Analysis on dynamics in the fecal microbiome and antibiotic resistance genes in rainbow trout (Oncorhynchus mykiss) treated with antibiotics

Abstract

In aquaculture, the secretions of cultured organisms contribute to the development of aquatic antibiotic resistance. However, the impacts of antibiotic treatment on fish feces remain poorly understood. This study aimed to assess the changes and restoration of the fecal microbiome in rainbow trout (Oncorhynchus mykiss) upon antibiotic treatment. Groups of five fish were orally administered diets supplemented with oxytetracycline (OTC; 75 mg/kg of body weight/day) or sulfadiazine/trimethoprim (SDZ/TMP; 30 mg/kg of body weight/day) for 10 consecutive days, followed by a 25-day withdrawal period. Fecal samples were collected before antibiotic treatment (day 0), and at 1, 3, 7, and 10 days post antibiotic administration (dpa), as well as 1, 3, 7, 14, and 25 days post antibiotic cessation (dpc). The fecal microbiome community was profiled using both culture-dependent and -independent methods employing the Illumina iSeq system. The relative abundance of antibiotic resistance genes (ARGs) and the class 1 integron-integrase gene (intI1) in the feces were quantified using real-time PCR. The correlation between ARGs, intI1, and the fecal microbiome was analyzed. The result demonstrated that antibiotic treatment significantly reduced the number of cultured bacteria in the feces. Importantly, antibiotic treatment disrupted the fecal microbial communities, and this alteration persisted even after antibiotic cessation. Moreover, OTC treatment increased the relative abundance of tetracycline resistance genes, while sulfonamide and trimethoprim resistance genes increased in the SDZ/TMP-treated group. Notably, Flavobacterium, Pseudomonas, and Streptococcus exhibited a significant correlation with the abundance of ARGs, suggesting their potential role as carriers for ARGs. In conclusion, this study demonstrates that the fecal microbiome of rainbow trout was affected by antibiotic selection pressure, leading to a substantial shift in microbial composition and diversity. Additionally, the co-occurrence of horizontal gene transfer (HGT) and the proliferation of specific bacterial populations positively correlated with ARGs, contributing to the increased abundance of ARGs in the feces. These findings highlight the potential of fish feces to serve as a reservoir of antibiotic resistance in aquaculture systems, while also providing a non-invasive approach to predict changes in the fish gut microbiome and resistome.