Sensitive and rapid detection of Flavobacterium columnare in channel catfish Ictalurus punctatus by a loop-mediated isothermal amplification method

Journal of Applied Microbiology

Volumn 100, Issue 5, 2006, Pages 919-925

  Yeh, H Y ^a   Shoemaker, C A ^a   Klesius, P H ^a  

^a AQUATIC ANIMAL HEALTH RESEARCH UNIT   (United States)

Author keywords

Aquaculture; Columnaris diseases; Flavobacterium columnare; LAMP; Loop mediated isothermal amplification

Indexed keywords

COST EFFECTIVENESS; ELECTROPHORESIS; FISH; GENES; ISOTHERMS; POLYMERASE CHAIN REACTION; RNA;

16S RIBOSOMAL RNA; CHANNEL CATFISH; COLUMNARI DISEASE; FLAVOBACTERIUM COLUMNARE; GENOMIC DNA; IN-CHANNELS; LOOP MEDIATED ISOTHERMAL AMPLIFICATIONS; LOOP-MEDIATED ISOTHERMAL AMPLIFICATIONS; RAPID DETECTION; RNA GENES;

DIAGNOSIS;

BACTERIAL DNA; ETHIDIUM BROMIDE; GENE PRODUCT; GENOMIC DNA; RIBOSOME RNA;

AQUACULTURE; ASSAY; BACTERIUM; DETECTION METHOD; DNA; ELECTROKINESIS; FISH; GENOMICS; HATCHERY; RNA;

AGAR GEL ELECTROPHORESIS; ANIMAL EXPERIMENT; ANIMAL TISSUE; AQUACULTURE; ARTICLE; BACTERIAL GENE; BACTERIAL INFECTION; BACTERIUM DETECTION; BIOASSAY; CHANNEL CATFISH; CONTROLLED STUDY; COST EFFECTIVENESS ANALYSIS; DIAGNOSTIC ACCURACY; DNA TEMPLATE; FISH DISEASE; FLAVOBACTERIUM; FLAVOBACTERIUM COLUMNARE; GENE AMPLIFICATION; GENE IDENTIFICATION; LOOP MEDIATED ISOTHERMAL AMPLIFICATION METHOD; LYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; RNA GENE; STAINING; TEMPERATURE DEPENDENCE;

ANIMALIA; BACTERIA (MICROORGANISMS); FLAVOBACTERIUM; FLAVOBACTERIUM COLUMNARE; ICTALURUS PUNCTATUS;

EID: 33645853476     PISSN: 13645072     EISSN: 13652672     Source Type: Journal    
DOI: 10.1111/j.1365-2672.2006.02853.x     Document Type: Article

References (40)

1. Abu Al-Soud W. Jönsson L.J. Rådström P. 2000 Identification and characterization of immunoglobulin G in blood as a major inhibitor of diagnostic PCR. J Clin Microbiol 38 345 350.
2. Abu Al-Soud W. Rådström P. 2000 Effects of amplification facilitators on diagnostic PCR in the presence of blood, feces, and meat. J Clin Microbiol 38 4463 4470.
3. Altschul S.F. Madden T.L. Schäffer A.A. Zhang J. Zhang Z. Miller W. Lipman D.J. 1997 Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25 3389 3402.
4. Arias C.R. Shoemaker C.A. Evans J.J. Klesius P.H. 2003 A comparative study of Edwardsiella ictaluri parent (EILO) and E. ictaluri rifampicin-mutant (RE-33) isolates using lipopolysaccharides, outer membrane proteins, fatty acids, Biolog, API 20E and genomic analyses. J Fish Dis 26 415 421.
5. Bader J.A. Shoemaker C.A. Klesius P.H. 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.
6. Bader J.A. Shotts E.B. 1998 Identification of Flavobacterium and Flexibacter species by species-specific polymerase chain reaction primers to the 16S ribosomal RNA gene. J Aquat Anim Health 10 311 319.
7. Bernardet J.F. Grimont P.A.D. 1989 Deoxyribonucleic acid relatedness and phenotypic characterization of Flexibacter columnaris sp. nov. rev., Flexibacter psychrophilus sp. nov. rev. and Flexibacter maritimus. Int J Syst Bacteriol 39 346 354.
8. Bernardet J.F. Nakagawa Y. Holmes B. Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes. 2002 Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 52 1049 1070.
9. Bernardet J.F. Segers P. Vancanneyt M. Berthe F. Kersters K. Vandamme P. 1996 Cutting a Gordian Knot: emended classification and description of the genus Flavobacterium, emended description of the family Flavobacteriaceae, and proposal of Flavobacterium hydatis nom. nov. (Basonym, Cytophaga aquatilis Strohl and Tait 1978). Int J Syst Bacteriol 46 128 148.
10. Brugere C. Ridler N. 2004 Global aquaculture outlook in the next decades: an analysis of national aquaculture production forecasts 2030. FAO Fisheries Circular No. 1001, http://www.fao.org/fi/default.asp.
11. Darwish A.M. Ismaiel A.A. Newton J.C. Tang J. 2004 Identification of Flavobacterium columnare by a species-specific polymerase chain reaction and renaming of ATCC 43622 strain to Flavobacterium johnsoniae. Mol Cell Probes 18 421 427.
12. Decostere A. Haesebrouck F. Devriese L.A. 1998 Characterization of four Flavobacterium columnare (Flexibacter columnaris) strains isolated from tropical fish. Vet Microbiol 62 35 45.
13. Durborow R.M. Thune R.L. Hawke J.P. Camus A.C. 1998 Columnaris disease: a bacterial infection caused by Flavobacterium columnare. Southern Regional Aquaculture Center Publication No. 479 pp. 1 4.
14. de Franchis R. Cross N.C. Foulkes N.S. Cox T.M. 1988 A potent inhibitor of Taq polymerase copurifies with human genomic DNA. Nucleic Acids Res 16 10355.
15. Grab D.J. Lonsdale-Eccles J. Inoue N. 2005 Lamp for tadpoles. Nat Methods 2 635.
16. Hawke J.P. Khoo L.H. 2004 Infectious diseases. In Biology and Culture of Channel Catfish ed. Tucker C.S. Hargreaves J.A. pp. 387 443. Amsterdam, the Netherlands Elsevier B.V.
17. Ikadai H. Tanaka H. Shibahara N. Matsuu A. Uechi M. Itoh N. Oshiro S. Kudo N. et al. 2004 Molecular evidence of infections with Babesia gibsoni parasites in Japan and evaluation of the diagnostic potential of a loop-mediated isothermal amplification method. J Clin Microbiol 42 2465 2469.
18. Iwamoto T. Sonobe T. Hayashi K. 2003 Loop-mediated isothermal amplification for direct detection of Mycobacterium tuberculosis complex, M. avium, and M. intracellulare in sputum samples. J Clin Microbiol 41 2616 2622.
19. Königsson M.H. Ballagi A. Jansson E. Johansson K.-E. 2005 Detection of Renibacterium salmoninarum in tissue samples by sequence capture and fluorescent PCR based on the 16S rRNA gene. Vet Microbiol 105 235 243.
20. Lantz P.-G. Abu Al-Soud W. Knutsson R. Hahn-Hägerdal B. Rådström P. 2000 Biotechnical use of the polymerase chain reaction for microbial analysis of biological samples. In Biotechnology Annual Review vol. 5. ed. El-Gewely M.R. pp. 87 130. Amsterdam, the Netherlands Elsevier Science B.V.
21. Notomi T. Okayama H. Masubuchi H. Yonekawa T. Watanabe K. Amino N. Hase T. 2000 Loop-mediated isothermal amplification of DNA. Nucleic Acids Res 15 E63.
22. Okafuji T. Yoshida N. Fujino M. Motegi Y. Ihara T. Ota Y. Notomi T. Nakayama T. 2005 Rapid diagnostic method for detection of mumps virus genome by loop-mediated isothermal amplification. J Clin Microbiol 43 1625 1631.
23. Plumb J.A. 1994 Columnaris disease. In Health Maintenance of Cultured Fishes: Principal Microbial Diseases ed. Plumb J.A. pp. 135 141. New York Wiley.
24. PrimerExplorer V3 software program, http://primerexplorer.jp. Last accessed September 6, 2005.
25. Seki M. Yamashita Y. Torigoe H. Tsuda H. Sato S. Maeno M. 2005 Loop-mediated isothermal amplification method targeting the lytA gene for detection of Streptococcus pneumoniae. J Clin Microbiol 43 1581 1586.
26. Shamsudin M.N. 1994 Pathogenesis of Flexibacter columnaris and immunity in the channel catfish. PhD Dissertation Auburn University Auburn, AL, USA.
27. Shoemaker C.A. Arias C.R. Klesius P.H. Welker T.L. 2005 Technique for identifying Flavobacterium columnare using whole cell fatty acid profiles. J Aquat Anim Health 17 267 274.
28. Shotts E.B. Starliper C.E. 1999 Flavobacterial diseases: columnaris disease, cold-water disease and bacterial gill disease. In Fish Disease and Disorders, Viral, Bacterial and Fungal Infections vol. 3. ed. Woo P.T.K. Bruno D.W. pp. 559 576.
29. Song T. Toma C. Nakasone N. Iwanaga M. 2005 Sensitive and rapid detection of Shigella and enteroinvasive Escherichia coli by a loop-mediated isothermal amplification method. FEMS Microbiol Lett 243 259 263.
30. Suomalainen L.-R. Tiirola M.A. Valtonen E.T. 2005 Influence of rearing conditions on Flavobacterium columnare infection of rainbow trout, Oncorhynchus mykiss (Walbaum). J Fish Dis 28 271 277.
31. Tiirola M. Valtonen E.T. Rintamäki-Kinnunen P. Kulomaa M.S. 2002 Diagnosis of flavobacteriosis by direct amplification of rRNA genes. Dis Aquat Organ 51 93 100.
32. Toyama T. Kita-Tsukamoto K. Wakabayashi H. 1996 Identification of Flexibacter maritimus, Flavobacterium branchiophilum and Cytophaga columnaris by PCR targeted 16S ribosomal DNA. Fish Pathol 31 25 31.
33. United States Department of Agriculture, Agricultural Research Service National Programs; Aquaculture 2003a ) http://www.ars.usda.gov/research/programs.
34. United States Department of Agriculture, National Agricultural Statistics Service 2003b Catfish Production Report. http://jan.mannlib.cornell.edu/reports/nassr/other/pcf-bbc/2003/cfpd0203.pdf.
35. Ushikubo H. 2004 Principle of LAMP method-A simple and rapid gene amplification method. Uirusu 54 107 112 (in Japanese).
36. Wagner B.A. Wise D.J. Khoo L.H. Terhune J.S. 2002 The epidemiology of bacterial diseases in food-size channel catfish. J Aquat Anim Health 14 263 272.
37. Wakabayashi H. 1991 Effect of environmental conditions on the infectivity of Flexibacter columnaris to fish. J Fish Dis 14 279 290.
38. Welker T.L. Shoemaker C.A. Arias C.R. Klesius P.H. 2005 Transmission and detection of Flavobacterium columnare in channel catfish Ictalurus punctatus. Dis Aquat Org 63 129 138.
39. Yeh H. Shoemaker C.A. Klesius P.H. 2005 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.
40. Zavaleta A.I. Martinez-Murcia A.J. Rodriguez-Valera F. 1996 16S-23S rDNA intergenic sequences indicate that Leuconostoc oenos is phylogenetically homogeneous. Microbiology 142 2105 2114.