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• W1965081205 abstract "Recent changes in the epidemiology of candidiasis highlighted an increase in non- Candida albicans species emphasizing the need for reliable identification methods. Molecular diagnostics in fungal infections may improve species characterization, particularly in cases of the closely related species in the Candida complexes. We developed two PCR/restriction fragment length polymorphism assays, targeting either a part of the intergenic spacer 2 or the entire intergenic spacer (IGS) of ribosomal DNA using a panel of 270 isolates. A part of the intergenic spacer was used for discrimination between C. albicans and C. dubliniensis and between species of the C. glabrata complex (C. glabrata/C. bracarensis/C. nivariensis). The whole IGS was applied to C. parapsilosis, C. metapsilosis, and C. orthopsilosis, and to separate C. famata (Debaryomyces hansenii) from C. guilliermondii (Pichia guilliermondii) and from the other species within this complex (ie, C. carpophila, C. fermentati and C. xestobii). Sharing similar biochemical patterns, Pichia norvegensis and C. inconspicua exhibited specific IGS profiles. Our study confirmed that isolates of C. guilliermondii were frequently mis-identified as C. famata. As much as 67% of the clinical isolates phenotypically determined as C. famata were recognized mostly as true P. guilliermondii. Conversely, 44% of the isolates initially identified as C. guilliermondii were corrected by the IGS fingerprints as C. parapsilosis, C. fermentati, or C. zeylanoides. These two PCR/restriction fragment length polymorphism methods may be used as reference tools [either alternatively or adjunctively to the existing ribosomal DNA (26S or ITS) sequence comparisons] for unambiguous determination of the Candida species for which phenotypic characterization remains problematic. Recent changes in the epidemiology of candidiasis highlighted an increase in non- Candida albicans species emphasizing the need for reliable identification methods. Molecular diagnostics in fungal infections may improve species characterization, particularly in cases of the closely related species in the Candida complexes. We developed two PCR/restriction fragment length polymorphism assays, targeting either a part of the intergenic spacer 2 or the entire intergenic spacer (IGS) of ribosomal DNA using a panel of 270 isolates. A part of the intergenic spacer was used for discrimination between C. albicans and C. dubliniensis and between species of the C. glabrata complex (C. glabrata/C. bracarensis/C. nivariensis). The whole IGS was applied to C. parapsilosis, C. metapsilosis, and C. orthopsilosis, and to separate C. famata (Debaryomyces hansenii) from C. guilliermondii (Pichia guilliermondii) and from the other species within this complex (ie, C. carpophila, C. fermentati and C. xestobii). Sharing similar biochemical patterns, Pichia norvegensis and C. inconspicua exhibited specific IGS profiles. Our study confirmed that isolates of C. guilliermondii were frequently mis-identified as C. famata. As much as 67% of the clinical isolates phenotypically determined as C. famata were recognized mostly as true P. guilliermondii. Conversely, 44% of the isolates initially identified as C. guilliermondii were corrected by the IGS fingerprints as C. parapsilosis, C. fermentati, or C. zeylanoides. These two PCR/restriction fragment length polymorphism methods may be used as reference tools [either alternatively or adjunctively to the existing ribosomal DNA (26S or ITS) sequence comparisons] for unambiguous determination of the Candida species for which phenotypic characterization remains problematic. Current changes in the epidemiology of invasive mycoses highlighted a shift in the Candida species involved with a reduced proportion of C. albicans and an increase in non-C. albicans species.1Groll A.H. Walsh T.J. Uncommon opportunistic fungi: new nosocomial threats.Clin Microbiol Infect. 2001; 7: 8-24Crossref PubMed Google Scholar, 2Nucci M. Marr K.A. Emerging fungal diseases.Clin Infect Dis. 2005; 41: 521-526Crossref PubMed Scopus (310) Google Scholar, 3Pfaller M.A. Diekema D.J. Epidemiology of invasive candidiasis: a persistent public health problem.Clin Microbiol Rev. 2007; 20: 133-163Crossref PubMed Scopus (3082) Google Scholar, 4Lass-Florl C. The changing face of epidemiology of invasive fungal disease in Europe.Mycoses. 2009; 52: 197-205Crossref PubMed Scopus (293) Google Scholar In the most recent series, including the large cohort of 2019 patients with candidemia enrolled from 2004 through 2008, C. albicans accounts for less than one half of the isolates.3Pfaller M.A. Diekema D.J. Epidemiology of invasive candidiasis: a persistent public health problem.Clin Microbiol Rev. 2007; 20: 133-163Crossref PubMed Scopus (3082) Google Scholar, 5Patterson T.F. Advances and challenges in management of invasive mycoses.Lancet. 2005; 366: 1013-1025Abstract Full Text Full Text PDF PubMed Scopus (199) Google Scholar, 6Hachem R. Hanna H. Kontoyiannis D. Jiang Y. Raad I. The changing epidemiology of invasive candidiasis: Candida glabrata and Candida krusei as the leading causes of candidemia in hematologic malignancy.Cancer. 2008; 112: 2493-2499Crossref PubMed Scopus (252) Google Scholar, 7Kung H.C. Wang J.L. Chang S.C. Wang J.T. Sun H.Y. Hsueh P.R. Chen Y.C. Community-onset candidemia at a university hospital, 1995–2005.J Microbiol Immunol Infect. 2007; 40: 355-363PubMed Google Scholar, 8Xess I. Jain N. Hasan F. Mandal P. Banerjee U. Epidemiology of candidemia in a tertiary care centre of north India: 5-year study.Infection. 2007; 35: 256-259Crossref PubMed Scopus (84) Google Scholar, 9Pappas P.G. Rex J.H. Lee J. Hamill R.J. Larsen R.A. Powderly W. Kauffman C.A. Hyslop N. Mangino J.E. Chapman S. Horowitz H.W. Edwards J.E. Dismukes W.E. NIAID Mycoses Study GroupA prospective observational study of candidemia: epidemiology, therapy, and influences on mortality in hospitalized adult and pediatric patients.Clin Infect Dis. 2003; 37: 634-643Crossref PubMed Scopus (692) Google Scholar, 10Pappas P.G. Invasive candidiasis.Infect Dis Clin North Am. 2006; 20: 485-506Abstract Full Text Full Text PDF PubMed Scopus (233) Google Scholar, 11Pfaller M.A. Diekema D.J. Role of sentinel surveillance of candidemia: trends in species distribution and antifungal susceptibility.J Clin Microbiol. 2002; 40: 3551-3557Crossref PubMed Scopus (211) Google Scholar, 12Horn D.L. Neofytos D. Anaissie E.J. Fishman J.A. Steinbach W.J. Olyaei A.J. Marr K.A. Pfaller M.A. Chang C.H. Webster K.M. Epidemiology and outcomes of candidemia in 2019 patients: data from the prospective antifungal therapy alliance registry.Clin Infect Dis. 2009; 48: 1695-1703Crossref PubMed Scopus (715) Google Scholar Although C. albicans antifungal susceptibility remains the rule, and reports on resistant isolates are very scarce, other species such as C. krusei, C. glabrata, C. bracarensis, C. nivariensis, C. parapsilosis, and C. guilliermondii are either innately resistant or show decreased susceptibility patterns to azoles, amphotericin B, or echinocandins.13Espinel-Ingroff A. In vitro antifungal activities of anidulafungin and micafungin, licensed agents and the investigational triazole posaconazole as determined by NCCLS methods for 12,052 fungal isolates: review of the literature.Rev Iberoam Micol. 2003; 20: 121-136PubMed Google Scholar, 14Marr K.A. Seidel K. White T.C. Bowden R.A. Candidemia in allogeneic blood and marrow transplant recipients: evolution of risk factors after the adoption of prophylactic fluconazole.J Infect Dis. 2000; 181: 309-316Crossref PubMed Scopus (429) Google Scholar, 15Marr K.A. The changing spectrum of candidemia in oncology patients: therapeutic implications.Curr Opin Infect Dis. 2000; 13: 615-620Crossref PubMed Scopus (34) Google Scholar, 16Lockhart S.R. Messer S.A. Pfaller M.A. Diekema D.J. Identification and Susceptibility Profile of Candida fermentati from a worldwide collection of Candida guilliermondii clinical isolates.J Clin Microbiol. 2009; 47: 242-244Crossref PubMed Scopus (38) Google Scholar, 17Fujita S. Senda Y. Okusi T. Ota Y. Takada H. Yamada K. Kawano M. Catheter-related fungemia due to fluconazole-resistant Candida nivariensis..J Clin Microbiol. 2007; 45: 3459-3461Crossref PubMed Scopus (47) Google Scholar, 18Lockhart S.R. Messer S.A. Gherna M. Bishop J.A. Merz W.G. Pfaller M.A. Diekema D.J. Identification of Candida nivariensis and Candida bracarensis in a large global collection of Candida glabrata isolates: comparison to the literature.J Clin Microbiol. 2009; 47: 1216-1217Crossref PubMed Scopus (86) Google Scholar, 19Cappelletty D. Eiselstein-McKitrick K. The echinocandins.Pharmacotherapy. 2007; 27: 369-388Crossref PubMed Scopus (199) Google Scholar, 20Borman A.M. Petch R. Linton C.J. Palmer M.D. Bridge P.D. Johnson E.M. Candida nivariensis, an emerging pathogenic fungus with multidrug resistance to antifungal agents.J Clin Microbiol. 2008; 46: 933-938Crossref PubMed Scopus (104) Google Scholar, 21Cendejas-Bueno E. Gomez-Lopez A. Mellado E. Rodriguez-Tudela J.L. Cuenca-Estrella M. Identification of Pathogenic Rare Yeast Species in Clinical Samples: Comparison between Phenotypical and Molecular Methods.J Clin Microbiol. 2010; 48: 1895-1899Crossref PubMed Scopus (51) Google Scholar Thus, the therapeutic impact of this shift might be critical and should be considered in patient management. Consistent with this trend, the recent revision of the consensus guidelines actually recommends an adjustment of the treatment according to the isolated Candida species.22Pappas P.G. Kauffman C.A. Andes D. Benjamin Jr., D.K. Calandra T.F. Edwards Jr., J.E. Filler S.G. Fisher J.F. Kullberg B.J. Ostrosky-Zeichner L. Reboli A.C. Rex J.H. Walsh T.J. Sobel J.D. Infectious Diseases Society of AmericaClinical practice guidelines for the management of candidiasis: 2009 update by the Infectious Diseases Society of America.Clin Infect Dis. 2009; 48: 503-535Crossref PubMed Scopus (1058) Google Scholar In yeasts, there is no transfer of resistance between cells and acquisition of resistance, which is mainly observed in restricted clinical settings such as allogeneic blood marrow transplant or AIDS patients under sustained prolonged azole treatment.5Patterson T.F. Advances and challenges in management of invasive mycoses.Lancet. 2005; 366: 1013-1025Abstract Full Text Full Text PDF PubMed Scopus (199) Google Scholar, 14Marr K.A. Seidel K. White T.C. Bowden R.A. Candidemia in allogeneic blood and marrow transplant recipients: evolution of risk factors after the adoption of prophylactic fluconazole.J Infect Dis. 2000; 181: 309-316Crossref PubMed Scopus (429) Google Scholar, 23Ruhnke M. Eigler A. Tennagen I. Geiseler B. Engelmann E. Trautmann M. Emergence of fluconazole-resistant strains of Candida albicans in patients with recurrent oropharyngeal candidosis and human immunodeficiency virus infection.J Clin Microbiol. 1994; 32: 2092-2098PubMed Google Scholar Therefore, species identification remains basically predictive of drug susceptibility. Current methods for yeast identification in clinical practice are based on phenotypic features and carbohydrate assimilation tests that require 2 to 5 days or even longer in the case of unusual species.24Freydiere A.M. Guinet R. Boiron P. Yeast identification in the clinical microbiology laboratory: phenotypical methods.Med Mycol. 2001; 39: 9-33Crossref PubMed Google Scholar, 25Pincus D.H. Orenga S. Chatellier S. Yeast identification–past, present, and future methods.Med Mycol. 2007; 45: 97-121Crossref PubMed Scopus (113) Google Scholar These phenotypic methods including the automated ones may lead to mis-identification, particularly in the case of the closely related species.16Lockhart S.R. Messer S.A. Pfaller M.A. Diekema D.J. Identification and Susceptibility Profile of Candida fermentati from a worldwide collection of Candida guilliermondii clinical isolates.J Clin Microbiol. 2009; 47: 242-244Crossref PubMed Scopus (38) Google Scholar, 18Lockhart S.R. Messer S.A. Gherna M. Bishop J.A. Merz W.G. Pfaller M.A. Diekema D.J. Identification of Candida nivariensis and Candida bracarensis in a large global collection of Candida glabrata isolates: comparison to the literature.J Clin Microbiol. 2009; 47: 1216-1217Crossref PubMed Scopus (86) Google Scholar, 26Sanguinetti M. Porta R. Sali M. La Sorda M. Pecorini G. Fadda G. Posteraro B. Evaluation of VITEK 2 and RapID yeast plus systems for yeast species identification: experience at a large clinical microbiology laboratory.J Clin Microbiol. 2007; 45: 1343-1346Crossref PubMed Scopus (60) Google Scholar, 27Hata D.J. Hall L. Fothergill A.W. Larone D.H. Wengenack N.L. Multicenter evaluation of the new VITEK 2 advanced colorimetric yeast identification card.J Clin Microbiol. 2007; 45: 1087-1092Crossref PubMed Scopus (51) Google Scholar, 28Majoros L. Kardos G. Belák A. Maráz A. Asztalos L. Csánky E. Barta Z. Szabó B. Restriction enzyme analysis of ribosomal DNA shows that Candida inconspicua clinical isolates can be misidentified as Candida norvegensis with traditional diagnostic procedures.J Clin Microbiol. 2003; 41: 5250-5253Crossref PubMed Scopus (29) Google Scholar, 29Williams D.W. Wilson M.J. Lewis M.A. Potts A.J. Identification of Candida species by PCR and restriction fragment length polymorphism analysis of intergenic spacer regions of ribosomal DNA.J Clin Microbiol. 1995; 33: 2476-2479PubMed Google Scholar, 30Desnos-Ollivier M. Ragon M. Robert V. Raoux D. Gantier J.C. Dromer F. Debaryomyces hansenii (Candida famata), a rare human fungal pathogen often misidentified as Pichia guilliermondii (Candida guilliermondii).J Clin Microbiol. 2008; 46: 3237-3242Crossref PubMed Scopus (108) Google Scholar, 31Loiez C. Wallet F. Sendid B. Courcol R.J. Evaluation of VITEK 2 colorimetric cards versus fluorimetric cards for identification of yeasts.Diagn Microbiol Infect Dis. 2006; 56: 455-457Abstract Full Text Full Text PDF PubMed Scopus (17) Google Scholar Several molecular approaches have been developed and were designed mostly for the ribosomal RNA (rRNA) genes: targeting either the D1D2 domain of the 26S rRNA large subunit or the internal transcribed spacer regions ITS1 and ITS2.25Pincus D.H. Orenga S. Chatellier S. Yeast identification–past, present, and future methods.Med Mycol. 2007; 45: 97-121Crossref PubMed Scopus (113) Google Scholar, 29Williams D.W. Wilson M.J. Lewis M.A. Potts A.J. Identification of Candida species by PCR and restriction fragment length polymorphism analysis of intergenic spacer regions of ribosomal DNA.J Clin Microbiol. 1995; 33: 2476-2479PubMed Google Scholar, 30Desnos-Ollivier M. Ragon M. Robert V. Raoux D. Gantier J.C. Dromer F. Debaryomyces hansenii (Candida famata), a rare human fungal pathogen often misidentified as Pichia guilliermondii (Candida guilliermondii).J Clin Microbiol. 2008; 46: 3237-3242Crossref PubMed Scopus (108) Google Scholar, 32Lau A. Chen S. Sleiman S. Sorrell T. Current status and future perspectives on molecular and serological methods in diagnostic mycology.Future Microbiol. 2009; 4: 1185-1222Crossref PubMed Scopus (44) Google Scholar, 33Putignani L. Paglia M.G. Bordi E. Nebuloso E. Pucillo L.P. Visca P. Identification of clinically relevant yeast species by DNA sequence analysis of the D2 variable region of the 25-28S rRNA gene.Mycoses. 2008; 51: 209-227Crossref PubMed Scopus (34) Google Scholar Restriction enzyme analysis of the intergenic spacer 1 (IGS1) region from the 26S to the 5S ribosomal DNA (rDNA), was used for identifying species of the Saccharomyces sensu stricto complex.34Molina F.I. Jong S.C. Huffman J.L. PCR amplification of the 3′ external transcribed and intergenic spacers of the ribosomal DNA repeat unit in three species of Saccharomyces..FEMS Microbiol Lett. 1993; 108: 259-263PubMed Google Scholar Later, the NTS2 region (from 5S to ETS1) part of the IGS2 was shown to be more appropriate.35Nguyen H.V. Pulvirenti A. Gaillardin C. Rapid differentiation of the closely related Kluyveromyces lactis var. lactis and K. marxianus strains isolated from dairy products using selective media and PCR/RFLP of the rDNA non transcribed spacer 2.Can J Microbiol. 2000; 46: 1115-1122Crossref PubMed Scopus (24) Google Scholar Several basidiomycetous yeasts include the pathogen Cryptococcus neoformans and Trichosporon species may also be determined by using the IGS1 or the whole IGS region from the 26S to the 18S rRNA genes.36Diaz M.R. Boekhout T. Theelen B. Fell J.W. Molecular sequence analyses of the intergenic spacer (IGS) associated with rDNA of the two varieties of the pathogenic yeast, Cryptococcus neoformans..Syst Appl Microbiol. 2000; 23: 535-545Crossref PubMed Scopus (91) Google Scholar, 37Diaz M.R. Boekhout T. Kiesling T. Fell J.W. Comparative analysis of the intergenic spacer regions and population structure of the species complex of the pathogenic yeast Cryptococcus neoformans..FEMS Yeast Res. 2005; 5: 1129-1140Crossref PubMed Scopus (78) Google Scholar, 38Sugita T. Nakajima M. Ikeda R. Matsushima T. Shinoda T. Sequence analysis of the ribosomal DNA intergenic spacer 1 regions of Trichosporon species.J Clin Microbiol. 2002; 40: 1826-1830Crossref PubMed Scopus (182) Google Scholar In the same way, it has been reported that IGS fingerprints are reliable to distinguish Candida famata var. famata from Candida famata var. flareri and 21 other species of the genus Debaryomyces.39Nguyen H.V. Gaillardin C. Neuveglise C. Differentiation of Debaryomyces hansenii and Candida famata by rRNA gene intergenic spacer fingerprinting and reassessment of phylogenetic relationships among D. hansenii, C. famata, D. fabryi, C. flareri (=D. subglobosus) and D. prosopidis: description of D. vietnamensis sp. nov. closely related to D. nepalensis.FEMS Yeast Res. 2009; 9: 641-662Crossref PubMed Scopus (47) Google Scholar Thus, PCR/restriction fragment length polymorphism (RFLP) fingerprints or sequencing of the IGS domain39Nguyen H.V. Gaillardin C. Neuveglise C. Differentiation of Debaryomyces hansenii and Candida famata by rRNA gene intergenic spacer fingerprinting and reassessment of phylogenetic relationships among D. hansenii, C. famata, D. fabryi, C. flareri (=D. subglobosus) and D. prosopidis: description of D. vietnamensis sp. nov. closely related to D. nepalensis.FEMS Yeast Res. 2009; 9: 641-662Crossref PubMed Scopus (47) Google Scholar can be used as alternative or adjunct to D1D2 sequence (26S rDNA)40Kurtzman C.P. Robnett C.J. Identification of clinically important ascomycetous yeasts based on nucleotide divergence in the 5′ end of the large-subunit (26S) ribosomal DNA gene.J Clin Microbiol. 1997; 35: 1216-1223PubMed Google Scholar, 41Kurtzman C.P. Robnett C.J. Phylogenetic relationships among yeasts of the ‘Saccharomyces complex’ determined from multigene sequence analyses.FEMS Yeast Res. 2003; 3: 417-432Crossref PubMed Scopus (537) Google Scholar or ITS sequencing.30Desnos-Ollivier M. Ragon M. Robert V. Raoux D. Gantier J.C. Dromer F. Debaryomyces hansenii (Candida famata), a rare human fungal pathogen often misidentified as Pichia guilliermondii (Candida guilliermondii).J Clin Microbiol. 2008; 46: 3237-3242Crossref PubMed Scopus (108) Google Scholar, 33Putignani L. Paglia M.G. Bordi E. Nebuloso E. Pucillo L.P. Visca P. Identification of clinically relevant yeast species by DNA sequence analysis of the D2 variable region of the 25-28S rRNA gene.Mycoses. 2008; 51: 209-227Crossref PubMed Scopus (34) Google Scholar, 42Esteve-Zarzoso B. Belloch C. Uruburu F. Querol A. Identification of yeasts by RFLP analysis of the 5.8S rRNA gene and the two ribosomal internal transcribed spacers.Int J Syst Bacteriol. 1999; 49: 329-337Crossref PubMed Scopus (780) Google Scholar Here, we selected primers for partial amplification of the IGS (IGS2) and we established the specific patterns of C. albicans, C. dubliniensis, C. glabrata, C. bracarensis, C. nivariensis and C. tropicalis. Other primers, described in reference 39Nguyen H.V. Gaillardin C. Neuveglise C. Differentiation of Debaryomyces hansenii and Candida famata by rRNA gene intergenic spacer fingerprinting and reassessment of phylogenetic relationships among D. hansenii, C. famata, D. fabryi, C. flareri (=D. subglobosus) and D. prosopidis: description of D. vietnamensis sp. nov. closely related to D. nepalensis.FEMS Yeast Res. 2009; 9: 641-662Crossref PubMed Scopus (47) Google Scholar, were used to amplify the complete IGS domain leading to the discrimination of other closely related yeast species: C. parapsilosis, C. metapsilosis, C. orthopsilosis, C. famata (Debaryomyces hansenii), C. guilliermondii (Pichia guilliermondii), C. carpophila, C. fermentati, C. xestobii, P. norvegensis, C. inconspicua, Clavispora lusitaniae, C. pararugosa, C. rugosa, C. catenulata, C. zeylanoides, Kluyveromyces marxianus, K. lactis, C. palmioleophila, C. pseudoglaebosa, and Saccharomyces cerevisiae. We further report on the evaluation of this new set of two PCR/RFLP methods for accurate identification of the Candida species for which phenotypic characterization remains uncertain. A panel of 270 isolates of most medically relevant species was investigated. Isolates are listed in Table 1, Table 2, as well as Supplemental Tables S1 and S2 (http://jmd.amjpathol.org). Reference strains were from The Centraalbureau voor Schimmelcultures (CBS) collection and the Belgian Co-ordinated Collections of Micro-organisms/IPH-Mycology (BCCM/IHEM) public collection and were kindly provided by Dr. Hiroshi Fukuhara and Dr. Françoise Symoens, respectively, or were purchased directly. Clinical isolates were collected mostly in mycology laboratories of Hôtel-Dieu in Paris and Lille University Hospital, France.Table 1List of Type and Collection Strains of Candida spp. Identified by the PCR/RFLP MethodSpecies/Strain⁎For collections and origin of the strains, see websites, last accession: July 16, 2010; CBS (www.cbs.knaw.nl/yeast/BioloMICS.aspx; http://www.cbs.knaw.nl/yeast/BioloMICS.aspx), DBVPG, (www.agr.unipg.it/dbvpg/), and BCCM/IHEM, (http://bccm.belspo.be/about/ihem.php#researc), NCPF, (http://www.hpacultures.org.uk/).PCR/RFLP profile accession number†Sequences with accession number starting with FN were determined in this study and are deposited in Gen Bank.PCR/RFLP identification (this study)C. albicans CBS 562§Type strain., CBS 1893, CBS 5982, CBS 5983, CBS 6431, CBS 8190ALBIC. albicansFN554375 SC5314, CBS 1949, CBS 2697, CBS 2707ALBI‡Polymorphic variant of the type strain pattern.C. albicansFN554376C. dubliniensis CBS 7987§Type strain., CBS 7988, CBS 8500¶Strains received from CBS, DBVPG, or IHEM., CBS 8501¶Strains received from CBS, DBVPG, or IHEM.DUBLC. dubliniensisFN554377C. glabrata CBS 138§Type strain., CBS 860, CBS 861, CBS 1528, CBS 2175, CBS 4692, CBS 7904, CBS 5691GLABFN554379C. glabrataC. bracarensisBRACC. bracarensis CBS 10154§Type strain.FN554380C. nivariensisNIVAC. nivariensis CBS 9983§Type strain., CBS 9984¶Strains received from CBS, DBVPG, or IHEM., CBS 9985¶Strains received from CBS, DBVPG, or IHEM.FN554381C. parapsilosis CBS 604§Type strain., CBS 1954, CBS 2152, CBS 2193, CBS 2194, CBS 2195, CBS 2197, CBS 2211, CBS 2215, CBS 2916, CBS 5301, CBS 6318, CBS 8050PPSIC. parapsilosisC. orthopsilosis NCPF 8795MPSIC. orthopsilosisC. metapsilosis NCPF 8789OPSIC. metapsilosisDebaryomyces hansenii CBS 767§Type strain., IHEM 711¶Strains received from CBS, DBVPG, or IHEM., IHEM 3438¶Strains received from CBS, DBVPG, or IHEM., IHEM 5768¶Strains received from CBS, DBVPG, or IHEM., IHEM 6275¶Strains received from CBS, DBVPG, or IHEM., IHEM 6826¶Strains received from CBS, DBVPG, or IHEM., IHEM 10430¶Strains received from CBS, DBVPG, or IHEM.∥Used as reference strain of C. famata.DEHAD. hansenii var. hansenii⁎⁎See Ref 38 for new nomenclatureDebaryomyces hansenii lineage Candida famata CBS 1795§Type strain.CAFAC. famata var. famata⁎⁎See Ref 38 for new nomenclatureAM992926Pichia guilliermondii CBS 2030§Type strain., CBS 2021, CBS 2024, CBS 2077, CBS 2083, CBS 2084, CBS 2672¶Strains received from CBS, DBVPG, or IHEM., CBS 4236, CBS 5265, CBS 5674, CBS 6109¶Strains received from CBS, DBVPG, or IHEM.As C. carpophila by the CBS, CBS 6557, CBS 7099, CBS 7232PIGUAM992960P. guilliermondiiCandida guilliermondii CBS 566§Type strain.PIGUC. guilliermondiiC. carpophila CBS 5256§Type strain., CBS 5258¶Strains received from CBS, DBVPG, or IHEM., CBS 7921¶Strains received from CBS, DBVPG, or IHEM., CBS 5257¶Strains received from CBS, DBVPG, or IHEM.CARPC. carpophilaFN554237C. fermentati (= Pichia caribbica) CBS 2022§Type strain., CBS 5059¶Strains received from CBS, DBVPG, or IHEM., CBS 5241¶Strains received from CBS, DBVPG, or IHEM.As P. guilliermondii by the CBS, CBS 6319¶Strains received from CBS, DBVPG, or IHEM., CBS 8302¶Strains received from CBS, DBVPG, or IHEM., CBS 8303¶Strains received from CBS, DBVPG, or IHEM.FERMC. fermentatiFN554235C. xestobii CBS 5975§Type strain.XESTC. xestobiiFN554238Pichia norvegensis CBS 6564§Type strain., CBS 1911, CBS 1953, CBS 2327, CBS 5304, CBS 6917PINOP. norvegensisFN554245 CBS 1921, CBS 2125, CBS 2145, CBS 6639PINO(‡Polymorphic variant of the type strain pattern.)P. norvegensisFN554246 CBS 2126PINO(‡Polymorphic variant of the type strain pattern.)P. norvegensis CBS 2128, CBS 2144PINO(‡Polymorphic variant of the type strain pattern.)P. norvegensisCandida norvegensis CBS 1922§Type strain.¶Strains received from CBS, DBVPG, or IHEM., DBVPG 6871§Type strain.¶Strains received from CBS, DBVPG, or IHEM.PINOP. norvegensis CBS 1922Strain from Dr. Hiroshi FukuharaZEYLC. zeylanoidesFN554768C. inconspicua CBS 180§Type strain., CBS 990, CBS 2833INCOC. inconspicuaFN554239 CBS 620INCO(‡Polymorphic variant of the type strain pattern.)C. inconspicua For collections and origin of the strains, see websites, last accession: July 16, 2010; CBS (www.cbs.knaw.nl/yeast/BioloMICS.aspx; http://www.cbs.knaw.nl/yeast/BioloMICS.aspx), DBVPG, (www.agr.unipg.it/dbvpg/), and BCCM/IHEM, (http://bccm.belspo.be/about/ihem.php#researc), NCPF, (http://www.hpacultures.org.uk/).† Sequences with accession number starting with FN were determined in this study and are deposited in Gen Bank.‡ Polymorphic variant of the type strain pattern.§ Type strain.¶ Strains received from CBS, DBVPG, or IHEM.∥ Used as reference strain of C. famata. See Ref 38Sugita T. Nakajima M. Ikeda R. Matsushima T. Shinoda T. Sequence analysis of the ribosomal DNA intergenic spacer 1 regions of Trichosporon species.J Clin Microbiol. 2002; 40: 1826-1830Crossref PubMed Scopus (182) Google Scholar for new nomenclature†† As C. carpophila by the CBS‡‡ As P. guilliermondii by the CBS§§ Strain from Dr. Hiroshi Fukuhara Open table in a new tab Table 2List of Clinical and Environmental Candida IsolatesFirst identification/StrainSite of isolationPCR/RFLP profile accession numberPCR/RFLP (this study) identificationCandida albicans HD PasqMouthALBIC. albicans HD KounMouthALBI⁎Polymorphic variant of the type strain pattern.C. albicans HD 10Biliary fluidALBIC. albicans HD 13, HD 31, HD 38BAL†Bronchoalveolar lavage.ALBIC. albicans HD 14BA‡Bronchial aspirate.ALBIC. albicans HD 37SputumALBI⁎Polymorphic variant of the type strain pattern.C. albicansC. dubliniensis HD RouMouthDUBLC. dubliniensis HD Ara, Lil 7MouthDUBL⁎Polymorphic variant of the type strain pattern.C. dubliniensisFN554378 L 1, L 3, L 10, L 480, L 513SputumDUBLC. dubliniensis L 11TracheaDUBL⁎Polymorphic variant of the type strain pattern.C. dubliniensis L 12StoolDUBLC. dubliniensis L 16VaginaDUBLC. dubliniensis L 479, L 481, L 512TongueDUBLC. dubliniensis L 522TongueDUBL⁎Polymorphic variant of the type strain pattern.C. dubliniensisC. glabrata HD 67, HD 68, HD 69, HD 71, HD 73BAGLABC. glabrata HD 70, HD 72SputumGLABC. glabrata HD 74, HD 75StoolGLABC. glabrataC. parapsilosis MC 2, MC 7, MC 18BAPPSIC. parapsilosis M 3, MC 8, MC 58BloodPPSIC. parapsilosis AM06/0207C. inconspicuaINCOC. inconspicua MC 1BloodFN5542408121 4335Debaryomyces hansenii/Candida famata Cfa4SputumDEHAD. hansenii var. hansenii§See Ref. 39 for new nomenclature. Cfa 6, Boc1128MouthCAFAC. famata var. famata§See Ref. 39 for new nomenclature. Cfa 2, CHR7305500SkinPIGUPichia guilliermondii Cfa 5NailPIGUP. guilliermondii CHR6009704SputumPGLAC. pseudoglaebosa CHR6005538SkinPALMC. palmiolephila Cfa 3StoolKLMAK. marxianusPichia guilliermondii HD 354SputumPIGUP. guilliermondii HD 520BALPIGUP. guilliermondii CHR004648, CHR993206, CHR00555181, CHR06173BloodPIGUP. guilliermondiiFN554234 CHR5000373, CHR7009193, CHR7005511TracheaPIGUP. guilliermondii CHR6006940TonguePIGUP. guilliermondii CHR6008052Gastric fluidPIGUP. guilliermondii CHR6008164, CHR700196, CHR3009257MouthPIGUP. guilliermondii CHR4006637Bronchial aspirateFERMC. fermentati CHR3008385StoolFERMC. fermentatiFN554236Wild strains CXB5Green Lemon skin, Viet NamPIGUP. guilliermondii CXB2, CXB7Green Lemon skin, Viet NamFERMC. fermentati XT1Mango skin, Viet NamPPSIC. parapsilosisFN554242 CXB6, CXB13Green Lemon skin, Viet NamZEYLC. zeylanoides Kam494, Kam522, Kam531, Kam544, Kam592Wild, Kamchatska, RussiaPPSIC. parapsilosis Polymorphic variant of the type strain pattern.† Bronchoalveolar lavage.‡ Bronchial aspirate.§ See Ref. 39Nguyen H.V. Gaillardin C. Neuveglise C. Differentiation of Debaryomyces hansenii and Candida famata by rRNA gene intergenic spacer fingerprinting and reassessment of phylogenetic relationships among D. hansenii, C. famata, D. fabryi, C. flareri (=D. subglobosus) and D. prosopidis: description of D. vietnamensis sp. nov. closely related to D. nepalensis.FEMS Yeast Res. 2009; 9: 641-662Crossref PubMed Scopus (47) Google Scholar for new nomenclature. Open table in a new tab Clinical isolates were routinely cultured either on Sabouraud dextrose agar supplemented with chloramphenicol and gentamicin (Bio-Rad; Marnes" @default.
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