Metagenomic analysis of antibiotic resistant bacteria and antibiotic resistance genes in koi carp, cultivated carp and wild carp

This study aims to provide detailed insights into the disparities of resistant bacteria and resistance genes found in the intestines of wild carp, cultivated carp, and koi carp through metagenomic analysis. By characterizing antibiotic-resistant bacteria and resistance genes in samples from major aquaculture producing countries worldwide, we have discovered that cultivated carp and koi carp exhibit a higher abundance and prevalence of resistant bacteria and resistance genes compared to their wild counterparts. Spearman correlation analysis revealed a richer co-occurrence relationship between resistant bacteria and resistance genes in the intestines of koi. Notably, the genes tetD and Aeromonas genus were identified as potential key resistance genes and resistant bacteria, respectively, within the koi carp gastrointestinal tract. A correlation was established between the intestinal samples and the aquaculture water samples in terms of resistant bacteria and resistance genes. This suggests that resistance genes in the intestines of cultivated fish may likely transfer to the surrounding water through mechanisms such as defecation and feeding, thereby increasing the risk of their dissemination in the aquatic environment.