Grad Student Competition
Aggregate sampling to detect pathogens and antimicrobial resistance genes associated with bovine respiratory disease in US feedlots: A Pilot Study
| Date/Time: |
9/12/2025
08:30
|
| Author: |
Erin Jobman |
| Clinic: |
PAC/University of Illinois |
| City, State, ZIP: |
Blue Hill, NE 68930 |
Erin Jobman, DVM, MPH
1
;
Brian Vander Ley, DVM, PhD, DACPVM
2
;
John Dustin Loy, DVM, PhD, DACVM
2
;
Duan Sriyotee Loy, DVM, PhD
2
;
Nathan Meyer, MS, MBA, PhD, DVM
3
;
Dan Thomson, PhD, DVM
4
;
James Lowe, DVM, MS, DABVP
1
;
Shane Terrell, DVM, PhD
4
;
1Department of Veterinary Clinical Medicine, University of Illinois Urbana-Champaign, 2001 S. Lincoln Ave., Urbana, IL 61802
2School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, 1880 N 42 St., Lincoln, NE 68583
3Boehringer Ingelheim Animal Health USA, 3239 Satellite Blvd NW, Duluth, GA 30096
4Production Animal Consultation, 307 S. Main, Scott City, KS, 67871
Introduction:
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 tank as an aggregate sample substrate in pens of confined cattle.
Materials and methods:
Ten pens from two US commercial feedlots were enrolled in an observational pilot study. Five pens were sampled at each site; the same pens were sampled 10 times. All pens were of similar size and utilized identical concrete water tanks. Each pen had its own tank and did not share water sources with adjacent pens.
Two samples were collected at each sampling event including 50 mL of water and a 2x2” absorbent, cotton swab of the tank’s water-air interface. Samples were collected on day zero, while the pen was empty, following cleaning of the tank. Additional samples were collected on day 4, 7, 14, 21, 28, 35, 42, 49, and 56. All samples were subjected to total nucleic acid extraction followed by multiplexed real time quantification polymerase chain reaction (RT-qPCR) assays at the Nebraska Veterinary Diagnostic Center. The assays are designed to detect viruses, bacteria, and antimicrobial resistance genes associated with BRD.
Agreement between the water and swab samples was estimated with the kappa statistic and percent positive agreement. A Bayesian latent class analysis was used to estimate sensitivity and specificity, in this case reflecting the probability of detection, at each sampling event.
Results:
Viral, bacterial, and AMR components of BRD were detected throughout the first 60 days on feed in varying degrees. Visually observed respiratory morbidity was divided post-hoc into three categories: low, moderate, and high for morbidity <15%, 16-30%, and >31% respectively. Viral and bacterial PCR detections differed significantly among morbidity classes (Fisher’s exact p = 0.0139 water; p = 0.0222 swab). AMR gene detections were relatively stable over time. The prevalence of each multiplex component detected varied, thus wide ranges of kappa and PPA are observed. The overall kappa and Percent Positive Agreement were 0.72 and 84.01% among sample substrates.
Detections of viral and bacterial pathogens occurred early in the feeding period (<21 days) as visually observed morbidity increased. Pathogen detections plateaued before decreasing to an undetectable level as the feeding period progressed (>42 days) and morbidity plateaued. AMR genes detected tended to be detected early and remain detected throughout the feeding period. 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.
Significance:
Viruses, bacteria, and antimicrobial resistance genes associated with BRD were successfully detected in the water tanks during the same period of conventional, visual disease detection. Many limitations exist in this pilot study including small sample size, and lack of accounting for potential conditional dependence, seasonal effects, environmental pathogen longevity, and dilution effects within the tank. However, 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.
