Mapping Antimicrobial Resistance in Escherichia coli and Klebsiella pneumoniae from Complicated Urinary Tract Infections in Oman: Phenotypic and Genotypic Insights
Abstract
Background: Mapping the local etiology and antimicrobial susceptibility profile of pathogens causing complicated urinary tract infection (cUTI) is important for promoting evidence based antimicrobial prescribing. WGS plays an important role in genomic surveillance of AMR and understanding circulating clades. Methods: Antimicrobial susceptibility profile of patients presenting with cUTI were analysed. ESBLs, AmpC β-lactamases, and CRE were detected by combined disc test (ESBL), D69C AmpC detection set (AmpC) and KPC/IMP/NDM/VIM/OXA-48 Combo test kit (CRE). Whole genome sequencing (WGS) was carried out in eleven E. coli AmpC and twenty-two K. pneumoniae CRE isolates. Bioinformatic analysis was performed using online tools. Results: The susceptibility patterns of E. coli and K. pneumoniae were as follows: nitrofurantoin (96%, 38%), fosfomycin (100%,89%), fluoroquinolones (44%, 47%), aminoglycosides (93%, 82%), piperacillin-tazobactam (95%,72% ) and carbapenems (98%, 83%). The overall prevalence of ESBL among E. coli and K. pneumoniae was 37.2%, while the estimated prevalence of AmpC was 5.4% and the prevalence of CRE was 6.2%. E. coli was the predominant ESBL and AmpC producer, whereas K. pneumoniae was the major CRE producer. Nine E. coli MLST lineages were identified: ST-10, ST-69, ST-77, ST-131, ST-156, ST-167, ST-361, ST-1125 and ST-2520, while in K. pneumoniae 5 MLST lineages were observed: ST-2096, ST-231, ST-147, ST-1770 and ST-111. ST-2096 (12 isolates) and ST-147 (7…
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