E. coli PCR genotyping is a new addition to the Swine Health Information Center (SHIC)-funded Domestic Swine Disease Monitoring Report. SHIC says this continues to show support towards evidence-based herd health decision-making across the U.S. pork industry.
“E. coli is a significant pathogen in swine, most frequently associated with neonatal and post-weaning diarrhea,” SHIC reports.
With the inclusion of E.coli in the Swine Disease Reporting System, producers, veterinarians and researchers will now have access to real-time surveillance data on one of the most important and complex pathogens affecting pigs today.
“The decision to add E. coli was in response to requests from the SDRS Advisory Board and multiple stakeholders in the industry,” explain Giovani Trevisan, co-principal investigator, along with Daniel Linhares for the SDRS at Iowa State University. “E. coli is a significant and complex pathogen affecting swine health, responsible for a wide range of diseases.”
The SHIC Swine Bacterial Disease Matrix ranks E. coli as the fifth most prioritized and clinically important bacterium for the U.S. pork industry, with a score of 21.7, second only by a narrow margin to the 21.8 score for M. hyopneumoniae.
“That ranking underscores how concerning it truly is,” Trevisan and Linhares say.
A Major Challenge
E. coli remains a challenge for bacterial disease management within swine populations because of its diverse pathotypes and its capacity to cause severe economic loss, SHIC explains. Its clinical manifestations range from post-weaning diarrhea to edema disease, conditions that can undermine welfare while also inflating production costs.
“For years, stakeholders have recognized the value of broader surveillance of this pathogen,” SHIC reports. “With the integration of E. coli into the SHIC monthly reports, this information is now available for producers and veterinarians to use in the management of E. coli challenges.”
Building the infrastructure necessary to add E. coli to SDRS was a complex process, Trevisan says.
“The efforts to add E. coli started in February 2024, with a learning journey on how to report a complex pathogen such as E. coli,” he says. “The data organization and hub development began shortly after SHIC funded the proposal. What became clear was the need for extensive standardization across participating veterinary diagnostic labs.”
This process of data organization reflected the inherent complexity of the pathogen, SHIC reports. Unlike many viral targets characterized in SDRS, E. coli behaves both as a benign commensal organism and as a highly pathogenic agent.
“To interpret results meaningfully, the surveillance network needed to account for genotypes, virotypes and virulence factors that define pathogenic potential,” SHIC says. “Harmonizing submissions across laboratories to achieve this level of granularity requires significant cross-institutional collaboration.”
The inclusion of E. coli data in SDRS now provides unprecedented insight into bacterial disease dynamics on a national scale.
“With this expansion, producers, practitioners, researchers and other stakeholders have access to centralized, near-real-time data on testing results, including E. coli genotyping PCR targets, virotypes and pathotypes being detected,” Trevisan says. “The advantages are multifaceted.”
New Insights
The process of integrating E. coli into SDRS became part of the master of science degree thesis of Elisa de Conti. SHIC notes it has already yielded important learnings that further highlight the complexity of this pathogen.
“We learned that E. coli’s complex ecology demands a reporting system that is both comprehensive and flexible,” Trevisan says. “Reporting must occur at the sample level, understanding what was detected within each isolate or sample submitted for genotyping PCR. This approach enabled us to classify submissions as potentially pathogenic or not, which is fundamental for epidemiological interpretation.”
Several findings have surfaced during this preparation.
- Approximately one-third of tested samples lacked pathogenic potential, demonstrating the need for nuanced reporting.
- Since 2017, detections of fimbriae have shifted, with F18 steadily increasing while K88 (F4) declined.
- Among virotypes, the combination of F18:LT:STa:STb:Stx2e emerged as the most frequently found across multiple states. Specifically, this F18:LT:STa:STb:Stx2e virotype was the most frequently detected in 2024, representing 37.8% (389/1,030) of the virotypes.
- Since 2021, hybrid ETEC/STEC pathotypes have been detected more frequently than classic ETEC strains, signaling a significant epidemiological shift in circulating E. coli populations.
“These trends provide actionable intelligence,” SHIC notes. “For veterinarians, recognizing a rising prevalence of certain virulence factors can inform vaccine and treatment strategies tailored to herd needs. For the broader industry, an understanding of regional patterns supports collaborative approaches to mitigation and control.”
The benefits include:
- Diagnostic decision-making can be enhanced, especially considering emerging pathotypes such as the hybrid ETEC/STEC strains.
- Veterinarians can use SDRS data to identify regional or age-specific trends, allowing them to proactively adapt herd health plans to shifting disease pressures.
- Targeting interventions—such as adjusting vaccine selection in response to shifts in fimbriae types like the growing prevalence of F18 over the declining K88 (F4)—can reduce unnecessary costs while improving effectiveness.
- The new system facilitates clearer distinctions between pathogenic and non-pathogenic sample findings, thereby supporting future investigations into population-level trends.
Growing System Capacity
“The addition of E. coli demonstrates how the SDRS can evolve with industry needs,” Trevisan says. “It also positions the system for future incorporation of other bacterial pathogens. Just as importantly, this module serves as proof of concept that cross-laboratory collaboration coupled with targeted data curation can yield practical, accessible tools for the field.”
SHIC says stakeholders have expressed interest in integrating bacterial culture results and antimicrobial susceptibility profiles into the reporting system. Such additions would create a more holistic view of E. coli, potentially connecting molecular detection trends with real-world treatment outcomes. For producers, this would translate into even faster access to actionable intelligence that drives profitability and herd well-being.
“The expansion of the SHIC Domestic Swine Disease Monitoring Reports to include E. coli genotyping and virotyping data provides valuable insights into the trends and geographic distribution of this pathogen,” SHIC reports. “This information can be used to identify regional trends in virulence genes, inform disease control strategies, and reduce the production impact of E. coli on U.S. swine.”
