The first phylogeographic population structure and analysis of transmission dynamics of M. africanum West African 1--combining molecular data from Benin, Nigeria and Sierra Leone

Florian Gehre, Martin Antonio, Frank Faïhun, Mathieu Odoun, Cecile Uwizeye, Pim de Rijk, Bouke C de Jong, Dissou Affolabi, Florian Gehre, Martin Antonio, Frank Faïhun, Mathieu Odoun, Cecile Uwizeye, Pim de Rijk, Bouke C de Jong, Dissou Affolabi

Abstract

Mycobacterium africanum is an important cause of tuberculosis (TB) in West Africa. So far, two lineages called M. africanum West African 1 (MAF1) and M. africanum West African 2 (MAF2) have been defined. Although several molecular studies on MAF2 have been conducted to date, little is known about MAF1. As MAF1 is mainly present in countries around the Gulf of Guinea we aimed to estimate its prevalence in Cotonou, the biggest city in Benin. Between 2005-06 we collected strains in Cotonou/Benin and genotyped them using spoligo- and 12-loci-MIRU-VNTR-typing. Analyzing 194 isolates, we found that 31% and 6% were MAF1 and MAF2, respectively. Therefore Benin is one of the countries with the highest prevalence (37%) of M. africanum in general and MAF1 in particular. Moreover, we combined our data from Benin with publicly available genotyping information from Nigeria and Sierra Leone, and determined the phylogeographic population structure and genotypic clustering of MAF1. Within the MAF1 lineage, we identified an unexpected great genetic variability with the presence of at least 10 sub-lineages. Interestingly, 8 out of 10 of the discovered sub-lineages not only clustered genetically but also geographically. Besides showing a remarkable local restriction to certain regions in Benin and Nigeria, the sub-lineages differed dramatically in their capacity to transmit within the human host population. While identifying Benin as one of the countries with the highest overall prevalence of M. africanum, this study also contains the first detailed description of the transmission dynamics and phylogenetic composition of the MAF1 lineage.

Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1. Geographical location of various study…
Figure 1. Geographical location of various study sites in Benin and Nigeria and the prevalence of M. africanum West Africa 1 (MAF1) and West Africa 2 (MAF2).
Data from Benin was generated in the present study, the prevalence in Ibadan, Abuja and Nnewi was extracted and estimated from Lawson et al., whereas the prevalence in the Cross River State derived from Thumamo et al..
Figure 2. Population structure of M. africanum…
Figure 2. Population structure of M. africanum West Africa 1 (MAF1).
A UPGMA tree was constructed including 141 MAF1 isolates from Benin, Sierra Leone and Nigeria. Ten sub-lineages were identified. Seven isolates could not be assigned to any of the defined sub-lineages.
Figure 3. Geographical distribution of identified M.…
Figure 3. Geographical distribution of identified M. africanum West Africa 1 (MAF1) sub-lineages.
(CRS = Cross River State).

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