Genetic diversity of clinical isolates of Mycobacterium tuberculosis complex circulating in Western Kenya

Abstract

Tuberculosis (TB) remains a burden in many countries, including Kenya, especially, Western Kenya. Mycobacterium tuberculosis complex (MTBC) is the etiological agent of tuberculosis. TB burden is majorly linked to development of drug resistant strains. For treatment of TB, there is need for close surveillance of MTBC circulating in a given region. Hence, this study aimed to determine the proportion of MTBC species, strains and genetic diversity in circulation in an HIV prevalent region, western Kenya. Clinical isolates archived between 2013 and 2014 at Moi Teaching and Referral Hospital, Eldoret, Kenya with confirmed tuberculosis following Lowenstein-Jensen medium cultures were used. A 12-loci MIRU-VNTR genotyping was performed to determine the circulating species and strains of MTBC using www.MIRU-VNTRplus web platform. Allelic diversity was calculated using Hunters-Gaston diversity index (HGDI). The species identified in this population were M. tuberculosis, M. bovis and M. africanum, M. pinnipedii, M. microti, M. caprae and M. canetti. The strains were Beijing, Latin American Mediterranean (LAM), Uganda 1 and 2, East African Indian (EAI), Ilama, West African 1 and 2, Haelem, URAL, Ghana, Seal, Cameroon, Vole etc. Notably, some isolates had unknown (new/unassigned) species. The strains were grouped into nine clusters with clustering rate of 31.18%. The study revealed that there are multiple species and strains of Mycobacterium circulating in Western Kenya. These strains were moderately diverse as seen in the high allelic diversity index of 0.53. The present findings suggest that there is need for more awareness among healthcare and other stakeholders on the existence of foreign MTBC species and strains in Kenya. Furthermore, 12-loci MIRU-VNTR may not be suitable for surveillance of MTBC strains in circulation. 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. The knowledge will be crucial in curbing TB, giving insights into new drug development, TB prevention, control and treatment strategies.