Phenotypic and genomic profiling of multidrug-resistant Escherichia coli and Klebsiella pneumoniae isolated from Intensive Care Unit patients in Kenya

Abstract Background The global rise of multidrug-resistant Enterobacterales, particularly extended-spectrum beta-lactamase (ESBL)- and carbapenemase-producing Escherichia coli and Klebsiella pneumoniae, poses a critical threat to intensive care unit (ICU) patients. Despite the clinical importance of these pathogens in sub-Saharan Africa, studies on their molecular characterization remains scarce. Methods We performed antibiotic susceptibility testing and whole-genome sequencing (WGS) on 22 multidrug-resistant isolates (15 E. coli and 7 K. pneumoniae) recovered from ICU patients at Kenya’s public referral hospital between January and June 2021. Isolates were obtained from blood, tracheal aspirates, urine, and pus swabs. We characterized antimicrobial resistance genes, virulence determinants, plasmid replicons, and genetic lineages, and assessed phenotype-genotype concordance. Results All isolates exhibited resistance to third-generation cephalosporins, with resistance rates exceeding 80% for at least 10 antibiotics. The ESBL gene bla CTX−M−15 was detected in 93% of E. coli and 100% of K. pneumoniae isolates. The concordance between phenotypic resistance and genotypic determinants was highest for β-lactams and lowest for aminoglycosides, trimethoprim-sulfamethoxazole and carbapenems. MLST revealed considerable genetic diversity among E. coli, including high-risk clones STc131 and ST648. Virulence genes (e.g., fimH, chuA, fyuA) were more prevalent in E. coli, particularly among isolates from urine and tracheal aspirate samples. Plasmid profiling revealed greater replicon diversity in E. coli, with frequent detection of IncFII and IncFIB plasmids, suggesting a stronger capacity for horizontal gene transfer. Conclusion These findings underscore the complexity of multidrug-resistant pathogen dynamics in ICU environments. They emphasize the need for species-specific surveillance, rapid diagnostics, and context-informed stewardship strategies to guide infection control and therapeutic interventions. While limited in scale, this study adds to the genomic landscape of multidrug-resistant pathogens in African ICUs and highlights critical targets for infection control and therapeutic interventions.