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Real-Time Polymerase Chain Reaction (PCR) Based Identification and Detection of Fungi Belongs to Genus Fusarium

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Molecular Markers in Mycology

Part of the book series: Fungal Biology ((FUNGBIO))

Abstract

The genus Fusarium is of great importance, since members of this genus are plant-pathogens as well as human-pathogens, and the secondary metabolites produced by Fusarium species are hazardous to agricultural products, wildlife, livestock and humans. The classical method of identification and detection based on morphological characteristics are time consuming and erroneous, which complicate timely disease management decisions. The real-time PCR based molecular techniques are more specific, sensitive and accurate than traditional methods. Early and reliable detection is crucial for implementation of disease control strategies, and for the disease management. These assays can function as a basis for clinical labs, regulatory personnel, and other diagnosticians to adapt or implement for detection of human, plant and animal pathogenic Fusarium species. In the present chapter, we present overview on the basic technique of real-time PCR for the accurate quantification, detection and diagnosis of plant and human pathogenic Fusarium species.

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References

  • Abd-Elsalam KA, Asran-Amal A, Schnieder F, Migheli Q Verreet JA. Molecular detection of Fusarium oxysporum f.sp. vasinfectum in cotton roots by PCR and real-time PCR assay. J Plant Dis Protect. 2006;113:14–19.

    Google Scholar 

  • Ahmad S, Khan ZU, Theyyathel AM. Development of a nested PCR assay for the detection of Fusarium solani DNA and its evaluation in the diagnosis of invasive fusariosis using an experimental mouse model. Mycoses. 2010;53:40–7.

    CAS  PubMed  Google Scholar 

  • Al-Hatmi AM, Bonifaz A, de Hoog G, Vazquez-Maya L, Garcia-Carmona K, Meis JF, van Diepeningen AD. Keratitis by Fusarium temperatum, a novel opportunist. BMC Infect Dis. 2014;14:588.

    PubMed  PubMed Central  Google Scholar 

  • Armstrong GM, Armstrong JK (1981) Formae specialis and races of Fusarium oxysporum causing wilt diseases. In: Fusarium: Diseuses, Biology and Taxonomy, Pennsylvania State University Press, University Park (US) pp 391–99.

    Google Scholar 

  • Bernal-Martínez L, Buitrago MJ, Castelli MV, Rodríguez-Tudela JL, Cuenca-Estrella M. Detection of invasive infection caused by Fusarium solani and non-Fusarium solani species using a duplex quantitative PCR-based assay in a murine model of fusariosis. Med Mycol. 2012;50:270–5.

    PubMed  Google Scholar 

  • Bluhm BH, Cousin MA, Woloshuk CP. Multiplex real-time PCR detection of fumonisin-producing and trichothecene-producing groups of Fusarium species. J Food Prot. 2004;67:536–43.

    CAS  PubMed  Google Scholar 

  • Borneman J, and Hartin RJ. PCR primers that amplify fungal rRNA genes from environmental samples. Appl. Environ. Microbiol. 2000;66:4356–60.

    Google Scholar 

  • De Hoog GS, Guarro J, Gené J, Figueras MJ. Atlas of clinical fungi, vol. 3. Utrecht: CD-ROM, CBS-KNAW Fungal Biodiversity Centre; 2011.

    Google Scholar 

  • de Sousa MV, Machado JC, Simmons HE, Munkvold GP. Real-time quantitative PCR assays for the rapid detection and quantification of Fusarium oxysporum f. sp. phaseoli in Phaseolus vulgaris (common bean) seeds. Plant Pathol. 2015;64:478–88.

    Google Scholar 

  • Demeke T, Gräfenhan T, Clear RM, Phan A, Ratnayaka I, Chapadps J, Patrick SK, Gaba D, Levesque CA, Seifert KA. Development of a specific TaqMan® real-time PCR assay for quantification of Fusarium graminearum clade 7 and comparison of fungal biomass determined by PCR with deoxynivalenol content in wheat and barley. Int J Food Microbiol. 2010;141:45–50.

    CAS  PubMed  Google Scholar 

  • Edel V, Steinberg C, Gautheron N, Alabouvette C. Evaluation of restriction analysis of polymerase chain reaction (PCR)- amplified ribosomal DNA for the identification of Fusarium species. Mycol Res. 1997;101:179–87.

    CAS  Google Scholar 

  • Edel-Hermann V, Aimé S, Cordier C, Olivain C, Steinberg C. Development of a strain-specific real-time PCR assay for the detection and quantification of the biological control agent Fo47 in root tissues. FEMS Microbiol Lett. 2011;322:34–40.

    CAS  PubMed  Google Scholar 

  • Faria CB, Abe CA, da Silva CN, Tessmann DJ, Barbosa-Tessmann IP. New PCR assays for the identification of Fusarium verticillioides, Fusarium subglutinans, and other species of the Gibberellafujikuroi complex. Int J Mol Sci. 2012;13:115–32.

    PubMed  Google Scholar 

  • Fredlund E, Gidlund A, Sulyok M, Börjesson T, Krska R, Olsen M, Lindblad M. Deoxynivalenol and other selected Fusarium toxins in Swedish oats – occurrence and correlation to specific Fusarium species. Int J Food Microbiol. 2013;167:276–83.

    CAS  PubMed  Google Scholar 

  • Gutleb AC, Morrison E, Murk AJ. Cytotoxicity assays for mycotoxins produced by Fusarium strains: a review. Environ Toxicol Pharmacol. 2002;11:309–20.

    CAS  PubMed  Google Scholar 

  • Hatsch D, Phalip V, Jeltsch JM. Use of genes encoding cellobiohydrolase-C and topoisomerase II as targets for phylogenetic analysis and identification of Fusarium, Research in Microbiology 2004;155:290–96.

    Google Scholar 

  • Higgins JA, Nasarabadi S, Karns JS, Shelton DR, Cooper M, Gbakima A, Koopman RP. A handheld real time thermal cycler for bacterial pathogen detection. Biosens Bioelectr 2003;18:1115–23.

    Google Scholar 

  • Jurado M, Vázquez C, Patiño B, González-Jaén MT. PCR detection assays for the trichothecene-producing species Fusarium graminearum, Fusarium culmorum, Fusarium poae, Fusarium equiseti and Fusarium sporotrichioides. Syst Appl Microbiol. 2005;28:562–8.

    CAS  PubMed  Google Scholar 

  • Kandel YR, Haudenshield JS, Srour AY, Islam KT, Fakhoury AM, Santos P, Wang J, Chilvers MI, Hartman GL, Malvick DK, Floyd CM, Mueller DS, Leandro LF. Multilaboratory comparison of quantitative PCR assays for detection and quantification of Fusarium virguliforme from soybean roots and soil. Phytopathology. 2015;105:1601–11.

    Google Scholar 

  • Kappe R, Fauser C, Okeke CN, Maiwald M. Universal fungus-specific primer systems and group-specific hybridization oligonucleotides for 18S rDNA. Mycoses. 1996;39:25–30.

    Google Scholar 

  • Kim YT, Lee YR, Jin J, Han KH, Kim H, Kim JC, Lee T, Yun SH, Lee YW. Two different polyketide synthase genes are required for synthesis of zearalenone in Gibberellazeae. Mol Microbiol. 2005;58:1102–13.

    CAS  PubMed  Google Scholar 

  • Kulik T, Pszczółkowska A, FordoÅ„ski G, Olszewski J. PCR approach based on the esyn1 gene for the detection of potential enniatin-producing Fusarium species. Int J Food Microbiol. 2007;116:319–24.

    Google Scholar 

  • Landlinger C, Baskova L, Preuner S, Willinger B, Buchta V, Lion T. Identification of fungal species by fragment length analysis of the internally transcribed spacer 2 region. Eur J Clin Microbiol Infect Dis. 2009;28:613–22.

    CAS  PubMed  Google Scholar 

  • Lau A, Sorrell TC, Lee O, Stanley K, Halliday C. Colony multiplex-tandem PCR for rapid, accurate identification of fungal cultures. J Clin Microbiol. 2008;46:4058–60.

    PubMed  PubMed Central  Google Scholar 

  • Leslie JF, Summerell BA. The Fusarium laboratory manual. Oxford: Blackwell Publishing Ltd.; 2006.

    Google Scholar 

  • Lievens B, Claes L, Vakalounakis DJ, Vanachter ACRC, Thomma BPHJ. A robust identification and detection assay to discriminate the cucumber pathogens Fusarium oxysporum f.sp. cucumerinum and f.sp. radicis-cucumerinum. Environ Microbiol. 2007;9:2145–61.

    Google Scholar 

  • Lievens B, Brouwer M, Vanachter ACRC, Lévesque CA, Cammue BPA, Thomma BPHJ. Design and development of a DNA array for rapid detection and identification of multiple tomato vascular wilt pathogens. FEMS Microbiol Lett. 2003;223:113–22.

    Google Scholar 

  • Lin Z, Xu S, Que Y, Wang J, Comstock JC, Wei J, McCord PH, Chen B, Chen R, Zhang M. Species-specific detection and identification of Fusarium species complex, the causal agent of sugarcane Pokkah Boeng in China. PLoS One. 2014;9:e104195.

    PubMed  PubMed Central  Google Scholar 

  • Lindblad M, Gidlund A, Sulyok M, Börjesson T, Krska R, Olsen M, Fredlund E. Deoxynivalenol and other selected Fusarium toxins in Swedish wheat – occurrence and correlation to specific Fusarium species. Int J Food Microbiol. 2013;167:284–91.

    CAS  PubMed  Google Scholar 

  • Lortholary O, Obenga G, Biswas P, Caillot D, Chachaty E, Bienvenu AL, Cornet M, Greene J, Herbrecht R, Lacroix C, Grenouillet F, Raad I, Sitbon K, Troke P, French Mycoses Study Group. International retrospective analysis of 73 cases of invasive fusariosis treated with voriconazole. Antimicrob Agents Chemother. 2010;54:4446–50.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Migheli Q, Balmas V, Harak H, Sanna S, Scherm B, Aoki T, O’Donnell K. Molecular phylogenetic diversity of dermatologic and other human pathogenic fusarial isolates from hospitals in Northern and Central Italy. J Clin Microbiol. 2010;48:1076–84.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Muraosa Y, Schreiber AZ, Trabasso P, Matsuzawa T, Taguchi H, Moretti LM, Mikami Y, Kamei K. Development of cycling probe-based real-time PCR system to detect Fusarium species and Fusarium solani species complex (FSSC). Int J Med Microbiol. 2014;304:505–11.

    CAS  PubMed  Google Scholar 

  • Nelson PE, Dignani MC, Anaissie EJ. Taxonomy, biology, and clinical aspects of Fusarium species. Clin Microbiol Rev. 1994;7:479.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Nicholson P, Simpson DR, Weston G, Rezanoor HN, Lees AK, Parry DW, Joyce D. Detection and quantification of Fusarium culmorum and Fusarium graminearum in cereals using PCR assays. Physiol Mol Plant Pathol. 1998;53:17–37.

    Google Scholar 

  • Nicolaisen M, SupronienÄ— S, Nielsen LK, Lazzaro I, Spliid NH, Justesen AF. Real-time PCR for quantification of eleven individual Fusarium species in cereals. J Microbiol Meth. 2009;76:234–40.

    CAS  Google Scholar 

  • Nucci M, Anaissie E. Fusarium infections in immunocompromised patients. Clin Microbiol Rev. 2007;20:695.

    CAS  PubMed  PubMed Central  Google Scholar 

  • O’Donnell K, Sutton DA, Fothergill A, McCarthy D, Rinaldi MG, Brandt ME, Zhang N, Geiser DM. Molecular phylogenetic diversity, multilocus haplotype nomenclature, and in vitro antifungal resistance within the Fusarium solani species complex. J Clin Microbiol. 2008;46:2477–90.

    PubMed  PubMed Central  Google Scholar 

  • O’Donnell K1, Sarver BA, Brandt M, Chang DC, Noble-Wang J, Park BJ, Sutton DA, Benjamin L, Lindsley M, Padhye A, Geiser DM, Ward TJ. Phylogenetic diversity and microsphere array-based genotyping of human pathogenic Fusaria, including isolates from the multistate contact lens-associated U.S. keratitis outbreaks of 2005 and 2006. J Clin Microbiol. 2007 Jul;45:2235–48.

    Google Scholar 

  • O’Donnell K, Gueidan C, Sink S, Johnston PR, Crous PW, Glenn A, Riley R, Zitomer NC, Colyer P, Waalwijk C, Lee TV, Moretti A, Kang S, Kim HS, Geiser DM, Juba JH, Baayen RP, Cromey MG, Bithell S, Sutton DA, Skovgaard K, Ploetz R, Corby Kistler H, Elliott M, Davis M, Sarver BA. A two-locus DNA sequence database for typing plant and human pathogens within the Fusarium oxysporum species complex. Fungal Genet Biol. 2009;46:936–48.

    PubMed  Google Scholar 

  • O’Donnell K, Sutton DA, Rinaldi MG, Gueidan C, Crous PW, Geiser DM. Novel multilocus sequence typing scheme reveals high genetic diversity of human pathogenic members of the Fusarium incarnatum, F. equiseti and F. chlamydosporum species complexes within the United States. J Clin Microbiol. 2010a;47:3851–61.

    Google Scholar 

  • O’Donnell K, Sutton DA, Rinaldi MG, et al. Internet-accessible DNA sequence database for identifying Fusaria from human and animal infections. J Clin Microbiol. 2010b;48:3708–18.

    PubMed  PubMed Central  Google Scholar 

  • Pasquali M, Marena L, Fiora E, Piatti P, Gullino ML, Garibaldi A. Real-time PCR for the identification of a highly pathogenic group of Fusarium oxysporum f.sp. chrysanthemi on Argyranthemum frutescens L. J Plant Pathol. 2004;86:51–57.

    Google Scholar 

  • Peng J, Zhang H, Chen F, Zhang X, Xie Y, Hou X, Li G, Pu J. Rapid and quantitative detection of Fusarium oxysporum f. sp. cubense race 4 in soil by real-time fluorescence loop-mediated isothermal amplification. J Appl Microbiol. 2014;117:1740–9.

    CAS  PubMed  Google Scholar 

  • Reischer GH, Lemmens M, Farnleitner A, Adler A, Mach RL. Quantification of Fusarium graminearum in infected wheat by species specific real-time PCR applying a TaqMan probe. J Microbiol Methods. 2004;59:141–6.

    CAS  PubMed  Google Scholar 

  • Sarver BAJ, Ward TJ, Gale LR, Broz K, Corby Kistler H, Aoki T, Nicholson P, Carter J, O’Donnell K. Novel Fusarium head blight pathogens from Nepal and Louisiana revealed by multilocus genealogical concordance. Fungal Genet Biol. 2011;48:1096–107.

    PubMed  Google Scholar 

  • Scauflaire J, Godet M, Gourgue M, Liénard C, Munaut F. A multiplex real-time PCR method using hybridization probes for the detection and the quantification of Fusarium proliferatum, F. subglutinans, F. temperatum, and F. verticillioides. Fungal Biol. 2012;116:1073–80.

    CAS  PubMed  Google Scholar 

  • Schena L, Franco N, Ippolito A, Gallitelli D. Real-time quantitative PCR: a new technology to detect and study phytopathogenic and antagonistic fungi. Eur J Plant Pathol. 2004;110: 893–908.

    Google Scholar 

  • Smit E, Leeflang P, Glandorf B, van Elass JD, Wernars K. Analysis of fungal diversity in the wheat rhizosphere by sequencing of cloned PCR-amplified genes encoding 18S rRNA and temperature gradient gel electrophoresis. Appl. Environ. Microbiol. 1999;65:2614–21.

    Google Scholar 

  • Sugawara Y, Nakase K, Nakamura A. Clinical utility of a panfungal polymerase chain reaction assay for invasive fungal diseases in patients with haematologic disorders. Eur J Haematol. 2013;90(4):331–9.

    CAS  PubMed  Google Scholar 

  • Tortorano AM, Richardson M, Roilides E. ESCMID & ECMM joint guidelines on diagnosis and management of hyalohyphomycosis: Fusarium spp, Scedosporium spp, and others. Clin Microbiol Infect. 2014;20:27–46.

    CAS  PubMed  Google Scholar 

  • van der Wolf JM, van Beckhoven JRCM, Bonanats PJM, Schoen CD (2001) New technologies for sensitive and specific routine detection of plant pathogenic bacteria. In: de Boer, SH Ed Plant pathogenic bacteria Kluwer, Dordrecht, pp 75–77.

    Google Scholar 

  • van Diepeningen AD, Brankovics B, Iltes J, van der Lee TA, Waalwijk C. Diagnosis of Fusarium infections: approaches to identification by the clinical mycology laboratory. Curr Fungal Infect Rep. 2015a;9(3):135–43.

    PubMed  PubMed Central  Google Scholar 

  • van Diepeningen AD, Feng P, Ahmed S, Sudhadham M, Bunyaratavej S, de Hoog GS. Spectrum of Fusarium infections in tropical dermatology evidenced by multilocus sequencing typing diagnostics. Mycoses. 2015b;58(1):48–57.

    PubMed  Google Scholar 

  • Vegi A, Wolf-Hall CE. Multiplex real-time PCR method for detection and quantification of mycotoxigenic fungi belonging to three different genera. J Food Sci. 2013;78:70–6.

    Google Scholar 

  • Waalwijk C, van der Heide R, de Vries I, van der Lee T, Schoen C, Costrel-de Corainville G, Häuser-Hahn I, Kastelein P, Kohl J, Lonnet P, Demarquet T, Kema GHJ. Quantitative detection of Fusarium species in wheat using TaqMan. Eur J Plant Pathol. 2004;110:481–94.

    Google Scholar 

  • White TJ, Bruns T, Lee S, Taylor J. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. Mycologia. 1990;18:315–22.

    Google Scholar 

  • Wang J, Jacobs JL, Byrne JM, Chilvers MI. Improved diagnoses and quantification of Fusarium virguliforme, causal agent of soybean sudden death syndrome. Phytopathology. 2014;105:378–87.

    Google Scholar 

  • Wickern GM. Fusarium allergic fungal sinusitis. J Allergy Clin Immunol. 1993;92:624.

    CAS  PubMed  Google Scholar 

  • Yadav MK, Babu BK, Saxena AK, Singh BP, Singh K, Arora DK. Real-time PCR assay based on topoisomerase-II gene for detection of Fusarium udum. Mycopathologia. 2011;171:373–81.

    Google Scholar 

  • Yli-Mattila T, Paavanen-Huhtala S, Jestoi M, Parikka P, Hietaniemi V, Gagkaeva T, Sarlin T, Haikara A, Laaksonen S, Rizzo A. Real-time PCR detection and quantification of Fusarium poae, F. graminearum, F. sporotrichioides and F. langsethiae in cereal grains in Finland and Russia. Arch Phytopathol Plant Prot. 2008;41:243–60.

    CAS  Google Scholar 

  • Zambounis AG, Paplomatas E, Tsaftaris AS. Intergenic spacer–RFLP analysis and direct quantification of Australian Fusarium oxysporum f sp vasinfectum isolates from soil and infected cotton tissues. Plant Dis. 2007; 91:1564–73.

    Google Scholar 

  • Zhang X, Zhang H, Pu J, Qi Y, Yu Q, Xie Y, Penj J. Development of a real-time fluorescence loop-mediated isothermal amplification assay for rapid and quantitative detection of Fusarium oxysporum f. sp. cubense tropical race 4 in soil. PLoS One. 2013;8:e82841.

    PubMed  PubMed Central  Google Scholar 

  • Zhang Z, Zhang J, Wang Y, Zheng X. Molecular detection of Fusarium oxysporum f.sp. niveum and Mycosphaerella melonis in infected plant tissues and soil. FEMS Microbiol Lett 2005;249:39–47.

    Google Scholar 

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Yadav, M.K., Singh, B.P. (2017). Real-Time Polymerase Chain Reaction (PCR) Based Identification and Detection of Fungi Belongs to Genus Fusarium. In: Singh, B.P., Gupta, V.K. (eds) Molecular Markers in Mycology. Fungal Biology. Springer, Cham. https://doi.org/10.1007/978-3-319-34106-4_4

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