Characterization of multidrug-resistant diarrheagenic Escherichia coli isolated from 2009-2020 among patients with acute diarrhea at Kisumu County Referral Hospital, Kenya

Background Antimicrobial resistance and multidrug resistance (MDR) among diarrheagenic Escherichia coli (DEC) increasingly compromise empiric therapy for enteric infections. Recent reports from Kenya indicate that multidrug resistance is increasingly common among diarrheagenic Escherichia coli , with approximately 30% of isolates reported as multidrug resistant in Dagoretti South, Nairobi. Data on resistance patterns of DEC in western Kenya remain limited. This study examined the epidemiology, antimicrobial susceptibility profiles, and multidrug resistance patterns of DEC isolates from patients with acute diarrhea at Kisumu County Referral Hospital between 2009 and 2020. Methods A retrospective laboratory-based case series study analyzed 181 archived diarrheagenic Escherichia coli (DEC) isolates collected between 2009 and 2020. Isolates were confirmed by multiplex PCR detection of pathotype-specific virulence genes. Antimicrobial susceptibility testing was performed using the Kirby–Bauer disk diffusion method on Mueller–Hinton agar and interpreted according to applicable Clinical and Laboratory Standards Institute guidelines. Results Of the 181 DEC isolates, the distribution across age groups differed significantly (χ² = 32.02, df = 15, p < 0.001), with the highest proportion occurring among children aged 1–4 years (75/181; 41.4%). EAEC was the predominant pathotype (89/181; 49.2%), followed by EPEC (33/181; 18.2%), EIEC (19/181; 10.5%), ETEC (19/181; 10.5%), and EHEC (8/181; 4.4%). Mixed-pathotype isolates were identified in 13 isolates (7.2%), comprising EAEC/EPEC, EAEC/EIEC, and ETEC/EPEC virulence-gene combinations. High phenotypic resistance was observed to trimethoprim–sulfamethoxazole (165/181; 91.2%) and ampicillin (131/181; 72.4%), while carbapenem non-susceptibility remained low (11/181; 6.1%). MDR occurred in 61/181 (33.7%) of the isolates. Among these MDR isolates, resistance most frequently involved ampicillin and trimethoprim–sulfamethoxazole (58/61; 95.1% each), followed by amoxicillin–clavulanate (46/61; 75.4%). Resistance to tetracycline (34.4%), quinolones (27.9%), aminoglycosides (19.7%), and third-generation cephalosporins (16.4%) was less common. Conclusions DEC remains an important cause of acute diarrheal disease in western Kenya, with sustained predominance of EAEC and widespread multidrug resistance across pathotypes. Persistently high resistance to ampicillin and trimethoprim–sulfamethoxazole indicates substantially reduced reliability of first-line empirical therapy. Although resistance to higher-tier antimicrobials remained comparatively low, detection of early non-susceptibility to last-resort agents calls for a sustained antimicrobial stewardship, diagnostic-guided therapy, and continuous resistance surveillance.