In pork production, we often focus on epidemic disease agents, such as Porcine Reproductive and Respiratory Syndrome (PRRS), Porcine Epidemic Diarrhea (PED), or the threat of foreign animal diseases like African Swine Fever. Lurking behind these headline-grabbing viral challenges are endemic bacterial agents such as Streptococcus suis or Glaesserella parasuis. These bacteria might not make the nightly news, but they’re commonly found in pigs’ respiratory tracts, where they’re a constant threat to herd health, animal well-being and performance potential.
A relatively new technology is helping swine veterinarians and pork producers better control diseases caused by these endemic agents.
Next generation gene sequencing
In the past, veterinarians could only broadly identify and diagnose disease-causing bacteria by culturing samples in the lab. Yet, many of these bacteria were difficult to culture. If they could be cultured, researchers could only identify the agent by species.
Now, next generation sequencing (NGS) can differentiate between strains of bacteria at the genetic level and identify strains that, although related, act differently in the pig or the barn environment.
“Beginning about three years ago, we were able to confirm that different strains have different impacts, and different pig flows carry different strains,” says Dr. Maria Jose Clavijo, a research associate professor at Iowa State University and a health assurance veterinarian with Pig Improvement Company (PIC). “It’s an obvious concept, and it’s what we expected, but we didn’t have the tools or the methodology to characterize the differences before next generation sequencing became available.”
By differentiating strains, veterinarians can precisely select antibiotics, vaccines and management strategies. Such accurate identification of a bacterial strain helps veterinarians and producers implement the best possible disease management protocols to control the pathogen.
The triple threat to pig health
While accurate identification of bacteria strains is crucial to managing endemic diseases, the pathogen is only one of the three factors creating a risk of disease outbreak. Jose Clavijo refers to the triple threat to pig health as “the epidemiological triad,” which includes the pathogen, the host animal and the barn environment.
“It’s the interaction between all three that you need to be aware of to better control endemic disease,” Jose Clavijo says. “You need to understand the pathogen. You need to understand the susceptibilities of the pig, including potential co-infections. And, you need to understand environmental factors like humidity, temperature, comingling pigs and more.”
In the case of endemic bacteria, NGS gives veterinarians and pork producers a clear picture of one of the three “threats” of a disease challenge: detailed information about the pathogen. This information can help strengthen a multifaceted approach to managing endemic disease agents. Successful strategies might include:1
- Minimizing triggers such as co-infections
- Selecting the correct pig to use for collecting diagnostic samples and sending high-quality samples to the laboratory
- Continuous monitoring of pig populations
- Strategically combining pig flows, including replacement gilts and weaned pigs
- Informed selection of vaccine types
“Next generation sequencing can provide significant value for control programs,” Jose Clavijo says. “By understanding the pathogen, how it could potentially interact with the pig, and how it could be impacted by the barn environment, veterinarians and pork producers can create strategic plans to minimize the risk of infections caused by endemic bacterial agents.”
Cases on the rise
Although endemic bacteria tend to take a back seat to epidemic diseases, Jose Clavijo and her colleagues at the ISU Veterinary Diagnostic Laboratory demonstrated that detection and diagnosis of endemic bacterial agents are on the rise.
The team analyzed data collected over a 10-year period. The study included five bacterial species identified by the Swine Health Information Center as being among the top endemic bacteria of concern for the U.S. swine industry, including S. suis and G. parasuis. The results showed an increase in cases of disease attributed to both species.
Reasons for the increase could include the growth of the U.S. sow herd by 500,000 head between 2015 and 2019. The expansion meant the herd likely had more and younger gilts with less developed immunity.
Other reasons for the increase in endemic disease diagnosis include changes in antimicrobial resistance or reduced antimicrobial use across the industry. Finally, spikes in confirmed cases could also be attributed to increases in sample submissions for testing and improved data management and coding.
While endemic bacterial agents don’t always get the same level of attention as epidemic diseases in pork production, the data shows a long-term increase of high-risk endemic bacteria diagnosed in the U.S. swine herd. Utilizing next generation sequencing tools to identify strains of endemic bacteria is the first step to designing strategic protocols to protect and manage your herd’s health.
 Clavijo1,2, Maria J., DVM, Ph.D.; Mugabi1, Robert, DVM, MS, Ph.D.; Ganwu Li1, MS, Ph.D. 2021. Next generation sequencing (NGS) for control of endemic diseases. 1Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, IA
2PIC®, Hendersonville, Tennessee