Phylogenetic diversity of Mycobacterium tuberculosis in two geographically distinct locations in Botswana - The Kopanyo Study

Abstract

Mycobacterium tuberculosis complex (MTBC) is divided into several major phylogenetic lineages, with differential distribution globally. Using population-based data collected over a three year period, we performed 24-locus Mycobacterial Interspersed Repeat Unit - Variable Number Tandem Repeat (MIRU-VNTR) genotyping on all culture isolates from two districts of the country that differ in tuberculosis (TB) incidence (Gaborone, the capital, and Ghanzi in the Western Kalahari). The study objective was to characterize the molecular epidemiology of TB in these districts. Overall phylogenetic diversity mirrored that reported from neighboring Republic of South Africa, but differences in the two districts were marked. All four major lineages of M. tuberculosis were found in Gaborone, but only three of the four major lineages were found in Ghanzi. Strain diversity was lower in Ghanzi, with a large proportion (38%) of all isolates having an identical MIRU-VNTR result, compared to 6% of all isolates in Gaborone with the same MIRU-VNTR result. This study demonstrates localized differences in strain diversity by two districts in Botswana, and contributes to a growing characterization of MTBC diversity globally.

Keywords: Botswana; Diversity; Lineage; Molecular epidemiology; Tuberculosis.

Fig. 1.

Unrooted UPGMA tree of study strains and MIRU-VNTRplus international reference strains. Reference strains are shown by color according to MIRU-VNTRplus lineage nomenclature; study strains are shown in white. Corresponding species are M. africanum (West African I and II), M. canettii (“Canetti” in the MIRU-VNTRplus reference set), M. caprae (“Caprae”), M. microti (“Vole”, “Llama”), M. pinnipedii (“Seal”), M. bovis (“Bovis”), and M. tuberculosis (all others). One representative of each genotype among study strains (n = 686) was used to determine phylogenetic relatedness to reference strains. Corresponding LSP-based nomenclature lineage names shown with colored lines.

Fig. 2.

Strain diversity by district. Unrooted UPGMA trees of MIRU-VNTRplus reference strains and all study strains in (a) Gaborone and (b) Ghanzi are shown.

Fig. 3.

Minimal spanning trees of study strains by district and lineage. Minimal spanning trees for study strains with (A) East African-Indian lineage, (B) East Asian lineage, (C) Indo-Oceanic lineage, (D) Euro-American lineage. Each circle represents a single MIRU-VNTR pattern. The size each circle corresponds to the number of strains with the same genotype (indicated as ‘pieces’ of the circle). Lines between circles indicate genetic distance between genotypes, with shorter lines indicating more genetic similarity. Blue circles indicate patient-isolates from Gaborone; pink from Ghanzi.

Fig. 4.

Minimal spanning trees of study strains in (a) Gaborone and (B) Ghanzi. Lineages are indicated by colors as specified in the key. Each circle represents a single MIRU-VNTR pattern. The size each circle corresponds to the number of strains with the same genotype (indicated as ‘pieces’ of the circle). Lines between circles indicate genetic distance between genotypes, with shorter lines indicating more genetic similarity.