Molecular diagnosis, epidemiology and taxonomy of emerging medically important filamentous fungi

Reviews and Research in Medical Microbiology

Volumn 15, Issue 4, 2004, Pages 153-162

  Nagy, Elisabeth ^a,b   Kredics, László ^b   Antal, Zsuzsanna ^b   Papp, Tamás ^b,c  

^a UNIVERSITY OF SZEGED   (Hungary)

^b UNIVERSITY OF SZEGED   (Hungary)

^c UNIVERSITY OF SZEGED   (Hungary)

Author keywords

Diagnosis; Emerging filamentous fungi; Epidemiology; Molecular techniques; Taxonomy

Indexed keywords

DNA 18S; INTERNAL TRANSCRIBED SPACER;

ACREMONIUM; DIAGNOSTIC PROCEDURE; EPIDEMIOLOGY; FILAMENTOUS FUNGUS; FUNGUS; FUSARIUM; GENOTYPE; IMMUNE DEFICIENCY; IN SITU HYBRIDIZATION; MICROSATELLITE MARKER; MOLECULAR BIOLOGY; MOULD; OPPORTUNISTIC INFECTION; PENICILLIUM MARNEFFEI; PRIORITY JOURNAL; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; REVIEW; SCEDOSPORIUM; SEQUENCE ANALYSIS; SPECIES DIFFERENCE; TAXONOMY; TRICHODERMA; ZYGOMYCETES;

EID: 12244305838     PISSN: 0954139X     EISSN: None     Source Type: Journal    
DOI: 10.1097/00013542-200410000-00004     Document Type: Review

References (86)

1. Dignani MC, Anaissie E. Human fusariosis. Clin Microbiol Infect 2004, 10(Suppl 1):67-75.
2. Dóczi I, Gyetvai T, Kredics L, Nagy E. Involvement of Fusarium spp. in fungal keratitis. Clin Microbiol Infect 2004, 10:773-776.
3. Walsh TJ, Groll A, Hiemenz J, Fleming R, Roilides E, Anaissie E. Infections due to emerging and uncommon medically important fungal pathogens. Clin Microbiol Infect 2004, 10(Suppl 1):48-66.
4. Defontaine A, Zouhair R, Cimon B, Carrere J, Bailly E, Symoens F, et al. Genotyping study of Scedosporium apiospermum isolates from patients with cystic fibrosis. J Clin Microbiol 2002, 40:2108-2114.
5. Sole M, Cano J, Rodriguez-Tudela JL, Ponton J, Sutton DA, Perrie R, et al. Molecular typing of clinical and environmental isolates of Scedosporium prolificans by inter-simple-sequence-repeat polymerase chain reaction. Med Mycol 2003, 41:293-300.
6. Vanittanakom N, Vanittanakom P, Hay RJ. Rapid identification of Penicillium marneffei by PCR-based detection of specific sequences on the rRNA gene. J Clin Microbiol 2002, 40:1739-1742.
7. Vanittanakom N, Cooper CR, Chariyalertsak S, Youngchim S, Nelson KE, Sirisanthana T. Restriction endonuclease analysis of Penicillium marneffei. J Clin Microbiol 1996, 34:1834-1836.
8. Kredics L, Antal Z, Dóczi I, Manczinger L, Kevei F, Nagy E. Clinical importance of the genus Trichoderma. A review. Acta Microbiol Immunol Hung 2003, 50:105-117.
9. Müller E, Petrini O, Fischer PJ, Samuels GJ, Rossman AY. Taxonomy and anamorphs of the Herpotrichiellaceae with notes on generic synonymy. Trans Br Mycol Soc 1987, 88:63-74.
10. Nishimura K, Miyaii M, Taguchi H, Tanaka R. Fungi in bathwater and sludge of bathroom pipes. I. Frequent isolation of Exophiala species. Mycopathologia 1987, 97:17-23.
11. Nosanchuk JD, Casadevall A. The contribution of melanin to microbial pathogenesis. Cell Microbiol 2003, 5:203-223.
12. McGinnis MR, Hill C. Chromoblastomycosis and phaeohyphomycosis: new concepts, diagnosis and mycology. J Am Acad Dermatol 1983, 8:1-16.
13. Ribes JA, Vanover-Sams CL, Baker DJ. Zygomycetes in human disease. Clin Microbiol Rev 2000, 13:236-301.
14. Eucker J, Sezer O, Graf B, Possinger K. Mucormycoses. Mycoses 2001, 44:253-260.
15. Iwen PC, Hinrichs SH, Rupp ME. Utilization of the internal transcribed spacer regions as molecular targets to detect and identify human fungal pathogens. Med Mycol 2002, 40:87-109.
16. Hue FX, Huerre M, Rouffault MA, De Bievre C. Specific detection of Fusarium species in blood and tissues by a PCR technique. J Clin Microbiol 1999, 37:2434-2438.
17. Hayden RT, Isotalo PA, Parrett T, Wolk DM, Qian X, Roberts GD, et al. In situ hybridization for the differentiation of Aspergillus, Fusarium, and Pseudallescheria species in tissue section. Diagn Mol Pathol 2003, 12:21-26.
18. Hennequin C, Abachin E, Symoens F, Lavarde V, Reboux C, Nolard N, et al. Identification of Fusarium species involved in human infections by 28S rRNA gene sequencing. J Clin Microbiol 1999, 37:3586-3589.
19. Wedde M, Muller D, Tintelnot K, De Hoog GS, Stahl U. PCR-based identification of clinically relevant Pseudallescheria/Scedosporium strains. Med Mycol 1998, 36:61-67.
20. Pryce TM, Palladino S, Kay ID, Coombs GW. Rapid identification of fungi by sequencing the ITS1 and ITS2 regions using an automated capillary electrophoresis system. Med Mycol 2003, 41:369-381.
21. LoBuglio KF, Taylor JW. Phylogeny and PCR identification of the human pathogenic fungus Penicillium marneffei. J Clin Microbiol 1995, 33:85-89.
22. Tsunemi Y, Takahashi T, Tamaki T. Penicillium marneffei infection diagnosed by polymerase chain reaction from the skin specimen. J Am Acad Dermatol 2003, 49:344-346.
23. Vanittanakom N, Merz WG, Sittisombut N, Khamwan C, Nelson KE, Sirisanthana T. Specific identification of Penicillium marneffei by a polymerase chain reaction/hybridization technique. Med Mycol 1998, 36:169-175.
24. Prariyachatigul C, Chaiprasert A, Geenkajorn K, Kappe R, Chuchottaworn C, Termsetjaroen S, et al. Development and evaluation of a one-tube seminested PCR assay for the detection and identification of Penicillium marneffei. Mycoses 2003, 46:447-454.
25. Abliz P, Fukushima K, Takizawa K, Miyaji M, Nishimura K. Specific oligonucleotide primers for identification of Hortaea werneckii, a causative agent of tinea nigra. Diagn Microbiol Infect Dis 2003, 46:89-93.
26. Abliz P, Fukushima K, Takizawa K, Nieda N, Miyaji M, Nishimura K. Rapid identification of the genus Fonsecaea by PCR with specific oligonucleotide primers. J Clin Microbiol 2003, 41:873-876.
27. Abliz P, Fukushima K, Takizawa K, Nishimura K. Specific oligonucleotide primers for identification of Cladophialophora carrionii, a causative agent of chromoblastomycosis. J Clin Microbiol 2004, 42:404-407.
28. Abliz P, Fukushima K, Takizawa K, Nishimura K. Identification of pathogenic dematiaceous fungi and related taxa based on large subunit ribosomal DNA D1/D2 domain sequence analysis. FEMS Immunol Med Microbiol 2004, 40:41-49.
29. Yamagishi Y, Kawasaki K, Ishizaki H. Mitochondrial DNA analysis of Phialophora verrucosa. Mycoses 1997, 40:329-334.
30. Kusaba M, Tsuge T. Phylogeny of Alternaria fungi known to produce host-specific toxins on the basis of variation in internal transcribed spacers of ribosomal DNA. Curr Genet 1995, 28:491-498.
31. De Hoog GS, Horre R. Molecular taxonomy of the Alternaria and Ulocladium species from humans and their identification in the routine laboratory. Mycoses 2002, 45:259-276.
32. Van Burik J-A, Myerson D, Schreckhise RW, Bowden RA. Panfungal PCR assay for detection of fungal infection in human blood specimens. J Clin Microbiol 1998, 36:1169-1175.
33. Voigt K, Cigelnik E, O'Donnell K. Phylogeny and PCRidentification of clinically important zygomycetes based on nuclear ribosomal-DNA sequence data. J Clin Microbiol 1999, 7:3957-3964.
34. Wu Z, Tsumura Y, Blomquist G, Wang X-R. 18S rRNA gene variation among common airborne fungi, and development of specific oligonucleotide probes for the detection of fungal isolates. Appl Environ Microbiol 2003, 69:5389-5397.
35. Hall L, Wohlfiel S, Roberts GD. Experience with the MicroSeq D2 large-subunit ribosomal DNA sequencing kit for the identification of filamentous fungi encountered in the clinical laboratory. J Clin Microbiol 2004, 42:622-626.
36. Imhof A, Schaer C, Schoedon G, Schaer DJ, Walter RB, Schaffner A, et al. Rapid detection of pathogenic fungi from clinical specimens using LightCycler real-time fluorescence PCR. Eur J Clin Microbiol Infect Dis 2003, 22:558-560.
37. Anaissie EJ, Kuchar RT, Rex JH, Francesconi A, Kasai M, Muller FMC, et al. Fusariosis associated with pathogenic Fusarium species colonization of a hospital water system: A new paradigm for the epidemiology of opportunistic mold infections. Clin infect Dis 2001, 33:1871-1878.
38. Raad I, Tarrand J, Hanna H, Albitar M, Janssen E, Boktour M, et al. Epidemiology, molecular mycology, and environmental sources of Fusarium infection in patients with cancer. Infect Control Hosp Epidemiol 2002, 23:532-537.
39. San Millan R, Quindos G, Garaizar J, Salesa R, Guarro J, Ponton J. Characterization of Scedosporium prolificans clinical isolates by randomly amplified polymorphic DNA analysis. J Clin Microbiol 1997, 35:2270-2274.
40. Ruiz-Diez B, Martin-Diez F, Rodriguez-Tudela JL, Alvarez M, Martinez-Suarez JV. Use of random amplification of polymorphic DNA (RAPD) and PCR-fingerprinting for genotyping a Scedosporium prolificans (inflatum) outbreak in four leukemic patients. Curr Microbiol 1997, 35:186-190.
41. Zouhair R, Defontaine A, Ollivier C, Cimon B, Symoens F, Hallet JN, et al. Typing of Scedosporium apiospermum by multilocus enzyme electrophoresis and random amplification of polymorphic DNA. J Med Microbiol 2001, 50:925-932.
42. Williamson ECM, Speers D, Arthur IH, Harnett G, Ryan G, Inglis TJJ. Molecular epidemiology of Scedosporium apiospermum infection determined by PCR amplification of ribosomal intergenic spacer sequences in patients with chronic lung disease. J Clin Microbiol 2001, 39:47-50.
43. Hsueh PR, Teng LJ, Hung CC, Hsu JH, Yang PC, Ho SW, et al. Molecular evidence for strain dissemination of Penicillium marneffei: an emerging pathogen in Taiwan. J Infect Dis 2000, 181:1706-1712.
44. Trewatcharegon S, Sirisinha S, Romsai A, Eampokalap B, Teanpaisan R, Chaiyaroj SC. Molecular typing of Penicillium marneffei isolates from Thailand by Not1 macrorestriction and pulsed-field gel electrophoresis. J Clin Microbiol 2001, 39:4544-4548.
45. Lasker BA, Ran Y. Analysis of polymorphic microsatellite markers for typing Penicillium marneffei isolates. J Clin Microbiol 2004, 42:1483-1490.
46. Kawasaki M, Aoki M, Ishizaki H, Nishimura K, Nishimoto K, Matsumoto T, et al. Molecular epidemiology of Fonsecaea pedrosoi using mitochondrial DNA analysis. Med Mycol 1999, 37:435-440.
47. Matos T, Haase G, Van Den Ende AHGG, De Hoog GS. Molecular diversity of oligotrophic and neurotropic members of the black yeast genus Exophiala, with accent on E. dermatitidis. Anton Leeuw Int J Gen Mol Microbiol 2003, 83:293-303.
48. Chakrabarti A, Ghosh A, Prasad GS, David JK, Gupta S, Das A, et al. Apophysomyces elegans: an emerging zygomycete in India. J Clin Microbiol 2003, 41:783-788.
49. Lemmer K, Losert H, Rickerts V, Just-Nubling G, Sander A, Kerkmann ML, et al. Identification of Cunninghamella spec. by molecular methods. Mycoses 2002, 45(Suppl 1):31-36.
50. Guarro J, Gene J, Stchigel AM. Developments in fungal taxonomy. Clin Microbiol Rev 1999, 12:454-500.
51. Summerbell RC, Schroers HJ. Analysis of phylogenetic relationship of Cylindrocarpon lichenicola and Acremonium falciforme to the Fusarium solani species complex and a review of similarities in the spectrum of opportunistic infections caused by these fungi. J Clin Microbiol 2002, 40:2866-2875.
52. Novicki TJ, LaFe K, Bui L, Bui U, Geise R, Marr K, et al. Genetic diversity among clinical isolates of Acremonium strictum determined during an investigation of a fatal mycosis. J Clin Microbiol 2003, 41:2623-2628.
53. Gueho E, De Hoog GS. Taxonomy of the medical species Pseudallescheria and Scedosporium. J Mycol Med 1991, 118:3-9.
54. Lennon PA, Cooper CR, Salkin IF, Lee SB. Ribosomal DNA internal transcribed spacer analysis supports synonomy of Scedosporium inflatum and Lomentospora prolificans. J Clin Microbiol 1994, 32:2413-2416.
55. Issakainen J, Jalava J, Eerola E, Campbell CK. Relatedness of Pseudallescheria, Scedosporium and Graphium pro parte based on SSU rDNA sequences. J Med Vet Mycol 1997, 35:389-398.
56. Rainer J, De Hoog GS, Wedde M, Graser Y, Gilges S. Molecular variability of Pseudallescheria boydii, a neurotropic opportunist. J Clin Microbiol 2000, 38:3267-3273.
57. Varga J, Tóth B. Genetic variability and reproductive mode of Aspergillus fumigatus: a review. Infect Genet Evol 2003, 3:3-17.
58. Kuhls K, Lieckfeldt E, Börner T, Gueho E. Molecular reidentification of human pathogenic Trichoderma isolates as Trichoderma longibrachiatum and Trichoderma citrinoviride. Med Mycol 1999, 37:25-33.
59. Kredics L, Antal Z, Varga J, Manczinger L, Szekeres A, Kocsubé S. et al. Genetic variability and antifungal susceptibilities of clinical Trichoderma isolates. In Proceedings of Trends in Medical Mycology, 9th Congress of the European Confederation of Medical Mycology and 7th Trends in Invasive Fungal Infections. Amsterdam, The Netherlands, September-October 2003. Bologna: Monduzzi Editore. pp. 133-136.
60. Kullnig-Gradinger CM, Szakács G, Kubicek CP. Phylogeny and evolution of the genus Trichoderma: a multigenic approach. Mycol Res 2002, 106:757-767.
61. Berbee ML, Pirseyedi M, Hubbard S. Cochliobolus phylogenetics and the origin of known, highly virulent pathogens, inferred from ITS and glyceraldehyde-3-phosphate dehydrogenase gene sequences. Mycologia 1999, 91:964-977.
62. Pryor BM, Gilbertson RL. Molecular phylogenetic relationships amongst Alternaria species and related fungi based upon analysis of nuclear ITS and mt SSU rDNA sequences. Mycol Res 2000, 104:1312-1321.
63. Simmons EG. Alternaria themes and variations (22-26). Mycotaxon 1986, 25:287-309.
64. Masclaux F, Gueho E, De Hoog GS, Christen R. Phylogenetic relationships of human-pathogenic Cladosporium (Xylohypha) species inferred from partial LS rRNA sequences. J Med Vet Mycol 1995, 33:327-338.
65. Spatafora JW, Mitchell TG, Vilgalys R. Analysis of genes coding for small subunit ribosomal RNA sequences in studying phylogenetics of dematiaceous fungal pathogens. J Clin Microbiol 1995, 33:1322-1326.
66. Untereiner WA, Straus NA, Malloch D. A molecular-morphotaxonomic approach to the systematics of the Herpotrichiellaceae and allied black yeasts. Mycol Res 1995, 99:897-913.
67. De Hoog GS, Bowman B, Graser Y, Haase G, El Fari M, Van Den Ende AHGG, et al. Molecular phylogeny and taxonomy of medically important fungi. Med Mycol 1998, 36(Suppl 1):52-56.
68. Untereiner WA, Naveau FA. Molecular systematics of the Herpotrichiellaceae with an assessment of the phylogenetic positions of Exophiala dermatitidis and Phialophora americana. Mycologia 1999, 91:67-83.
69. Haase G, Sonntag L, Melzer-Krick B, De Hoog GS. Phylogenetic inference by SSU-gene analysis of members of the Herpotrichielllaceae with special reference to human pathogenic species. Stud Mycol 1999, 43:80-97.
70. De Hoog GS, Vicente V, Caligiorne RB, Kantarcioglu S, Tintelnot K, Van Den Ende AHGG, et al. Species diversity and polymorphism in the Exophiala spinifera clade containing opportunistic black yeast-like fungi. J Clin Microbiol 2003, 41:4767-4778.
71. Wang L, Yokoyama K, Miyaji M, Nishimura K. Identification, classification, and phylogeny of the pathogenic species Exophiala jeanselmei and related species by mitochondrial cytochrome b gene analysis. J Clin Microbiol 2001, 39:4462-4467.
72. Kawasaki M, Ishizaki H, Matsumoto T, Matsuda T, Nishimura K, Miyaji M. Mitochondrial DNA analysis of Exophiala jeanselmei var. lecanii-corni and Exophiala castellanii. Mycopathologia 1999, 146:75-77.
73. Kawasaki M, Ishizaki H, Nishimura K, Miyaji M. Mitochondrial DNA analysis of Exophiala jeanselmei and Exophiala dermatitidis. Mycopathologia 1990, 110:107-112.
74. Kawasaki M, Ishizaki H, Nishimura K, Miyaji M. Mitochondrial DNA analysis of Exophiala moniliae. Mycopathologia 1993, 121:7-10.
75. Ishizaki H, Kawasaki M, Nishimura K, Miyaji M. Mitochondrial DNA analysis of Exophiala spinifera. Mycopathologia 1995, 131:67-70.
76. Kawasaki M, Ishizaki H, Miyaji M, Nishimura K, Matsumoto T, Hombo S, et al. Molecular epidemiology of Cladosporium carrionii. Mycopathologia 1993, 124:149-152.
77. De Cook AWAM. Population biology of Hortaea werneckii based on restriction patterns of mitochondrial DNA. Anton Leeuw Int J Gen Mol Microbiol 1994, 65:21-28.
78. Van ZH, Rogers SO, Wang CJK. Assessment of Phialophora species based on ribosomal DNA internal transcribed spacers and morphology. Mycologia 1995, 87:72-83.
79. Voigt K, Wöstemeyer J. Phylogeny and origin of 82 zygomycetes from all 54 genera of the Mucorales and Mortierellales based on combined analysis of actin and translation elongation factor EF-1 alpha genes. Gene 2001, 270:113-120.
80. O'Donnel K, Lutzoni FM, Ward TJ, Benny GL. Evolutionary relationships among mucoralean fungi (Zygomycota): Evidence for family polyphyly on a large scale. Mycologia 2001, 93:286-296.
81. Jensen AB, Gargas A, Eilenberg J, Rosendahl S. Relationships of the insect-pathogenic order Entomophthorales (Zygomycota, Fungi) based on phylogenetic analyses of nuclear small subunit ribosomal DNA sequences (SSU rDNA). Fung Genet Biol 1998, 24:325-334.
82. Vágvölgyi C, Vastag M, Ács K, Papp T. Rhizomucor tauricus: a questionable species of the genus. Mycol Res 1999, 103:1318-1322.
83. Vastag M, Papp T, Kasza Z, Vágvölgyi C. Intraspecific variation in two species of Rhizomucor assessed by random amplified polymorphic DNA analysis. J Basic Microbiol 2000, 40:269-277.
84. Vágvölgyi C, Heinrich H, Ács K, Rapp T. Genetic variability in the species Rhizopus stolonifer, assessed by random amplified polymorphic DNA analysis. Anton Leeuw Int J Gen Mol Microbiol 2004, 86:181-188.
85. Hsu MC, Chen KW, Lo HJ, Chen YC, Liao MH, Lin YH, et al. Species identification of medically important fungi by use of real-time LightCycler PCR. J Med Microbiol 2003, 52:1071-1076.
86. Lasker BA. Evaluation of performance of four genotyping methods for studying the genetic epidemiology of Aspergillus fumigatus isolates. J Clin Microbiol 2002, 40:2886-2992.