Kenyan water harvesting ponds harbour hundreds of antibiotic resistance genes, study finds

Water harvesting ponds that supply smallholder farms across rural Kenya carry a substantial load of antibiotic resistance genes, according to a new shotgun metagenomics study published in the journal Environmental Microbiome. The research characterised the microbiome and resistome of 16 rural Kenyan ponds, detecting 582 antibiotic resistance gene subtypes belonging to 27 different classes.

The analysis showed that a small number of resistance gene types dominated the ponds. Five types, conferring resistance to bacitracin, multiple drugs, polymyxins, beta-lactams and rifamycin, together accounted for 90.6 percent of the antibiotic resistance genes detected. This concentration suggests that a limited set of resistance mechanisms underpins much of the resistome in these water bodies.

Using genome-resolved analyses, the researchers recovered 1,542 metagenome-assembled genomes from the pond samples. Among these were non-tuberculous Mycolicibacterium organisms carrying rifamycin resistance via the rbpA gene, along with virulence factors including type VII secretion systems, dormancy regulators and the antigen 85 complex.

Not all findings pointed to high risk. Co-localisation between antibiotic resistance genes and mobile genetic elements was rare in the samples, and resistome risk scores were moderate at approximately 22.4. The authors report that this indicates limited potential for horizontal gene transfer compared with ponds or water systems influenced by agricultural or hospital effluents.

Despite that moderate risk profile, the study concludes that the ponds act as persistent environmental reservoirs of antimicrobial resistance linked to farming practices.

The researchers suggest that strengthened antimicrobial stewardship, improved manure management and vegetative buffer zones could help mitigate the dissemination of resistance genes and support safer rural water systems under a One Health framework. The work was published as an open access article on 17 October 2026, and the version currently available is an accepted manuscript shared early, subject to further edits before the final version of record.

Subject of Research: Metagenomic analysis of antibiotic resistance genes in rural Kenyan water harvesting ponds

Article Title: Shotgun metagenomics reveals the microbiome and resistome of water harvesting ponds used by Kenyan rural smallholders

Article References: Gregson, B. H., Bani, A., Steinfield, L., Holt, D., Vamos, E. E., Connell, R., Whitby, C., & Ferguson, R. M. W. (2026). Shotgun metagenomics reveals the microbiome and resistome of water harvesting ponds used by Kenyan rural smallholders. Environmental Microbiome. https://doi.org/10.1186/s40793-026-00978-5

Image Credits: AI Generated

DOI: 10.1186/s40793-026-00978-5

Keywords: antimicrobial resistance, shotgun metagenomics, water harvesting ponds, Kenya, smallholder farming, resistome, Mycolicibacterium, One Health, environmental microbiome, mobile genetic elements, Shotgun, metagenomics