Metode Loop-Mediated Isothermal Amplification (LAMP) dan Aplikasinya untuk Deteksi Penyakit Ikan

https://doi.org/10.22146/jfs.156

Murwantoko Murwantoko(1*)

(1) Jurusan Perikanan, Fakultas Pertanian, Universitas Gadjah Mada
(*) Corresponding Author

Abstract


Polymerase chain reaction (PCR) is a method that amplifies DNA which have been widely used in molecular biology technique. Based on the PCR, many methods have been developed on isothermal condition and the useful one is loop-mediated isothermal amplification of DNA (LAMP). LAMP reaction employs a Bst DNA polymerase and a set of four specific primers that recognizes a total of six distinct sequences of the target DNA and produces amount of different size of DNA. Many advantages have been achieved in LAMP such as the simple equipment for reaction and observation, short time, highly specific and sensitive procedure. LAMP has been used as a tools for detection many pathogens for human, animals and plants. Some fish pathogens as parasites, bacteria and viruses have been detected by LAMP. The principles and application of LAMP method are discussed in this paper.

Keywords


Detection, Loop-mediated isothermal amplification (LAMP), Pathogen, PCR

Full Text:

Full Article (PDF)


References

Altinok, I., J.M. Grizzle, and Z. Liu. 2001. Detection of Yersinia ruckeri in rainbow trout blood by use of the polymerase chain reaction. Dis. Aquat. Organ. 44: 29-34.

Bader, J.A., C.A. Shoemaker, and P.H. Klesius. 2003. Rapid detection of columnaris disease in channel catfish (Ictalurus punctatus) with a new species-specific 16-S rRNA gene-based PCR primer for Flavobacterium columnare. J. Microbiol. Methods. 52: 209-220.

Bell, A.S., H. Yokohama, T. Aoki, M. Takahashi, and K. Maruyama. 1999. Single and nested polymerase chain reaction assays for the detection of Microsporidium seriolae (Microspora), the causative agent of 'Beko' disease in yellowtail Seriola quinqueradiata. Dis. Aquat. Organ. 37: 127-134.

Blake, S.L., W.B. Schill, P.E. Mc Allister, M.K. Lee, J.T. Singer, and B.L. Nicholson. 1995. Detection and identification of aquatic birnaviruses by PCR assay. J. Clin. Microbiol. 33: 835-839.

Boyle, J. and J. Blackwell. 1991. Use of polymerase chain reaction to detect latent channel catfish virus. Am. J. Vet. Res. 52: 1965-1968

Caipang, C.M., I. Haraguchi, T Ohira, I. Hirono, and T. Aoki. 2004. Rapid detection of a fish iridovirus using loop-mediated isothermal amplifica-tion (LAMP). J. Virol. Methods. 121: 155-161.

Compton, I. 1991. Nucleic acid sequence-based amplification. Nature. 350: 91-92.

El-Matbouli, M. and H. Soliman. 2005a. Rapid diagnosis of Tetracapsuloides bryosalmonae, the causative agent of proliferative kidney disease (PKD) in salmonid fish by a novel DNA amplification method, loop-mediated isothermal amplification (LAMP). Parasitol. Res. 96: 277-284.

El-Matbouli, M. and H. Soliman. 2005b. Development of a rapid assay for the diagnosis of Myxobulus cerebralis in fish and oligochaetes using loop-mediated isotemal amplification. J. Fish. Disease 28: 549-557.

Fukuta, S., K. Ohishi, K. Yoshida, Y. Mizukumi, A. Ishida, and M. Kanbe. 2004. Development of immuno-capture reverse transcription loop-mediated isothermal amplification for the detection of tomato spotted wilt virus from chrysanthemum. J. Virol. Methods. 121: 49-55.

Gilad, O., S. Yun, K.B. Andree, M.A. Adkison, A. Zlotkin, H. Bercovier, A. Eldar, and R.P. Hedrick. 2002. Initial characteristics of koi herpesvirus and development of a polymerase chain reaction assay to detect the virus in koi (Cyprinus carpio). Dis. Aq. Org, 48: 101-108.

Gonzalez, S.F., C.R. Osorio, and Y. Santos. 2003. Development of a PCR-based method for the detection of Listonella anguillarum in fish tissues and blood samples. Dis. Aquat. Organ. 55:1 09-115.

Guatelli, J.C., K.M. Whitefield, D.Y. Kwoh, K.J. Barringer, D.D. Richman, and T.R. Gingeras. 1990. Isothermal, in vitro amplification of nucleic acids by a multi enzyme reaction modeled after retroviral replication. Proc. Natl. Acad. Sci. USA. 87: 7797.

Gunimaladevi, I., T. Kono, M.N. Venugopal, and M. Sakai. 2004. Detection of koi herpesvirus in common carp, Cyprinus carpio L., by loop-mediated isothermal ampli-fication. J. Fish. Disease 27: 583-589.

Gunimaladevi, I., T. Kono, S.E. Lapatra, and M. Sakai. 2005. A loop-mediated isothermal amplification (LAMP) method for detection of infectious hematopoietic necrosis virus (IHNV) in rainbow trout (Oncorhynchus mykiss). Arch. Virol. 50: 899-909.

Heath, S., S. Pak, S. Marshall, E.M. Prager, and C. Orrego, 2000. Monitoring Piscirickettsia salmonis by denaturant gel electrophoresis and competitive PCR. Dis. Aquat. Organ. 41: 19-29.

Iwamoto, T., T. Sonobe, and K. Hayashi. 2003. Loop-mediated isothermal amplification for direct detection of Mycobacterium tuberculosis com-plex, M. avium and M. intracellulare in sputum samples. J. Clin. Microbiol. 41: 2616-2622.

Kelley, G.O., F.J. Zagnutt-Vergara, C.M. Leutenegger, K.A. Myklebust, M.A. Adkison, T.S. McDowell, G.D. Marty, A.L. Kahler, A.I. Bush, I.A. Gardner, and R.P. Hedrick. 2004. Evaluation of five diagnostic methods for the detection and quantification of Myxobolus cerebralis. J. Vet. Diagn. Invest. 16: 202-11.

Kibenge, F.S., S.K. Whyte, K.L. Hammell, D. Rainnie, M.T. Kibenge, and C.K. Martin. 2000. A dual infection of infectious salmon anaemia (ISA) virus and a togavirus-like virus in ISA of Atlantic salmon Salmo salar in New Brunswick. Canada. Dis. Aquat. Organ. 42: 11-15.

Kibenge, M.T., B. Opazo, A.H. Rojas, and F.S. Kibenge. 2002. Serological evi-dence of infectious salmon anaemia virus (ISAV) infection in farmed fishes, using an indirect enzyme-linked immunosorbent assay (ELISA). Dis. Aquat. Organ. 51: 1-11.

Kono, T., R. Savan, M. Sakai, and T. Itami. 2004. Detection of white spot syndrome virus in shrimp by loop-mediated isothermal amplification. J. Virol. Methods.115: 59-65.

Kuboki, N., N. Inoue, T. Sakurai, F. Di Cello, D.J. Grab, H. Suzuki, C. Sugimoto, and I. Igarashi. 2003. Loop-mediated isothermal amplifica-tion for detection of African trypanoso-mes. J. Clin. Microbiol. 41: 5517-5524.

Leon, G., N. Maulen, J. Figueroa, J. Villaneuva, C. Rodiguez, M.I. Vera, and M. Krauskopf. 1994. A PCR-based assay for the identification of the fish pathogen Renibacterium salmoninarum. FEMS Microbiol. Lett. 115: 131-136.

Miller, T.A. , J. Rapp, U. Wastlhuber, R.W. Hoffmann, and P.J. Enzmann. 1988. Rapid and sensitive reverse transcrip-tase-polymerase chain reaction based detection and differential diagnosis of fish pathogenic rhabdoviruses in organ samples and cultured cells. Dis. Aquat. Organ. 34: 13-20.

Mori, Y., M. Kitao, N. Tomita, and T. Notomi. 2004. Real-time turbidimetry of LAMP reaction for quantifying template DNA. J. Biochem. Biophys. Methods. 59: 145-157.

Notomi, T., H. Okayama, H. Masubuchi, T. Yonekawa, K. Watanabe, N. Amino, and T. Hase, 2000. Loop-mediated isothermal amplification of DNA. Nucleic Acid Research 28:e63.

Oreshkova, S.F., I.S. Shchelkunov, N.V. Tikunova, T.I. Shchelkunova, A.T. Puzyrev, and A.A. Ilyichev. 1999. Detection of spring viremia of carp virus isolates by hybridization with non-radioactive probes and amplifi-cation by polymerase chain reac-tion. Virus. Res. 63: 3-10.

Oshima, S., J. Hata, N. Hirasawa, T. Ohtaka, I. Hirono, T. Aoki, and S. Yamashita. 1988. Rapid diagnosis of red sea bream iridovirus infection using the polymerase chain reaction. Dis. Aquat. Organ. 32: 87-90.

Sambrook, J. and D.W. Russell. 2001. Molecular cloning, a laboratory manual. Volume 2. 3rd Ed. CSHL Press. New York. p. 8.11-8.53.

Savan, R., A. Igarashi, S. Matsuoka, and M. Sakai, 2004. Sensitive and rapid detection of Edwardsiellosis in fish by a loop-mediated isothermal amplifica-tion method. App. Environ. Microbiol. 70: 621-624.

Seng, E.K, Q. Fang, T.J. Lam, and Y.M. Sin. 2004. Development of a rapid, sensitive and specific diagnostic assay for fish Aquareovirus based on RT-PCR. J. Virol. Methods. 118: 111-122.

Thai, H.T.C., M.Q. Le, C.D. Vuong, M. Parida, H. Minekawa, F. Hasabe, and K. Morita. 2004. Development and evaluation of a novel loop-mediated isothermal amplification method for rapid detection of severe acute respiratory syndrome corona-virus. J. Clin. Microbiol. 42: 1956-1961.

Thiery, R., J.C. Raymond, and J. Castric. 1999. Natural outbreak of viral encephalopathy and retinopathy in juvenile sea bass, Dicentrarchus labrax: study by nested reverse transcriptase-polymerase chain reac-tion Virus. Res. 63: 11-17.

Urdaci, M.C., C. Chakroun, D. Faure, and J.F. Bernardet. 1998. Development of a polymerase chain reaction assay for identification and detection of the fish pathogen Flavobacterium psychrophilum. Res. Microbiol. 149: 519-530.

Walker, G.T., M.S. Fraiser, J.L. Schram, M.C. Little, J.G. Nadeau, and D.P. Malinowski. 1992. Strand displace-ment amplification an isothermal, in vitro DNA amplification technique. Nucleic Acids Res. 20: 1691-1696.

Yeh, H.Y., C.A. Shoemaker, and P.H. Klesius. 2005a. Evaluation of a loop-mediated isothermal amplification method for rapid detection of channel catfish Ictalurus punctatus important bacterial pathogen Edwardsiella ictaluri. J. Microbiol. Methods 63: 36-44.

Yeh, H.Y., C.A. Shoemaker, and P.H. Klesius. 2005. Rapid, specific and sensitive detection of Flavobacterium columnare by a loop-mediated ampli-fication method. American Society of Microbiologists Abstract.

Yoshikawa, T., M. Ihira, S. Akimoto, C. Usui, F. Miyake, S. Suga, Y. Enomoto, R. Suzuki, Y. Nishiyama, and Y. Asano. 2004. Detection of human herpesvirus 7 DNA by loop-mediated isothermal amplification. J. Clin. Microbiol. 42: 1348-1352.



DOI: https://doi.org/10.22146/jfs.156

Article Metrics

Abstract views : 5161 | views : 11771

Refbacks

  • There are currently no refbacks.


Bookmark and Share


Copyright (c)



Jurnal Perikanan Universitas Gadjah Mada (print ISSN 0853-6384; online ISSN 2502-5066) is published by Department of Fisheries, Universitas Gadjah Mada in collaboration with Semnaskan UGM (Seminar Nasional Tahunan Hasil Perikanan dan Kelautan) and ISMFR (International Symposium on Marine and Fisheries Research).

 

View My Stats