Genetic diversities of Mycobacterium tuberculosis complex species in Western Kenya

Tuberculosis (TB) remains a high-burden infectious disease worldwide. Mycobacterium tuberculosis complex (MTBC) is the aetiological agent of TB.

The TB burden is significantly linked to the development of drug-resistant strains. Thus, there is an urgent need for close surveillance of MTBC circulating in a given region, such as Western Kenya, for treatment of TB.

To determine the proportion of MTBC species, strains and genetic diversities in circulation in HIV/AIDS-prevalent regions, and Western Kenya in particular. The clinical MTBC isolates were collected from Moi Teaching and Referral Hospital (MTRH) at Eldoret-Kenya during 2013-14. All clinical MTBC isolates were confirmed by the gold standard method (Löwenstein-Jensen medium culture) before inclusion in the investigation.

Twelve-loci mycobacterium interspersed repetitive unit - variable-number tandem repeats (MIRU-VNTR) genotyping was performed to determine the circulating species/strains of MTBC using the www.miru-vntrplus.org web platform. Allelic diversity was calculated using the Hunter-Gaston diversity index (HGDI).

The species M. tuberculosis, Mycobacterium bovis, Mycobacterium africanum, Mycobacterium pinnipedii, Mycobacterium microti, Mycobacterium caprae and Mycobacterium canetti were identified in the MTBC population. These strains were found in the Beijing, Latin American Mediterranean, Uganda 1/2, East African Indian, Ilama, West African 1/2, Harlem, URAL, Ghana, Seal, Cameroon and Vole etc. regions of Western Kenya. Notably, some isolates had unknown (new/unassigned) species. The strains were grouped into nine clusters with a clustering rate of 31.18 % and a high allelic diversity index of 0.53 was observed.

The present findings suggest that there is an urgent need for more awareness among healthcare professionals and stakeholders concerning the existence of foreign MTBC species/strains in Kenya. Furthermore, 12-loci MIRU-VNTR may not be suitable for the surveillance of MTBC strains in circulation in Kenya. Thus, high-resolution techniques such as whole-genome sequencing need to be adopted to resolve the genetic diversity and establish evolutionary trends for future and archived samples. This knowledge will be crucial in restraining TB, providing insights into new drug development, and developing prevention, control and treatment strategies for TB.