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

Abstract

Streptococcus suis 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 S. suis 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 S. suis 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 in silico 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, p < 0.001) and non-systemic (Kruskal–Wallis, p < 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 dltA [Fisher's test (FT), p < 0.001], luxS (FT, p = 0.01), and troA (FT, p = 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 tetO conferring resistance to tetracycline and ermB conferring resistance to macrolide, lincosamide, and streptogramin. The wide distribution of VAFs genes in S. suis isolates in this study suggests that other host and environmental factors may contribute to S. suis disease development.

Comparative virulence and antimicrobial resistance distribution of Streptococcus suis isolates obtained from the United States

“…The most prevalent AMR element found among the isolates was tetO, followed by ermB, lsaE, lnuB, ant(9)-Ia, and ant(6)-Ia. While differences in MICs between countries have been described, high prevalence rates for macrolide and tetracycline resistance, along with low prevalence rates for β-lactam resistance have been previously reported (Gurung et al, 2015;Aradanas et al, 2021;Dechene-Tempier et al, 2021;Hadjirin et al, 2021;Ma et al, 2021;Matiasovic et al, 2021;Cucco et al, 2022). This has been a global trend for several decades now, and the genetic basis for these resistances has been extensively studied (Varela et al, 2013;Gurung et al, 2015;Seitz et al, 2016;Dechene-Tempier et al, 2021).…”

Comparative analysis of Streptococcus suis genomes identifies novel candidate virulence-associated genes in North American isolates

“…High predicted resistance to tetracyclines (93%, predominantly tet ( O )) and erythromycin (70%, erm ( B )) was observed similar to previous reports of resistance genes in S. suis in North America, Asia, and Europe [ 63 , 64 ]. Previous studies indicate a higher prevalence of antibiotic resistance among commensal strains, which may act as reservoirs for resistance genes [ 65 , 66 ]. There was no major difference in the distribution of resistance genes by pathotype, but the commensal and possibly opportunistic pathotypes did tend to have more resistance genes.…”

“…Our results indicated a lack of correlation between the presence of MGE-associated VAGs and pathotype. The presence of VAGs in a majority of the commensal pathotype provides further evidence that commensal strains may act as gene reservoirs [ 66 , 71 ]. Although the 89 K PAI (a S. suis MGE) was absent in all isolates in this study, the in silico detection of 89 K PAI sequences (CH1/CH2 and CH5/CH6) and the presence of PAI VAGs suggest some genetic similarity between North American isolates and the virulent S. suis strain 05ZYH33 [ 45 ].…”

A Streptococcus suis infection causing pneumonia in Indonesia: A case report

“…There are currently 29 known serotypes of S. suis [13] , [14] , [15] . Reliable multiplex PCR techniques are replacing traditional biochemical-based approaches for detecting these serotypes.…”