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Volume 30, Number 3—March 2024
Dispatch

Newly Identified Mycobacterium africanum Lineage 10, Central Africa

Christophe Guyeux, Gaetan Senelle, Adrien Le Meur, Philip Supply, Cyril Gaudin, Jody E. Phelan, Taane G Clark, Leen Rigouts, Bouke de Jong, Christophe Sola, and Guislaine RefrégierComments to Author 
Author affiliations: University Bourgogne Franche-Comté (UBFC), Besançon, France (C. Guyeux, G. Senelle); Université Paris-Saclay–AgroParisTech, Gif-sur-Yvette, France (A. Le Meur, G. Refrégier); Institut Pasteur de Lille Center for Infection and Immunity of Lille, Lille, France (P. Supply, C. Gaudin); London School of Hygiene and Tropical Medicine, London, UK (J.E. Phelan, T.G. Clark, L. Rigouts, B. de Jong); Université Paris-Saclay, Saint-Aubin, France (C. Sola); Université Paris Cité, Paris (C. Sola)

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Figure

Global Mycobacterium phylogeny including newly identified M. africanum L10 (proposed) strains (green shading). We selected M. africanum samples for harboring RD9 deletion, having documented country of origin (for the purpose of additional analyses; Appendix 2, Figure 2), and refined our selection to retain a sole representative of each sublineage for each country. This sample represents representing the genetic and geographic diversity of M. africanum in Africa. Specifically for this phylogenetic reconstruction, single-nucleotide polymorphisms were identified in comparison with an M. tuberculosis ancestor (11) and reincorporated into the whole genome to avoid biases in the molecular model or need for Lewis correction. Phylogeny was rooted with M. canettii, subsequently removed for better visualization. Bootstrap support was computed using 100 replicates and shown when ≥0.6. Circles confirm the large support of almost all branches, especially of L10 and its sister branches. L10 branching point lies between L9 and the La_A1 lineage grouping chimpanzee and Dassie bacillus. Scale bar indicates nucleotide substitutions per site.

Figure. Global Mycobacterium phylogeny including newly identified M. africanum L10 (proposed) strains (green shading). We selected M. africanum samples for harboring RD9 deletion, having documented country of origin (for the purpose of additional analyses; Appendix 2, Figure 2), and refined our selection to retain a sole representative of each sublineage for each country. This sample represents representing the genetic and geographic diversity of M. africanum in Africa. Specifically for this phylogenetic reconstruction, single-nucleotide polymorphisms were identified in comparison with an M. tuberculosis ancestor (11) and reincorporated into the whole genome to avoid biases in the molecular model or need for Lewis correction. Phylogeny was rooted with M. canettii, subsequently removed for better visualization. Bootstrap support was computed using 100 replicates and shown when ≥0.6. Circles confirm the large support of almost all branches, especially of L10 and its sister branches. L10 branching point lies between L9 and the La_A1 lineage grouping chimpanzee and Dassie bacillus. Scale bar indicates nucleotide substitutions per site.

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References
  1. Gagneux  S. Ecology and evolution of Mycobacterium tuberculosis. Nat Rev Microbiol. 2018;16:202–13. DOIPubMedGoogle Scholar
  2. Ngabonziza  JCS, Loiseau  C, Marceau  M, Jouet  A, Menardo  F, Tzfadia  O, et al. A sister lineage of the Mycobacterium tuberculosis complex discovered in the African Great Lakes region. Nat Commun. 2020;11:2917. DOIPubMedGoogle Scholar
  3. Coscolla  M, Gagneux  S, Menardo  F, Loiseau  C, Ruiz-Rodriguez  P, Borrell  S, et al. Phylogenomics of Mycobacterium africanum reveals a new lineage and a complex evolutionary history. Microb Genom. 2021;7:00047. DOIPubMedGoogle Scholar
  4. Napier  G, Campino  S, Merid  Y, Abebe  M, Woldeamanuel  Y, Aseffa  A, et al. Robust barcoding and identification of Mycobacterium tuberculosis lineages for epidemiological and clinical studies. Genome Med. 2020;12:114. DOIPubMedGoogle Scholar
  5. Phelan  JE, O’Sullivan  DM, Machado  D, Ramos  J, Oppong  YEA, Campino  S, et al. Integrating informatics tools and portable sequencing technology for rapid detection of resistance to anti-tuberculous drugs. Genome Med. 2019;11:41. DOIPubMedGoogle Scholar
  6. Chen  W, Biswas  T, Porter  VR, Tsodikov  OV, Garneau-Tsodikova  S. Unusual regioversatility of acetyltransferase Eis, a cause of drug resistance in XDR-TB. Proc Natl Acad Sci U S A. 2011;108:9804–8. DOIPubMedGoogle Scholar
  7. Dupuy  P, Ghosh  S, Adefisayo  O, Buglino  J, Shuman  S, Glickman  MS. Distinctive roles of translesion polymerases DinB1 and DnaE2 in diversification of the mycobacterial genome through substitution and frameshift mutagenesis. Nat Commun. 2022;13:4493. DOIPubMedGoogle Scholar
  8. Guyeux  C, Sola  C, Noûs  C, Refrégier  G. CRISPRbuilder-TB: “CRISPR-builder for tuberculosis”. Exhaustive reconstruction of the CRISPR locus in mycobacterium tuberculosis complex using SRA. PLOS Comput Biol. 2021;17:e1008500. DOIPubMedGoogle Scholar
  9. Couvin  D, David  A, Zozio  T, Rastogi  N. Macro-geographical specificities of the prevailing tuberculosis epidemic as seen through SITVIT2, an updated version of the Mycobacterium tuberculosis genotyping database. Infect Genet Evol. 2019;72:31–43. DOIPubMedGoogle Scholar
  10. Kayomo  MK, Mbula  VN, Aloni  M, André  E, Rigouts  L, Boutachkourt  F, et al. Targeted next-generation sequencing of sputum for diagnosis of drug-resistant TB: results of a national survey in Democratic Republic of the Congo. Sci Rep. 2020;10:10786. DOIPubMedGoogle Scholar
  11. Comas  I, Chakravartti  J, Small  PM, Galagan  J, Niemann  S, Kremer  K, et al. Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved. Nat Genet. 2010;42:498–503. DOIPubMedGoogle Scholar
  12. Coscolla  M, Lewin  A, Metzger  S, Maetz-Rennsing  K, Calvignac-Spencer  S, Nitsche  A, et al. Novel Mycobacterium tuberculosis complex isolate from a wild chimpanzee. Emerg Infect Dis. 2013;19:969–76. DOIPubMedGoogle Scholar

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Page updated: February 22, 2024
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