Mycobacterium africanum--review of an important cause of human tuberculosis in West Africa

Abstract

Mycobacterium africanum consists of two phylogenetically distinct lineages within the Mycobacterium tuberculosis complex, known as M. africanum West African 1 and M. africanum West African 2. These lineages are restricted to West Africa, where they cause up to half of human pulmonary tuberculosis. In this review we discuss the definition of M. africanum, describe the prevalence and restricted geographical distribution of M. africanum West African 1 and 2, review the occurrence of M. africanum in animals, and summarize the phenotypic differences described thus far between M. africanum and M. tuberculosis sensu stricto.

Figure 1. Nomenclature of M. africanum as related to its biochemical and molecular classification.

Biochemical classification is reviewed in Table 1. LSPs, large sequence polymorphisms . Spoligotype signatures are reviewed in .

Figure 2. The position of M. africanum in the global phylogeny of the M. tuberculosis complex (MTBC) as originally published by Hershberg et al..

This phylogeny is based on over 65 kb of DNA sequence data (89 concatenated gene sequences) in each of 108 strains of the MTBC and was inferred using maximum parsimony, which resulted in a single tree with negligable homoplasy . Analysis by the neighbor-joining method resulted in an identical tree topology with high statistical support for all main branches . This phylogeny has been referred to as the most robust and most detailed phylogeny of the MTBC to date, and thus should be considered as the new gold standard for classification of the MTBC . The six main MTBC lineages adapted to humans and the animal strains are indicated in different colors. The human MTBC lineages include four M. tuberculosis lineages and the two M. africanum type I lineages. The “Uganda” genotype (formally referred to as M. africanum type II), which is a sub-lineage within M. tuberculosis lineage 4 (also known as the Euro-American lineage), is also shown. These lineages are completely congruent to previous classifications based on LSPs , , . Black arrows indicate genomic regions or regions of difference (RDs) that are deleted in all descendent strains belonging to a particular lineage or sub-lineage. The scale indicates the genetic distance as number of SNPs (adapted from Figure 1 in with additional data from [5]).

Figure 3. M. africanum prevalence in Western African countries.

Prevalence figures were derived from the most recently published studies from Table 2 and unpublished data from Tunisia, Senegal, Cote d'Ivoire, Cameroon, and the Central African Republic extracted from the SITVIT2 proprietary database of Institut Pasteur de la Guadeloupe. If studies did not list the prevalence of MAF1 and/or MAF2, the estimates were based on interpretation of the spoligotype patterns. Areas with MAF1 are shaded in brown and areas with MAF2 are shaded in green, with striped shading if prevalence of MAF1 and MAF2 exceeds 5% each. Map courtesy of http://www.theodora.com/maps/, used with permission.