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

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.