Molecular characterization of Carbapenem-resistant Escherichia coli isolates from sewage at Mulago National Referral Hospital, Kampala: a cross-sectional study

Abstract Background Escherichia coli (E. coli) is one of the most frequent causes of fatal bacterial infections affecting both humans and animals. The resistance to Carbapenems is mainly associated with enzyme-mediated resistance mechanism, through the acquisition of Carbapenemase genes. In Uganda, no studies have been done to detect presence of Carbapenem-resistant E. coli in sewage. We therefore carried out a study to characterize Carbapenem-resistant E. coli from sewage from Mulago National Referral Hospital. Methods and results In this cross-sectional study, a total of 104, sewage samples were aseptically collected, cultured on MacConkey agar supplemented with Meropenem 1 µg/ml with other standard microbiology methods to screen for Carbapenem-resistant E. coli (CREC). Antimicrobial susceptibility testing was performed on the CREC, using Imipenem (10 mg/disc) and Meropenem (10 mg/disc), Carbapenem drugs readily available on market. Multiplex PCR was performed on selected Carbapenem-resistant and susceptible isolates to detect Carbapenemase genes. Later the isolates were pathotyped for virulence genes that included pathogenicity islands (PAIs) and phylogenetic markers. The results showed that the Carbapenem-resistant E. coli isolates were more resistant to Meropenem (64%) than Imipenem (60%). KPC gene was the most predominant (75%), followed by NDM gene (30%) while no OXA-48, IMP-1, and IMP-2 genes were detected. Pathotyping of virulence genes showed presence of eae gene, as the most predominant (40%), followed by elt gene (25%) and negative for stx and aggR genes. For PAI markers, only the PAI IV536 gene was detected at 10%. Then, pathotyping of the phylogenetic markers was present in 85% of the typed isolates with yjaA gene the most abundant (60%) while both chuA and TSPE4.C2 were detected in 5% of the isolates. Conclusion Both pathogenic and non-pathogenic Carbapenem-resistant E. coli strains are present in the sewage of Mulago National Referral Hospital in Uganda.