Emergence of Staphylococcus saprophyticus as the predominant uropathogen in febrile children under five years at Alupe Sub-County Referral Hospital, Busia County, Kenya

Abstract

Urinary tract infections (UTIs) remain among the most common bacterial infections in febrile children under five, yet their etiological patterns are changing across sub-Saharan Africa. In resource-limited settings such as rural Kenya, diagnostic dilemmas compound this burden. A cross-sectional study was conducted between November 2024 and March 2025, enrolling about 200 febrile children aged 1 to 5 years. The sample size was calculated using the single population qualitative variable formula. Children presenting with fever are defined as having an axillary temperature ≥37.5°C measured using a calibrated digital thermometer. The clean-catch method was used to collect the urine samples in sterile urine bottles and cultured on standard media. Cysteine Lactose Electrolyte Deficient Agar (CLED) was used for primary culture, MacConkey agar for selective isolation, and subcultured on Blood Agar. A culture-confirmed UTI was defined as ≥10⁵ CFU/mL of a single organism from a clean-catch midstream urine sample. Mixed cultures or bacterial counts below this cut-off were considered non-significant, and colony-count criteria (>10⁵ CFU/mL plus pyuria) minimized false positives. Socio-demographic data were obtained through structured caregiver interviews. Associations between infection status and fever were analyzed using chi-square and Fisher’s exact tests, with p<0.05 considered significant.  Urine cultures yielding microbial growth were identified using standard bacteriological techniques. Seventy-seven (38.5%) children had culture-confirmed urinary tract infections. Staphylococcus saprophyticus was the most frequent pathogen (46.3%), followed by Escherichia coli (19.2%) and Staphylococcus aureus (12.8%). Other isolates included Klebsiella pneumoniae (5.2%), Pseudomonas aeruginosa (3.9%), Streptococcus pneumoniae (2.6%), and several other minor species. While the primary focus of this study was on bacterial uropathogens, Candida albicans (3.9%) was also isolated in some specimens.  Infection rates were slightly higher in boys (21.5%) than in girls (17.0%), though this difference was not significant (p=0.101). Fever was not associated with infection (p=0.7). Staphylococcus saprophyticus has emerged as a dominant uropathogen among the febrile children in this rural Kenyan setting, indicating a potential shift in local etiology. Continuous local surveillance and health education are essential for the prevention and early management of urinary tract infections.