Strain diversity of mycobacterium tuberculosis non-Uganda isolates from patients with pulmonary tuberculosis in Kawempe

Abstract

Background: Tuberculosis is a major public health problem in peri-urban areas of Kampala and Uganda in general. To date there is inconclusive information about strain diversity of Mycobacterium tuberculosis of the non Ugandan lineages, yet evidence continues to mount that Mycobacterium tuberculosis (MTB) is so diverse. Therefore in this study we sought to ascertain the genetic diversity of MTB as an avenue of generating information geared at controlling tuberculosis. Methods and Results: we analyzed 446 isolates previously identified as belonging to the non-Ugandan lineages by single nucleotide polymorphism (SNP) typing. Two hundred and eighty (280) belonged to the Euro-American non-Ugandan lineage, 136 belonged to the Central Asian lineage (CAS) while 30 were un-identified by SNP typing and were referred to as unknown. All isolates were first analyzed with Spoligotype and those that were orphans were re-analyzed with Mycobacterial Interspersed Repetitive Units-Variable Number Tandem Repeats (MIRU-VNTR) to rule out multiple infections; a possible cause of orphan spoligotype signatures. We observed a high spoligotype diversity with up to 104 spoligotype patterns from the 446 isolates. The Latin American Mediterranean strain (LAM) (36.7%) and T families (16.3%) of strains were the most predominant in the Euro-American non-Ugandan lineage, while CAS1-Delhi (62%) was the most predominant in the CAS lineage. Of the 30 ―unknown‖ isolates only three (10 %) were identified by spoligotype and they had a characteristic Beijing spoligotype. Other identified strains included X2 (0.98%), X1 (0.98%), S (5.9%), MANU (0.98%), and H3 (9.5) for the Euro-American non-Ugandan lineage and CAS1-Killi (16.6%)i, CAS2 (6.02%) and EAI5 (0.75%) for the Central Asian Lineage. Conclusion: The strain diversity of Mycobacterium tuberculosis is greater than previously reported with Latin American Mediterranean (LAM) and CAS1-Delhi family of strains being the most predominant in the Euro-American non-Ugandan lineage and Central Asian Lineage respectively.