The 'species complex' issue in clinically relevant fungi: A case study in Scedosporium apiospermum

Fungal Biology

Volumn 120, Issue 2, 2016, Pages 137-146

  Chen, Min ^a,b,c   Zeng, Jingsi ^d   De Hoog, G Sybren ^{a,b,c,e,f,g,h}   Stielow, Benjamin ^b   Gerrits Van Den Ende, A H G ^b   Liao, Wanqing ^a   Lackner, Michaela ⁱ  

^a SECOND MILITARY MEDICAL UNIVERSITY   (China)

^b CBS KNAW FUNGAL BIODIVERSITY CENTRE   (Netherlands)

^c UNIVERSITY OF AMSTERDAM   (Netherlands)

^d HUAZHONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

^e SUN YAT SEN UNIVERSITY   (China)

^f PEKING UNIVERSITY FIRST HOSPITAL   (China)

^g KING ABDULAZIZ UNIVERSITY   (Saudi Arabia)

^h FEDERAL UNIVERSITY OF PARANÁ   (Brazil)

ⁱ INNSBRUCK MEDICAL UNIVERSITY   (Austria)

Author keywords

ITS rDNA; Populations; Primary barcode; Secondary barcode

Indexed keywords

DNA FINGERPRINTING; FUNGUS;

FUNGI; PSEUDALLESCHERIA ANGUSTA; PSEUDALLESCHERIA BOYDII; SCEDOSPORIUM; SCEDOSPORIUM AURANTIACUM;

ACTIN; FUNGAL PROTEIN; TUBULIN;

CLASSIFICATION; GENETICS; HUMAN; ISOLATION AND PURIFICATION; MICROBIOLOGICAL EXAMINATION; MICROBIOLOGY; MOLECULAR GENETICS; MYCOSIS; PHYLOGENY; SCEDOSPORIUM;

ACTINS; FUNGAL PROTEINS; HUMANS; MOLECULAR SEQUENCE DATA; MYCOLOGICAL TYPING TECHNIQUES; MYCOSES; PHYLOGENY; SCEDOSPORIUM; TUBULIN;

EID: 84954228134     PISSN: 18786146     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.funbio.2015.09.003     Document Type: Article

References (28)

1. Al-Hatmi A.M.S., Gerrits V.D.E., Stielow A.H.G., Diepeningen B.V., Seifert A.D., Mccormick K.A., Assabgui W., Gräfenhan R.T., De Hoog Sybren, André Levesque G.C. Evaluation of two novel barcodes for species recognition of opportunistic pathogens in Fusarium. Fungal Biology 2016, 120(2):231-245.
2. Bensch K., Braun U., Groenewald J.Z., Crous P.W. The genus Cladosporium. Studies in Mycology 2012, 72:1-401.
3. Bissett J. A revision of the genus Trichoderma. III. Section Pachybasium. Canadian Journal of Botany 1991, 69:2373-2417.
4. Brown S.D.J., Collins R.A., Boyer S., Lefort M-C., Malumbres-Olarte J., Vink C.J., Cruickshank R. Spider: an R package for the analysis of species identity and evolution, with particular reference to DNA barcoding. Molecular Ecology Resource 2012, 12:562-565.
5. Druzhinina I.S., Kopchinskiy A.G., Komoń M., Bissett J., Szakacs G., Kubicek C.P. An oligonucleotide barcode for species identification in Trichoderma and Hypocrea. Fungal Genetics and Biology 2005, 42:813-828.
6. Geiser D.M., Klich M.A., Frisvad J.C., Peterson S.W., Varga J., Samson R.A. The current status of species recognition and identification in Aspergillus. Studies in Mycology 2007, 59:1-10.
7. Gilgado F., Cano J., Gené J., Guarro J. Molecular phylogeny of the Pseudallescheria boydii species complex: proposal of two new species. Journal of Clinical Microbiology 2005, 43:4930-4942.
8. Hagen F., Khayhan K., Theelen B., Kolecka A., Polacheck I., Sionov E., Falk R., Parnmen S., Lumbsch H.T., Boekhout T. Recognition of seven species in the Cryptococcus gattii/Cryptococcus neoformans species complex. Fungal Genetics and Biology 2015, 78:16-48.
9. Hall T.A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series 1999, 41:95-98.
10. Heinrichs G., de Hoog G.S., Haase G. Barcode identifiers as a practical tool for reliable species assignment of medically important black yeast species. Journal of Clinical Microbiology 2012, 50:3023-3030.
11. Hong S.B., Go S.J., Shin H.D., Frisvad J.C., Samson R.A. Polyphasic taxonomy of Aspergillus fumigatus and related species. Mycologia 2005, 97:1316-1329.
12. Howard S.J., Harrison E., Bowyer P., Varga J., Denning D.W. Cryptic species and azole resistance in the Aspergillus niger complex. Antimicrobial Agents and Chemotherapy 2011, 55:4802-4809.
13. Irinyi L., Serena C., Garcia-Hermoso D., Arabatzis M., Desnos-Ollivier M., Vu D., Cardinali G., Arthur I., Normand A.C., Giraldo A., da Cunha K.C., Sandoval-Denis M., Hendrickx M., Nishikaku A.S., de Azevedo Melo A.S., Merseguel K.B., Khan A., Parente Rocha J.A., Sampaio P., da Silva Briones M.R., e Ferreira R.C., de Medeiros Muniz M., Castañón-Olivares L.R., Estrada-Barcenas D., Cassagne C., Mary C., Duan S.Y., Kong F., Sun A.Y., Zeng X., Zhao Z., Gantois N., Botterel F., Robbertse B., Schoch C., Gams W., Ellis D., Halliday C., Chen S., Sorrell T.C., Piarroux R., Colombo A.L., Pais C., de Hoog S., Zancopé-Oliveira R.M., Taylor M.L., Toriello C., de Almeida Soares C.M., Delhaes L., Stubbe D., Dromer F., Ranque S., Guarro J., Cano-Lira J.F., Robert V., Velegraki A., Meyer W. International Society of Human and Animal Mycology (ISHAM)-ITS reference DNA barcoding database-the quality controlled standard tool for routine identification of human and animal pathogenic fungi. Medical Mycology 2015, 53:313-337.
14. Kaltseis J., Rainer J., De Hoog G.S. Ecology of Pseudallescheria and Scedosporium species in human-dominated and natural environments and their distribution in clinical samples. Medical Mycology 2009, 47:398-405.
15. Katsu M., Kidd S., Ando A., Moretti-Branchini M.L., Mikami Y., Nishimura K., Meyer W. The internal transcribed spacers and 5.8S rRNA gene show extensive diversity among isolates of the Cryptococcus neoformans species complex. FEMS Yeast Research 2004, 4:377-388.
16. Kwon-Chung K.J., Varma A. Do major species concepts support one, two or more species within Cryptococcus neoformans?. FEMS Yeast Research 2006, 6:574-587.
17. Lackner M., Hagen F., Meis J.F., Gerrits van den Ende A.H., Vu D., Robert V., Fritz J., Moussa T.A., de Hoog G.S. Susceptibility and diversity in the therapy-refractory genus Scedosporium. Antimicrobial Agents and Chemotherapy 2014, 58:5877-5885.
18. Lackner M., de Hoog G.S., Yang L.Y., Moreno L.F., Ahmed S.A., Fritz A., Kaltseis J., Nagl M., Lass-Flörl C., Risslegger B., Rambach G., Speth C., Robert V., Buzina W., Chen S., Bouchara J.P., Cano-Lira J.F., Guarro J., Gené J., Silva F.F., Haido R., Haase G., Havlicek V., Garcia-Hermoso D., Meis Jacques F., Hagen F., Kirchmair M., Rainer J., Schwabenbauer K., Zoderer M., Meyer W., Gilgado F., Schwabenbauer K., Vicente V.A., Piecková E., Regenermel M., Rath P.M., Steinmann J., de Alencar X.W., Symoens F., Tintelnot K., Ulfig K., Velegraki A., Tortorano A.M., Giraud S., Mina S., Rigler-Hohenwarter K., Hernando F.L., Ramirez-Garcia A., Pellon A., Kaur J., Bergter E.B., de Meirelles J.V., da Silva I.D., Delhaes L., Alastruey-Izquerdo A., Li R.Y., Lu Q.Y., Moussa T., Almaghrabi O., Al-Zahrani H., Okada G., Deng S.W., Liao W.Q., Zeng J.S., Issakainen J., Lopes L.C.L. Proposed nomenclature for Pseudallescheria, Scedosporium and related genera. Fungal Diversity 2014, 67:1-10.
19. Manamgoda D.S., Cai L., McKenzie E.H.C., Crous P.W., Madrid H., Chukeatirote E., Shivas R.G., Tan Y.P., Hyde K.D. A phylogenetic and taxonomic re-evaluation of the Bipolaris - Cochliobolus - Curvularia complex. Fungal Diversity 2012, 56:131-144.
20. Nylander J. MrModeltest v2. Program Distributed by the Author 2004, vol. 2:1-2. Evolutionary Biology Centre Uppsala University.
21. O'Donnell K., Humber R.A., Geiser D.M., Kang S., Park B., Robert V.A., Crous P.W., Johnston P.R., Aoki T., Rooney A.P., Rehner S.A. Phylogenetic diversity of insecticolous fusaria inferred from multilocus DNA sequence data and their molecular identification via FUSARIUM-ID and Fusarium MLST. Mycologia 2012, 104:427-445.
22. Reedy J.L., Floyd A.M., Heitman J. Mechanistic plasticity of sexual reproduction and meiosis in the Candida pathogenic species complex. Current Biology 2009, 19:891-899.
23. Stielow J.B., Lévesque C.A., Seifert K.A., Meyer W., Irinyi L. One fungus, which genes? Development and assessment of universal primers for potential secondary fungal DNA barcodes. Persoonia 2015, (submitted for publication).
24. 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. Molecular Biology and Evolution 2011, 28:2731-2739.
25. Tammer I., Tintelnot K., Braun-Dullaeus R.C., Mawrin C., Scherlach C., Schlüter D., König W. Infections due to Pseudallescheria/Scedosporium species in patients with advanced HIV disease - a diagnostic and therapeutic challenge. International Journal of Infectious Diseases 2011, 15:e422-429.
26. Téllez M.D., Batista-Duharte A., Portuondo D., Quinello C., Bonne-Hernández R., Carlos I.Z. Sporothrix schenckii complex biology: environment and fungal pathogenicity. Microbiology 2014, 160:2352-2365.
27. Treviño-Rangel Rde J., Garza-González E., González J.G., Bocanegra-García V., Llaca J.M., González G.M. Molecular characterization and antifungal susceptibility of the Candida parapsilosis species complex of clinical isolates from Monterrey, Mexico. Medical Mycology 2012, 50:781-784.
28. Zhang Y., Hagen F., Stielow B., Rodrigues A.M., Samerpitak K., Zhou X., Feng P., Yang L., Chen M., Deng S., Li S., Liao W., Li R., Li F., Meis J.F., Guarro J., Teixeira M., Al-Zahrani H.S., Camargo Z.P., Zhang L., de Hoog G.S. Phylogeography and evolutionary patterns in Sporothrix spanning more than 14 000 human and animal case reports. Persoonia 2015, 35:1-20.