10754/566083en
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.en
dc.publisherElsevier BVen
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/en
dc.subjectPakistanen
dc.subjectTuberculosisen
dc.titleCharacterization of genomic variations in SNPs of PE_PGRS genes reveals deletions and insertions in extensively drug resistant (XDR) M. tuberculosis strains from Pakistanen
dc.typePresentationen
dc.contributor.departmentPathogen Genomics Laboratoryen
dc.identifier.journalInternational Journal of Mycobacteriologyen
dc.conference.nameThe 1st Asian-African Congress of International Journal of Mycobacteriology, Iranen
dc.contributor.institutionAga Khan University, Karachi, Pakistanen
dc.contributor.institutionLondon School of Hygiene & Tropical Medicine (LSHTM), 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.authorPain, Arnaben
kaust.authorNair, Mridulen
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