Enrofloxacin treatment alters cecal microbiota and metabolites and selects for fluoroquinolone-resistant Campylobacter jejuni in chickens

ABSTRACT Campylobacter is a leading cause of foodborne illness and is commonly present in the poultry gut. Fluoroquinolone (FQ)-resistant Campylobacter quickly emerges in chickens infected with FQ-susceptible Campylobacter and treated with an FQ antibiotic via drinking water due to selection and expansion of FQ-resistant mutants. However, it is unclear whether FQ treatment alters the gut microbiota and metabolome, and consequently provides a favorable environment for FQ-resistant Campylobacter to rapidly expand in the intestine. Here, we investigated cecal microbiota and metabolome profiles of broiler chickens infected with Campylobacter jejuni and treated with enrofloxacin (ENRO). Although ENRO treatment initially reduced Campylobacter colonization, rapid selection and expansion of FQ-resistant C. jejuni mutants followed in treated birds. 16S rRNA gene sequencing revealed significant decreases in the relative abundance of phylum Actinobacteriota and several genera, including Proteus , Blautia , Romboutsia , Erysipelotrichaceae_uncultured , Candidatus_Arthromitus , Weissella , Butyricicoccus , and Clostridia _ vadinBB60_group , in ENRO-treated birds. Untargeted metabolomics analyses indicated notable differences in amino acid, lipid, carbohydrate, cofactor, vitamin, and xenobiotic metabolites between ENRO-treated and control groups. Interestingly, the ENRO-treated group had a significantly higher concentration of phenethylamine. Correlation analysis found several significantly correlated pairs of bacterial taxa and metabolomic features. These results indicate that gut microbiota diversity, composition, and metabolites were significantly altered by ENRO treatment, which may facilitate the rapid propagation of FQ-resistant Campylobacter in the chicken gut. Future studies are needed to identify specific microbiota members and metabolites linked to the emergence and proliferation of FQ resistance, ultimately aiding the development of antibiotic resistance mitigation strategies. IMPORTANCE Campylobacter is a major foodborne bacterium often linked to poultry, and antibiotic-resistant strains can make infections harder to treat. This study shows that treating chickens with enrofloxacin, an antibiotic in the fluoroquinolone family, quickly selected for resistant Campylobacter and also changed the gut bacterial community and chemical makeup of the chicken intestine. These changes may help resistant Campylobacter grow and persist after treatment. By linking antibiotic treatment with changes in gut bacteria and metabolites, this work provides a broader view of how antimicrobial use can unintentionally promote resistance in food animals. The findings highlight the need to consider the whole gut environment when designing strategies to limit antibiotic resistance and improve poultry-related food safety.