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

Abstract

<i>Streptococcus suis</i> is ubiquitous in swine, and yet, only a small percentage of pigs become clinically ill. The objective of this study was to describe the distribution of serotypes, virulence-associated factor (VAF), and antimicrobial resistance (AMR) genes in <i>S. suis</i> isolates recovered from systemic (blood, meninges, spleen, and lymph node) and non-systemic (tonsil, nasal cavities, ileum, and rectum) sites of sick and healthy pigs using whole-genome sequencing. In total, 273 <i>S. suis</i> isolates recovered from 112 pigs (47 isolates from systemic and 136 from non-systemic sites of 65 sick pigs; 90 isolates from non-systemic sites of 47 healthy pigs) on 17 Ontario farms were subjected to whole-genome sequencing. Using <i>in silico</i> typing, 21 serotypes were identified with serotypes 9 (13.9%) and 2 (8.4%) as the most frequent serotypes, whereas 53 (19.4%) isolates remained untypable. The relative frequency of VAF genes in isolates from systemic (Kruskal-Wallis, <i>p</i> < 0.001) and non-systemic (Kruskal-Wallis, <i>p</i> < 0.001) sites in sick pigs was higher compared with isolates from non-systemic sites in healthy pigs. Although many VAF genes were abundant in all isolates, three genes, including <i>dltA</i> [Fisher's test (FT), <i>p</i> < 0.001], <i>luxS</i> (FT, <i>p</i> = 0.01), and <i>troA</i> (FT, <i>p</i> = 0.02), were more prevalent in isolates recovered from systemic sites compared with non-systemic sites of pigs. Among the isolates, 98% had at least one AMR gene, and 79% had genes associated with at least four drug classes. The most frequently detected AMR genes were <i>tetO</i> conferring resistance to tetracycline and <i>ermB</i> conferring resistance to macrolide, lincosamide, and streptogramin. The wide distribution of VAFs genes in <i>S. suis</i> isolates in this study suggests that other host and environmental factors may contribute to <i>S. suis</i> disease development.