New Mycobacterium tuberculosis Complex Sublineage, Brazzaville, Congo

Abstract

Tuberculosis is a leading cause of illness and death in Congo. No data are available about the population structure and transmission dynamics of the Mycobacterium tuberculosis complex strains prevalent in this central Africa country. On the basis of single-nucleotide polymorphisms detected by whole-genome sequencing, we phylogenetically characterized 74 MTBC isolates from Brazzaville, the capital of Congo. The diversity of the study population was high; most strains belonged to the Euro-American lineage, which split into Latin American Mediterranean, Uganda I, Uganda II, Haarlem, X type, and a new dominant sublineage named Congo type (n = 26). Thirty strains were grouped in 5 clusters (each within 12 single-nucleotide polymorphisms), from which 23 belonged to the Congo type. High cluster rates and low genomic diversity indicate recent emergence and transmission of the Congo type, a new Euro-American sublineage of MTBC.

Keywords: Brazzaville; Congo; Genetic diversity; Mycobacterium tuberculosis; bacteria; epidemiology; phylogeny; transmission; tuberculosis and other mycobacteria.

Figure 1

Maximum-likelihood tree of Mycobacterium tuberculosis complex isolates from Congo (black branch tips) and 65 reference strains (red branch tips). The tree was calculated by using the general time reversible substitution model with gamma distribution based on single-nucleotide polymorphisms identified by whole-genome sequencing. Models were tested and the tree generated by using MetaPiga software version 3.1 (18) and the maximum-likelihood ratio test. Midpoint rooting was performed. Distinct colors were chosen for the lineages identified; leaves with white background represent strains that initially were not assigned to particular lineages because of ambiguous typing patterns from mycobacterial interspersed repetitive unit, restriction fragment length polymorphism, or spoligo analysis (data not shown). The numerical code assigned to the respective lineages at the outer rim of the circular tree shows the Coll-nomenclature inferred from the whole-genome sequencing data. EAI, East African Indian; LAM, Latin American Mediterranean; TUR, Turkish. Scale bar indicates nucleotide substitutions per site.

Figure 2

Maximum parsimony tree of Mycobacterium tuberculosis complex isolates from Congo. The tree was calculated on the basis of the concatenated single-nucleotide polymorphism (SNP) list. Branch labels indicate SNP distances; node labels represent the strain identifiers. Clusters based on pairwise comparisons were plotted on the tree: clusters <5 SNPs, nodes filled in black; clusters <12 SNPs, nodes with bold black outlines.