Whole-Genome Sequencing of Mycobacterium tuberculosis From 14 Sub-Saharan African Countries: Drug Resistance Profiles, Lineage Distribution, and Transmission Cluster Analysis

This study investigates drug resistance profiles, lineage distribution, and genomic transmission cluster analysis from whole-genome sequencing of M. tuberculosis clinical isolates across 14 sub-Saharan African countries within the context of infectious disease genomics and TB epidemiology, an area of growing scientific importance given its implications for national TB drug resistance surveillance, genomic epidemiology-informed outbreak response, and WHO resistance mutation catalog validation for WGS diagnostic deployment. Using Illumina NextSeq WGS (>50x coverage), resistance mutation calling against WHO mutation catalog v2, lineage assignment by Coll 2014 SNP barcodes, and transmission cluster analysis by 5 SNP threshold pairwise distance, we examine acquired drug resistance accumulating via sequential mutation selection under incomplete treatment, amplified by ongoing transmission of pre-resistant strains within high-burden communities lacking adequate infection control in 4,284 M. tuberculosis isolates from 14 countries (2018-2024): 3,484 new cases, 800 previously treated; phenotypic DST available for 2,840 (66%) drawn from 14 national TB programs: South Africa, Kenya, Tanzania, Uganda, Ethiopia, Nigeria, Ghana, DRC, Cameroon, Mozambique, Zambia, Zimbabwe, Malawi, Rwanda with centralized WGS at Cape Town and Nairobi nodes. Results indicate that RR/MDR-TB prevalence 6.4% (new cases) and 28.4% (previously treated); pre-XDR-TB 2.4% of all isolates; Lineage 4 dominant (64.2%) with Lineage 2 (Beijing, 18.4%) significantly enriched in MDR clusters; 38.4% of MDR isolates within genomic transmission clusters (p < 0.001), with MDR: 6.4% new, 28.4% retreated; 38.4% MDR in transmission clusters; L2 enriched 2.8x in MDR as the primary quantitative benchmark. Concordance between primary and confirmatory measurement approaches exceeded 93%, validating the analytical framework. These findings contribute empirically to infectious disease genomics and TB epidemiology and carry actionable implications for the design of programs and policies targeting national TB drug resistance surveillance, genomic epidemiology-informed outbreak response, and WHO resistance mutation catalog validation for WGS diagnostic deployment.