Molecular characterisation of carbapenem resistant escherichia coli isolates from sewage within Mulago national referral hospital, Kampala
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Escherichia coli, an etiological agent emerging as one of the most frequent cause of fatal bacterial infections affecting both humans and animals. The resistance to carbapenems is mainly associated with enzyme mediated resistance mechanism, effected through the acquisition of carbapenemase genes. In Uganda, no studies have been done to detect presence of carbapenem resistant Escherichia coli in sewage. We therefore carried out a study to characterize carbapenem resistant Escherichia coli from sewage from Mulago National Referral Hospital. In this cross-sectional study, a total of 104, sewage samples were aseptically collected, cultured on MacConkey agar supplemented with meropenem 1µg/ml with other standard microbiology methods to screen for carbapenem resistant Escherichia coli (CREC). Antimicrobial susceptibility testing was performed on the CREC, using imipenem (10mg/disc) and meropenem (10mg/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 and pathotyped for virulence genes that included pathogenicity islands (PAIs) and phylogenetic markers. The result showed that the carbapenem resistant Escherichia 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 were 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. The presence of pathogenic and non-pathogenic carbapenem resistant Escherichia coli in the sewage is a threat to management of bacterial infections in clinical settings in Uganda. This would require regular surveillance of hospital sewage treatment and release into the common waste and close monitoring to eliminate potential health risks for humans and animals.