IncL plasmid-mediated dissemination of OXA-48 β-lactamase and <i>bla</i> _CTX-M-15 gene amplification identified <i>via</i> long-read sequencing in carbapenem-resistant Enterobacterales

<h4>Background</h4>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.<h4>Methods</h4>In 2021, stool samples (<i>n</i> = 538) and rectal swabs (<i>n</i> = 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.<h4>Results</h4>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 <i>Klebsiella pneumoniae</i> (<i>n</i> = 25), <i>Escherichia coli</i> (<i>n</i> = 1), and <i>Enterobacter cloacae</i> (<i>n</i> = 1). In CRE, 29.6% (8/27) were carbapenemase-producing Enterobacterales (CPE), carrying the <i>bla</i> _OXA-48 (<i>n</i> = 7) or <i>bla</i> _NDM-1 (<i>n</i> = 1) genes. The remaining 70.4% (19/27) were non-carbapenemase-producing CRE isolates (non-CP-CRE). The <i>bla</i> _OXA-48 gene was localized on identical IncL plasmids with an inverted Tn<i>1999.2</i> 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 <i>bla</i> _CTX-M-15 gene along with mutations in porin genes.<h4>Conclusions</h4>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 <i>bla</i> _CTX-M-15 gene amplification, demonstrating its added value for antimicrobial resistance monitoring.