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A Brief Overview of Bovine Respiratory Disease Sequencing Study

Sherry Agrawal

11/23/2024
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Table 1:Research Activities (Bovine Pathogen Sequencing)_____________________________________________3

Table 2: BRD Tested____________________________________________________________________________4
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Many large-scale genomics projects in progress today relate to sequencing human

genomes, and finding relationships between certain sequences and disease, in addition to creating

large storehouses of genetic data for later research. Most goals of genomic projects relate to

strategies for early detection, prevention, and cures for diseases. However, a lesser-known area

of genomic research is that of farm animals, particularly those that are integral to the national

food supply. By understanding many of the same correlations and sequencing patterns found in

human genomic research, farm animal genomics can foster practices that lead to increased

livestock health and productivity, and the bioengineering of new animal-related technologies.

Additionally, research related to farm-animal genetics proves valuable for humans, as farm

animals are often models for physiological and pathological studies.

A developing area of livestock genomics is that of pathogen sequencing. Specifically, the

Agricultural Research Service (ARS) branch of the United States Department of Agriculture

(USDA) is conducting a genetics study to sequence the respiratory microbiome and virome

associated with Bovine Respiratory Disease (BRD) in beef cattle (Institute for Bovine Research,

2023, p. 31). This disease is one of the most costly and prevalent diseases within the cattle

industry, causing severe respiratory distress that usually results in death. As such, BRD results in

lost revenue for cattle farmers each year. To combat this, in 2021 the ARS began following

specific populations of beef cattle in the US and Ireland to study the microbiome and virome

profiles at various points of time during the animal’s life cycle. Specifically, profiles are

evaluated in calves prior to weaning and again after entering the feedlot, at which time the

animal is most likely to contract BRD. This study will continue through 2022.

Objectives of the study are three-fold; to gather information about the prevalence of

BRD, develop scientific methods to identify the pathogenic agents that cause the disease, and to
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understand the dynamics of secondary infection in cattle that contract the disease a second time,

provided the first infection is survived (United States Department of Agriculture, 2021). These

objectives will help researchers uncover and understand any connections between microbiome

profiles of cattle that develop BRD and those that do not. Consequently, this study has the

potential for large positive impacts to the beef cattle industry. As detailed in Table 1, several

research activities are ongoing, contributing to the understanding of pathogen sequencing in

cattle.

Research Activity URL

Microbiome Cattle Conservation https://mcca.ars.edu

University of Castleberry Bovine Studies https://uc.bovine.edu/research2/?54689

USDA Temple Station (Bovine Unit) https://usda.gov/temple-bovine

Table 1:Research Activities (Bovine Pathogen Sequencing)

The approach of the study includes sampling upper respiratory tracts of calves as they

move from birth to the feedlot. Next, microbiome profiles will be gleaned from the samples

using high-throughput 16S rRNA sequencing, and specific viral pathogens found will be profiled

using qRT-PCR. After the initial sampling, additional upper respiratory tract samples will be

harvested from the same animals at three different points in time, which include pre-breeding,

pre-conditioning, and weaning. As the calves transition to the feedlot after weaning, more

samples will be collected from those who contract BRD, and exhibit symptoms.1 From these sick

animals, viral DNA will be collected using a nasopharyngeal swab, and then extracted and

amplified using standard PCR technologies. This will allow researchers to then extract RNA and

reverse transcribe to determine if any viral pathogens are present. Finally, the microbiomes of

infected animals will be employed to determine if cattle treated for BRD have any different

1
A diagnosis of BRD will be confirmed by attending veterinarians.
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pathogenic profiles as compared to healthy control herds at points in time before weaning and

when diagnosed with BRD.

BRD Tested Number

Independent genome sequences from cattle 103

microbiome

Novel bacteria viruses 188

Antimicrobial-resistant genes found 94

Table 2: BRD Tested

At the completion of the study in 2024, there will hopefully exist a better awareness and

understanding of any genomic factors that contribute to the probability of cattle contracting

Bovine Respiratory Disease. From this information, new and better strategies can be

implemented to reduce contraction of BRD and help to reduce instances of lost revenue from

sick and/or dead cattle. Additionally, cattle populations should benefit from insights gleaned

from this study, as better practices can be put in place to provide for healthier cattle.
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References

Institute for Bovine Research. (2023, October 18). BRD and Cattle: What You Should Know.

Agriculture Today, pp. 26-34.

United States Department of Agriculture. (2021, July 15). Recent advances in sequencing

technologies to characterize the respiratory microbiome and virome associated with

Bovine Respiratory Disease. Retrieved from USDA Agricultural Research Service:

https://www.ars.usda.gov/research/project/?accnNO=435841
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B P

Bovine Respiratory Disease, 1, 3, 5, 6 pathogen, 3, 4

genomics, 3