Campylobacter has been the most commonly reported cause of bacterial diarrheal disease in humans in the European Union since 2005. Most broiler batches at slaughter are colonized with Campylobacter, and the major source of infection is contaminated poultry meat. The aim of this study was to characterize a selection of Campylobacter jejuni and Campylobacter coli isolates from broilers through whole-genome sequencing (WGS). A total of 16 isolates (C. jejuni = 12 and C. coli = 4) from five broiler farms from Catalonia (northeastern Spain) were analyzed. A phylogenetic analysis based on 8420 single-nucleotide polymorphisms showed two main cluster grouping strains by species. Phenotypic resistances to quinolones (100%), tetracycline (81%), streptomycin (75%), erythromycin (56%), and gentamicin (13%) were found. All the isolates carried the C257T point mutation in the subunit A of the DNA gyrase gene (Thr86Ile) conferring resistance to quinolones, while all the isolates showing resistance to tetracycline carried the tet(O) gene. The genes aph(3′)-III and aadE conferring resistance to aminoglycosides were identified in the two isolates (one C. jejuni and one C. coli) resistant to streptomycin and gentamicin. The point mutation A2075G on the 23S rDNA conferring high resistance to macrolides was detected in three C. coli isolates. The CmeABC multidrug efflux pump was also detected, both in C. jejuni and C. coli isolates. All C. jejuni and C. coli isolates were positive for most of the 34 virulence-associated genes studied related to motility, chemotaxis, adhesion, and invasion. Interestingly, the wlaN gene involved in the Guillain–Barré syndrome was found in two isolates. The results underline the power of WGS for investigation of virulence, clonality, and antimicrobial resistance in Campylobacter.

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