Abstract
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), a single treatment of enrofloxacin, or a single treatment of tulathromycin. Fecal samples were collected at days 4, 14, 56 and 112 days after enrollment, and DNA extraction and sequencing was conducted. The effect of antibiotic treatment on each taxon and genetic functional level by time (including Day 0 as a covariate) revealed few changes in the microbiota. At the genus level, enrofloxacin group had higher relative abundance of Blautia, Coprococcus and Desulfovibrio and lower abundance of Bacteroides when compared to other study groups. The SEED database was used for genetic functional analyses, which showed that calves in the enrofloxacin group started with a higher relative 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 relative abundance between study groups. “Resistance to fluoroquinolones” increased during the study period regardless of study group. Despite small differences over the first weeks between study groups, at Day 112 the microbiota composition and genetic functional profile was similar among all study groups. In our study, enrofloxacin or tulathromycin had minimal impacts on the microbial composition and genetic functional microbiota of calves over the study period.
Highlights
There is urgent need for the judicious use of antimicrobial drugs to extend the effectiveness of currently available therapies [1,2]
We focused on enrofloxacin and tulathromycin, a fluoroquinolone and a macrolide, respectively
The farm was selected because preventive antimicrobial treatment was indicated based on a prior history of calfhood respiratory disease identified by the herd veterinarian, as well as conditions that resulted in calves being at high risk of developing bovine respiratory disease (BRD), warranting use of antibiotic for control of BRD as per drug label
Summary
There is urgent need for the judicious use of antimicrobial drugs to extend the effectiveness of currently available therapies [1,2]. Antimicrobials may be used to control and prevent the spread of the disease in production animals at high risk of developing a bacterial infectious disease. This practice is referred to as metaphylaxis. In the United States, several drugs are approved for this use in cattle, including in dairy calves, at risk of bovine respiratory disease (BRD). In 2014 in the United States 12% of pre-weaned calves were affected with respiratory disease and almost 95% of those were treated with antimicrobial drugs [11]. We focused on enrofloxacin and tulathromycin, a fluoroquinolone and a macrolide, respectively These are injectable, single dose antimicrobials, labeled for treatment and control of BRD
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