{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,5]],"date-time":"2026-11-05T12:40:34Z","timestamp":1793882434416,"version":"4.7.0"},"reference-count":221,"publisher":"MDPI AG","issue":"7","license":[{"start":{"date-parts":[[2024,6,26]],"date-time":"2024-06-26T00:00:00Z","timestamp":1719360000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["JoF"],"abstract":"<jats:p>Invasive fungal diseases (IFDs) comprise a growing healthcare burden, especially given the expanding population of immunocompromised hosts. Early diagnosis of IFDs is required to optimise therapy with antifungals, especially in the setting of rising rates of antifungal resistance. Molecular techniques including nucleic acid amplification tests and whole genome sequencing have potential to offer utility in overcoming limitations with traditional phenotypic testing. However, standardisation of methodology and interpretations of these assays is an ongoing undertaking. The utility of targeted Aspergillus detection has been well-defined, with progress in investigations into the role of targeted assays for Candida, Pneumocystis, Cryptococcus, the Mucorales and endemic mycoses. Likewise, whilst broad-range polymerase chain reaction assays have been in use for some time, pathology stewardship and optimising diagnostic yield is a continuing exercise. As costs decrease, there is also now increased access and experience with whole genome sequencing, including metagenomic sequencing, which offers unparalleled resolution especially in the investigations of potential outbreaks. However, their role in routine diagnostic use remains uncommon and standardisation of techniques and workflow are required for wider implementation.<\/jats:p>","DOI":"10.3390\/jof10070447","type":"journal-article","created":{"date-parts":[[2024,6,26]],"date-time":"2024-06-26T09:29:33Z","timestamp":1719394173000},"page":"447","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":44,"title":["Molecular Diagnostics for Invasive Fungal Diseases: Current and Future Approaches"],"prefix":"10.3390","volume":"10","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0953-4063","authenticated-orcid":false,"given":"David","family":"Pham","sequence":"first","affiliation":[{"name":"Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8834-892X","authenticated-orcid":false,"given":"Varsha","family":"Sivalingam","sequence":"additional","affiliation":[{"name":"Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Helen M.","family":"Tang","sequence":"additional","affiliation":[{"name":"Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James M.","family":"Montgomery","sequence":"additional","affiliation":[{"name":"Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sharon C.-A.","family":"Chen","sequence":"additional","affiliation":[{"name":"Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia"},{"name":"Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia"},{"name":"Sydney Infectious Diseases Institute, The University of Sydney, Westmead, NSW 2145, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0301-7110","authenticated-orcid":false,"given":"Catriona L.","family":"Halliday","sequence":"additional","affiliation":[{"name":"Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2024,6,26]]},"reference":[{"key":"ref_1","unstructured":"World Health Organization (2022). WHO Fungal Priority Pathogens List to Guide Research, Development and Public Health Action, WHO."},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Bongomin, F., Gago, S., Oladele, R., and Denning, D. (2017). Global and Multi-National Prevalence of Fungal Diseases\u2014Estimate Precision. J. Fungi, 3.","DOI":"10.3390\/jof3040057"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1021","DOI":"10.1111\/myc.13148","article-title":"Breakthrough Invasive Fungal Infections: Who Is at Risk?","volume":"63","author":"Jenks","year":"2020","journal-title":"Mycoses"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1136\/ejhpharm-2020-002604","article-title":"Antifungal Drug Resistance: An Update","volume":"29","author":"Denning","year":"2022","journal-title":"Eur. J. Hosp. Pharm."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"E428","DOI":"10.1016\/S1473-3099(23)00692-8","article-title":"Global Incidence and Mortality of Severe Fungal Disease","volume":"24","author":"Denning","year":"2024","journal-title":"Lancet Infect. Dis."},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Nnadi, N.E., and Carter, D.A. (2021). Climate Change and the Emergence of Fungal Pathogens. PLoS Pathog., 17.","DOI":"10.1371\/journal.ppat.1009503"},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Kidd, S.E., Chen, S.C.-A., Meyer, W., and Halliday, C.L. (2020). A New Age in Molecular Diagnostics for Invasive Fungal Disease: Are We Ready?. Front. Microbiol., 10.","DOI":"10.3389\/fmicb.2019.02903"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"1135","DOI":"10.1080\/14737159.2023.2267977","article-title":"An Update on Current and Novel Molecular Diagnostics for the Diagnosis of Invasive Fungal Infections","volume":"23","author":"Jenks","year":"2023","journal-title":"Expert. Rev. Mol. Diagn."},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Gudisa, R., Harchand, R., and Rudramurthy, S.M. (2024). Nucleic-Acid-Based Molecular Fungal Diagnostics: A Way to a Better Future. Diagnostics, 14.","DOI":"10.3390\/diagnostics14050520"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1080\/14737159.2022.2037423","article-title":"An Overview of Using Fungal DNA for the Diagnosis of Invasive Mycoses","volume":"22","author":"White","year":"2022","journal-title":"Expert. Rev. Mol. Diagn."},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Cruciani, M., White, P.L., Barnes, R.A., Loeffler, J., Donnelly, J.P., Rogers, T.R., Heinz, W.J., Warris, A., Morton, C.O., and Lengerova, M. (2023). An Overview of Systematic Reviews of Polymerase Chain Reaction (PCR) for the Diagnosis of Invasive Aspergillosis in Immunocompromised People: A Report of the Fungal PCR Initiative (FPCRI)\u2014An ISHAM Working Group. J. Fungi, 9.","DOI":"10.3390\/jof9100967"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1367","DOI":"10.1093\/cid\/ciz1008","article-title":"Revision and Update of the Consensus Definitions of Invasive Fungal Disease from the European Organization for Research and Treatment of Cancer and the Mycoses Study Group Education and Research Consortium","volume":"71","author":"Donnelly","year":"2020","journal-title":"Clin. Infect. Dis."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1038\/s41576-019-0113-7","article-title":"Clinical Metagenomics","volume":"20","author":"Chiu","year":"2019","journal-title":"Nat. Rev. Genet."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"S46","DOI":"10.1016\/j.pathol.2022.12.145","article-title":"Panfungal PCR on Formalin Fixed Paraffin Embedded Tissue\u2014To Proceed or Not Proceed?","volume":"55","author":"Sparks","year":"2023","journal-title":"Pathology"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"S60","DOI":"10.1093\/mmy\/myx091","article-title":"Diagnosis of Aspergillosis by PCR: Clinical Considerations and Technical Tips","volume":"56","author":"Barnes","year":"2018","journal-title":"Med. Mycol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"1231","DOI":"10.1128\/JCM.01767-09","article-title":"Aspergillus PCR: One Step Closer to Standardization","volume":"48","author":"White","year":"2010","journal-title":"J. Clin. Microbiol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"5122","DOI":"10.1128\/JCM.43.10.5122-5128.2005","article-title":"Comparison of Six DNA Extraction Methods for Recovery of Fungal DNA as Assessed by Quantitative PCR","volume":"43","author":"Fredricks","year":"2005","journal-title":"J. Clin. Microbiol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1016\/j.mimet.2005.06.008","article-title":"An Assessment of the Efficiency of Fungal DNA Extraction Methods for Maximizing the Detection of Medically Important Fungi Using PCR","volume":"65","author":"Karakousis","year":"2006","journal-title":"J. Microbiol. Methods"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"S331","DOI":"10.1093\/infdis\/jiz151","article-title":"From the Pipeline to the Bedside: Advances and Challenges in Clinical Metagenomics","volume":"221","author":"Dekker","year":"2020","journal-title":"J. Infect. Dis."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"e02437-21","DOI":"10.1128\/jcm.02437-21","article-title":"Utility of Broad-Range PCR Sequencing for Infectious Diseases Clinical Decision Making: A Pediatric Center Experience","volume":"60","author":"Nakamura","year":"2022","journal-title":"J. Clin. Microbiol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"e00952-23","DOI":"10.1128\/jcm.00952-23","article-title":"Universal PCR for Bacteria, Mycobacteria, and Fungi: A 10-Year Retrospective Review of Clinical Indications and Patient Outcomes","volume":"61","author":"Kubiak","year":"2023","journal-title":"J. Clin. Microbiol."},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Valero, C., Mart\u00edn-G\u00f3mez, M.T., and Buitrago, M.J. (2022). Molecular Diagnosis of Endemic Mycoses. J. Fungi, 9.","DOI":"10.3390\/jof9010059"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1007\/s15010-020-01395-7","article-title":"Clinical Evaluation of an In-House Panfungal Real-Time PCR Assay for the Detection of Fungal Pathogens","volume":"48","author":"Camp","year":"2020","journal-title":"Infection"},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Zhu, A., Zembower, T., and Qi, C. (2021). Molecular Detection, Not Extended Culture Incubation, Contributes to Diagnosis of Fungal Infection. BMC Infect. Dis., 21.","DOI":"10.1186\/s12879-021-06838-6"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"584","DOI":"10.1016\/j.pathol.2020.03.013","article-title":"Knowledge at What Cost? An Audit of the Utility of Panfungal PCR Performed on Bronchoalveolar Lavage Fluid Specimens at a Tertiary Mycology Laboratory","volume":"52","author":"Garnham","year":"2020","journal-title":"Pathology"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"669","DOI":"10.1016\/j.pathol.2023.03.011","article-title":"Panfungal PCR on Formalin-Fixed, Paraffin-Embedded Tissue: To Proceed or Not Proceed?","volume":"55","author":"Sparks","year":"2023","journal-title":"Pathology"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1554","DOI":"10.1093\/cid\/ciz1245","article-title":"Clinical Utility of Universal Broad-Range Polymerase Chain Reaction Amplicon Sequencing for Pathogen Identification: A Retrospective Cohort Study","volume":"71","author":"Kerkhoff","year":"2020","journal-title":"Clin. Infect. Dis."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1558","DOI":"10.1093\/cid\/ciz1246","article-title":"A Laboratory\u2019s Guide to the Universe of Broad-Range Polymerase Chain Reactions","volume":"71","author":"Schuetz","year":"2020","journal-title":"Clin. Infect. Dis."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"e00955-21","DOI":"10.1128\/JCM.00955-21","article-title":"High Clinical Impact of Broad-Range Fungal PCR in Suspected Fungal Sinusitis","volume":"59","author":"Lieberman","year":"2021","journal-title":"J. Clin. Microbiol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"380","DOI":"10.1128\/JCM.01862-06","article-title":"Development and Clinical Application of a Panfungal PCR Assay to Detect and Identify Fungal DNA in Tissue Specimens","volume":"45","author":"Lau","year":"2007","journal-title":"J. Clin. Microbiol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"e24209","DOI":"10.1002\/jcla.24209","article-title":"Evaluating a Semi-nested PCR to Support Histopathology Reports of Fungal Rhinosinusitis in Formalin-fixed Paraffin-embedded Tissue Samples","volume":"36","author":"Ashraf","year":"2022","journal-title":"J. Clin. Lab. Anal."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"e01083-17","DOI":"10.1128\/AAC.01083-17","article-title":"Development and Validation of a High-Resolution Melting Assay to Detect Azole Resistance in Aspergillus fumigatus","volume":"61","author":"Gil","year":"2017","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_33","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."},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Radmard, S., Reid, S., Ciryam, P., Boubour, A., Ho, N., Zucker, J., Sayre, D., Greendyke, W.G., Miko, B.A., and Pereira, M.R. (2019). Clinical Utilization of the FilmArray Meningitis\/Encephalitis (ME) Multiplex Polymerase Chain Reaction (PCR) Assay. Front. Neurol., 10.","DOI":"10.3389\/fneur.2019.00281"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1016\/j.diagmicrobio.2015.10.023","article-title":"Clinical and Economic Impact of Antimicrobial Stewardship Interventions with the FilmArray Blood Culture Identification Panel","volume":"84","author":"Pardo","year":"2016","journal-title":"Diagn. Microbiol. Infect. Dis."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"779","DOI":"10.1093\/mmy\/myz115","article-title":"The Fungal PCR Initiative\u2019s Evaluation of in-House and Commercial Pneumocystis jirovecii QPCR Assays: Toward a Standard for a Diagnostics Assay","volume":"58","author":"White","year":"2020","journal-title":"Med. Mycol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"126","DOI":"10.1093\/mmy\/myaa036","article-title":"Interlaboratory Evaluation of Mucorales PCR Assays for Testing Serum Specimens: A Study by the Fungal PCR Initiative and the Modimucor Study Group","volume":"59","author":"Rocchi","year":"2021","journal-title":"Med. Mycol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"myac004","DOI":"10.1093\/mmy\/myac004","article-title":"Assessment of Panfungal PCR Performance with Formalin-Fixed Paraffin-Embedded Tissue Specimens","volume":"60","author":"Clark","year":"2022","journal-title":"Med. Mycol."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1309\/AJCPNSU2SDZD9WPW","article-title":"Utility of DNA Sequencing for Direct Identification of Invasive Fungi from Fresh and Formalin-Fixed Specimens","volume":"140","author":"Moncada","year":"2013","journal-title":"Am. J. Clin. Pathol."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"1737","DOI":"10.1128\/JCM.00328-14","article-title":"Performance of Panfungal- and Specific-PCR-Based Procedures for Etiological Diagnosis of Invasive Fungal Diseases on Tissue Biopsy Specimens with Proven Infection: A 7-Year Retrospective Analysis from a Reference Laboratory","volume":"52","author":"Buitrago","year":"2014","journal-title":"J. Clin. Microbiol."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1093\/mmy\/myv008","article-title":"International Society of Human and Animal Mycology (ISHAM)-ITS Reference DNA Barcoding Database\u2014The Quality Controlled Standard Tool for Routine Identification of Human and Animal Pathogenic Fungi","volume":"53","author":"Irinyi","year":"2015","journal-title":"Med. Mycol."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"S95","DOI":"10.1093\/cid\/ciaa1865","article-title":"Aspergillus Polymerase Chain Reaction\u2014An Update on Technical Recommendations, Clinical Applications, and Justification for Inclusion in the Second Revision of the EORTC\/MSGERC Definitions of Invasive Fungal Disease","volume":"72","author":"White","year":"2021","journal-title":"Clin. Infect. Dis."},{"key":"ref_43","first-page":"402","article-title":"Determining the Analytical Specificity of PCR-Based Assays for the Diagnosis of IA: What Is Aspergillus?","volume":"55","author":"Morton","year":"2016","journal-title":"Med. Mycol."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"2838","DOI":"10.1128\/JCM.00906-15","article-title":"Analytical Comparison of in vitro -Spiked Human Serum and Plasma for PCR-Based Detection of Aspergillus fumigatus DNA: A Study by the European Aspergillus PCR Initiative","volume":"53","author":"Loeffler","year":"2015","journal-title":"J. Clin. Microbiol."},{"key":"ref_45","first-page":"CD009551","article-title":"Polymerase Chain Reaction Blood Tests for the Diagnosis of Invasive Aspergillosis in Immunocompromised People","volume":"2019","author":"Cruciani","year":"2019","journal-title":"Cochrane Database Syst. Rev."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"e48","DOI":"10.1016\/S2213-2600(20)30237-X","article-title":"Prevalence of Putative Invasive Pulmonary Aspergillosis in Critically Ill Patients with COVID-19","volume":"8","author":"Alanio","year":"2020","journal-title":"Lancet Respir. Med."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"3842","DOI":"10.1128\/JCM.05316-11","article-title":"Evaluation of Aspergillus PCR Protocols for Testing Serum Specimens","volume":"49","author":"White","year":"2011","journal-title":"J. Clin. Microbiol."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"635","DOI":"10.1093\/jac\/dkaa498","article-title":"The Impact of Anti-Mould Prophylaxis on Aspergillus PCR Blood Testing for the Diagnosis of Invasive Aspergillosis","volume":"76","author":"Cruciani","year":"2021","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1093\/cid\/ciad141","article-title":"Clinical Impact of Polymerase Chain Reaction\u2013Based Aspergillus and Azole Resistance Detection in Invasive Aspergillosis: A Prospective Multicenter Study","volume":"77","author":"Huygens","year":"2023","journal-title":"Clin. Infect. Dis."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"1120","DOI":"10.1016\/j.cmi.2022.02.026","article-title":"The Impact of the Updated EORTC\/MSG Criteria on the Classification of Hematological Patients with Suspected Invasive Pulmonary Aspergillosis","volume":"28","author":"Lamberink","year":"2022","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_51","doi-asserted-by":"crossref","unstructured":"Fan, L.-C., Lu, H.-W., Cheng, K.-B., Li, H.-P., and Xu, J.-F. (2013). Evaluation of PCR in Bronchoalveolar Lavage Fluid for Diagnosis of Pneumocystis jirovecii Pneumonia: A Bivariate Meta-Analysis and Systematic Review. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0073099"},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"1230","DOI":"10.1111\/myc.13354","article-title":"Performance of the RealStar\u00ae Pneumocystis jirovecii PCR Kit for the Diagnosis of Pneumocystis Pneumonia","volume":"64","author":"Mercier","year":"2021","journal-title":"Mycoses"},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"myad032","DOI":"10.1093\/mmy\/myad032","article-title":"Evaluation of the PneumoGenius\u00ae PCR Assay for the Diagnosis of Pneumocystis Pneumonia and the Detection of Pneumocystis Dihydropteroate Synthase Mutations in Respiratory Samples","volume":"61","author":"Guegan","year":"2023","journal-title":"Med. Mycol."},{"key":"ref_54","doi-asserted-by":"crossref","unstructured":"Delli\u00e8re, S., Gits-Muselli, M., White, P.L., Mengoli, C., Bretagne, S., and Alanio, A. (2019). Quantification of Pneumocystis jirovecii: Cross-Platform Comparison of One QPCR Assay with Leading Platforms and Six Master Mixes. J. Fungi, 6.","DOI":"10.3390\/jof6010009"},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"S114","DOI":"10.1093\/cid\/ciaa1805","article-title":"Pneumocystis jirovecii Disease: Basis for the Revised EORTC\/MSGERC Invasive Fungal Disease Definitions in Individuals without Human Immunodeficiency Virus","volume":"72","author":"Lagrou","year":"2021","journal-title":"Clin. Infect. Dis."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1016\/j.cmi.2021.08.017","article-title":"Non-Invasive Diagnosis of Pneumocystis jirovecii Pneumonia: A Systematic Review and Meta-Analysis","volume":"28","author":"Smyth","year":"2022","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"1375","DOI":"10.1016\/j.cmi.2020.01.007","article-title":"Evaluation of the Biofire FilmArray Meningitis\/Encephalitis Assay for the Detection of Cryptococcus neoformans\/gattii","volume":"26","author":"Van","year":"2020","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"3021","DOI":"10.1128\/JCM.00689-08","article-title":"Multiplex Tandem PCR: A Novel Platform for Rapid Detection and Identification of Fungal Pathogens from Blood Culture Specimens","volume":"46","author":"Lau","year":"2008","journal-title":"J. Clin. Microbiol."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"408","DOI":"10.1093\/mmy\/myz064","article-title":"False Negative Diagnostic Errors with Polymerase Chain Reaction for the Detection of Cryptococcal Meningoencephalitis","volume":"58","author":"Lewis","year":"2020","journal-title":"Med. Mycol."},{"key":"ref_60","doi-asserted-by":"crossref","unstructured":"Tay, E., Chen, S.C.-A., Green, W., Lopez, R., and Halliday, C.L. (2022). Development of a Real-Time PCR Assay to Identify and Distinguish between Cryptococcus neoformans and Cryptococcus gattii Species Complexes. J. Fungi, 8.","DOI":"10.3390\/jof8050462"},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"e261","DOI":"10.1016\/S2666-5247(23)00362-2","article-title":"Development and Validation of Quantitative PCR Assays for HIV-Associated Cryptococcal Meningitis in Sub-Saharan Africa: A Diagnostic Accuracy Study","volume":"5","author":"Mbangiwa","year":"2024","journal-title":"Lancet Microbe"},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1007\/s12281-021-00421-x","article-title":"Molecular Diagnosis of Yeast Infections","volume":"15","author":"White","year":"2021","journal-title":"Curr. Fungal. Infect. Rep."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"665","DOI":"10.1128\/JCM.01602-10","article-title":"PCR Diagnosis of Invasive Candidiasis: Systematic Review and Meta-Analysis","volume":"49","author":"Avni","year":"2011","journal-title":"J. Clin. Microbiol."},{"key":"ref_64","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":"ref_65","doi-asserted-by":"crossref","first-page":"ofz136","DOI":"10.1093\/ofid\/ofz136","article-title":"Diagnostic Performance of T2Candida among ICU Patients with Risk Factors for Invasive Candidiasis","volume":"6","author":"Arendrup","year":"2019","journal-title":"Open Forum Infect. Dis."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"789","DOI":"10.1093\/mmy\/myz123","article-title":"Roles of the Multiplex Real-Time PCR Assay and \u03b2-D-Glucan in a High-Risk Population for Intra-Abdominal Candidiasis (IAC)","volume":"58","author":"Buitrago","year":"2020","journal-title":"Med. Mycol."},{"key":"ref_67","doi-asserted-by":"crossref","unstructured":"Zacharioudakis, I., Zervou, F., and Mylonakis, E. (2018). T2 Magnetic Resonance Assay: Overview of Available Data and Clinical Implications. J. Fungi, 4.","DOI":"10.3390\/jof4020045"},{"key":"ref_68","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":"ref_69","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":"ref_70","doi-asserted-by":"crossref","unstructured":"Tang, D.-L., Chen, X., Zhu, C.-G., Li, Z., Xia, Y., and Guo, X.-G. (2019). Pooled Analysis of T2Candida for Rapid Diagnosis of Candidiasis. BMC Infect. Dis., 19.","DOI":"10.1186\/s12879-019-4419-z"},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"858","DOI":"10.1093\/ajcp\/aqw063","article-title":"T2Candida Provides Rapid and Accurate Species Identification in Pediatric Cases of Candidemia","volume":"145","author":"Hamula","year":"2016","journal-title":"Am. J. Clin. Pathol."},{"key":"ref_72","doi-asserted-by":"crossref","unstructured":"Fuchs, S., Lass-Fl\u00f6rl, C., and Posch, W. (2019). Diagnostic Performance of a Novel Multiplex PCR Assay for Candidemia among ICU Patients. J. Fungi, 5.","DOI":"10.3390\/jof5030086"},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"E1","DOI":"10.1111\/j.1469-0691.2012.03976.x","article-title":"Development of a Single Tube Multiplex Real-Time PCR to Detect the Most Clinically Relevant Mucormycetes Species","volume":"19","author":"Buitrago","year":"2013","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"e95","DOI":"10.1093\/cid\/cit094","article-title":"Quantitative Polymerase Chain Reaction Detection of Circulating DNA in Serum for Early Diagnosis of Mucormycosis in Immunocompromised Patients","volume":"56","author":"Millon","year":"2013","journal-title":"Clin. Infect. Dis."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1099\/jmm.0.000218","article-title":"Development and Application of Two Independent Real-Time PCR Assays to Detect Clinically Relevant Mucorales Species","volume":"65","author":"Springer","year":"2016","journal-title":"J. Med. Microbiol."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"2824","DOI":"10.1128\/JCM.00637-14","article-title":"Rapid Detection and Identification of Mucormycetes in Bronchoalveolar Lavage Samples from Immunocompromised Patients with Pulmonary Infiltrates by Use of High-Tesolution Melt Snalysis","volume":"52","author":"Lengerova","year":"2014","journal-title":"J. Clin. Microbiol."},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"e00746-18","DOI":"10.1128\/JCM.00746-18","article-title":"PCR-Based Approach Targeting Mucorales-Specific Gene Family for Diagnosis of Mucormycosis","volume":"56","author":"Baldin","year":"2018","journal-title":"J. Clin. Microbiol."},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"777","DOI":"10.1093\/cid\/ciab1066","article-title":"Evaluation of Serum Mucorales Polymerase Chain Reaction (PCR) for the Diagnosis of Mucormycoses: The MODIMUCOR Prospective Trial","volume":"75","author":"Millon","year":"2022","journal-title":"Clin. Infect. Dis."},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1016\/j.jinf.2020.05.051","article-title":"Evaluation of MucorGenius\u00ae Mucorales PCR Assay for the Diagnosis of Pulmonary Mucormycosis","volume":"81","author":"Guegan","year":"2020","journal-title":"J. Infect."},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"810.e1","DOI":"10.1016\/j.cmi.2015.12.006","article-title":"Early Diagnosis and Monitoring of Mucormycosis by Detection of Circulating DNA in Serum: Retrospective Analysis of 44 Cases Collected through the French Surveillance Network of Invasive Fungal Infections (RESSIF)","volume":"22","author":"Millon","year":"2016","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"e01409-22","DOI":"10.1128\/jcm.01409-22","article-title":"A Multiplex PCR and DNA-Sequencing Workflow on Serum for the Diagnosis and Species Identification for Invasive Aspergillosis and Mucormycosis","volume":"61","author":"Imbert","year":"2023","journal-title":"J. Clin. Microbiol."},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"1581","DOI":"10.1007\/s10096-019-03600-4","article-title":"Essential in vitro Diagnostics for Advanced HIV and Serious Fungal Diseases: International Experts\u2019 Consensus Recommendations","volume":"38","author":"Bongomin","year":"2019","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis."},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"774","DOI":"10.1111\/myc.13603","article-title":"A Multicentre External Quality Assessment: A First Step to Standardise PCR Protocols for the Diagnosis of Histoplasmosis and Coccidioidomycosis","volume":"66","author":"Wilmes","year":"2023","journal-title":"Mycoses"},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"1506","DOI":"10.1128\/JCM.39.4.1506-1509.2001","article-title":"Diagnosis and Monitoring of Murine Histoplasmosis by a Nested PCR Assay","volume":"39","author":"Bialek","year":"2001","journal-title":"J. Clin. Microbiol."},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"665","DOI":"10.1007\/s10096-006-0207-y","article-title":"Detection of Imported Histoplasmosis in Serum of HIV-Infected Patients Using a Real-Time PCR-Based Assay","volume":"25","author":"Buitrago","year":"2006","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis."},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"1168","DOI":"10.1128\/JCM.02895-13","article-title":"A Multiplex Real-Time PCR Assay for Identification of Pneumocystis jirovecii, Histoplasma capsulatum, and Cryptococcus neoformans\/Cryptococcus gattii in Samples from AIDS Patients with Opportunistic Pneumonia","volume":"52","author":"Gago","year":"2014","journal-title":"J. Clin. Microbiol."},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"1295","DOI":"10.1128\/JCM.41.3.1295-1298.2003","article-title":"Identification of Histoplasma capsulatum from Culture Extracts by Real-Time PCR","volume":"41","author":"Shrestha","year":"2003","journal-title":"J. Clin. Microbiol."},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1016\/j.diagmicrobio.2009.10.010","article-title":"Detection of Histoplasma capsulatum DNA in Human Samples by Real-Time Polymerase Chain Reaction","volume":"66","author":"Simon","year":"2010","journal-title":"Diagn. Microbiol. Infect. Dis."},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"698","DOI":"10.1016\/j.jmoldx.2021.02.007","article-title":"Evaluation of a New Histoplasma spp. Quantitative RT-PCR Assay","volume":"23","author":"Alanio","year":"2021","journal-title":"J. Mol. Diagn."},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"1753","DOI":"10.1128\/JCM.41.4.1753-1755.2003","article-title":"Molecular Detection of Histoplasma capsulatum var. capsulatum in Human Clinical Samples","volume":"41","author":"Bracca","year":"2003","journal-title":"J. Clin. Microbiol."},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1128\/JCM.41.2.535-539.2003","article-title":"PCR Assay for Identification of Histoplasma capsulatum Based on the Nucleotide Sequence of the M Antigen","volume":"41","author":"Muniz","year":"2003","journal-title":"J. Clin. Microbiol."},{"key":"ref_92","doi-asserted-by":"crossref","unstructured":"L\u00f3pez, L.F., Mu\u00f1oz, C.O., C\u00e1ceres, D.H., Tob\u00f3n, \u00c1.M., Loparev, V., Clay, O., Chiller, T., Litvintseva, A., Gade, L., and Gonz\u00e1lez, \u00c1. (2017). Standardization and Validation of Real Time PCR Assays for the Diagnosis of Histoplasmosis Using Three Molecular Targets in an Animal Model. PLoS ONE, 12.","DOI":"10.1371\/journal.pone.0190311"},{"key":"ref_93","doi-asserted-by":"crossref","first-page":"441","DOI":"10.1016\/j.diagmicrobio.2007.03.008","article-title":"Histoplasmosis Diagnosis Using a Polymerase Chain Reaction Method. Application on Human Samples in French Guiana, South America","volume":"58","author":"Maubon","year":"2007","journal-title":"Diagn. Microbiol. Infect. Dis."},{"key":"ref_94","doi-asserted-by":"crossref","first-page":"821","DOI":"10.1007\/s10096-002-0833-y","article-title":"Rapid PCR-Based Diagnosis of Disseminated Histoplasmosis in an AIDS Patient","volume":"21","author":"Rickerts","year":"2002","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis."},{"key":"ref_95","doi-asserted-by":"crossref","unstructured":"Gallo, J.E., Torres, I., G\u00f3mez, O.M., Rishishwar, L., Vannberg, F., Jordan, I.K., McEwen, J.G., and Clay, O.K. (2021). New Histoplasma Diagnostic Assays Designed via Whole Genome Comparisons. J. Fungi, 7.","DOI":"10.3390\/jof7070544"},{"key":"ref_96","doi-asserted-by":"crossref","first-page":"256","DOI":"10.1016\/j.riam.2013.03.004","article-title":"Comparison of PCR Protocols for Detecting Histoplasma capsulatum DNA through a Multicenter Study","volume":"30","author":"Buitrago","year":"2013","journal-title":"Rev. Iberoam. Micol."},{"key":"ref_97","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":"ref_98","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1128\/JCM.01776-06","article-title":"Detection of Coccidioides Species in Clinical Specimens by Real-Time PCR","volume":"45","author":"Binnicker","year":"2007","journal-title":"J. Clin. Microbiol."},{"key":"ref_99","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1016\/j.diagmicrobio.2014.01.029","article-title":"Development and Validation of a Quantitative Real-Time PCR Assay for the Early Diagnosis of Coccidioidomycosis","volume":"79","author":"Gago","year":"2014","journal-title":"Diagn. Microbiol. Infect. Dis."},{"key":"ref_100","doi-asserted-by":"crossref","first-page":"778","DOI":"10.1128\/JCM.42.2.778-783.2004","article-title":"PCR Assays for Identification of Coccidioides posadasii Based on the Nucleotide Sequence of the Antigen 2\/Proline-Rich Antigen","volume":"42","author":"Bialek","year":"2004","journal-title":"J. Clin. Microbiol."},{"key":"ref_101","doi-asserted-by":"crossref","unstructured":"Zangeneh, T.T., and Al-Obaidi, M.M. (2023). Diagnostic Approach to Coccidioidomycosis in Solid Organ Transplant Recipients. J. Fungi, 9.","DOI":"10.3390\/jof9050513"},{"key":"ref_102","doi-asserted-by":"crossref","first-page":"e01277-17","DOI":"10.1128\/JCM.01277-17","article-title":"Multicenter Clinical Validation of a Cartridge-Based Real-Time PCR System for Detection of Coccidioides spp. in Lower Respiratory Specimens","volume":"56","author":"Saubolle","year":"2018","journal-title":"J. Clin. Microbiol."},{"key":"ref_103","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1016\/j.micpath.2018.05.039","article-title":"Paracoccidioidomycosis: Detection of Paracoccidioides brasiliensis\u2019 Genome in Biological Samples by Quantitative Chain Reaction Polymerase (QPCR)","volume":"121","author":"Machado","year":"2018","journal-title":"Microb. Pathog."},{"key":"ref_104","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1016\/j.bjid.2015.04.008","article-title":"Validation and Clinical Application of a Nested PCR for Paracoccidioidomycosis Diagnosis in Clinical Samples from Colombian Patients","volume":"19","author":"Gaviria","year":"2015","journal-title":"Braz. J. Infect. Dis."},{"key":"ref_105","doi-asserted-by":"crossref","first-page":"879","DOI":"10.3109\/13693780802713208","article-title":"Utility of Real-Time PCR for the Detection of Paracoccidioides brasiliensis DNA in the Diagnosis of Imported Paracoccidioidomycosis","volume":"47","author":"Buitrago","year":"2009","journal-title":"Med. Mycol."},{"key":"ref_106","doi-asserted-by":"crossref","first-page":"1783","DOI":"10.1128\/JCM.00310-12","article-title":"Real-Time PCR Assay for Identification of Blastomyces dermatitidis in Culture and in Tissue","volume":"50","author":"Sidamonidze","year":"2012","journal-title":"J. Clin. Microbiol."},{"key":"ref_107","doi-asserted-by":"crossref","first-page":"3204","DOI":"10.1128\/JCM.00673-11","article-title":"Detection of Blastomyces dermatitidis and Histoplasma capsulatum from Culture Isolates and Clinical Specimens by Use of Real-Time PCR","volume":"49","author":"Babady","year":"2011","journal-title":"J. Clin. Microbiol."},{"key":"ref_108","doi-asserted-by":"crossref","first-page":"487","DOI":"10.1111\/j.1439-0507.2008.01653.x","article-title":"Development of TaqMan Real-time Polymerase Chain Reaction for the Detection and Identification of Penicillium marneffei","volume":"52","author":"Pornprasert","year":"2009","journal-title":"Mycoses"},{"key":"ref_109","doi-asserted-by":"crossref","first-page":"549","DOI":"10.1080\/13693780802484875","article-title":"Application of Nested PCR to Detect Penicillium marneffei in Serum Samples","volume":"47","author":"Pongpom","year":"2009","journal-title":"Med. Mycol."},{"key":"ref_110","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1111\/j.1574-695X.2009.00647.x","article-title":"Development and Evaluation of Loop-Mediated Isothermal Amplification (LAMP) for the Rapid Diagnosis of Penicillium marneffei in Archived Tissue Samples","volume":"58","author":"Sun","year":"2010","journal-title":"FEMS Immunol. Med. Microbiol."},{"key":"ref_111","doi-asserted-by":"crossref","first-page":"162","DOI":"10.1093\/mmy\/myv068","article-title":"Whole Blood Nested PCR and Real-Time PCR Amplification of Talaromyces marneffei Specific DNA for Diagnosis","volume":"54","author":"Lu","year":"2016","journal-title":"Med. Mycol."},{"key":"ref_112","first-page":"181","article-title":"Evaluation of Quantitative Real-Time PCR and Platelia Galactomannan Assays for the Diagnosis of Disseminated Talaromyces marneffei Infection","volume":"58","author":"Li","year":"2019","journal-title":"Med. Mycol."},{"key":"ref_113","doi-asserted-by":"crossref","first-page":"e00069-19","DOI":"10.1128\/CMR.00069-19","article-title":"Antifungal Susceptibility Testing: Current Approaches","volume":"33","author":"Berkow","year":"2020","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_114","doi-asserted-by":"crossref","first-page":"198","DOI":"10.1111\/myc.12469","article-title":"Epidemiology and Molecular Mechanisms of Antifungal Resistance in Candida and Aspergillus","volume":"59","author":"Souza","year":"2016","journal-title":"Mycoses"},{"key":"ref_115","doi-asserted-by":"crossref","first-page":"1602.e1","DOI":"10.1016\/j.cmi.2023.08.030","article-title":"Mutations in TAC1 and ERG11 Are Major Drivers of Triazole Antifungal Resistance in Clinical Isolates of Candida parapsilosis","volume":"29","author":"Doorley","year":"2023","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_116","doi-asserted-by":"crossref","first-page":"e00889-22","DOI":"10.1128\/aac.00889-22","article-title":"Evolution of Fluconazole Resistance Mechanisms and Clonal Types of Candida parapsilosis Isolates from a Tertiary Care Hospital in South Korea","volume":"66","author":"Kim","year":"2022","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_117","doi-asserted-by":"crossref","first-page":"ofaa158","DOI":"10.1093\/ofid\/ofaa158","article-title":"Genetic Heterogeneity of Australian Candida auris Isolates: Insights from a Nonoutbreak Setting Using Whole-Genome Sequencing","volume":"7","author":"Biswas","year":"2020","journal-title":"Open Forum Infect. Dis."},{"key":"ref_118","doi-asserted-by":"crossref","first-page":"792","DOI":"10.1016\/j.cmi.2019.03.028","article-title":"Resistance of Candida to Azoles and Echinocandins Worldwide","volume":"25","author":"Pristov","year":"2019","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_119","doi-asserted-by":"crossref","unstructured":"Spampinato, C., and Leonardi, D. (2013). Candida Infections, Causes, Targets, and Resistance Mechanisms: Traditional and Alternative Antifungal Agents. Biomed. Res. Int., 2013.","DOI":"10.1155\/2013\/204237"},{"key":"ref_120","doi-asserted-by":"crossref","first-page":"S458","DOI":"10.1093\/infdis\/jix121","article-title":"Culture-Independent Molecular Methods for Detection of Antifungal Resistance Mechanisms and Fungal Identification","volume":"216","author":"Perlin","year":"2017","journal-title":"J. Infect. Dis."},{"key":"ref_121","doi-asserted-by":"crossref","unstructured":"Czajka, K.M., Venkataraman, K., Brabant-Kirwan, D., Santi, S.A., Verschoor, C., Appanna, V.D., Singh, R., Saunders, D.P., and Tharmalingam, S. (2023). Molecular Mechanisms Associated with Antifungal Resistance in Pathogenic Candida Species. Cells, 12.","DOI":"10.3390\/cells12222655"},{"key":"ref_122","doi-asserted-by":"crossref","unstructured":"Ferrari, S., Ischer, F., Calabrese, D., Posteraro, B., Sanguinetti, M., Fadda, G., Rohde, B., Bauser, C., Bader, O., and Sanglard, D. (2009). Gain of Function Mutations in CgPDR1 of Candida glabrata Not Only Mediate Antifungal Resistance but Also Enhance Virulence. PLoS Pathog., 5.","DOI":"10.1371\/journal.ppat.1000268"},{"key":"ref_123","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1016\/j.jgar.2022.05.004","article-title":"Azole Resistance in Candida glabrata Clinical Isolates from Global Surveillance Is Associated with Efflux Overexpression","volume":"29","author":"Castanheira","year":"2022","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"ref_124","doi-asserted-by":"crossref","unstructured":"Rybak, J.M., Cuomo, C.A., and David Rogers, P. (2022). The Molecular and Genetic Basis of Antifungal Resistance in the Emerging Fungal Pathogen Candida auris. Curr. Opin. Microbiol., 70.","DOI":"10.1016\/j.mib.2022.102208"},{"key":"ref_125","doi-asserted-by":"crossref","unstructured":"Arrieta-Aguirre, I., Men\u00e9ndez-Manj\u00f3n, P., Carrano, G., Diez, A., Fernandez-de-Larrinoa, \u00cd., and Moragues, M.-D. (2023). Molecular Identification of Fungal Species through Multiplex-QPCR to Determine Candidal Vulvovaginitis and Antifungal Susceptibility. J. Fungi, 9.","DOI":"10.20944\/preprints202311.0196.v1"},{"key":"ref_126","doi-asserted-by":"crossref","first-page":"3626","DOI":"10.1128\/AAC.00123-14","article-title":"Positions and Numbers of FKS Mutations in Candida albicans Selectively Influence in vitro and in vivo Susceptibilities to Echinocandin Treatment","volume":"58","author":"Lackner","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_127","doi-asserted-by":"crossref","first-page":"3390","DOI":"10.1021\/acs.chemrev.0c00199","article-title":"Antifungal Drug Resistance: Molecular Mechanisms in Candida albicans and Beyond","volume":"121","author":"Lee","year":"2021","journal-title":"Chem. Rev."},{"key":"ref_128","doi-asserted-by":"crossref","unstructured":"Posteraro, B., Torelli, R., Vella, A., Leone, P.M., De Angelis, G., De Carolis, E., Ventura, G., Sanguinetti, M., and Fantoni, M. (2020). Pan-Echinocandin-Resistant Candida glabrata Bloodstream Infection Complicating COVID-19: A Fatal Case Report. J. Fungi, 6.","DOI":"10.20944\/preprints202008.0198.v1"},{"key":"ref_129","doi-asserted-by":"crossref","unstructured":"Szymankiewicz, M., Kamecki, K., Jarzynka, S., Koryszewska-Bagi\u0144ska, A., Ol\u0119dzka, G., and Nowikiewicz, T. (2021). Case Report: Echinocandin-Resistance Candida glabrata FKS Mutants from Patient Following Radical Cystoprostatectomy Due to Muscle-Invasive Bladder Cancer. Front. Oncol., 11.","DOI":"10.3389\/fonc.2021.794235"},{"key":"ref_130","first-page":"e56714","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":"ref_131","doi-asserted-by":"crossref","unstructured":"Khalaf, R.A., Fattouh, N., Medvecky, M., and Hrabak, J. (2021). Whole Genome Sequencing of a Clinical Drug Resistant Candida albicans Isolate Reveals Known and Novel Mutations in Genes Involved in Resistance Acquisition Mechanisms. J. Med. Microbiol., 70.","DOI":"10.1099\/jmm.0.001351"},{"key":"ref_132","doi-asserted-by":"crossref","first-page":"286","DOI":"10.1111\/lam.13516","article-title":"Targeted Amplification and MinION Nanopore Sequencing of Key Azole and Echinocandin Resistance Determinants of Clinically Relevant Candida spp. from Blood Culture Bottles","volume":"73","author":"Chew","year":"2021","journal-title":"Lett. Appl. Microbiol."},{"key":"ref_133","doi-asserted-by":"crossref","first-page":"2053","DOI":"10.1093\/jac\/dkac161","article-title":"Molecular Mechanisms of Acquired Antifungal Drug Resistance in Principal Fungal Pathogens and EUCAST Guidance for Their Laboratory Detection and Clinical Implications","volume":"77","author":"Rogers","year":"2022","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_134","doi-asserted-by":"crossref","first-page":"e03333-20","DOI":"10.1128\/mBio.03333-20","article-title":"Genome-Wide Analysis of Experimentally Evolved Candida auris Reveals Multiple Novel Mechanisms of Multidrug Resistance","volume":"12","author":"Carolus","year":"2021","journal-title":"mBio"},{"key":"ref_135","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1038\/s44259-023-00007-2","article-title":"Molecular Mechanisms Governing Antifungal Drug Resistance","volume":"1","author":"Lee","year":"2023","journal-title":"npj Antimicrob. Resist."},{"key":"ref_136","doi-asserted-by":"crossref","first-page":"599","DOI":"10.1016\/j.ijantimicag.2017.05.012","article-title":"Molecular Basis of Antifungal Drug Resistance in Yeasts","volume":"50","author":"Morio","year":"2017","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref_137","doi-asserted-by":"crossref","first-page":"e00761-23","DOI":"10.1128\/msphere.00761-23","article-title":"Functional Genetic Characterization of Stress Tolerance and Biofilm Formation in Nakaseomyces (Candida) glabrata via a Novel CRISPR Activation System","volume":"9","author":"Maroc","year":"2024","journal-title":"mSphere"},{"key":"ref_138","doi-asserted-by":"crossref","first-page":"jkac301","DOI":"10.1093\/g3journal\/jkac301","article-title":"Development and Applications of a CRISPR Activation System for Facile Genetic Overexpression in Candida albicans","volume":"13","author":"Gervais","year":"2023","journal-title":"G3 Genes Genomes Genet."},{"key":"ref_139","doi-asserted-by":"crossref","first-page":"e00536-15","DOI":"10.1128\/mBio.00536-15","article-title":"Genomic Context of Azole Resistance Mutations in Aspergillus fumigatus Determined Using Whole-Genome Sequencing","volume":"6","author":"Abdolrasouli","year":"2015","journal-title":"mBio"},{"key":"ref_140","doi-asserted-by":"crossref","first-page":"419","DOI":"10.1111\/myc.13426","article-title":"Azole Resistance in Aspergillus fumigatus. The First 2-year\u2019s Data from the Danish National Surveillance Study, 2018\u20132020","volume":"65","author":"Risum","year":"2022","journal-title":"Mycoses"},{"key":"ref_141","doi-asserted-by":"crossref","first-page":"S83","DOI":"10.1093\/mmy\/myx144","article-title":"Triazole Resistance Surveillance in Aspergillus fumigatus","volume":"56","author":"Lagrou","year":"2018","journal-title":"Med. Mycol."},{"key":"ref_142","doi-asserted-by":"crossref","first-page":"e01277-17","DOI":"10.1128\/AAC.01277-17","article-title":"Emergence of Echinocandin Resistance Due to a Point Mutation in the Fks1 Gene of Aspergillus fumigatus in a Patient with Chronic Pulmonary Aspergillosis","volume":"61","author":"Moore","year":"2017","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_143","doi-asserted-by":"crossref","unstructured":"Satish, S., and Perlin, D.S. (2019). Echinocandin Resistance in Aspergillus fumigatus Has Broad Implications for Membrane Lipid Perturbations That Influence Drug-Target Interactions. Microbiol. Insights, 12.","DOI":"10.1177\/1178636119897034"},{"key":"ref_144","doi-asserted-by":"crossref","first-page":"e01803-21","DOI":"10.1128\/mBio.01803-21","article-title":"Genomic Diversity of Azole-Resistant Aspergillus fumigatus in the United States","volume":"12","author":"Etienne","year":"2021","journal-title":"mBio"},{"key":"ref_145","doi-asserted-by":"crossref","unstructured":"Nargesi, S., Valadan, R., Abastabar, M., Kaboli, S., Thekkiniath, J., and Hedayati, M.T. (2022). A Whole Genome Sequencing-Based Approach to Track down Genomic Variants in Itraconazole-Resistant Species of Aspergillus from Iran. J. Fungi, 8.","DOI":"10.3390\/jof8101091"},{"key":"ref_146","doi-asserted-by":"crossref","first-page":"e05188-22","DOI":"10.1128\/spectrum.05188-22","article-title":"HapE and Hmg1 Mutations Are Drivers of Cyp51A-Independent Pan-Triazole Resistance in an Aspergillus fumigatus Clinical Isolate","volume":"11","author":"Souza","year":"2023","journal-title":"Microbiol. Spectr."},{"key":"ref_147","doi-asserted-by":"crossref","unstructured":"G\u00f3mez Londo\u00f1o, L.F., and Brewer, M.T. (2023). Detection of Azole-Resistant Aspergillus fumigatus in the Environment from Air, Plant Debris, Compost, and Soil. PLoS ONE, 18.","DOI":"10.1371\/journal.pone.0282499"},{"key":"ref_148","doi-asserted-by":"crossref","unstructured":"van der Torre, M.H., Novak-Frazer, L., and Rautemaa-Richardson, R. (2020). Detecting Azole-Antifungal Resistance in Aspergillus fumigatus by Pyrosequencing. J. Fungi, 6.","DOI":"10.3390\/jof6010012"},{"key":"ref_149","doi-asserted-by":"crossref","first-page":"e00865-19","DOI":"10.1128\/AAC.00865-19","article-title":"Molecular Identification, Antifungal Susceptibility Testing, and Mechanisms of Azole Resistance in Aspergillus Species Received within a Surveillance Program on Antifungal Resistance in Spain","volume":"63","author":"Medina","year":"2019","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_150","doi-asserted-by":"crossref","unstructured":"Scharmann, U., Kirchhoff, L., Hain, A., Buer, J., Koldehoff, M., Steinmann, J., and Rath, P.-M. (2021). Evaluation of Three Commercial PCR Assays for the Detection of Azole-Resistant Aspergillus fumigatus from Respiratory Samples of Immunocompromised Patients. J. Fungi, 7.","DOI":"10.3390\/jof7020132"},{"key":"ref_151","doi-asserted-by":"crossref","first-page":"41","DOI":"10.3314\/mmj.21-00001","article-title":"Rapid Molecular Detection of Terbinafine-Resistant Dermatophytes","volume":"62","author":"Kano","year":"2021","journal-title":"Med. Mycol. J."},{"key":"ref_152","doi-asserted-by":"crossref","first-page":"721","DOI":"10.1111\/myc.13271","article-title":"Evaluation of DermaGenius\u00ae Resistance Real-time Polymerase Chain Reaction for Rapid Detection of Terbinafine-resistant Trichophyton Species","volume":"64","author":"Singh","year":"2021","journal-title":"Mycoses"},{"key":"ref_153","doi-asserted-by":"crossref","first-page":"1935","DOI":"10.1128\/AAC.36.9.1935","article-title":"Activities of Antifolate, Antiviral, and Other Drugs in an Immunosuppressed Rat Model of Pneumocystis carinii Pneumonia","volume":"36","author":"Walzer","year":"1992","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_154","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1128\/AAC.39.2.279","article-title":"Trimethoprim and Sulfonamide Resistance","volume":"39","author":"Huovinen","year":"1995","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_155","doi-asserted-by":"crossref","unstructured":"Singh, A., Sharma, B., Mahto, K.K., Meis, J.F., and Chowdhary, A. (2020). High-Frequency Direct Detection of Triazole Resistance in Aspergillus fumigatus from Patients with Chronic Pulmonary Fungal Diseases in India. J. Fungi, 6.","DOI":"10.3390\/jof6020067"},{"key":"ref_156","doi-asserted-by":"crossref","unstructured":"Tsang, C.-C., Teng, J.L.L., Lau, S.K.P., and Woo, P.C.Y. (2021). Rapid Genomic Diagnosis of Fungal Infections in the Age of Gext-Generation Sequencing. J. Fungi, 7.","DOI":"10.3390\/jof7080636"},{"key":"ref_157","doi-asserted-by":"crossref","unstructured":"Jiang, S., Chen, Y., Han, S., Lv, L., and Li, L. (2022). Next-Generation Sequencing Applications for the Study of Fungal Pathogens. Microorganisms, 10.","DOI":"10.3390\/microorganisms10101882"},{"key":"ref_158","doi-asserted-by":"crossref","unstructured":"Douglas, A.P., Stewart, A.G., Halliday, C.L., and Chen, S.C.-A. (2023). Outbreaks of Fungal Infections in Hospitals: Epidemiology, Detection, and Management. J. Fungi, 9.","DOI":"10.3390\/jof9111059"},{"key":"ref_159","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1186\/s13756-018-0338-9","article-title":"Healthcare-Associated Fungal Outbreaks: New and Uncommon Species, New Molecular Tools for Investigation and Prevention","volume":"7","author":"Bougnoux","year":"2018","journal-title":"Antimicrob. Resist. Infect. Control"},{"key":"ref_160","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1186\/s43008-020-00033-z","article-title":"Unambiguous Identification of Fungi: Where Do We Stand and How Accurate and Precise Is Fungal DNA Barcoding?","volume":"11","author":"Aime","year":"2020","journal-title":"IMA Fungus"},{"key":"ref_161","doi-asserted-by":"crossref","unstructured":"Gostin\u010dar, C. (2020). Towards Genomic Criteria for Delineating Fungal Species. J. Fungi, 6.","DOI":"10.3390\/jof6040246"},{"key":"ref_162","doi-asserted-by":"crossref","unstructured":"Salem-Bango, Z., Price, T.K., Chan, J.L., Chandrasekaran, S., Garner, O.B., and Yang, S. (2023). Fungal Whole-Genome Sequencing for Species Identification: From Test Development to Clinical Utilization. J. Fungi, 9.","DOI":"10.3390\/jof9020183"},{"key":"ref_163","doi-asserted-by":"crossref","unstructured":"Lumpe, J., Gumbleton, L., Gorzalski, A., Libuit, K., Varghese, V., Lloyd, T., Tadros, F., Arsimendi, T., Wagner, E., and Stephens, C. (2023). GAMBIT (Genomic Approximation Method for Bacterial Identification and Tracking): A Methodology to Rapidly Leverage Whole Genome Sequencing of Bacterial Isolates for Clinical Identification. PLoS ONE, 18.","DOI":"10.1371\/journal.pone.0277575"},{"key":"ref_164","doi-asserted-by":"crossref","unstructured":"Ambrosio, F.J., Scribner, M.R., Wright, S.M., Otieno, J.R., Doughty, E.L., Gorzalski, A., Siao, D.D., Killian, S., Hua, C., and Schneider, E. (2023). TheiaEuk: A Species-Agnostic Bioinformatics Workflow for Fungal Genomic Characterization. Front. Public Health, 11.","DOI":"10.3389\/fpubh.2023.1198213"},{"key":"ref_165","doi-asserted-by":"crossref","unstructured":"Yu, P.-L., Fulton, J.C., Hudson, O.H., Huguet-Tapia, J.C., and Brawner, J.T. (2023). Next-Generation Fungal Identification Using Target Enrichment and Nanopore Sequencing. BMC Genom., 24.","DOI":"10.1186\/s12864-023-09691-w"},{"key":"ref_166","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1016\/j.nmni.2016.07.003","article-title":"Whole Genome Sequencing of Emerging Multidrug Resistant Candida auris Isolates in India Demonstrates Low Genetic Variation","volume":"13","author":"Sharma","year":"2016","journal-title":"New Microbes New Infect."},{"key":"ref_167","doi-asserted-by":"crossref","first-page":"e00029-17","DOI":"10.1128\/CMR.00029-17","article-title":"Candida auris: A Review of the Literature","volume":"31","author":"Taori","year":"2018","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_168","doi-asserted-by":"crossref","unstructured":"dos Santos, R.A.C., Steenwyk, J.L., Rivero-Menendez, O., Mead, M.E., Silva, L.P., Bastos, R.W., Alastruey-Izquierdo, A., Goldman, G.H., and Rokas, A. (2020). Genomic and Phenotypic Heterogeneity of Clinical Isolates of the Human Pathogens Aspergillus fumigatus, Aspergillus lentulus, and Aspergillus fumigatiaffinis. Front. Genet., 11.","DOI":"10.3389\/fgene.2020.00459"},{"key":"ref_169","doi-asserted-by":"crossref","first-page":"myae012","DOI":"10.1093\/mmy\/myae012","article-title":"Whole Genome Characterization of Trichophyton indotineae Isolated in Singapore","volume":"62","author":"Teo","year":"2024","journal-title":"Med. Mycol."},{"key":"ref_170","doi-asserted-by":"crossref","unstructured":"Spettel, K., Barousch, W., Makristathis, A., Zeller, I., Nehr, M., Selitsch, B., Lackner, M., Rath, P.-M., Steinmann, J., and Willinger, B. (2019). Analysis of Antifungal Resistance Genes in Candida albicans and Candida glabrata Using next Generation Sequencing. PLoS ONE, 14.","DOI":"10.1371\/journal.pone.0210397"},{"key":"ref_171","doi-asserted-by":"crossref","unstructured":"Alastruey-Izquierdo, A., and Mart\u00edn-Galiano, A.J. (2023). The Challenges of the Genome-Based Identification of Antifungal Resistance in the Clinical Routine. Front. Microbiol., 14.","DOI":"10.3389\/fmicb.2023.1134755"},{"key":"ref_172","doi-asserted-by":"crossref","first-page":"e00402-20","DOI":"10.1128\/AAC.00402-20","article-title":"Antifungal Susceptibility of Clinical Yeast Isolates from a Large Canadian Reference Laboratory and Application of Whole-Genome Sequence Analysis to Elucidate Mechanisms of Acquired Resistance","volume":"64","author":"McTaggart","year":"2020","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_173","doi-asserted-by":"crossref","first-page":"e00291-21","DOI":"10.1128\/AAC.00291-21","article-title":"Long Terminal Repeat Retrotransposon Afut4 Promotes Azole Resistance of Aspergillus fumigatus by Enhancing the Expression of Sac1 Gene","volume":"65","author":"Hu","year":"2021","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_174","doi-asserted-by":"crossref","unstructured":"Uddin, W., Dhabalia, D., Prakash, S.M.U., and Kabir, M.A. (2021). Systematic Truncations of Chromosome 4 and Their Responses to Antifungals in Candida albicans. J. Genet. Eng. Biotechnol., 19.","DOI":"10.1186\/s43141-021-00197-0"},{"key":"ref_175","doi-asserted-by":"crossref","first-page":"2031","DOI":"10.3201\/eid2609.200341","article-title":"Saprochaete clavata Outbreak Infecting Cancer Center through Dishwasher","volume":"26","author":"Menu","year":"2020","journal-title":"Emerg. Infect. Dis."},{"key":"ref_176","doi-asserted-by":"crossref","unstructured":"Di Pilato, V., Codda, G., Ball, L., Giacobbe, D.R., Willison, E., Mikulska, M., Magnasco, L., Crea, F., Vena, A., and Pelosi, P. (2021). Molecular Epidemiological Investigation of a Nosocomial Cluster of C. auris: Evidence of Recent Emergence in Italy and Ease of Transmission during the COVID-19 Pandemic. J. Fungi, 7.","DOI":"10.3390\/jof7020140"},{"key":"ref_177","doi-asserted-by":"crossref","unstructured":"Gorzalski, A., Ambrosio, F.J., Massic, L., Scribner, M.R., Siao, D.D., Hua, C., Dykema, P., Schneider, E., Njoku, C., and Libuit, K. (2023). The Use of Whole-Genome Sequencing and Development of Bioinformatics to Monitor Overlapping Outbreaks of Candida auris in Southern Nevada. Front. Public Health, 11.","DOI":"10.3389\/fpubh.2023.1198189"},{"key":"ref_178","doi-asserted-by":"crossref","unstructured":"Hiel, S.J.P., Hendriks, A.C.A., Eijkenboom, J.J.A., Bosch, T., Coolen, J.P.M., Melchers, W.J.G., Anr\u00f6chte, P., Camps, S.M.T., Verweij, P.E., and Zhang, J. (2024). Aspergillus Outbreak in an Intensive Care Unit: Source Analysis with Whole Genome Sequencing and Short Tandem Repeats. J. Fungi, 10.","DOI":"10.3390\/jof10010051"},{"key":"ref_179","doi-asserted-by":"crossref","first-page":"101758","DOI":"10.1016\/j.pmpp.2021.101758","article-title":"A Rapid Fungal DNA Extraction Method Suitable for PCR Screening Fungal Mutants, Infected Plant Tissue and Spore Trap Samples","volume":"117","author":"Pilo","year":"2022","journal-title":"Physiol. Mol. Plant Pathol."},{"key":"ref_180","doi-asserted-by":"crossref","unstructured":"Bellemare, A., John, T., and Marqueteau, S. (2018). Fungal Genomic DNA Extraction Methods for Rapid Genotyping and Genome Sequencing. Methods in Molecular Biology, Humana Press.","DOI":"10.1007\/978-1-4939-7804-5_2"},{"key":"ref_181","first-page":"816","article-title":"High Molecular Weight DNA Extraction Methods Lead to High Quality Filamentous Ascomycete Fungal Genome Assemblies Using Oxford Nanopore Sequencing","volume":"8","author":"Petersen","year":"2022","journal-title":"Microb. Genom."},{"key":"ref_182","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1016\/j.fgb.2015.08.010","article-title":"Mind the Gap; Seven Reasons to Close Fragmented Genome Assemblies","volume":"90","author":"Thomma","year":"2016","journal-title":"Fungal Genet. Biol."},{"key":"ref_183","doi-asserted-by":"crossref","unstructured":"Araujo, R., and Sampaio-Maia, B. (2018). Fungal Genomes and Genotyping. Advances in Applied Microbiology, Elsevier.","DOI":"10.1016\/bs.aambs.2017.10.003"},{"key":"ref_184","doi-asserted-by":"crossref","unstructured":"Farrer, R.A., and Fisher, M.C. (2017). Describing Genomic and Epigenomic Traits Underpinning Emerging Fungal Pathogens. Advances in Genetics, Elsevier.","DOI":"10.1016\/bs.adgen.2017.09.009"},{"key":"ref_185","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":"ref_186","doi-asserted-by":"crossref","unstructured":"Matute, D.R., and Sep\u00falveda, V.E. (2019). Fungal Species Boundaries in the Genomics Era. Fungal Genet. Biol., 131.","DOI":"10.1016\/j.fgb.2019.103249"},{"key":"ref_187","doi-asserted-by":"crossref","unstructured":"Stengel, A., Stanke, K.M., Quattrone, A.C., and Herr, J.R. (2022). Improving Taxonomic Delimitation of Fungal Species in the Age of Genomics and Phenomics. Front. Microbiol., 13.","DOI":"10.3389\/fmicb.2022.847067"},{"key":"ref_188","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1139\/gen-2020-0022","article-title":"Fungal Species Concepts in the Genomics Era","volume":"63","author":"Xu","year":"2020","journal-title":"Genome"},{"key":"ref_189","doi-asserted-by":"crossref","unstructured":"Ahrendt, S.R., Mondo, S.J., Haridas, S., and Grigoriev, I.V. (2023). MycoCosm, the JGI\u2019s Fungal Genome Portal for Comparative Genomic and Multiomics Data Analyses. Methods in Molecular Biology, Humana.","DOI":"10.1007\/978-1-0716-2871-3_14"},{"key":"ref_190","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":"ref_191","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":"ref_192","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":"ref_193","doi-asserted-by":"crossref","unstructured":"Basenko, E., Pulman, J., Shanmugasundram, A., Harb, O., Crouch, K., Starns, D., Warrenfeltz, S., Aurrecoechea, C., Stoeckert, C., and Kissinger, J. (2018). FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes. J. Fungi, 4.","DOI":"10.3390\/jof4010039"},{"key":"ref_194","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."},{"key":"ref_195","doi-asserted-by":"crossref","first-page":"e52","DOI":"10.1016\/S2666-5247(23)00244-6","article-title":"Performance of Clinical Metagenomics in France: A Prospective Observational Study","volume":"5","author":"Fourgeaud","year":"2024","journal-title":"Lancet Microbe"},{"key":"ref_196","doi-asserted-by":"crossref","first-page":"20297","DOI":"10.1038\/s41598-023-47685-6","article-title":"Blood Plasma Metagenomic Next-Generation Sequencing for Identifying Pathogens of Febrile Neutropenia in Acute Leukemia Patients","volume":"13","author":"Qi","year":"2023","journal-title":"Sci. Rep."},{"key":"ref_197","doi-asserted-by":"crossref","unstructured":"Xie, F., Duan, Z., Zeng, W., Xie, S., Xie, M., Fu, H., Ye, Q., Xu, T., and Xie, L. (2021). Clinical Metagenomics Assessments Improve Diagnosis and Outcomes in Community-Acquired Pneumonia. BMC Infect. Dis., 21.","DOI":"10.1186\/s12879-021-06039-1"},{"key":"ref_198","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":"ref_199","doi-asserted-by":"crossref","unstructured":"Hilt, E.E., and Ferrieri, P. (2022). Next Generation and Other Sequencing Technologies in Diagnostic Microbiology and Infectious Diseases. Genes, 13.","DOI":"10.3390\/genes13091566"},{"key":"ref_200","doi-asserted-by":"crossref","first-page":"447","DOI":"10.1016\/j.cll.2020.08.003","article-title":"Clinical Pathogen Genomics","volume":"40","author":"Cameron","year":"2020","journal-title":"Clin. Lab. Med."},{"key":"ref_201","doi-asserted-by":"crossref","first-page":"833","DOI":"10.1038\/nbt.3935","article-title":"Shotgun Metagenomics, from Sampling to Analysis","volume":"35","author":"Quince","year":"2017","journal-title":"Nat. Biotechnol."},{"key":"ref_202","doi-asserted-by":"crossref","first-page":"1502","DOI":"10.1001\/jama.2013.3231","article-title":"A Culture-Independent Sequence-Based Metagenomics Approach to the Investigation of an Outbreak of Shiga-Toxigenic Escherichia coli O104:H4","volume":"309","author":"Loman","year":"2013","journal-title":"JAMA"},{"key":"ref_203","doi-asserted-by":"crossref","unstructured":"Oniciuc, E., Likotrafiti, E., Alvarez-Molina, A., Prieto, M., Santos, J., and Alvarez-Ord\u00f3\u00f1ez, A. (2018). The Present and Future of Whole Genome Sequencing (WGS) and Whole Metagenome Sequencing (WMS) for Surveillance of Antimicrobial Resistant Microorganisms and Antimicrobial Resistance Genes across the Food Chain. Genes, 9.","DOI":"10.3390\/genes9050268"},{"key":"ref_204","doi-asserted-by":"crossref","first-page":"e01055","DOI":"10.1016\/j.idcr.2021.e01055","article-title":"Rapid Diagnosis of Talaromyces marneffei Infection Assisted by Metagenomic Next-Generation Sequencing in a HIV-Negative Patient","volume":"23","author":"Zhang","year":"2021","journal-title":"IDCases"},{"key":"ref_205","doi-asserted-by":"crossref","first-page":"567","DOI":"10.2147\/IDR.S235182","article-title":"Metagenomic Next-Generation Sequencing versus Traditional Pathogen Detection in the Diagnosis of Peripheral Pulmonary Infectious Lesions","volume":"13","author":"Huang","year":"2020","journal-title":"Infect. Drug Resist."},{"key":"ref_206","doi-asserted-by":"crossref","unstructured":"Lin, P., Chen, Y., Su, S., Nan, W., Zhou, L., Zhou, Y., and Li, Y. (2022). Diagnostic Value of Metagenomic Next-Generation Sequencing of Bronchoalveolar Lavage Fluid for the Diagnosis of Suspected Pneumonia in Immunocompromised Patients. BMC Infect. Dis., 22.","DOI":"10.1186\/s12879-022-07381-8"},{"key":"ref_207","doi-asserted-by":"crossref","first-page":"e02473-21","DOI":"10.1128\/spectrum.02473-21","article-title":"Improving Suspected Pulmonary Infection Diagnosis by Bronchoalveolar Lavage Fluid Metagenomic Next-Generation Sequencing: A Multicenter Retrospective Study","volume":"10","author":"Jin","year":"2022","journal-title":"Microbiol. Spectr."},{"key":"ref_208","doi-asserted-by":"crossref","unstructured":"Sun, H., Wang, F., Zhang, M., Xu, X., Li, M., Gao, W., Wu, X., Han, H., Wang, Q., and Yao, G. (2022). Diagnostic Value of Bronchoalveolar Lavage Fluid Metagenomic Next-Generation Sequencing in Pneumocystis jirovecii Pneumonia in Non-HIV Immunosuppressed Patients. Front. Cell Infect. Microbiol., 12.","DOI":"10.3389\/fcimb.2022.872813"},{"key":"ref_209","doi-asserted-by":"crossref","unstructured":"Guo, Y., Li, H., Chen, H., Li, Z., Ding, W., Wang, J., Yin, Y., Jin, L., Sun, S., and Jing, C. (2021). Metagenomic Next-Generation Sequencing to Identify Pathogens and Cancer in Lung Biopsy Tissue. eBioMedicine, 73.","DOI":"10.1016\/j.ebiom.2021.103639"},{"key":"ref_210","doi-asserted-by":"crossref","unstructured":"Wang, J., Han, Y., and Feng, J. (2019). Metagenomic Next-Generation Sequencing for Mixed Pulmonary Infection Diagnosis. BMC Pulm. Med., 19.","DOI":"10.1186\/s12890-019-1022-4"},{"key":"ref_211","doi-asserted-by":"crossref","first-page":"e00586-23","DOI":"10.1128\/spectrum.00586-23","article-title":"Joint Application of Metagenomic Next-Generation Sequencing and Histopathological Examination for the Diagnosis of Pulmonary Infectious Disease","volume":"12","author":"Yang","year":"2024","journal-title":"Microbiol. Spectr."},{"key":"ref_212","doi-asserted-by":"crossref","first-page":"947","DOI":"10.1001\/jamaneurol.2018.0463","article-title":"Chronic Meningitis Investigated via Metagenomic Next-Generation Sequencing","volume":"75","author":"Wilson","year":"2018","journal-title":"JAMA Neurol."},{"key":"ref_213","doi-asserted-by":"crossref","unstructured":"Qian, M., Li, C., Zhang, M., Zhan, Y., Zhu, B., Wang, L., Shen, Q., Yue, L., Chen, H., and Cheng, Y. (2023). Blood Metagenomics Next-Generation Sequencing Has Advantages in Detecting Difficult-to-Cultivate Pathogens, and Mixed Infections: Results from a Real-World Cohort. Front. Cell Infect. Microbiol., 13.","DOI":"10.3389\/fcimb.2023.1268281"},{"key":"ref_214","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1038\/s41591-020-1105-z","article-title":"Rapid Pathogen Detection by Metagenomic Next-Generation Sequencing of Infected Body Fluids","volume":"27","author":"Gu","year":"2021","journal-title":"Nat. Med."},{"key":"ref_215","doi-asserted-by":"crossref","first-page":"e36745","DOI":"10.1097\/MD.0000000000036745","article-title":"Clinical Application of Metagenomic Next-Generation Sequencing in Patients with Different Organ System Infection: A Retrospective Observational Study","volume":"103","author":"Zhang","year":"2024","journal-title":"Medicine"},{"key":"ref_216","doi-asserted-by":"crossref","unstructured":"Jia, K., Huang, S., Shen, C., Li, H., Zhang, Z., Wang, L., Zhao, G., Wu, Z., Lin, Y., and Xia, H. (2023). Enhancing Urinary Tract Infection Diagnosis for Negative Culture Patients with Metagenomic Next-Generation Sequencing (MNGS). Front. Cell Infect. Microbiol., 13.","DOI":"10.3389\/fcimb.2023.1119020"},{"key":"ref_217","doi-asserted-by":"crossref","unstructured":"Hoang, M.T.V., Irinyi, L., Hu, Y., Schwessinger, B., and Meyer, W. (2022). Long-Reads-Based Metagenomics in Clinical Diagnosis with a Special Focus on Fungal Infections. Front. Microbiol., 12.","DOI":"10.3389\/fmicb.2021.708550"},{"key":"ref_218","doi-asserted-by":"crossref","unstructured":"McIntyre, A.B.R., Ounit, R., Afshinnekoo, E., Prill, R.J., H\u00e9naff, E., Alexander, N., Minot, S.S., Danko, D., Foox, J., and Ahsanuddin, S. (2017). Comprehensive Benchmarking and Ensemble Approaches for Metagenomic Classifiers. Genome Biol., 18.","DOI":"10.1186\/s13059-017-1299-7"},{"key":"ref_219","doi-asserted-by":"crossref","first-page":"663","DOI":"10.1038\/s41564-018-0349-6","article-title":"Analytical and Clinical Validation of a Microbial Cell-Free DNA Sequencing Test for Infectious Disease","volume":"4","author":"Blauwkamp","year":"2019","journal-title":"Nat. Microbiol."},{"key":"ref_220","doi-asserted-by":"crossref","first-page":"831","DOI":"10.1101\/gr.238170.118","article-title":"Laboratory Validation of a Clinical Metagenomic Sequencing Assay for Pathogen Detection in Cerebrospinal Fluid","volume":"29","author":"Miller","year":"2019","journal-title":"Genome Res."},{"key":"ref_221","doi-asserted-by":"crossref","first-page":"776","DOI":"10.5858\/arpa.2016-0539-RA","article-title":"Validation of Metagenomic Next-Generation Sequencing Tests for Universal Pathogen Detection","volume":"141","author":"Schlaberg","year":"2017","journal-title":"Arch. Pathol. Lab. 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