Nairobi study links resistant E. coli in the gut to local strains and antibiotic use

In a dense informal settlement in Nairobi, the antibiotic-resistant E. coli people carried in their guts varied with the area they lived in: the resistant strains already established nearby and the type of antibiotic used most there were both associated with what people carried. That is the finding of a paper by Eric Ng'eno of the University of Kansas, published in PLOS ONE on 24 June 2026.

Ng'eno, a PhD candidate in ecology and evolutionary biology, explained the work in The Conversation Africa on 15 October 2026. The World Health Organization (WHO) says E. coli is commonly found in the lower intestine of warm-blooded animals, including humans, and that most strains are harmless, though some cause serious food poisoning. The samples in the study came from people without symptoms.

WHO's fact sheet on antimicrobial resistance, dated 16 July 2026, says infections caused by microbes that no longer respond to medicines become hard or impossible to treat. It estimates that bacterial resistance was associated with more than 4.7 million deaths worldwide in 2021, and says about 1 in 6 laboratory-confirmed bacterial infections in 2023 were resistant to antibiotics.

The paper re-examines data from a population-based infectious disease surveillance platform and an earlier study of carriage. It describes the settlement as having inadequate sanitation, a high burden of infectious disease, high antibiotic use and high carriage of resistant E. coli. Between 1 September 2015 and 22 January 2016, 2,320 stool samples were collected from households at 195 locations: 1,212 (52.2 per cent) from children under five and 1,108 (47.8 per cent) from adults aged 18 and over. The surveillance covers roughly 26,000 residents in about 0.4 square kilometres.

An E. coli isolate was scored resistant to a drug if it grew fully in its presence. Carriage of resistant strains ranged from 57 of 2,320 samples (2.5 per cent) for kanamycin to 2,098 (90.4 per cent) for trimethoprim. Only 425 samples (18.3 per cent) held susceptible E. coli alone. Resistance to ampicillin, streptomycin, sulfamethoxazole, tetracycline and trimethoprim tended to occur together.

Ng'eno then estimated each area's antibiotic exposure from prescriptions filled between 2010 and 2015, and tested it, along with distance to water, toilets, dump sites and clinics, hygiene practices and weather, against what was found in the samples. Areas frequently exposed to bactericidal antibiotics, which kill bacteria, were “dominated by locally established resistant strains”, the paper says. Areas frequently exposed to bacteriostatic antibiotics, which stop bacteria multiplying, had more less-established strains. The paper describes cloxacillin as bactericidal and erythromycin as bacteriostatic. Higher cloxacillin exposure was linked to the common resistant strains. Higher erythromycin exposure was linked to strains resistant to ceftazidime and ciprofloxacin, and to fully susceptible strains.

Ng'eno wrote in The Conversation that when antibiotics severely disrupted the gut microbiota, the native microbes were “quickly displaced by microbial communities” from the surrounding environment. Milder drugs left more of the original bacteria in place, he wrote, and outcomes varied more.

The paper says hygiene practices, including frequent toilet cleaning, regular handwashing and sharing toilets, “were unexpectedly associated with increased risk of resistant bacteria carriage”. Ng'eno wrote that vaccines and hygiene practices that lower the risk of disease “can help reduce the need for antibiotics”.

The paper lists its own limits. The models explained 10 per cent of the variance in resistant E. coli strain diversity in the area, and a considerable part of what they explained was attributed to unmeasured spatial factors. It used no genomic data, which it says could clarify which resistant strains were colonising people, and it considered only interactions among E. coli strains. It studied “a relatively small, highly interactive area”, and the samples date from 2015 and early 2016.

The paper concludes that its findings point to “context-specific approaches to antibiotic stewardship and hygiene interventions”. In Kenya, Capital FM reported on 5 July 2026 that Mary Muthoni Muriuki, Principal Secretary for Public Health and Professional Standards at the Ministry of Health, urged Kenyans to avoid self-medication and to use antibiotics only as prescribed by qualified healthcare professionals. “Responsible use of antibiotics is critical in the fight against antimicrobial resistance,” she said at a church service in Karen, Nairobi, as quoted by Capital FM. WHO lists misuse and overuse of antimicrobials and poor access to clean water, sanitation and hygiene among the causes of resistance.

The news site Eastleigh Voice reported on 18 November 2025 that health officials, in a Ministry of Health statement released that day, said misuse of antibiotics, such as stopping treatment early or buying drugs without prescriptions, was feeding the problem.