Repository series · ncbi-prjna1240580

E. coli and Klebsiella pneumoniae isolated from patients with complicated UTI

Mapping the local etiology and antibiogram of common pathogens causing complicated urinary tract infection (cUTI) is important for promoting evidence based antimicrobial prescribing. Evaluating the prevalence of extended spectrum beta lactamases (ESBL), AmpC beta lactamases (AmpC) and carbapenemase producing Enterobacterales (CPE), is equally important as it informs treatment guidelines and empiric management. Whole genome sequencing (WGS) enhances antimicrobial resistance (AMR) surveillance by complementing phenotypic antimicrobial susceptibility testing, offering deeper insights into resistance mechanisms, transmission, and evolution. Integrating it into routine AMR monitoring can significantly improve global efforts to combat antimicrobial resistance. Methods: Antimicrobial susceptibility profile of isolates from cUTI were collected from patients presenting with Sultan Qaboos University Hospital, Muscat and Suhar Hospital, Suhar, Oman. Automated systems as well as manual methods were used for detection of ESBL and CPE. ESBLs, AmpC beta-lactamases, and CPE were further detected by manual methods: double disc synergy test for ESBL; disc approximation assay and D69C AmpC detection set for AmpC and CIM/mCIM and KPC/IMP/NDM/VIM/OXA-48 Combo test kit for CPE. WGS was carried out in 11 FOX resistant E. coli and 22 K. pneumoniae CPE isolates with varying susceptibilities to identify circulating clades, AMR genes and plasmids. Bioinformatic analysis was performed using online tools.