Differentiation and identification of filamentous fungi by high-throughput FTIR spectroscopic analysis of mycelia

International Journal of Food Microbiology

Volumn 168-169, Issue , 2014, Pages 32-41

  Lecellier, A ^a   Mounier, J ^b   Gaydou, V ^a   Castrec, L ^b   Barbier, G ^b   Ablain, W ^c   Manfait, M ^a   Toubas, D ^a,d   Sockalingum, G D ^a  

^a UNIVERSITÉ DE BREST   (France)

^b TECHNOPÔLE BREST IROISE   (France)

^c BIOMÉRIEUX   (France)

^d HÔPITAL MAISON BLANCHE   (France)

Author keywords

Fungi; High throughput FTIR spectroscopy; Identification; PLS DA

Indexed keywords

ALTERNARIA ALTERNATA; ARTICLE; ASPERGILLUS; ASPERGILLUS FLAVUS; ASPERGILLUS NIGER; ASPERGILLUS VERSICOLOR; AUREOBASIDIUM PULLULANS; CALIBRATION; CHEMOMETRIC ANALYSIS; CUNNINGHAMELLA BINARIAE; CUNNINGHAMELLA BLAKESLEEANA; CUNNINGHAMELLA ELEGANS; DNA SEQUENCE; EMERICELLA NIDULANS; EUROTIUM AMSTELODAMI; EUROTIUM CHEVALIERI; FUNGAL STRAIN; FUNGUS IDENTIFICATION; FUSARIUM; FUSARIUM MONILIFORME; FUSARIUM OXYSPORUM; GALACTOMYCES GEOTRICHUM; HIGH THROUGHPUT SEQUENCING; INFRARED SPECTROSCOPY; LECANICILLIUM LECANII; LITCHTHEIMIA CORYMBIFERA; MUCOR CIRCINELLOIDES; MUCOR RACEMOSUS; MUCOR SPINOSUS; MYCELIUM; NONHUMAN; NUCLEOTIDE SEQUENCE; PENICILLIUM; PENICILLIUM BREVICOMPACTUM; PENICILLIUM CHRYSOGENUM; PENICILLIUM CORYLOPHILUM; PENICILLIUM EXPANSUM; PENICILLIUM GLABRUM; PENICILLIUM NALGIOVENSE; PENICILLIUM OXALICUM; PENICILLIUM ROQUEFORTI; PENICILLIUM VERRUCULOSUM; PHYLUM; REFERENCE DATABASE; RHIZOPUS ORYZAE; STATISTICAL ANALYSIS; SYNCEPHALASTRUM MONOSPORUM; SYNCEPHALASTRUM RACEMOSUM;

FUNGI;

EID: 84887525631     PISSN: 01681605     EISSN: 18793460     Source Type: Journal    
DOI: 10.1016/j.ijfoodmicro.2013.10.011     Document Type: Article

References (49)

1. Bastert J., Korting H.C., Traenkle P., Schmalreck A.F. Identification of dermatophytes by Fourier transform infrared spectroscopy (FT-IR). Mycoses 1999, 42:525-528.
2. Bertrand, D., Dufour, E., 2006. La spectroscopie infrarouge et ses applications analytiques, 2nd edn. Technique et Documentation (ed) ed., Paris.
3. Bylesjö M., Cloarec O., Rantalainen M. Normalization and closure. Compr. Chemom. 2009, 2(7):109-127.
4. Cantu D., Greve L.C., Labavitch J.M., Powell A.L. Characterization of the cell wall of the ubiquitous plant pathogen Botrytis cinerea. Mycol. Res. 2009, 113:1396-1403.
5. Cassagne C., Ranque S., Normand A.C., Fourquet P., Thiebault S., Planard C., Hendrickx M., Piarroux R. Mould routine identification in the clinical laboratory by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. PLoS One 2011, 6:e28425.
6. Chaiwun B., Vanittanakom N., Jiviriyawat Y., Rojanasthien S., Thorner P. Investigation of dogs as a reservoir of Penicillium marneffei in northern Thailand. Int. J. Infect. Dis. 2011, 15:e236-e239.
7. De Carolis E., Posteraro B., Lass-Florl C., Vella A., Florio A.R., Torelli R., Girmenia C., Colozza C., Tortorano A.M., Sanguinetti M., Fadda G. Species identification of Aspergillus, Fusarium and Mucorales with direct surface analysis by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Clin. Microbiol. Infect. 2012, 18:475-484.
8. Fischer G., Braun S., Thissen R., Dott W. FT-IR spectroscopy as a tool for rapid identification and intra-species characterization of airborne filamentous fungi. J. Microbiol. Methods 2006, 64:63-77.
9. Garon D., El Kaddoumi A., Carayon A., Amiel C. FT-IR spectroscopy for rapid differentiation of Aspergillus flavus, Aspergillus fumigatus, Aspergillus parasiticus and characterization of aflatoxigenic isolates collected from agricultural environments. Mycopathologia 2010, 170:131-142.
10. Gaydou V., Kister J., Dupuy N. Evaluation of multiblock NIR/MIR PLS predictive models to detect adulteration of diesel/biodiesel blends by vegetal oil. Chemom. Intell. Lab. Syst. 2009, 106:190-197.
11. Geiser D.M., Gueidan C., Miadlikowska J., Lutzoni F., Kauff F., Hofstetter V., Fraker E., Schoch C.L., Tibell L., Untereiner W.A., Aptroot A. Eurotiomycetes: Eurotiomycetidae and Chaetothyriomycetidae. Mycologia 2006, 98:1053-1064.
12. Glass N.L., Donaldson G.C. Development of primer sets designed for use with the PCR to amplify conserved genes from filamentous ascomycetes. Appl. Environ. Microbiol. 1995, 61:1323-1330.
13. Helm D., Labischinski H., Naumann D. Elaboration of a procedure for identification of bacteria using Fourier-Transform IR spectral libraries: a stepwise correlation approach. J. Microbiol. Methods 1991, 14:127-142.
14. Hermet A., Meheust D., Mounier J., Barbier G., Jany J.L. Molecular systematics in the genus Mucor with special regards to species encountered in cheese. Fungal Biol. 2012, 116:692-705.
15. Hibbett D.S., Binder M., Bischoff J.F., Blackwell M., Cannon P.F., Eriksson O.E., Huhndorf S., James T., Kirk P.M., Lucking R., Thorsten Lumbsch H., Lutzoni F., Matheny P.B., McLaughlin D.J., Powell M.J., Redhead S., Schoch C.L., Spatafora J.W., Stalpers J.A., Vilgalys R., Aime M.C., Aptroot A., Bauer R., Begerow D., Benny G.L., Castlebury L.A., Crous P.W., Dai Y.C., Gams W., Geiser D.M., Griffith G.W., Gueidan C., Hawksworth D.L., Hestmark G., Hosaka K., Humber R.A., Hyde K.D., Ironside J.E., Koljalg U., Kurtzman C.P., Larsson K.H., Lichtwardt R., Longcore J., Miadlikowska J., Miller A., Moncalvo J.M., Mozley-Standridge S., Oberwinkler F., Parmasto E., Reeb V., Rogers J.D., Roux C., Ryvarden L., Sampaio J.P., Schussler A., Sugiyama J., Thorn R.G., Tibell L., Untereiner W.A., Walker C., Wang Z., Weir A., Weiss M., White M.M., Winka K., Yao Y.J., Zhang N. A higher-level phylogenetic classification of the Fungi. Mycol. Res. 2007, 111:509-547.
16. Houbraken J., Samson R.A. Phylogeny of Penicillium and the segregation of Trichocomaceae into three families. Stud. Mycol. 2011, 70:1-51.
17. Inderbitzin P., Bostock R.M., Davis R.M., Usami T., Platt H.W., Subbarao K.V. Phylogenetics and taxonomy of the fungal vascular wilt pathogen Verticillium, with the descriptions of five new species. PLoS One 2011, 6:e28341.
18. Kohler A., Bocker U., Warringer J., Blomberg A., Omholt S.W., Stark E., Martens H. Reducing inter-replicate variation in Fourier transform infrared spectroscopy by extended multiplicative signal correction. Appl. Spectrosc. 2009, 63:296-305.
19. Kummerle M., Scherer S., Seiler H. Rapid and reliable identification of food-borne yeasts by Fourier-transform infrared spectroscopy. Appl. Environ. Microbiol. 1998, 64:2207-2214.
20. Lay J.O. MALDI-TOF mass spectrometry of bacteria. Mass Spectrom. Rev. 2001, 20:172-194.
21. Liang Y.Z., Kvalheim O. Robust methods for multivariate analysis. Chemom. Intell. Lab. Syst. 1996, 32:1-10.
22. Nie M., Zhang W.Q., Xiao M., Luo J.L., Bao K., Chen J.K., Li B. FT-IR spectroscopy and artificial neural network identification of Fusarium species. J. Phytopathol. 2007, 155:364-367.
23. Nilsson R.H., Ryberg M., Abarenkov K., Sjokvist E., Kristiansson E. The ITS region as a target for characterization of fungal communities using emerging sequencing technologies. FEMS Microbiol. Lett. 2009, 296:97-101.
24. Nucci M., Anaissie E. Fusarium infections in immunocompromised patients. Clin. Microbiol. Rev. 2007, 20:695-704.
25. O'Donnell K., Kistler H.C., Cigelnik E., Ploetz R.C. Multiple evolutionary origins of the fungus causing Panama disease of banana: concordant evidence from nuclear and mitochondrial gene genealogies. Proc. Natl. Acad. Sci. U. S. A. 1998, 95:2044-2049.
26. Peterson S.W. Phylogenetic analysis of Aspergillus species using DNA sequences from four loci. Mycologia 2008, 100:205-226.
27. Pitt J.I. The current role of Aspergillus and Penicillium in human and animal health. J. Med. Vet. Mycol. 1994, 32(Suppl. 1):17-32.
28. Pitt J.I., Hocking A.D. Fungi and Food Spoilage 2009, Springer, New York. 3rd edn.
29. Rozynek P., Gilges S., Bruning T., Wilhelm M. Quality test of the MicroSeq D2 LSU Fungal Sequencing Kit for the identification of fungi. Int. J. Hyg. Environ. Health 2004, 207:297-299.
30. Santos C., Fraga M.E., Kozakiewicz Z., Lima N. Fourier transform infrared as a powerful technique for the identification and characterization of filamentous fungi and yeasts. Res. Microbiol. 2010, 161:168-175.
31. Santos C., Paterson R.R., Venancio A., Lima N. Filamentous fungal characterizations by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. J. Appl. Microbiol. 2010, 108:375-385.
32. Savitzky A., Golay M.J.E. Smoothing and differentiation of data by simplified least squares procedures. Anal. Chem. 1964, 36:1627-1639.
33. Schmitt I., Crespo A., Divakar P.K., Fankhauser J.D., Herman-Sackett E., Kalb K., Nelsen M.P., Nelson N.A., Rivas-Plata E., Shimp A.D., Widhelm T., Lumbsch H.T. New primers for promising single-copy genes in fungal phylogenetics and systematics. Persoonia 2009, 23:35-40.
34. Schoch C.L., Seifert K.A., Huhndorf S., Robert V., Spouge J.L., Levesque C.A., Chen W. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for fungi. Proc. Natl. Acad. Sci. U. S. A. 2012, 109:6241-6246.
35. Shapaval V., Moretro T., Suso H.P., Asli A.W., Schmitt J., Lillehaug D., Martens H., Bocker U., Kohler A. A high-throughput microcultivation protocol for FTIR spectroscopic characterization and identification of fungi. J. Biophotonics 2010, 3:512-521.
36. Shapaval V., Schmitt J., Moretro T., Suso H.P., Skaar I., Asli A.W., Lillehaug D., Kohler A. Characterization of food spoilage fungi by FTIR spectroscopy. J. Appl. Microbiol. 2013, 114:788-796.
37. Skiada A., Pagano L., Groll A., Zimmerli S., Dupont B., Lagrou K., Lass-Florl C., Bouza E., Klimko N., Gaustad P., Richardson M., Hamal P., Akova M., Meis J.F., Rodriguez-Tudela J.L., Roilides E., Mitrousia-Ziouva A., Petrikkos G. Zygomycosis in Europe: analysis of 230 cases accrued by the registry of the European Confederation of Medical Mycology (ECMM) Working Group on Zygomycosis between 2005 and 2007. Clin. Microbiol. Infect. 2011, 17:1859-1867.
38. Stone M. Cross-validation choice and assessment of statistical predictions. J. R. Stat. Soc. Ser. B Stat. Methodol. 1974, 36:111-147.
39. Suh S.O., Blackwell M., Kurtzman C.P., Lachance M.A. Phylogenetics of Saccharomycetales, the ascomycete yeasts. Mycologia 2006, 98:1006-1017.
40. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 2011, 28:2731-2739.
41. Tenenhaus M. La régression PLS: théorie et pratique 1998, Technip, Paris. M. Tenenhaus (Ed.).
42. Verscheure M., Lognay G., Marlier M. Revue bibliographique: les méthodes chimiques d'identification et de classification des champignons. Biotechnol. Agron. Soc. Environ. 2002, 6:131-142.
43. Vitale R.G., de Hoog G.S., Schwarz P., Dannaoui E., Deng S., Machouart M., Voigt K., van de Sande W.W., Dolatabadi S., Meis J.F., Walther G. Antifungal susceptibility and phylogeny of opportunistic members of the order Mucorales. J. Clin. Microbiol. 2011, 50:66-75.
44. Walker D.M., Castlebury L.A., Rossman A.Y., White J.F. New molecular markers for fungal phylogenetics: two genes for species-level systematics in the Sordariomycetes (Ascomycota). Mol. Phylogenet. Evol. 2012, 64:500-512.
45. Wang Y., Geng Y., Ma J., Wang Q., Zhang X.G. Sinomyces: a new genus of anamorphic Pleosporaceae. Fungal Biol. 2012, 115:188-195.
46. White T.J., Bruns T., Lee S., Taylor J. PCR Protocols: A Guide to Methods and Applications 1990, Academic Press, San Diego. M.A. Innis, D.H. Gelfand, J.J. Sninsky, T.J. White (Eds.).
47. Wu W., Guo Q., Jouan-Rimbaud D., Massart D.L. Using contrasts as data pretreatment method in pattern recognition of multivariate data. Chemom. Intell. Lab. Syst. 1999, 45:39-53.
48. Zhang N., Castlebury L.A., Miller A.N., Huhndorf S.M., Schoch C.L., Seifert K.A., Rossman A.Y., Rogers J.D., Kohlmeyer J., Volkmann-Kohlmeyer B., Sung G.H. An overview of the systematics of the Sordariomycetes based on a four-gene phylogeny. Mycologia 2006, 98:1076-1087.
49. Zhang Y., Crous P.W., Schoch C.L., Hyde K.D. Pleosporales. Fungal Divers. 2012, 53:1-221.