Factors associated with non-Typhoidal Salmonella infection in children under 5 years in an urban informal settlement in Nairobi, Kenya

Non-Typhoidal Salmonella (NTS) is a common cause of bacteremia among children under five in sub-Saharan Africa. The risk of infection is high in urban informal settlements due to limited access to clean drinking water, poor sanitation, and improper solid waste disposal. Consequently, in this study, we investigated the social demographic, environmental, sanitation and hygiene factors that increase the risk for NTS infection among children under five. Between March 2023 and July 2025, children presenting with fever (≥ 38° C), with or without diarrhoea, were recruited from four outpatient health facilities. Fecal and blood samples collected were subjected to culture for isolation of NTS. Questionnaires were used to collect data on socio-economic-environmental, demographic factors and clinical characteristics. Associations and risk factors for NTS infection were assessed using descriptive statistics, chi-square tests, and multivariable binary logistic regression. Among the 3,780 enrolled children, NTS was isolated from 1.1% (42/3780), of which Salmonella Typhimurium was 0.6% (22/3780) and Salmonella Enteritidis 0.5% (20/3780). Children aged 12–24 months had higher odds of infection compared with those aged < 12 months (aOR = 1.83; 95% CI: 0.79–4.23). However, there was no significant association between the occurrence of NTS and gender, age, or contact with animals. The use of open containers for water storage, specifically drums, was potentially associated with NTS infection (aOR = 2.38; 95% CI: 1.27–4.45, p = 0.007). Having malignancy as a comorbidity was also associated with NTS infection (aOR = 30.05; 95% CI: 2.83–319.65, p = 0.005). This study highlights the need for improving Water, Sanitation and Hygiene (WASH) infrastructure and practice to reduce the risk associated with transmission of NTS in endemic settings. In the short-to medium-term, there is a need for introduction of vaccines for prevention and control of NTS disease.