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

Abstract

16The increasing concerns with antimicrobial resistance highlights the need for studies 17 evaluating the impacts of antimicrobial use in livestock on antimicrobial resistance using new 18 sequencing technologies. Through shotgun sequencing, we investigated the changes in the fecal 19 microbiome composition and function, with a focus on functions related to antimicrobial 20 resistance, of dairy calves. Heifers 2 to 3 weeks old, which were not treated with antibiotics by the 21 farm before enrollment, were randomly allocated to one of three study groups: control (no 22 treatment), enrofloxacin, or tulathromycin. Fecal samples were collected at days 4, 14, 56 and 112 23 days after enrollment, and DNA extraction and sample preparation and sequencing was conducted. 2 24 The effect of antibiotic treatment on each taxon and functional level by time (including Day 0 as 25 a covariate) revealed few changes in the microbiota. At the genus level, enrofloxacin group had 26 higher abundance of Blautia, Coprococcus and Desulfovibrio and lower abundance of Bacteroides 27when compared to other treatment groups. The SEED database was used for functional analyses, 28 which showed that calves in the enrofloxacin group started with a higher abundance of "Resistance 29 to antibiotics and toxic compounds" function on Day 0, however an increase in antibiotic resistance 30 genes after treatment with enrofloxacin was not observed. "Resistance to Fluoroquinolones" and 31 "Erythromycin resistance", of relevance given the study groups, were not statistically different in 32 abundance between treatment groups. "Resistance to fluoroquinolones" increased during the study 33 period regardless of treatment group. Despite small differences over the first weeks between 34 treatment groups, at Day 112 the microbiota composition and functional profile was similar among 35 all study groups. These findings show that metaphylaxis treatment of dairy calves with either 36 enrofloxacin or tulathromycin have minimal impacts on the microbial composition and functional 37 microbiota of dairy calves over time. 38 39 40 42 45and resistance genes are present even in places that were never inhabited by humans [3,4] and in 46 wild animals [5]. However, the use of antibiotics in human and animal medicine, as well as in plant 3 47 agriculture and animal production systems, has resulted in an acceleration in the selection and 48 spread of antimicrobial resistance [1,6]. Antimicrobial resistant enteric bacteria can be transmitted 49 from livestock to humans through the fecal-oral route, or contamination in the food chain and 50 environment [1,7,8]. Together with prevention of disease and infectious agent transmission, the 51 prudent use of antibiotics is extremely important to preserve treatment effectiveness and decrease 52 the dissemination of resistant bacteria. 53Antimicrobials may be used to control and prevent the spread of the disease in production 54 animals at high risk of developing a bacterial infectious disease. This practice is referred to as 55 metaph...