Molecular Characterization of Extended-Spectrum Beta-Lactamase-Producing Enterobacteriaceae from Stool of Patients with Gastrointestinal Infections at Kisii Teaching and Referral Hospital

Abstract

Antimicrobial resistance (AMR) is a significant global health challenge, with Extended-Spectrum Beta-Lactamase (ESBL)-producing Enterobacteriaceae contributing notably to multidrug-resistant infections. ESBLs were prioritized in this study given their central role in beta-lactam resistance and their disproportionate contribution to treatment failure in resource-limited settings, where third-generation cephalosporins remain a mainstay of empirical therapy. Despite this burden, no prior study had characterized the prevalence, susceptibility patterns, or molecular epidemiology of ESBL-producing Enterobacteriaceae at Kisii Teaching and Referral Hospital (KTRH) or within Kisii County more broadly. This study assessed the prevalence, antimicrobial susceptibility patterns, and molecular characteristics of ESBL-producing Enterobacteriaceae isolated from stool samples of patients with gastrointestinal infections at KTRH, southwestern Kenya. In this cross-sectional study, stool specimens were collected from 200 patients presenting with symptoms of gastrointestinal infection, including diarrhoea, fever, vomiting, and mucoid/bloody stool, and cultured to identify bacterial isolates. Antimicrobial susceptibility was determined using the Kirby-Bauer disk diffusion method, with phenotypic ESBL confirmation via the Modified Double-Disk Synergy Test (MDDST) and molecular detection of blaTEM, blaSHV, and blaCTX-M variants by PCR. Associations between ESBL phenotype and participant characteristics were assessed using Chi-square and Fisher's exact tests, with significance set at p<0.05. A total of 187 isolates were recovered from the 200 samples analyzed, predominantly Escherichia coli (n=139/187, 74.3%), followed by Salmonella spp. (n=23/187, 12.3%), Klebsiella spp. (n=16/187, 8.6%), and Shigella spp. (n=9/187, 4.8%). Resistance was highest to Ampicillin (74.9%), Piperacillin-tazobactam (73.3%), and Amoxicillin-clavulanate (54.5%), and comparatively lower to Imipenem (25.7%) and Amikacin (24.6%). No participant characteristic, including age, sex, occupation, or water source, was significantly associated with ESBL phenotype (all p>0.05), though occupation approached significance (p=0.083). Of the 187 isolates, 84 (44.9%) were confirmed ESBL producers by MDDST. Molecular analysis revealed blaTEM (63.1%, n=53/84) and blaCTX-M-15 (48.8%, n=41/84) as the most prevalent genes, followed by blaSHV (38.1%), blaCTX-M-8 (28.6%), and blaCTX-M-9 (9.5%), with prevalence differing significantly across genes (χ²=36.75, p<0.001). Eighteen distinct co-carriage patterns were identified, and blaTEM and blaCTX-M-15 co-occurred significantly more often than expected by chance (OR=8.10, p<0.001), consistent with shared carriage on mobile genetic elements. These findings demonstrate a substantial, genetically diverse ESBL burden at KTRH, broadly distributed across the patient population rather than confined to an identifiable risk group, underscoring the need for heightened AMR surveillance, strengthened antimicrobial stewardship, and targeted infection control in resource-limited settings.