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Ramage G, Andersen ÅB. APMIS focus issue 2023-fungal infections: diagnostics and therapeutics. APMIS 2023; 131:559-560. [PMID: 37712200 DOI: 10.1111/apm.13350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 06/29/2023] [Indexed: 09/16/2023]
Affiliation(s)
- Gordon Ramage
- Safeguarding Health through Infection Prevention (SHIP) Research Group, Research Centre for Health, Glasgow Caledonian University, Glasgow, UK
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Lin L, Shen K, Xiao L, lin Y, Feng E, Zhang Y. Identification of prosthetic joint infection by Candida using metagenomic shotgun sequencing. Access Microbiol 2023; 5:000425. [PMID: 37970089 PMCID: PMC10634495 DOI: 10.1099/acmi.0.000425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 10/03/2023] [Indexed: 11/17/2023] Open
Abstract
Background Periprosthetic joint infection (PJI) is a serious complication after total knee arthroplasty. Fungal infections are prone to biofilm formation, which makes it hard to diagnose and clarify the pathogenic species. Case Presentation This case study provides evidence of a novel PJI pathogen that is otherwise difficult to detect using conventional methods. A patient was reviewed with persistent postoperative pain, swelling and eventually drainage around the left knee after undergoing a bilateral total knee arthroplasty 2 years previously for progressive osteoarthritis. By using metagenomic shotgun sequencing to analyse both bacterial and fungal agent sequences, we were able to identify fungal strains of Candida tropicalis, a rarely reported and difficult-to-culture PJI pathogen. Conclusion Metagenomic shotgun sequencing enables the detection of difficult-to-detect pathogens and the formulation of treatment recommendations for fungal infections with low positive rates based on gene content analysis.
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Affiliation(s)
- Liqiong Lin
- Department of Orthopedics, Fuzhou Second Hospital, Fuzhou, PR China
- Fujian Provincial Clinical Medical Research Center for First Aid and Rehabilitation in Orthopaedic Trauma, Fuzhou, PR China
| | - Kaiwei Shen
- Institute for Biochemistry and Molecularbiology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Lili Xiao
- Department of Orthopedics, Fuzhou Second Hospital, Fuzhou, PR China
- Fujian Provincial Clinical Medical Research Center for First Aid and Rehabilitation in Orthopaedic Trauma, Fuzhou, PR China
| | - Yu lin
- Department of Orthopedics, Fuzhou Second Hospital, Fuzhou, PR China
- Fujian Provincial Clinical Medical Research Center for First Aid and Rehabilitation in Orthopaedic Trauma, Fuzhou, PR China
| | - Eryou Feng
- Department of Orthopedics, Fuzhou Second Hospital, Fuzhou, PR China
- Fujian Provincial Clinical Medical Research Center for First Aid and Rehabilitation in Orthopaedic Trauma, Fuzhou, PR China
| | - Yiyuan Zhang
- Department of Orthopedics, Fuzhou Second Hospital, Fuzhou, PR China
- Fujian Provincial Clinical Medical Research Center for First Aid and Rehabilitation in Orthopaedic Trauma, Fuzhou, PR China
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Jenks JD, White PL, Kidd SE, Goshia T, Fraley SI, Hoenigl M, Thompson GR. An update on current and novel molecular diagnostics for the diagnosis of invasive fungal infections. Expert Rev Mol Diagn 2023; 23:1135-1152. [PMID: 37801397 PMCID: PMC10842420 DOI: 10.1080/14737159.2023.2267977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 10/04/2023] [Indexed: 10/08/2023]
Abstract
BACKGROUND Invasive fungal infections cause millions of infections annually, but diagnosis remains challenging. There is an increased need for low-cost, easy to use, highly sensitive and specific molecular assays that can differentiate between colonized and pathogenic organisms from different clinical specimens. AREAS COVERED We reviewed the literature evaluating the current state of molecular diagnostics for invasive fungal infections, focusing on current and novel molecular tests such as polymerase chain reaction (PCR), digital PCR, high-resolution melt (HRM), and metagenomics/next generation sequencing (mNGS). EXPERT OPINION PCR is highly sensitive and specific, although performance can be impacted by prior/concurrent antifungal use. PCR assays can identify mutations associated with antifungal resistance, non-Aspergillus mold infections, and infections from endemic fungi. HRM is a rapid and highly sensitive diagnostic modality that can identify a wide range of fungal pathogens, including down to the species level, but multiplex assays are limited and HRM is currently unavailable in most healthcare settings, although universal HRM is working to overcome this limitation. mNGS offers a promising approach for rapid and hypothesis-free diagnosis of a wide range of fungal pathogens, although some drawbacks include limited access, variable performance across platforms, the expertise and costs associated with this method, and long turnaround times in real-world settings.
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Affiliation(s)
- Jeffrey D Jenks
- Durham County Department of Public Health, Durham, North Carolina, USA
- Division of Infectious Diseases, Department of Medicine, Duke University, Durham, North Carolina, USA
| | - P Lewis White
- Public Health Wales Microbiology Cardiff, UHW, United Kingdom and Centre for trials research/Division of Infection/Immunity, Cardiff University, Cardiff, UK
| | - Sarah E Kidd
- National Mycology Reference Centre, SA Pathology, Adelaide, Australia
- School of Biological Sciences, Faculty of Sciences, University of Adelaide, Adelaide, Australia
| | - Tyler Goshia
- Department of Bioengineering, University of California, San Diego, CA, USA
| | - Stephanie I Fraley
- Department of Bioengineering, University of California, San Diego, CA, USA
| | - Martin Hoenigl
- Division of Infectious Diseases, Medical University of Graz, Graz, Austria
- BioTechMed, Graz, Austria
| | - George R Thompson
- University of California Davis Center for Valley Fever, Sacramento, CA, USA
- Department of Internal Medicine, Division of Infectious Diseases, University of California Davis Medical Center, Sacramento, CA, USA
- Department of Medical Microbiology and Immunology, University of California Davis, Davis, CA, USA
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White PL. Developments in Fungal Serology. CURRENT FUNGAL INFECTION REPORTS 2023; 17:1-12. [PMID: 37360856 PMCID: PMC10099008 DOI: 10.1007/s12281-023-00462-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2023] [Indexed: 06/28/2023]
Abstract
Purpose of Review The true incidence of fungal disease is hampered by conventionally poor diagnostic tests, limited access to advanced diagnostics, and limited surveillance. The availability of serological testing has been available for over two decades and generally underpins the modern diagnosis of the most common forms of fungal disease. This review will focus on technical developments of serological tests for the diagnosis of fungal disease, describing advances in clinical performance when available. Recent Findings Despite their longevity, technical, clinical, and performance limitations remain, and tests specific for fungal pathogens outside the main pathogens are lacking. The availability of LFA and automated systems, capable of running multiple different tests, represents significant developments, but clinical performance data is variable and limited. Summary Fungal serology has significantly advanced the diagnosis of the main fungal infections, with LFA availability increasing accessibility to testing. Combination testing has the potential to overcome performance limitations.
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Affiliation(s)
- P. Lewis White
- Public Health Wales Mycology Reference Laboratory and Cardiff University Centre for Trials Research/Division of Infection and Immunity, UHW, Heath Park, Cardiff, CF14 4XW UK
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Salem-Bango Z, Price TK, Chan JL, Chandrasekaran S, Garner OB, Yang S. Fungal Whole-Genome Sequencing for Species Identification: From Test Development to Clinical Utilization. J Fungi (Basel) 2023; 9:jof9020183. [PMID: 36836298 PMCID: PMC9965959 DOI: 10.3390/jof9020183] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/23/2023] [Accepted: 01/27/2023] [Indexed: 01/31/2023] Open
Abstract
Using next-generation sequencing (NGS), we developed and validated a whole-genome sequencing (WGS)-based clinical test for fungal species identification on clinical isolates. The identification is mainly based on the fungal ribosomal internal transcribed spacer (ITS) region as the primary marker, and additional marker and genomic analysis applied for species within the Mucorales family (using the 28S rRNA gene) and Aspergillus genus (using the beta-tubulin gene and k-mer tree-based phylogenetic clustering). The validation study involving 74 unique fungal isolates (22 yeasts, 51 molds, and 1 mushroom-forming fungus) showed high accuracy, with 100% (74/74) concordance on the genus-level identifications and 89.2% (66/74) concordance on the species level. The 8 discrepant results were due to either the limitation of conventional morphology-based methodology or taxonomic changes. After one year of implementation in our clinical laboratory, this fungal NGS test was utilized in 29 cases; the majority of them were transplant and cancer patients. We demonstrated the utility of this test by detailing five case studies, in which accurate fungal species identification led to correct diagnosis, treatment adjustment or was ruled out for hospital acquired infection. This study provides a model for validation and implementation of WGS for fungal identification in a complex health system that serves a large immunocompromised patient population.
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Wu S, Guo W, Li B, Zhou H, Meng H, Sun J, Li R, Guo D, Zhang X, Li R, Qu W. Progress of polymer-based strategies in fungal disease management: Designed for different roles. Front Cell Infect Microbiol 2023; 13:1142029. [PMID: 37033476 PMCID: PMC10073610 DOI: 10.3389/fcimb.2023.1142029] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 02/22/2023] [Indexed: 04/11/2023] Open
Abstract
Fungal diseases have posed a great challenge to global health, but have fewer solutions compared to bacterial and viral infections. Development and application of new treatment modalities for fungi are limited by their inherent essential properties as eukaryotes. The microorganism identification and drug sensitivity analyze are limited by their proliferation rates. Moreover, there are currently no vaccines for prevention. Polymer science and related interdisciplinary technologies have revolutionized the field of fungal disease management. To date, numerous advanced polymer-based systems have been developed for management of fungal diseases, including prevention, diagnosis, treatment and monitoring. In this review, we provide an overview of current needs and advances in polymer-based strategies against fungal diseases. We high light various treatment modalities. Delivery systems of antifungal drugs, systems based on polymers' innate antifungal activities, and photodynamic therapies each follow their own mechanisms and unique design clues. We also discuss various prevention strategies including immunization and antifungal medical devices, and further describe point-of-care testing platforms as futuristic diagnostic and monitoring tools. The broad application of polymer-based strategies for both public and personal health management is prospected and integrated systems have become a promising direction. However, there is a gap between experimental studies and clinical translation. In future, well-designed in vivo trials should be conducted to reveal the underlying mechanisms and explore the efficacy as well as biosafety of polymer-based products.
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Affiliation(s)
- Siyu Wu
- Department of Hand Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Wenlai Guo
- Department of Hand Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Bo Li
- Department of Cardiovascular Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Huidong Zhou
- Department of Hand Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Hongqi Meng
- Department of Hand Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Junyi Sun
- Changchun American International School, Changchun, China
| | - Ruiyan Li
- Orthpoeadic Medical Center, The Second Hospital of Jilin University, Changchun, China
- Jilin Provincial Key Laboratory of Orhtopeadics, Changchun, China
| | - Deming Guo
- Orthpoeadic Medical Center, The Second Hospital of Jilin University, Changchun, China
- Jilin Provincial Key Laboratory of Orhtopeadics, Changchun, China
| | - Xi Zhang
- Department of Burn Surgery, The First Hospital of Jilin University, Changchun, China
- *Correspondence: Xi Zhang, ; Rui Li, ; Wenrui Qu,
| | - Rui Li
- Department of Hand Surgery, The Second Hospital of Jilin University, Changchun, China
- *Correspondence: Xi Zhang, ; Rui Li, ; Wenrui Qu,
| | - Wenrui Qu
- Department of Hand Surgery, The Second Hospital of Jilin University, Changchun, China
- *Correspondence: Xi Zhang, ; Rui Li, ; Wenrui Qu,
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Fathima AS, Mounika VL, Kumar VU, Gupta AK, Garapati P, Ravichandiran V, Dhingra S, Murti K. Mucormycosis: A triple burden in patients with diabetes during COVID-19 Pandemic. HEALTH SCIENCES REVIEW (OXFORD, ENGLAND) 2021; 1:100005. [PMID: 34977914 PMCID: PMC8639489 DOI: 10.1016/j.hsr.2021.100005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 11/18/2021] [Accepted: 11/30/2021] [Indexed: 02/07/2023]
Abstract
With the upsurge in the cases of COVID-19 around the world, plenty of potential COVID-19 complications are becoming more prevalent, including a higher risk of secondary bacterial and fungal infections. Mucormycosis is one such condition which has high prevalence among individuals with diabetes who were infected with COVID-19.The usage of steroids in the treatment further inflates the risk of infection and exacerbation of disease in pre-existent mucormycosis patients. Generally, Corticosteroid-induced diabetes can arise on long-term steroid medication, increasing the likelihood of mucormycosis. In patients with COVID-19, the indications and dose of corticosteroids should be properly regulated, and persons with diabetes who take insulin or oral anti-diabetic medicines should be cautious. To avoid poor outcomes, strategies to improve glycemic management should be emphasized. This narrative review elucidates different disciplines on rampant use of steroids, iron and zinc supplements as well as the methods utilized as primary or adjunctive treatment of this fatal condition. This article may help to pave the way for robust research that needs to be done to tackle the deadly triple burden of the disease.
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Affiliation(s)
- A S Fathima
- Department of Pharmacy Practice, National Institute of Pharmaceutical Education and Research, Hajipur, Bihar 844102, India
| | - Vakada Lakshmi Mounika
- Department of Pharmacy Practice, National Institute of Pharmaceutical Education and Research, Hajipur, Bihar 844102, India
| | - V Udaya Kumar
- Department of Pharmacy Practice, National Institute of Pharmaceutical Education and Research, Hajipur, Bihar 844102, India
| | - Ashok Kumar Gupta
- Department of Pharmacy, School of Medical and Allied Sciences, Galgotia University, Uttar Pradesh, India
| | - Pavan Garapati
- Department of Pharmacy Practice, National Institute of Pharmaceutical Education and Research, Hajipur, Bihar 844102, India
| | - V Ravichandiran
- Department of Pharmacy Practice, National Institute of Pharmaceutical Education and Research, Hajipur, Bihar 844102, India
| | - Sameer Dhingra
- Department of Pharmacy Practice, National Institute of Pharmaceutical Education and Research, Hajipur, Bihar 844102, India
| | - Krishna Murti
- Department of Pharmacy Practice, National Institute of Pharmaceutical Education and Research, Hajipur, Bihar 844102, India
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Groll AH, Gordon K, Buchheidt D, Willinger B, Heinz WJ, Kurzai O, Rickerts V, Cornely OA. State of Medical Mycology at German Academic Medical Centres: A Survey of the German-Speaking Mycological Society (DMYKG) and the Paul-Ehrlich-Society for Chemotherapy (PEG). Mycoses 2021; 64:1177-1182. [PMID: 34180098 DOI: 10.1111/myc.13346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 11/28/2022]
Abstract
BACKGROUND Little is known about the infrastructure to translate advances in the management of patients at risk to develop invasive opportunistic fungal diseases. To assess the current state of Medical Mycology support in Germany, we conducted a survey among all 36 academic medical centres. METHODS The survey consisted of a 3-pages questionnaire sent out in the first half of 2019. Information included details of infrastructure, education and teaching; consultation services and interdisciplinary conferences; research activities and participation in network groups; radiology, microbiology and pharmacology support; publication activity; and European Confederation for Medical Mycology (ECMM) Excellence Center designation, if assigned. RESULTS Information was returned from 24 centres (67%). Thirteen institutions (54%) reported an independent infectious disease, and two a separate Medical Mycology department (8%); a Medical Mycology working group was reported for nine institutions (38%). An infectious disease consultation service was existent in 16 institutions (67%) and a multidisciplinary conference in 13 (54%). Fifteen institutions reported a separate study office with activities in infectious disease studies (63%). Laboratory capability for fungal identification and susceptibility testing was confirmed by all 24 institutions; testing of galactomannan by 23 (96%), cryptococcal antigen by 21 (88%), ß-D-Glucan by 9 (38%), and panfungal and Pneumocystis PCR by 21 and 22 (88% and 92%), respectively. Therapeutic drug monitoring of voriconazole was reported to be available in 15 (63%) institutions with a turnaround of ≤24 h during weekdays in 10 (42%). Two of the 24 University hospitals (8%) reported ECMM Diamond Excellence Status. CONCLUSIONS The results of this survey document the continuing need to improve the availability of specialised Medical Mycology support in German academic medical centres.
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Affiliation(s)
- Andreas H Groll
- Infectious Disease Research Program, Center for Bone Marrow Transplantation and Department of Pediatric Hematology/Oncology, University Children's Hospital Münster, Münster, Germany
| | - Kathrin Gordon
- Infectious Disease Research Program, Center for Bone Marrow Transplantation and Department of Pediatric Hematology/Oncology, University Children's Hospital Münster, Münster, Germany
| | - Dieter Buchheidt
- Department of Hematology and Oncology, Mannheim University Hospital, Heidelberg University, Mannheim, Germany
| | - Birgit Willinger
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Werner J Heinz
- Department of Internal Medicine II, Caritas Hospital Bad Mergentheim, Bad Mergentheim, Germany
| | - Oliver Kurzai
- Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany.,National Reference Center for Invasive Fungal Infections NRZMyk, Leibniz Institut für Naturstoff-Forschung und Infektionsbiologie - Hans-Knöll-Institut, Jena, Germany
| | - Volker Rickerts
- Unit 16, Mycotic and Parasitic Agents and Mycobacteria, Robert Koch Institute Berlin, Berlin, Germany
| | - Oliver A Cornely
- Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Excellence Center for Medical Mycology (ECMM), Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Ageing-Associated Diseases (CECAD), and German Centre for Infection Research (DZIF) Partner Site Bonn-Cologne, University of Cologne, Cologne, Germany
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Emerging Fungi and Diagnosis of Fungal Infections: Current Knowledge and New Developments. J Fungi (Basel) 2021; 7:jof7040316. [PMID: 33921558 PMCID: PMC8074204 DOI: 10.3390/jof7040316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 04/15/2021] [Indexed: 12/18/2022] Open
Abstract
I would like to thank all the authors contributing to this Special Issue [...].
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White PL, Price JS, Cordey A, Backx M. Molecular Diagnosis of Yeast Infections. CURRENT FUNGAL INFECTION REPORTS 2021; 15:67-80. [PMID: 34178207 PMCID: PMC8212580 DOI: 10.1007/s12281-021-00421-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/27/2021] [Indexed: 02/06/2023]
Abstract
PURPOSE OF REVIEW The use of molecular tests to aid the diagnosis of invasive yeast infection, in particular invasive candidosis, has been described for over two decades, yet widespread application is limited, and diagnosis remains heavily dependent on classical microbiology. This article will review developments from the past decade in attempt to build on existing knowledge. It will highlight clinical performance and limitations while reviewing developments on recognized procedures; it will also provide insight into novel approaches incorporated in response to clinical demand (e.g. C. auris and antifungal resistance) or technological advances (e.g. next-generation sequencing). RECENT FINDINGS Limited methodological standardization and, until recently, unavailability of commercial options have hindered the integration of molecular diagnostics for yeasts. The development of certain, novel commercial methods has received considerable evaluation allowing a greater understanding of individual assay performance, but widespread multicentre evaluation of most commercial kits is lacking. The detection of emerging pathogens (e.g. C. auris) has been enhanced by the development of molecular tests. Molecular methods are providing a better understanding of the mycobiome, mechanisms of resistance and epidemiology/phylogeny. SUMMARY Despite over two decades of use, the incorporation of molecular methods to enhance the diagnosis of yeast infections remains limited to certain specialist centres. While the development of commercial tests will provide stimulus for broader application, further validation and reduced costs are required. Over the same period of time, Aspergillus PCR has become more widely accepted driven by international efforts to standardize methodology; it is critical that yeast PCR follows suit. Next-generation sequencing will provide significant information on the mycobiome, antifungal resistance mechanism and even broad-range detection directly from the specimen, which may be critical for the molecular detection of yeasts other than Candida species, which is currently limited.
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Affiliation(s)
- P. Lewis White
- grid.241103.50000 0001 0169 7725Mycology Reference Laboratory, Public Health Wales, Microbiology Cardiff, UHW, Heath Park, Cardiff, CF14 4XW UK
| | - Jessica S. Price
- grid.241103.50000 0001 0169 7725Mycology Reference Laboratory, Public Health Wales, Microbiology Cardiff, UHW, Heath Park, Cardiff, CF14 4XW UK
| | - Alan Cordey
- grid.241103.50000 0001 0169 7725Mycology Reference Laboratory, Public Health Wales, Microbiology Cardiff, UHW, Heath Park, Cardiff, CF14 4XW UK
| | - Matthijs Backx
- grid.241103.50000 0001 0169 7725Mycology Reference Laboratory, Public Health Wales, Microbiology Cardiff, UHW, Heath Park, Cardiff, CF14 4XW UK
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