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ORIGINAL RESEARCH article

Front. Microbiol.
Sec. Antimicrobials, Resistance and Chemotherapy
Volume 16 - 2025 | doi: 10.3389/fmicb.2025.1540210

A One Health approach for the genomic characterization of antibioticresistant Campylobacter isolates using Nanopore whole-genome sequencing

Provisionally accepted
Ana Hurtado Ana Hurtado 1*Medelin Ocejo Medelin Ocejo 1Beatriz Alda Oporto Beatriz Alda Oporto 1José Luis Lavín José Luis Lavín 2Ruth Rodríguez Ruth Rodríguez 3María Ángeles Marco María Ángeles Marco 3Mikel Urrutikoetxea-Gutiérrez Mikel Urrutikoetxea-Gutiérrez 4Miriam Alkorta Miriam Alkorta 5José María Marimon José María Marimon 5
  • 1 Animal Health Department, NEIKER Basque Institute for Agricultural Research and Development, Bilbao, Basque Country, Spain
  • 2 Applied Mathematics Department, NEIKER Basque Institute for Agricultural Research and Development, Bilbao, Basque Country, Spain
  • 3 Laboratorio de Salud Pública de Gipuzkoa, Donostia-San Sebastián, Spain
  • 4 Biobizkaia Health Research Institute, Barakaldo, Spain
  • 5 Biogipuzkoa Health Research Institute, Donostia-San Sebastian, Spain

The final, formatted version of the article will be published soon.

    In response to the growing threat posed by the spread of antimicrobial resistance in zoonotic Campylobacter, a One-Health approach was used to examine the genomic diversity, phylogenomic relationships and the distribution of genetic determinants of resistance (GDR) in C. jejuni and C. coli isolates from humans, animals (ruminants, swine, chickens), and avian food products collected during a regionally (Basque Country, Spain) and temporally (mostly 2021-2022) restricted sampling. Eighty-three C. jejuni and 71 C. coli isolates, most exhibiting resistance to ciprofloxacin and/or erythromycin, were whole-genome sequenced using Oxford-Nanopore Technologies long-fragment sequencing (ONT). MLST analysis identified a high genomic diversity among isolates. Phylogenomic analysis showed that clustering based on the core genome was aligned with MLST profiles, regardless of the sample source. In contrast, accessory genome content sometimes discriminated isolates within the same ST, and occasionally differentiated isolates from different sources. Most of the identified GDRs were present in isolates from different sources and a good correlation was observed between GDR distribution and phenotypic susceptibility profiles (based on minimum inhibitory concentrations interpreted according to the EUCAST epidemiological cut-off values). Genotypic resistance profiles were independent of genotypes, indicating no apparent association between resistance and phylogenetic origin. This study demonstrates that ONT sequencing is a powerful tool for molecular surveillance of bacterial pathogens in the One Health framework.

    Keywords: Campylobacter jejuni, Campylobacter coli, Antimicrobial resistance (AMR), Wholegenome sequencing (WGS), Nanopore long-fragment sequencing, One Health, pangenome, resistome

    Received: 05 Dec 2024; Accepted: 02 Jan 2025.

    Copyright: © 2025 Hurtado, Ocejo, Oporto, Lavín, Rodríguez, Marco, Urrutikoetxea-Gutiérrez, Alkorta and Marimon. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence: Ana Hurtado, Animal Health Department, NEIKER Basque Institute for Agricultural Research and Development, Bilbao, Basque Country, Spain

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