Streptococcus canis Are a Single Population Infecting Multiple Animal Hosts Despite the Diversity of the Universally Present M-Like Protein SCM

Abstract

Streptococcus canis is an animal pathogen which occasionally causes infections in humans. The S. canis M-like protein (SCM) encoded by the scm gene, is its best characterized virulence factor but previous studies suggested it could be absent in a substantial fraction of isolates. We studied the distribution and variability of the scm gene in 188 S. canis isolates recovered from companion animals (n = 152), wild animal species (n = 20), and humans (n = 14). Multilocus sequence typing, including the first characterization of wildlife isolates, showed that the same lineages are present in all animal hosts, raising the possibility of extensive circulation between species. Whole-genome analysis revealed that emm-like genes found previously in S. canis correspond to divergent scm genes, indicating that what was previously believed to correspond to two genes is in fact the same scm locus. We designed primers allowing for the first time the successful amplification of the scm gene in all isolates. Analysis of the scm sequences identified 12 distinct types, which could be divided into two clusters: group I (76%, n = 142) and group II (24%, n = 46) sharing little sequence similarity. The predicted group I SCM showed extensive similarity with each other outside of the N-terminal hypervariable region and a conserved IgG binding domain. This domain was absent from group II SCM variants found in isolates previously thought to lack the scm gene, which also showed greater amino acid variability. Further studies are necessary to elucidate the possible host interacting partners of the group II SCM variants and their role in virulence.

Keywords: M-like protein (SCM) gene; Streptococcus canis; genome; multilocus sequence typing; wildlife.

FIGURE 1

goeBURST diagram of S. canis isolates recovered from animal and human infections. The diagram includes the 188 isolates studied plus the 3 S. canis isolates with publicly available genomes (from which MLST data was extracted). Numbers inside the circles identify the ST and numbers near the lines indicate the number of alleles different between the two connected STs. The size of each circle is proportional to the number of isolates in a logarithmic scale. The number of isolates with the same characteristic is proportional to the respective color. Putative CC founders are identified by an outer light green circle and correspond to the STs with the higher number of SLVs.

FIGURE 2

Neighbor-joining tree of scm alleles found among S. canis isolates. The scm alleles found in the current study are shown in bold and the numbers of isolates presenting each allele are indicated in brackets. Sequences from other studies are identified by their GenBank accession number and include those previously described by Timoney et al. (2017), the original scm sequence (FJ594772) described by Yang et al. (2010) and those extracted from S. canis genomes (indicated by an asterisk following the accession number and the name of the strain). scm alleles 1.16 to 1.18 have premature stop codons and were not included in the tree. Branches supported in the bootstrap test (1,000 replicates) by > 75%, have the values shown next to the branches. The tree is drawn to scale, with branch lengths being in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed by the Kimura two-parameter method and are in units of number of base substitutions per site. #indicates scm types that correspond to previously identified emm types, namely stG1389 (scm8), stg1451 (scm9), and stG663 (scm10).

FIGURE 3

Alignment of predicted amino acid sequences of IgG binding regions in SCM group I proteins. The IgG binding region derived from isolate G361 comprising amino acids 173 to 225 of the mature protein (Bergmann et al., 2017) was used as reference and corresponds to the consensus of predicted SCM group I proteins. Representative alleles of sequences found in our study are indicated by their numbers and sequences found elsewhere by their GenBank numbers.