Epidemiology and carbapenemase gene distribution among carbapenem-resistant enterobacterales: a two-year retrospective study in a Saudi tertiary hospital

Carbapenem-resistant Enterobacterales (CREs) present a significant public health challenge due to their rapid dissemination, high mortality, and limited treatment options. Ongoing assessment of their epidemiology is essential for detecting shifts in species distribution and resistance patterns, as well as the emergence of carbapenemase variants. This retrospective study aimed to examine the epidemiological, microbiological, and molecular characteristics of CRE isolates collected from January 2023 to January 2025 at a tertiary hospital in Saudi Arabia. Data from 131 isolates were analyzed, including species identification, antimicrobial susceptibility testing (AST), and carbapenemase gene profiles (blaOXA-48, blaNDM, blaKPC, blaVIM, and blaIMP). Patients’ demographic and clinical data, including 30-day mortality, were also analyzed. Klebsiella pneumoniae was the most common species (74.8%), followed by Escherichia coli (12.9%). The predominant carbapenemase genes were blaOXA-48 (42.7%) and blaNDM (28.2%), with co-carriage of blaNDM and blaOXA-48 and blaNDM and blaKPC in 16.0% and 3.5% of isolates, respectively. AST revealed high resistance to β-lactams, fluoroquinolones, and aminoglycosides. Resistance to colistin and ceftazidime-avibactam was observed in 23.5% and 24.1% of isolates, respectively, a finding that is clinically concerning given the reliance on colistin as salvage therapy and on ceftazidime–avibactam as a key targeted treatment option for CREs in Saudi Arabia. Tigecycline remained effective, with 7% resistance. Importantly, phenotypic–genotypic discrepancies were identified in a small proportion of isolates. Eight isolates (6.1%) were phenotypically carbapenem-resistant but tested negative for the screened carbapenemase genes, as well as carbapenemase gene–positive isolates that were phenotypically susceptible to imipenem (nine isolates) and meropenem (eight isolates). The overall 30-day mortality was 35.1%, with ICU admission significantly associated with higher mortality (RR = 1.85; 95% CI: 1.32–2.59). This study provides updated insights into the molecular epidemiology of CREs in Saudi Arabia. The dominance of blaOXA-48 and blaNDM genes indicates that these remain the primary carbapenemase genes circulating in the region. The observed discrepancies between phenotype and genotype highlight the limitations of current PCR-based assays and emphasize the need for surveillance strategies that integrate both phenotypic and molecular methods to enhance diagnostics and strengthen infection control measures.