Kisumu’s water carries invisible passengers—superbugs and resistance genes—slipping from lake to home, threatening families, defying treatment, and revealing how delicate life becomes when the sources we trust betray us
By Faith Anene, Kakamega
A new scientific study has raised concerns about the safety of water flowing from Lake Victoria into homes in Kisumu, warning that antibiotic-resistant bacteria and potentially harmful pathogens are present not only in rivers and wastewater but also in treated tap water.
The research, published in Tropical Medicine & International Health, used advanced metagenomic sequencing to trace microbial communities from the lake through treatment facilities to household supply points.
The study was led by Prof Oleg Reva of the University of Pretoria and Prof William Shivoga Prof Francis Orata Omoto and Dr Anthony Wawire of Masinde Muliro University of Science and Technology (Mmust) alongside collaborators from the Water and Sanitation Company (KIWASCO) in Kisumu, the Department of Microbiology and Immunology at Busitema University in Uganda, Manchester Metropolitan University in the UK, and the South African Medical Research Council’s Office of AIDS and TB.
Samples were collected from Lake Victoria, River Wigwa, wastewater stabilisation ponds, the Dunga Water Treatment Plant and a post-treatment tap outlet in Kisumu on 23 October 2023, at the end of the short rainy season when flooding and runoff can intensify contamination.
“We wanted to characterise the microbial and resistome landscapes of natural and industrial water reservoirs in Kisumu,” Prof Shivoga said
Using shotgun metagenomic sequencing, the researchers analysed millions of DNA fragments to identify bacteria, viruses, virulence factors and antibiotic resistance genes (ARGs).
“We wanted to characterise the microbial and resistome landscapes of natural and industrial water reservoirs in Kisumu,” Prof Shivoga said, noting that traditional culture-based methods often underestimate microbial diversity and resistance risks.
The results revealed 121 bacterial classes across the samples. Cyanobacteria, particularly Planktothrix were abundant in both lake and tap water.
More concerning was the detection of major human pathogens at nearly all sampling sites, including Pseudomonas aeruginosa, Klebsiella pneumoniae, Escherichia coli, Acinetobacter baumannii and Bacillus cereus/anthracis. Some were found at unexpectedly high prevalence in treated tap water.
Beyond pathogens, the study identified what researchers described as a “rich resistome” — a wide array of antibiotic resistance genes, including β-lactamases, aminoglycoside-modifying enzymes, vancomycin-resistance operons and disinfectant-resistance determinants.
Strikingly, the highest frequencies of antibiotic resistance and virulence genes were detected not in raw lake water, but in tap water and treatment-plant samples.
“This suggests that incomplete disinfection and biofilm persistence promote the proliferation and exchange of ARGs between environmental and pathogenic taxa,” he said
Prof Reva said ageing infrastructure may be contributing to the problem. “Cracks and clogs in the ageing municipal water-supply infrastructure create ideal conditions for biofilm formation, while suboptimal disinfectant concentrations within the system select for antimicrobial resistance,”
By contrast, Lake Victoria water showed lower levels of resistance genes, likely due to natural self-purification processes such as microbial grazing, sedimentation, ultraviolet radiation and dilution. However, the researchers cautioned that natural purification does not eliminate risk.
“Although the concentrations of waterborne pathogens decrease within the lake, they remain sufficiently abundant to pose continued public-health risks,” the study notes.
The open design of wastewater stabilisation ponds may further compound the problem. According to the researchers, inadequate treatment combined with open systems creates an “optimal environment for the evolution of antibiotic-resistant pathogens through ARG selection and horizontal gene transfer”.
The team also detected viral indicators of faecal contamination in the water including adenoviruses, enteroviruses and torque teno viruses across the water system.
Prof Shivoga said environmental reservoirs can act as long-term storage sites for resistance genes, which may re-enter clinical settings through water or food chains. “Addressing antimicrobial resistance and waterborne infections requires a One Health approach recognising links between human, animal and environmental systems,”.
One notable finding was that bacterial abundance did not always match resistance impact. Even species present in small numbers could disproportionately influence resistance gene pools, depending on environmental pressures and mobile genetic elements such as plasmids and phages.
The researchers say these complex microbial interactions are of “great practical importance” for predicting disease outbreaks and assessing the risk of multidrug-resistant infections.
They argue that conventional monitoring systems may be insufficient in rapidly urbanising regions with dense populations and limited sanitation infrastructure.
“The detection of clinically relevant pathogens and high-risk antibiotic resistance genes in treated and tap water identifies critical weaknesses in the municipal water treatment and distribution system,” said Prof Francis Orata, one of the researchers.
The team is calling for metagenomic surveillance to be integrated into routine monitoring and national One Health strategies to strengthen early warning systems for antimicrobial resistance.
The study will now expand into longer-term analyses to track environmental and human influences on pathogen and resistance gene distribution in the Lake Victoria basin, which serves an estimated 30 to 35 million people.
