{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,9]],"date-time":"2026-10-09T15:53:47Z","timestamp":1791561227264,"version":"4.3.4"},"reference-count":405,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2019,6,3]],"date-time":"2019-06-03T00:00:00Z","timestamp":1559520000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"European Union\u2019s Horizon 2020 research"},{"name":"Marie Sklodowska-Curie","award":["H2020-MSCA-ITN-2014\u2013642 095"],"award-info":[{"award-number":["H2020-MSCA-ITN-2014\u2013642 095"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,9,1]]},"abstract":"<jats:title>ABSTRACT<\/jats:title><jats:p>The incidence of opportunistic yeast infections in humans has been increasing over recent years. These infections are difficult to treat and diagnose, in part due to the large number and broad diversity of species that can underlie the infection. In addition, resistance to one or several antifungal drugs in infecting strains is increasingly being reported, severely limiting therapeutic options and showcasing the need for rapid detection of the infecting agent and its drug susceptibility profile. Current methods for species and resistance identification lack satisfactory sensitivity and specificity, and often require prior culturing of the infecting agent, which delays diagnosis. Recently developed high-throughput technologies such as next generation sequencing or proteomics are opening completely new avenues for more sensitive, accurate and fast diagnosis of yeast pathogens. These approaches are the focus of intensive research, but translation into the clinics requires overcoming important challenges. In this review, we provide an overview of existing and recently emerged approaches that can be used in the identification of yeast pathogens and their drug resistance profiles. Throughout the text we highlight the advantages and disadvantages of each methodology and discuss the most promising developments in their path from bench to bedside.<\/jats:p>","DOI":"10.1093\/femsre\/fuz015","type":"journal-article","created":{"date-parts":[[2019,5,31]],"date-time":"2019-05-31T19:11:14Z","timestamp":1559329874000},"page":"517-547","source":"Crossref","is-referenced-by-count":123,"title":["Recent trends in molecular diagnostics of yeast infections: from PCR to NGS"],"prefix":"10.1093","volume":"43","author":[{"name":"Consortium OPATHY","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"A","family":"Arastehfar","sequence":"additional","affiliation":[{"name":"Westerdijk Fungal Biodiversity Institute, 3584 CT, Utrecht, The Netherlands"},{"name":"Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, 1012 WX, Amsterdam, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"T","family":"Boekhout","sequence":"additional","affiliation":[{"name":"Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, 1012 WX, Amsterdam, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"G","family":"Butler","sequence":"additional","affiliation":[{"name":"School of Biomedical and Biomolecular Science and UCD Conway Institute of Biomolecular and Biomedical Research, Conway Institute, University College Dublin, Belfield, Dublin, Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"G Buda","family":"De Cesare","sequence":"additional","affiliation":[{"name":"MRC Centre for Medical Mycology at University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"E","family":"Dolk","sequence":"additional","affiliation":[{"name":"QVQ Holding BV, Yalelaan 1, 3584 CL Utrecht, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"T","family":"Gabald\u00f3n","sequence":"additional","affiliation":[{"name":"Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain"},{"name":"Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain"},{"name":"Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats (ICREA), Passeig Llu\u00eds Companys 23, 08010 Barcelona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"A","family":"Hafez","sequence":"additional","affiliation":[{"name":"Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain"},{"name":"Biotechvana, Calle\/Catedr\u00e1tico Agust\u00edn Escardino No. 9, Scientific Park Universitat de Val\u00e8ncia, 46980 Paterna, Valencia, Spain"},{"name":"Faculty of Computers and Information, Menia University, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"B","family":"Hube","sequence":"additional","affiliation":[{"name":"Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute (HKI), Jena, Germany; Friedrich Schiller University, Jena, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"F","family":"Hagen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"H","family":"Hovhannisyan","sequence":"additional","affiliation":[{"name":"Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain"},{"name":"Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"E","family":"Iracane","sequence":"additional","affiliation":[{"name":"School of Biomedical and Biomolecular Science and UCD Conway Institute of Biomolecular and Biomedical Research, Conway Institute, University College Dublin, Belfield, Dublin, Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M","family":"Kostrzewa","sequence":"additional","affiliation":[{"name":"Bruker Daltonik GmbH, Fahrenheitstr. 4, 28359 Bremen, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M","family":"Lackner","sequence":"additional","affiliation":[{"name":"Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Sch\u00f6pfstrasse 41, 6020 Innsbruck, Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"C","family":"Lass-Fl\u00f6rl","sequence":"additional","affiliation":[{"name":"Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Sch\u00f6pfstrasse 41, 6020 Innsbruck, Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"C","family":"Llorens","sequence":"additional","affiliation":[{"name":"Biotechvana, Calle\/Catedr\u00e1tico Agust\u00edn Escardino No. 9, Scientific Park Universitat de Val\u00e8ncia, 46980 Paterna, Valencia, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"V","family":"Mix\u00e3o","sequence":"additional","affiliation":[{"name":"Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain"},{"name":"Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"C","family":"Munro","sequence":"additional","affiliation":[{"name":"MRC Centre for Medical Mycology at University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J","family":"Oliveira-Pacheco","sequence":"additional","affiliation":[{"name":"School of Biomedical and Biomolecular Science and UCD Conway Institute of Biomolecular and Biomedical Research, Conway Institute, University College Dublin, Belfield, Dublin, Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M","family":"Pekmezovic","sequence":"additional","affiliation":[{"name":"Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute (HKI), Jena, Germany; Friedrich Schiller University, Jena, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"A","family":"P\u00e9rez-Hansen","sequence":"additional","affiliation":[{"name":"Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Sch\u00f6pfstrasse 41, 6020 Innsbruck, Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"A Rodriguez","family":"Sanchez","sequence":"additional","affiliation":[{"name":"Laboratory Bacteriology Research, Department Clinical Chemistry, Microbiology & Immunology, Faculty of Medicine & Health Sciences, Ghent University, Flanders, Belgium; Medical Research Building II, 1st Floor, Ghent University Hospital, Entrance 38, Heymanslaan 10, 9000 Gent, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"F M","family":"Sauer","sequence":"additional","affiliation":[{"name":"Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, 1012 WX, Amsterdam, The Netherlands"},{"name":"QVQ Holding BV, Yalelaan 1, 3584 CL Utrecht, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"K","family":"Sparbier","sequence":"additional","affiliation":[{"name":"Bruker Daltonik GmbH, Fahrenheitstr. 4, 28359 Bremen, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"A A","family":"Stavrou","sequence":"additional","affiliation":[{"name":"Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, 1012 WX, Amsterdam, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M","family":"Vaneechoutte","sequence":"additional","affiliation":[{"name":"Laboratory Bacteriology Research, Department Clinical Chemistry, Microbiology & Immunology, Faculty of Medicine & Health Sciences, Ghent University, Flanders, Belgium; Medical Research Building II, 1st Floor, Ghent University Hospital, Entrance 38, Heymanslaan 10, 9000 Gent, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M","family":"Vatanshenassan","sequence":"additional","affiliation":[{"name":"Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, 1012 WX, Amsterdam, The Netherlands"},{"name":"Bruker Daltonik GmbH, Fahrenheitstr. 4, 28359 Bremen, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Toni","family":"Gabald\u00f3n","sequence":"additional","affiliation":[{"name":"Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain"},{"name":"Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain"},{"name":"ICREA, Pg Llu\u00eds Companys 23, 08010 Barcelona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2019,6,3]]},"reference":[{"key":"2021041201471724600_bib1","doi-asserted-by":"crossref","first-page":"3635","DOI":"10.1128\/JCM.01461-12","article-title":"Accurate and rapid identification of Candida spp. frequently associated with fungemia by using PCR and the microarray-based prove-it Sepsis assay","volume":"50","author":"Aittakorpi","year":"2012","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib2","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1590\/S0036-46652015000700011","article-title":"Susceptibility test for fungi: clinical and laboratorial correlations in medical mycology","volume":"57 Suppl 19","author":"Alastruey-Izquierdo","year":"2015","journal-title":"Rev Inst Med Trop Sao Paulo"},{"key":"2021041201471724600_bib3","doi-asserted-by":"crossref","first-page":"3324","DOI":"10.1039\/c3cs60439j","article-title":"Rolling circle amplification: a versatile tool for chemical biology, materials science and medicine","volume":"43","author":"Ali","year":"2014","journal-title":"Chem Soc Rev"},{"key":"2021041201471724600_bib4","doi-asserted-by":"crossref","first-page":"e1005471","DOI":"10.1371\/journal.ppat.1005471","article-title":"In vivo transcriptional profiling of human pathogenic fungi during infection: reflecting the real life?","volume":"12","author":"Allert","year":"2016","journal-title":"PLoS Pathog"},{"key":"2021041201471724600_bib5","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1155\/2012\/540490","article-title":"Raman spectroscopy of bacterial species and strains cultivated under reproducible conditions","volume":"27","author":"Almarashi","year":"2012","journal-title":"J Spectrosc"},{"key":"2021041201471724600_bib6","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1111\/omi.12050","article-title":"The development and validation of a rapid genetic method for species identification and genotyping of medically important fungal pathogens using high-resolution melting curve analysis","volume":"29","author":"Alnuaimi","year":"2014","journal-title":"Mol Oral Microbiol"},{"key":"2021041201471724600_bib7","doi-asserted-by":"crossref","first-page":"762","DOI":"10.1128\/JB.172.2.762-770.1990","article-title":"Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology","volume":"172","author":"Amann","year":"1990","journal-title":"J Bacteriol"},{"key":"2021041201471724600_bib8","doi-asserted-by":"crossref","first-page":"baw103","DOI":"10.1093\/database\/baw103","article-title":"HPIDB 2.0: a curated database for host\u2013pathogen interactions","volume":"2016","author":"Ammari","year":"2016","journal-title":"Database"},{"key":"2021041201471724600_bib9","volume-title":"AmpliSens Candida albicans - FEP PCR kit","author":"AmpliSens\u00ae","year":"2018"},{"key":"2021041201471724600_bib10","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1016\/j.mimet.2015.11.003","article-title":"Matrix-assisted laser desorption\/ionization time of flight mass spectrometry (MALDI-TOF MS) and Bayesian phylogenetic analysis to characterize Candida clinical isolates","volume":"119","author":"Angeletti","year":"2015","journal-title":"J Microbiol Methods"},{"key":"2021041201471724600_bib11","volume-title":"Clinical and Laboratory Standards Institute","author":"Antifungal Susceptibility Testing Files & Resources","year":"2019"},{"key":"2021041201471724600_bib12","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1016\/j.diagmicrobio.2010.10.003","article-title":"Rapid, simple, and low-cost identification of Candida species using high-resolution melting analysis","volume":"69","author":"Arancia","year":"2011","journal-title":"Diagn Microbiol Infect Dis"},{"key":"2021041201471724600_bib13","doi-asserted-by":"crossref","first-page":"112","DOI":"10.1016\/j.diagmicrobio.2018.09.007","article-title":"YEAST PANEL multiplex PCR for identification of clinically important yeast species: stepwise diagnostic strategy, useful for developing countries","volume":"93","author":"Arastehfar","year":"2019","journal-title":"Diagn Microbiol Infect Dis"},{"key":"2021041201471724600_bib14","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1111\/1469-0691.12360","article-title":"ESCMID and ECMM joint clinical guidelines for the diagnosis and management of rare invasive yeast infections","volume":"20 Suppl 3","author":"Arendrup","year":"2014","journal-title":"Clin Microbiol Infect"},{"key":"2021041201471724600_bib15","doi-asserted-by":"crossref","first-page":"484","DOI":"10.1097\/QCO.0000000000000111","article-title":"Echinocandin resistance: an emerging clinical problem?","volume":"27","author":"Arendrup","year":"2014","journal-title":"Curr Opin Infect Dis"},{"key":"2021041201471724600_bib16","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1007\/s12281-014-0212-z","article-title":"The state-of-the-art mycology laboratory: visions of the future","volume":"9","author":"Arendrup","year":"2014","journal-title":"Curr Fungal Infect Rep"},{"key":"2021041201471724600_bib17","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1586\/14737159.5.2.209","article-title":"Basic principles of real-time quantitative PCR","volume":"5","author":"Arya","year":"2005","journal-title":"Expert Rev Mol Diagn"},{"key":"2021041201471724600_bib18","volume-title":"Next Generation Sequencing in Public Health Laboratories","author":"Association of Public Health Laboratories","year":"2015"},{"key":"2021041201471724600_bib19","doi-asserted-by":"crossref","first-page":"1612","DOI":"10.1128\/JCM.02430-16","article-title":"Laboratory diagnostics for histoplasmosis","volume":"55","author":"Azar","year":"2017","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib21","first-page":"195","article-title":"Opportunistic invasive fungal infections: diagnosis & clinical management","volume":"139","author":"Badiee","year":"2014","journal-title":"Indian J Med Res"},{"key":"2021041201471724600_bib22","doi-asserted-by":"crossref","first-page":"286","DOI":"10.1016\/j.trac.2016.06.006","article-title":"Lateral flow assays: Principles, designs and labels","volume":"82","author":"Bahad\u0131r","year":"2016","journal-title":"Trends Analyt Chem"},{"key":"2021041201471724600_bib23","doi-asserted-by":"crossref","first-page":"304","DOI":"10.1093\/nar\/28.1.304","article-title":"The ENZYME database in 2000","volume":"28","author":"Bairoch","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"2021041201471724600_bib24","doi-asserted-by":"crossref","first-page":"492","DOI":"10.1128\/JCM.06375-11","article-title":"Detection of yeasts in blood cultures by the Luminex xTAG fungal assay","volume":"50","author":"Balada-Llasat","year":"2012","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib25","doi-asserted-by":"crossref","first-page":"2058","DOI":"10.1128\/AAC.01653-05","article-title":"Assessing resistance to the echinocandin antifungal drug caspofungin in Candida albicans by profiling mutations in FKS1","volume":"50","author":"Balashov","year":"2006","journal-title":"Antimicrob Agents Chemother"},{"key":"2021041201471724600_bib26","doi-asserted-by":"crossref","first-page":"E39","DOI":"10.3390\/jof4010039","article-title":"FungiDB: an integrated bioinformatic resource for fungi and oomycetes","volume":"4","author":"Basenko","year":"2018","journal-title":"J Fungi (Basel)"},{"key":"2021041201471724600_bib27","doi-asserted-by":"crossref","first-page":"2092","DOI":"10.1007\/s00134-013-3109-3","article-title":"A research agenda on the management of intra-abdominal candidiasis: results from a consensus of multinational experts","volume":"39","author":"Bassetti","year":"2013","journal-title":"Intensive Care Med"},{"key":"2021041201471724600_bib28","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1016\/j.riam.2014.06.004","article-title":"A flow cytometry method for testing the susceptibility of Cryptococcus spp. to amphotericin B","volume":"32","author":"Benaducci","year":"2015","journal-title":"Rev Iberoam Micol"},{"key":"2021041201471724600_bib29","doi-asserted-by":"crossref","first-page":"680","DOI":"10.2144\/04374DD04","article-title":"DNA nucleic acid sequence-based amplification-based genotyping for polymorphism analysis","volume":"37","author":"Berard","year":"2004","journal-title":"BioTechniques"},{"key":"2021041201471724600_bib30","doi-asserted-by":"crossref","first-page":"365","DOI":"10.3732\/ajb.1100309","article-title":"Next-generation sequencing applications for wheat crop improvement","volume":"99","author":"Berkman","year":"2012","journal-title":"Am J Bot"},{"key":"2021041201471724600_bib31","doi-asserted-by":"crossref","first-page":"34841","DOI":"10.1038\/srep34841","article-title":"Network diffusion-based analysis of high-throughput data for the detection of differentially enriched modules","volume":"6","author":"Bersanelli","year":"2016","journal-title":"Sci Rep"},{"key":"2021041201471724600_bib32","doi-asserted-by":"crossref","first-page":"714","DOI":"10.1093\/mmy\/myw032","article-title":"Rapid detection of fungal pathogens in bronchoalveolar lavage samples using panfungal PCR combined with high resolution melting analysis","volume":"54","author":"Bezdicek","year":"2016","journal-title":"Med Mycol"},{"key":"2021041201471724600_bib33","doi-asserted-by":"crossref","first-page":"1988","DOI":"10.1128\/CVI.00446-12","article-title":"Comparison of four assays for the detection of cryptococcal antigen","volume":"19","author":"Binnicker","year":"2012","journal-title":"Clin Vaccine Immunol"},{"key":"2021041201471724600_bib34","volume-title":"RealLine Candida albicans\/ Gardnerella vaginalis Str Format","author":"Bioron","year":"2016"},{"key":"2021041201471724600_bib35","doi-asserted-by":"publisher","DOI":"10.3791\/56714","article-title":"Whole genome sequencing of Candida glabrata for detection of markers of antifungal drug resistance","volume":"130","author":"Biswas","year":"2017","journal-title":"J Vis Exp"},{"key":"2021041201471724600_bib36","doi-asserted-by":"crossref","first-page":"487","DOI":"10.1186\/s13059-014-0487-y","article-title":"Improved characterization of medically relevant fungi in the human respiratory tract using next-generation sequencing","volume":"15","author":"Bittinger","year":"2014","journal-title":"Genome Biol"},{"key":"2021041201471724600_bib37","doi-asserted-by":"crossref","first-page":"161","DOI":"10.4137\/EBO.S8989","article-title":"Selection of marker genes using whole-genome DNA polymorphism analysis","volume":"8","author":"Bohle","year":"2012","journal-title":"Evol Bioinform Online"},{"key":"2021041201471724600_bib38","doi-asserted-by":"crossref","first-page":"9419","DOI":"10.1021\/acs.analchem.6b01016","article-title":"Automated high-throughput identification and characterization of clinically important bacteria and fungi using rapid evaporative ionization mass spectrometry","volume":"88","author":"Bolt","year":"2016","journal-title":"Anal Chem"},{"key":"2021041201471724600_bib39","doi-asserted-by":"crossref","first-page":"57","DOI":"10.3390\/jof3040057","article-title":"Global and multi-national prevalence of fungal diseases\u2013estimate precision","volume":"3","author":"Bongomin","year":"2017","journal-title":"J Fungi (Basel)"},{"key":"2021041201471724600_bib40","doi-asserted-by":"crossref","first-page":"E6","DOI":"10.3390\/jof3010006","article-title":"Cutaneous disseminated and extracutaneous sporotrichosis: current status of a complex disease","volume":"3","author":"Bonifaz","year":"2017","journal-title":"J Fungi (Basel)"},{"key":"2021041201471724600_bib41","doi-asserted-by":"crossref","first-page":"551","DOI":"10.1007\/s15010-015-0796-4","article-title":"Diagnosis of prosthetic joint infections using UMD-Universal Kit and the automated multiplex-PCR Unyvero i60 ITI(\u00ae) cartridge system: a pilot study","volume":"43","author":"Borde","year":"2015","journal-title":"Infection"},{"key":"2021041201471724600_bib42","first-page":"487","article-title":"Clinical evaluation of a NASBA-based assay for detection of Candida spp. in blood and blood cultures","volume":"48","author":"Borst","year":"2002","journal-title":"Clin Lab"},{"key":"2021041201471724600_bib44","doi-asserted-by":"crossref","first-page":"1026","DOI":"10.1053\/j.gastro.2017.06.004","article-title":"Intestinal fungal dysbiosis is associated with visceral hypersensitivity in patients with irritable bowel syndrome and rats","volume":"153","author":"Botschuijver","year":"2017","journal-title":"Gastroenterology"},{"key":"2021041201471724600_bib45","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1016\/0027-5107(93)90211-W","article-title":"PCR amplification of specific alleles: rapid detection of known mutations and polymorphisms","volume":"288","author":"Bottema","year":"1993","journal-title":"Mutat Res"},{"key":"2021041201471724600_bib46","doi-asserted-by":"crossref","first-page":"1874","DOI":"10.1128\/JCM.00223-07","article-title":"Identification of genotypically diverse Cryptococcus neoformans and Cryptococcus gattii isolates by Luminex xMAP technology","volume":"45","author":"Bovers","year":"2007","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib47","doi-asserted-by":"crossref","first-page":"165rv13","DOI":"10.1126\/scitranslmed.3004404","article-title":"Hidden killers: human fungal infections","volume":"4","author":"Brown","year":"2012","journal-title":"Sci Transl Med"},{"key":"2021041201471724600_bib52","volume-title":"Bruker Expands Portfolio for Testing of Candida Auris, an Emerging, Multidrug-Resistant Pathogen in Human Healthcare","author":"Bruker","year":"2018"},{"key":"2021041201471724600_bib48","volume-title":"Fungiplex\u00ae Aspergillus Azole-R IVD Real-Time PCR Kit","author":"Bruker","year":"2018"},{"key":"2021041201471724600_bib50","volume-title":"Fungiplex\u00ae Candida Auris RUO Real-Time PCR Kit","author":"Bruker","year":"2018"},{"key":"2021041201471724600_bib49","volume-title":"Fungiplex\u00ae Universal RUO Real-Time PCR Kit","author":"Bruker","year":"2018"},{"key":"2021041201471724600_bib51","volume-title":"IR Biotyper - Microbial Typing for Real-Time Epidemiology","author":"Bruker","year":"2018"},{"key":"2021041201471724600_bib53","doi-asserted-by":"crossref","first-page":"e00182","DOI":"10.1128\/mBio.00182-15","article-title":"Transcriptomic analysis of vulvovaginal candidiasis identifies a role for the NLRP3 inflammasome","volume":"6","author":"Bruno","year":"2015","journal-title":"MBio"},{"key":"2021041201471724600_bib54","doi-asserted-by":"crossref","first-page":"611","DOI":"10.1373\/clinchem.2008.112797","article-title":"The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments","volume":"55","author":"Bustin","year":"2009","journal-title":"Clin Chem"},{"key":"2021041201471724600_bib55","doi-asserted-by":"crossref","first-page":"1456","DOI":"10.1101\/gr.3672305","article-title":"The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species","volume":"15","author":"Byrne","year":"2005","journal-title":"Genome Res"},{"key":"2021041201471724600_bib43","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1016\/j.fsigen.2015.02.002","article-title":"Next generation sequencing and its applications in forensic genetics","volume":"18","author":"B\u00f8rsting","year":"2015","journal-title":"Forensic Sci Int Genet"},{"key":"2021041201471724600_bib56","doi-asserted-by":"crossref","first-page":"172","DOI":"10.1007\/s00284-016-1039-3","article-title":"Principles of a new protocol for prediction of azole resistance in Candida albicans infections on the basis of ERG11 polymorphisms","volume":"73","author":"Caban","year":"2016","journal-title":"Curr Microbiol"},{"key":"2021041201471724600_bib57","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1016\/j.jinf.2016.07.008","article-title":"First report of Candida auris in America: Clinical and microbiological aspects of 18 episodes of candidemia","volume":"73","author":"Calvo","year":"2016","journal-title":"J Infect"},{"key":"2021041201471724600_bib58","doi-asserted-by":"crossref","first-page":"36788","DOI":"10.1038\/srep36788","article-title":"Rapid Evaporative Ionisation Mass Spectrometry (REIMS) provides accurate direct from culture species identification within the genus Candida","volume":"6","author":"Cameron","year":"2016","journal-title":"Sci Rep"},{"issue":"2","key":"2021041201471724600_bib59","first-page":"1304","article-title":"The preparation and clinical application of diagnostic DNA microarray for the detection of pathogens in intracranial bacterial and fungal infections","volume":"16","author":"Cao","year":"2018","journal-title":"Exp Ther Med"},{"key":"2021041201471724600_bib60","doi-asserted-by":"crossref","first-page":"e54","DOI":"10.1093\/nar\/gku071","article-title":"A phylogenomics approach for selecting robust sets of phylogenetic markers","volume":"42","author":"Capella-Gutierrez","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2021041201471724600_bib62","doi-asserted-by":"crossref","first-page":"447","DOI":"10.1016\/j.chom.2012.04.004","article-title":"Immunoglobulins in defense, pathogenesis, and therapy of fungal diseases","volume":"11","author":"Casadevall","year":"2012","journal-title":"Cell Host Microbe"},{"key":"2021041201471724600_bib63","doi-asserted-by":"crossref","first-page":"3641","DOI":"10.1128\/JCM.02248-12","article-title":"Reclassification of the Candida haemulonii complex as Candida haemulonii (C. haemulonii group I), C. duobushaemulonii sp. nov. (C. haemulonii group II), and C. haemulonii var. vulnera var. nov.: three multiresistant human pathogenic yeasts","volume":"50","author":"Cendejas-Bueno","year":"2012","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib64","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1111\/ppa.12957","article-title":"Diagnosis of plant diseases using the Nanopore sequencing platform","volume":"68","author":"Chalupowicz","year":"2019","journal-title":"Plant Pathol"},{"key":"2021041201471724600_bib65","doi-asserted-by":"crossref","first-page":"2249","DOI":"10.1128\/JCM.42.5.2249-2251.2004","article-title":"Collaborative study of the NCCLS and flow cytometry methods for antifungal susceptibility testing of Candida albicans","volume":"42","author":"Chaturvedi","year":"2004","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib66","doi-asserted-by":"crossref","first-page":"504","DOI":"10.1039\/C5AN00382B","article-title":"Microfluidics for research and applications in oncology","volume":"141","author":"Chaudhuri","year":"2016","journal-title":"Analyst"},{"key":"2021041201471724600_bib67","doi-asserted-by":"crossref","first-page":"2632","DOI":"10.1093\/jac\/dkt214","article-title":"Clinical features of patients with infections caused by Candida guilliermondii and Candida fermentati and antifungal susceptibility of the isolates at a medical centre in Taiwan, 2001-10","volume":"68","author":"Chen","year":"2013","journal-title":"J Antimicrob Chemother"},{"key":"2021041201471724600_bib69","doi-asserted-by":"crossref","first-page":"e25527","DOI":"10.1371\/journal.pone.0025527","article-title":"Development of a PNA probe for fluorescence in situ hybridization detection of Prorocentrum donghaiense","volume":"6","author":"Chen","year":"2011","journal-title":"PLoS One"},{"key":"2021041201471724600_bib68","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1189\/jlb.1210702","article-title":"The dectin-1\/inflammasome pathway is responsible for the induction of protective T-helper 17 responses that discriminate between yeasts and hyphae of Candida albicans","volume":"90","author":"Cheng","year":"2011","journal-title":"J Leukoc Biol"},{"key":"2021041201471724600_bib73","doi-asserted-by":"crossref","first-page":"1647","DOI":"10.1128\/JCM.02018-07","article-title":"Immunoglobulin G responses to a panel of Candida albicans antigens as accurate and early markers for the presence of systemic candidiasis","volume":"46","author":"Clancy","year":"2008","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib70","doi-asserted-by":"crossref","first-page":"1284","DOI":"10.1093\/cid\/cit006","article-title":"Finding the \u201cmissing 50%\u201d of invasive candidiasis: how nonculture diagnostics will improve understanding of disease spectrum and transform patient care","volume":"56","author":"Clancy","year":"2013","journal-title":"Clin Infect Dis"},{"key":"2021041201471724600_bib72","doi-asserted-by":"crossref","first-page":"E27","DOI":"10.3390\/jof4010027","article-title":"Non-culture diagnostics for invasive candidiasis: promise and unintended consequences","volume":"4","author":"Clancy","year":"2018","journal-title":"J Fungi (Basel)"},{"key":"2021041201471724600_bib71","doi-asserted-by":"crossref","first-page":"iv2","DOI":"10.1093\/jac\/dky050","article-title":"T2 magnetic resonance for the diagnosis of bloodstream infections: charting a path forward","volume":"73","author":"Clancy","year":"2018","journal-title":"J Antimicrob Chemother"},{"key":"2021041201471724600_bib74","volume-title":"CLSI M100-ED29:2019 Performance Standards for Antimicrobial Susceptibility Testing","author":"CLSI","year":"2019","edition":"29th edition"},{"key":"2021041201471724600_bib75","doi-asserted-by":"crossref","first-page":"D633","DOI":"10.1093\/nar\/gkt1244","article-title":"Ribosomal Database Project: data and tools for high throughput rRNA analysis","volume":"42","author":"Cole","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2021041201471724600_bib76","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1093\/clinchem\/46.7.996","article-title":"Multiplexed genotyping of beta-globin variants from PCR-amplified newborn blood spot DNA by hybridization with allele-specific oligodeoxynucleotides coupled to an array of fluorescent microspheres","volume":"46","author":"Colinas","year":"2000","journal-title":"Clin Chem"},{"key":"2021041201471724600_bib77","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1038\/350091a0","article-title":"Nucleic acid sequence-based amplification","volume":"350","author":"Compton","year":"1991","journal-title":"Nature"},{"key":"2021041201471724600_bib78","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1111\/1469-0691.12039","article-title":"ESCMID* guideline for the diagnosis and management of Candida diseases 2012: non-neutropenic adult patients","volume":"18 Suppl 7","author":"Cornely","year":"2012","journal-title":"Clin Microbiol Infect"},{"key":"2021041201471724600_bib79","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1155\/2015\/456479","article-title":"A comparison of variant calling pipelines using Genome in a Bottle as a reference","volume":"2015","author":"Cornish","year":"2015","journal-title":"Biomed Res Int"},{"key":"2021041201471724600_bib80","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1111\/1469-0691.12038","article-title":"ESCMID* guideline for the diagnosis and management of Candida diseases 2012: diagnostic procedures","volume":"18 Suppl 7","author":"Cuenca-Estrella","year":"2012","journal-title":"Clin Microbiol Infect"},{"key":"2021041201471724600_bib81","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1089\/omi.2015.0185","article-title":"Systems biology approaches for host-fungal interactions: an expanding multi-omics frontier","volume":"20","author":"Culibrk","year":"2016","journal-title":"OMICS"},{"key":"2021041201471724600_bib82","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1007\/s12281-017-0276-7","article-title":"Harnessing whole genome sequencing in medical mycology","volume":"11","author":"Cuomo","year":"2017","journal-title":"Curr Fungal Infect Rep"},{"key":"2021041201471724600_bib61","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1016\/j.mimet.2004.07.009","article-title":"Comparative evaluation of four commercial tests for presumptive identification of Candida albicans","volume":"59","author":"C\u00e1rdenes","year":"2004","journal-title":"J Microbiol Methods"},{"key":"2021041201471724600_bib224","doi-asserted-by":"crossref","first-page":"E24","DOI":"10.3390\/jof3020024","article-title":"Revisiting species distribution and antifungal susceptibility of Candida bloodstream isolates from Latin American medical centers","volume":"3","author":"da\u00a0Matta","year":"2017","journal-title":"J Fungi (Basel)"},{"key":"2021041201471724600_bib83","doi-asserted-by":"crossref","first-page":"863","DOI":"10.1111\/j.1469-0691.2009.02997.x","article-title":"Comparison of antifungal MICs for yeasts obtained using the EUCAST method in a reference laboratory and the Etest in nine different hospital laboratories","volume":"16","author":"Dannaoui","year":"2010","journal-title":"Clin Microbiol Infect"},{"key":"2021041201471724600_bib84","doi-asserted-by":"crossref","first-page":"847","DOI":"10.1128\/MMBR.64.4.847-867.2000","article-title":"Microbial biofilms: from ecology to molecular genetics","volume":"64","author":"Davey","year":"2000","journal-title":"Microbiol Mol Biol Rev"},{"key":"2021041201471724600_bib85","doi-asserted-by":"crossref","first-page":"1111","DOI":"10.1109\/TKDE.2005.131","article-title":"Knowledge accumulation and resolution of data inconsistencies during the integration of microbial information sources","volume":"17","author":"Dawyndt","year":"2005","journal-title":"IEEE Trans Knowl Data Eng"},{"key":"2021041201471724600_bib86","doi-asserted-by":"crossref","first-page":"1660","DOI":"10.1128\/AAC.45.6.1660-1670.2001","article-title":"Genomic profiling of the response of Candida albicans to itraconazole treatment using a DNA microarray","volume":"45","author":"De\u00a0Backer","year":"2001","journal-title":"Antimicrob Agents Chemother"},{"key":"2021041201471724600_bib87","doi-asserted-by":"crossref","first-page":"475","DOI":"10.1111\/j.1469-0691.2011.03599.x","article-title":"Species identification of Aspergillus, Fusarium and Mucorales with direct surface analysis by matrix-assisted laser desorption ionization time-of-flight mass spectrometry","volume":"18","author":"De\u00a0Carolis","year":"2012","journal-title":"Clin Microbiol Infect"},{"key":"2021041201471724600_bib88","doi-asserted-by":"crossref","first-page":"2479","DOI":"10.1128\/JCM.00224-12","article-title":"Use of matrix-assisted laser desorption ionization-time of flight mass spectrometry for caspofungin susceptibility testing of Candida and Aspergillus species","volume":"50","author":"De\u00a0Carolis","year":"2012","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib89","doi-asserted-by":"crossref","first-page":"1081","DOI":"10.3855\/jidc.3623","article-title":"Application of MALDI-TOF mass spectrometry in clinical diagnostic microbiology","volume":"8","author":"De\u00a0Carolis","year":"2014","journal-title":"J Infect Dev Ctries"},{"key":"2021041201471724600_bib90","doi-asserted-by":"crossref","first-page":"664","DOI":"10.1186\/1756-0500-5-664","article-title":"Optimization of quantitative polymerase chain reactions for detection and quantification of eight periodontal bacterial pathogens","volume":"5","author":"Decat","year":"2012","journal-title":"BMC Res Notes"},{"key":"2021041201471724600_bib91","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1016\/j.resmic.2012.10.017","article-title":"Rapid and accurate identification of isolates of Candida species by melting peak and melting curve analysis of the internally transcribed spacer region 2 fragment (ITS2-MCA)","volume":"164","author":"Decat","year":"2013","journal-title":"Res Microbiol"},{"key":"2021041201471724600_bib92","doi-asserted-by":"crossref","first-page":"E1796","DOI":"10.3390\/ijms18081796","article-title":"Immune-response patterns and next generation sequencing diagnostics for the detection of Mycoses in patients with septic shock-results of a combined clinical and experimental investigation","volume":"18","author":"Decker","year":"2017","journal-title":"Int J Mol Sci"},{"key":"2021041201471724600_bib93","doi-asserted-by":"crossref","first-page":"1992","DOI":"10.1111\/pce.12106","article-title":"RNAseq-based transcriptome analysis of Lactuca sativa infected by the fungal necrotroph Botrytis cinerea","volume":"36","author":"De\u00a0Cremer","year":"2013","journal-title":"Plant Cell Environ"},{"key":"2021041201471724600_bib94","doi-asserted-by":"crossref","first-page":"1360","DOI":"10.1126\/science.2466341","article-title":"Phylogenetic stains: ribosomal RNA-based probes for the identification of single cells","volume":"243","author":"DeLong","year":"1989","journal-title":"Science"},{"key":"2021041201471724600_bib95","doi-asserted-by":"crossref","first-page":"1191","DOI":"10.1111\/j.1469-0691.2003.00719.x","article-title":"PCR-RFLP detection and species identification of fungal pathogens in patients with febrile neutropenia","volume":"9","author":"Dendis","year":"2003","journal-title":"Clin Microbiol Infect"},{"key":"2021041201471724600_bib96","doi-asserted-by":"crossref","first-page":"1107","DOI":"10.1007\/s00431-016-2753-3","article-title":"Magicplex(TM) Sepsis Real-Time test to improve bloodstream infection diagnostics in children","volume":"175","author":"Denina","year":"2016","journal-title":"Eur J Pediatr"},{"key":"2021041201471724600_bib97","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1128\/JCM.01763-16","article-title":"Performance of matrix-assisted laser desorption ionization-time of flight mass spectrometry for identifying clinical Malassezia isolates","volume":"55","author":"Denis","year":"2017","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib98","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1016\/j.jbiotec.2016.12.022","article-title":"Application of next generation sequencing in clinical microbiology and infection prevention","volume":"243","author":"Deurenberg","year":"2017","journal-title":"J Biotechnol"},{"key":"2021041201471724600_bib99","doi-asserted-by":"crossref","first-page":"216","DOI":"10.1111\/cei.12746","article-title":"Chronic mucocutaneous candidiasis: characterization of a family with STAT-1 gain-of-function and development of an ex-vivo assay for Th17 deficiency of diagnostic utility","volume":"184","author":"Dhalla","year":"2016","journal-title":"Clin Exp Immunol"},{"key":"2021041201471724600_bib100","doi-asserted-by":"crossref","first-page":"1197","DOI":"10.1099\/jmm.0.46630-0","article-title":"Microcoding and flow cytometry as a high-throughput fungal identification system for Malassezia species","volume":"55","author":"Diaz","year":"2006","journal-title":"J Med Microbiol"},{"key":"2021041201471724600_bib101","doi-asserted-by":"crossref","first-page":"3269","DOI":"10.1128\/AAC.00556-06","article-title":"Biofilm formation by the emerging fungal pathogen Trichosporon asahii: development, architecture, and antifungal resistance","volume":"50","author":"Di\u00a0Bonaventura","year":"2006","journal-title":"Antimicrob Agents Chemother"},{"key":"2021041201471724600_bib103","doi-asserted-by":"crossref","first-page":"e00843","DOI":"10.1128\/JCM.00843-18","article-title":"Typing and species identification of clinical Klebsiella isolates by Fourier transform infrared spectroscopy and matrix-assisted laser desorption ionization-time of flight mass spectrometry","volume":"56","author":"Dinkelacker","year":"2018","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib104","doi-asserted-by":"crossref","first-page":"e1007138","DOI":"10.1371\/journal.ppat.1007138","article-title":"Population genomics shows no distinction between pathogenic Candida krusei and environmental Pichia kudriavzevii: One species, four names","volume":"14","author":"Douglass","year":"2018","journal-title":"PLoS Pathog"},{"key":"2021041201471724600_bib105","doi-asserted-by":"crossref","first-page":"2609","DOI":"10.1128\/JCM.01038-14","article-title":"Set of classical PCRs for detection of mutations in Candida glabrata FKS genes linked with echinocandin resistance","volume":"52","author":"Dudiuk","year":"2014","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib106","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1016\/j.cccn.2005.06.023","article-title":"Applications of Luminex xMAP technology for rapid, high-throughput multiplexed nucleic acid detection","volume":"363","author":"Dunbar","year":"2006","journal-title":"Clin Chim Acta"},{"key":"2021041201471724600_bib107","first-page":"235","article-title":"A review on computational systems biology of pathogen-host interactions","volume":"6","author":"Durmu\u015f","year":"2015","journal-title":"Front Microbiol"},{"key":"2021041201471724600_bib108","doi-asserted-by":"crossref","first-page":"e0132149","DOI":"10.1371\/journal.pone.0132149","article-title":"Validation of high resolution melting analysis (HRM) of the amplified ITS2 region for the detection and identification of yeasts from clinical samples: comparison with culture and MALDI-TOF based identification","volume":"10","author":"Duyvejonck","year":"2015","journal-title":"PLoS One"},{"key":"2021041201471724600_bib109","doi-asserted-by":"crossref","first-page":"566","DOI":"10.1038\/365566a0","article-title":"PNA hybridizes to complementary oligonucleotides obeying the Watson-Crick hydrogen-bonding rules","volume":"365","author":"Egholm","year":"1993","journal-title":"Nature"},{"key":"2021041201471724600_bib110","first-page":"65","article-title":"Laboratory diagnosis of invasive candidiasis","volume":"43 Spec No","author":"Ellepola","year":"2005","journal-title":"J Microbiol"},{"key":"2021041201471724600_bib111","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1007\/s00281-014-0466-0","article-title":"The protective role of immunoglobulins in fungal infections and inflammation","volume":"37","author":"Elluru","year":"2015","journal-title":"Semin Immunopathol"},{"key":"2021041201471724600_bib112","doi-asserted-by":"crossref","first-page":"1604","DOI":"10.1111\/j.1469-0691.2010.03368.x","article-title":"Application and use of various mass spectrometry methods in clinical microbiology","volume":"16","author":"Emonet","year":"2010","journal-title":"Clin Microbiol Infect"},{"key":"2021041201471724600_bib113","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1111\/j.1574-6968.2004.tb09518.x","article-title":"Detection of gp43 of Paracoccidioides brasiliensis by the loop-mediated isothermal amplification (LAMP) method","volume":"234","author":"Endo","year":"2004","journal-title":"FEMS Microbiol Lett"},{"key":"2021041201471724600_bib114","doi-asserted-by":"crossref","first-page":"E7","DOI":"10.3390\/jof2010007","article-title":"Transcriptomic crosstalk between fungal invasive pathogens and their host cells: opportunities and challenges for next-generation sequencing methods","volume":"2","author":"Enguita","year":"2016","journal-title":"J Fungi (Basel)"},{"key":"2021041201471724600_bib115","volume-title":"Aspergillus, Candida albicans Molecular Detection Kit (Real-time PCR)","author":"Era Biology","year":"2018"},{"key":"2021041201471724600_bib116","doi-asserted-by":"crossref","first-page":"618","DOI":"10.1007\/s12275-016-6017-8","article-title":"Application of high-resolution melting analysis for differentiation of spoilage yeasts","volume":"54","author":"Erdem","year":"2016","journal-title":"J Microbiol"},{"key":"2021041201471724600_bib117","volume-title":"Breakpoint Tables for Interpretation of MICs","author":"European Committee on Antimicrobial Susceptibility Testing","year":"2018"},{"key":"2021041201471724600_bib118","doi-asserted-by":"crossref","first-page":"16092","DOI":"10.1038\/nmicrobiol.2016.92","article-title":"Drug resistance in eukaryotic microorganisms","volume":"1","author":"Fairlamb","year":"2016","journal-title":"Nat Microbiol"},{"key":"2021041201471724600_bib119","doi-asserted-by":"crossref","first-page":"1567","DOI":"10.1373\/clinchem.2013.205211","article-title":"Current methods for fluorescence-based universal sequence-dependent detection of nucleic acids in homogenous assays and clinical applications","volume":"59","author":"Faltin","year":"2013","journal-title":"Clin Chem"},{"key":"2021041201471724600_bib120","doi-asserted-by":"crossref","first-page":"318","DOI":"10.1016\/j.ijantimicag.2017.05.019","article-title":"Epidemiology of antifungal resistance in human pathogenic yeasts: current viewpoint and practical recommendations for management","volume":"50","author":"Farmakiotis","year":"2017","journal-title":"Int J Antimicrob Agents"},{"key":"2021041201471724600_bib121","doi-asserted-by":"crossref","first-page":"1125","DOI":"10.1039\/b500248f","article-title":"DNA detection by surface enhanced resonance Raman scattering (SERRS)","volume":"130","author":"Faulds","year":"2005","journal-title":"Analyst"},{"key":"2021041201471724600_bib122","doi-asserted-by":"crossref","first-page":"3190","DOI":"10.1128\/JCM.01297-14","article-title":"Development of two molecular approaches for differentiation of clinically relevant yeast species closely related to Candida guilliermondii and Candida famata","volume":"52","author":"Feng","year":"2014","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib123","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1016\/0732-8893(95)00199-9","article-title":"Comparison of the Murex Candida albicans CA50 test with germ tube production for identification of C. albicans","volume":"24","author":"Fenn","year":"1996","journal-title":"Diagn Microbiol Infect Dis"},{"key":"2021041201471724600_bib124","doi-asserted-by":"crossref","first-page":"290","DOI":"10.1186\/1471-2164-11-290","article-title":"Analysis of gene evolution and metabolic pathways using the Candida Gene Order Browser","volume":"11","author":"Fitzpatrick","year":"2010","journal-title":"BMC Genomics"},{"key":"2021041201471724600_bib125","doi-asserted-by":"publisher","first-page":"1","DOI":"10.4172\/2469-9861.1000106","article-title":"Diagnosis of bloodstream infections by mass spectrometry: present and future","volume":"01","author":"Florio","year":"2015","journal-title":"Mass Spectrom Purif Tech"},{"key":"2021041201471724600_bib126","doi-asserted-by":"crossref","first-page":"2085","DOI":"10.1128\/JCM.42.5.2085-2093.2004","article-title":"Rapid quantification of drug resistance gene expression in Candida albicans by reverse transcriptase LightCycler PCR and fluorescent probe hybridization","volume":"42","author":"Frade","year":"2004","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib127","first-page":"80","article-title":"Rapid identification of 6328 isolates of pathogenic yeasts using MALDI-ToF MS and a simplified, rapid extraction procedure that is compatible with the Bruker Biotyper platform and database","volume":"54","author":"Fraser","year":"2016","journal-title":"Med Mycol"},{"key":"2021041201471724600_bib128","doi-asserted-by":"crossref","first-page":"877","DOI":"10.1128\/JCM.35.4.877-880.1997","article-title":"Evaluation of latex reagents for rapid identification of Candida albicans and C. krusei colonies","volume":"35","author":"Freydiere","year":"1997","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib129","doi-asserted-by":"crossref","first-page":"1749","DOI":"10.1093\/clinchem\/43.9.1749","article-title":"Advanced multiplexed analysis with the FlowMetrix system","volume":"43","author":"Fulton","year":"1997","journal-title":"Clin Chem"},{"key":"2021041201471724600_bib130","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1111\/myc.12426","article-title":"Molecular identification of Histoplasma capsulatum using rolling circle amplification","volume":"59","author":"Furuie","year":"2016","journal-title":"Mycoses"},{"key":"2021041201471724600_bib131","doi-asserted-by":"crossref","first-page":"fow064","DOI":"10.1093\/femsyr\/fow064","article-title":"Evolutionary genomics of yeast pathogens in the Saccharomycotina","volume":"16","author":"Gabald\u00f3n","year":"2016","journal-title":"FEMS Yeast Res"},{"key":"2021041201471724600_bib132","doi-asserted-by":"crossref","first-page":"1616","DOI":"10.1128\/JCM.29.8.1616-1619.1991","article-title":"Comparison of the PREMIER cryptococcal antigen enzyme immunoassay and the latex agglutination assay for detection of cryptococcal antigens","volume":"29","author":"Gade","year":"1991","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib134","doi-asserted-by":"crossref","first-page":"e112","DOI":"10.1093\/cid\/ciw360","article-title":"2016 Infectious Diseases Society of America (IDSA) clinical practice guideline for the treatment of coccidioidomycosis","volume":"63","author":"Galgiani","year":"2016","journal-title":"Clin Infect Dis"},{"key":"2021041201471724600_bib133","doi-asserted-by":"crossref","first-page":"372","DOI":"10.1016\/j.eimc.2014.10.003","article-title":"Evaluation of mass spectrometry for the identification of clinically interesting yeasts","volume":"33","author":"Gal\u00e1n","year":"2015","journal-title":"Enferm Infecc Microbiol Clin"},{"key":"2021041201471724600_bib135","doi-asserted-by":"crossref","first-page":"987","DOI":"10.1111\/j.1567-1364.2006.00108.x","article-title":"Use of DNA microarray technology and gene expression profiles to investigate the pathogenesis, cell biology, antifungal susceptibility and diagnosis of Candida albicans","volume":"6","author":"Garaizar","year":"2006","journal-title":"FEMS Yeast Res"},{"key":"2021041201471724600_bib136","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1111\/nyas.13739","article-title":"New pathogens, new tricks: emerging, drug-resistant fungal pathogens and future prospects for antifungal therapeutics","volume":"1435","author":"Geddes-McAlister","year":"2018","journal-title":"Ann N Y Acad Sci"},{"key":"2021041201471724600_bib137","doi-asserted-by":"crossref","first-page":"3126","DOI":"10.1128\/AAC.00118-10","article-title":"Correlation between azole susceptibilities, genotypes, and ERG11 mutations in Candida albicans isolates associated with vulvovaginal candidiasis in China","volume":"54","author":"Ge","year":"2010","journal-title":"Antimicrob Agents Chemother"},{"key":"2021041201471724600_bib138","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1016\/S0065-2164(10)71006-6","article-title":"Microbial fingerprinting using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) applications and challenges","volume":"71","author":"Giebel","year":"2010","journal-title":"Adv Appl Microbiol"},{"key":"2021041201471724600_bib139","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1111\/myc.12519","article-title":"Identification and typing of the emerging pathogen Candida auris by matrix-assisted laser desorption ionisation time of flight mass spectrometry","volume":"59","author":"Girard","year":"2016","journal-title":"Mycoses"},{"key":"2021041201471724600_bib140","doi-asserted-by":"crossref","first-page":"340","DOI":"10.1089\/cmb.2016.0100","article-title":"New algorithm and software (BNOmics) for inferring and visualizing Bayesian networks from heterogeneous big biological and genetic data","volume":"24","author":"Gogoshin","year":"2017","journal-title":"J Comput Biol"},{"key":"2021041201471724600_bib141","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1007\/s11046-016-0074-8","article-title":"Expression patterns of ABC transporter genes in fluconazole-resistant Candida glabrata","volume":"182","author":"Gohar","year":"2017","journal-title":"Mycopathologia"},{"key":"2021041201471724600_bib142","doi-asserted-by":"crossref","first-page":"e01888","DOI":"10.1128\/mBio.01888-15","article-title":"Making the leap from research laboratory to clinic: challenges and opportunities for next-generation sequencing in infectious disease diagnostics","volume":"6","author":"Goldberg","year":"2015","journal-title":"MBio"},{"key":"2021041201471724600_bib143","doi-asserted-by":"crossref","first-page":"194","DOI":"10.1016\/S1130-1406(06)70044-4","article-title":"FISH and Calcofluor staining techniques to detect in situ filamentous fungal biofilms in water","volume":"23","author":"Gon\u00e7alves","year":"2006","journal-title":"Rev Iberoam Micol"},{"key":"2021041201471724600_bib144","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1038\/nrg.2016.49","article-title":"Coming of age: ten years of next-generation sequencing technologies","volume":"17","author":"Goodwin","year":"2016","journal-title":"Nat Rev Genet"},{"key":"2021041201471724600_bib145","doi-asserted-by":"crossref","first-page":"112","DOI":"10.1038\/nrmicro2711","article-title":"Candida albicans morphogenesis and host defence: discriminating invasion from colonization","volume":"10","author":"Gow","year":"2011","journal-title":"Nat Rev Microbiol"},{"key":"2021041201471724600_bib146","doi-asserted-by":"crossref","first-page":"D699","DOI":"10.1093\/nar\/gkt1183","article-title":"MycoCosm portal: gearing up for 1000 fungal genomes","volume":"42","author":"Grigoriev","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2021041201471724600_bib147","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1016\/j.mmcr.2016.12.004","article-title":"Recurrent episodes of Candidemia due to and with acquired echinocandin resistance","volume":"14","author":"Grosset","year":"2016","journal-title":"Med Mycol Case Rep"},{"key":"2021041201471724600_bib149","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1128\/CMR.00053-10","article-title":"Histopathologic diagnosis of fungal infections in the 21st century","volume":"24","author":"Guarner","year":"2011","journal-title":"Clin Microbiol Rev"},{"key":"2021041201471724600_bib148","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1146\/annurev-pathmechdis-012418-012751","article-title":"Clinical metagenomic next-generation sequencing for pathogen detection","volume":"14","author":"Gu","year":"2019","journal-title":"Annu Rev Pathol"},{"key":"2021041201471724600_bib150","doi-asserted-by":"crossref","first-page":"3424","DOI":"10.1128\/AAC.00462-08","article-title":"Antifungal resistance of Candida glabrata vaginal isolates and development of a quantitative reverse transcription-PCR-based azole susceptibility assay","volume":"52","author":"Gygax","year":"2008","journal-title":"Antimicrob Agents Chemother"},{"key":"2021041201471724600_bib151","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1016\/j.fgb.2015.02.009","article-title":"Recognition of seven species in the Cryptococcus gattii\/Cryptococcus neoformans species complex","volume":"78","author":"Hagen","year":"2015","journal-title":"Fungal Genet Biol"},{"key":"2021041201471724600_bib152","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1111\/j.1574-695X.2012.00968.x","article-title":"Towards diagnostic guidelines for biofilm-associated infections","volume":"65","author":"Hall-Stoodley","year":"2012","journal-title":"FEMS Immunol Med Microbiol"},{"key":"2021041201471724600_bib153","doi-asserted-by":"crossref","first-page":"513","DOI":"10.1007\/s11046-017-0238-1","article-title":"A retrospective assessment of four antigen assays for the detection of invasive candidiasis among high-risk hospitalized patients","volume":"183","author":"Hartl","year":"2018","journal-title":"Mycopathologia"},{"key":"2021041201471724600_bib154","doi-asserted-by":"crossref","first-page":"1910","DOI":"10.2146\/ajhp110604","article-title":"Impact of a rapid peptide nucleic acid fluorescence in situ hybridization assay on treatment of Candida infections","volume":"69","author":"Heil","year":"2012","journal-title":"Am J Health Syst Pharm"},{"key":"2021041201471724600_bib155","doi-asserted-by":"crossref","first-page":"1158","DOI":"10.1128\/JCM.02473-12","article-title":"Comparison of (1-&gt;3)-\u03b2-D-glucan, mannan\/anti-mannan antibodies, and Cand-Tec Candida antigen as serum biomarkers for candidemia","volume":"51","author":"Held","year":"2013","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib156","doi-asserted-by":"crossref","first-page":"1451","DOI":"10.3389\/fmicb.2016.01451","article-title":"Development of a lateral flow immunoassay for the rapid diagnosis of invasive candidiasis","volume":"7","author":"He","year":"2016","journal-title":"Front Microbiol"},{"key":"2021041201471724600_bib157","doi-asserted-by":"crossref","first-page":"4566","DOI":"10.1128\/AEM.69.8.4566-4574.2003","article-title":"Rapid identification of Candida species by using nuclear magnetic resonance spectroscopy and a statistical classification strategy","volume":"69","author":"Himmelreich","year":"2003","journal-title":"Appl Environ Microbiol"},{"key":"2021041201471724600_bib159","doi-asserted-by":"crossref","first-page":"360","DOI":"10.1128\/JCM.01057-16","article-title":"Host-based peripheral blood gene expression analysis for diagnosis of infectious diseases","volume":"55","author":"Holcomb","year":"2017","journal-title":"J Clin Microbiol"},{"issue":"8401","key":"2021041201471724600_bib162","first-page":"1","article-title":"Knowledge discovery and data mining in biomedical informatics: the future is in integrative, interactive machine learning solutions","author":"Holzinger","year":"2014","journal-title":"Lect Notes Comput Sci"},{"key":"2021041201471724600_bib161","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-319-50478-0","volume-title":"Machine Learning for Health Informatics: State-of-the-Art and Future Challenges","author":"Holzinger","year":"2016"},{"key":"2021041201471724600_bib160","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1007\/978-3-662-43968-5_19","article-title":"On topological data mining","author":"Holzinger","year":"2014","journal-title":"Lect Notes Comput Sci"},{"key":"2021041201471724600_bib163","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/82_2018_122","article-title":"Transcriptome sequencing approaches to elucidate host-microbe interactions in opportunistic human fungal pathogens","volume":"8401","author":"Hovhannisyan","year":"2018","journal-title":"Curr Top Microbiol Immunol"},{"key":"2021041201471724600_bib164","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1007\/s12550-018-0313-6","article-title":"Development of a droplet digital PCR assay for population analysis of aflatoxigenic and atoxigenic Aspergillus flavus mixtures in soil","volume":"34","author":"Hua","year":"2018","journal-title":"Mycotoxin Res"},{"key":"2021041201471724600_bib165","doi-asserted-by":"crossref","first-page":"336","DOI":"10.1016\/j.mib.2004.06.003","article-title":"From commensal to pathogen: stage- and tissue-specific gene expression of Candida albicans","volume":"7","author":"Hube","year":"2004","journal-title":"Curr Opin Microbiol"},{"key":"2021041201471724600_bib166","doi-asserted-by":"crossref","first-page":"334","DOI":"10.1016\/j.tim.2013.04.002","article-title":"The emerging world of the fungal microbiome","volume":"21","author":"Huffnagle","year":"2013","journal-title":"Trends Microbiol"},{"key":"2021041201471724600_bib167","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1093\/femsre\/fuw047","article-title":"Forgotten fungi-the gut mycobiome in human health and disease","volume":"41","author":"Huseyin","year":"2017","journal-title":"FEMS Microbiol Rev"},{"key":"2021041201471724600_bib168","doi-asserted-by":"crossref","first-page":"553","DOI":"10.1038\/bjc.2016.452","article-title":"Tissue-based next generation sequencing: application in a universal healthcare system","volume":"116","author":"Hynes","year":"2017","journal-title":"Br J Cancer"},{"key":"2021041201471724600_bib158","doi-asserted-by":"crossref","first-page":"S1","DOI":"10.1016\/j.cmi.2014.10.024","article-title":"ESCMID\u2217 guideline for the diagnosis and treatment of biofilm infections 2014","volume":"21","author":"H\u00f8iby","year":"2015","journal-title":"Clin Microbiol Infect"},{"key":"2021041201471724600_bib170","doi-asserted-by":"crossref","first-page":"353","DOI":"10.1111\/j.1469-0691.2005.01103.x","article-title":"Rapid identification of Candida spp. in peritonitis patients by Raman spectroscopy","volume":"11","author":"Ibelings","year":"2005","journal-title":"Clin Microbiol Infect"},{"key":"2021041201471724600_bib169","first-page":"16","article-title":"Update on the diagnosis of invasive fungal infection","volume":"30 Suppl 1","author":"Ib\u00e1\u00f1ez-Mart\u00ednez","year":"2017","journal-title":"Rev Esp Quimioter"},{"key":"2021041201471724600_bib171","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1264\/jsme2.ME16085","article-title":"Application of locked nucleic acid (LNA) primer and PCR clamping by LNA oligonucleotide to enhance the amplification of internal transcribed spacer (ITS) regions in investigating the community structures of plant-associated fungi","volume":"31","author":"Ikenaga","year":"2016","journal-title":"Microbes Environ"},{"key":"2021041201471724600_bib172","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1016\/j.funbio.2015.04.007","article-title":"DNA barcoding of fungi causing infections in humans and animals","volume":"120","author":"Irinyi","year":"2016","journal-title":"Fungal Biol"},{"key":"2021041201471724600_bib173","doi-asserted-by":"crossref","first-page":"192","DOI":"10.1007\/s13337-018-0450-8","article-title":"Development of a rapid test for detection of foot-and-mouth disease virus specific antibodies using gold nanoparticles","volume":"29","author":"Jain","year":"2018","journal-title":"Virusdisease"},{"key":"2021041201471724600_bib174","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1186\/s40246-015-0031-5","article-title":"Clinical application of next-generation sequencing for Mendelian diseases","volume":"9","author":"Jamuar","year":"2015","journal-title":"Hum Genomics"},{"key":"2021041201471724600_bib175","doi-asserted-by":"crossref","first-page":"634","DOI":"10.1093\/ajcp\/109.5.634","article-title":"Comparison of two rapid latex agglutination tests for detection of cryptococcal capsular polysaccharide","volume":"109","author":"Jaye","year":"1998","journal-title":"Am J Clin Pathol"},{"key":"2021041201471724600_bib176","doi-asserted-by":"crossref","first-page":"219","DOI":"10.3389\/fgene.2015.00219","article-title":"From next-generation sequencing to systematic modeling of the gut microbiome","volume":"6","author":"Ji","year":"2015","journal-title":"Front Genet"},{"key":"2021041201471724600_bib177","doi-asserted-by":"crossref","first-page":"e62108","DOI":"10.1371\/journal.pone.0062108","article-title":"Rapid diagnosis of bloodstream infections with PCR followed by mass spectrometry","volume":"8","author":"Jordana-Lluch","year":"2013","journal-title":"PLoS One"},{"key":"2021041201471724600_bib178","doi-asserted-by":"crossref","first-page":"1823","DOI":"10.1128\/JCM.00367-15","article-title":"Multidrug-resistant Candida auris misidentified as Candida haemulonii: characterization by matrix-assisted laser desorption ionization-time of flight mass spectrometry and DNA sequencing and its antifungal susceptibility profile variability by Vitek 2, CLSI broth microdilution, and Etest method","volume":"53","author":"Kathuria","year":"2015","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib179","doi-asserted-by":"crossref","first-page":"D574","DOI":"10.1093\/nar\/gkv1209","article-title":"Ensembl Genomes 2016: more genomes, more complexity","volume":"44","author":"Kersey","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2021041201471724600_bib180","doi-asserted-by":"crossref","first-page":"1201","DOI":"10.1586\/eri.09.104","article-title":"PCR-based diagnosis of human fungal infections","volume":"7","author":"Khot","year":"2009","journal-title":"Expert Rev Anti Infect Ther"},{"key":"2021041201471724600_bib181","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1016\/j.tibtech.2007.07.008","article-title":"Proteomics of filamentous fungi","volume":"25","author":"Kim","year":"2007","journal-title":"Trends Biotechnol"},{"key":"2021041201471724600_bib182","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1016\/j.mimet.2006.07.011","article-title":"Development of a new real-time TaqMan PCR assay for quantitative analyses of Candida albicans resistance genes expression","volume":"68","author":"Kofla","year":"2007","journal-title":"J Microbiol Methods"},{"key":"2021041201471724600_bib183","doi-asserted-by":"crossref","first-page":"332","DOI":"10.1111\/bjd.12680","article-title":"Efficient identification of Malassezia yeasts by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)","volume":"170","author":"Kolecka","year":"2014","journal-title":"Br J Dermatol"},{"key":"2021041201471724600_bib184","doi-asserted-by":"crossref","first-page":"2491","DOI":"10.1128\/JCM.00470-13","article-title":"Identification of medically relevant species of arthroconidial yeasts by use of matrix-assisted laser desorption ionization-time of flight mass spectrometry","volume":"51","author":"Kolecka","year":"2013","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib186","article-title":"MALDI-TOF Mass Spectrometry in Microbiology","author":"Kostrzewa"},{"key":"2021041201471724600_bib185","volume-title":"MALDI-TOF Mass Spectrometry in Microbiology","author":"Kostrzewa","year":"2016"},{"key":"2021041201471724600_bib187","doi-asserted-by":"crossref","first-page":"328","DOI":"10.1097\/MD.0b013e318274cd77","article-title":"Central nervous system aspergillosis: a series of 14 cases from a general hospital and review of 123 cases from the literature","volume":"91","author":"Kourkoumpetis","year":"2012","journal-title":"Medicine (Baltimore)"},{"key":"2021041201471724600_bib188","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1038\/nrc3721","article-title":"Principles and methods of integrative genomic analyses in cancer","volume":"14","author":"Kristensen","year":"2014","journal-title":"Nat Rev Cancer"},{"key":"2021041201471724600_bib189","doi-asserted-by":"crossref","first-page":"E461","DOI":"10.3390\/genes9090461","article-title":"Evolutionary emergence of drug resistance in Candida opportunistic pathogens","volume":"9","author":"Ksiezopolska","year":"2018","journal-title":"Genes"},{"key":"2021041201471724600_bib191","doi-asserted-by":"crossref","first-page":"1445","DOI":"10.1056\/NEJMra1315399","article-title":"Invasive candidiasis","volume":"373","author":"Kullberg","year":"2015","journal-title":"N Engl J Med"},{"key":"2021041201471724600_bib192","doi-asserted-by":"crossref","first-page":"S16","DOI":"10.1186\/1471-2105-11-S6-S16","article-title":"HPIDB\u2013a unified resource for host-pathogen interactions","volume":"11 Suppl 6","author":"Kumar","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2021041201471724600_bib193","volume-title":"The Yeasts: A Taxonomic Study","author":"Kurtzman","year":"2011"},{"key":"2021041201471724600_bib194","doi-asserted-by":"crossref","first-page":"1216","DOI":"10.1128\/JCM.35.5.1216-1223.1997","article-title":"Identification of clinically important ascomycetous yeasts based on nucleotide divergence in the 5\u2019 end of the large-subunit (26S) ribosomal DNA gene","volume":"35","author":"Kurtzman","year":"1997","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib190","doi-asserted-by":"crossref","first-page":"2919","DOI":"10.1128\/JCM.00830-11","article-title":"Evaluation of commercial universal rRNA gene PCR plus sequencing tests for identification of bacteria and fungi associated with infectious endocarditis","volume":"49","author":"K\u00fchn","year":"2011","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib195","doi-asserted-by":"crossref","first-page":"683","DOI":"10.2217\/fmb.14.23","article-title":"Laboratory diagnosis of mucormycosis: current status and future perspectives","volume":"9","author":"Lackner","year":"2014","journal-title":"Future Microbiol"},{"key":"2021041201471724600_bib196","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1007\/978-1-4939-6515-1_4","article-title":"Commercial molecular tests for fungal diagnosis from a practical point of view","volume":"1508","author":"Lackner","year":"2017","journal-title":"Methods Mol Biol"},{"key":"2021041201471724600_bib197","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1016\/j.jcv.2006.10.002","article-title":"Evaluation of NucliSens EasyQ HIV-1 assay for quantification of HIV-1 subtypes prevalent in South-east Asia","volume":"38","author":"Lam","year":"2007","journal-title":"J Clin Virol"},{"key":"2021041201471724600_bib198","doi-asserted-by":"crossref","first-page":"1063","DOI":"10.1128\/JCM.01558-08","article-title":"Species-specific identification of a wide range of clinically relevant fungal pathogens by use of Luminex xMAP technology","volume":"47","author":"Landlinger","year":"2009","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib199","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1016\/j.ins.2012.12.051","article-title":"A review on evolutionary algorithms in Bayesian network learning and inference tasks","volume":"233","author":"Larra\u00f1aga","year":"2013","journal-title":"Inf Sci"},{"key":"2021041201471724600_bib200","first-page":"1061","article-title":"Multi-omics approach identifies molecular mechanisms of plant-fungus mycorrhizal interaction","volume":"6","author":"Larsen","year":"2015","journal-title":"Front Plant Sci"},{"key":"2021041201471724600_bib201","doi-asserted-by":"crossref","first-page":"25","DOI":"10.3389\/fcimb.2014.00025","article-title":"The diagnosis of infectious diseases by whole genome next generation sequencing: a new era is opening","volume":"4","author":"Lecuit","year":"2014","journal-title":"Front Cell Infect Microbiol"},{"key":"2021041201471724600_bib202","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1007\/s00122-004-1827-1","article-title":"Comparison of four flow cytometric SNP detection assays and their use in plant improvement","volume":"110","author":"Lee","year":"2004","journal-title":"Theor Appl Genet"},{"key":"2021041201471724600_bib203","doi-asserted-by":"crossref","first-page":"4943","DOI":"10.1128\/JCM.43.10.4943-4953.2005","article-title":"Development of a DNA microarray for detection and identification of fungal pathogens involved in invasive mycoses","volume":"43","author":"Leinberger","year":"2005","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib204","doi-asserted-by":"crossref","first-page":"802","DOI":"10.1128\/CVI.00035-07","article-title":"Evaluation of the IMMY ALPHA Histoplasma antigen enzyme immunoassay for diagnosis of histoplasmosis marked by antigenuria","volume":"14","author":"LeMonte","year":"2007","journal-title":"Clin Vaccine Immunol"},{"key":"2021041201471724600_bib206","doi-asserted-by":"crossref","first-page":"e41","DOI":"10.1016\/j.ijid.2011.09.016","article-title":"Ten-year experience with fungal peritonitis in peritoneal dialysis patients: antifungal susceptibility patterns in a North-American center","volume":"16","author":"Levallois","year":"2012","journal-title":"Int J Infect Dis"},{"key":"2021041201471724600_bib205","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1186\/s13054-016-1324-3","article-title":"Contribution of Candida biomarkers and DNA detection for the diagnosis of invasive candidiasis in ICU patients with severe abdominal conditions","volume":"20","author":"Le\u00f3n","year":"2016","journal-title":"Crit Care"},{"key":"2021041201471724600_bib207","doi-asserted-by":"crossref","first-page":"473","DOI":"10.1093\/bib\/bbq015","article-title":"A survey of sequence alignment algorithms for next-generation sequencing","volume":"11","author":"Li","year":"2010","journal-title":"Brief Bioinform"},{"key":"2021041201471724600_bib208","doi-asserted-by":"crossref","first-page":"1679","DOI":"10.1093\/cid\/cis460","article-title":"Executive summary: 2012 Infectious Diseases Society of America clinical practice guideline for the diagnosis and treatment of Diabetic foot Infectionsa","volume":"54","author":"Lipsky","year":"2012","journal-title":"Clin Infect Dis"},{"key":"2021041201471724600_bib209","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1111\/myc.12432","article-title":"1,3-\u00df-D-glucan concentrations in blood products predict false positive post-transfusion results","volume":"59","author":"Liss","year":"2016","journal-title":"Mycoses"},{"key":"2021041201471724600_bib210","doi-asserted-by":"crossref","first-page":"3435","DOI":"10.1128\/JCM.01283-12","article-title":"Species identification and antifungal susceptibility testing of Candida bloodstream isolates from population-based surveillance studies in two U.S. cities from 2008 to 2011","volume":"50","author":"Lockhart","year":"2012","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib211","doi-asserted-by":"crossref","first-page":"1405","DOI":"10.1586\/14737159.2015.1088385","article-title":"The main challenges that remain in applying high-throughput sequencing to clinical diagnostics","volume":"15","author":"Loeffelholz","year":"2015","journal-title":"Expert Rev Mol Diagn"},{"key":"2021041201471724600_bib212","doi-asserted-by":"crossref","first-page":"631","DOI":"10.1093\/clinchem\/46.5.631","article-title":"Rapid detection of point mutations by fluorescence resonance energy transfer and probe melting curves in Candida species","volume":"46","author":"Loeffler","year":"2000","journal-title":"Clin Chem"},{"key":"2021041201471724600_bib213","doi-asserted-by":"crossref","first-page":"S31","DOI":"10.1086\/344658","article-title":"Antifungal drug resistance","volume":"36","author":"Loeffler","year":"2003","journal-title":"Clin Infect Dis"},{"key":"2021041201471724600_bib214","doi-asserted-by":"crossref","first-page":"848","DOI":"10.3109\/13693786.2011.582889","article-title":"Performance of the new Platelia Candida Plus assays for the diagnosis of invasive Candida infection in patients undergoing myeloablative therapy","volume":"49","author":"Lunel","year":"2011","journal-title":"Med Mycol"},{"key":"2021041201471724600_bib215","doi-asserted-by":"crossref","first-page":"2023","DOI":"10.3390\/cancers7040874","article-title":"Next-generation sequencing in clinical molecular diagnostics of cancer: advantages and challenges","volume":"7","author":"Luthra","year":"2015","journal-title":"Cancers"},{"key":"2021041201471724600_bib216","doi-asserted-by":"crossref","first-page":"1281","DOI":"10.1093\/molbev\/mst042","article-title":"Comparative genome analysis and gene finding in Candida species using CGOB","volume":"30","author":"Maguire","year":"2013","journal-title":"Mol Biol Evol"},{"key":"2021041201471724600_bib217","doi-asserted-by":"crossref","first-page":"2603","DOI":"10.1099\/mic.0.028712-0","article-title":"Detection and identification of specific bacteria in wound biofilms using peptide nucleic acid fluorescent in situ hybridization (PNA FISH)","volume":"155","author":"Malic","year":"2009","journal-title":"Microbiology"},{"key":"2021041201471724600_bib218","doi-asserted-by":"crossref","first-page":"91","DOI":"10.2353\/jmoldx.2010.090085","article-title":"High-throughput identification and quantification of Candida species using high resolution derivative melt analysis of panfungal amplicons","volume":"12","author":"Mandviwala","year":"2010","journal-title":"J Mol Diagn"},{"key":"2021041201471724600_bib219","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1016\/S0167-7012(02)00127-6","article-title":"Identification of medically relevant microorganisms by vibrational spectroscopy","volume":"51","author":"Maquelin","year":"2002","journal-title":"J Microbiol Methods"},{"key":"2021041201471724600_bib220","doi-asserted-by":"crossref","first-page":"4627","DOI":"10.1002\/pmic.200900152","article-title":"MALDI-TOF MS-based drug susceptibility testing of pathogens: the example of Candida albicans and fluconazole","volume":"9","author":"Marinach","year":"2009","journal-title":"Proteomics"},{"key":"2021041201471724600_bib221","doi-asserted-by":"crossref","first-page":"2912","DOI":"10.1128\/JCM.00389-09","article-title":"Matrix-assisted laser desorption ionization-time of flight mass spectrometry for fast and reliable identification of clinical yeast isolates","volume":"47","author":"Marklein","year":"2009","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib222","doi-asserted-by":"crossref","first-page":"138","DOI":"10.1128\/JCM.44.1.138-142.2006","article-title":"Development and evaluation of a rapid latex agglutination test using a monoclonal antibody to identify Candida dubliniensis colonies","volume":"44","author":"Marot-Leblond","year":"2006","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib223","doi-asserted-by":"crossref","first-page":"25","DOI":"10.4103\/0255-0857.19890","article-title":"Detection of biofilm formation among the clinical isolates of Staphylococci: an evaluation of three different screening methods","volume":"24","author":"Mathur","year":"2006","journal-title":"Indian J Med Microbiol"},{"key":"2021041201471724600_bib225","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1080\/14737159.2018.1420476","article-title":"Profile of GenMark's ePlex\u00ae blood culture identification fungal pathogen panel","volume":"18","author":"Maubon","year":"2018","journal-title":"Expert Rev Mol Diagn"},{"key":"2021041201471724600_bib226","doi-asserted-by":"crossref","first-page":"435","DOI":"10.1016\/j.ccm.2017.04.006","article-title":"Clinical manifestations and treatment of blastomycosis","volume":"38","author":"McBride","year":"2017","journal-title":"Clin Chest Med"},{"key":"2021041201471724600_bib227","doi-asserted-by":"publisher","first-page":"1637","DOI":"10.1093\/ofid\/ofw172.1337","article-title":"Echinocandin resistance in Candida glabrata bloodstream infection 2009\u20132015 at a single institution","volume":"3","author":"Mccarty","year":"2016","journal-title":"Open Forum Infect Dis"},{"key":"2021041201471724600_bib228","doi-asserted-by":"crossref","first-page":"619","DOI":"10.1099\/jmm.0.000277","article-title":"Performance of the FilmArray\u00ae blood culture identification panel utilized by non-expert staff compared with conventional microbial identification and antimicrobial resistance gene detection from positive blood cultures","volume":"65","author":"McCoy","year":"2016","journal-title":"J Med Microbiol"},{"key":"2021041201471724600_bib229","doi-asserted-by":"crossref","first-page":"1948","DOI":"10.1128\/JCM.00057-13","article-title":"Evaluation of the NucliSENS EasyQ KPC assay for detection of Klebsiella pneumoniae carbapenemase-producing Enterobacteriaceae","volume":"51","author":"McEwan","year":"2013","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib230","doi-asserted-by":"crossref","first-page":"3732","DOI":"10.1128\/JCM.00921-09","article-title":"High interlaboratory reproducibility of matrix-assisted laser desorption ionization-time of flight mass spectrometry-based species identification of nonfermenting bacteria","volume":"47","author":"Mellmann","year":"2009","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib231","doi-asserted-by":"crossref","first-page":"224","DOI":"10.2174\/1874285801711010224","article-title":"Paracoccidioidomycosis: current perspectives from Brazil","volume":"11","author":"Mendes","year":"2017","journal-title":"Open Microbiol J"},{"key":"2021041201471724600_bib232","doi-asserted-by":"crossref","first-page":"e0158186","DOI":"10.1371\/journal.pone.0158186","article-title":"The IRIDICA BAC BSI Assay: rapid, sensitive and culture-independent identification of bacteria and Candida in blood","volume":"11","author":"Metzgar","year":"2016","journal-title":"PLoS One"},{"key":"2021041201471724600_bib233","doi-asserted-by":"crossref","first-page":"R222","DOI":"10.1186\/cc9365","article-title":"The use of mannan antigen and anti-mannan antibodies in the diagnosis of invasive candidiasis: recommendations from the Third European Conference on Infections in Leukemia","volume":"14","author":"Mikulska","year":"2010","journal-title":"Crit Care"},{"key":"2021041201471724600_bib234","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1016\/j.ygeno.2010.03.001","article-title":"Assembly algorithms for next-generation sequencing data","volume":"95","author":"Miller","year":"2010","journal-title":"Genomics"},{"key":"2021041201471724600_bib235","doi-asserted-by":"crossref","first-page":"2586","DOI":"10.1128\/JCM.43.6.2586-2589.2005","article-title":"Flow cytometry susceptibility testing for the antifungal caspofungin","volume":"43","author":"Mitchell","year":"2005","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib236","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1002\/yea.3242","article-title":"Hybridization and emergence of virulence in opportunistic human yeast pathogens","volume":"35","author":"Mix\u00e3o","year":"2018","journal-title":"Yeast"},{"key":"2021041201471724600_bib237","doi-asserted-by":"crossref","first-page":"334","DOI":"10.1002\/jcla.1860090509","article-title":"(1\u2013&gt;3)-beta-D-glucan in culture fluid of fungi activates factor G, a limulus coagulation factor","volume":"9","author":"Miyazaki","year":"1995","journal-title":"J Clin Lab Anal"},{"key":"2021041201471724600_bib238","doi-asserted-by":"crossref","first-page":"3115","DOI":"10.1128\/JCM.33.12.3115-3118.1995","article-title":"Plasma (1\u2013&gt;3)-beta-D-glucan and fungal antigenemia in patients with candidemia, aspergillosis, and cryptococcosis","volume":"33","author":"Miyazaki","year":"1995","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib239","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1081\/MC-200045819","article-title":"Latex immunoagglutination assays","volume":"45","author":"Molina-Bol\u00edvar","year":"2005","journal-title":"J Macromol Sci Part C Polymer Rev"},{"key":"2021041201471724600_bib240","doi-asserted-by":"crossref","first-page":"2795","DOI":"10.1099\/mic.0.027441-0","article-title":"Genomic DNA microarray comparison of gene expression patterns in Paracoccidioides brasiliensis mycelia and yeasts in vitro","volume":"155","author":"Monteiro","year":"2009","journal-title":"Microbiology"},{"key":"2021041201471724600_bib241","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1007\/978-1-4939-1459-3_18","article-title":"In situ hybridization for fungal ribosomal RNA sequences in paraffin-embedded tissues using biotin-labeled locked nucleic acid probes","volume":"1211","author":"Montone","year":"2014","journal-title":"Methods Mol Biol"},{"key":"2021041201471724600_bib242","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1016\/j.jbbm.2003.12.005","article-title":"Real-time turbidimetry of LAMP reaction for quantifying template DNA","volume":"59","author":"Mori","year":"2004","journal-title":"J Biochem Biophys Methods"},{"key":"2021041201471724600_bib243","doi-asserted-by":"crossref","first-page":"150","DOI":"10.1006\/bbrc.2001.5921","article-title":"Detection of loop-mediated isothermal amplification reaction by turbidity derived from magnesium pyrophosphate formation","volume":"289","author":"Mori","year":"2001","journal-title":"Biochem Biophys Res Commun"},{"key":"2021041201471724600_bib244","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1016\/j.chom.2010.08.002","article-title":"A biphasic innate immune MAPK response discriminates between the yeast and hyphal forms of Candida albicans in epithelial cells","volume":"8","author":"Moyes","year":"2010","journal-title":"Cell Host Microbe"},{"key":"2021041201471724600_bib245","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1038\/nature17625","article-title":"Candidalysin is a fungal peptide toxin critical for mucosal infection","volume":"532","author":"Moyes","year":"2016","journal-title":"Nature"},{"key":"2021041201471724600_bib246","first-page":"263","article-title":"Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction","volume":"51 Pt 1","author":"Mullis","year":"1986","journal-title":"Biotechnology"},{"key":"2021041201471724600_bib247","doi-asserted-by":"crossref","first-page":"1309","DOI":"10.1007\/s10096-016-2666-0","article-title":"Mammary candidiasis: molecular-based detection of Candida species in human milk samples","volume":"35","author":"Mutschlechner","year":"2016","journal-title":"Eur J Clin Microbiol Infect Dis"},{"key":"2021041201471724600_bib248","doi-asserted-by":"crossref","first-page":"775","DOI":"10.1146\/annurev-biochem-063011-092449","article-title":"Nanobodies: natural single-domain antibodies","volume":"82","author":"Muyldermans","year":"2013","journal-title":"Annu Rev Biochem"},{"key":"2021041201471724600_bib249","doi-asserted-by":"crossref","first-page":"892","DOI":"10.1093\/cid\/ciu959","article-title":"T2 magnetic resonance assay for the rapid diagnosis of candidemia in whole blood: a clinical trial","volume":"60","author":"Mylonakis","year":"2015","journal-title":"Clin Infect Dis"},{"key":"2021041201471724600_bib250","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1006\/mcpr.2002.0415","article-title":"Accelerated reaction by loop-mediated isothermal amplification using loop primers","volume":"16","author":"Nagamine","year":"2002","journal-title":"Mol Cell Probes"},{"key":"2021041201471724600_bib251","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1016\/j.cca.2014.10.017","article-title":"Real-time PCR detection chemistry","volume":"439","author":"Navarro","year":"2015","journal-title":"Clin Chim Acta"},{"key":"2021041201471724600_bib252","doi-asserted-by":"crossref","first-page":"D8","DOI":"10.1093\/nar\/gkx1095","article-title":"Database resources of the National Center for Biotechnology Information","volume":"46","author":"NCBI Resource Coordinators","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2021041201471724600_bib253","doi-asserted-by":"crossref","first-page":"182ra54","DOI":"10.1126\/scitranslmed.3005377","article-title":"T2 magnetic resonance enables nanoparticle-mediated rapid detection of candidemia in whole blood","volume":"5","author":"Neely","year":"2013","journal-title":"Sci Transl Med"},{"key":"2021041201471724600_bib254","doi-asserted-by":"crossref","first-page":"e0116940","DOI":"10.1371\/journal.pone.0116940","article-title":"Rapid identification of medically important Candida isolates using high resolution melting analysis","volume":"10","author":"Nemcova","year":"2015","journal-title":"PLoS One"},{"key":"2021041201471724600_bib255","doi-asserted-by":"crossref","first-page":"fov081","DOI":"10.1093\/femsyr\/fov081","article-title":"Candida albicans commensalism in the gastrointestinal tract","volume":"15","author":"Neville","year":"2015","journal-title":"FEMS Yeast Res"},{"key":"2021041201471724600_bib256","doi-asserted-by":"crossref","first-page":"89","DOI":"10.3389\/fmicb.2015.00089","article-title":"The lung mycobiome: an emerging field of the human respiratory microbiome","volume":"6","author":"Nguyen","year":"2015","journal-title":"Front Microbiol"},{"key":"2021041201471724600_bib257","doi-asserted-by":"crossref","first-page":"1497","DOI":"10.1126\/science.1962210","article-title":"Sequence-selective recognition of DNA by strand displacement with a thymine-substituted polyamide","volume":"254","author":"Nielsen","year":"1991","journal-title":"Science"},{"key":"2021041201471724600_bib258","doi-asserted-by":"crossref","first-page":"e0195569","DOI":"10.1371\/journal.pone.0195569","article-title":"Accuracy of rapid diagnosis of Talaromyces marneffei: A systematic review and meta-analysis","volume":"13","author":"Ning","year":"2018","journal-title":"PLoS One"},{"key":"2021041201471724600_bib259","doi-asserted-by":"crossref","first-page":"541","DOI":"10.2334\/josnusd.16-0717","article-title":"Rapid detection of Candida albicans in oral exfoliative cytology samples by loop-mediated isothermal amplification","volume":"59","author":"Noguchi","year":"2017","journal-title":"J Oral Sci"},{"key":"2021041201471724600_bib260","doi-asserted-by":"crossref","first-page":"434","DOI":"10.1016\/S0968-0004(98)01302-4","article-title":"Contrasting lifestyles of rolling-circle phages and plasmids","volume":"23","author":"Novick","year":"1998","journal-title":"Trends Biochem Sci"},{"key":"2021041201471724600_bib261","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1111\/myc.12444","article-title":"Comparison of biotyping methods as alternative identification tools to molecular typing of pathogenic Cryptococcus species in sub-Saharan Africa","volume":"59","author":"Nyazika","year":"2016","journal-title":"Mycoses"},{"key":"2021041201471724600_bib262","doi-asserted-by":"crossref","first-page":"1216","DOI":"10.1056\/NEJMp1606181","article-title":"Predicting the future - big data, machine learning, and clinical medicine","volume":"375","author":"Obermeyer","year":"2016","journal-title":"N Engl J Med"},{"key":"2021041201471724600_bib263","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1128\/JCM.05267-11","article-title":"Diagnostic accuracy of serum 1,3-\u03b2-D-glucan for pneumocystis jiroveci pneumonia, invasive candidiasis, and invasive aspergillosis: systematic review and meta-analysis","volume":"50","author":"Onishi","year":"2012","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib264","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1186\/cc12718","article-title":"Limitation of (1\u21923)-\u03b2-D-glucan monitoring in major elective surgery involving cardiopulmonary bypass","volume":"17","author":"Otto","year":"2013","journal-title":"Crit Care"},{"key":"2021041201471724600_bib265","doi-asserted-by":"publisher","DOI":"10.1111\/tid.12664","article-title":"Pseudozyma and other non-Candida opportunistic yeast bloodstream infections in a large stem cell transplant center","volume":"19","author":"Pande","year":"2017","journal-title":"Transpl Infect Dis"},{"key":"2021041201471724600_bib266","doi-asserted-by":"crossref","first-page":"e1003550","DOI":"10.1371\/journal.ppat.1003550","article-title":"Emerging and emerged pathogenic Candida species: beyond the Candida albicans paradigm","volume":"9","author":"Papon","year":"2013","journal-title":"PLoS Pathog"},{"key":"2021041201471724600_bib267","doi-asserted-by":"crossref","first-page":"e1","DOI":"10.1093\/cid\/civ933","article-title":"Clinical practice guideline for the management of candidiasis: 2016 update by the Infectious Diseases Society of America","volume":"62","author":"Pappas","year":"2016","journal-title":"Clin Infect Dis"},{"key":"2021041201471724600_bib268","doi-asserted-by":"crossref","first-page":"647","DOI":"10.1111\/j.1524-475X.2012.00836.x","article-title":"A review of the scientific evidence for biofilms in wounds","volume":"20","author":"Percival","year":"2012","journal-title":"Wound Repair Regen"},{"key":"2021041201471724600_bib270","doi-asserted-by":"crossref","first-page":"1","DOI":"10.3109\/10408410903241444","article-title":"Epidemiology of invasive mycoses in North America","volume":"36","author":"Pfaller","year":"2010","journal-title":"Crit Rev Microbiol"},{"key":"2021041201471724600_bib271","doi-asserted-by":"crossref","first-page":"103","DOI":"10.2217\/fmb.15.111","article-title":"T2MR and T2Candida: novel technology for the rapid diagnosis of candidemia and invasive candidiasis","volume":"11","author":"Pfaller","year":"2016","journal-title":"Future Microbiol"},{"key":"2021041201471724600_bib269","doi-asserted-by":"crossref","first-page":"217","DOI":"10.3390\/jof1020217","article-title":"Application of culture-independent rapid diagnostic tests in the management of invasive candidiasis and cryptococcosis","volume":"1","author":"Pfaller","year":"2015","journal-title":"J Fungi (Basel)"},{"key":"2021041201471724600_bib272","doi-asserted-by":"crossref","first-page":"790","DOI":"10.1128\/JCM.03378-13","article-title":"Development of a Luminex-based multiplex assay for detection of mutations conferring resistance to Echinocandins in Candida glabrata","volume":"52","author":"Pham","year":"2014","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib273","doi-asserted-by":"crossref","first-page":"2950","DOI":"10.1128\/JCM.01010-13","article-title":"Identification of Salmonella enterica serovar Typhi genotypes by use of rapid multiplex ligation-dependent probe amplification","volume":"51","author":"Pham\u00a0Thanh","year":"2013","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib274","doi-asserted-by":"crossref","first-page":"629","DOI":"10.1007\/s11739-017-1627-7","article-title":"Usefulness of procalcitonin in differentiating Candida and bacterial blood stream infections in critically ill septic patients outside the intensive care unit","volume":"12","author":"Pieralli","year":"2017","journal-title":"Intern Emerg Med"},{"key":"2021041201471724600_bib275","doi-asserted-by":"crossref","first-page":"1494","DOI":"10.1038\/nprot.2008.141","article-title":"A simple and reproducible 96-well plate-based method for the formation of fungal biofilms and its application to antifungal susceptibility testing","volume":"3","author":"Pierce","year":"2008","journal-title":"Nat Protoc"},{"key":"2021041201471724600_bib276","doi-asserted-by":"crossref","first-page":"4674","DOI":"10.1128\/JCM.43.9.4674-4679.2005","article-title":"Comparison of two probes for testing susceptibilities of pathogenic yeasts to voriconazole, itraconazole, and caspofungin by flow cytometry","volume":"43","author":"Pina-Vaz","year":"2005","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib277","doi-asserted-by":"crossref","first-page":"947","DOI":"10.2217\/fmb.14.55","article-title":"The future of fungal susceptibility testing","volume":"9","author":"Posteraro","year":"2014","journal-title":"Future Microbiol"},{"key":"2021041201471724600_bib278","doi-asserted-by":"crossref","first-page":"2472","DOI":"10.1128\/JCM.00737-12","article-title":"Matrix-assisted laser desorption ionization-time of flight mass spectrometry-based method for discrimination between molecular types of Cryptococcus neoformans and Cryptococcus gattii","volume":"50","author":"Posteraro","year":"2012","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib279","doi-asserted-by":"crossref","first-page":"423","DOI":"10.1007\/978-1-4939-6515-1_24","article-title":"Molecular detection of resistance to azole components","volume":"1508","author":"Posteraro","year":"2017","journal-title":"Methods Mol Biol"},{"key":"2021041201471724600_bib280","doi-asserted-by":"crossref","first-page":"178","DOI":"10.2174\/1871526517666170531114335","article-title":"Expression of major efflux pumps in fluconazole-resistant Candida albicans","volume":"17","author":"Pourakbari","year":"2017","journal-title":"Infect Disord Drug Targets"},{"key":"2021041201471724600_bib281","doi-asserted-by":"crossref","first-page":"277.e1","DOI":"10.1016\/j.cmi.2015.10.022","article-title":"Evidence of genotypic diversity among Candida auris isolates by multilocus sequence typing, matrix-assisted laser desorption ionization time-of-flight mass spectrometry and amplified fragment length polymorphism","volume":"22","author":"Prakash","year":"2016","journal-title":"Clin Microbiol Infect"},{"key":"2021041201471724600_bib282","doi-asserted-by":"crossref","first-page":"1069","DOI":"10.1093\/gbe\/evu082","article-title":"Genome comparison of Candida orthopsilosis clinical strains reveals the existence of hybrids between two distinct subspecies","volume":"6","author":"Pryszcz","year":"2014","journal-title":"Genome Biol Evol"},{"key":"2021041201471724600_bib284","doi-asserted-by":"crossref","first-page":"439","DOI":"10.1007\/s00216-008-2288-1","article-title":"MALDI-TOF mass signatures for differentiation of yeast species, strain grouping and monitoring of morphogenesis markers","volume":"392","author":"Qian","year":"2008","journal-title":"Anal Bioanal Chem"},{"key":"2021041201471724600_bib285","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1016\/j.bios.2018.03.065","article-title":"Isothermal exponential amplification techniques: From basic principles to applications in electrochemical biosensors","volume":"110","author":"Qi","year":"2018","journal-title":"Biosens Bioelectron"},{"key":"2021041201471724600_bib286","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nature08821","article-title":"A human gut microbial gene catalogue established by metagenomic sequencing","volume":"464","author":"Qin","year":"2010","journal-title":"Nature"},{"key":"2021041201471724600_bib287","doi-asserted-by":"crossref","first-page":"1263","DOI":"10.1128\/JCM.35.5.1263-1265.1997","article-title":"Evaluation of bichro-latex albicans, a new method for rapid identification of Candida albicans","volume":"35","author":"Quindos","year":"1997","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib288","doi-asserted-by":"publisher","DOI":"10.1002\/biot.201700449","article-title":"An overview of the evolution of infrared spectroscopy applied to bacterial typing","volume":"13","author":"Quintelas","year":"2018","journal-title":"Biotechnol J"},{"key":"2021041201471724600_bib289","doi-asserted-by":"crossref","first-page":"654","DOI":"10.1093\/mmy\/myw012","article-title":"Evaluation of PNA FISH\u00ae Yeast Traffic Light in identification of Candida species from blood and non-blood culture specimens","volume":"54","author":"Radic","year":"2016","journal-title":"Med Mycol"},{"key":"2021041201471724600_bib290","doi-asserted-by":"crossref","first-page":"915","DOI":"10.3389\/fmicb.2016.00915","article-title":"A prospective surveillance study of candidaemia: epidemiology, risk factors, antifungal treatment and outcome in hospitalized patients","volume":"7","author":"Rajendran","year":"2016","journal-title":"Front Microbiol"},{"key":"2021041201471724600_bib291","doi-asserted-by":"crossref","first-page":"979","DOI":"10.1111\/j.1567-1364.2006.00117.x","article-title":"Candida biofilms on implanted biomaterials: a clinically significant problem","volume":"6","author":"Ramage","year":"2006","journal-title":"FEMS Yeast Res"},{"key":"2021041201471724600_bib292","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1016\/j.ijantimicag.2013.10.023","article-title":"Strength in numbers: antifungal strategies against fungal biofilms","volume":"43","author":"Ramage","year":"2014","journal-title":"Int J Antimicrob Agents"},{"key":"2021041201471724600_bib293","doi-asserted-by":"crossref","first-page":"2475","DOI":"10.1128\/AAC.45.9.2475-2479.2001","article-title":"Standardized method for in vitro antifungal susceptibility testing of Candida albicans biofilms","volume":"45","author":"Ramage","year":"2001","journal-title":"Antimicrob Agents Chemother"},{"key":"2021041201471724600_bib295","doi-asserted-by":"publisher","DOI":"10.1136\/bmjopen-2012-002175","article-title":"A pilot study of rapid whole-genome sequencing for the investigation of a Legionella outbreak","volume":"3","author":"Reuter","year":"2013","journal-title":"BMJ Open"},{"key":"2021041201471724600_bib296","doi-asserted-by":"crossref","first-page":"643","DOI":"10.1128\/CMR.14.4.643-658.2001","article-title":"Antifungal susceptibility testing: practical aspects and current challenges","volume":"14","author":"Rex","year":"2001","journal-title":"Clin Microbiol Rev"},{"key":"2021041201471724600_bib297","doi-asserted-by":"crossref","first-page":"2195","DOI":"10.1128\/JCM.00622-13","article-title":"Development and evaluation of a next-generation digital PCR diagnostic assay for ocular Chlamydia trachomatis infections","volume":"51","author":"Roberts","year":"2013","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib298","doi-asserted-by":"crossref","first-page":"371","DOI":"10.5598\/imafungus.2013.04.02.16","article-title":"MycoBank gearing up for new horizons","volume":"4","author":"Robert","year":"2013","journal-title":"IMA Fungus"},{"key":"2021041201471724600_bib299","first-page":"1715985","article-title":"Embracing integrative multiomics approaches","volume":"2016","author":"Rotroff","year":"2016","journal-title":"Int J Genomics Proteomics"},{"key":"2021041201471724600_bib300","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1146\/annurev-genom-090413-025552","article-title":"Translating genomics for precision cancer medicine","volume":"15","author":"Roychowdhury","year":"2014","journal-title":"Annu Rev Genomics Hum Genet"},{"key":"2021041201471724600_bib301","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1016\/j.jmoldx.2017.11.003","article-title":"Standards and guidelines for validating next-generation sequencing bioinformatics pipelines","volume":"20","author":"Roy","year":"2018","journal-title":"J Mol Diagn"},{"key":"2021041201471724600_bib302","doi-asserted-by":"crossref","first-page":"249","DOI":"10.3354\/dao02420","article-title":"Fast quantitative PCR, locked nucleic acid probes and reduced volume reactions are effective tools for detecting Batrachochytrium dendrobatidis DNA","volume":"97","author":"Ruthig","year":"2012","journal-title":"Dis Aquat Organ"},{"key":"2021041201471724600_bib303","doi-asserted-by":"crossref","first-page":"687","DOI":"10.1128\/JCM.01679-15","article-title":"Evaluation of the FilmArray Blood Culture Identification Panel: results of a multicenter controlled trial","volume":"54","author":"Salimnia","year":"2016","journal-title":"J Clin Microbiol"},{"issue":"4","key":"2021041201471724600_bib304","doi-asserted-by":"crossref","first-page":"1174","DOI":"10.1128\/AAC.45.4.1174-1183.2001","article-title":"Role of ATP-binding-cassette transporter genes in high-frequency acquisition of resistance to azole antifungals in Candida glabrata","volume":"45","author":"Sanglard","year":"2001","journal-title":"Antimicrob Agents Chemother"},{"key":"2021041201471724600_bib305","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1126\/science.1439758","article-title":"Immuno-PCR: very sensitive antigen detection by means of specific antibody-DNA conjugates","volume":"258","author":"Sano","year":"1992","journal-title":"Science"},{"key":"2021041201471724600_bib306","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1111\/j.1365-2672.2009.04448.x","article-title":"Filamentous fungal characterizations by matrix-assisted laser desorption\/ionization time-of-flight mass spectrometry","volume":"108","author":"Santos","year":"2010","journal-title":"J Appl Microbiol"},{"key":"2021041201471724600_bib307","doi-asserted-by":"crossref","first-page":"736","DOI":"10.1093\/mmy\/myv046","article-title":"Detection of triazole resistance among Candida species by matrix-assisted laser desorption\/ionization-time of flight mass spectrometry (MALDI-TOF MS)","volume":"53","author":"Saracli","year":"2015","journal-title":"Med Mycol"},{"key":"2021041201471724600_bib308","doi-asserted-by":"crossref","first-page":"2357","DOI":"10.1128\/JCM.02185-09","article-title":"Simple PCR-based DNA microarray system to identify human pathogenic fungi in skin","volume":"48","author":"Sato","year":"2010","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib309","doi-asserted-by":"crossref","first-page":"1575","DOI":"10.1128\/AAC.01799-13","article-title":"Phylogenetic relationships matter: antifungal susceptibility among clinically relevant yeasts","volume":"58","author":"Schmalreck","year":"2014","journal-title":"Antimicrob Agents Chemother"},{"key":"2021041201471724600_bib310","doi-asserted-by":"crossref","first-page":"567","DOI":"10.1016\/j.jprot.2008.11.010","article-title":"The UniProtKB\/Swiss-Prot knowledgebase and its Plant Proteome Annotation Program","volume":"72","author":"Schneider","year":"2009","journal-title":"J Proteomics"},{"key":"2021041201471724600_bib311","doi-asserted-by":"crossref","first-page":"6241","DOI":"10.1073\/pnas.1117018109","article-title":"Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi","volume":"109","author":"Schoch","year":"2012","journal-title":"Proc Natl Acad Sci USA"},{"key":"2021041201471724600_bib312","doi-asserted-by":"crossref","first-page":"e57","DOI":"10.1093\/nar\/gnf056","article-title":"Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification","volume":"30","author":"Schouten","year":"2002","journal-title":"Nucleic Acids Res"},{"key":"2021041201471724600_bib313","doi-asserted-by":"crossref","first-page":"1014","DOI":"10.1111\/j.1365-2672.2012.05384.x","article-title":"PCR inhibitors - occurrence, properties and removal","volume":"113","author":"Schrader","year":"2012","journal-title":"J Appl Microbiol"},{"key":"2021041201471724600_bib314","doi-asserted-by":"crossref","first-page":"e1006404","DOI":"10.1371\/journal.pgen.1006404","article-title":"Multiple origins of the pathogenic yeast Candida orthopsilosis by separate hybridizations between two parental species","volume":"12","author":"Schr\u00f6der","year":"2016","journal-title":"PLoS Genet"},{"key":"2021041201471724600_bib315","doi-asserted-by":"crossref","first-page":"2145","DOI":"10.1007\/s10096-018-3351-2","article-title":"Evaluation of the Bruker\u00ae MBT Sepsityper IVD module for the identification of polymicrobial blood cultures with MALDI-TOF MS","volume":"37","author":"Scohy","year":"2018","journal-title":"Eur J Clin Microbiol Infect Dis"},{"key":"2021041201471724600_bib316","volume-title":"Allplex\u2122 STI\/BV Panel Assays","author":"Seegene","year":"2019"},{"key":"2021041201471724600_bib317","doi-asserted-by":"crossref","first-page":"241","DOI":"10.2217\/fmb-2017-0172","article-title":"Emerging mechanisms of antimicrobial resistance in bacteria and fungi: advances in the era of genomics","volume":"13","author":"Sekyere","year":"2018","journal-title":"Future Microbiol"},{"key":"2021041201471724600_bib318","doi-asserted-by":"crossref","first-page":"1733","DOI":"10.2217\/fmb.10.127","article-title":"MALDI-TOF-mass spectrometry applications in clinical microbiology","volume":"5","author":"Seng","year":"2010","journal-title":"Future Microbiol"},{"key":"2021041201471724600_bib319","doi-asserted-by":"crossref","first-page":"2099","DOI":"10.1128\/JCM.32.9.2099-2102.1994","article-title":"Comparison of broth macrodilution, broth microdilution, and E test antifungal susceptibility tests for fluconazole","volume":"32","author":"Sewell","year":"1994","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib320","first-page":"DC04","article-title":"Identification of HIV mutation as diagnostic biomarker through next generation sequencing","volume":"10","author":"Shaw","year":"2016","journal-title":"J Clin Diagn Res"},{"key":"2021041201471724600_bib321","doi-asserted-by":"crossref","first-page":"1314","DOI":"10.1039\/C6LC00249H","article-title":"Droplet-based microfluidics in drug discovery, transcriptomics and high-throughput molecular genetics","volume":"16","author":"Shembekar","year":"2016","journal-title":"Lab Chip"},{"key":"2021041201471724600_bib322","doi-asserted-by":"crossref","first-page":"1396","DOI":"10.1128\/JCM.03332-12","article-title":"Outbreak investigation using high-throughput genome sequencing within a diagnostic microbiology laboratory","volume":"51","author":"Sherry","year":"2013","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib323","doi-asserted-by":"crossref","first-page":"681","DOI":"10.3109\/13693780802549594","article-title":"Biofilms of non-Candida albicans Candida species: quantification, structure and matrix composition","volume":"47","author":"Silva","year":"2009","journal-title":"Med Mycol"},{"key":"2021041201471724600_bib324","doi-asserted-by":"crossref","first-page":"464","DOI":"10.1016\/j.ijantimicag.2011.11.017","article-title":"Invasive fungal infections in patients with cancer in the Intensive Care Unit","volume":"39","author":"Sipsas","year":"2012","journal-title":"Int J Antimicrob Agents"},{"key":"2021041201471724600_bib325","doi-asserted-by":"crossref","first-page":"D592","DOI":"10.1093\/nar\/gkw924","article-title":"The Candida Genome Database (CGD): incorporation of Assembly 22, systematic identifiers and visualization of high throughput sequencing data","volume":"45","author":"Skrzypek","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2021041201471724600_bib326","doi-asserted-by":"crossref","first-page":"715","DOI":"10.5021\/ad.2015.27.6.715","article-title":"Antifungal susceptibility testing with Etest for Candida Species isolated from patients with oral candidiasis","volume":"27","author":"Song","year":"2015","journal-title":"Ann Dermatol"},{"key":"2021041201471724600_bib327","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1016\/j.diagmicrobio.2014.11.004","article-title":"Implementation and performance of the BioFire FilmArray\u00ae Blood Culture Identification panel with antimicrobial treatment recommendations for bloodstream infections at a midwestern academic tertiary hospital","volume":"81","author":"Southern","year":"2015","journal-title":"Diagn Microbiol Infect Dis"},{"key":"2021041201471724600_bib328","doi-asserted-by":"crossref","first-page":"3743","DOI":"10.1128\/JCM.00942-07","article-title":"DNA microarray-based detection and identification of fungal pathogens in clinical samples from neutropenic patients","volume":"45","author":"Spiess","year":"2007","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib329","doi-asserted-by":"crossref","first-page":"4258","DOI":"10.1128\/AEM.66.10.4258-4265.2000","article-title":"A bead-based method for multiplexed identification and quantitation of DNA sequences using flow cytometry","volume":"66","author":"Spiro","year":"2000","journal-title":"Appl Environ Microbiol"},{"key":"2021041201471724600_bib330","doi-asserted-by":"crossref","first-page":"D675","DOI":"10.1093\/nar\/gkr918","article-title":"FungiDB: an integrated functional genomics database for fungi","volume":"40","author":"Stajich","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2021041201471724600_bib331","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1002\/yea.3303","article-title":"Misidentification of genome assemblies in public databases: The case of Naumovozyma dairenensis and proposal of a protocol to correct misidentifications","volume":"35","author":"Stavrou","year":"2018","journal-title":"Yeast"},{"key":"2021041201471724600_bib332","doi-asserted-by":"crossref","first-page":"2707","DOI":"10.1128\/JCM.01224-16","article-title":"Cerebrospinal fluid (1,3)-beta-d-glucan testing is useful in diagnosis of coccidioidal meningitis","volume":"54","author":"Stevens","year":"2016","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib333","first-page":"1","article-title":"Sepsis: the LightCycler SeptiFast Test MGRADE\u00ae, SepsiTestTM and IRIDICA BAC BSI assay for rapidly identifying bloodstream bacteria and fungi \u2013 a systematic review and economic evaluation","volume":"20","author":"Stevenson","year":"2016","journal-title":"Health Technol Assess (Rockv)"},{"key":"2021041201471724600_bib335","doi-asserted-by":"crossref","first-page":"2234","DOI":"10.1093\/jac\/dkt180","article-title":"Predicting antimicrobial susceptibilities for Escherichia coli and Klebsiella pneumoniae isolates using whole genomic sequence data","volume":"68","author":"Stoesser","year":"2013","journal-title":"J Antimicrob Chemother"},{"key":"2021041201471724600_bib336","doi-asserted-by":"crossref","first-page":"1301","DOI":"10.1128\/JCM.00028-13","article-title":"Evaluation of PNA-FISH yeast traffic light for rapid identification of yeast directly from positive blood cultures and assessment of clinical impact","volume":"51","author":"Stone","year":"2013","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib337","doi-asserted-by":"crossref","first-page":"34G","DOI":"10.1016\/0002-9149(90)90957-3","article-title":"Significance of coronary circulation in hypertensive heart disease for development and prevention of heart failure","volume":"65","author":"Strauer","year":"1990","journal-title":"Am J Cardiol"},{"key":"2021041201471724600_bib338","doi-asserted-by":"crossref","first-page":"6188","DOI":"10.1039\/c3cc42015a","article-title":"Analysis of intact bacteria using rapid evaporative ionisation mass spectrometry","volume":"49","author":"Strittmatter","year":"2013","journal-title":"Chem Commun"},{"key":"2021041201471724600_bib334","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1002\/jrs.4844","article-title":"The application of Raman spectroscopy for the detection and identification of microorganisms: Raman spectroscopy for microorganism detection and identification","volume":"47","author":"St\u00f6ckel","year":"2016","journal-title":"J Raman Spectrosc"},{"key":"2021041201471724600_bib339","doi-asserted-by":"crossref","first-page":"390","DOI":"10.1016\/j.mimet.2013.07.021","article-title":"Ribosomal proteins as biomarkers for bacterial identification by mass spectrometry in the clinical microbiology laboratory","volume":"94","author":"Suarez","year":"2013","journal-title":"J Microbiol Methods"},{"key":"2021041201471724600_bib340","doi-asserted-by":"crossref","first-page":"1826","DOI":"10.1128\/JCM.40.5.1826-1830.2002","article-title":"Sequence analysis of the ribosomal DNA Intergenic Spacer 1 regions of Trichosporon species","volume":"40","author":"Sugita","year":"2002","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib341","doi-asserted-by":"crossref","first-page":"1480","DOI":"10.1128\/JCM.37.5.1480-1483.1999","article-title":"Comparison of E-test and broth microdilution methods for antifungal drug susceptibility testing of molds","volume":"37","author":"Szekely","year":"1999","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib342","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1016\/j.ijvsm.2013.03.001","article-title":"Use of Fourier transform infrared spectroscopy (FTIR) spectroscopy for rapid and accurate identification of Yeasts isolated from human and animals","volume":"1","author":"Taha","year":"2013","journal-title":"Int J Vet Sci Med"},{"key":"2021041201471724600_bib344","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1016\/j.cca.2015.03.018","article-title":"Rapid single nucleotide polymorphism based method for hematopoietic chimerism analysis and monitoring using high-speed droplet allele-specific PCR and allele-specific quantitative PCR","volume":"445","author":"Taira","year":"2015","journal-title":"Clin Chim Acta"},{"key":"2021041201471724600_bib343","doi-asserted-by":"crossref","first-page":"406","DOI":"10.1186\/1471-2334-14-406","article-title":"A multiplex nested PCR for the detection and identification of Candida species in blood samples of critically ill paediatric patients","volume":"14","author":"Taira","year":"2014","journal-title":"BMC Infect Dis"},{"key":"2021041201471724600_bib345","doi-asserted-by":"crossref","first-page":"552","DOI":"10.1093\/mmycol\/myu016","article-title":"Uncommon opportunistic yeast bloodstream infections from Qatar","volume":"52","author":"Taj-Aldeen","year":"2014","journal-title":"Med Mycol"},{"key":"2021041201471724600_bib346","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1007\/s15010-013-0570-4","article-title":"Epidemiology of candidemia in Qatar, the Middle East: performance of MALDI-TOF MS for the identification of Candida species, species distribution, outcome, and susceptibility pattern","volume":"42","author":"Taj-Aldeen","year":"2014","journal-title":"Infection"},{"key":"2021041201471724600_bib347","doi-asserted-by":"crossref","first-page":"1680","DOI":"10.1128\/JCM.32.7.1680-1684.1994","article-title":"Comparison of commercial kits for detection of cryptococcal antigen","volume":"32","author":"Tanner","year":"1994","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib348","doi-asserted-by":"crossref","first-page":"1455","DOI":"10.1128\/JCM.00243-07","article-title":"Genotyping of Candida orthopsilosis clinical isolates by amplification fragment length polymorphism reveals genetic diversity among independent isolates and strain maintenance within patients","volume":"45","author":"Tavanti","year":"2007","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib350","doi-asserted-by":"crossref","first-page":"3555","DOI":"10.1128\/JCM.01868-13","article-title":"Evaluation of an enzyme immunoassay for detection of Histoplasma capsulatum antigen from urine specimens","volume":"51","author":"Theel","year":"2013","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib349","doi-asserted-by":"crossref","first-page":"D1049","DOI":"10.1093\/nar\/gku1179","article-title":"Gene Ontology Consortium: going forward","volume":"43","author":"The Gene Ontology Consortium","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2021041201471724600_bib351","doi-asserted-by":"crossref","first-page":"85","DOI":"10.3389\/fmicb.2012.00085","article-title":"An interspecies regulatory network inferred from simultaneous RNA-seq of Candida albicans invading innate immune cells","volume":"3","author":"Tierney","year":"2012","journal-title":"Front Microbiol"},{"key":"2021041201471724600_bib352","doi-asserted-by":"crossref","first-page":"367","DOI":"10.1128\/JCM.36.2.367-374.1998","article-title":"Rapid differentiation of closely related Candida species and strains by pyrolysis-mass spectrometry and Fourier transform-infrared spectroscopy","volume":"36","author":"Timmins","year":"1998","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib353","doi-asserted-by":"crossref","first-page":"3418","DOI":"10.1128\/JCM.01709-12","article-title":"Microbiological applications of high-resolution melting analysis","volume":"50","author":"Tong","year":"2012","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib354","doi-asserted-by":"crossref","first-page":"186","DOI":"10.1111\/j.1365-2958.2008.06143.x","article-title":"The ATP-binding cassette transporter-encoding gene CgSNQ2 is contributing to the CgPDR1-dependent azole resistance of Candida glabrata","volume":"68","author":"Torelli","year":"2008","journal-title":"Mol Microbiol"},{"key":"2021041201471724600_bib355","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1007\/s11046-014-9830-9","article-title":"Isolation and drug susceptibility of Candida parapsilosis sensu lato and other species of C. parapsilosis complex from patients with blood stream infections and proposal of a novel LAMP identification method for the species","volume":"179","author":"Trabasso","year":"2015","journal-title":"Mycopathologia"},{"key":"2021041201471724600_bib356","doi-asserted-by":"crossref","first-page":"3308","DOI":"10.1128\/AAC.00535-10","article-title":"Microarray and molecular analyses of the azole resistance mechanism in Candida glabrata oropharyngeal isolates","volume":"54","author":"Tsai","year":"2010","journal-title":"Antimicrob Agents Chemother"},{"key":"2021041201471724600_bib357","doi-asserted-by":"crossref","first-page":"e33705","DOI":"10.1371\/journal.pone.0033705","article-title":"Risk factors and outcomes of candidemia caused by biofilm-forming isolates in a Tertiary Care Hospital","volume":"7","author":"Tumbarello","year":"2012","journal-title":"PLoS One"},{"key":"2021041201471724600_bib358","doi-asserted-by":"crossref","first-page":"3950","DOI":"10.1128\/JCM.01930-13","article-title":"Precise dissection of an Escherichia coli O157:H7 outbreak by single nucleotide polymorphism analysis","volume":"51","author":"Turabelidze","year":"2013","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib359","doi-asserted-by":"crossref","first-page":"11971","DOI":"10.1038\/s41598-017-11887-6","article-title":"Towards an ultra-rapid smartphone-connected test for infectious diseases","volume":"7","author":"Turb\u00e9","year":"2017","journal-title":"Sci Rep"},{"key":"2021041201471724600_bib360","doi-asserted-by":"crossref","DOI":"10.12705\/Code.2018","volume-title":"International Code of Nomenclature for Algae, Fungi, and Plants (Shenzhen Code): Adopted by the Nineteenth International Botanical Congress, Shenzhen, China, July, 2017","author":"Turland","year":"2018"},{"key":"2021041201471724600_bib361","doi-asserted-by":"crossref","first-page":"a019778","DOI":"10.1101\/cshperspect.a019778","article-title":"The Candida pathogenic species complex","volume":"4","author":"Turner","year":"2014","journal-title":"Cold Spring Harb Perspect Med"},{"key":"2021041201471724600_bib362","doi-asserted-by":"crossref","first-page":"50","DOI":"10.1099\/jmm.0.47216-0","article-title":"Development of a loop-mediated isothermal amplification method for diagnosing Pneumocystis pneumonia","volume":"57","author":"Uemura","year":"2008","journal-title":"J Med Microbiol"},{"key":"2021041201471724600_bib363","doi-asserted-by":"crossref","first-page":"e1","DOI":"10.1016\/j.cmi.2018.01.002","article-title":"Diagnosis and management of Aspergillus diseases: executive summary of the 2017 ESCMID-ECMM-ERS guideline","volume":"24 Suppl 1","author":"Ullmann","year":"2018","journal-title":"Clin Microbiol Infect"},{"key":"2021041201471724600_bib364","doi-asserted-by":"crossref","first-page":"D604","DOI":"10.1093\/nar\/gkw1089","article-title":"PHI-base: a new interface and further additions for the multi-species pathogen-host interactions database","volume":"45","author":"Urban","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2021041201471724600_bib365","doi-asserted-by":"crossref","first-page":"605","DOI":"10.3389\/fpls.2015.00605","article-title":"Using the pathogen-host interactions database (PHI-base) to investigate plant pathogen genomes and genes implicated in virulence","volume":"6","author":"Urban","year":"2015","journal-title":"Front Plant Sci"},{"key":"2021041201471724600_bib366","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1111\/j.1439-0507.2006.01243.x","article-title":"Antifungal susceptibility testing by flow cytometry: is it the future?","volume":"49","author":"Vale-Silva","year":"2006","journal-title":"Mycoses"},{"key":"2021041201471724600_bib102","doi-asserted-by":"crossref","first-page":"418","DOI":"10.1016\/j.tig.2014.07.001","article-title":"Ten years of next-generation sequencing technology","volume":"30","author":"van\u00a0Dijk","year":"2014","journal-title":"Trends Genet"},{"key":"2021041201471724600_bib367","doi-asserted-by":"crossref","first-page":"884","DOI":"10.1038\/nbt.3017","article-title":"Bringing RNA-seq closer to the clinic","volume":"32","author":"Van\u00a0Keuren-Jensen","year":"2014","journal-title":"Nat Biotechnol"},{"key":"2021041201471724600_bib368","doi-asserted-by":"crossref","first-page":"i237","DOI":"10.1093\/bioinformatics\/btq182","article-title":"Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM","volume":"26","author":"Vaske","year":"2010","journal-title":"Bioinformatics"},{"key":"2021041201471724600_bib369","doi-asserted-by":"crossref","first-page":"e00420","DOI":"10.1128\/JCM.00420-18","article-title":"Proof of concept for MBT ASTRA, a rapid matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)-based method to detect caspofungin resistance in Candida albicans and Candida glabrata","volume":"56","author":"Vatanshenassan","year":"2018","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib370","doi-asserted-by":"crossref","first-page":"20","DOI":"10.3389\/fcimb.2019.00020","article-title":"Candida auris identification and rapid antifungal susceptibility testing against echinocandins by MALDI-TOF MS","volume":"9","author":"Vatanshenassan","year":"2019","journal-title":"Front Cell Infect Microbiol"},{"key":"2021041201471724600_bib371","doi-asserted-by":"crossref","first-page":"2964","DOI":"10.1128\/JCM.00903-13","article-title":"Rapid antifungal susceptibility testing by matrix-assisted laser desorption ionization-time of flight mass spectrometry analysis","volume":"51","author":"Vella","year":"2013","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib372","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1016\/j.syapm.2013.11.002","article-title":"StrainInfo introduces electronic passports for microorganisms","volume":"37","author":"Verslyppe","year":"2014","journal-title":"Syst Appl Microbiol"},{"key":"2021041201471724600_bib373","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1590\/S0036-46652015000700008","article-title":"Lateral flow assay for cryptococcal antigen: an important advance to improve the continuum of HIV care and reduce cryptococcal meningitis-related mortality","volume":"57 Suppl 19","author":"Vidal","year":"2015","journal-title":"Rev Inst Med Trop Sao Paulo"},{"key":"2021041201471724600_bib374","doi-asserted-by":"crossref","first-page":"3023","DOI":"10.1128\/JCM.00563-14","article-title":"Interlaboratory comparison of sample preparation methods, database expansions, and cutoff values for identification of yeasts by matrix-assisted laser desorption ionization-time of flight mass spectrometry using a yeast test panel","volume":"52","author":"Vlek","year":"2014","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib375","doi-asserted-by":"crossref","first-page":"9236","DOI":"10.1073\/pnas.96.16.9236","article-title":"Digital PCR","volume":"96","author":"Vogelstein","year":"1999","journal-title":"Proc Natl Acad Sci USA"},{"key":"2021041201471724600_bib376","doi-asserted-by":"crossref","first-page":"4407","DOI":"10.1093\/nar\/23.21.4407","article-title":"AFLP: a new technique for DNA fingerprinting","volume":"23","author":"Vos","year":"1995","journal-title":"Nucleic Acids Res"},{"key":"2021041201471724600_bib377","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1586\/erm.13.8","article-title":"Next-generation sequencing in clinical microbiology","volume":"13","author":"Wain","year":"2013","journal-title":"Expert Rev Mol Diagn"},{"key":"2021041201471724600_bib378","doi-asserted-by":"crossref","first-page":"136","DOI":"10.1002\/cyto.990140205","article-title":"Optimizing fluorescent in situ hybridization with rRNA-targeted oligonucleotide probes for flow cytometric identification of microorganisms","volume":"14","author":"Wallner","year":"1993","journal-title":"Cytometry"},{"key":"2021041201471724600_bib379","first-page":"1","article-title":"Using RNA-seq for analysis of differential gene expression in fungal species","author":"Wang","year":"2016","journal-title":"Methods Mol Biol"},{"key":"2021041201471724600_bib380","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1186\/1471-2180-9-167","article-title":"Rapid detection of ERG11 gene mutations in clinical Candida albicans isolates with reduced susceptibility to fluconazole by rolling circle amplification and DNA sequencing","volume":"9","author":"Wang","year":"2009","journal-title":"BMC Microbiol"},{"key":"2021041201471724600_bib381","first-page":"307","article-title":"Latex agglutination: diagnose the early Cryptococcus neoformans test of capsular polysaccharide antigen","volume":"28","author":"Wang","year":"2015","journal-title":"Pak J Pharm Sci"},{"key":"2021041201471724600_bib382","doi-asserted-by":"crossref","first-page":"1007","DOI":"10.1002\/jcb.24762","article-title":"Recent advances in thiol and sulfide reactive probes","volume":"115","author":"Wang","year":"2014","journal-title":"J Cell Biochem"},{"key":"2021041201471724600_bib384","doi-asserted-by":"crossref","first-page":"7111","DOI":"10.1007\/s00253-013-5087-3","article-title":"Identification of microorganisms by FTIR spectroscopy: perspectives and limitations of the method","volume":"97","author":"Wenning","year":"2013","journal-title":"Appl Microbiol Biotechnol"},{"key":"2021041201471724600_bib385","doi-asserted-by":"crossref","first-page":"618","DOI":"10.1038\/nrmicro2852","article-title":"Dual RNA-seq of pathogen and host","volume":"10","author":"Westermann","year":"2012","journal-title":"Nat Rev Microbiol"},{"key":"2021041201471724600_bib386","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1002\/mgg3.281","article-title":"The cost and cost trajectory of whole-genome analysis guiding treatment of patients with advanced cancers","volume":"5","author":"Weymann","year":"2017","journal-title":"Mol Genet Genomic Med"},{"key":"2021041201471724600_bib387","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1186\/2049-2618-1-6","article-title":"CloVR-ITS: automated internal transcribed spacer amplicon sequence analysis pipeline for the characterization of fungal microbiota","volume":"1","author":"White","year":"2013","journal-title":"Microbiome"},{"key":"2021041201471724600_bib388","doi-asserted-by":"crossref","first-page":"3536","DOI":"10.1128\/JCM.01135-14","article-title":"Evaluation of a commercially developed semiautomated PCR-Surface-Enhanced raman scattering assay for diagnosis of invasive fungal disease","volume":"52","author":"White","year":"2014","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib389","doi-asserted-by":"crossref","first-page":"2832","DOI":"10.1128\/JCM.00905-15","article-title":"Clinical performance of Aspergillus PCR for testing serum and plasma: a study by the European Aspergillus PCR Initiative","volume":"53","author":"White","year":"2015","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib390","doi-asserted-by":"crossref","first-page":"e184","DOI":"10.1371\/journal.ppat.0030184","article-title":"Self-regulation of Candida albicans population size during GI colonization","volume":"3","author":"White","year":"2007","journal-title":"PLoS Pathog"},{"key":"2021041201471724600_bib1_279_1561025390594"},{"key":"2021041201471724600_bib391","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1016\/S0167-7012(99)00079-2","article-title":"Nucleic acid sequence-based amplification (NASBA) detection of medically important Candida species","volume":"38","author":"Widjojoatmodjo","year":"1999","journal-title":"J Microbiol Methods"},{"key":"2021041201471724600_bib392","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1186\/1471-2164-14-90","article-title":"Genotyping 1000 yeast strains by next-generation sequencing","volume":"14","author":"Wilkening","year":"2013","journal-title":"BMC Genomics"},{"key":"2021041201471724600_bib393","doi-asserted-by":"crossref","first-page":"2408","DOI":"10.1056\/NEJMoa1401268","article-title":"Actionable diagnosis of neuroleptospirosis by next-generation sequencing","volume":"370","author":"Wilson","year":"2014","journal-title":"N Engl J Med"},{"key":"2021041201471724600_bib394","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1016\/j.tim.2011.05.004","article-title":"TARDIS-based microbial metabolomics: time and relative differences in systems","volume":"19","author":"Winder","year":"2011","journal-title":"Trends Microbiol"},{"key":"2021041201471724600_bib395","doi-asserted-by":"crossref","first-page":"e01514","DOI":"10.1128\/mBio.01514-16","article-title":"Global identification of biofilm-specific proteolysis in Candida albicans","volume":"7","author":"Winter","year":"2016","journal-title":"MBio"},{"key":"2021041201471724600_bib396","doi-asserted-by":"crossref","first-page":"853","DOI":"10.1373\/49.6.853","article-title":"High-resolution genotyping by amplicon melting analysis using LCGreen","volume":"49","author":"Wittwer","year":"2003","journal-title":"Clin Chem"},{"key":"2021041201471724600_bib397","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1016\/j.ijmm.2010.06.002","article-title":"MALDI-TOF MS fingerprinting allows for discrimination of major methicillin-resistant Staphylococcus aureus lineages","volume":"301","author":"Wolters","year":"2011","journal-title":"Int J Med Microbiol"},{"key":"2021041201471724600_bib398","doi-asserted-by":"crossref","first-page":"1888","DOI":"10.1101\/gr.190901","article-title":"BADGE, BeadsArray for the detection of gene expression, a high-throughput diagnostic bioassay","volume":"11","author":"Yang","year":"2001","journal-title":"Genome Res"},{"key":"2021041201471724600_bib399","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1351\/pac198557040583","article-title":"Enzyme immunoassays for the detection of microbial antigens in body fluids: an overview","volume":"57","author":"Yolken","year":"1985","journal-title":"J Macromol Sci Part A Pure Appl Chem"},{"key":"2021041201471724600_bib400","doi-asserted-by":"crossref","first-page":"3371","DOI":"10.1002\/smll.201100633","article-title":"Combining a nanowire SERRS sensor and a target recycling reaction for ultrasensitive and multiplex identification of pathogenic fungi","volume":"7","author":"Yoo","year":"2011","journal-title":"Small"},{"key":"2021041201471724600_bib401","doi-asserted-by":"crossref","first-page":"305","DOI":"10.1007\/978-1-4939-6515-1_18","article-title":"T2 magnetic resonance for fungal diagnosis","volume":"1508","author":"Zervou","year":"2017","journal-title":"Methods Mol Biol"},{"key":"2021041201471724600_bib402","doi-asserted-by":"crossref","first-page":"152","DOI":"10.2353\/jmoldx.2010.090070","article-title":"Direct DNA amplification from crude clinical samples using a PCR enhancer cocktail and novel mutants of Taq","volume":"12","author":"Zhang","year":"2010","journal-title":"J Mol Diagn"},{"key":"2021041201471724600_bib403","doi-asserted-by":"crossref","first-page":"12491","DOI":"10.1021\/acs.chemrev.5b00428","article-title":"Isothermal amplification of nucleic acids","volume":"115","author":"Zhao","year":"2015","journal-title":"Chem Rev"},{"key":"2021041201471724600_bib404","doi-asserted-by":"crossref","first-page":"6573","DOI":"10.1128\/AAC.01574-16","article-title":"Rapid detection of FKS-associated echinocandin resistance in Candida glabrata","volume":"60","author":"Zhao","year":"2016","journal-title":"Antimicrob Agents Chemother"},{"key":"2021041201471724600_bib405","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1007\/978-1-62703-257-5_6","article-title":"Quantitative detection of Aspergillus spp. by real-time nucleic acid sequence-based amplification","volume":"968","author":"Zhao","year":"2013","journal-title":"Methods Mol Biol"},{"key":"2021041201471724600_bib406","doi-asserted-by":"crossref","first-page":"2423","DOI":"10.1128\/JCM.00420-08","article-title":"Practical method for detection and identification of Candida, Aspergillus, and Scedosporium spp. by use of rolling-circle amplification","volume":"46","author":"Zhou","year":"2008","journal-title":"J Clin Microbiol"},{"key":"2021041201471724600_bib407","doi-asserted-by":"crossref","first-page":"e0148714","DOI":"10.1371\/journal.pone.0148714","article-title":"A murine, bispecific monoclonal antibody simultaneously recognizing \u03b2-glucan and MP65 determinants in Candida species","volume":"11","author":"Zito","year":"2016","journal-title":"PLoS One"},{"key":"2021041201471724600_bib408","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1007\/s12281-016-0253-6","article-title":"Next-generation sequencing in the Mycology Lab","volume":"10","author":"Zoll","year":"2016","journal-title":"Curr Fungal Infect Rep"}],"container-title":["FEMS Microbiology Reviews"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/femsre\/advance-article-pdf\/doi\/10.1093\/femsre\/fuz015\/28788428\/fuz015.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/femsre\/article-pdf\/43\/5\/517\/37020972\/fuz015.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/femsre\/article-pdf\/43\/5\/517\/37020972\/fuz015.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,7,18]],"date-time":"2024-07-18T23:52:23Z","timestamp":1721346743000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/femsre\/article\/43\/5\/517\/5510456"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,6,3]]},"references-count":405,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2019,6,3]]},"published-print":{"date-parts":[[2019,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/femsre\/fuz015","relation":{},"ISSN":["1574-6976"],"issn-type":[{"value":"1574-6976","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,9]]},"published":{"date-parts":[[2019,6,3]]}}}