Journal of Microbiology and Biotechnology

  • 제34권5호
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  • Pages.1146-1153
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  • 2024
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  • 1017-7825(pISSN)
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  • 1738-8872(eISSN)
한국미생물·생명공학회 (The Korean Society for Microbiology and Biotechnology)
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The Use of the Internal Transcribed Spacer Region for Phylogenetic Analysis of the Microsporidian Parasite Enterocytozoon hepatopenaei Infecting Whiteleg Shrimp (Penaeus vannamei) and for the Development of a Nested PCR as Its Diagnostic Tool

  • Ju Hee Lee (Laboratory of Aquatic Biomedicine, College of Veterinary Medicine, Kyungpook National University) ;
  • Hye Jin Jeon (Laboratory of Aquatic Biomedicine, College of Veterinary Medicine, Kyungpook National University) ;
  • Sangsu Seo (Laboratory of Aquatic Biomedicine, College of Veterinary Medicine, Kyungpook National University) ;
  • Chorong Lee (Laboratory of Aquatic Biomedicine, College of Veterinary Medicine, Kyungpook National University) ;
  • Bumkeun Kim (Laboratory of Aquatic Biomedicine, College of Veterinary Medicine, Kyungpook National University) ;
  • Dong-Mi Kwak (Laboratory of Aquatic Biomedicine, College of Veterinary Medicine, Kyungpook National University) ;
  • Man Hee Rhee (Laboratory of Aquatic Biomedicine, College of Veterinary Medicine, Kyungpook National University) ;
  • Patharapol Piamsomboon (Department of Veterinary Medicine, Faculty of Veterinary Science, Chulalongkorn University) ;
  • Yani Lestari Nuraini (Fish Health and Environmental Laboratory, Brackishwater Aquaculture Development Center) ;
  • Chang Uook Je (Ministry of Agriculture, Food and Rural Affairs) ;
  • Seon Young Park (Division of Animal and Dairy Sciences, College of Agriculture and Life Science, Chungnam National University) ;
  • Ji Hyung Kim (Department of Food Science and Biotechnology, Gachon University) ;
  • Jee Eun Han (Laboratory of Aquatic Biomedicine, College of Veterinary Medicine, Kyungpook National University)
  • 투고 : 2024.01.10
  • 심사 : 2024.02.14
  • 발행 : 2024.05.28
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초록

The increasing economic losses associated with growth retardation caused by Enterocytozoon hepatopenaei (EHP), a microsporidian parasite infecting penaeid shrimp, require effective monitoring. The internal transcribed spacer (ITS)-1 region, the non-coding region of ribosomal clusters between 18S and 5.8S rRNA genes, is widely used in phylogenetic studies due to its high variability. In this study, the ITS-1 region sequence (~600-bp) of EHP was first identified, and primers for a polymerase chain reaction (PCR) assay targeting that sequence were designed. A newly developed nested-PCR method successfully detected the EHP in various shrimp (Penaeus vannamei and P. monodon) and related samples, including water and feces collected from Indonesia, Thailand, South Korea, India, and Malaysia. The primers did not cross-react with other hosts and pathogens, and this PCR assay is more sensitive than existing PCR detection methods targeting the small subunit ribosomal RNA (SSU rRNA) and spore wall protein (SWP) genes. Phylogenetic analysis based on the ITS-1 sequences indicated that the Indonesian strain was distinct (86.2% nucleotide sequence identity) from other strains collected from Thailand and South Korea, and also showed the internal diversity among Thailand (N = 7, divided into four branches) and South Korean (N = 5, divided into two branches) samples. The results revealed the ability of the ITS-1 region to determine the genetic diversity of EHP from different geographical origins.

키워드

과제정보

This research was supported by the Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (NRF2019R1C1C1006212 and NRF-2022R1I1A3066435). The work was also supported by the Development of technology for biomaterialization of marine fisheries byproducts of the Korea Institute of Marine Science & Technology Promotion (KIMST) funded by the Ministry of Oceans and Fisheries (KIMST-20220128).

참고문헌

  1. Chayaburakul K, Nash G, Pratanpipat P, Sriurairatana S, Withyachumnarnkul B. 2004. Multiple pathogens found in growth-retarded black tiger shrimp Penaeus monodon cultivated in Thailand. Dis. Aquat. Org. 60: 89-96. https://doi.org/10.3354/dao060089
  2. Tourtip S, Wongtripop S, Stentiford GD, Bateman KS, Sriurairatana S, Chavadej J, et al. 2009. Enterocytozoon hepatopenaei sp. nov.(Microsporida: Enterocytozoonidae), a parasite of the black tiger shrimp Penaeus monodon (Decapoda: Penaeidae): fine structure and phylogenetic relationships. J. Invertebr. Pathol. 102: 21-29. https://doi.org/10.1016/j.jip.2009.06.004
  3. Tang KF, Pantoja CR, Redman RM, Han JE, Tran LH, Lightner DV. 2015. Development of in situ hybridization and PCR assays for the detection of Enterocytozoon hepatopenaei (EHP), a microsporidian parasite infecting penaeid shrimp. J. Invertebr. Pathol. 130: 37-41. https://doi.org/10.1016/j.jip.2015.06.009
  4. Tang KF, Aranguren LF, Piamsomboon P, Han JE, Maskaykina IY, Schmidt MM. 2017. Detection of the microsporidian Enterocytozoon hepatopenaei (EHP) and Taura syndrome virus in Penaeus vannamei cultured in Venezuela. Aquaculture 480: 17-21. https://doi.org/10.1016/j.aquaculture.2017.07.043
  5. Ma C, Fan S, Wang Y, Yang H, Qiao Y, Jiang G, et al. 2021. Rapid detection of Enterocytozoon hepatopenaei infection in shrimp with a real-time isothermal recombinase polymerase amplification assay. Front. Cell. Infect. Microbiol. 11: 631960.
  6. Jaroenlak P, Sanguanrut P, Williams BA, Stentiford GD, Flegel TW, Sritunyalucksana K, et al. 2016. A nested PCR assay to avoid false positive detection of the microsporidian Enterocytozoon hepatopenaei (EHP) in environmental samples in shrimp farms. PLoS One 11: e0166320.
  7. Vijayan, K.K., 2018. Visual loop-mediated isothermal amplification (LAMP) for the rapid diagnosis of Enterocytozoon hepatopenaei (EHP) infection. Parasitol. Res. 117: 1485-1493. https://doi.org/10.1007/s00436-018-5828-4
  8. Piamsomboon P, Choi SK, Hanggono B, Nuraini YL, Wati F Tang, K, et al. 2019. Quantification of Enterocytozoon hepatopenaei (EHP) in penaeid shrimps from Southeast Asia and Latin America using taqman probe-based quantitative PCR. Pathogens 8: 233.
  9. Froeschke, G., von der Heyden, S. 2014. A review of molecular approaches for investigating patterns of coevolution in marine hostparasite relationships. Adv. Parasitol. 84: 209-252. https://doi.org/10.1016/B978-0-12-800099-1.00004-1
  10. Chu, K.H., Li, C.P., Ho, H.Y. 2001. The first internal transcribed spacer (ITS-1) of ribosomal DNA as a molecular marker for phylogenetic and population analyses in crustacea. Mar. Biotechnol. 3: 355-361. https://doi.org/10.1007/s10126001-0014-5
  11. Mahe S, Duhamel M, Le Calvez T, Guillot L, Sarbu L, Bretaudeau A, et al. 2012. PHYMYCO-DB: a curated database for analyses of fungal diversity and evolution. PLoS One 7: e43117.
  12. Mirjalali H, Mirhendi H, Meamar AR, Mohebali M, Askari Z, Mirsamadi ES, et al. 2015. Genotyping and molecular analysis of Enterocytozoon bieneusi isolated from immunocompromised patients in Iran. Infect. Genet. Sel. Evol. 36: 244-249. https://doi.org/10.1016/j.meegid.2015.09.022
  13. Henriques-Gil N, Haro M, Izquierdo F, Fenoy S, del Aguila C. 2010. Phylogenetic approach to the variability of the microsporidian Enterocytozoon bieneusi and its implications for inter-and intrahost transmission. Appl. Environ. Microbiol. 76: 3333-3342. https://doi.org/10.1128/AEM.03026-09
  14. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19: 455-477. https://doi.org/10.1089/cmb.2012.0021
  15. Kajitani R, Yoshimura D, Okuno M, Minakuchi Y, Kagoshima H, Fujiyama A, et al. 2019. Platanus-allee is a de novo haplotype assembler enabling a comprehensive access to divergent heterozygous regions. Nat. Commun. 10: 1702.
  16. Wiredu Boakye D, Jaroenlak P, Prachumwat A, Williams TA, Bateman KS, Itsathitphaisarn, O, et al. 2017. Decay of the glycolytic pathway and adaptation to intranuclear parasitism within Enterocytozoonidae microsporidia. Environ. Microbiol. 19: 2077-2089. https://doi.org/10.1111/1462-2920.13734
  17. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, et al. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947-2948. https://doi.org/10.1093/bioinformatics/btm404
  18. Hall, T.A. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 41: 95-98.
  19. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. 2018. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35: 1547-1549. https://doi.org/10.1093/molbev/msy096
  20. Ha NTH, Ha DT, Thuy NT, Lien VTK. 2010. Enterocytozoon hepatopenaei parasitizing on tiger shrimp (Penaeus monodon) infected by white feces culture in Vietnam, has been detected. Agric. Rural Dev. Sci. Technol. (translation from Vietnamese) 12: 45-50.
  21. Rajendran KV, Shivam S, Praveena PE, Rajan JJS, Kumar TS, Avunje S, et al. 2016. Emergence of Enterocytozoon hepatopenaei (EHP) in farmed Penaeus (Litopenaeus) vannamei in India. Aquaculture 454: 272-280. https://doi.org/10.1016/j.aquaculture.2015.12.034
  22. Biju N, Sathiyaraj G, Raj M, Shanmugam V, Baskaran B, Govindan U, et al. 2016. High prevalence of Enterocytozoon hepatopenaei in shrimps Penaeus monodon and Litopenaeus vannamei sampled from slow growth ponds in India. Dis. Aquat. Org. 120: 225-230. https://doi.org/10.3354/dao03036
  23. Kim JH, Lee C, Jeon HJ, Kim BK, Lee NK, Choi SK, et al. 2022. First report on Enterocytozoon hepatopenaei (EHP) infection in Pacific white shrimp (Penaeus vannamei) cultured in Korea. Aquaculture 547: 737525.
  24. Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL, Levesque CA, Chen W, Fungal Barcoding Consortium. 2012. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for fungi. Proc. Natl. Acad. Sci. USA 109: 6241-6246. https://doi.org/10.1073/pnas.1117018109
  25. Yarza P, Yilmaz P, Panzer K, Glockner FO, Reich M. 2017. A phylogenetic framework for the kingdom fungi based on 18S rRNA gene sequences. Mar. Genom. 36: 33-39. https://doi.org/10.1016/j.margen.2017.05.009
  26. Luton K, Walker D, Blair D. 1992. Comparisons of ribosomal internal transcribed spacers from two congeneric species of flukes (Platyhelminthes: Trematoda: Digenea). Mol. Biochem. Parasitol. 56: 323-327. https://doi.org/10.1016/0166-6851(92)90181-I
  27. Coleman AW. 2015. Nuclear rRNA transcript processing versus internal transcribed spacer secondary structure. Trends Genet. 31: 157-163. https://doi.org/10.1016/j.tig.2015.01.002