Comparative Virulence and Genomic Analysis of Streptococcus suis Isolates

Abstract

Streptococcus suis is a zoonotic bacterial swine pathogen causing substantial economic and health burdens to the pork industry. Mechanisms used by S. suis to colonize and cause disease remain unknown and vaccines and/or intervention strategies currently do not exist. Studies addressing virulence mechanisms used by S. suis have been complicated because different isolates can cause a spectrum of disease outcomes ranging from lethal systemic disease to asymptomatic carriage. The objectives of this study were to evaluate the virulence capacity of nine United States S. suis isolates following intranasal challenge in swine and then perform comparative genomic analyses to identify genomic attributes associated with swine-virulent phenotypes. No correlation was found between the capacity to cause disease in swine and the functional characteristics of genome size, serotype, sequence type (ST), or in vitro virulence-associated phenotypes. A search for orthologs found in highly virulent isolates and not found in non-virulent isolates revealed numerous predicted protein coding sequences specific to each category. While none of these predicted protein coding sequences have been previously characterized as potential virulence factors, this analysis does provide a reliable one-to-one assignment of specific genes of interest that could prove useful in future allelic replacement and/or functional genomic studies. Collectively, this report provides a framework for future allelic replacement and/or functional genomic studies investigating genetic characteristics underlying the spectrum of disease outcomes caused by S. suis isolates.

Serotypes, Virulence-Associated Factors, and Antimicrobial Resistance of Streptococcus suis Isolates Recovered From Sick and Healthy Pigs Determined by Whole-Genome Sequencing

“…There was a high rate of carriage of AMR genes in S. suis isolates in this study, and similar to previous S. suis genotypic AMR studies globally ( 20 , 22 , 23 ), most of the isolates carried genes associated with resistance to tetracycline, lincosamides, and macrolides. Consistent with those studies, tet(O) was the most prevalent tetracycline resistance gene detected in the S. suis isolates.…”

“…The recent increase in the prevalence of disease caused by serotype 9 isolates globally requires more attention to understanding the pathogenesis mechanisms that may be unique to each serotype. There was a high rate of carriage of AMR genes in S. suis isolates in this study, and similar to previous S. suis genotypic AMR studies globally (20,22,23), most of the isolates carried genes associated with resistance to tetracycline, lincosamides, and macrolides. Consistent with those studies, tet(O) was the most prevalent tetracycline resistance gene detected in the S. suis isolates.…”

“…Over time, there has been a global trend of increased resistance to tetracycline, aminoglycosides, fluoroquinolones, macrolides, and cephalosporins (8,20,21) in S. suis. Recent metagenomic studies have also supported the trend of increased resistance and broad distribution of AMR-associated genes globally (20,22,23). Recombination plays a key role in the evolutionary history of S. suis (24), and it has been suggested that S. suis has the potential to act as an AMR reservoir (8).…”

Peptidomics Analysis of Virulent Peptides Involved in Streptococcus suis Pathogenesis

“…The tetracycline-resistance gene, tet M, encoded TetM protein responsible for the inhibitory effect of tetracycline, is distributed among virulent S. suis. [ 34 , 35 , 36 ]. An outbreak report in China demonstrated that the tetracycline-resistance strains were associated with S. suis infections in both pigs and humans [ 34 ].…”

Genomic Characterization of Streptococcus suis Serotype 24 Clonal Complex 221/234 From Human Patients

“…Among 29 serotypes, WGS has been applied to the serotype 2 strains worldwide for, as examples, characterization of outbreaks, evaluation of S. suis reinfection, determining the population structure of S. suis strains, and identifying pathotypes or virulence traits ( Estrada et al, 2019 ; Hatrongjit et al, 2020 ). Several studies have also been conducted on serotypes other than serotype 2 including serotypes 3–9, 14, 16, 19, 20, 21, 22, 26, and unencapsulated strains, although most of them were of swine origin ( Hu et al, 2011 ; Wang et al, 2013a , b , 2014 ; Baig et al, 2015 ; Yoshida et al, 2017 ; Zheng et al, 2018 ; Niemann et al, 2019 ; Stevens et al, 2019 ; Bunk et al, 2021 ; Liang et al, 2021 ; Nicholson et al, 2021 ). To date, there has been no WGS performed on S. suis serotype 24 strains recovered from humans.…”