Molecular Epidemiology of Underreported Emerging Zoonotic Pathogen Streptococcus suis in Europe

Abstract

Streptococcus suis, a zoonotic bacterial pathogen circulated through swine, can cause severe infections in humans. Because human S. suis infections are not notifiable in most countries, incidence is underestimated. We aimed to increase insight into the molecular epidemiology of human S. suis infections in Europe. To procure data, we surveyed 7 reference laboratories and performed a systematic review of the scientific literature. We identified 236 cases of human S. suis infection from those sources and an additional 87 by scanning gray literature. We performed whole-genome sequencing to type 46 zoonotic S. suis isolates and combined them with 28 publicly available genomes in a core-genome phylogeny. Clonal complex (CC) 1 isolates accounted for 87% of typed human infections; CC20, CC25, CC87, and CC94 also caused infections. Emergence of diverse zoonotic clades and notable severity of illness in humans support classifying S. suis infection as a notifiable condition.

Keywords: Europe; Streptococcus suis; bacteria; molecular epidemiology; pathogens; pigs; porcine diseases; pork; swine; systematic review; whole genome sequencing; zoonoses.

Figure 1

Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) search flowchart for systematic review of Streptococcus suis in Europe during 1990–2022.

Figure 2

Reported cases of human Streptococcus suis infections across Europe during 1990–2022. We pooled reported cases collected in the survey study and systematic search study. The color of the countries represents the relative number of cases: the darker the tone, the higher the number of reported cases. Scale bar indicated substitutions per site. Purple stars indicate reference laboratory participating in the survey study within that country. Countries in black were not included in the study.

Figure 3

Genome population structure of zoonotic Streptococcus suis in Europe. The maximum-likelihood tree was reconstructed using IQ-TREE (18) with a core genome alignment produced with Panaroo (16). Color triangles at branch tips indicate country of collection; color rings indicate lineage (CC). The inner color ring indicates ST and is labeled accordingly. The outer color ring indicates the serotype as determined by the antigenic properties of the cps. We used iTOL (https://itol.embl.de) to visualize the tree. cps, capsular polysaccharide; NA, not available; ST, sequence type.

Figure 4

Presence/absence matrix of 46 genes putatively associated with zoonotic potential in study of zoonotic Streptococcus suis in Europe. The same phylogenetic tree presented in Figure 3 was used. Blue squares indicate presence of the gene while red squares indicate absence. The colored branches indicate CCs and follow the same pattern as in Figure 3 (blue, CC1; red, CC20; purple, CC87; yellow, CC94; green, CC25). We defined gene presence with 80% protein identity and coverage. We used Phandango (19) to visualize the tree. Bios, biosynthesis; CC, clonal complex; CS, complement system evasion.