IncL plasmid-mediated dissemination of OXA-48 β-lactamase and blaCTX-M-15 gene amplification identified via long-read sequencing in carbapenem-resistant Enterobacterales

TL;DR

This study found that long-read sequencing helps track antibiotic resistance genes in hospital patients, revealing how resistance spreads through plasmids.

Contribution

The study demonstrates the added value of long-read sequencing in identifying plasmid-mediated resistance gene dissemination in clinical settings.

Findings

30% of samples showed intestinal carriage of ESBL-producing Enterobacterales, and 3.4% showed CRE carriage.

Long-read sequencing identified IncL plasmid-mediated spread of the blaOXA-48 gene and blaCTX-M-15 gene amplification.

Non-CP-CRE isolates showed resistance to meropenem and carried multiple copies of the blaCTX-M-15 gene.

Abstract

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.

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.

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 blaOXA-48 (n = 7) or blaNDM-1 (n = 1) genes. The remaining 70.4% (19/27) were non-carbapenemase-producing CRE isolates (non-CP-CRE). The blaOXA-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 blaCTX-M-15 gene along with mutations in porin genes.

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 blaCTX-M-15 gene amplification, demonstrating its added value for antimicrobial resistance monitoring.

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