Detection of extended-spectrum beta-lactamase (ESBL)-producing Klebsiella pneumoniae in samples from meat rabbits

Vanessa Silva; Adriana Silva; Manuela Caniça; Rani Rivière; Patrícia Poeta; Gilberto Igrejas

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Detection of extended-spectrum beta-lactamase (ESBL)-producing Klebsiella pneumoniae in samples from meat rabbits

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¹ LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
² Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
³ Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
⁴ Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
⁵ Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisboa, Lisboa, 2829-516 Caparica, Portugal
⁶ National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections (NRL-AMR/HAI), Department of Infectious Diseases, National Institute of Health Dr Ricardo Jorge, Av. Padre Cruz, 1649-016, Lisbon, Portugal
⁷ Centre for the Studies of Animal Science, Institute of Agrarian and Agri-Food Sciences and Technologies, Oporto University, 4049-021 Porto, Portugal
⁸ CECAV-Veterinary and Animal Research Centre, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal
⁹ Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
¹⁰ Department of Genetics and Biotechnology, Functional Genomics and Proteomics' Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal

Academic Editor: Marc Maresca

Published: 19 May 2025 by MDPI in The 4th International Electronic Conference on Antibiotics session Antibiotics and One Health

Abstract:

Klebsiella pneumoniae is an opportunistic pathogen that can acquire multiple antimicrobial resistance mechanisms. The presence of multidrug-resistant K. pneumoniae in food-producing animals raises concerns about its potential role in the dissemination of resistance genes. This study aimed to investigate the occurrence of K. pneumoniae in healthy meat rabbits and characterize its antimicrobial resistance and virulence profiles.

A total of 295 fecal samples were collected from 20 rabbit farms in northern Portugal. Samples were incubated in BHI broth and plated on Chromocult Coliform Agar with cefotaxime (2 µg/mL). Pink colonies were subcultured on BHI agar and identified by MALDI-TOF MS. Antimicrobial susceptibility was assessed by the Kirby–Bauer method, and whole-genome sequencing was performed to detect resistance and virulence genes, as well as clonal lineages.

Out of the 295 samples, only 6 (2%) ESBL-producing K. pneumoniae were isolated. All isolates were multidrug-resistant, as they were resistant to at least three classes of antibiotics. All isolates carried ESBL-related genes, including bla_TEM-1(5/6), bla_CTX-M-15 (2/6), and bla_SHV variants (bla_SHV-1, bla_SHV-28, bla_SHV-38, bla_SHV-61), as well as bla_OXA-1 in two isolates. Genes associated with aminoglycoside resistance were identified in all isolates, such as aph(3'')-Ib, aph(6)-Id, and aac(3)-IIe/IVa. Tetracycline resistance was mainly mediated by tet(A) and tet(D), while sulfonamide resistance was conferred by sul1 and sul2. Among fluoroquinolone resistance genes, qnrB1 and qnrS1 were detected. The fosA gene, conferring resistance to fosfomycin, was also present. Genes associated with heavy-metal resistance (sil and pco) were found in all isolates. All isolates carried regulators such as ramA, marA, and baeR, which modulate efflux pump. Isolates were ascribed to ST307, ST45, ST193, and ST2026.

These findings reinforce the need for the continuous monitoring of antimicrobial resistance in K. pneumoniae from food-producing animals, as their potential role in the spread of resistance genes poses a risk to public health.

Keywords: Klebsiella pneumoniae; rabbits; antimicrobial resistance; whole-genome sequencing

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