Characterization of genomic variations in SNPs of PE_PGRS genes reveals deletions and insertions in extensively drug resistant (XDR) M. tuberculosis strains from Pakistan
Hill-Cawthorne, Grant A.
Clark, Taane G.
KAUST DepartmentPathogen Genomics Laboratory
Permanent link to this recordhttp://hdl.handle.net/10754/552321
MetadataShow full item record
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.
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
- Variation of the Mycobacterium tuberculosis PE_PGRS 33 gene among clinical isolates.
- Authors: Talarico S, Cave MD, Marrs CF, Foxman B, Zhang L, Yang Z
- Issue date: 2005 Oct
- Single nucleotide polymorphisms in efflux pumps genes in extensively drug resistant Mycobacterium tuberculosis isolates from Pakistan.
- Authors: Kanji A, Hasan R, Ali A, Zaver A, Zhang Y, Imtiaz K, Shi W, Clark TG, McNerney R, Phelan J, Rao S, Shafiq S, Hasan Z
- Issue date: 2017 Dec
- Sequence diversity in the pe_pgrs genes of Mycobacterium tuberculosis is independent of human T cell recognition.
- Authors: Copin R, Coscollá M, Seiffert SN, Bothamley G, Sutherland J, Mbayo G, Gagneux S, Ernst JD
- Issue date: 2014 Jan 14
- Whole genome sequencing based characterization of extensively drug-resistant Mycobacterium tuberculosis isolates from Pakistan.
- Authors: Ali A, Hasan Z, McNerney R, Mallard K, Hill-Cawthorne G, Coll F, Nair M, Pain A, Clark TG, Hasan R
- Issue date: 2015
- Mycobacterium tuberculosis PE_PGRS16 and PE_PGRS26 genetic polymorphism among clinical isolates.
- Authors: Talarico S, Zhang L, Marrs CF, Foxman B, Cave MD, Brennan MJ, Yang Z
- Issue date: 2008 Jul