BACKGROUND: Increasing resistance to broad-spectrum beta-lactams and carbapenems is a significant concern in healthcare settings. This study aimed to determine the prevalence of intestinal carriage of extended-spectrum β-lactamase (ESBL)-producing and carbapenem-resistant Enterobacterales (CRE) in a tertiary care hospital and to evaluate the utility of long-read sequencing for carbapenem resistance surveillance. METHODS: In 2021, stool samples (n = 538) and rectal swabs (n = 256) from hospitalized patients were cultured after enrichment on selective chromogenic medium to detect ESBL and CRE carriage. CRE isolates were characterized by antimicrobial susceptibility testing and whole-genome sequencing. RESULTS: Among 794 patient samples, 239 (30%) Enterobacterales isolates grew on ESBL media. On CRE agar, 28 Enterobacterales were cultured, 27 confirmed carbapenem-resistant and identified as Klebsiella pneumoniae (n = 25), Escherichia coli (n = 1), and Enterobacter cloacae (n = 1). In CRE, 29.6% (8/27) were carbapenemase-producing Enterobacterales (CPE), carrying the bla OXA-48 (n = 7) or bla NDM-1 (n = 1) genes. The remaining 70.4% (19/27) were non-carbapenemase-producing CRE isolates (non-CP-CRE). The bla OXA-48 gene was localized on identical IncL plasmids with an inverted Tn1999.2 transposon in non-clonally related isolates. CPE isolates exhibited distinct resistance patterns to carbapenems, β-lactam/β-lactamase inhibitor combinations, with 87.5% resistant to cefiderocol. All non-CP-CRE isolates remained susceptible to imipenem; two were resistant to meropenem and carried either five or six copies of the bla CTX-M-15 gene along with mutations in porin genes. CONCLUSIONS: A 30% prevalence of intestinal carriage of ESBL-producing Enterobacterales and a 3.4% carriage prevalence of CRE were found. Long-read sequencing revealed IncL plasmid-mediated dissemination of OXA-48 β-lactamase and bla CTX-M-15 gene amplification, demonstrating its added value for antimicrobial resistance monitoring.

Department of Medical Microbiology 2nd Faculty of Medicine Charles University and Motol University Hospital 5 Uvalu 84 Praha 5 Prague 150 06 Czech Republic

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