Population Structure and Genetic Diversity of Streptococcus suis Isolates Obtained from the United States

Authors: Nicholson, Tracy; KALALAH, ANWAR - University Of Texas At San Antonio; EPPINGER, MARK - University Of Texas At San Antonio

Submitted to: Frontiers in Immunology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/22/2023
Publication Date: 9/21/2023
Citation: Nicholson, T.L., Kalalah, A.A., Eppinger, M. 2023. Population Structure and Genetic Diversity of Streptococcus suis Isolates Obtained from the United States. Frontiers in Immunology. https://doi.org/10.3389/fmicb.2023.1250265.
DOI: https://doi.org/10.3389/fmicb.2023.1250265

Interpretive Summary: Streptococcus suis is a zoonotic swine pathogen capable of causing a spectrum of clinical disease outcomes in pigs including pneumonia, endocarditis, septicemia, and meningitis. Most genomic sequence data needed to evaluate any potential risks attributed to S. suis due to occupational exposure is derived from isolates obtained outside the U.S. To help fill this gap, this study applied whole genome sequencing and core genome (cg) multilocus sequence typing (MLST) based method to compare the population structure and genetic relatedness among S. suis isolates obtained within the U.S. The resulting high-resolution phylogenomic framework revealed extensive genomic variation and diversity among all the sampled S. suis isolates, with isolates obtained from countries outside the U.S. found interspersed throughout the cgMLST-based tree. S. suis isolates obtained within the U.S. did not cluster by state or geographic location, however, isolates with similar serotypes, both obtained from within and outside the U.S., generally clustered together. Average nucleotide identity (ANI) were additionally determined for the S. suis isolates and were extensively broad, and correlated with the phylogenetic group distribution of the cgMLST-based tree. Collectively, the data in this report provides information needed to address S. suis biosurveillance as well as providing needed information regarding the population structure of among U.S. S. suis isolates and how U.S. S. suis isolates compare with isolates obtained from various countries outside the U.S.

Technical Abstract: Diseases caused by S. suis are a substantial economic problem as well as an animal welfare concern for the global swine industry. Previous studies have evaluated the genomic diversity and population structure of S. suis isolates, however, the majority of these studies utilized S. suis isolates obtained from countries other than U.S. This study applied whole genome sequencing and cgMLST-based typing to compare the population structure and genetic relatedness among S. suis isolates obtained within the U.S. The resulting high-resolution phylogenomic framework revealed extensive genomic variation and diversity among all the sampled S. suis isolates, with isolates obtained from countries outside the U.S. found interspersed throughout the cgMLST-based tree. S. suis isolates obtained within the U.S. did not cluster by state or geographic location, however, isolates with similar serotypes, both obtained from within and outside the U.S., generally clustered together. Average nucleotide identity (ANI) values determined for the S. suis isolates were extensively broad, approaching the recommended species demarcation value, and correlated with the phylogenetic group distribution of the cgMLST-based tree. Collectively, the data in this report provides information needed to address S. suis biosurveillance as well as providing needed information regarding the population structure of among U.S. S. suis isolates and how they compare with isolates obtained from various countries outside the U.S.