Phenotypic and whole genome characterization of multidrug-resistant Campylobacter coli from chicken liver

Campilobacteriosis is the most frequently reported zoonosis in the European Union. Poultry and poultry products are the primary sources of human infection. The high occurrence of antibiotic-resistant (AR) Campylobacter strains is particularly concerning, as it complicates treatment and poses a serious public health threat. Therefore, this study assessed the prevalence of AR C. coli recovered from the gut and liver of broiler chickens from northeastern Spain. Using the broth microdilution method and whole genome sequencing (WGS) with Illumina HiSeq, the AR of 40 C. coli strains (n = 18 from liver; n = 22 from gut) was assessed. Phenotypically, all isolates were resistant to ciprofloxacin (100%), followed by tetracycline (95%), while co-resistance to both constituted the most prevalent profile (25%). Moderate to high resistance frequencies were observed to erythromycin (53%), ertapenem (28%) and gentamicin (23%). Overall, 70% of the isolates showed a multidrug resistant (MDR) phenotype. The origin of the strain (caeca or liver) did not influence the occurrence of AR. WGS revealed that all isolates harbored the gyrA T86I mutation conferring ciprofloxacin resistance while most tetracycline-resistant isolates (80%) carried the tet(O) gene. Macrolide-resistant isolates either exhibited a point mutation in the 23S rDNA or the 50S ribosomal L22 protein gene, or harbored ermB and erm(53) genes. BlaOXA genes were present in 72.5% of the ertapenem-resistant strains; however, ertapenem-specific resistance was not identified and might involve the CmeABC efflux pump with certain blaOXA genes. Among gentamicin resistant strains, 78% harbored the aph(2″) gene conferring resistance to this antibiotic. All isolates carried genes coding for the CmeABC and CmeDEF efflux pumps conferring unspecific AR. Overall, a strong concordance between phenotypes and genotypes was seen, with WGS analysis also revealing additional putative resistance determinants and predicting 92.5% MDR strains. This study highlights the potential risk of chickens and chicken livers as a source of AR C. coli and emphasizes WGS as a valuable tool providing significant additional information on the AR potential of C. coli isolates.