Streptococcus halichoeri: Comparative Genomics of an Emerging Pathogen

Abstract

Streptococcus halichoeri is an emerging pathogen with a variety of host species and zoonotic potential. It has been isolated from grey seals and other marine mammals as well as from human infections. Beginning in 2010, two concurrent epidemics were identified in Finland, in fur animals and domestic dogs, respectively. The fur animals suffered from a new disease fur animal epidemic necrotic pyoderma (FENP) and the dogs presented with ear infections with poor treatment response. S. halichoeri was isolated in both studies, albeit among other pathogens, indicating a possible role in the disease etiologies. The aim was to find a possible common origin of the fur animal and dog isolates and study the virulence factors to assess pathogenic potential. Isolates from seal, human, dogs, and fur animals were obtained for comparison. The whole genomes were sequenced from 20 different strains using the Illumina MiSeq platform and annotated using an automatic annotation pipeline RAST. The core and pangenomes were formed by comparing the genomes against each other in an all-against-all comparison. A phylogenetic tree was constructed using the genes of the core genome. Virulence factors were assessed using the Virulence Factor Database (VFDB) concentrating on the previously confirmed streptococcal factors. A core genome was formed which encompassed approximately half of the genes in Streptococcus halichoeri. The resulting core was nearly saturated and would not change significantly by adding more genomes. The remaining genes formed the pangenome which was highly variable and would still evolve after additional genomes. The results highlight the great adaptability of this bacterium possibly explaining the ease at which it switches hosts and environments. Virulence factors were also analyzed and were found primarily in the core genome. They represented many classes and functions, but the largest single category was adhesins which again supports the marine origin of this species.

Clinical Laboratory Perspective on Streptococcus halichoeri, an Unusual Nonhemolytic, Lancefield Group B Streptococcus Causing Human Infections

“…16S rRNA gene sequencing confirmed its placement in the genus Streptococcus , but the >3% divergence from described taxa suggested it was a novel species ( 1 ). S. halichoeri was also isolated from a European badger with pyogranulomatous pleuropneumonia ( 9 ) and from several canine and fur-producing animal species, including companion animals ( 14 , 15 ). These observations indicate a much broader host range than originally described for this organism.…”

“…It is unclear if S. halichoeri represents an emerging zoonosis or a rare but still underdiagnosed infection, or if it is simply being recognized only now because of improved identification methods (e.g., MALDI-TOF mass spectrometry). The source for infection with S. halichoeri is certainly not limited to marine life, because the organism has been isolated from both domestic and wild terrestrial mammals ( 14 ). Patients in the cases presented here had no known exposures to animals; therefore, reservoirs for infection by S. halichoeri might be more widespread than once thought.…”

Streptococcal Infections in Marine Mammals

“…hominis for strains associated with human infections. The core genome of 20 S. halichoeri isolates from different hosts including dogs and minks contained 19 different streptococcal virulence factors, of which most were associated with adherence followed by proteases and toxins emphasizing its pathogenic potential [ 120 , 121 ].…”

“…phocae showed host specificity by the immunoglobulin G degrading enzyme ideP that solely cleaves IgG of grey and harbor seals, but not from harbor porpoises or non-marine mammals indicating functional adaptation [ 192 ]. S. halichoeri is assumed to have marine origin, although it has also been isolated from dog, bluefox, finnraccoon, and mink, as it has a great number of adhesins and salt tolerance proteins [ 120 ]. Lateral gene transfer between different streptococcal species is discussed as potential way of host adaptation [ 214 ].…”

“…S. iniae and S. agalactiae were also isolated from wild fish indicating fish as potential source for streptococci [ 217 , 218 ]. In addition, S. halichoeri is supposed to be transmitted to mink and Finnish dogs via fed fish [ 120 ]. S. phocae is also a well-known pathogen of Atlantic salmon [ 143 ].…”