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This study presents one of the first integrated applications of shotgun metagenomic and metatranscriptomic sequencing to investigate Mycobacterium communities in wastewater across six TB-endemic countries: Cameroon, Ghana, Kenya, Nigeria, South Africa, and Uganda. Twelve untreated and treated wastewater samples were analysed to characterise taxonomic composition, strain-level diversity, and transcriptional activity. Metagenomic analyses revealed diverse Mycobacterium communities, including M. tuberculosis, M. canettii, M. bovis, and members of the M. avium complex. Metatranscriptomic data detected MTBC-associated transcripts, indicating transcriptional activity and\/or persistence of MTBC RNA signals in wastewater, with higher signal predominance in influent samples, consistent with community-level shedding. Metagenome-assembled genomes (MAGs) recovered from South Africa, Cameroon, and Uganda showed &amp;gt;82% completeness and included zoonotic species. MTBC strains clustered into Lineages 1, 2, 4, and 6, with animal-adapted strains linked to livestock and rodents, highlighting One Health relevance. Overall, this dual-omics approach supports wastewater-based epidemiology as a scalable tool for TB surveillance in high-burden settings.<\/jats:p>","DOI":"10.2166\/wh.2026.129","type":"journal-article","created":{"date-parts":[[2026,2,21]],"date-time":"2026-02-21T09:48:08Z","timestamp":1771667288000},"page":"109-127","update-policy":"https:\/\/doi.org\/10.2166\/iwapcrossmarkpolicypage","source":"Crossref","is-referenced-by-count":0,"title":["Decoding mycobacterial ecology in Sub-Saharan African wastewater: metagenomic and metatranscriptomic insights for tuberculosis surveillance"],"prefix":"10.2166","volume":"24","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4184-204X","authenticated-orcid":false,"given":"Hlengiwe N.","family":"Mtetwa","sequence":"first","affiliation":[{"name":"a Institute for Water and Wastewater Technology (IWWT), Durban University of Technology, P.O. Box 1334, Durban, 4000, South Africa"},{"name":"b Department of Community Health Studies, Faculty of Health Sciences, Durban University of Technology, P.O. Box 1334, Durban, 4000, South Africa"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0131-3442","authenticated-orcid":false,"given":"Isaac D.","family":"Amoah","sequence":"additional","affiliation":[{"name":"c Department of Environmental Science, University of Arizona, Tucson, AZ 85721, Usa"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4800-4006","authenticated-orcid":false,"given":"Nonsikelelo P.","family":"Mthethwa-Hlongwa","sequence":"additional","affiliation":[{"name":"d Stellenbosch University, Microbiology, Faculty of Science, School for Data Science and Computational Thinking, Stellenbosch, 7600, South Africa"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0619-0058","authenticated-orcid":false,"given":"Rian","family":"Pieerneef","sequence":"additional","affiliation":[{"name":"e Centre for Bioinformatics and Computational Biology, University of Pretoria, Pretoria, 0001, South Africa"},{"name":"f Department of Biochemistry, Genetics and Microbiology, DSI\/NRF SARChI in Marine Microbiomics, Pretoria, 0001, South Africa"},{"name":"g Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0001, South Africa"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3436-8263","authenticated-orcid":false,"given":"Sheena","family":"Kumari","sequence":"additional","affiliation":[{"name":"a Institute for Water and Wastewater Technology (IWWT), Durban University of Technology, P.O. 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