1887

Abstract

The virulence of is variable depending on its virulence determinants. A strain, in which the virulence is governed by the and genes, can cause acute hepatopancreatic necrosis disease (AHPND) in shrimps. Some that are non-AHPND strains also cause shrimp diseases and result in huge economic losses, while their pathogenicity and pathogenesis remain unclear. In this study, a non-AHPND , TJA114, was isolated from diseased associated with a high mortality. To understand its virulence and adaptation to the external environment, whole-genome sequencing of this isolate was conducted, and its phenotypic profiles including pathogenicity, growth characteristics and nutritional requirements were investigated. Shrimps following artificial infection with this isolate presented similar clinical symptoms to the naturally diseased ones and generated obvious pathological lesions. The growth characteristics indicated that the isolate TJA114 could grow well under different salinity (10–55 p.p.t.), temperature (23–37 °C) and pH (6–10) conditions. Phenotype MicroArray results showed that this isolate could utilize a variety of carbon sources, amino acids and a range of substrates to help itself adapt to the high hyperosmotic and alkaline environments. Antimicrobial-susceptibility test showed that it was a multidrug-resistant bacterium. The whole-genomic analysis showed that this possessed many important functional genes associated with multidrug resistance, stress response, adhesions, haemolysis, putative secreted proteases, dedicated protein secretion systems and a variety of nutritional metabolic mechanisms. These annotated functional genes were confirmed by the phenotypic profiles. The results in this study indicated that this isolate possesses a high pathogenicity and strong environmental adaptability.

Funding
This study was supported by the:
  • the Scientific Research and Innovation Project of Tianjin Agricultural University in 2019 (Award 2019XY038)
    • Principle Award Recipient: XueZhang
  • the Science and Technology Project in the Field of Social Development in Tianjin Binhai New Area (Award BHXQKJXM-SF-2018-34)
    • Principle Award Recipient: YadongHuang
  • the Science and Technology Innovation Project of Shandong province (Award 2018SDKJ0406-4)
    • Principle Award Recipient: HongliQi
  • The Scientific Programs of Tianjin City (Award 19JCTPJC60100)
    • Principle Award Recipient: LimeiChen
  • the Innovation Team of Tianjin Fisheries Research System (Award ITTFRS2017009)
    • Principle Award Recipient: SunJingfeng
  • This is an open-access article distributed under the terms of the Creative Commons Attribution NonCommercial License.
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2021-05-05
2022-01-24
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References

  1. López-Cuadros I, García-Gasca A, Gomez-Anduro G, Escobedo-Fregoso C, Llera-Herrera RA et al. Isolation of the sex-determining gene Sex-lethal (Sxl) in Penaeus (Litopenaeus) vannamei (Boone, 1931) and characterization of its embryogenic, gametogenic, and tissue-specific expression. Gene 2018; 668:33–47 [View Article][PubMed]
    [Google Scholar]
  2. Thornber K, Verner-Jeffreys D, Hinchliffe S, Rahman MM, Bass D et al. Evaluating antimicrobial resistance in the global shrimp industry. Rev Aquac 2020; 12:966–986 [View Article][PubMed]
    [Google Scholar]
  3. Flegel TW. Historic emergence, impact and current status of shrimp pathogens in Asia. J Invertebr Pathol 2012; 110:166–173 [View Article][PubMed]
    [Google Scholar]
  4. Morales-Covarrubias MS, Cuéllar-Anjel J, Varela-Mejías A, Elizondo-Ovares C. Shrimp bacterial infections in Latin America: a review. Asian Fish Sci 2018; 31S:76–87
    [Google Scholar]
  5. Lee C-T, Chen I-T, Yang Y-T, Ko T-P, Huang Y-T et al. The opportunistic marine pathogen Vibrio parahaemolyticus becomes virulent by acquiring a plasmid that expresses a deadly toxin. Proc Natl Acad Sci USA 2015; 112:10798–10803 [View Article][PubMed]
    [Google Scholar]
  6. Ghenem L, Elhadi N, Alzahrani F, Nishibuchi M, Nishibuchi M. Vibrio parahaemolyticus: a review on distribution, pathogenesis, virulence determinants and epidemiology. Saudi J Med Med Sci 2017; 5:93–103 [View Article][PubMed]
    [Google Scholar]
  7. Garin-Fernandez A, Glöckner FO, Wichels A. Genomic characterization of filamentous phage vB_VpaI_VP-3218, an inducible prophage of Vibrio parahaemolyticus . Mar Genomics 2020; 53:100767 [View Article][PubMed]
    [Google Scholar]
  8. Shanmugasundaram S, Mayavu P, Manikandarajan T, Suriva M, Eswar A et al. Isolation and identification of Vibrio sp. in the hepatopancreas of cultured white Pacific shrimp (Litopenaeus vannamei). Int Lett Nat Sci 2015; 46:52–59 [View Article]
    [Google Scholar]
  9. Ananda Raja R, Sridhar R, Balachandran C, Palanisammi A, Ramesh S et al. Pathogenicity profile of Vibrio parahaemolyticus in farmed Pacific white shrimp, Penaeus vannamei . Fish Shellfish Immunol 2017; 67:368–381 [View Article][PubMed]
    [Google Scholar]
  10. Petronella N, Ronholm J. The mechanisms that regulate Vibrio parahaemolyticus virulence gene expression differ between pathotypes. Microb Genom 2018; 4:e000182 [View Article][PubMed]
    [Google Scholar]
  11. Soto-Rodriguez SA, Gomez-Gil B, Lozano-Olvera R, Bolan-Mejía M, Aguilar-Rendon KG et al. Pathological, genomic and phenotypical characterization of Vibrio parahaemolyticus, causative agent of acute hepatopancreatic necrosis disease (AHPND) in Mexico. Asian Fish Sci 2018; 31S:102–111 [View Article]
    [Google Scholar]
  12. Zhang BC, Liu F, Bian HH, Liu J, Pan LQ et al. Isolation, identification, and pathogenicity analysis of a Vibrio parahaemolyticus strain from Litopenaeus vannamei . Prog Fishery Sci 2012; 33:56–62
    [Google Scholar]
  13. Phiwsaiya K, Charoensapsri W, Taengphu S, Dong HT, Sangsuriya P et al. A natural Vibrio parahaemolyticus ΔpirAVp pirBVp+ mutant kills shrimp but produces neither PirVp toxins nor acute hepatopancreatic necrosis disease lesions. Appl Environ Microbiol 2017; 83:e00680-17 [View Article]
    [Google Scholar]
  14. Identification and toxicity analysis of a virulent Vibrio parahaemolyticus isolated from Litopenaeus vannamei . Marine Fisheries 2013; 35:479–484
    [Google Scholar]
  15. Kwong JC, McCallum N, Sintchenko V, Howden BP. Whole genome sequencing in clinical and public health microbiology. Pathology 2015; 47:199–210 [View Article][PubMed]
    [Google Scholar]
  16. Tagini F, Greub G. Bacterial genome sequencing in clinical microbiology: a pathogen-oriented review. Eur J Clin Microbiol Infect Dis 2017; 36:2007–2020 [View Article][PubMed]
    [Google Scholar]
  17. Cao S, Geng Y, Yu Z, Deng L, Gan W et al. Acinetobacter lwoffii, an emerging pathogen for fish in Schizothorax genus in China. Transbound Emerg Dis 2018; 65:1816–1822 [View Article][PubMed]
    [Google Scholar]
  18. Hannula M, Hanninen ML. Phylogenetic analysis of Helicobacter species based on partial gyrB gene sequences. Int J Syst Evol Microbiol 2007; 57:444–449 [View Article][PubMed]
    [Google Scholar]
  19. Han Z, Sun J, Lv A, Sung Y, Shi H et al. Isolation, identification and characterization of Shewanella algae from reared tongue sole, Cynoglossus semilaevis Günther. Aquaculture 2017; 468:356–362 [View Article]
    [Google Scholar]
  20. Bej AK, Patterson DP, Brasher CW, Vickery MC, Jones DD et al. Detection of total and hemolysin-producing Vibrio parahaemolyticus in shellfish using multiplex PCR amplification of tl, tdh and trh . J Microbiol Methods 1999; 36:215–225 [View Article][PubMed]
    [Google Scholar]
  21. Lai HC, Ng TH, Ando M, Lee C-T, Chen I-T et al. Pathogenesis of acute hepatopancreatic necrosis disease (AHPND) in shrimp. Fish Shellfish Immunol 2015; 47:1006–1014 [View Article][PubMed]
    [Google Scholar]
  22. Xian YY, Wei S, Yu C, Li ZY, MY Y. Novel multiplex polymerase chain reaction assay to detect virulence-related genes in Vibrio parahaemolyticus . Mod Food Sci Technol 2015; 31:309–315
    [Google Scholar]
  23. Ardui S, Ameur A, Vermeesch JR, Hestand MS. Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics. Nucleic Acids Res 2018; 46:2159–2168 [View Article][PubMed]
    [Google Scholar]
  24. Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS. PHAST: a fast phage search tool. Nucleic Acids Res 2011; 39:W347–W352 [View Article][PubMed]
    [Google Scholar]
  25. Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M et al. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 2006; 34:D354–D357 [View Article][PubMed]
    [Google Scholar]
  26. Li W, Jaroszewski L, Godzik A. Tolerating some redundancy significantly speeds up clustering of large protein databases. Bioinformatics 2002; 18:77–82 [View Article][PubMed]
    [Google Scholar]
  27. Eichinger V, Nussbaumer T, Platzer A, Jehl M-A, Arnold R et al. EffectiveDB – updates and novel features for a better annotation of bacterial secreted proteins and type III, IV, VI secretion systems. Nucleic Acids Res 2016; 44:D669–D674 [View Article][PubMed]
    [Google Scholar]
  28. Chen L, Xiong Z, Sun L, Yang J, Jin Q. VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors. Nucleic Acids Res 2012; 40:D641–D645 [View Article][PubMed]
    [Google Scholar]
  29. Jia B, Raphenya AR, Alcock B, Waglechner N, Guo P et al. CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database. Nucleic Acids Res 2017; 45:D566–D573 [View Article][PubMed]
    [Google Scholar]
  30. Maralit BA, Jaree P, Boonchuen P, Tassanakajon A, Somboonwiwat K. Differentially expressed genes in hemocytes of Litopenaeus vannamei challenged with Vibrio parahaemolyticus AHPND (VPAHPND) and VPAHPND toxin. Fish Shellfish Immunol 2018; 81:284–296 [View Article][PubMed]
    [Google Scholar]
  31. Deng Y, Su Y, Liu S, Guo Z, Cheng C et al. Identification of a novel small RNA srvg23535 in Vibrio alginolyticus ZJ-T and its characterization with phenotype microarray technology. Front Microbiol 2018; 9:2394 [View Article][PubMed]
    [Google Scholar]
  32. Buchanan RE, Gibbons NE. Bergey’s Manual of Determinative Bacteriology, 8th edn. Baltimore, MA: Williams and Wilkins; 1974
    [Google Scholar]
  33. Liu L, Xiao J, Zhang M, Zhu W, Xia X et al. A Vibrio owensii strain as the causative agent of AHPND in cultured shrimp, Litopenaeus vannamei . J Invertebr Pathol 2018; 153:156–164 [View Article][PubMed]
    [Google Scholar]
  34. Jeon HJ, Noda M, Matoba Y, Kumagai T, Sugiyama M. Crystal structure and mutagenic analysis of a bacteriocin immunity protein, Mun-im. Biochem Biophys Res Commun 2009; 378:574–578 [View Article][PubMed]
    [Google Scholar]
  35. Gerth U, Krüger E, Derré I, Msadek T, Hecker M. Stress induction of the Bacillus subtilis clpP gene encoding a homologue of the proteolytic component of the Clp protease and the involvement of ClpP and ClpX in stress tolerance. Mol Microbiol 1998; 28:787–802 [View Article][PubMed]
    [Google Scholar]
  36. Li X, Zeng Y, Gao Y, Zheng X, Zhang Q et al. The ClpP protease homologue is required for the transmission traits and cell division of the pathogen Legionella pneumophila . BMC Microbiol 2010; 10:54 [View Article][PubMed]
    [Google Scholar]
  37. Fu S, Wang L, Tian H, Wei D, Liu Y. Pathogenicity and genomic characterization of Vibrio parahaemolyticus strain PB1937 causing shrimp acute hepatopancreatic necrosis disease in China. Ann Microbiol 2018; 68:175–184 [View Article]
    [Google Scholar]
  38. McCarter LL. Polar flagellar motility of the Vibrionaceae . Microbiol Mol Biol Rev 2001; 65:445–462 [View Article][PubMed]
    [Google Scholar]
  39. Aagesen AM, Häse CC. Sequence analyses of type IV pili from Vibrio cholerae, Vibrio parahaemolyticus, and Vibrio vulnificus . Microb Ecol 2012; 64:509–524 [View Article][PubMed]
    [Google Scholar]
  40. Lee K-J, Lee NY, Han Y-S, Kim J, Lee K-H et al. Functional characterization of the IlpA protein of Vibrio vulnificus as an adhesin and its role in bacterial pathogenesis. Infect Immun 2010; 78:2408–2417 [View Article][PubMed]
    [Google Scholar]
  41. Krachler AM, Ham H, Orth K. Outer membrane adhesion factor multivalent adhesion molecule 7 initiates host cell binding during infection by Gram-negative pathogens. Proc Natl Acad Sci USA 2011; 108:11614–11619 [View Article][PubMed]
    [Google Scholar]
  42. Yildiz FH, Visick KL. Vibrio biofilms: so much the same yet so different. Trends Microbiol 2009; 17:109–118 [View Article][PubMed]
    [Google Scholar]
  43. Sudheesh PS, Xu H-S. Pathogenicity of Vibrio parahaemolyticus in tiger prawn Penaeus monodon Fabricius: possible role of extracellular proteases. Aquaculture 2001; 196:37–46 [View Article]
    [Google Scholar]
  44. Wang R, Zhong Y, Gu X, Yuan J, Saeed AF et al. Corrigendum: the pathogenesis, detection, and prevention of Vibrio parahaemolyticus . Front Microbiol 2015; 6:437 [View Article][PubMed]
    [Google Scholar]
  45. Weaver EA, Wyckoff EE, Mey AR, Morrison R, Payne SM. FeoA and FeoC are essential components of the Vibrio cholerae ferrous iron uptake system, and FeoC interacts with FeoB. J Bacteriol 2013; 195:4826–4835 [View Article][PubMed]
    [Google Scholar]
  46. Bach FH. Heme oxygenase-1: a therapeutic amplification funnel. FASEB J 2005; 19:1216–1219 [View Article][PubMed]
    [Google Scholar]
  47. Sandkvist M. Type II secretion and pathogenesis. Infect Immun 2001; 69:3523–3535 [View Article][PubMed]
    [Google Scholar]
  48. Chernyatina AA, Low HH. Core architecture of a bacterial type II secretion system. Nat Commun 2019; 10:5437 [View Article][PubMed]
    [Google Scholar]
  49. Bhattacharjee RN, Park KS, Kumagai Y, Okada K, Yamamoto M et al. VP1686, a Vibrio type III secretion protein, induces Toll-like receptor-independent apoptosis in macrophage through NF-κB inhibition. J Biol Chem 2006; 281:36897–36904 [View Article][PubMed]
    [Google Scholar]
  50. Burdette DL, Seemann J, Orth K. Vibrio VopQ induces PI3-kinase-independent autophagy and antagonizes phagocytosis. Mol Microbiol 2009; 73:639–649 [View Article][PubMed]
    [Google Scholar]
  51. Salomon D, Guo Y, Kinch LN, Grishin NV, Gardner KH et al. Effectors of animal and plant pathogens use a common domain to bind host phosphoinositides. Nat Commun 2013; 4:2973 [View Article][PubMed]
    [Google Scholar]
  52. Waddell B, Southward CM, McKenna N, DeVinney R. Identification of VPA0451 as the specific chaperone for the Vibrio parahaemolyticus chromosome 1 type III-secreted effector VPA0450. FEMS Microbiol Lett 2014; 353:141–150 [View Article][PubMed]
    [Google Scholar]
  53. Okada N, Iida T, Park KS, Goto N, Yasunaga T et al. Identification and characterization of a novel type III secretion system in trh-positive Vibrio parahaemolyticus strain TH3996 reveal genetic lineage and diversity of pathogenic machinery beyond the species level. Infect Immun 2009; 77:904–913 [View Article][PubMed]
    [Google Scholar]
  54. Kumar BK, Deekshit VK, Rai P, Shekar M, Karunasagar I et al. Presence of T3SS2β genes in trh+ Vibrio parahaemolyticus isolated from seafood harvested along Mangalore Coast, India. Lett Appl Microbiol 2014; 58:440–446 [View Article][PubMed]
    [Google Scholar]
  55. Backert S, Meyer TF. Type IV secretion systems and their effectors in bacterial pathogenesis. Curr Opin Microbiol 2006; 9:207–217 [View Article][PubMed]
    [Google Scholar]
  56. Hachani A, Wood TE, Filloux A. Type VI secretion and anti-host effectors. Curr Opin Microbiol 2016; 29:81–93 [View Article][PubMed]
    [Google Scholar]
  57. Yu Y, Fang L, Zhang Y, Sheng H, Fang W. VgrG2 of type VI secretion system 2 of Vibrio parahaemolyticus induces autophagy in macrophages. Front Microbiol 2015; 6:168 [View Article][PubMed]
    [Google Scholar]
  58. Deutscher J, Francke C, Postma PW. How phosphotransferase system-related protein phosphorylation regulates carbohydrate metabolism in bacteria. Microbiol Mol Biol Rev 2006; 70:939–1031 [View Article][PubMed]
    [Google Scholar]
  59. Wang Q, Yang M, Xiao J, Wu H, Wang X et al. Genome sequence of the versatile fish pathogen Edwardsiella tarda provides insights into its adaptation to broad host ranges and intracellular niches. PLoS One 2009; 4:e7646 [View Article][PubMed]
    [Google Scholar]
  60. Hayrapetyan H, Tempelaars M, Groot MN, Abee T. Bacillus cereus ATCC 14579 RpoN (sigma 54) is a pleiotropic regulator of growth, carbohydrate metabolism, motility, biofilm formation and toxin production. PLoS One 2015; 10:e0134872 [View Article][PubMed]
    [Google Scholar]
  61. Missiakas D, Mayer MP, Lemaire M, Georgopoulos C, Raina S. Modulation of the Escherichia coli σE (RpoE) heat-shock transcription-factor activity by the RseA, RseB and RseC proteins. Mol Microbiol 1997; 24:355–371 [View Article][PubMed]
    [Google Scholar]
  62. Wösten MMSM, Van Dijk L, Veenendaal AKJ, De Zoete MR, Bleumink-Pluijm NMC et al. Temperature-dependent FlgM/FliA complex formation regulates Campylobacter jejuni flagella length. Mol Microbiol 2010; 75:1577–1591 [View Article][PubMed]
    [Google Scholar]
  63. Vasudevan P, Venkitanarayanan K. Role of the rpoS gene in the survival of Vibrio parahaemolyticus in artificial seawater and fish homogenate. J Food Prot 2006; 69:1438–1442 [View Article][PubMed]
    [Google Scholar]
  64. Liu T, Wang KY, Wang J, Chen DF, Huang XL et al. Genome sequence of the fish pathogen Yersinia ruckeri SC09 provides insights into niche adaptation and pathogenic mechanism. Int J Mol Sci 2016; 17:557 [View Article][PubMed]
    [Google Scholar]
  65. Nakayama H, Yoshida K, Ono H, Murooka Y, Shinmyo A. Ectoine, the compatible solute of Halomonas elongata, confers hyperosmotic tolerance in cultured tobacco cells. Plant Physiol 2000; 122:1239–1247 [View Article][PubMed]
    [Google Scholar]
  66. Tanaka Y, Kimura B, Takahashi H, Watanabe T, Obata H et al. Lysine decarboxylase of Vibrio parahaemolyticus: kinetics of transcription and role in acid resistance. J Appl Microbiol 2008; 104:1283–1293 [View Article][PubMed]
    [Google Scholar]
  67. Ongagna-Yhombi SY, Boyd EF. Biosynthesis of the osmoprotectant ectoine, but not glycine betaine, is critical for survival of osmotically stressed Vibrio parahaemolyticus cells. Appl Environ Microbiol 2013; 79:5038–5049 [View Article][PubMed]
    [Google Scholar]
  68. Le TTT, Mawatari K, Maetani M, Yamamoto T, Hayashida S et al. VP2118 has major roles in Vibrio parahaemolyticus response to oxidative stress. Biochim Biophys Acta 2012; 1820:1686–1692 [View Article][PubMed]
    [Google Scholar]
  69. Lightner DV, Redman RM, Pantoja CR, Tran L. Early mortality syndrome affects shrimp in Asia. Glob Aquacul Advocate 2012; 15:40
    [Google Scholar]
  70. Williams SL, Jensen RV, Kuhn DD, Stevens AM. Analyzing the metabolic capabilities of a Vibrio parahaemolyticus strain that causes early mortality syndrome in shrimp. Aquaculture 2017; 476:44–48
    [Google Scholar]
  71. Stülke J, Hillen W. Carbon catabolite repression in bacteria. Curr Opin Microbiol 1999; 2:195–201 [View Article]
    [Google Scholar]
  72. Tan CW, Rukayadi Y, Hasan H, Thung TY, Lee E et al. Prevalence and antibiotic resistance patterns of Vibrio parahaemolyticus isolated from different types of seafood in Selangor, Malaysia. Saudi J Biol Sci 2020; 27:1602–1608 [View Article][PubMed]
    [Google Scholar]
  73. Jia D, Shi C, Huang J, Zhang Q, Wan X et al. Identification and pathogenicity analysis of bacterial pathogen associated with acute hepatopancreatic necrosis disease (AHPND) in the Pacific shrimp Litopenaeus vannamei . Prog Fishery Sci 2018; 39:103–111
    [Google Scholar]
  74. Shaw KS, Rosenberg Goldstein RE, He X, Jacobs JM, Crump BC et al. Antimicrobial susceptibility of Vibrio vulnificus and Vibrio parahaemolyticus recovered from recreational and commercial areas of Chesapeake Bay and Maryland Coastal Bays. PLoS One 2014; 9:e89616 [View Article][PubMed]
    [Google Scholar]
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