High gastrointestinal carriage rates of extended-spectrum-β-lactamase-producing enterobacterales and associated factors among hospitalized and nonhospitalized children in Kenya.

Gastrointestinal carriage of extended-spectrum β-lactamase-producing Enterobacterales (ESBL-E) presents a critical public health threat globally. However, in resource-constrained countries with poor sanitation, inadequate drinking water, and limited microbiology laboratories like Kenya, epidemiological data of these strains is limited. This study assessed the gastrointestinal carriage of ESBL-E and the risk factors for colonization among children (≤ 5 years) in the inpatient department (IPD) and outpatient department (OPD). This was a hospital-based cross-sectional study at Thika Level 5 Hospital, Kenya, from February to June 2023. In total, 540 participants (OPD: 270, IPD: 270) were recruited, using systematic random sampling and consecutive sampling in OPD and IPD, respectively. Children admitted for less than 48 h in the paediatrics ward and those with a prior history of hospitalization (≤ 3 months) in OPD were excluded. Demographic data were collected using a well-structured questionnaire. Following the standard microbiology methods, stool or rectal swab samples were cultured, with the identity and antimicrobial susceptibility of isolates elucidated by automated platforms. The overall ESBL-E gastrointestinal carriage rate was 35.4% (191/540), and was highest among outpatients at 40.4% (109/270). Isolates demonstrated co-resistance to aminoglycosides (43–52%), quinolones (52–62%), carbapenems (44–50%), and sulfonamides (92–97%). They were more susceptible to piperacillin/tazobactam (67–95%) and colistin (96–99%). Carbapenemase-producing Enterobacterales (CPE) co-carriage rate was 17.6% (16/91), with similar rates for inpatients (50%, 8/16) and outpatients (50%, 8/16). Escherichia coli was the predominant ESBL-E overall (82.2%, 157/191), among outpatients (83.5%, 91/109), and inpatients (80.5%, 66/82), and was also the main CPE (overall: 81.3%, 13/16; OPD: 75%, 6/8; IPD: 87.5%, 7/8). Independent predictors of colonization included child age (adjusted odds ratio (OR): 1.60, p = 0.045) and a history of antimicrobial use from retail pharmacies without a clinician’s prescription (adjusted OR: 0.18, p = 0.047). This study demonstrates a substantial burden of gastrointestinal carriage of ESBL-E and CPE co-carriage among children (≤ 5 years), with E. coli being the predominant organism. Age less than two years and a history of exposure to non-prescribed antimicrobials were independent factors for colonization. Efforts to limit exposure to contaminated environments and targeted antimicrobial stewardship initiatives are required to mitigate AMR in the current study setting.