Streptococcus halichoeri: Comparative Genomics of an Emerging Pathogen
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...
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| Format: | Article |
| Language: | English |
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Wiley
2020-01-01
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| Series: | International Journal of Genomics |
| Online Access: | http://dx.doi.org/10.1155/2020/8708305 |
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| author | Kirsi Aaltonen Ravi Kant Marjut Eklund Mirja Raunio-Saarnisto Lars Paulin Olli Vapalahti Thomas Grönthal Merja Rantala Tarja Sironen |
| author_facet | Kirsi Aaltonen Ravi Kant Marjut Eklund Mirja Raunio-Saarnisto Lars Paulin Olli Vapalahti Thomas Grönthal Merja Rantala Tarja Sironen |
| author_sort | Kirsi Aaltonen |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-e71a03e6d4654c1b8bc1387970624a82 |
| institution | Kabale University |
| issn | 2314-436X 2314-4378 |
| language | English |
| publishDate | 2020-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | International Journal of Genomics |
| spelling | doaj-art-e71a03e6d4654c1b8bc1387970624a822025-02-03T01:26:58ZengWileyInternational Journal of Genomics2314-436X2314-43782020-01-01202010.1155/2020/87083058708305Streptococcus halichoeri: Comparative Genomics of an Emerging PathogenKirsi Aaltonen0Ravi Kant1Marjut Eklund2Mirja Raunio-Saarnisto3Lars Paulin4Olli Vapalahti5Thomas Grönthal6Merja Rantala7Tarja Sironen8Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, FinlandDepartment of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, FinlandDepartment of Equine and Small Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, FinlandFinnish Food Authority, Seinäjoki, FinlandInstitute of Biotechnology, University of Helsinki, Helsinki, FinlandDepartment of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, FinlandDepartment of Equine and Small Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, FinlandDepartment of Equine and Small Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, FinlandDepartment of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, FinlandStreptococcus 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.http://dx.doi.org/10.1155/2020/8708305 |
| spellingShingle | Kirsi Aaltonen Ravi Kant Marjut Eklund Mirja Raunio-Saarnisto Lars Paulin Olli Vapalahti Thomas Grönthal Merja Rantala Tarja Sironen Streptococcus halichoeri: Comparative Genomics of an Emerging Pathogen International Journal of Genomics |
| title | Streptococcus halichoeri: Comparative Genomics of an Emerging Pathogen |
| title_full | Streptococcus halichoeri: Comparative Genomics of an Emerging Pathogen |
| title_fullStr | Streptococcus halichoeri: Comparative Genomics of an Emerging Pathogen |
| title_full_unstemmed | Streptococcus halichoeri: Comparative Genomics of an Emerging Pathogen |
| title_short | Streptococcus halichoeri: Comparative Genomics of an Emerging Pathogen |
| title_sort | streptococcus halichoeri comparative genomics of an emerging pathogen |
| url | http://dx.doi.org/10.1155/2020/8708305 |
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