1887

Abstract

A recently described emergent disease of ornamental fish has been associated with an species positive for the surface protective antigen () C gene. Whole genome sequencing was performed on five isolates from diseased ornamental fish. In addition, these isolates were compared to and other -positive species isolated from terrestrial and marine mammals, birds and fish using multi-locus sequence analysis (MLSA). The genomes of fish pathogenic isolates were genetically distinct from , sharing 86.61–86.94 % average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values of 31.6–32.2 %, but 99.01–99.11 % ANI and 90.8–91.9 % dDDH values with the uncharacterized -positive sp. strain 2 isolated from swine. The findings indicate the -positive fish and swine isolates are conspecific and represent a previously unrecognized taxon. While phylogenies inferred from MLSA sequences confirm this conclusion, slight genetic differences between the fish isolates and swine strain 2 were indicated. Bath immersion challenge trials were conducted using tiger barbs () exposed by immersion to 10 c.f.u. ml of three fish pathogenic species, and three and two isolates as a model of infection. Thirty days post-challenge, cumulative mean percentage survival was 37 % for the , 100 % for the and 13 % for the isolates, revealing differences in virulence among the various genotypes in fish. Genetic findings and observed differences in virulence demonstrate the fish pathogenic isolates represent a novel species, for which the name sp. nov. is proposed. The type strain is 15TAL0474 (=NRRL B-65533=ATCC-TSD-175=DSM 110099).

Keyword(s): emergent , ornamental and aquaculture
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2019-11-04
2019-11-17
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References

  1. Reboli AC, Farrar WE. Erysipelothrix rhusiopathiae: an occupational pathogen. Clin Microbiol Rev 1989;2:354–359 [CrossRef]
    [Google Scholar]
  2. Pomaranski EK, Reichley SR, Yanong R, Shelley J, Pouder DB et al. Characterization of spaC-type Erysipelothrix sp. isolates causing systemic disease in ornamental fish. J Fish Dis 2018;41:49–60 [CrossRef]
    [Google Scholar]
  3. Chong RSM, Shinwari MW, Amigh MJ, Aravena-Roman M, Riley TV. First report of Erysipelothrix rhusiopathiae- associated septicaemia and histologic changes in cultured Australian eels, Anguilla reinhardtii (Steindachner, 1867) and A. australis (Richardson, 1841). J Fish Dis 2015;38:839–847 [CrossRef]
    [Google Scholar]
  4. Wang LT, Lee FL, Tai CJ, Kasai H. Comparison of gyrB gene sequences, 16S rRNA gene sequences and DNA-DNA hybridization in the Bacillus subtilis group. Int J Syst Evol Microbiol 2007;57:1846–1850 [CrossRef]
    [Google Scholar]
  5. To H, Nagai S. Genetic and antigenic diversity of the surface protective antigen proteins of Erysipelothrix rhusiopathiae. Clin Vaccine Immunol 2007;14:813–820 [CrossRef]
    [Google Scholar]
  6. Shen HG, Bender JS, Opriessnig T. Identification of surface protective antigen (spa) types in Erysipelothrix reference strains and diagnostic samples by spa multiplex real-time and conventional PCR assays. J Appl Microbiol 2010;109:1227–1233 [CrossRef]
    [Google Scholar]
  7. Ingebritson AL, Roth JA, Hauer PJ. Erysipelothrix rhusiopathiae: association of Spa-type with serotype and role in protective immunity. Vaccine 2010;28:2490–2496 [CrossRef]
    [Google Scholar]
  8. Takeshi K, Makino S, Ikeda T, Takada N, Nakashiro A et al. Direct and rapid detection by PCR of Erysipelothrix sp. DNAs prepared from bacterial strains and animal tissues. J Clin Microbiol 1999;37:4093–4098
    [Google Scholar]
  9. Takahashi T, Fujisawa T, Tamura Y, Suzuki S, Muramatsu M et al. DNA relatedness among Erysipelothrix rhusiopathiae strains representing all twenty-three serovars and Erysipelothrix tonsillarum. Int J Syst Bacteriol 1992;42:469–473 [CrossRef]
    [Google Scholar]
  10. Bender JS, Shen HG, Irwin CK, Schwartz KJ, Opriessnig T. Characterization of Erysipelothrix species isolates from clinically affected pigs, environmental samples, and vaccine strains from six recent swine erysipelas outbreaks in the United States. Clin Vaccine Immunol 2010;17:1605–1611 [CrossRef]
    [Google Scholar]
  11. Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH et al. Canu: scalable and accurate long-read assembly via adaptive κ-mer weighting and repeat separation. Genome Res 2017
    [Google Scholar]
  12. Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 2014;9:e112963 [CrossRef]
    [Google Scholar]
  13. Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M et al. Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 2012;28:1647–1649 [CrossRef]
    [Google Scholar]
  14. Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S et al. RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep 2015;5:8365 [CrossRef]
    [Google Scholar]
  15. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. Ncbi prokaryotic genome annotation pipeline. Nucleic Acids Res 2016;44:66146624 [CrossRef]
    [Google Scholar]
  16. Ogawa Y, Ooka T, Shi F, Ogura Y, Nakayama K et al. The genome of Erysipelothrix rhusiopathiae, the causative agent of swine erysipelas, reveals new insights into the evolution of Firmicutes and the organism's intracellular adaptations. J Bacteriol 2011;193:2959–2971 [CrossRef]
    [Google Scholar]
  17. Tang HB, Xie J, Wang L, Liu F, Wu J. Complete genome sequence of Erysipelothrix rhusiopathiae strain GXBY-1 isolated from acute swine erysipelas outbreaks in South China. Genom Data 2016;8:70–71 [CrossRef]
    [Google Scholar]
  18. Kwok AHY, Li Y, Jiang J, Jiang P, Leung FC. Complete genome assembly and characterization of an outbreak strain of the causative agent of swine erysipelas – Erysipelothrix rhusiopathiae SY1027. BMC Microbiol 2014;14:176 [CrossRef]
    [Google Scholar]
  19. Rodriguez-R LM, Konstantinidis KT. The enveomics collection : a toolbox for specialized analyses of microbial genomes and metagenomes. Peer J Prepr 2016
    [Google Scholar]
  20. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013;14:60 [CrossRef]
    [Google Scholar]
  21. Alikhan N-F, Petty NK, Ben Zakour NL, Beatson SA. Blast ring image generator (BRIG): simple prokaryote genome comparisons. BMC Genomics 2011;12:402 [CrossRef]
    [Google Scholar]
  22. Tatusov RL, Galperin MY, Natale DA, Koonin EV. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 2000;28:33–36 [CrossRef]
    [Google Scholar]
  23. Janßen T, Voss M, Kühl M, Semmler T, Philipp H-C et al. A combinational approach of multilocus sequence typing and other molecular typing methods in unravelling the epidemiology of Erysipelothrix rhusiopathiae strains from poultry and mammals. Vet Res 2015;46:84 [CrossRef]
    [Google Scholar]
  24. Edgar RC. Muscle: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004;32:1792–1797 [CrossRef]
    [Google Scholar]
  25. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17:368–376 [CrossRef]
    [Google Scholar]
  26. Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 1993;10:512–526
    [Google Scholar]
  27. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0. Molecular biology and evolution. Mol Biol Evol
    [Google Scholar]
  28. Reichley SR, Ware C, Steadman J, Gaunt PS, García JC et al. Comparative phenotypic and genotypic analysis of Edwardsiella isolates from different hosts and geographic origins, with emphasis on isolates formerly classified as E. tarda, and evaluation of diagnostic methods. J Clin Microbiol 2017;55:3466–3491 [CrossRef]
    [Google Scholar]
  29. Kim M, Oh H-S, Park S-C, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014;64:346–351 [CrossRef]
    [Google Scholar]
  30. Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ani analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 2018;9:5114 [CrossRef]
    [Google Scholar]
  31. Stackebrandt E, Goebel BM. Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Evol Microbiol 1994
    [Google Scholar]
  32. Forde T, Biek R, Zadoks R, Workentine ML, De Buck J et al. Genomic analysis of the multi-host pathogen Erysipelothrix rhusiopathiae reveals extensive recombination as well as the existence of three generalist clades with wide geographic distribution. BMC Genomics 2016;17:461 [CrossRef]
    [Google Scholar]
  33. Richter M, Rossello-Mora R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci 2009
    [Google Scholar]
  34. Konstantinidis KT, Ramette A, Tiedje JM.The bacterial species definition in the genomic era Philosophical Transactions of the Royal Society B: Biological Sciences361 2006; pp1929–1940 [CrossRef]
    [Google Scholar]
  35. Harada K, Furui Y, Takahashi T. Spa type of Erysipelothrix strains and its association with virulence of Erysipelothrix strains in mice and swine. African J Microbiol Res 2012;6:7123–7127
    [Google Scholar]
  36. Stackebrandt E, Reboli AC, Farrar WE.The genus Erysipelothrix The Prokaryotes Springer; 2006; pp492–510
    [Google Scholar]
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