Identification of <i>Streptococcus suis</i> putative zoonotic virulence factors: A systematic review and genomic meta-analysis

Roodsant, Thomas J.; Putten, Boas C L van der; Tamminga, Sara M.; Schultsz, Constance; Ark, Kees C. H. van der

doi:10.1080/21505594.2021.1985760

Cited by 20 publications

(41 citation statements)

References 92 publications

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“…A dataset containing 1703 curated S. suis genomes [46] was used in combination with genomes generated in this study to reconstruct the phylogeny of the global S. suis population (Table S1). The core genome and pangenome were inferred by clustering genes from the annotated draft assemblies into homology groups using Roary v3.13.0 [47].…”

Section: Phylogenetic Analysismentioning

confidence: 99%

“…The plasmid acquired by the outbreak strain was visualized using ApE v3.0.8 [58] and a blastn [59] search was performed against bacterial reference genomes. To assess the presence of potential genes of interest, ABRicate (https://github.com/tseemann/ abricate) was used with a custom database containing the sequences of 52 genes previously found to be putatively associated with zoonotic potential of S. suis strains [46].…”

Section: Acquisition Of Mobile Genetic Elements and Antimicrobial Res...mentioning

confidence: 99%

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Streptococcus suis outbreak caused by an emerging zoonotic strain with acquired multi-drug resistance in Thailand

et al. 2023

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Streptococcus suis is an emerging zoonotic swine pathogen which can cause severe infections in humans. In March 2021, an outbreak of S. suis infections with 19 confirmed cases of septicemia and meningitis leading to two deaths, occurred in Nakhon Ratchasima province, Thailand. We characterized the outbreak through an epidemiological investigation combined with Illumina and Nanopore whole genome sequencing (WGS). The source of the outbreak was traced back to a raw pork dish prepared from a single pig during a Buddhist ceremony attended by 241 people. WGS analysis revealed that a single S. suis serotype 2 strain belonging to a novel sequence type (ST) of the emergent Thai zoonotic clade CC233/379, was responsible for the infections. The outbreak clone grouped together with other Thai zoonotic strains from CC233/379 and CC104 in a global S. suis phylogeny and capsule switching events between serotype 2 zoonotic strains and serotype 7 porcine strains were identified. The outbreak strain showed reduced susceptibility to penicillin corresponding with mutations in key residues in the penicillin binding proteins (PBPs). Furthermore, the outbreak strain was resistant to tetracycline, erythromycin, clindamycin, linezolid and chloramphenicol, having acquired an integrative and conjugative element (ICE) carrying resistance genes tetO and ermB, as well as a transposon from the IS1216 family carrying optrA and ermA. This investigation demonstrates that multi-drug resistant zoonotic lineages of S. suis which pose a threat to human health continue to emerge.

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Section: Phylogenetic Analysismentioning

confidence: 99%

Section: Acquisition Of Mobile Genetic Elements and Antimicrobial Res...mentioning

confidence: 99%

Streptococcus suis outbreak caused by an emerging zoonotic strain with acquired multi-drug resistance in Thailand

et al. 2023

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“…Clarifying the mechanism of pathogenicity increase of epidemic strains is urgently needed to develop effective control and treatment strategies. To date, over 100 virulence genes have been reported to be involved in the pathogenesis of S. suis virulent strains [ 6–10 ]. They were classified into four categories based on their properties and functions, including surface/secreted elements, enzymes/proteases, transcription factors/regulatory systems, and transporters/secretion systems [ 7 ].…”

Section: Introductionmentioning

confidence: 99%

Comparative transcriptomic analysis reveal genes involved in the pathogenicity increase of Streptococcus suis epidemic strains

et al. 2022

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Streptococcus suis epidemic strains were responsible for two outbreaks in China and possessed increased pathogenicity which was featured prominently by inducing an excessive inflammatory response at the early phase of infection. To discover the critical genes responsible for the pathogenicity increase of S. suis epidemic strains, the genome-wide transcriptional profiles of epidemic strain SC84 were investigated at the early phase of interaction with BV2 cells. The overall low expression levels of 89K pathogenicity island (PAI) and 129 known virulence genes in the SC84 interaction groups indicated that its pathogenicity increase should be attributed to novel mechanisms. Using highly pathogenic strain P1/7 and intermediately pathogenic strain 89–1591 as controls, 11 pathogenicity increase crucial genes (PICGs) and 38 pathogenicity increase-related genes (PIRGs) were identified in the SC84 incubation groups. The PICGs encoded proteins related to the methionine biosynthesis/uptake pathway and played critical roles in the pathogenicity increase of epidemic strains. A high proportion of PIRGs encoded surface proteins related to host cell adherence and immune escape, which may be conducive to the pathogenicity increase of epidemic strains by rapidly initiating infection. The fact that none of PICGs and PIRGs belonged to epidemic strain-specific gene indicated that the pathogenicity increase of epidemic strain may be determined by the expression level of genes, rather than the presence of them. Our results deepened the understanding on the mechanism of the pathogenicity increase of S. suis epidemic strains and provided novel approaches to control the life-threatening infections of S. suis epidemic strains.

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“…We annotated the genomes using Prokka v1.14.5 and clustered all protein coding genes at 80% residue identity using mmseqs easy-cluster (–min-seq-id 0.8 –cluster-mode 2 – cov-mode 1). We used previously published metadata covering 1703 assemblies [21]. We determined the association of each cluster with presence in clinical and non-clinical strains by calculating the ratio of percent presence in each group.…”

Section: Methodsmentioning

confidence: 99%

“…Tonsillar colonization by different S. suis strains may also impact on invasive disease risk [13,20]. While S. suis has been described as an opportunistic pathogen, different strains have varying virulent potential and can be grouped into commensal and pathogenic clades [21][22][23].…”

Section: Introductionmentioning

confidence: 99%

Streptococcus suis infection on European farms is associated with an altered tonsil microbiome and resistome

Fredriksen

Neila‐Ibáñez

Hennig-Pauka

et al. 2022

Preprint

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Introduction Streptoccocus suis is a Gram-positive opportunistic pathogen causing systemic disease in piglets around weaning age. Outbreaks of S. suis disease are controlled by metaphylactic use of antibiotics, leading to high levels of antimicrobial resistance in S. suis isolates. This is an issue for both animal and human health due to the zoonotic disease potential of S. suis. The mechanisms facilitating invasive disease are not known but may involve host and environmental factors. The palatine tonsils are considered a portal of entry for pathogenic strains to cause systemic disease. We hypothesised that tonsil colonization by pathogenic and commensal bacteria may impact on disease risk via colonization resistance and co-infections. We conducted a case-control study on 9 European farms, comparing the tonsil microbiome of piglets with S. suis systemic disease with asymptomatic controls. We also compared these to piglets on control farms and piglets reared naturally in a forest. Results We found a small but significant difference in the tonsil microbiota composition of case and control piglets. Case-control associations varied between amplicon sequence variants (ASVs) and metagenome assembled genomes (MAGs) within the same species. Variants of putatively commensal taxa including Rothia nasimurium were reduced in abundance in case piglets compared to asymptomatic controls. Case piglets had higher relative abundance of Fusobacterium gastrosuis, Bacteroides heparinolyticus, and uncultured Prevotella and Alloprevotella species. There was, however, no higher abundance of S. suis itself at the species-level or of clinical strain marker genes in case piglets. Piglets sampled prospectively weeks prior to developing clinical signs had reduced microbiota alpha diversity. Despite case-control pairs receiving equal antimicrobial treatment, case piglets had higher abundance of antimicrobial resistance genes (ARGs) conferring resistance to antimicrobial classes used to treat S. suis. Conclusions The tonsillar microbiota of S. suis case piglets had increased abundance of taxa not previously linked to S. suis disease. This coincided with increased ARG abundance in case piglets, possibly due to adaptation of the disease-associated microbiota to frequent antimicrobial treatment.

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Identification of Streptococcus suis putative zoonotic virulence factors: A systematic review and genomic meta-analysis

Cited by 20 publications

References 92 publications

Streptococcus suis outbreak caused by an emerging zoonotic strain with acquired multi-drug resistance in Thailand

Streptococcus suis outbreak caused by an emerging zoonotic strain with acquired multi-drug resistance in Thailand

Comparative transcriptomic analysis reveal genes involved in the pathogenicity increase of Streptococcus suis epidemic strains

Streptococcus suis infection on European farms is associated with an altered tonsil microbiome and resistome

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