Next-generation sequencing provides valuable insights on endemic disease agents


“Cutting-edge molecular technologies offer novel insights into the molecular epidemiology of systemic bacterial agents,” said Maria Clavijo, DVM, PhD, in a recent paper.1 The health-assurance veterinarian for PIC North America and research assistant professor in the Veterinary Diagnostic and Production Animal Medicine Department at Iowa State University said next-generation sequencing (NGS) may provide valuable information for researchers. “Swine practitioners can utilize this information to identify the most frequent strains found in disease- associated cases, improve vaccine-candidate selection or antimicrobial use on the farm, and optimize mixing of pig populations.”

Endemic agents like Streptococcus suis (Strep suis) and Glaesserella parasuis (GPS) are frequent causes of systemic disease in pig populations.

“Recent data from the Iowa State Veterinary Diagnostic Laboratory (ISU VDL) show that the diagnosis and detection for these agents has increased in the last couple of years,” she noted.

According to Clavijo, the agents are normal colonizers of the upper respiratory tract of pigs, and both pathogenic and commensal strains can co-exist, which complicates diagnosis.

NGS provides the best resolution for strain characterization, unlike conventional typing methods, Clavijo said. It can serve as a robust surveillance system for these bacterial agents when used in conjunction with other relevant information, including clinical history, histopathology and sourcing.

Key learning on Strep suis

“Control of pathogenic strains hinges on proper diagnosis, minimizing triggering or predisposing factors, effective vaccines based on the farm’s strains and strategic use of medication,” she said.

A total of 531 Strep suis isolates submitted between 2014 and 2020 to ISU-VDL were whole-genome sequenced and analyzed in a study. Strains originated from Canada, Mexico, Chile, Peru and Spain. Those strains included 25 different serotypes and 183 isolates that were untypeable, representing 34.5% of the isolates.

The strains that were untypeable tended to have two unique genetic features, Clavijo said: an overabundance of antimicrobial resistance genes and a lack of putative virulence factors.

“It’s important to highlight that serotyping can tell an incomplete picture on the clinical relevance of an isolate,” she explained. “Further characterizing these strains is a critical step for the identification and management of clinically important isolates within a flow.”

The data show a wide diversity of Strep suis strains, but usually one or two strains were predominant within a farm or flow in disease-associated cases.

“In our experience, it is important that repeated tissue submissions be carried out to increase the likelihood of capturing the clinically relevant strains and have a good understanding of the diversity and frequency of disease-associated strains found in a farm,” Clavijo said.

Key learning on GPS

More than 100 GPS isolates were submitted to the ISU-VDL over the same time period as the Strep suis isolates and were whole-genome sequenced and analyzed.

“Similar to Strep suis, multiple serotypes were distributed in multiple clusters, suggesting that further characterization is needed for proper identification and determining their relevance,” Clavijo said.

Systematic approach

Obtaining the right isolates requires a systematic approach, she added. This includes selecting the right pigs that show clinical signs, collecting the right strains and making sure sample handling and submission are performed properly. Each tissue should be bagged individually with the identified agent on the associated lesions.

“A baseline of current strains in a flow can be obtained, and routine incorporation of clinical strains can help identify the emergence of new pathotypes and changes in prevalence,” Clavijo said.

For example, one client submitted 75 strains of Strep suis. Of those, 25 were opportunistic and shouldn’t be included in a vaccine, she said. A third of the samples included strains known to be pathogenic, and she recommended they be included in a vaccine.

Producers should avoid mixing flows with different endemic-disease profiles.

“We can improve how populations of pigs are mixed,” she said. “Endemic agents from multiple farms have allowed practitioners to better determine how to source gilts.”

In summary, Clavijo advises swine practitioners to keep four key points in mind:

  1. Endemic bacteria continue to challenge the health and productivity of production systems.
  2. Obtaining the right isolates requires a systematic approach, including selecting the right pigs and samples.
  3. ISU-VDL offers NGS for endemic bacterial pathogens and maintains a well-characterized database with routine submissions.
  4. NGS provides valuable and actionable information that aids prevention and control programs for these endemic pathogens.

“This is a continuous process that depends on the relevance of the isolates and systematic collection and analysis,” Clavijo said.



1 Clavijo J, Mugabi R, Li G. Iowa State University Veterinary Diagnostic Laboratory, Department of Veterinary Diagnostic and Production Animal Medicine, Ames, Iowa. Friend or foe: what next generation sequencing can tell you about the endemic agents in your herd. Presented at Am Assoc Swine Vet annual meeting, March 2021.