Genetic diversity and distribution of Mycobacterium tuberculosis genotypes in Limpopo, South Africa

Abstract

BackgroundTuberculosis remains a major health problem and knowledge of the diversity of Mycobacterium tuberculosis strains in specific geographical regions can contribute to the control of the disease. This study describes the genetic profile of M. tuberculosis in five districts of Limpopo Province.MethodsA total 487 isolates were collected from the National Health Laboratory Services from all regions/districts of Limpopo Province. Only 215 isolates were confirmed to be M. tuberculosis by Bactec Mycobacterium Growth Indicator Tube 960® and Rhodamine-Auramine staining. Isolates were subcultured on Löwenstein-Jensen medium agar slants to validate purity. They were spoligotyped and data analysed using the international spoligotyping database 4 (SpolDB4).ResultsOf the 215 isolates, 134 (62.3%) were genotyped into 21 genotype families while 81 (37.7%) were orphans. The 81 orphans were further subjected to resolution employing SpolDB3/RIM. Overall, the study revealed a high diversity of strains of 32 predominantly the non-Beijing lineages: the LAM- LAM3 (9.8%), LAM9 (4.7%) and LAM11- ZWE (3.3%), the T-T1(15.0%), T2 (0.9%), T2-T3 (1.4%), the CAS-CAS1-Delhi 5 (1.9%) and CAS1-KILI (1.4%) the MANU2 (1.4%), U (0.5%), X-X1(1.4%), X3 (1.9%), S (9.8%), CAS (1.4%), LAM7(0.9%), T3(0.5%), LAM8(4.7%), T4(1.4%), X2(0.4%), AI5(1.9%), LAM1(0.5%), FAMILY33 (1.9%), EAI4(1.4%), M. microti (1.9%). The Beijing and Beijing-like families were (14.9%) and (0.9%), respectively. A total of 28(13%) clusters and 77(36%) unique cases were identified. Beijing strain (SIT 1) formed the biggest cluster constituting 14%, followed by LAM3 (SIT 33), T1 (SIT 53) and LAM4 (SIT 811) with 7%, 5.1% and 2.8%, respectively. The Beijing family was the only genotype found in all the five districts and was predominant in Mopani (18.8%), Sekhukhune (23.7%) and Vhembe (23.3%). Dominant genotypes in Capricorn and Waterberg were LAM3 (11.9%) and T1 (13.3%), respectively.ConclusionA wide diversity of lineages was demonstrated at district level. A high number of clusters per district provided evidence of on-going transmission in this Province.

Pathogenomic analyses of Mycobacterium microti, an ESX-1-deleted member of the Mycobacterium tuberculosis complex causing disease in various hosts

“…al [5]), France [27] and the Czech Republic [28], but also recently in South Africa, where among the spoligotypes of 215 tested human isolates, 4 corresponded to M. microti -specific patterns [29]. Yet, prevalence of M.…”

Genetic diversity of Mycobacterium tuberculosis strains circulating in Botswana

“…Monitoring circulating M . tb strains remains a critical part of any TB control program as it can help improve our understanding of transmission dynamics in specific geographical locations [17]. Studies were previously conducted in Botswana by Lockman et al .…”

Machine learning reveals Mycobacterium tuberculosis genotypes and anatomic disease site impacts drug resistance and disease transmission among patients with proven extra-pulmonary tuberculosis

“…The key finding is the hierachical and nonlinear association between key EPTB disease sites (mainly lymphatic, skin and meningeal) and spoligotypes (mainly to impact both disease transmission and drug resistance. The association between Beijing strains and both TB disease transmission and drug resistance has been well described in South Africa and across the world and the results have been mixed [2,[23][24][25][46][47][48]. Our study demonstrates that those relationships are conditional, complex and characterized by several nonlinear interactions (Figures 3 and 4).. For example, two-way interactions between EPTB disease site and another variable explained >20% of the variance in clustering and almost 10% of drug resistance.…”