Online databases for taxonomy and identification of pathogenic fungi and proposal for a cloud-based dynamic data network platform

Journal of Clinical Microbiology

Volumn 55, Issue 4, 2017, Pages 1011-1024

  Prakash, Peralam Yegneswaran ^a,b,c   Irinyi, Laszlo ^b   Halliday, Catriona ^c   Chen, Sharon ^b,c   Robert, Vincent ^d   Meyer, Wieland ^b  

^a KASTURBA MEDICAL COLLEGE   (India)

^b UNIVERSITY OF SYDNEY   (Australia)

^c WESTMEAD HOSPITAL   (Australia)

^d CBS KNAW FUNGAL BIODIVERSITY CENTRE   (Netherlands)

Author keywords

Databases; Fungi; Nomenclature; Pathogenic; Taxonomy

Indexed keywords

ARTICLE; CLOUD COMPUTING; DNA BARCODING; FUNGAL GENOME; FUNGAL STRAIN; FUNGUS IDENTIFICATION; GENE LOCUS; GENE SEQUENCE; GENETIC DATABASE; GENOMICS; MULTILOCUS SEQUENCE TYPING; NONHUMAN; ONLINE SYSTEM; SEQUENCE DATABASE; TAXONOMIC IDENTIFICATION; WHOLE GENOME SEQUENCING; ANIMAL; CLASSIFICATION; FACTUAL DATABASE; FUNGUS; HUMAN; ISOLATION AND PURIFICATION; MICROBIOLOGICAL EXAMINATION; MICROBIOLOGY; MYCOSES; PROCEDURES;

ANIMALS; DATABASES, FACTUAL; FUNGI; HUMANS; MICROBIOLOGICAL TECHNIQUES; MYCOSES;

EID: 85016193487     PISSN: 00951137     EISSN: 1098660X     Source Type: Journal    
DOI: 10.1128/JCM.02084-16     Document Type: Article

References (60)

1. Brown GD, Denning DW, Gow NA, Levitz SM, Netea MG, White TC. 2012. Hidden killers: human fungal infections. Sci Transl Med 4:165rv113. https://doi.org/10.1126/scitranslmed.3004404.
2. Pfaller MA, Pappas PG, Wingard JR. 2006. Invasive fungal pathogens: current epidemiological trends. Clin Infect Dis 43:S3-S14. https://doi.org/10.1086/504490.
3. Panackal AA. 2011. Global climate change and infectious diseases: invasive mycoses. J Earth Sci Climate Change 1:108.
4. Armstrong-James D, Meintjes G, Brown GD. 2014. A neglected epidemic: fungal infections in HIV/AIDS. Trends Microbiol 22:120-127. https://doi.org/10.1016/j.tim.2014.01.001.
5. Fisher MC, Henk DA, Briggs CJ, Brownstein JS, Madoff LC, McCraw SL, Gurr SJ. 2012. Emerging fungal threats to animal, plant and ecosystem health. Nature 484:186-194. https://doi.org/10.1038/nature10947.
6. Sleiman S, Halliday CL, Chapman B, Brown M, Nitschke J, Lau AF, Chen SC. 2016. Performance of matrix-assisted laser desorption ionization-time of flight mass spectrometry for identification of Aspergillus, Scedosporium, and Fusarium spp. in the Australian clinical setting. J Clin Microbiol 54:2182-2186.
7. Rizzato C, Lombardi L, Zoppo M, Lupetti A, Tavanti A. 2015. Pushing the Limits of MALDI-TOF mass spectrometry: beyond fungal species identification. J Fungi 1:367. https://doi.org/10.3390/jof1030367.
8. Chen SC, Sorrell TC, Chang CC, Paige EK, Bryant PA, Slavin MA. 2014. Consensus guidelines for the treatment of yeast infections in the haematology, oncology and intensive care setting, 2014. Intern Med J 44: 1315-1332. https://doi.org/10.1111/imj.12597.
9. Westblade LF, Jennemann R, Branda JA, Bythrow M, Ferraro MJ, Garner OB, Ginocchio CC, Lewinski MA, Manji R, Mochon AB, Procop GW, Richter SS, Rychert JA, Sercia L, Burnham CA. 2013. Multicenter study evaluating the Vitek MS system for identification of medically important yeasts. J Clin Microbiol 51:2267-2272. https://doi.org/10.1128/JCM.00680-13.
10. Hebert PD, Cywinska A, Ball SL, deWaard JR. 2003. Biological identifications through DNA barcodes. Proc Biol Sci 270:313-321. https://doi.org/10.1098/rspb.2002.2218.
11. Frézal L, Leblois R. 2008. Four years of DNA barcoding: current advances and prospects. Infect Genet Evol 8:727-736. https://doi.org/10.1016/j.meegid.2008.05.005.
12. Schoch CL, Robbertse B, Robert V, Vu D, Cardinali G, Irinyi L, Meyer W, Nilsson RH, Hughes K, Miller AN, Kirk PM, Abarenkov K, Aime MC, Ariyawansa HA, Bidartondo M, Boekhout T, Buyck B, Cai Q, Chen J, Crespo A, Crous PW, Damm U, De Beer ZW, Dentinger BT, Divakar PK, Dueñas M, Feau N, Fliegerova K, García MA, Ge ZW, Griffith GW, Groenewald JZ, Groenewald M, Grube M, Gryzenhout M, Gueidan C, Guo L, Hambleton S, Hamelin R, Hansen K, Hofstetter V, Hong SB, Houbraken J, Hyde KD, Inderbitzin P, Johnston PR, Karunarathna SC, Kõljalg U, Kovács GM, Kraichak E, et al. 2014. Finding needles in haystacks: linking scientific names, reference specimens and molecular data for fungi. Database (Oxford) 2014:bau061.
13. Nakamura Y, Cochrane G, Karsch-Mizrachi I, International Nucleotide Sequence Database Collaboration. 2013. The international nucleotide sequence database collaboration. Nucleic Acids Res 41:D21-D24. https://doi.org/10.1093/nar/gks1084.
14. Irinyi L, Serena C, Garcia-Hermoso D, Arabatzis M, Desnos-Ollivier M, Vu D, Cardinali G, Arthur I, Normand AC, Giraldo A, da Cunha KC, Sandoval-Denis M, Hendrickx M, Nishikaku AS, de Azevedo Melo AS, Merseguel KB, Khan A, Parente Rocha JA, Sampaio P, da Silva Briones MR, e Ferreira RC, de Medeiros Muniz M, Castanon-Olivares LR, Estrada-Barcenas D, Cassagne C, Mary C, Duan SY, Kong F, Sun AY, Zeng X, Zhao Z, Gantois N, Botterel F, Robbertse B, Schoch C, Gams W, Ellis D, Halliday C, Chen S, Sorrell TC, Piarroux R, Colombo AL, Pais C, de Hoog S, Zancope-Oliveira RM, Taylor ML, Toriello C, de Almeida Soares CM, Delhaes L, Stubbe D, et al. 2015. 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. Med Mycol 53:313-337. https://doi.org/10.1093/mmy/myv008.
15. Kõljalg U, Nilsson RH, Abarenkov K, Tedersoo L, Taylor AFS, Bahram M, Bates ST, Bruns TD, Bengtsson-Palme J, Callaghan TM, Douglas B, Drenkhan T, Eberhardt U, Dueñas M, Grebenc T, Griffith GW, Hartmann M, Kirk PM, Kohout P, Larsson E, Lindahl BD, Lücking R, Martín MP, Matheny PB, Nguyen NH, Niskanen T, Oja J, Peay KG, Peintner U, Peterson M, Põldmaa K, Saag L, Saar I, Schüßler A, Scott JA, Senés C, Smith ME, Suija A, Taylor DL, Telleria MT, Weiss M, Larsson K-H. 2013. Towards a unified paradigm for sequence-based identification of Fungi. Mol Ecol 22:5271-5277. https://doi.org/10.1111/mec.12481.
16. Ratnasingham S, Hebert PD. 2007. BOLD: the Barcode of Life Data system (http://www.barcodinglife.org). Mol Ecol Notes 7:355-364. https://doi.org/10.1111/j.1471-8286.2007.01678.x.
17. Delgado-Serrano L, Restrepo S, Bustos JR, Zambrano MM, Anzola JM. 2016. Mycofier: a new machine learning-based classifier for fungal ITS sequences. BMC Res Notes 9:1-8. https://doi.org/10.1186/s13104-015-1837-x.
18. Samson RA, Visagie CM, Houbraken J, Hong SB, Hubka V, Klaassen CHW, Perrone G, Seifert KA, Susca A, Tanney JB, Varga J, Kocsubé S, Szigeti G, Yaguchi T, Frisvad JC. 2014. Phylogeny, identification and nomenclature of the genus Aspergillus. Stud Mycol 78:141-173. https://doi.org/10.1016/j.simyco.2014.07.004.
19. Gilgado F, Cano J, Gené J, Guarro J. 2005. Molecular phylogeny of the Pseudallescheria boydii species complex: proposal of two new species. J Clin Microbiol 43:4930-4942. https://doi.org/10.1128/JCM.43.10.4930-4942.2005.
20. Short DP, O'Donnell K, Thrane U, Nielsen KF, Zhang N, Juba JH, Geiser DM. 2013. Phylogenetic relationships among members of the Fusarium solani species complex in human infections and the descriptions of F. keratoplasticum sp. Nov. and F. petroliphilum stat. Nov. Fungal Genet Biol 53:59-70. https://doi.org/10.1016/j.fgb.2013.01.004.
21. Chagas-Neto TC, Chaves GM, Melo AS, Colombo AL. 2009. Bloodstream infections due to Trichosporon spp.: species distribution, Trichosporon asahii genotypes determined on the basis of ribosomal DNA intergenic spacer 1 sequencing, and antifungal susceptibility testing. J Clin Microbiol 47:1074-1081. https://doi.org/10.1128/JCM.01614-08.
22. Garcia-Hermoso D, Hoinard D, Gantier JC, Grenouillet F, Dromer F, Dannaoui E. 2009. Molecular and phenotypic evaluation of Lichtheimia corymbifera (formerly Absidia corymbifera) complex isolates associated with human mucormycosis: rehabilitation of L. ramosa. J Clin Microbiol 47:3862-3870. https://doi.org/10.1128/JCM.02094-08.
23. Robert V, Szöke S, Eberhardt U, Cardinali G, Seifert KA, Lévesque CA, Lewis CT, Meyer W. 2011. The quest for a general and reliable fungal DNA barcode. Open Appl Inform J 5:45-61. https://doi.org/10.2174/1874136301105010045.
24. Stielow JB, Lévesque CA, Seifert KA, Meyer W, Iriny L, Smits D, Renfurm R, Verkley GJM, Groenewald M, Chaduli D, Lomascolo A, Welti S, Lesage-Meessen L, Favel A, Al-Hatmi AMS, Damm U, Yilmaz N, Houbraken J, Lombard L, Quaedvlieg W, Binder M, Vaas LAI, Vu D, Yurkov A, Begerow D, Roehl O, Guerreiro M, Fonseca A, Samerpitak K, van Diepeningen AD, Dolatabadi S, Moreno LF, Casaregola S, Mallet S, Jacques N, Roscini L, Egidi E, Bizet C, Garcia-Hermoso D, Martín MP, Deng S, Groenewald JZ, Boekhout T, de Beer ZW, Barnes I, Duong TA, Wingfield MJ, de Hoog GS, Crous PW, Lewis CT, et al. 2015. One fungus, which genes?. Development and assessment of universal primers for potential secondary fungal DNA barcodes. Persoonia 35:242-263.
25. Crous PW, Gams W, Stalpers D, Robert V, Stegehuis G. 2004. MycoBank: an online initiative to launch mycology into the 21st century. Stud Mycol 50:19-22.
26. Robert V, Vu D, Amor AB, van de Wiele N, Brouwer C, Jabas B, Szoke S, Dridi A, Triki M, Ben Daoud S, Chouchen O, Vaas L, de Cock A, Stalpers JA, Stalpers D, Verkley GJ, Groenewald M, Dos Santos FB, Stegehuis G, Li W, Wu L, Zhang R, Ma J, Zhou M, Gorjon SP, Eurwilaichitr L, Ingsriswang S, Hansen K, Schoch C, Robbertse B, Irinyi L, Meyer W, Cardinali G, Hawksworth DL, Taylor JW, Crous PW. 2013. MycoBank gearing up for new horizons. IMA Fungus 4:371-379. https://doi.org/10.5598/imafungus.2013.04.02.16.
27. Benson DA, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. 2014. GenBank. Nucleic Acids Res 42:D32-D37. https://doi.org/10.1093/nar/gkt1030.
28. Nilsson R, Ryberg M, Kristiansson E, Abarenkov K, Larsson K, Kõljalg U. 2006. Taxonomic reliability of DNA sequences in public sequence databases: a fungal perspective. PLoS One 1:e59. https://doi.org/10.1371/journal.pone.0000059.
29. Celio GJ, Padamsee M, Dentinger BT, Bauer R, McLaughlin DJ. 2006. Assembling the Fungal Tree of Life: constructing the structural and biochemical database. Mycologia 98:850-859. https://doi.org/10.3852/mycologia.98.6.850.
30. O'Donnell K, Ward TJ, Robert VARG, Crous PW, Geiser DM, Kang S. 2015. DNA sequence-based identification of Fusarium: current status and future directions. Phytoparasitica 43:583-595. https://doi.org/10.1007/s12600-015-0484-z.
31. Geiser DM, del Mar Jiménez-Gasco M, Kang S, Makalowska I, Veeraraghavan N, Ward TJ, Zhang N, Kuldau GA, O'Donnell K. 2004. FUSARIUM-ID v. 1.0: a DNA sequence database for identifying Fusarium. Eur J Plant Pathol 110:473-479. https://doi.org/10.1023/B:EJPP.0000032386.75915.a0.
32. Park B, Park J, Cheong KC, Choi J, Jung K, Kim D, Lee YH, Ward TJ, O'Donnell K, Geiser DM, Kang S. 2011. Cyber infrastructure for Fusarium: three integrated platforms supporting strain identification, phylogenetics, comparative genomics and knowledge sharing. Nucleic Acids Res 39:D640-D646. https://doi.org/10.1093/nar/gkq1166.
33. O'Donnell K, Sutton DA, Rinaldi MG, Sarver BA, Balajee SA, Schroers HJ, Summerbell RC, Robert VA, Crous PW, Zhang N, Aoki T, Jung K, Park J, Lee YH, Kang S, Park B, Geiser DM. 2010. Internet-accessible DNA sequence database for identifying fusaria from human and animal infections. J Clin Microbiol 48:3708-3718. https://doi.org/10.1128/JCM.00989-10.
34. Visagie CM, Houbraken J, Frisvad JC, Hong SB, Klaassen CHW, Perrone G, Seifert KA, Varga J, Yaguchi T, Samson RA. 2014. Identification and nomenclature of the genus Penicillium. Stud Mycol 78:343-371. https://doi.org/10.1016/j.simyco.2014.09.001.
35. Meyer W, Aanensen DM, Boekhout T, Cogliati M, Diaz MR, Esposto MC, Fisher M, Gilgado F, Hagen F, Kaocharoen S, Litvintseva AP, Mitchell TG, Simwami SP, Trilles L, Viviani MA, Kwon-Chung J. 2009. Consensus multi-locus sequence typing scheme for Cryptococcus neoformans and Cryptococcus gattii. Med Mycol 47:561-570. https://doi.org/10.1080/13693780902953886.
36. Bernhardt A, Sedlacek L, Wagner S, Schwarz C, Wurstl B, Tintelnot K. 2013. Multilocus sequence typing of Scedosporium apiospermum and Pseudallescheria boydii isolates from cystic fibrosis patients. J Cyst Fibros 12:592-598. https://doi.org/10.1016/j.jcf.2013.05.007.
37. Pham CD, Purfield AE, Fader R, Pascoe N, Lockhart SR. 2015. Development of a multilocus sequence typing system for medically relevant Bipolaris species. J Clin Microbiol 53:3239-3246. https://doi.org/10.1128/JCM.01546-15.
38. Phipps LM, Chen SC, Kable K, Halliday CL, Firacative C, Meyer W, Wong G, Nankivell BJ. 2011. Nosocomial Pneumocystis jirovecii pneumonia: lessons from a cluster in kidney transplant recipients. Transplantation 92:1327-1334. https://doi.org/10.1097/TP.0b013e3182384b57.
39. Aanensen DM, Spratt BG. 2005. The multilocus sequence typing network: mlst.net. Nucleic Acids Res 33:W728-W733. https://doi.org/10.1093/nar/gki415.
40. Bougnoux ME, Tavanti A, Bouchier C, Gow NA, Magnier A, Davidson AD, Maiden MC, D'Enfert C, Odds FC. 2003. Collaborative consensus for optimized multilocus sequence typing of Candida albicans. J Clin Microbiol 41:5265-5266. https://doi.org/10.1128/JCM.41.11.5265-5266.2003.
41. Dodgson AR, Pujol C, Denning DW, Soll DR, Fox AJ. 2003. Multilocus sequence typing of Candida glabrata reveals geographically enriched clades. J Clin Microbiol 41:5709-5717. https://doi.org/10.1128/JCM.41.12.5709-5717.2003.
42. Jacobsen MD, Gow NA, Maiden MC, Shaw DJ, Odds FC. 2007. Strain typing and determination of population structure of Candida krusei by multilocus sequence typing. J Clin Microbiol 45:317-323. https://doi.org/10.1128/JCM.01549-06.
43. Tavanti A, Davidson AD, Johnson EM, Maiden MC, Shaw DJ, Gow NA, Odds FC. 2005. Multilocus sequence typing for differentiation of strains of Candida tropicalis. J Clin Microbiol 43:5593-5600. https://doi.org/10.1128/JCM.43.11.5593-5600.2005.
44. Cerqueira GC, Arnaud MB, Inglis DO, Skrzypek MS, Binkley G, Simison M, Miyasato SR, Binkley J, Orvis J, Shah P, Wymore F, Sherlock G, Wortman JR. 2014. The Aspergillus genome database: multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations. Nucleic Acids Res 42:D705-D710. https://doi.org/10.1093/nar/gkt1029.
45. White TC, Oliver BG, Graser Y, Henn MR. 2008. Generating and testing molecular hypotheses in the dermatophytes. Eukaryot Cell 7:1238-1245. https://doi.org/10.1128/EC.00100-08.
46. Yang J, Chen L, Wang L, Zhang W, Liu T, Jin Q. 2007. TrED: the Trichophyton rubrum Expression Database. BMC Genomics 8:250. https://doi.org/10.1186/1471-2164-8-250.
47. Inglis DO, Arnaud MB, Binkley J, Shah P, Skrzypek MS, Wymore F, Binkley G, Miyasato SR, Simison M, Sherlock G. 2011. The Candida genome database incorporates multiple Candida species: multispecies search and analysis tools with curated gene and protein information for Candida albicans and Candida glabrata. Nucleic Acids Res 40:D667-D674. https://doi.org/10.1093/nar/gkr945.
48. Stajich JE, Harris T, Brunk BP, Brestelli J, Fischer S, Harb OS, Kissinger JC, Li W, Nayak V, Pinney DF, Stoeckert CJ, Jr, Roos DS. 2012. FungiDB: an integrated functional genomics database for fungi. Nucleic Acids Res 40:D675-D681. https://doi.org/10.1093/nar/gkr918.
49. Grigoriev IV, Nikitin R, Haridas S, Kuo A, Ohm R, Otillar R, Riley R, Salamov A, Zhao X, Korzeniewski F, Smirnova T, Nordberg H, Dubchak I, Shabalov I. 2014. MycoCosm portal: gearing up for 1000 fungal genomes. Nucleic Acids Res 42:D699-D704. https://doi.org/10.1093/nar/gkt1183.
50. Taylor JW. 2011. One fungus one name: DNA and fungal nomenclature twenty years after PCR. IMA Fungus 2:113-120. https://doi.org/10.5598/imafungus.2011.02.02.01.
51. Hawksworth DL, Crous PW, Redhead SA, Reynolds DR, Samson RA, Seifert KA, Taylor JW, Wingfield MJ, Abaci O, Aime C, Asan A, Bai F-Y, de Beer ZW, Begerow D, Berikten D, Boekhout T, Buchanan PK, Burgess T, Buzina W, Cai L, Cannon PF, Crane JL, Damm U, Daniel H-M, van Diepeningen AD, Druzhinina I, Dyer PS, Eberhardt U, Fell JW, Frisvad JC, Geiser DM, Geml J, Glienke C, Gräfenhan T, Groenewald JZ, Groenewald M, de Gruyter J, Guého-Kellermann E, Guo L-D, Hibbett DS, Hong S-B, de Hoog GS, Houbraken J, Huhndorf SM, Hyde KD, Ismail A, Johnston PR, Kadaifciler DG, Kirk PM, Kõljalg U, et al. 2011. The Amsterdam Declaration on Fungal Nomenclature. IMA Fungus 2:105-112. https://doi.org/10.5598/imafungus.2011.02.01.14.
52. Lindahl BD, Nilsson RH, Tedersoo L, Abarenkov K, Carlsen T, Kjøller R, Kõljalg U, Pennanen T, Rosendahl S, Stenlid J, Kauserud H. 2013. Fungal community analysis by high-throughput sequencing of amplified markers-A user's guide. New Phytol 199:288-299. https://doi.org/10.1111/nph.12243.
53. Jayasiri SC, Hyde KD, Ariyawansa HA, Bhat J, Buyck B, Cai L, Dai Y-C, Abd-Elsalam KA, Ertz D, Hidayat I, Jeewon R, Jones EBG, Bahkali AH, Karunarathna SC, Liu J-K, Luangsa-ard JJ, Lumbsch HT, Maharachchikumbura SSN, McKenzie EHC, Moncalvo J-M, Ghobad-Nejhad M, Nilsson H, Pang K-L, Pereira OL, Phillips AJL, Raspé O, Rollins AW, Romero AI, Etayo J, Selçuk F, Stephenson SL, Suetrong S, Taylor JE, Tsui CKM, Vizzini A, Abdel-Wahab MA, Wen T-C, Boonmee S, Dai DQ, Daranagama DA, Dissanayake AJ, Ekanayaka AH, Fryar SC, Hongsanan S, Jayawardena RS, Li W-J, Perera RH, Phookamsak R, de Silva NI, Thambugala KM, et al. 2015. The Faces of Fungi database: fungal names linked with morphology, phylogeny and human impacts. Fungal Divers 74:3-18. https://doi.org/10.1007/s13225-015-0351-8.
54. Saxena V, Doddavula SK, Jain A. 2012. Implementation of a secure genome sequence search platform on public cloud-leveraging open source solutions. J Cloud Comp Adv Syst Appl 1:1-14. https://doi.org/10.1186/2192-113X-1-1.
55. Boixo S, Ronnow TF, Isakov SV, Wang Z, Wecker D, Lidar DA, Martinis JM, Troyer M. 2014. Evidence for quantum annealing with more than one hundred qubits. Nat Phys 10:218-224. https://doi.org/10.1038/nphys2900.
56. Yu YW, Daniels NM, Danko DC, Berger B. 2015. Entropy-scaling search of massive biological data. Cell Syst 1:130-140. https://doi.org/10.1016/j.cels.2015.08.004.
57. Vu D, Szoke S, Wiwie C, Baumbach J, Cardinali G, Rottger R, Robert V. 2014. Massive fungal biodiversity data re-annotation with multi-level clustering. Sci Rep 4:6837. https://doi.org/10.1038/srep06837.
58. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, Park SC, Jeon YS, Lee JH, Yi H, Won S, Chun J. 2012. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716-721. https://doi.org/10.1099/ijs.0.038075-0.
59. Jolley KA, Chan M-S, Maiden MC. 2004. mlstdbNet-distributed multilocus sequence typing (MLST) databases. BMC Bioinformatics 5:1-8. https://doi.org/10.1186/1471-2105-5-1.
60. Petti CA, Bosshard PP, Brandt ME, Clarridge JE, Feldblyum TV, Foxall P, Furtado MR, Pace N, Procop G. 2008. Interpretive criteria for identification of bacteria and fungi by DNA target sequencing; approved guideline-vol 28, no.12. CLSI document MM18-A. Clinical and Laboratory Standards Institute, Wayne, PA.