{ "abstract": "Introduction: Mycobacterium africanum is responsible for up to half of tuberculosis cases in West Africa and comprises four sub lineages. Its genomic diversity remains undescribed in Sénégal where M. africanum was first described and where the present study was conducted. Results: Whole Genome Sequencing (WGS) identified one M. africanum lineage L5 isolate and 50 M. africanum lineage L6 isolates, with a predominance of sub lineage L6.1.1 (24/50, 43.7%) across seven of eight regions of Sénégal. The Dakar region gathered all the sub lineages (L5.3, L6.1, L6.1.1, L6.1.3, L6.2.3, L6.3.1, L6.3.2, L6.3.3, unclassified L6), except for sub lineage L6.2. Further Single Nucleotide Polymorphisms (SNPs) analysis revealed substantial genetic diversity among the lineage L6 isolates with mean value of 668.54 (±239.61), while themedian was 465 SNPs (interquartile range = 400, median absolute deviation:163.09). According to the World health Organization Catalogue of mutations in the Mycobacterium tuberculosis complex and their association with drug resistance, WGS predicted antibiotic resistance in 16 strains. Comparing Drug Susceptibility Testing (DST) and WGS results showed complete concordance across 19 DST tested strains. Conclusion: This study highlights the diversity of M. africanum in Sénégal, with intra-lineage genomic variability and predicted antimicrobial resistance. The presence of synonymous mutations in the absence of resistance-associated variants suggests that WGS–based predictions of drug resistance should be interpreted with caution. Author summary: Senegal is the country where Mycobacterium africanum was first described. Mycobacterium africanum is a Mycobacterium tuberculosis complex pathogen responsible for a significant part of tuberculosis cases in some regions in West Africa, including Sénégal. Here whole genome sequencing of 51 M. africanum isolates recovered from eight regions in Sénégal, unprecedently found that one M. africanum lineage 5 isolate and a novel lineage 6 sub lineage, both participated to geographically structure the population of M. africanum in this country. This observation raises questions regarding weight of the multiple determinants of this situation, opening doors for next works aiming to question the zoonotic and environmental contributions.", "abstract_shown": true, "affiliations": [ "Mycobacteriology Unit, Bacteriology-Virology Laboratory, CHU Aristide Le Dantec Hospital, Dakar, Senegal", "Department of Biological and Pharmaceutical Sciences, Faculty of Medicine, Pharmacy and Odontology, Cheikh Anta Diop University, Dakar, Senegal", "MEPHI, Aix-Marseille University, Marseille, France", "Institut de Recherche en Santé, de Surveillance Épidémiologique et de Formations (IRESSEF), Dakar, Senegal", "Assistance Publique-Hôpitaux de Marseille, Marseille, France", "Aix-Marseille University, IRD, SSA, MINES, Marseille, France", "Aix-Marseille University, SSA, RITMES, Marseille, France", "IHU Méditerranée Infection, Marseille, France", "Faculty of Health Sciences, Gaston Berger University, Saint-Louis, Senegal" ], "article_type": "Research Article", "arxiv": null, "author_total": 9, "authors": [ { "affs": [ 0, 1 ], "name": "Awa Ba Diallo" }, { "affs": [ 2, 3 ], "name": "Joséphine Badiane" }, { "affs": [ 4 ], "name": "Mamadou Beye" }, { "affs": [ 0 ], "name": "Khardiata Gueye" }, { "affs": [ 5, 6, 7 ], "name": "Sébastien Cortaredona" }, { "affs": [ 8 ], "name": "Seynabou Lo" }, { "affs": [ 2, 7 ], "name": "Michel Drancourt", "orcid": "0000-0003-0768-1139" }, { "affs": [ 2, 7 ], "name": "Ghiles Grine" }, { "affs": [ 0, 1 ], "name": "Makhtar Camara" } ], "bibtex": "https://research.draconitic.com/paper/ftnh5ya2s6rdr.bib", "cited_by": 0, "doi": "10.1371/journal.pntd.0014770", "fulltext_url": "https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0014770", "id": "ftnh5ya2s6rdr", "issns": [ "1935-2735", "1935-2727" ], "landing_url": "https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0014770", "language": "en", "licence": "CC-BY-4.0", "licence_label": "CC BY 4.0", "licence_source": "article", "licence_url": "https://creativecommons.org/licenses/by/4.0/", "metadata_licence": null, "native_subjects": [ [ "heading", "Actinobacteria" ], [ "heading", "Africa" ], [ "heading", "African People" ], [ "heading", "Antibiotic Resistance" ], [ "heading", "Antibiotics" ], [ "heading", "Antimicrobial Resistance" ], [ "heading", "Antimicrobials" ], [ "heading", "Bacteria" ], [ "heading", "Biology and Life Sciences" ], [ "heading", "Drugs" ], [ "heading", "Ecological Metrics" ], [ "heading", "Ecology" ], [ "heading", "Ecology and Environmental Sciences" ], [ "heading", "Ethnicities" ], [ "heading", "Genetics" ], [ "heading", "Genomics" ], [ "heading", "Geographical Locations" ], [ "heading", "Medicine and Health Sciences" ], [ "heading", "Microbial Control" ], [ "heading", "Microbiology" ], [ "heading", "Mycobacterium Tuberculosis" ], [ "heading", "Organisms" ], [ "heading", "People and Places" ], [ "heading", "Pharmacology" ], [ "heading", "Population Groupings" ], [ "heading", "Research Article" ], [ "heading", "Senegal" ], [ "heading", "Single Nucleotide Polymorphisms" ], [ "heading", "Species Diversity" ], [ "heading", "Streptomycin" ], [ "openalex", "2725|Tuberculosis Research and Epidemiology" ], [ "plos", "/Biology and life sciences/Ecology/Ecological metrics/Species diversity" ], [ "plos", "/Biology and life sciences/Genetics/Genomics" ], [ "plos", "/Biology and life sciences/Genetics/Single nucleotide polymorphisms" ], [ "plos", "/Biology and life sciences/Microbiology/Microbial control/Antimicrobial resistance/Antibiotic resistance" ], [ "plos", "/Biology and life sciences/Microbiology/Microbial control/Antimicrobials/Antibiotics/Streptomycin" ], [ "plos", "/Biology and life sciences/Organisms/Bacteria/Actinobacteria/Mycobacterium tuberculosis" ], [ "plos", "/Ecology and environmental sciences/Ecology/Ecological metrics/Species diversity" ], [ "plos", "/Medicine and health sciences/Pharmacology/Antimicrobial resistance/Antibiotic resistance" ], [ "plos", "/Medicine and health sciences/Pharmacology/Drugs/Antimicrobials/Antibiotics/Streptomycin" ], [ "plos", "/People and places/Geographical locations/Africa/Senegal" ], [ "plos", "/People and places/Population groupings/Ethnicities/African people" ] ], "openalex": "W7223663375", "pdf_url": "https://journals.plos.org/plosntds/article/file?id=10.1371/journal.pntd.0014770&type=printable", "pmcid": "PMC13727044", "pmid": "42932393", "published": "2026-10-26", "publisher": "Public Library of Science", "ris": "https://research.draconitic.com/paper/ftnh5ya2s6rdr.ris", "sources": [ { "first_seen": "2026-10-30T12:17:17Z", "native_id": "10.1371/journal.pntd.0014770", "source": "plos", "url": "https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0014770" }, { "first_seen": "2026-11-05T12:23:15Z", "native_id": "PMC13727044", "source": "pmc", "url": "https://doi.org/10.1371/journal.pntd.0014770" } ], "subjects": [ { "field": "biology", "origin": "plos:ecology", "subfield": "ecology" }, { "field": "biology", "origin": "plos:genomics", "subfield": "genetics-genomics" }, { "field": "biology", "origin": "plos:microbiology", "subfield": "microbiology" }, { "field": "medicine", "origin": "heading:Pharmacology", "subfield": "pharmacology-toxicology" } ], "title": "Genomic microdiversity of Mycobacterium africanum in Sénégal", "title_text": "Genomic microdiversity of Mycobacterium africanum in Sénégal", "type": "peer-reviewed", "updated_at": "2026-11-06T12:22:51Z", "url": "https://research.draconitic.com/paper/ftnh5ya2s6rdr", "venue": "PLOS Neglected Tropical Diseases", "versions": [] }