Genomic characterization of Streptococcus equi subspecies zooepidemicus from a 2021 outbreak in Indiana with increased sow mortality

Abstract

ABSTRACT Streptococcus equi subspecies zooepidemicus ( S. zooepidemicus ) was reported to cause epizootic outbreaks in swine, resulting in significant economic losses in Asia in the 1970s and in North America in 2019. In February 2021, another outbreak due to S. zooepidemicus occurred in 2-year-old adult sows in a production system in Indiana. Whole-genome sequencing analysis of three outbreak isolates from Indiana revealed that all were genetically distant from the isolates of a strain that caused high mortality events in Ohio and Tennessee in 2019, as well as from the ATCC 35246 strain that caused outbreaks in China in the 1970s. The Indiana outbreak isolates were also distantly related to outbreak-unrelated swine isolate AZ-45470 from Arizona but closely related to an S. zooepidemicus equine isolate from Iowa. Comparative genomic analysis revealed that one genomic island, GI-13, was unique to the genome of a representative Indiana outbreak isolate, IN-6992. The genomic islands GI-1, GI-3, and GI-10 were also present in IN-6992 but absent from the Ohio and Tennessee outbreak isolates. In addition, the ATCC 35246-type szM gene and the Fic domain-containing protein gene ( bifA ) were absent from IN-6992, while present in all isolates from the Ohio and Tennessee outbreaks. Our findings have significant implications for understanding, monitoring, and developing control measures against diseases caused by S. zooepidemicus . IMPORTANCE This study highlights a Streptococcus equi subspecies zooepidemicus ( S. zooepidemicus ) strain isolated from an outbreak in Indiana, which resulted in mortality events among a swine herd in 2021. The Indiana outbreak strain was found to be genetically and phylogenetically distant to a strain isolated from the 2019 outbreaks in Ohio and Tennessee, which caused high swine mortality. We also discovered multiple unique genetic features in the Indiana outbreak strain, including distinct S. zooepidemicus genomic islands, and notable S. zooepidemicus virulence genes—many of which could serve as biomarkers for the diagnosis of this strain. These findings provide significant insights into monitoring and potentially preventing severe outbreaks caused by the Indiana outbreak strain in the future.