Resistance to tetracyclines and fluoroquinolones reaches rates higher than 50% in many parts of Europe, while resistance to macrolides is lower and generally more prevalent in C. A particular concern is its resistance to the antimicrobial agents of choice (macrolides for laboratory-confirmed cases and fluoroquinolones for cases of diarrhoea), which compromises the therapeutic efficacy 8, 9. However, antimicrobial resistance (AMR) is increasing globally at an alarming rate in Campylobacter from human and animal sources, resistance rates being usually higher in C. Antimicrobial therapy is only recommended in systemic and severe Campylobacter infections or immunocompromised patients. Campylobacter is highly prevalent in ruminants worldwide and the Basque Country (northern Spain) 3, 4, 5, and there is increasing evidence of the significant contribution of ruminant Campylobacter to human campylobacteriosis 6, 7. Both species asymptomatically colonise the intestinal tract of a wide range of wild and domestic mammals and birds, and livestock constitute a significant source for human infection through consumption of contaminated food and water, or by contact with animals 1. Updated resistance gene databases and detailed analysis of the matched open reading frames are needed to avoid errors when using WGS-based analysis pipelines for AMR detection in the absence of phenotypic data.Д¬ampylobacter is a leading cause of bacterial gastroenteritis throughout the industrialized world, most cases being attributed to infection with Campylobacter jejuni and to a lesser extent with Campylobacter coli 1, 2. coli, describe possible new alleles of bla OXA-61-like genes, and decipher the genetic context of aminoglycoside resistance genes, as well as the plasmid/chromosomal location of the different AMR genes and their implication for resistance spread. Detailed sequence analysis allowed us to detect the recently described mosaic tet(O/M/O) gene in one C. A high correlation was observed between phenotypic resistance to a given antimicrobial and the presence of the corresponding known resistance genes. Resistance genotypes were identified by screening assembled sequences with BLASTn and ABRicate, and additional sequence alignments were performed to search for frameshift mutations and gene modifications. Genome analysis showed extensive genetic diversity that clearly separated both species. Considering the significant contribution of ruminants as reservoirs of resistant Campylobacter, Illumina whole-genome sequencing was used to characterise the mechanisms of AMR in Campylobacter jejuni and Campylobacter coli recovered from beef cattle, dairy cattle, and sheep in northern Spain. Campylobacter, a leading cause of gastroenteritis in humans, asymptomatically colonises the intestinal tract of a wide range of animals.Although antimicrobial treatment is restricted to severe cases, the increase of antimicrobial resistance (AMR) is a concern.

N gene sequence snapgene viewer