Whole genome sequencing identifies a novel species of the genus Capnocytophaga isolated from dog and cat bite wounds in humans

Abstract

C. canimorsus and C. cynodegmi are dog and cat commensals which can be transmitted to humans via bites or scratches and can cause sepsis, meningitis, endocarditis, and eye- or wound infections. Recently an additional Capnocytophaga species was identified as part of the oral flora of healthy dogs and was given the name "C. canis". We previously identified a Capnocytophaga isolate that could not be typed with available diagnostic tests including MALDI-TOF, 16S rRNA sequencing or species-specific PCR. This strain and 21 other Capnocytophaga spp isolated in Sweden from clinical blood- or wound-cultures were subjected to whole genome sequencing using the Illumina platform. Phylogenetic analysis revealed that the previously non-typable isolate belongs to the putative new species "C. canis". Since this strain was isolated from a wound it also shows that members of "C. canis" have the potential to be pathogenic. In addition, our phylogenetic analysis uncovered an additional species of Capnocytophaga, which can be transmitted from dogs and cats to humans, suggesting a speciation within the Capnocytophaga family that has not been observed before. We propose the name of "C. stomatis" for this putative novel species.

Figure 1. Phylogenetic analysis of Capnocytophaga strains.

Maximum-likelihood trees inferred from concatenations of 43 housekeeping-gene proteins. F. johnsoniae UW101 was used as the outgroup. Strains isolated from blood and wounds are designated with “B” and “W”, respectively. CCD38, CCD93 and CCD95 and W13 represent the recently described species “C. canis”. W5, W10 and W12 represent the novel species, with the proposed name “C. stomatis”. Strains genome-sequenced in this study are indicated with blue text. The size and color of the circles indicate the reliability of the corresponding split in the tree using the Shimodaira-Hasegawa test (with 1 being the maximum possible value).

Figure 2. Heat-map representation of the presence (red = 1) or absence (blue = 0) of COGs in the different Capnocytophaga genomes.

CCA, C. canimorsus, CCY, C. cynodegmi and Cc, “C. canis”.

Figure 3. A Venn-diagram showing clusters of orthologous groups of genes (COGs) for the four clusters of strains.

Cluster 1: C. canimorsus (pink); cluster 2: “C. canis”(isolates CCD38, CCD93, CCD95 and W13, beige); cluster 3: C. cynodegmi (green) and cluster 4: The novel species with the proposed name “C. stomatis” (isolates W5, W10 and W12, purple). Note that a COG was considered to be present in a cluster only if it was present in all genomes in the cluster.

Figure 4. Colony morphology.

(A) C. canimorsus, C. cynodegmi, W13, W5, W10 and W12 colony morphology on blood agar, 72 h culture, 37° C, 5% CO₂ atmosphere. (B) Alpha hemolytic activity of C. canimorsus, C. cynodegmi and W13. Beta hemolytic activity of W5, W10 and W12 on blood agar, 72 h culture, 37° C, 5% CO₂ atmosphere.