title: MIRU-VNTR profiles of three major Mycobacterium tuberculosis spoligotypes found in western India.
abstract: We performed 12 loci MIRU-VNTR on 327 Mycobacterium tuberculosis (Mtb) isolates belonging to three major spoligotypes MANU1, CAS1_Delhi and Beijing from Mumbai, western India and two proximal rural locations. Complete allele and drug susceptibility data was available for 232 isolates. These included 143 MANU1 (ST100), 65 CAS1_Delhi (ST26) and 24 Beijing (ST1) isolates. Of the 232 isolates, 26 were rural consisting 6 CAS1_Delhi and 20 MANU1 isolates. Using eBURST multi-locus sequence typing (MLST), cluster analyses was performed for each of the spoligotypes and drug susceptibility profiles. MANU1 MLST consisted of 90 related isolates (clustered and grouped) and 53 singletons; CAS1_Delhi MLST consisted of 44 related isolates and 21 singletons; Beijing MLST consisted of 10 related isolates and 14 singletons. Although the number of related isolates were different in MANU1 (63%), CAS1_Delhi (68%) and Beijing (42%) clusters, it was not statistically significant. Furthermore, it was observed that while MANU1 and CAS1_Delhi singletons (n = 74) had only 12 (16%) MDR isolates, the Beijing MLST had 8/14 (57%) MDR singleton isolates. Phylogenetic ananlysis using minimum spanning tree (MST) and a UPGMA radial tree revealed MANU1 had the largest number of nodes as compared to the CAS1_Delhi and Beijing spoligotypes. Additionally the CAS isolates were more homogeneous than the MANU1 isolates. The 12 loci MIRU-VNTR was used to provide greater discrimination than spoligotyping, but 6 of the 12 loci provided less than 50% discriminatory power. The highest discrimination was achieved using locus 26 (80%). Our results concur with recent reports that the most discriminatory MIRU-VNTR combination varied across different lineages. The results also highlight the need for more robust genetic markers for studying the transmission of Mtb in endemic regions like India.
authors.affiliation: The Foundation for Medical Research, 84-A, R.G. Thadani Marg, Worli, Bombay 400018, India.
authors.forename: Anirvan
authors.initials: A
authors.lastname: Chatterjee
authors.forename: Nerges
authors.initials: N
authors.lastname: Mistry
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D015373:Bacterial Typing Techniques / Q000379:methods; D016000:Cluster Analysis; D024881:Drug Resistance, Bacterial / Q000235:genetics; D005819:Genetic Markers; D005838:Genotype; D006801:Humans; D020071:Interspersed Repetitive Sequences / Q000235:genetics*; D008826:Microbial Sensitivity Tests; D008875:Middle Aged; D018598:Minisatellite Repeats / Q000235:genetics*; D058885:Multilocus Sequence Typing / Q000379:methods; D009169:Mycobacterium tuberculosis / Q000145:classification* / Q000187:drug effects / Q000235:genetics / Q000302:isolation & purification; D010802:Phylogeny; D012423:Rural Health / Q000706:statistics & numerical data; D014397:Tuberculosis, Pulmonary / Q000382:microbiology*; D014504:Urban Health / Q000706:statistics & numerical data; D055815:Young Adult
chemical_list: D005819:Genetic Markers