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

Sep 30, 2026

Increasing resistance to broad-spectrum beta-lactams and carbapenems poses a major challenge in healthcare. This study assessed how often ESBL-producing and carbapenem-resistant Enterobacterales (CRE) were carried in a tertiary hospital and tested whether long-read sequencing improves CRE surveillance. Stool and rectal samples from hospitalized patients were cultured and CRE isolates were characterized using susceptibility testing and whole-genome approaches. Results showed a 30% ESBL carriage rate and CRE carriage of 3.4%, with IncL plasmids driving dissemination of blaOXA-48 and blaCTX-M-15 amplification.

LanguageEnglish

CategoryHealthcare

FormatPDF

Pages13

Reading Time33 min

AccessFree to download

Background

Methods

Results

Conclusions

Introduction

Materials and methods

Samples, culture, species identification and antimicrobial susceptibility testing

JAC Antimicrob Resist [https://doi.org/10.1093/jacamr/dlaf254](https://doi.org/10.1093/jacamr/dlaf254) JACAntimicrobial Resistance IncL plasmid-mediated dissemination of OXA-48 β-lactamase and blaCTX-M-15 gene amplification identified via long-read sequencing in carbapenem-resistant Enterobacterales Suhanya Prasad1, Barbora Dratvova1, Anezka Gryndlerova1, Marie Brajerova1, Petra Kabelikova1, Jan Tkadlec1, Pavel Drevinek1 and Marcela Krutova 1* 1Department of Medical Microbiology, Second Faculty of Medicine, Charles University, and Motol University Hospital, V Uvalu 84, Praha 5, Prague 150 06, Czech Republic *Corresponding [author. E-mail: marcela.krutova@lfmotol.cuni.cz](author. E-mail: marcela.krutova@lfmotol.cuni.cz) Received 1 September 2025; accepted 12 December 2025 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 carbapenemaseproducing 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 Tn 1999.2 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. 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 blaCTX-M-15 gene amplification, demonstrating its added value for antimicrobial resistance monitoring. Introduction Increasing resistance to broad-spectrum beta-lactams and carbapenems is a significant concern in healthcare settings. In addition, carbapenem-resistant Enterobacterales (CRE) infections are associated with high morbidity and mortality, particularly in patients with comorbidities, and treatment options remain severely limited.1,2 Carbapenem resistance in Enterobacterales is primarily mediated by plasmid-encoded carbapenemase enzymes, which enable their rapid spread among bacterial species. These plasmids often co-carry additional antimicrobial resistance genes, contributing to multidrug resistance against cephalosporins, aminoglycosides, sulphonamides, and quinolones.3–5 Non-carbapenemase-producing CRE (non-CP-CRE) typically develop resistance through alternative mechanisms, such asporin inactivation and efflux pump overexpression, which reduce antibiotic concentration in the periplasmic space.6 Although extended-spectrum β-lactamases (ESBLs) do not confer carbapenem resistance directly, growing evidence indicates that increased gene copy number, particularly in combination with porin loss, can contribute to reduced susceptibility

FAQs

What was the main goal of the study?

The study aimed to determine the prevalence of intestinal carriage of ESBL-producing Enterobacterales and CRE in a tertiary care hospital and to evaluate long-read sequencing for carbapenem resistance surveillance.

How were samples collected and analyzed in 2021?

Stool samples and rectal swabs from hospitalized patients were enriched and cultured on selective chromogenic media to detect ESBL and CRE carriage, followed by characterization of CRE isolates using antimicrobial susceptibility testing and sequencing.

What were the key carriage prevalence findings for ESBL and CRE?

Among 794 patient samples, ESBL-producing Enterobacterales were detected at 30%. CRE carriage prevalence was 3.4%, based on isolates confirmed as carbapenem-resistant.

Sep 30, 2026

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