The recent addition of E. coli PCR genotyping to the SHIC-funded Domestic Swine Disease Monitoring Report continues to show support towards evidence-based herd health decision-making across the US pork industry. E. coli is a significant pathogen in swine, most frequently associated with neonatal and post-weaning diarrhea. With the inclusion of E.coli in the Swine Disease Reporting System published in monthly SHIC communications, producers, veterinarians, and researchers now gain access to real-time surveillance data on one of the most important and complex pathogens affecting pigs today.
Find the industry summary for Swine Health Information Center project #24-017 here.
Dr. Giovani Trevisan, co-principal investigator with Dr. Daniel Linhares for the SDRS at Iowa State University, explained, “The decision to add E. coli was in response to requests from the SDRS Advisory Board and multiple stakeholders in the industry. 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 5th most prioritized and clinically important bacterium for the US 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.”
Understanding and Reporting on this Significant Pathogen
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. 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. 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.
According to Dr. Trevisan, building the infrastructure necessary to add E. coli to SDRS was a complex process. “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. 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. 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. 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. As Dr. Trevisan described, “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. The advantages are multifaceted.”
Insights Gained in Developing the E. coli Report
The process of integrating E. coli into SDRS was championed and became part of the master of science degree thesis of Elisa de Conti and has already yielded important learnings that further highlight the complexity of this pathogen. Dr. Trevisan observed, “We learned that E. coli’s complex ecology demands a reporting system that is both comprehensive and flexible. 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. Perhaps most notably, 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. 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 are highly practical. Diagnostic decision-making can be enhanced, especially considering emerging pathotypes such as the hybrid ETEC/STEC strains. These variants, increasingly documented in SDRS since 2021, present new challenges in field diagnosis and require close monitoring. On a herd level, veterinarians can use SDRS data to identify regional or age-specific trends, allowing them to proactively adapt herd health plans to shifting disease pressures.
Economic implications are also significant. 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. For epidemiologists and researchers, the new system facilitates clearer distinctions between pathogenic and non-pathogenic sample findings, thereby supporting future investigations into population-level trends.
Growing System Capacity for the Future
Dr. Trevisan stressed the broader implications of this report stating, “The addition of E. coli demonstrates how the SDRS can evolve with industry needs. 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.”
Future enhancements are being discussed for consideration. 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. 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 US swine.
SDRS
SHIC-funded Domestic Disease Surveillance Program: A collaborative project among multiple VDLs, with the goal to aggregate swine diagnostic data and report in an intuitive format (web dashboards and monthly PDF report), describing dynamics of pathogen detection by PCR-based assays over time, specimen, age group, and geographical area. Data is from the Iowa State University VDL, South Dakota State University ADRDL, University of Minnesota VDL, Kansas State University VDL, Ohio Animal Disease and Diagnostic Laboratory, and Purdue ADDL. For PRRSV ORF5 Lineages, RFLP, and variant classification data are also available from all participant d-labs. Specifically for syndromic dashboards, the results are from Iowa State University VDL.
SHIC
The Swine Health Information Center, launched in 2015 with Pork Checkoff funding, protects and enhances the health of the US swine herd by minimizing the impact of emerging disease threats through preparedness, coordinated communications, global disease monitoring, analysis of swine health data, and targeted research investments. As a conduit of information and research, SHIC encourages sharing of its publications and research. Forward, reprint, and quote SHIC material freely. For more information, visit http://www.swinehealth.org or contact Dr. Megan Niederwerder at [email protected] or Dr. Lisa Becton at [email protected].