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Peer-reviewedCC BY 4.0PLOS Neglected Tropical Diseases

Genomic microdiversity of Mycobacterium africanum in Sénégal

  • Awa Ba Diallo1,2
  • Joséphine Badiane3,4
  • Mamadou Beye5
  • Khardiata Gueye1
  • Sébastien Cortaredona6,7,8
  • Seynabou Lo9
  • Michel Drancourt3,8
  • Ghiles Grine3,8
  • Makhtar Camara1,2
9 affiliations
  1. 1Mycobacteriology Unit, Bacteriology-Virology Laboratory, CHU Aristide Le Dantec Hospital, Dakar, Senegal
  2. 2Department of Biological and Pharmaceutical Sciences, Faculty of Medicine, Pharmacy and Odontology, Cheikh Anta Diop University, Dakar, Senegal
  3. 3MEPHI, Aix-Marseille University, Marseille, France
  4. 4Institut de Recherche en Santé, de Surveillance Épidémiologique et de Formations (IRESSEF), Dakar, Senegal
  5. 5Assistance Publique-Hôpitaux de Marseille, Marseille, France
  6. 6Aix-Marseille University, IRD, SSA, MINES, Marseille, France
  7. 7Aix-Marseille University, SSA, RITMES, Marseille, France
  8. 8IHU Méditerranée Infection, Marseille, France
  9. 9Faculty of Health Sciences, Gaston Berger University, Saint-Louis, Senegal
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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.

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Cite

BibTeXRIS
BibTeX
@article{diallo2026genomic,
  title = {{Genomic microdiversity of Mycobacterium africanum in Sénégal}},
  author = {Awa Ba Diallo and Joséphine Badiane and Mamadou Beye and Khardiata Gueye and Sébastien Cortaredona and Seynabou Lo and Michel Drancourt and Ghiles Grine and Makhtar Camara},
  journal = {PLOS Neglected Tropical Diseases},
  year = {2026},
  month = oct,
  doi = {10.1371/journal.pntd.0014770},
  url = {https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0014770},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - Genomic microdiversity of Mycobacterium africanum in Sénégal
AU  - Awa Ba Diallo
AU  - Joséphine Badiane
AU  - Mamadou Beye
AU  - Khardiata Gueye
AU  - Sébastien Cortaredona
AU  - Seynabou Lo
AU  - Michel Drancourt
AU  - Ghiles Grine
AU  - Makhtar Camara
PY  - 2026
DA  - 2026/10/26
JO  - PLOS Neglected Tropical Diseases
DO  - 10.1371/journal.pntd.0014770
UR  - https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0014770
AB  - 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.
SN  - 1935-2735
SN  - 1935-2727
ER  -