High mortality events due to Streptococcus equi subspecies zooepidemicus in U.S. swine were first reported in Ohio and Tennessee in September and October 2019. In February 2021, two-year-old adult sows from a production system in Indiana experienced increased sow death loss. To investigate if the Indiana outbreak isolates were similar to or different from isolates from Ohio and Tennessee S. zooepidemicus outbreaks, Swine Health Information Center-funded whole genome sequencing analysis was performed.

In Indiana, there were 66 deaths in the affected 2,400-sow production herd within a six-week period. Four outbreak isolates from Indiana were genetically distant to those isolates causing high mortality events in Ohio and Tennessee in the spring of 2019, while closely related to a S. zooepidemicus isolate from a horse in Iowa. These results suggest more than one strain of S. zooepidemicus could cause high mortality events in the United States.

The genome sequence of the Indiana outbreak isolate was further closed using Nanopore sequencing. Comparative genomic analysis was performed, and genomic islands and putative virulence genes were identified. Two genomic islands (GI-3 and GI-13) were identified specifically only in the Indiana outbreak isolates, thus could serve as the biomarker for the diagnosis of this particular strain. In addition, M-like protein gene (szM) and the Fic domain-containing protein gene (bifA) were positive in those Ohio and Tennessee outbreak isolates, but absent from the Indiana outbreak isolates.

The findings provide significant and timely insights into the genetic diversity of S. zooepidemicus strains that are capable of causing high mortality outbreaks and understanding, tracking and possibly preventing these outbreaks caused by S. zooepidemicus. In addition, identification of specific virulence genes and genomic islands may provide the basis for future investigation of identification techniques, virulence mechanisms and control measures.

SHIC, launched by the National Pork Board in 2015 solely with Pork Checkoff funding, continues to focus efforts on prevention, preparedness and response to novel and emerging swine disease for the benefit of U.S. swine health. SHIC is funded by America's pork producers to fulfill its mission to protect and enhance the health of the U.S. swine herd.

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