Detection of different carbapenemases and clonality analysis of carbapenem-resistant Enterobacter cloacae

To identify antibiotic resistant genes and assess the clonality of carbapenem-resistant Enterobacter cloacae (CRECL) isolates from a hospital setting, altogether fifty-two clinical CRECL isolates were collected from 2012 to 2023. Antibiotic resistance genes including blaNDM, blaVIM, blaIMP, blaOXA-48, blaCTX-M-1 and blaTEM, were analyzed by PCR and nucleic acid sequencing. Sequence data were compared with those in the National Center for Biotechnology Information database. Clonality analysis was performed by ERIC-PCR. Among the 52 isolates, urine samples (23.1%) were the most common source, followed by puncture fluid (13.5%). The isolates were predominately obtained from urology (15.4%), followed by hepatobiliary surgery (11.5%). All isolates exhibited carbapenem resistance, with resistance rates of 88.5%, 84.6%, and 94.2% to imipenem, meropenem, and ertapenem, respectively. This was frequently accompanied by co-resistance to fluoroquinolones (67.2% to ciprofloxacin) and aminoglycosides (61.5% to tobramycin), likely due to the co-existence of multiple resistance genes on mobile genetic elements such as plasmids. However, all isolates remained sensitive to polymyxins, 67.2% to tigecycline and 50% to amikacin. Several carbapenem resistance genes were detected in isolates, with blaNDM-1 being the most abundant (40.4%), followed by blaNDM-5 (21.2%). Additionally, blaOXA-48 (3.8%), blaIMP-6 (1.9%) and blaVIM-1 gene (1.9%) have also been found in a few isolates. Among β-lactam resistance genes, blaTEM-1 (42.3%) is the most prevalent, followed by blaCTX-M-1 gene (23.1%). Clonality analysis classified the isolates into five clusters (A-E). Multiple strains exhibited >86% similarity, indicating clonal spread. In conclusion, CRECL isolates demonstrated extensive antimicrobial resistance, primarily mediated by blaNDM-1 and blaTEM. Clonality analysis revealed the presence of clonally related strains across different hospital departments, suggesting potential nosocomial transmission. Enhanced surveillance, strict disinfection and isolation measures are necessary to prevent the spread of CRECL and mitigate nosocomial infections and dissemination of epidemics.