Shigella flexneri and Shigella sonnei among children under five in Kenya’s urban informal settlement

Abstract Background Shigella species are a significant global public health threat with the highest burden of Shigella-associated diarrhoea in children under five years of age, particularly in low- and middle-income countries. Given the high burden of shigellosis in these settings, there is a need for continuous surveillance to identify the prevalent species, risk factors, and determine appropriate intervention strategies. Methods This study aimed to determine the prevalence of Shigella flexneri (S. flexneri) and Shigella sonnei (S. sonnei), assess risk factors and identify Antimicrobial Resistance (AMR) genes present in samples positive for either species among children under five in Mukuru informal settlement. Between August 2023 and November 2024, 386 children presenting with diarrhoea at any of the four selected health facilities in Mukuru were enrolled. Stool samples or rectal swabs were collected and subjected to TaqMan Polymerase Chain Reaction (TAC PCR) for the detection of S. flexneri, S. sonnei and selected AMR genes. Case Report Forms (CRF) and structured questionnaires were used to collect medical history, behavioural and socioeconomic data, respectively. Results The prevalence of S. flexneri and S. sonnei among the 386 participants was 15.54% (60/386). Positivity for S. flexneri and S. sonnei by age group was highest among children aged 12–23 months (24.84%, 40/161) and lowest among those aged 24–59 months (2.08%, 2/96). S. flexneri was the most prevalent species, with serotypes 2 and X being the most detected. Among the samples positive for S. flexneri and S. sonnei, the mphA gene was detected in 98.33% (59/60), the β-lactamase gene CTX-M1-9 was present in 85% (51/60), and CTX-M2-8-25 was identified in 26.67% (16/60) of samples. Age (aOR = 1.025, 95% CI: 1.003–1.047, P = 0.027) and obtaining vegetables from the market (aOR = 2.737, 95% CI: 1.081–6.930, P = 0.034) were significantly associated with shigellosis. Conclusions These findings show that shigellosis due to S. flexneri and S. sonnei remains a significant contributor to the burden of diarrheal disease, particularly among young children. The high prevalence of AMR genes, especially mphA and CTX-M β-lactamases, indicates widespread resistance to macrolides and extended-spectrum β-lactams. Addressing this challenge may require a multifaceted approach, including enhanced antimicrobial resistance surveillance, strengthened Water, Sanitation, and Hygiene (WASH) interventions, and the potential deployment of Shigella vaccines among vulnerable populations.