{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,2]],"date-time":"2026-09-02T05:20:05Z","timestamp":1788326405254,"version":"build-2803163510"},"reference-count":37,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2026,8,31]],"date-time":"2026-08-31T00:00:00Z","timestamp":1788134400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Federal Ministry of Economic Cooperation and Development","award":["BMZ001201"],"award-info":[{"award-number":["BMZ001201"]}]},{"award":["BMZ001201"],"award-info":[{"award-number":["BMZ001201"]}],"id":[{"id":"https:\/\/ror.org\/00e0ttj68","id-type":"ROR","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000877","name":"Rockefeller Foundation","doi-asserted-by":"publisher","award":["HTH 017"],"award-info":[{"award-number":["HTH 017"]}],"id":[{"id":"10.13039\/100000877","id-type":"DOI","asserted-by":"publisher"}]},{"award":["HTH 017"],"award-info":[{"award-number":["HTH 017"]}],"id":[{"id":"https:\/\/ror.org\/03sfkwk85","id-type":"ROR","asserted-by":"publisher"}]},{"name":"Africa CDC"},{"id":[{"id":"https:\/\/ror.org\/01d9dbd65","id-type":"ROR","asserted-by":"publisher"}]},{"name":"Global Health EDCTP3 Joint Undertaking"},{"DOI":"10.13039\/100000865","name":"Bill & Melinda Gates Foundation","doi-asserted-by":"crossref","award":["101103171"],"award-info":[{"award-number":["101103171"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"crossref"}]},{"award":["101103171"],"award-info":[{"award-number":["101103171"]}],"id":[{"id":"https:\/\/ror.org\/0456r8d26","id-type":"ROR","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004421","name":"World Bank","doi-asserted-by":"publisher","award":["TF0B8412"],"award-info":[{"award-number":["TF0B8412"]}],"id":[{"id":"10.13039\/100004421","id-type":"DOI","asserted-by":"publisher"}]},{"award":["TF0B8412"],"award-info":[{"award-number":["TF0B8412"]}],"id":[{"id":"https:\/\/ror.org\/00ae7jd04","id-type":"ROR","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001322","name":"SAMRC mRNA Vaccine Consortium","doi-asserted-by":"publisher","award":["SAMVAC"],"award-info":[{"award-number":["SAMVAC"]}],"id":[{"id":"10.13039\/501100001322","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Antibiotics"],"abstract":"<jats:p>Background: Wastewater and Environmental Surveillance (WES) has become a useful public health tool as an early-warning system revealing emergence\/re-emergence of pathogenic diseases and spread of antimicrobial resistance (AMR). We characterized the taxonomic composition, relative abundance, and antibiotic resistance genes (ARGs) of wastewater-identified bacterial pathogens across socioeconomically and epidemiologically diverse sewerage catchments in Nairobi, Kenya\u2014a key East African urban city representing a low- and middle-income country (LMIC). Results: Metagenomic analysis of Nairobi\u2019s wastewater revealed distinct bacterial and antimicrobial resistance (AMR) profiles. Campylobacteraceae (52.5% \u00b1 17.9%) and Bacteroidaceae (19.8% \u00b1 9.9%) dominated the communities. While Arcobacter cryaerophilus was ubiquitous, Bacteroides fragilis and A. suis abundances varied by neighborhood socioeconomic status. We detected critical clinical pathogens\u2014including Escherichia coli, Vibrio cholerae, Mycobacterium tuberculosis, and the ESKAPE species\u2014alongside 207 distinct ARGs conferring resistance to 11 antibiotic classes. Both taxonomic and ARG compositions showed high spatial heterogeneity, with maximum variation in low-income areas. Temporal analysis captured shifting pathogen dynamics, and metagenomic abundances for Vibrio cholerae and Klebsiella pneumoniae were validated via qPCR. Conclusions: Our findings underscore the utility of WES as a scalable, non-invasive public health tool. By capturing community-level pathogen composition and AMR dynamics, WES bypasses the limitations of clinical diagnostic access, providing a vital early-warning system for underserved urban populations. To maximize its public health utility, environmental genomic signals must serve as actionable triggers for coordinated One Health responses, including targeted clinical diagnostics, localized antimicrobial stewardship reviews, proactive risk communication, and prioritized sanitation infrastructure upgrades.<\/jats:p>","DOI":"10.3390\/antibiotics15090845","type":"journal-article","created":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T10:32:18Z","timestamp":1788258738000},"page":"845","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Wastewater Metagenomic Surveillance Reveals Socioeconomic Patterns of Pathogen Diversity and Antimicrobial Resistance in Nairobi, Kenya"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2214-5457","authenticated-orcid":false,"given":"Benard","family":"Mware","sequence":"first","affiliation":[{"name":"International Livestock Research Institute, Uthiru, Naivasha Road, P.O. Box 30709, Nairobi 00100, Kenya"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8043-5423","authenticated-orcid":false,"given":"Gilbert","family":"Kibet-Rono","sequence":"additional","affiliation":[{"name":"International Livestock Research Institute, Uthiru, Naivasha Road, P.O. Box 30709, Nairobi 00100, Kenya"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2561-1521","authenticated-orcid":false,"given":"Kennedy","family":"Mwangi","sequence":"additional","affiliation":[{"name":"International Livestock Research Institute, Uthiru, Naivasha Road, P.O. Box 30709, Nairobi 00100, Kenya"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"software","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"}]},{"given":"Doreen","family":"Lugano","sequence":"additional","affiliation":[{"name":"International Livestock Research Institute, Uthiru, Naivasha Road, P.O. Box 30709, Nairobi 00100, Kenya"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"}]},{"given":"Shebbar","family":"Osiany","sequence":"additional","affiliation":[{"name":"International Livestock Research Institute, Uthiru, Naivasha Road, P.O. Box 30709, Nairobi 00100, Kenya"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0513-8300","authenticated-orcid":false,"given":"Edward","family":"Kiritu","sequence":"additional","affiliation":[{"name":"International Livestock Research Institute, Uthiru, Naivasha Road, P.O. Box 30709, Nairobi 00100, Kenya"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8722-8301","authenticated-orcid":false,"given":"Paul O.","family":"Dobi","sequence":"additional","affiliation":[{"name":"International Livestock Research Institute, Uthiru, Naivasha Road, P.O. Box 30709, Nairobi 00100, Kenya"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1775-0468","authenticated-orcid":false,"given":"Collins","family":"Muli","sequence":"additional","affiliation":[{"name":"International Livestock Research Institute, Uthiru, Naivasha Road, P.O. Box 30709, Nairobi 00100, Kenya"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1481-5337","authenticated-orcid":false,"given":"John","family":"Juma","sequence":"additional","affiliation":[{"name":"International Livestock Research Institute, Uthiru, Naivasha Road, P.O. Box 30709, Nairobi 00100, Kenya"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"software","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"}]},{"given":"Regina","family":"Njeru","sequence":"additional","affiliation":[{"name":"International Livestock Research Institute, Uthiru, Naivasha Road, P.O. Box 30709, Nairobi 00100, Kenya"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1142-3442","authenticated-orcid":false,"given":"Eunice M.","family":"Machuka","sequence":"additional","affiliation":[{"name":"International Livestock Research Institute, Uthiru, Naivasha Road, P.O. Box 30709, Nairobi 00100, Kenya"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bernard","family":"Bett","sequence":"additional","affiliation":[{"name":"International Livestock Research Institute, Uthiru, Naivasha Road, P.O. Box 30709, Nairobi 00100, Kenya"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"investigation","vocabulary":"credit"},{"role":"resources","vocabulary":"credit"}]},{"given":"Ahmed","family":"Ogwell","sequence":"additional","affiliation":[{"name":"Africa Centres for Disease Control and Prevention, African Union Headquarters, Addis Ababa P.O. Box 200050, Ethiopia"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"funding-acquisition","vocabulary":"credit"},{"role":"resources","vocabulary":"credit"},{"role":"conceptualization","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0689-823X","authenticated-orcid":false,"given":"Edward O.","family":"Abworo","sequence":"additional","affiliation":[{"name":"International Livestock Research Institute, Uthiru, Naivasha Road, P.O. Box 30709, Nairobi 00100, Kenya"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tulio","family":"de Oliveira","sequence":"additional","affiliation":[{"name":"Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Francie van Zijl Drive, Tygerberg, Stellenbosch, Cape Town 7505, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"funding-acquisition","vocabulary":"credit"},{"role":"conceptualization","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6236-2280","authenticated-orcid":false,"given":"Dishon M.","family":"Muloi","sequence":"additional","affiliation":[{"name":"International Livestock Research Institute, Uthiru, Naivasha Road, P.O. Box 30709, Nairobi 00100, Kenya"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sofon\u00edas K.","family":"Tessema","sequence":"additional","affiliation":[{"name":"Africa Centres for Disease Control and Prevention, African Union Headquarters, Addis Ababa P.O. Box 200050, Ethiopia"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"funding-acquisition","vocabulary":"credit"},{"role":"conceptualization","vocabulary":"credit"},{"role":"resources","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6425-7345","authenticated-orcid":false,"given":"Samuel O.","family":"Oyola","sequence":"additional","affiliation":[{"name":"International Livestock Research Institute, Uthiru, Naivasha Road, P.O. 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