Uncovering hidden Campylobacter diversity in wild birds: a genomic comparison of free-living birds and wildlife rehabilitation centre residents reveals differences in virulence and antimicrobial resistance profiles

Abstract

Campylobacter spp. are among the leading causes of bacterial gastroenteritis worldwide and are commonly associated with poultry reservoirs. Although wild birds are frequently implicated in the environmental dissemination of Campylobacter , their actual epidemiological role remains poorly understood, particularly in relation to anthropogenic exposure and wildlife rehabilitation settings. In this study, 387 wild birds representing both strictly free-living populations and individuals admitted to wildlife rehabilitation centres were examined to assess the occurrence, genomic diversity, virulence-associated genes, antimicrobial resistance (AMR) determinants, and phylogenetic relationships of Campylobacter isolates. The overall prevalence reached 4.1% (16/387), with a markedly lower prevalence among free-living birds (1.0%; 3/315) compared with birds originating from wildlife rehabilitation centres (18.1%; 13/72, p  < 0.001). A total of 16 Campylobacter isolates underwent genomic characterisation. C. jejuni predominated (62.5%), while C. coli accounted for 37.5% of isolates. Virulence-associated genes linked to motility and adhesion, including flaA , flaB , flaC , and cadF , were highly conserved and detected in all isolates, whereas the complete cdtABC operon occurred in 37.5% of strains and was restricted to wildlife rehabilitation-derived C. jejuni . Type IV and type VI secretion system-associated genes were detected sporadically. Phylogenetic analysis revealed the presence of lineages previously associated with poultry, livestock, environmental, and human-derived Campylobacter , including CC-179 and CC-828. Phenotypic resistance to ciprofloxacin (37.5%) and tetracycline (25.0%) was detected exclusively among wildlife rehabilitation-derived isolates and was fully concordant with genotypic determinants, including the gyrA T86I mutation and the tet(O) gene. In contrast, all isolates remained susceptible to erythromycin and gentamicin. These findings suggest that Campylobacter occurrence, virulence profiles, and antimicrobial resistance patterns in wild birds may be associated with ecological context and anthropogenic exposure. The markedly higher prevalence and resistance burden observed among rehabilitation-associated birds indicate that wildlife rehabilitation centres may represent important interfaces where Campylobacter strains of diverse origins converge, rather than representing baseline wildlife health. In contrast, strictly free-living bird populations exhibited low carriage rates and limited resistance profiles, indicating that their role as major reservoirs for poultry-associated campylobacteriosis may be less prominent than previously assumed.