SHIC-Funded Genetic Characterization of S. Zooepidemicus Provides Preparedness Tools

June 17, 2020 — Paul Sundberg

Prior to September and October 2019, no high mortality events due to Streptococcus equi subspecies zooepidemicus (S. zooepidemicus) in swine had been reported in the US. Then outbreaks in Ohio and Tennessee at that time saw mortality up to 50% due to S. zooepidemicus septicemia in those cases. While no additional outbreaks have been diagnosed domestically since last fall, the Swine Health Information Center (SHIC) saw a need for more information on this high mortality disease. Consequently, SHIC funded a project conducted by researchers from Iowa State University and the National Veterinary Services Laboratory for a genomic epidemiological analysis on the limited occurrence. The study revealed eight isolates were clustered together with a strain causing outbreaks with high mortality elsewhere. This preparedness project equips the US swine industry with needed detail should another S. zooepidemicus outbreak occur and has implications for understanding, tracking, and possibly preventing related diseases as well.

S. zooepidemicus is most frequently isolated as an opportunistic pathogen of horses in the upper respiratory and lower genital tracts. It can also cause infections in a wide range of other animal species. The first high mortality event from S. zooepidemicus in North America was reported in Canada during March 2019. From late September to early October of 2019, three cases of cull sows and feeder pigs from Ohio and Tennessee were submitted to the Iowa State University Veterinary Diagnostic Lab (ISU VDL). High mortality ranging from 10% to 50% in groups of pigs was reported over the period of 8 to 10 days at the buying station in Ohio and similar high mortality (922 out of 2,222 sows in lairage) from an abattoir in Tennessee. The clinical signs included sudden death, weakness, lethargy, and high fever. Splenomegaly and haemorrhagic lymph nodes were the most consistent macroscopic findings. Microscopic lesions were consistent with acute bacterial septicaemia. A laboratory diagnosis of S. zooepidemicus septicemia was given, which was corroborated by histopathology, PCR, and bacterial culture.

To genetically characterize S. zooepidemicus strains associated with high mortality and gain insights into the epidemiology of these highly unusual and unexpected outbreaks, researchers performed whole-genome sequencing on eight isolates from the Ohio and Tennessee outbreaks, another outbreak-unrelated swine isolate from Arizona, and 15 S. zooepidemicus isolates from other animal species. Three full-length complete genome sequences were further assembled, and genomic epidemiological and comparative genomic analyses were conducted.

Findings from this project provide significant and timely insights for a better understanding of the epidemiology and virulence of S. zooepidemicus isolates associated with highly unexpected and severe outbreaks that occurred very recently in the US swine population. In addition, identification of specific virulence genes and genomic islands may lead to the development of novel molecular diagnostic tools, and provide the basis for future investigation of virulence mechanisms and control measures.

As the world deals with the COVID-19 pandemic, SHIC continues to focus efforts on prevention, preparedness, and response to novel and emerging swine disease for the benefit of US swine health. As a conduit of information and research, SHIC encourages sharing of its publications and research. Forward, reprint, and quote SHIC material freely. SHIC is funded by America's pork producers to fulfill its mission to protect and enhance the health of the US swine herd. For more information, visit

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Paul Sundberg, Executive Director, Swine Health Information Center