Genotypic diversity of Mycobacterium tuberculosis in pretoria

Abstract

Tuberculosis is a global health problem. Continuous efforts are needed to understand the genetic diversity and geographical distribution of Mycobacterium tuberculosis. The objective of this study was to determine the genetic diversity of M. tuberculosis strains in Soshanguve, Pretoria. Eighty-nine isolates that were sputum culture-positive in Mycobacterium Growth Indicator Tube 960®, and positively identified by Accuprobe Probe assay as M. tuberculosis complex, were used in the study. The samples were sub-cultured on Lowenstein-Jensen (L-J) slants to ensure purity. Spoligotyping was performed, with slight modifications according to the manufacturer’s specifications. Genotypic data were compared to the international spoligotyping database 4 (SpolDB4) and that suggested by Streicher et al. Spoligotyping identified 12 genotypes. Of the 89 isolates studied, 75 could be grouped into 11 clusters. The Beijing genotype family formed the largest group, with 21 isolates (28%). The remaining isolates were distributed among the Latino-American-Mediterranean (LAM) family: LAM3 (13%), LAM4 (4%), LAM9 (3%); the T family: T1 (23%), T2 (9%), and T3 (3%); the S family (8%); the X3 family (4%); CAS1-KILI (3%); and LAM11-ZWE (3%). Fourteen (16%) of the isolates had spoligotypes that did not match any of the spoligotype patterns deposited in the SpolDB4 database. Beijing was the most common genotype family, identified in 28% of the cases, followed by T1 (23%). The high prevalence of Beijing and T1 in this study reflects transmission of these genotype families within this community. The results of this study showed the dire need for more robust prevention strategies in tuberculosis control programmes. Other genotyping methods with a higher discriminatory power, such as restriction fragment length polymorphism, will be useful in defining the transmission patterns in this community