Genomic survey reveals hidden diversity of Mycobacterium africanum in Senegal

Mycobacterium africanum, the mycobacterium responsible for up to half of tuberculosis cases in West Africa, has now been genomically characterized in Senegal, the country where it was first described. Using whole-genome sequencing, researchers identified one isolate belonging to lineage L5 and 50 isolates belonging to lineage L6, with sub lineage L6.1.1 the most common, accounting for 24 of the 50 lineage L6 isolates, or 43.7 percent. The isolates were collected across seven of Senegal's eight regions.

The Dakar region stood out for its breadth of diversity, harboring all observed sub lineages — L5.3, L6.1, L6.1.1, L6.1.3, L6.2.3, L6.3.1, L6.3.2, L6.3.3 and an unclassified L6 group — with the sole exception of sub lineage L6.2. This concentration of distinct variants in the capital region suggests a heterogeneous circulating population, although the study was observational and cannot establish transmission routes. Single nucleotide polymorphism analysis revealed substantial genetic variability within lineage L6.

The mean pairwise SNP distance was 668.54, with a standard deviation of 239.61, while the median was 465 SNPs with an interquartile range of 400 and a median absolute deviation of 163.09. Applying the World Health Organization catalogue of mutations in the Mycobacterium tuberculosis complex associated with drug resistance, the team predicted antibiotic resistance in 16 of the sequenced strains. To test the reliability of these predictions, the researchers compared sequencing-based calls with conventional drug susceptibility testing in 19 strains and found complete concordance between the two approaches.

Despite this agreement, the authors urge caution. In strains lacking resistance-associated variants, synonymous mutations were present, and the team concludes that whole-genome sequencing-based predictions of drug resistance in M. africanum should be interpreted carefully.

Subject of Research: Genomic diversity and drug resistance prediction of Mycobacterium africanum isolates in Senegal

Article Title: Genomic microdiversity of Mycobacterium africanum in Sénégal

Article References: Ba Diallo, A., Badiane, J., Beye, M., Gueye, K., Cortaredona, S., Lo, S., Drancourt, M., Grine, G., & Camara, M. (2026). Genomic microdiversity of Mycobacterium africanum in Sénégal. PLOS Neglected Tropical Diseases, 20(10), e0014770. https://doi.org/10.1371/journal.pntd.0014770

Image Credits: AI Generated

DOI: 10.1371/journal.pntd.0014770

Keywords: Mycobacterium africanum, tuberculosis, whole-genome sequencing, lineage L6, Senegal, drug resistance, single nucleotide polymorphisms, drug susceptibility testing, West Africa, genomic epidemiology, WHO mutation catalogue, Genomic