Genomics of <i>Tenacibaculum</i> Species in British Columbia, Canada
<i>Tenacibaculum</i> is a genus of Gram-negative filamentous bacteria with a cosmopolitan distribution. The research describing <i>Tenacibaculum</i> genomes stems primarily from Norway and Chile due to their impacts on salmon aquaculture. Canadian salmon aquaculture also expe...
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| Format: | Article |
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MDPI AG
2023-01-01
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| Series: | Pathogens |
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| Online Access: | https://www.mdpi.com/2076-0817/12/1/101 |
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| author | Joseph P. Nowlan Ashton N. Sies Scott R. Britney Andrew D. S. Cameron Ahmed Siah John S. Lumsden Spencer Russell |
| author_facet | Joseph P. Nowlan Ashton N. Sies Scott R. Britney Andrew D. S. Cameron Ahmed Siah John S. Lumsden Spencer Russell |
| author_sort | Joseph P. Nowlan |
| collection | DOAJ |
| description | <i>Tenacibaculum</i> is a genus of Gram-negative filamentous bacteria with a cosmopolitan distribution. The research describing <i>Tenacibaculum</i> genomes stems primarily from Norway and Chile due to their impacts on salmon aquaculture. Canadian salmon aquaculture also experiences mortality events related to the presence of <i>Tenacibaculum</i> spp., yet no Canadian <i>Tenacibaculum</i> genomes are publicly available. Ribosomal DNA sequencing of 16S and four species-specific 16S quantitative-PCR assays were used to select isolates cultured from Atlantic salmon with mouthrot in British Columbia (BC), Canada. Ten isolates representing four known and two unknown species of <i>Tenacibaculum</i> were selected for shotgun whole genome sequencing using the Oxford Nanopore’s MinION platform. The genome assemblies achieved closed circular chromosomes for seven isolates and long contigs for the remaining three isolates. Average nucleotide identity analysis identified <i>T. ovolyticum</i>, <i>T. maritimum</i>, <i>T. dicentrarchi</i>, two genomovars of <i>T. finnmarkense</i>, and two proposed novel species <i>T. pacificus</i> sp. nov. type strain 18-2881-A<sup>T</sup> and <i>T. retecalamus</i> sp. nov. type strain 18-3228-7B<sup>T</sup>. Annotation in most of the isolates predicted putative virulence and antimicrobial resistance genes, most-notably toxins (i.e., hemolysins), type-IX secretion systems, and oxytetracycline resistance. Comparative analysis with the <i>T. maritimum</i> type-strain predicted additional toxins and numerous C-terminal secretion proteins, including an M12B family metalloprotease in the <i>T. maritimum</i> isolates from BC. The genomic prediction of virulence-associated genes provides important targets for studies of mouthrot disease, and the annotation of the antimicrobial resistance genes provides targets for surveillance and diagnosis in veterinary medicine. |
| first_indexed | 2024-03-09T11:29:37Z |
| format | Article |
| id | doaj.art-87fb02e29b134d5397a2e76c9e566561 |
| institution | Directory Open Access Journal |
| issn | 2076-0817 |
| language | English |
| last_indexed | 2024-03-09T11:29:37Z |
| publishDate | 2023-01-01 |
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| spelling | doaj.art-87fb02e29b134d5397a2e76c9e5665612023-11-30T23:53:44ZengMDPI AGPathogens2076-08172023-01-0112110110.3390/pathogens12010101Genomics of <i>Tenacibaculum</i> Species in British Columbia, CanadaJoseph P. Nowlan0Ashton N. Sies1Scott R. Britney2Andrew D. S. Cameron3Ahmed Siah4John S. Lumsden5Spencer Russell6Center for Innovation in Fish Health, Vancouver Island University, Nanaimo, BC V9R 5S5, CanadaDepartment of Biology, University of Regina, Regina, SK S4S 0A2, CanadaCenter for Innovation in Fish Health, Vancouver Island University, Nanaimo, BC V9R 5S5, CanadaDepartment of Biology, University of Regina, Regina, SK S4S 0A2, CanadaBC Center for Aquatic Health Sciences, Campbell River, BC V9W 2C2, CanadaDepartment of Pathobiology, University of Guelph, Guelph, ON N1G 2W1, CanadaCenter for Innovation in Fish Health, Vancouver Island University, Nanaimo, BC V9R 5S5, Canada<i>Tenacibaculum</i> is a genus of Gram-negative filamentous bacteria with a cosmopolitan distribution. The research describing <i>Tenacibaculum</i> genomes stems primarily from Norway and Chile due to their impacts on salmon aquaculture. Canadian salmon aquaculture also experiences mortality events related to the presence of <i>Tenacibaculum</i> spp., yet no Canadian <i>Tenacibaculum</i> genomes are publicly available. Ribosomal DNA sequencing of 16S and four species-specific 16S quantitative-PCR assays were used to select isolates cultured from Atlantic salmon with mouthrot in British Columbia (BC), Canada. Ten isolates representing four known and two unknown species of <i>Tenacibaculum</i> were selected for shotgun whole genome sequencing using the Oxford Nanopore’s MinION platform. The genome assemblies achieved closed circular chromosomes for seven isolates and long contigs for the remaining three isolates. Average nucleotide identity analysis identified <i>T. ovolyticum</i>, <i>T. maritimum</i>, <i>T. dicentrarchi</i>, two genomovars of <i>T. finnmarkense</i>, and two proposed novel species <i>T. pacificus</i> sp. nov. type strain 18-2881-A<sup>T</sup> and <i>T. retecalamus</i> sp. nov. type strain 18-3228-7B<sup>T</sup>. Annotation in most of the isolates predicted putative virulence and antimicrobial resistance genes, most-notably toxins (i.e., hemolysins), type-IX secretion systems, and oxytetracycline resistance. Comparative analysis with the <i>T. maritimum</i> type-strain predicted additional toxins and numerous C-terminal secretion proteins, including an M12B family metalloprotease in the <i>T. maritimum</i> isolates from BC. The genomic prediction of virulence-associated genes provides important targets for studies of mouthrot disease, and the annotation of the antimicrobial resistance genes provides targets for surveillance and diagnosis in veterinary medicine.https://www.mdpi.com/2076-0817/12/1/101phylogenetics<i>de novo</i> assemblyvirulenceantimicrobial resistancediversity<i>Tenacibaculum</i> |
| spellingShingle | Joseph P. Nowlan Ashton N. Sies Scott R. Britney Andrew D. S. Cameron Ahmed Siah John S. Lumsden Spencer Russell Genomics of <i>Tenacibaculum</i> Species in British Columbia, Canada Pathogens phylogenetics <i>de novo</i> assembly virulence antimicrobial resistance diversity <i>Tenacibaculum</i> |
| title | Genomics of <i>Tenacibaculum</i> Species in British Columbia, Canada |
| title_full | Genomics of <i>Tenacibaculum</i> Species in British Columbia, Canada |
| title_fullStr | Genomics of <i>Tenacibaculum</i> Species in British Columbia, Canada |
| title_full_unstemmed | Genomics of <i>Tenacibaculum</i> Species in British Columbia, Canada |
| title_short | Genomics of <i>Tenacibaculum</i> Species in British Columbia, Canada |
| title_sort | genomics of i tenacibaculum i species in british columbia canada |
| topic | phylogenetics <i>de novo</i> assembly virulence antimicrobial resistance diversity <i>Tenacibaculum</i> |
| url | https://www.mdpi.com/2076-0817/12/1/101 |
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