Effects of treatment with enrofloxacin or tulathromycin on fecal microbiota composition and function of dairy calves

The increasing concerns with antimicrobial resistance highlights the need for studies evaluating the impacts of antimicrobial use in livestock on antimicrobial resistance using new sequencing technologies. Through shotgun sequencing, we investigated the changes in the fecal microbiome composition and function, with a focus on functions related to antimicrobial resistance, of dairy calves. Heifers 2 to 3 weeks old, which were not treated with antibiotics by the farm before enrollment, were randomly allocated to one of three study groups: control (no treatment), enrofloxacin, or tulathromycin. Fecal samples were collected at days 4, 14, 56 and 112 days after enrollment, and DNA extraction and sample preparation and sequencing was conducted. The effect of antibiotic treatment on each taxon and functional level by time (including Day 0 as a covariate) revealed few changes in the microbiota. At the genus level, enrofloxacin group had higher abundance of Blautia, Coprococcus and Desulfovibrio and lower abundance of Bacteroides when compared to other treatment groups. The SEED database was used for functional analyses, which showed that calves in the enrofloxacin group started with a higher abundance of \"Resistance to antibiotics and toxic compounds\" function on Day 0, however an increase in antibiotic resistance genes after treatment with enrofloxacin was not observed. \"Resistance to Fluoroquinolones\" and \"Erythromycin resistance\", of relevance given the study groups, were not statistically different in abundance between treatment groups. \"Resistance to fluoroquinolones\" increased during the study period regardless of treatment group. Despite small differences over the first weeks between treatment groups, at Day 112 the microbiota composition and functional profile was similar among all study groups. These findings show that metaphylaxis treatment of dairy calves with either enrofloxacin or tulathromycin have minimal impacts on the microbial composition and functional microbiota of dairy calves over time.