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Article: Yeast identification by sequencing, biochemical kits, MALDI–TOF MS and rep-PCR DNA fingerprinting

TitleYeast identification by sequencing, biochemical kits, MALDI–TOF MS and rep-PCR DNA fingerprinting
Authors
KeywordsDNA sequencing
Identification
MALDI-TOF MS
rep-PCR DNA fingerprinting
Yeasts
Issue Date2017
PublisherInforma Healthcare. The Journal's web site is located at https://academic.oup.com/mmy/
Citation
Medical Mycology, 2017, v. 56 n. 7, p. 816-827 How to Cite?
AbstractNo study has comprehensively evaluated the performance of 28S nrDNA and ITS sequencing, commercial biochemical test kits, MALDI-TOF MS platforms, and the emerging rep-PCR DNA fingerprinting technology using a cohort of yeast strains collected from a clinical microbiology laboratory. In this study, using 71 clinically important yeast isolates (excluding Candida albicans) collected from a single centre, we determined the concordance of 28S nrDNA and ITS sequencing and evaluated the performance of two commercial test kits, two MALDI-TOF MS platforms, and rep-PCR DNA fingerprinting. 28S nrDNA and ITS sequencing showed complete agreement on the identities of the 71 isolates. Using sequencing results as the standard, 78.9% and 71.8% isolates were correctly identified using the API 20C AUX and Vitek 2 YST ID Card systems, respectively; and 90.1% and 80.3% isolates were correctly identified using the Bruker and Vitek MALDI-TOF MS platforms, respectively. Of the 18 strains belonging to the Candida parapsilosis species complex tested by DiversiLab automated rep-PCR DNA fingerprinting, all were identified only as Candida parapsilosis with similarities ≥93.2%, indicating the misidentification of Candida metapsilosis and Candida orthopsilosis. However, hierarchical cluster analysis of the rep-PCR DNA fingerprints of these three species within this species complex formed three different discrete clusters, indicating that this technology can potentially differentiate the three species. To achieve higher accuracies of identification, the databases of commercial biochemical test kits, MALDI-TOF MS platforms, and DiversiLab automated rep-PCR DNA fingerprinting needs further enrichment, particularly for uncommonly encountered yeast species.
Persistent Identifierhttp://hdl.handle.net/10722/250546
ISSN
2017 Impact Factor: 2.799
2015 SCImago Journal Rankings: 1.055
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorZhao, Y-
dc.contributor.authorTsang, CC-
dc.contributor.authorXiao, M-
dc.contributor.authorChan, JFW-
dc.contributor.authorLau, SKP-
dc.contributor.authorKong, F-
dc.contributor.authorXu, Y-
dc.contributor.authorWoo, PCY-
dc.date.accessioned2018-01-18T04:28:47Z-
dc.date.available2018-01-18T04:28:47Z-
dc.date.issued2017-
dc.identifier.citationMedical Mycology, 2017, v. 56 n. 7, p. 816-827-
dc.identifier.issn1369-3786-
dc.identifier.urihttp://hdl.handle.net/10722/250546-
dc.description.abstractNo study has comprehensively evaluated the performance of 28S nrDNA and ITS sequencing, commercial biochemical test kits, MALDI-TOF MS platforms, and the emerging rep-PCR DNA fingerprinting technology using a cohort of yeast strains collected from a clinical microbiology laboratory. In this study, using 71 clinically important yeast isolates (excluding Candida albicans) collected from a single centre, we determined the concordance of 28S nrDNA and ITS sequencing and evaluated the performance of two commercial test kits, two MALDI-TOF MS platforms, and rep-PCR DNA fingerprinting. 28S nrDNA and ITS sequencing showed complete agreement on the identities of the 71 isolates. Using sequencing results as the standard, 78.9% and 71.8% isolates were correctly identified using the API 20C AUX and Vitek 2 YST ID Card systems, respectively; and 90.1% and 80.3% isolates were correctly identified using the Bruker and Vitek MALDI-TOF MS platforms, respectively. Of the 18 strains belonging to the Candida parapsilosis species complex tested by DiversiLab automated rep-PCR DNA fingerprinting, all were identified only as Candida parapsilosis with similarities ≥93.2%, indicating the misidentification of Candida metapsilosis and Candida orthopsilosis. However, hierarchical cluster analysis of the rep-PCR DNA fingerprints of these three species within this species complex formed three different discrete clusters, indicating that this technology can potentially differentiate the three species. To achieve higher accuracies of identification, the databases of commercial biochemical test kits, MALDI-TOF MS platforms, and DiversiLab automated rep-PCR DNA fingerprinting needs further enrichment, particularly for uncommonly encountered yeast species.-
dc.languageeng-
dc.publisherInforma Healthcare. The Journal's web site is located at https://academic.oup.com/mmy/-
dc.relation.ispartofMedical Mycology-
dc.rightsMedical Mycology. Copyright © Informa Healthcare.-
dc.subjectDNA sequencing-
dc.subjectIdentification-
dc.subjectMALDI-TOF MS-
dc.subjectrep-PCR DNA fingerprinting-
dc.subjectYeasts-
dc.titleYeast identification by sequencing, biochemical kits, MALDI–TOF MS and rep-PCR DNA fingerprinting-
dc.typeArticle-
dc.identifier.emailTsang, CC: microbioct@connect.hku.hk-
dc.identifier.emailChan, JFW: jfwchan@hku.hk-
dc.identifier.emailLau, SKP: skplau@hkucc.hku.hk-
dc.identifier.emailWoo, PCY: pcywoo@hkucc.hku.hk-
dc.identifier.authorityTsang, CC=rp02492-
dc.identifier.authorityChan, JFW=rp01736-
dc.identifier.authorityLau, SKP=rp00486-
dc.identifier.authorityWoo, PCY=rp00430-
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.1093/mmy/myx118-
dc.identifier.pmid29228397-
dc.identifier.scopuseid_2-s2.0-85054956697-
dc.identifier.hkuros283893-
dc.identifier.volume56-
dc.identifier.issue7-
dc.identifier.spage816-
dc.identifier.epage827-
dc.identifier.isiWOS:000448007600007-
dc.publisher.placeUnited Kingdom-

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