Phenotypic and Genotypic Detection of Carbapenem Resistance in Urinary Enterobacterales Isolates: A Prospective...

Background Carbapenem-resistant Enterobacteriaceae (CRE)-induced urinary tract infections (UTI) pose increased mortality rates in critically ill patients. Carbapenem resistance is primarily due to the activity of Ambler Classes A, B, and D carbapenemase enzymes. Horizontal transmission of carbapenemase genes has propelled the increase in CRE prevalence. Newer carbapenemase inhibitors do not act against class B enzymes, hence early and precise detection of CRE is essential to advise targeted therapy and manage antimicrobial resistance. In our research, the prevalence of CRE among urinary Enterobacteriaceae isolates was determined, and the diagnostic performance of the Carba-NP test (bioMérieux, Marcy l'Étoile, France) was compared to multiplex polymerase chain reaction (PCR) for carbapenemase detection and the results were analysed. The phenotypic resistance patterns are correlated with particular carbapenemase gene expression. Materials and methods An 18-month prospective cross-sectional study was performed, during which 350 Enterobacteriaceae isolates from urine samples were isolated. Disc diffusion was performed according to the Clinical and Laboratory Standards Institute (CLSI) M100-2022 guidelines to screen for carbapenem resistance, and carbapenemase production was phenotypically determined using the Carba-NP test. Multiplex PCR was used to identify prevalent carbapenemase genes (NDM, IMP, KPC, OXA-48-like, VIM). Results Among 350 Enterobacteriaceae isolates, 110 were resistant to carbapenems by multiplex PCR. Eighty-one isolates were positive by Carba-NP. Multiplex PCR was positive for most prevalent genes like NDM and OXA-48-like, 44 had both NDM and OXA-48-like, and three had IMP genes. No KPC genes were found. The most common resistant species were Escherichia coli and Klebsiella pneumoniae.  Conclusion The increased prevalence of CRE among urinary Enterobacteriaceae, which is dominated by NDM and OXA-48-like carbapenemases, highlights the necessity for strong antimicrobial stewardship and infection control measures. The Carba-NP test was 100% specific but had only 73.64% sensitivity compared to PCR, emphasising molecular diagnostics' critical role in carbapenemase detection. Rapid detection of CRE is required to allow targeted treatment and control the dissemination of antimicrobial resistance in clinical environments.