Identification of the major molecular types of cryptococcus neoformans and C. gattii by hyperbranched rolling circle amplification

PLoS ONE

Volumn 9, Issue 4, 2014, Pages

  Trilles, Luciana ^a,b   Wang, Bin ^a   Firacative, Carolina ^a   Lazéra, Márcia Dos Santos ^b   Wanke, Bodo ^b   Meyer, Wieland ^a  

^a UNIVERSITY OF SYDNEY   (Australia)

^b Funda??o Oswaldo Cruz   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

FUNGAL DNA; OLIGONUCLEOTIDE PROBE; PRIMER DNA;

ARTICLE; CRYPTOCOCCUS GATTII; CRYPTOCOCCUS GATTII GENOTYPE VGI; CRYPTOCOCCUS GATTII GENOTYPE VGII; CRYPTOCOCCUS GATTII GENOTYPE VGIII; CRYPTOCOCCUS GATTII GENOTYPE VGIV; CRYPTOCOCCUS NEOFORMANS; CRYPTOCOCCUS NEOFORMANS GENOTYPE VNI; CRYPTOCOCCUS NEOFORMANS GENOTYPE VNII; CRYPTOCOCCUS NEOFORMANS GENOTYPE VNIV; DNA DETERMINATION; FUNGAL GENE; FUNGUS IDENTIFICATION; GENE AMPLIFICATION; GENE LOCUS; GENE SEQUENCE; HYPERBRANCHED ROLLING CIRCLE AMPLIFICATION; MOLECULAR TYPING; NONHUMAN; PLB1 GENE; POLYMERASE CHAIN REACTION; SEMI NESTED POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY; SINGLE NUCLEOTIDE POLYMORPHISM; CLASSIFICATION; GENETICS; HUMAN; NUCLEIC ACID AMPLIFICATION; OLIGONUCLEOTIDE PROBE; PROCEDURES; TIME;

CRYPTOCOCCUS NEOFORMANS; DNA PRIMERS; DNA, FUNGAL; GENETIC LOCI; HUMANS; MOLECULAR TYPING; NUCLEIC ACID AMPLIFICATION TECHNIQUES; OLIGONUCLEOTIDE PROBES; TIME FACTORS;

EID: 84899669812     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0094648     Document Type: Article

References (36)

1. Perfect JR, Dismukes WE, Dromer F, Goldman DL, Graybill JR, et al. (2010) Clinical practice guidelines for the management of cryptococcal disease: 2010 update by the infectious diseases society of America. Clin Infect Dis 50(3): 291-322.
2. Harris J, Lockhart S, Chiller T (2012) Cryptococcus gattii: where do we go from here? Med Mycol 50(2): 113-129.
3. Lazéra MS, Gutierrez-Galhardo MC, Cavalcanti MAS, Wanke B (2005) Criptococose. In: Coura JR, editor. Dinâmica das doenças infecciosas e parasitárias, Guanabara Koogan, Rio de Janeiro. 1223-1236.
4. Kidd SE, Hagen F, Tscharke RL, Huynh M, Bartlett KH, et al. (2004) A rare genotype of Cryptococcus gattii caused the cryptococcosis outbreak on Vancouver Island (British Columbia, Canada). Proc Natl Acad Sci U S A 101(49): 17258-17263. (Pubitemid 39627807)
5. Meyer M, Gilgado F, Ngamskulrungroj P, Trilles L, Hagen F, et al. (2011) Molecular Typing of the Cryptococcus neoformans/C. gattii species complex, p 327-357. In: Heitman J, Kozel T, Kwon-Chung J, Perfect J, Casadevall, editors, Cryptococcus: from human pathogen to model yeast. ASM Press, Washington, DC.
6. Trilles L, Meyer W, Wanke B, Guarro J, Lazéra MS (2012) Correlation of antifungal susceptibility and molecular type within the Cryptococcus neoformans/C. gattii species complex. Med Mycol 50(3): 328-332.
7. Sorrell TC (2001) Cryptococcus neoformans variety gattii. Med Mycol 39: 155-168. (Pubitemid 32377312)
8. Huston SM, Mody CH. (2009) Cryptococcosis: an emerging respiratory mycosis. Clin Chest Med 30(2): 253-264.
9. Byrnes EJ 3rd, Li W, Ren P, Lewit Y, Voelz K, et al. (2011) A diverse population of Cryptococcus gattii molecular type VGIII in Southern Californian HIV/AIDS patients. PloS Pathogens 7(9): e1002205.
10. Boekhout T, Theelen B, Diaz M, Fell JW, Hop WC, et al. (2001) Hybrid genotypes in the pathogenic yeast Cryptococcus neoformans. Microbiology 147(4): 891-907. (Pubitemid 32401329)
11. Meyer W, Castañeda A, Jackson S, Huynh M, Castañeda E, et al. (2003) Molecular typing of IberoAmerican Cryptococcus neoformans isolates. Emerg Infect Dis 9(2): 189-195. (Pubitemid 36231789)
12. Hanafy A, Kaocharoen S, Jover-Botella A, Katsu M, Iida S, et al. (2008) Multilocus microsatellite typing for Cryptococcus neoformans var. grubii. Med Mycol 46(7): 685-696.
13. Meyer W, Aanensen DM, Boekhout T, Cogliati M, Diaz MR, et al. (2009) Consensus multi-locus sequence typing scheme for Cryptococcus neoformans and Cryptococcus gattii. Med Mycol 47(6): 561-570.
14. Magee PT, Gale C, Berman J, Davis D (2003) Molecular genetic and genomic approaches to the study of medically important fungi. Infect Immun 71(5): 2299-2309. (Pubitemid 36519839)
15. Leaw SN, Chang HC, Sun HF, Barton R, Bouchara JP, et al. (2006) Identification of medically important yeast species by sequence analysis of the internal transcribed spacer regions. J Clin Microbiol 44(3): 693-699.
16. Bovers M, Diaz MR, Hagen F, Spanjaard L, Duim B, et al. (2007) Identification of genotypically diverse Cryptococcus neoformans and Cryptococcus gattii isolates by Luminex xMAP technology. J Clin Microbiol 45(6): 1874-1883. (Pubitemid 46933920)
17. Lizardi PM, Huang XH, Zhu ZG, Bray-Ward P, Thomas DC, et al. (1998) Mutation detection and single-molecule counting using isothermal rolling-circle amplification. Nat Genet 19: 225-232. (Pubitemid 28309332)
18. Nilsson M, Malmgren H, Samiotaki M, Kwiatkowski M, Chowdhary BP, et al. (1994) Padlock probes: circularizing oligonucleotides for localized DNA detection. Science 265: 2085-2088. (Pubitemid 24325689)
19. Alsmadi OA, Bornarth CJ, Song W, Wisniewski M, Du J, et al. (2003) High accuracy genotyping directly from genomic DNA using a rolling circle amplification based assay. BMC Genomics 4(1): 21.
20. Wang B, Dwyer DE, Chew CB, Kol C, He ZP, et al. (2009) Sensitive detection of the K103N non-nucleoside reverse transcriptase inhibitor resistance mutation in treatment-nave HIV-1 infected individuals by rolling circle amplification. J Virol Methods 161(1): 128-135.
21. Kurt K, Alderborn A, Nilsson M, Strommenger B, Witte W, et al. (2009) Multiplexed genotyping of methicillin-resistant Staphylococcus aureus isolates by use of padlock probes and tag microarrays. J Clin Microbiol 47(3): 577-585.
22. Kaocharoen S, Wang B, Tsui KM, Trilles L, Kong F, et al. (2008) Hyperbranched rolling circle amplification as a rapid and sensitive method for species identification within the Cryptococcus species complex. Electrophoresis 29(15): 3183-3191.
23. Lucas S, da Luz Martins M, Flores O, Meyer W, Spencer-Martins I, et al. (2010) Differentiation of Cryptococcus neoformans varieties and Cryptococcus gattii using CAP59-based loop-mediated isothermal DNA amplification. Clin Microbiol Infect 16(6): 711-714.
24. Aminnejad M, Diaz M, Arabatzis M, Castañeda E, Lazera M, et al. (2012) Identification of novel hybrids between Cryptococcus neoformans var. grubii VNI and Cryptococcus gattii VGII. Mycopathologia 173: 337-346.
25. Ferrer C, Colom F, Frasés S, Mulet E, Abad JL, et al. (2001) Detection and identification of fungal pathogens by PCR and by ITS2 and 5.8S ribosomal DNA typing in ocular infections. J Clin Microbiol 39(8): 2873-2879. (Pubitemid 32744004)
26. Litvintseva AP, Thakur R, Vilgalys R, Mitchell TG (2006) Multilocus sequence typing reveals three genetic subpopulations of Cryptococcus neoformans var. grubii (serotype A), including a unique population in Botswana. Genetics 172(4): 2223-2238.
27. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: Molecular Evolutionary Genetics Analysis using Likelihood, Distance, and Parsimony methods. Mol Biol Evol 28(10): 2731-2739.
28. Trilles L, Lazéra dos Santos M, Wanke B, Oliveira RV, Barbosa GG, et al. (2008) Regional pattern of the molecular types of Cryptococcus neoformans and Cryptococcus gattii in Brazil. Mem Inst Oswaldo Cruz 103(5): 455-462.
29. Thomas LB, Foulis PR, Mastorides SM, Djilan YA, Skinner O, et al. (2012) Hepatitis C genotype analysis: results in a large veteran population with review of the implications for clinical practice. Ann Clin Lab Sci 42(4): 355-362.
30. van der Velden WJ, Blijlevens NM, Donnelly JP (2011) Genetic variants and the risk for invasive mould disease in immunocompromised hematology patients. Curr. Opin Infect Dis 24(6): 554-563.
31. Johnson MD, Plantinga TS, van de Vosse E, Velez Edwards DR, Smith PB, et al. (2012) Cytokine gene polymorphisms and the outcome of invasive candidiasis: a prospective cohort study. Clin Infect Dis 54(4): 502-510.
32. Wiesner DL, Moskalenko O, Corcoran JM, McDonald T, Rolfes MA, et al. (2012) Cryptococcal genotype influences immunologic response and human clinical outcome after meningitis. MBio 25(5): e00196-12. 10.1128/mBio.00196-12.
33. Feng X, Fu X, Ling B, Wang L, Liao W, et al. (2013) Rapid differentiation or cryptic species within Cryptococcus gattii by a duplex PCR assay. JCM Doi:10.11.28/JCM.01455-13 published ahead of print 3 July 2013.
34. Skladny H, Buchheidt D, Baust C, Krieg-Schneider F, Seifarth W, et al. (1999) Specific detection of Aspergillus species in blood and bronchoalveolar lavage samples of immunocompromised patients by two-step PCR. J Clin Microbiol 37(12): 3865-3871.
35. Spiess B, Seifarth W, Hummel M, Frank O, Fabarius A, et al. (2007) DNA microarray-based detection and identification of fungal pathogens in clinical samples from neutropenic patients. J Clin Microbiol 45(11): 3743-3753. (Pubitemid 350156875)
36. Katsu M, Kidd S, Ando A, Moretti-Branchini ML, Mikami Y, et al. (2004) The internal transcribed spacers and 5.8S rRNA gene show extensive diversity among isolates of the Cryptococcus neoformans species complex. FEMS Yeast Res 4(4-5): 377-388. (Pubitemid 38156202)