Investigating Effects of Tulathromycin Metaphylaxis on the Fecal Resistome and Microbiome of Commercial Feedlot Cattle Early in the Feeding Period.

Enrique Doster,Paul S Morley,Christopher J Dean,Kenneth I Jones,Xiang Yang,Lyndsey Linke,Jamie Ruiz,Brandy A Burgess,Pablo Rovira,Roberta Magnuson,Margaret D Weinroth,Christina Boucher,Steven M Lakin,Noelle R Noyes,Keith E Belk

doi:10.3389/fmicb.2018.01715

Abstract

The objective was to examine effects of treating commercial beef feedlot cattle with therapeutic doses of tulathromycin, a macrolide antimicrobial drug, on changes in the fecal resistome and microbiome using shotgun metagenomic sequencing. Two pens of cattle were used, with all cattle in one pen receiving metaphylaxis treatment (800 mg subcutaneous tulathromycin) at arrival to the feedlot, and all cattle in the other pen remaining unexposed to parenteral antibiotics throughout the study period. Fecal samples were collected from 15 selected cattle in each group just prior to treatment (Day 1), and again 11 days later (Day 11). Shotgun sequencing was performed on isolated metagenomic DNA, and reads were aligned to a resistance and a taxonomic database to identify alignments to antimicrobial resistance (AMR) gene accessions and microbiome content. Overall, we identified AMR genes accessions encompassing 9 classes of AMR drugs and encoding 24 unique AMR mechanisms. Statistical analysis was used to identify differences in the resistome and microbiome between the untreated and treated groups at both timepoints, as well as over time. Based on composition and ordination analyses, the resistome and microbiome were not significantly different between the two groups on Day 1 or on Day 11. However, both the resistome and microbiome changed significantly between these two sampling dates. These results indicate that the transition into the feedlot—and associated changes in diet, geography, conspecific exposure, and environment—may exert a greater influence over the fecal resistome and microbiome of feedlot cattle than common metaphylactic antimicrobial drug treatment.

Highlights

One of the most critical periods in managing the health and wellbeing of beef cattle is when they are transitioned from less intensive production settings, such as pasture or backgrounding operations, to feedlots
Results of this study suggest that parenteral metaphylactic treatment of cattle with tulathromycin had minimal, if any, detectable short-term impact on the fecal resistome and microbiome of commercially raised feedlot cattle when evaluated using shotgun metagenomic sequencing
This is important because of critical concerns about public health in relation to antimicrobial drugs (AMDs) use in food-producing animals and because this is an important drug for treatment and control of life-threatening respiratory disease in feedlot cattle

Summary

Introduction

One of the most critical periods in managing the health and wellbeing of beef cattle is when they are transitioned from less intensive production settings, such as pasture or backgrounding operations, to feedlots. During this transition, animals are exposed to varied stressors associated with handling, transport, processing, commingling, and a shift to a high-energy feedlot diet (Sanderson et al, 2008). Treatment of animals with AMDs, especially mass treatment regimens, are subject to increasing concern and scrutiny because of the potential for public health impacts related to antimicrobial resistance in bacteria that may be transferred to consumers through the food chain or environmental routes

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