Phylodynamic analysis reveals disparate transmission dynamics of Mycobacterium tuberculosis complex lineages in Botswana

Abstract

Tuberculosis epidemics have traditionally been conceptualized as arising from a single uniform pathogen. However, Mycobacterium tuberculosis complex (Mtbc), the pathogen causing tuberculosis in humans, encompasses multiple lineages exhibiting genetic and phenotypic diversity that may be responsible for heterogeneity in tuberculosis transmission. We analysed a population-based dataset of 1,354 Mtbc whole-genome sequences collected over four years in Botswana, a country with high HIV and tuberculosis burden. We identified Lineage 4 (L4) as the most prevalent (87.4%), followed by L1 (6.4%), L2 (5.3%), and L3 (0.9%). Within L4, multiple sublineages were identified, with L4.3.4 being the predominant sublineage. Phylodynamic analysis revealed that L4.3.4 expanded steadily from the late 1800s to early 2000s. Conversely, L1, L4.4, and L4.3.2 showed population trajectories closely aligned with the HIV epidemic. Meanwhile, L2 saw rapid expansion throughout most of the 20th century but declined sharply in the early 1990s. Additionally, pairwise genome comparison of Mtbc highlighted differences in clustering proportions due to recent transmission at the sublineage level. These findings emphasize the diverse transmission dynamics of strains of different Mtbc lineages and highlight the potential for phylodynamic analysis of routine sequences to refine our understanding of lineage-specific behaviors.

Fig. 1

Maximum likelihood phylogeny of Mycobacterium tuberculosis–complex (Mtbc) isolates collected in Botswana, 2012–2016 (n = 1,354). (A) Phylogeny of Lineage 1 Indo-Oceanic Mtbc isolates (n = 86). (B) Phylogeny of Lineage 2 East Asian Mtbc isolates (n = 72). (C) Phylogeny of Lineage 3 East African-Indian Mtbc isolates (n = 12). (D) Phylogeny of Lineage 4 Euro-American Mtbc isolates (n = 1184). Tree tips are colored by Mtbc strains within a major lineage.

Fig. 2

Inferred effective population size over time for Mycobacterium tuberculosis– complex lineages circulating in Botswana.