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Predominant clones of Mycobacterium tuberculosis in Sub-Saharan African Countries

F Massou(1,2) W Mulders(2) A Gnamy(1) B C de Jong(3) D Affolabi(1) C DIAMA(1) L Rigouts(2,3) C J Meehan(3,4)

1:Laboratoire de Référence des Mycobactéries, Cotonou, Benin; 2:Biomedical Sciences, Antwerp University, Antwerpen, Belgium; 3:Mycobacteriology Unit, Institute of Tropical Medicine (ITM), Antwerpen, Belgium; 4:School of Science and Technology, Nottingham Trent University, Nottingham, The UK

Tuberculosis (TB) remains a major threat to global public health, with transmission dynamics of M. tuberculosis (Mtb) varying considerably across global regions. This study aims to assessing the presence and distribution of Mtb clones and -transmission clusters within and across different sub-Saharan African countries.

In the DIAMA study involving nine Africans countries, we sequenced isolates from consecutive rifampicin-resistant (RR-TB) patients and equal numbers of retreatment patients with RS-TB. Lineages were assigned using the TB Profiler v4.4.2 pipeline. Single nucleotide polymorphisms (SNPs) were identified from VCF files using H37Rv as a reference, and pairwise matrix distances per sub-lineage between samples were calculated using the Lyve-SET pipeline, with a cutoff of 5 SNPs to define clusters.

From 1586 isolates, we identified 49 transmission clusters comprising 1453 isolates, with clusters stratified as follows: Lineage 2 (1), Lineage 3 (3), Lineage 4 (35), Lineage 5 (9), and Lineage 8 (9). We found that 26% of clusters were country-specific, while 78% demonstrated cross-border transmission. Lineage 2 clusters predominated in Guinea (63%) and were confined to West Africa. Lineage 3 clusters were predominant in Ethiopia (79%) and limited to Eastern Africa. Lineage 4 was widespread, although some clusters were country-specific. Culture biases likely caused underestimation of Lineage 5 clusters, primarily found in Benin (41%), affecting West and Central Africa, while Lineage 8 was exclusive to Rwanda.

This comprehensive analysis reveals significant variability in the distribution of Mtb transmission clusters across sub-Saharan Africa. The predominance of multi-country clusters underscores the necessity of regional cooperation in TB control strategies.

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