BackgroundThe accumulation of resistance genes inEscherichia coli(E.coli)strains imposes limitations in the therapeutic options available for the treatment of infections caused byE.coli. Production ofKlebsiella pneumoniaecarbapenemase (KPC) byE.colirenders it resistant to broad-spectrum β-lactam antibiotics. Globally there is existing evidence of spread of carbapenem-resistantE.coliin both humans and livestock driven by acquisition of the several other carbapenemase genes. Overall, there is little information regarding the extent of KPC gene distribution inE.coli. We set out to determine the prevalence, and evaluate the phenotypic and genotypic patterns of KPC inE.coliisolated from humans and their livestock in rural south western Uganda.MethodsA laboratory-based, descriptive cross-sectional study was conducted involving 96 human and 96 livestock isolates collected from agro-pastoralist communities in Mbarara district in south western Uganda. Phenotypic and molecular methods (PCR) were used for presence and identification of KPC genes in theE.coliisolates. A chi-square test of independence was used to evaluate the differences in resistant patterns between carbapenems and isolates.ResultsThe overall prevalence of carbapenem resistance by disk diffusion susceptibility testing (DST) for both humans and livestock isolates were 41.7% (80/192). DST-based resistance was identical in both human and livestock isolates (41.7%). The prevalence of carbapenem resistance based on Modified Hodge Test (MHT) was 5% (2/40) and 10% (4/40) for humans and livestock isolates respectively. Both human and livestock isolates, 48.7% (95/192) had the KPC gene, higher than phenotypic expression; 41.7% (80/192).blaKPC gene prevalence was overall similar in human isolates (51%; 49/96) vs livestock isolates (47.9%; 46/96). Approximately, 19% (15/80) of the isolates were phenotypically resistant to carbapenems and over 70% (79/112) of the phenotypically sensitive strains harbored theblaKPC gene.ConclusionOur results suggest that both human and livestock isolates ofE.coliin our setting carry theblaKPC gene with a high percentage of strains not actively expressing the blaKPC gene. The finding of fewer isolates carrying the KPC gene than those phenotypically resistant to carbapenems suggests that other mechanisms are playing a role in this phenomenon, calling for further researcher into this phenomenon.