Pan-immune system, mobilome and resistome in Streptococcus suis

Abstract

Streptococcus suis is a bacterial pathogen responsible for infections in pigs and in wild fauna that can also lead to severe infections in humans. Increasing antimicrobial resistance (AMR) has been described for this zoonotic pathogen worldwide. Since most of these AMR genes are carried by mobile genetic elements (MGEs), they can largely disseminate by horizontal gene transfer. Taking advantage of the large set of genomes available for this species, an exhaustive search of integrative and conjugative elements (ICEs) and integrative and mobilizable elements (IMEs) was undertaken in a representative set of 400 selected high-quality genomes of S. suis. We examined how these elements vary across phylogenetic clades and ecotypes and their association with AMR genes and defence systems (DSs), including restriction-modification (RM), CRISPR and also less studied DSs. This investigation identified 569 ICEs, belonging to the 7 families previously described in streptococci, inserted in 12 distinct specific integration sites. Additionally, 1,035 IMEs characterized by 11 distinct relaxase families and integrated in 10 specific chromosomal sites were detected in the 400 genomes of S. suis. New associations between ICE/IME and AMR genes were discovered. A huge diversity of putative DSs was observed including 2,035 RM systems, 124 CRISPR systems and systems belonging to 20 other categories, most of them described as efficient against phages and plasmids. Furthermore, most of the spacers associated with CRISPR systems target these MGEs rather than integrative elements. In addition, many integrative elements appear to carry an orphan methylase that could help them escape RM systems. Altogether, this points out that ICEs and IMEs are spared by DSs and play a major role in AMR dissemination in S. suis. In addition, most of the strains have the full set of genes required for competence, i.e. for the acquisition of extracellular DNA by natural transformation. This suggests a high risk of AMR dissemination in S. suis.

Keywords: CRISPR; Streptococcus suis; antimicrobial resistance genes; competence; defence systems; integrative and conjugative elements; integrative and mobilizable elements; restriction–modification systems; virulence.

Fig. 1.. Characteristics of the 400 selected strains of S. suis. Genomes have been grouped in clades according to their phylogenetic distance determined by alignment of the persisting genes (see the ‘Methods’ section) as indicated by a phylogenetic tree at the left. STs previously described as associated with the pathogenic pathotype are indicated on the phylogenetic tree. Strains were also categorized according to their (i) host, (ii) isolation group, (iii) serotype, (iv) virulence cluster and (v) virulence-gene pattern. The virulence cluster of the strain was obtained by HCPC analysis (see the ‘Methods’ section). The grouping of the strains in four virulence clusters was made according to the presence (in blue) or absence (in white) of the most discriminant 25 virulence-associated genes (ordered by descending discriminatory power) among the 70 genes analysed. The colour code of clades and of other categories is shown at the bottom of the figure.

Fig. 2.. AMR gene pattern in the 400 genomes of S. suis according to the clade, host and isolation group of the strains. AMR genes have been classified per class of antibiotics targeted by the resistance determinant. Some AMR genes confer resistance to multiple antibiotics and thus appear several times on the diagram. Genomes have been grouped in clades according to their phylogenetic distance determined by alignment of the persisting genes as indicated by the phylogenetic tree at the left. The colour code of clades and of other categories is shown at the bottom of the figure.

Fig. 3.. Stacked histogram showing the families of (a) ICEs and (b) IMEs detected in the 400 genomes of S. suis and their integration sites (shown in different colours, see legend on the right). When the gene is interrupted by the integration of the element, it is mentioned by a delta symbol before the name of the target gene.

Fig. 4.. Co-occurrences of ICEs and IMEs identified in the 400 genomes of S. suis. The number of occurrences of each integrative element is indicated on the left with horizontal bars and the number of element co-occurrences by vertical histograms (with indication of the number of representatives on the top of the histogram). Combinations of elements are indicated in the centre of the figure by a circle in front of the elements in association, linked by a vertical line. Only those encountered at least twice are indicated on the figure.

Fig. 5.. Number of RM systems according to the clade of the strains. The box plots represent the data distribution with the IQR between the upper and lower quartiles, Q3 (75th percentile of the data dispersion) and Q1 (25th percentile of the data). The median values (middle 50% of the data) are indicated by a horizontal line inside the boxes. Outliers are indicated as black circles. The boxes are coloured differently according to the phylogenetic clade (see legend on the right).

Fig. 6.. Occurrence and associations of various categories of CRISPR systems found in the 400 genomes of S. suis. The number of occurrences of each CRISPR-Cas system is indicated on the left with horizontal bars and the number of system associations by vertical histograms (with indication of the number of representatives on the top of the histogram). Combinations of CRISPR-Cas systems are indicated in the centre of the figure by a circle in front of the systems in association, linked by a vertical line.

Fig. 7.. Pattern of DSs (excluding RM and CRISPR-Cas systems) in the 400 genomes of S. suis according to their phylogenetic clade, host and isolation site. Genomes have been grouped in clades according to their phylogenetic distance determined by alignment of the persisting genes as indicated by the phylogenetic tree at the left. The colour code of clades and of other categories is shown on the bottom of the figure.