# Aggregate Sampling to Detect Pathogens and Antimicrobial Resistance Genes Associated with Bovine Respiratory Disease in US Feedlots: A Pilot Study

## TL;DR

This study explores using water trough samples to detect pathogens and antimicrobial resistance genes linked to bovine respiratory disease in cattle feedlots.

## Contribution

The study introduces population-based aggregate sampling via water troughs as a novel non-invasive diagnostic method for bovine respiratory disease.

## Key findings

- Viral and bacterial pathogens associated with bovine respiratory disease were successfully detected in water trough samples.
- Aggregate sampling showed high agreement between water and swab substrates with a kappa of 0.72 and 84.01% positive agreement.
- AMR gene detection remained consistent in sensitivity and specificity throughout the sampling period.

## Abstract

This pilot study investigated a population-based sampling technique to detect pathogens associated with bovine respiratory disease. The US feedlot industry typically manages cattle in groups, at the lot, or pen level; however, current diagnostics reflect individual animals only. Population-based sampling could be advantageous to the cattle industry because it is non-invasive, reduces handling stress, and improves safety for the animals and personnel involved. The primary objective was to investigate the presence of pathogens in water troughs from pens of confined cattle. Viruses, bacteria, and antimicrobial resistance genes associated with bovine respiratory disease were successfully detected in the water tanks during the same period of conventional visual disease detection. These findings provide a foundation for population-based testing to better manage current bovine disease challenges and could be pivotal in the detection of emerging diseases.

Bovine respiratory disease (BRD) is the leading cause of feedlot morbidity and mortality. Field diagnosis is often limited to visual examination as available diagnostics reflect individual animals only and require labor, animal restraint, and time. Aggregate sampling techniques are valuable tools in other species but are lacking in the beef industry. This pilot study investigates the plausibility of using the water trough as an aggregate sample substrate in pens of confined cattle. Water and swab substrates from ten water tanks were collected at ten sampling events. Samples were subjected to a multiplex PCR to detect viruses, bacteria, and antimicrobial resistance (AMR) genes associated with BRD. Viral and bacterial PCR detections differed significantly among morbidity classes (Fisher’s exact p = 0.0139 water; p = 0.0222 swab). The overall kappa and Percent Positive Agreement were 0.72 and 84.01% among sample substrates. Bayesian latent class analysis was used to estimate the probability of detection. Viral and bacterial organisms reached peak sensitivity (21–79%) on days 4–21 and peak specificity (44–79%) on days 42–56. All AMR genes’ sensitivity and specificity remained relatively constant throughout the sampling period.