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Morrissey CO, Kim HY, Duong TMN, Moran E, Alastruey-Izquierdo A, Denning DW, Perfect JR, Nucci M, Chakrabarti A, Rickerts V, Chiller TM, Wahyuningsih R, Hamers RL, Cassini A, Gigante V, Sati H, Alffenaar JW, Beardsley J. Aspergillus fumigatus-a systematic review to inform the World Health Organization priority list of fungal pathogens. Med Mycol 2024; 62:myad129. [PMID: 38935907 PMCID: PMC11210617 DOI: 10.1093/mmy/myad129] [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: 09/16/2023] [Revised: 11/06/2023] [Accepted: 12/11/2023] [Indexed: 06/29/2024] Open
Abstract
Recognizing the growing global burden of fungal infections, the World Health Organization established a process to develop a priority list of fungal pathogens (FPPL). In this systematic review, we aimed to evaluate the epidemiology and impact of invasive infections caused by Aspergillus fumigatus to inform the first FPPL. The pre-specified criteria of mortality, inpatient care, complications and sequelae, antifungal susceptibility, risk factors, preventability, annual incidence, global distribution, and emergence were used to search for relevant articles between 1 January 2016 and 10 June 2021. Overall, 49 studies were eligible for inclusion. Azole antifungal susceptibility varied according to geographical regions. Voriconazole susceptibility rates of 22.2% were reported from the Netherlands, whereas in Brazil, Korea, India, China, and the UK, voriconazole susceptibility rates were 76%, 94.7%, 96.9%, 98.6%, and 99.7%, respectively. Cross-resistance was common with 85%, 92.8%, and 100% of voriconazole-resistant A. fumigatus isolates also resistant to itraconazole, posaconazole, and isavuconazole, respectively. The incidence of invasive aspergillosis (IA) in patients with acute leukemia was estimated at 5.84/100 patients. Six-week mortality rates in IA cases ranged from 31% to 36%. Azole resistance and hematological malignancy were poor prognostic factors. Twelve-week mortality rates were significantly higher in voriconazole-resistant than in voriconazole-susceptible IA cases (12/22 [54.5%] vs. 27/88 [30.7%]; P = .035), and hematology patients with IA had significantly higher mortality rates compared with solid-malignancy cases who had IA (65/217 [30%] vs. 14/78 [18%]; P = .04). Carefully designed surveillance studies linking laboratory and clinical data are required to better inform future FPPL.
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Affiliation(s)
- C Orla Morrissey
- Department of Infectious Diseases, Alfred Health and Monash University, Melbourne, Victoria, Australia
| | - Hannah Y Kim
- The University of Sydney Infectious Diseases Institute (Sydney ID), New South Wales, Australia
- Faculty of Medicine and Health, School of Pharmacy, The University of Sydney, New South Wales, Australia
- Westmead Hospital, Westmead, New South Wales, Australia
| | - Tra-My N Duong
- The University of Sydney Infectious Diseases Institute (Sydney ID), New South Wales, Australia
| | - Eric Moran
- Sinclair Dermatology, East Melbourne, Victoria, Australia
| | - Ana Alastruey-Izquierdo
- Mycology Reference Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - David W Denning
- Global Action for Fungal Infections, Geneva, Switzerland
- Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - John R Perfect
- Division of Infectious Diseases and International Health, Duke University School of Medicine, Durham, NC, USA
| | - Marcio Nucci
- Universidade Federal do Rio de Janeiro and Grupo Oncoclinicas, Rio de Janeiro, RJ, Brazil
| | | | - Volker Rickerts
- Robert Koch Institute Berlin, FG16, Seestrasse 10, 13353 Berlin, Germany
| | - Tom M Chiller
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Retno Wahyuningsih
- Department of Parasitology, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
- Department of Parasitology, Faculty of Medicine, Universitas Kristen, Jakarta, Indonesia
| | - Raph L Hamers
- Oxford University Clinical Research Unit Indonesia, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Alessandro Cassini
- Infectious Diseases Service, Lausanne University Hospital, Lausanne, Switzerland
- Public Health Department, Canton of Vaud, Lausanne, Switzerland
| | - Valeria Gigante
- AMR Division, World Health Organization, Geneva, Switzerland
| | - Hatim Sati
- AMR Division, World Health Organization, Geneva, Switzerland
| | - Jan-Willem Alffenaar
- The University of Sydney Infectious Diseases Institute (Sydney ID), New South Wales, Australia
- Faculty of Medicine and Health, School of Pharmacy, The University of Sydney, New South Wales, Australia
- Westmead Hospital, Westmead, New South Wales, Australia
| | - Justin Beardsley
- The University of Sydney Infectious Diseases Institute (Sydney ID), New South Wales, Australia
- Westmead Institute for Medical Research, Westmead, New South Wales, Australia
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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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3
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Mendonça A, Carvalho-Pereira J, Franco-Duarte R, Sampaio P. Optimization of a Quantitative PCR Methodology for Detection of Aspergillus spp. and Rhizopus arrhizus. Mol Diagn Ther 2022; 26:511-525. [PMID: 35710958 PMCID: PMC9202985 DOI: 10.1007/s40291-022-00595-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/02/2022] [Indexed: 11/25/2022]
Abstract
Introduction Multiplex quantitative polymerase chain reaction (qPCR) methods for the detection of Aspergillus spp. based only on SYBR Green and melting curve analysis of PCR products are difficult to develop because most targets are located within ITS regions. The aim of this study was to adapt our previously developed methodology based on a multiplex PCR assay coupled with GeneScan analysis to provide a qPCR method. Methods A SYBR Green-based real-time PCR assay was optimized to detect A. fumigatus, A. flavus, A. niger, A. terreus, and R. arrhizus in a multiplex assay and applied to cultured fungi and spiked plasma. Results Different melting temperatures allowed identification of all five pathogens and discrimination between them, even in samples with low amounts of fungal gDNA (from 1.3 to 33.0 pg/μL), which has been reported previously as problematic. No false-positive results were obtained for non-target species, including bacteria and human DNA. This method allowed detection of fungal pathogens in human plasma spiked with fungal DNA and in coinfections of A. niger/R. arrhizus. Discussion This work provides evidence for the use of a qPCR multiplex method based on SYBR Green and melting curve analysis of PCR products for the detection of A. fumigatus, A. flavus, A. niger, A. terreus, and R. arrhizus. The proposed method is simpler and less expensive than available kits based on fluorescent probes and can be used for aiding diagnosis of the most relevant invasive filamentous fungi, particularly in low-income health care institutions. Supplementary Information The online version contains supplementary material available at 10.1007/s40291-022-00595-1.
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Affiliation(s)
- Alexandre Mendonça
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Braga, Portugal
| | - Joana Carvalho-Pereira
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Braga, Portugal
| | - Ricardo Franco-Duarte
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Braga, Portugal.
| | - Paula Sampaio
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Braga, Portugal
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Rogers TR, Verweij PE, Castanheira M, Dannaoui E, White PL, Arendrup MC. OUP accepted manuscript. J Antimicrob Chemother 2022; 77:2053-2073. [PMID: 35703391 PMCID: PMC9333407 DOI: 10.1093/jac/dkac161] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The increasing incidence and changing epidemiology of invasive fungal infections continue to present many challenges to their effective management. The repertoire of antifungal drugs available for treatment is still limited although there are new antifungals on the horizon. Successful treatment of invasive mycoses is dependent on a mix of pathogen-, host- and antifungal drug-related factors. Laboratories need to be adept at detection of fungal pathogens in clinical samples in order to effectively guide treatment by identifying isolates with acquired drug resistance. While there are international guidelines on how to conduct in vitro antifungal susceptibility testing, these are not performed as widely as for bacterial pathogens. Furthermore, fungi generally are recovered in cultures more slowly than bacteria, and often cannot be cultured in the laboratory. Therefore, non-culture-based methods, including molecular tests, to detect fungi in clinical specimens are increasingly important in patient management and are becoming more reliable as technology improves. Molecular methods can also be used for detection of target gene mutations or other mechanisms that predict antifungal drug resistance. This review addresses acquired antifungal drug resistance in the principal human fungal pathogens and describes known resistance mechanisms and what in-house and commercial tools are available for their detection. It is emphasized that this approach should be complementary to culture-based susceptibility testing, given the range of mutations, resistance mechanisms and target genes that may be present in clinical isolates, but may not be included in current molecular assays.
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Affiliation(s)
| | | | | | | | | | - Maiken Cavling Arendrup
- Unit of Mycology, Statens Serum Institut, Copenhagen, Denmark
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
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Mendonça A, Santos H, Franco-Duarte R, Sampaio P. Fungal infections diagnosis - Past, present and future. Res Microbiol 2022; 173:103915. [PMID: 34863883 PMCID: PMC8634697 DOI: 10.1016/j.resmic.2021.103915] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/19/2021] [Accepted: 11/26/2021] [Indexed: 01/07/2023]
Abstract
Despite the scientific advances observed in the recent decades and the emergence of new methodologies, the diagnosis of systemic fungal infections persists as a problematic issue. Fungal cultivation, the standard method that allows a proven diagnosis, has numerous disadvantages, as low sensitivity (only 50% of the patients present positive fungal cultures), and long growth time. These are factors that delay the patient's treatment and, consequently, lead to higher hospital costs. To improve the accuracy and quickness of fungal infections diagnosis, several new methodologies attempt to be implemented in clinical microbiology laboratories. Most of these innovative methods are independent of pathogen isolation, which means that the diagnosis goes from being considered proven to probable. In spite of the advantage of being culture-independent, the majority of the methods lack standardization. PCR-based methods are becoming more and more commonly used, which has earned them an important place in hospital laboratories. This can be perceived now, as PCR-based methodologies have proved to be an essential tool fighting against the COVID-19 pandemic. This review aims to go through the main steps of the diagnosis for systemic fungal infection, from diagnostic classifications, through methodologies considered as "gold standard", to the molecular methods currently used, and finally mentioning some of the more futuristic approaches.
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Slavin MA, Chen YC, Cordonnier C, Cornely OA, Cuenca-Estrella M, Donnelly JP, Groll AH, Lortholary O, Marty FM, Nucci M, Rex JH, Rijnders BJA, Thompson GR, Verweij PE, White PL, Hargreaves R, Harvey E, Maertens JA. When to change treatment of acute invasive aspergillosis: an expert viewpoint. J Antimicrob Chemother 2021; 77:16-23. [PMID: 34508633 PMCID: PMC8730679 DOI: 10.1093/jac/dkab317] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Invasive aspergillosis (IA) is an acute infection affecting patients who are immunocompromised, as a result of receiving chemotherapy for malignancy, or immunosuppressant agents for transplantation or autoimmune disease. Whilst criteria exist to define the probability of infection for clinical trials, there is little evidence in the literature or clinical guidelines on when to change antifungal treatment in patients who are receiving prophylaxis or treatment for IA. To try and address this significant gap, an advisory board of experts was convened to develop criteria for the management of IA for use in designing clinical trials, which could also be used in clinical practice. For primary treatment failure, a change in antifungal therapy should be made: (i) when mycological susceptibility testing identifies an organism from a confirmed site of infection, which is resistant to the antifungal given for primary therapy, or a resistance mutation is identified by molecular testing; (ii) at, or after, 8 days of primary antifungal treatment if there is increasing serum galactomannan, or galactomannan positivity in serum, or bronchoalveolar lavage fluid when the antigen was previously undetectable, or there is sudden clinical deterioration, or a new clearly distinct site of infection is detected; and (iii) at, or after, 15 days of primary antifungal treatment if the patient is clinically stable but with ≥2 serum galactomannan measurements persistently elevated compared with baseline or increasing, or if the original lesions on CT or other imaging, show progression by >25% in size in the context of no apparent change in immune status.
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Affiliation(s)
- Monica A Slavin
- Department of Infectious Diseases, Peter MacCallum Cancer Centre, National Centre for Infections in Cancer, Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Yee-Chun Chen
- Department of Internal Medicine, National Taiwan University Hospital and College of Medicine, No. 7, Chung-Shan South Road, Taipei, 100, Taiwan
| | - Catherine Cordonnier
- Service d'Hématologie clinique et de Thérapie cellulaire, DMU Cancer, CHU Henri Mondor, 94000 Créteil, France
| | - Oliver A Cornely
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Excellence Center for Medical Mycology (ECMM), Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD); Clinical Trials Centre Cologne (ZKS Köln), Kerpener Str. 62, 50937 Cologne, Germany
| | - Manuel Cuenca-Estrella
- Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo Km2, Majadahonda, Madrid 28220, Spain
| | | | - Andreas H Groll
- Infectious Disease Research Program, Center for Bone Marrow Transplantation and Department of Pediatric Hematology and Oncology, University Children's Hospital Münster, Albert-Schweitzer-Campus 1, Building A1, 48149 Münster, Germany
| | - Olivier Lortholary
- Paris University, Necker Pasteur Center for Infectious Diseases and Tropical Medicine, IHU Imagine, Necker Enfants Malades University Hospital, and Institute Pasteur, CNRS, Molecular Mycology Unit, APHP 149, rue de Sèvres, 75015 Paris, France
| | | | - Marcio Nucci
- University Hospital, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - John H Rex
- F2G Ltd, Lankro Way, Eccles, Manchester, M30 0LX, UK.,McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Bart J A Rijnders
- Department of Internal Medicine, Section of Infectious Diseases and Department of Medical Microbiology and Infectious Diseases Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - George R Thompson
- Department of Internal Medicine, Division of Infectious Diseases, 4150 V Street, Suite G500, Sacramento, CA 95817, USA
| | - Paul E Verweij
- Radboudumc-CWZ Center of Expertise for Mycology, Radboud University Nijmegen Medical Center, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands.,Center for Infectious Disease Research, Diagnostics and Laboratory Surveillance National Institute for Public Health and the Environment (RIVM), P.O. Box 1, 3720 BA Bilthoven, The Netherlands
| | - P Lewis White
- Public Health Wales Mycology Reference Laboratory, University Hospital of Wales, Heath Park, Cardiff, UK
| | | | - Emma Harvey
- F2G Ltd, Lankro Way, Eccles, Manchester, M30 0LX, UK
| | - Johan A Maertens
- Department of Microbiology, Immunology, and Transplantation, K.U. Leuven, Leuven, Belgium.,Department of Hematology, U.Z. Leuven, Leuven, Belgium
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Brackin AP, Hemmings SJ, Fisher MC, Rhodes J. Fungal Genomics in Respiratory Medicine: What, How and When? Mycopathologia 2021; 186:589-608. [PMID: 34490551 PMCID: PMC8421194 DOI: 10.1007/s11046-021-00573-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/14/2021] [Indexed: 12/20/2022]
Abstract
Respiratory infections caused by fungal pathogens present a growing global health concern and are a major cause of death in immunocompromised patients. Worryingly, coronavirus disease-19 (COVID-19) resulting in acute respiratory distress syndrome has been shown to predispose some patients to airborne fungal co-infections. These include secondary pulmonary aspergillosis and mucormycosis. Aspergillosis is most commonly caused by the fungal pathogen Aspergillus fumigatus and primarily treated using the triazole drug group, however in recent years, this fungus has been rapidly gaining resistance against these antifungals. This is of serious clinical concern as multi-azole resistant forms of aspergillosis have a higher risk of mortality when compared against azole-susceptible infections. With the increasing numbers of COVID-19 and other classes of immunocompromised patients, early diagnosis of fungal infections is critical to ensuring patient survival. However, time-limited diagnosis is difficult to achieve with current culture-based methods. Advances within fungal genomics have enabled molecular diagnostic methods to become a fast, reproducible, and cost-effective alternative for diagnosis of respiratory fungal pathogens and detection of antifungal resistance. Here, we describe what techniques are currently available within molecular diagnostics, how they work and when they have been used.
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Affiliation(s)
- Amelie P Brackin
- MRC Centre for Global Disease Analysis, Imperial College London, London, UK
| | - Sam J Hemmings
- Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Matthew C Fisher
- Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Johanna Rhodes
- Department of Infectious Disease Epidemiology, Imperial College London, London, UK.
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8
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Arastehfar A, Carvalho A, Houbraken J, Lombardi L, Garcia-Rubio R, Jenks J, Rivero-Menendez O, Aljohani R, Jacobsen I, Berman J, Osherov N, Hedayati M, Ilkit M, Armstrong-James D, Gabaldón T, Meletiadis J, Kostrzewa M, Pan W, Lass-Flörl C, Perlin D, Hoenigl M. Aspergillus fumigatus and aspergillosis: From basics to clinics. Stud Mycol 2021; 100:100115. [PMID: 34035866 PMCID: PMC8131930 DOI: 10.1016/j.simyco.2021.100115] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The airborne fungus Aspergillus fumigatus poses a serious health threat to humans by causing numerous invasive infections and a notable mortality in humans, especially in immunocompromised patients. Mould-active azoles are the frontline therapeutics employed to treat aspergillosis. The global emergence of azole-resistant A. fumigatus isolates in clinic and environment, however, notoriously limits the therapeutic options of mould-active antifungals and potentially can be attributed to a mortality rate reaching up to 100 %. Although specific mutations in CYP 51A are the main cause of azole resistance, there is a new wave of azole-resistant isolates with wild-type CYP 51A genotype challenging the efficacy of the current diagnostic tools. Therefore, applications of whole-genome sequencing are increasingly gaining popularity to overcome such challenges. Prominent echinocandin tolerance, as well as liver and kidney toxicity posed by amphotericin B, necessitate a continuous quest for novel antifungal drugs to combat emerging azole-resistant A. fumigatus isolates. Animal models and the tools used for genetic engineering require further refinement to facilitate a better understanding about the resistance mechanisms, virulence, and immune reactions orchestrated against A. fumigatus. This review paper comprehensively discusses the current clinical challenges caused by A. fumigatus and provides insights on how to address them.
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Affiliation(s)
- A. Arastehfar
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, 07110, USA
| | - A. Carvalho
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's - PT Government Associate Laboratory, Guimarães/Braga, Portugal
| | - J. Houbraken
- Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands
| | - L. Lombardi
- UCD Conway Institute and School of Medicine, University College Dublin, Dublin 4, Ireland
| | - R. Garcia-Rubio
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, 07110, USA
| | - J.D. Jenks
- Department of Medicine, University of California San Diego, San Diego, CA, 92103, USA
- Clinical and Translational Fungal-Working Group, University of California San Diego, La Jolla, CA, 92093, USA
| | - O. Rivero-Menendez
- Medical Mycology Reference Laboratory, National Center for Microbiology, Instituto de Salud Carlos III, Madrid, 28222, Spain
| | - R. Aljohani
- Department of Infectious Diseases, Imperial College London, London, UK
| | - I.D. Jacobsen
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology—Hans Knöll Institute, Jena, Germany
- Institute for Microbiology, Friedrich Schiller University, Jena, Germany
| | - J. Berman
- Research Group Microbial Immunology, Leibniz Institute for Natural Product Research and Infection Biology—Hans Knöll Institute, Jena, Germany
| | - N. Osherov
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine Ramat-Aviv, Tel-Aviv, 69978, Israel
| | - M.T. Hedayati
- Invasive Fungi Research Center/Department of Medical Mycology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - M. Ilkit
- Division of Mycology, Department of Microbiology, Faculty of Medicine, Çukurova University, 01330, Adana, Turkey
| | | | - T. Gabaldón
- Life Sciences Programme, Supercomputing Center (BSC-CNS), Jordi Girona, Barcelona, 08034, Spain
- Mechanisms of Disease Programme, Institute for Research in Biomedicine (IRB), Barcelona, Spain
- ICREA, Pg. Lluís Companys 23, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010, Barcelona, Spain
| | - J. Meletiadis
- Clinical Microbiology Laboratory, Attikon University Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | | | - W. Pan
- Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, 200003, China
| | - C. Lass-Flörl
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - D.S. Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, 07110, USA
| | - M. Hoenigl
- Department of Medicine, University of California San Diego, San Diego, CA, 92103, USA
- Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, 8036, Graz, Austria
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, San Diego, CA 92093, USA
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Novak-Frazer L, Anees-Hill SP, Hassan D, Masania R, Moore CB, Richardson MD, Denning DW, Rautemaa-Richardson R. Deciphering Aspergillus fumigatus cyp51A-mediated triazole resistance by pyrosequencing of respiratory specimens. J Antimicrob Chemother 2021; 75:3501-3509. [PMID: 32862231 PMCID: PMC7662182 DOI: 10.1093/jac/dkaa357] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 07/16/2020] [Indexed: 12/16/2022] Open
Abstract
Background Infections caused by triazole drug-resistant Aspergillus fumigatus are an increasing problem. The sensitivity of standard culture is poor, abrogating susceptibility testing. Early detection of resistance can improve patient outcomes, yet tools for this purpose are limited. Objectives To develop and validate a pyrosequencing technique to detect resistance-conferring cyp51A polymorphisms from clinical respiratory specimens and A. fumigatus isolates. Methods Method validation was performed by Sanger sequencing and pyrosequencing of 50 A. fumigatus isolates with a spectrum of triazole susceptibility patterns. Then, 326 Aspergillus quantitative PCR (qPCR)-positive respiratory samples collected over a 27 month period (January 2017–March 2019) from 160 patients at the UK National Aspergillosis Centre were assessed by cyp51A pyrosequencing. The Sanger sequencing and pyrosequencing results were compared with those from high-volume culture and standard susceptibility testing. Results The cyp51A genotypes of the 50 isolates analysed by pyrosequencing and Sanger sequencing matched. Of the 326 Aspergillus qPCR-positive respiratory specimens, 71.2% were reported with no A. fumigatus growth. Of these, 56.9% (132/232) demonstrated a WT cyp51A genotype and 31.5% (73/232) a resistant genotype by pyrosequencing. Pyrosequencing identified the environmental TR34/L98H mutation in 18.7% (61/326) of the samples in contrast to 6.4% (21/326) pan-azole resistance detected by culture. Importantly, pyrosequencing detected resistance earlier than culture in 23.3% of specimens. Conclusions The pyrosequencing assay described could detect a wide range of cyp51A polymorphisms associated with triazole resistance, including those not identified by commercial assays. This method allowed prompt recognition of resistance and the selection of appropriate antifungal treatment when culture was negative.
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Affiliation(s)
- Lilyann Novak-Frazer
- Mycology Reference Centre Manchester, ECMM Centre of Excellence, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Wythenshawe Hospital, Manchester, UK.,The University of Manchester, Faculty of Biology, Medicine and Health, Division of Infection, Inflammation and Respiratory Medicine, Manchester, UK
| | - Samuel P Anees-Hill
- Mycology Reference Centre Manchester, ECMM Centre of Excellence, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Wythenshawe Hospital, Manchester, UK
| | - Darin Hassan
- Mycology Reference Centre Manchester, ECMM Centre of Excellence, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Wythenshawe Hospital, Manchester, UK
| | - Rikesh Masania
- Mycology Reference Centre Manchester, ECMM Centre of Excellence, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Wythenshawe Hospital, Manchester, UK
| | - Caroline B Moore
- Mycology Reference Centre Manchester, ECMM Centre of Excellence, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Wythenshawe Hospital, Manchester, UK.,The University of Manchester, Faculty of Biology, Medicine and Health, Division of Infection, Inflammation and Respiratory Medicine, Manchester, UK
| | - Malcolm D Richardson
- Mycology Reference Centre Manchester, ECMM Centre of Excellence, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Wythenshawe Hospital, Manchester, UK.,The University of Manchester, Faculty of Biology, Medicine and Health, Division of Infection, Inflammation and Respiratory Medicine, Manchester, UK
| | - David W Denning
- The University of Manchester, Faculty of Biology, Medicine and Health, Division of Infection, Inflammation and Respiratory Medicine, Manchester, UK.,National Aspergillosis Centre, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Wythenshawe Hospital, Manchester, UK
| | - Riina Rautemaa-Richardson
- Mycology Reference Centre Manchester, ECMM Centre of Excellence, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Wythenshawe Hospital, Manchester, UK.,The University of Manchester, Faculty of Biology, Medicine and Health, Division of Infection, Inflammation and Respiratory Medicine, Manchester, UK.,National Aspergillosis Centre, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Wythenshawe Hospital, Manchester, UK
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10
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Recognition of Diagnostic Gaps for Laboratory Diagnosis of Fungal Diseases: Expert Opinion from the Fungal Diagnostics Laboratories Consortium (FDLC). J Clin Microbiol 2021; 59:e0178420. [PMID: 33504591 DOI: 10.1128/jcm.01784-20] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Fungal infections are a rising threat to our immunocompromised patient population, as well as other nonimmunocompromised patients with various medical conditions. However, little progress has been made in the past decade to improve fungal diagnostics. To jointly address this diagnostic challenge, the Fungal Diagnostics Laboratory Consortium (FDLC) was recently created. The FDLC consists of 26 laboratories from the United States and Canada that routinely provide fungal diagnostic services for patient care. A survey of fungal diagnostic capacity among the 26 members of the FDLC was recently completed, identifying the following diagnostic gaps: lack of molecular detection of mucormycosis; lack of an optimal diagnostic algorithm incorporating fungal biomarkers and molecular tools for early and accurate diagnosis of Pneumocystis pneumonia, aspergillosis, candidemia, and endemic mycoses; lack of a standardized molecular approach to identify fungal pathogens directly in formalin-fixed paraffin-embedded tissues; lack of robust databases to enhance mold identification with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry; suboptimal diagnostic approaches for mold blood cultures, tissue culture processing for Mucorales, and fungal respiratory cultures for cystic fibrosis patients; inadequate capacity for fungal point-of-care testing to detect and identify new, emerging or underrecognized, rare, or uncommon fungal pathogens; and performance of antifungal susceptibility testing. In this commentary, the FDLC delineates the most pressing unmet diagnostic needs and provides expert opinion on how to fulfill them. Most importantly, the FDLC provides a robust laboratory network to tackle these diagnostic gaps and ultimately to improve and enhance the clinical laboratory's capability to rapidly and accurately diagnose fungal infections.
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11
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Brackin AP, Shelton JMG, Abdolrasouli A, Fisher MC, Sewell TR. A Low-Cost Tebuconazole-Based Screening Test for Azole-Resistant Aspergillus fumigatus. ACTA ACUST UNITED AC 2021; 58:e112. [PMID: 32857921 DOI: 10.1002/cpmc.112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The global emergence of azole resistance in Aspergillus fumigatus is resulting in health and food security concerns. Rapid diagnostics and environmental surveillance methods are key to understanding the distribution and prevalence of azole resistance. However, such methods are often associated with high costs and are not always applicable to laboratories based in the least-developed countries. Here, we present and validate a low-cost screening protocol that can be used to differentiate between azole-susceptible "wild-type" and azole-resistant A. fumigatus isolates. © 2020 The Authors. Basic Protocol 1: Preparation of Tebucheck multi-well plates Basic Protocol 2: Inoculation of Tebucheck multi-well plates.
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Affiliation(s)
- Amelie P Brackin
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Jennifer M G Shelton
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Alireza Abdolrasouli
- Diagnostic Mycology Service, Department of Medical Microbiology, North West London Pathology, Imperial College Healthcare National Health Service Trust, London, United Kingdom
| | - Matthew C Fisher
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Thomas R Sewell
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
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12
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White PL, Bretagne S, Caliendo AM, Loeffler J, Patterson TF, Slavin M, Wingard JR. Aspergillus Polymerase Chain Reaction-An Update on Technical Recommendations, Clinical Applications, and Justification for Inclusion in the Second Revision of the EORTC/MSGERC Definitions of Invasive Fungal Disease. Clin Infect Dis 2021; 72:S95-S101. [PMID: 33709129 DOI: 10.1093/cid/ciaa1865] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Aspergillus polymerase chain reaction testing of blood and respiratory samples has recently been included in the second revision of the EORTC/MSGERC definitions for classifying invasive fungal disease. This is a result of considerable efforts to standardize methodology, the availability of commercial assays and external quality control programs, and additional clinical validation. This supporting article provides both clinical and technical justifications for its inclusion while also summarizing recent advances and likely future developments in the molecular diagnosis of invasive aspergillosis.
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Affiliation(s)
- P Lewis White
- Public Health Wales Mycology Reference Laboratory, Cardiff, United Kingdom
| | - Stephane Bretagne
- Mycology Laboratory, Saint Louis Hospital, Paris and Université de Paris, France
| | - Angela M Caliendo
- Department of Medicine, Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
| | - Juergen Loeffler
- Department of Molecular Biology and Infection, University Hospital Wuerzburg, Medical Hospital II, Wuerzburg, Germany
| | - Thomas F Patterson
- Department of Medicine, University of Texas Health San Antonio and the South Texas Veterans Health Care System, San Antonio, Texas, USA
| | - Monica Slavin
- National Centre for Infections in Cancer, Sir Peter MacCallum Department of Medical Oncology, University of Melbourne, Melbourne, Australia
| | - John R Wingard
- Department of Medicine, University of Florida College of Medicine, Gainesville, Florida, USA
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13
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Neofytos D, Garcia-Vidal C, Lamoth F, Lichtenstern C, Perrella A, Vehreschild JJ. Invasive aspergillosis in solid organ transplant patients: diagnosis, prophylaxis, treatment, and assessment of response. BMC Infect Dis 2021; 21:296. [PMID: 33761875 PMCID: PMC7989085 DOI: 10.1186/s12879-021-05958-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 03/04/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Invasive aspergillosis (IA) is a rare complication in solid organ transplant (SOT) recipients. Although IA has significant implications on graft and patient survival, data on diagnosis and management of this infection in SOT recipients are still limited. METHODS Discussion of current practices and limitations in the diagnosis, prophylaxis, and treatment of IA and proposal of means of assessing treatment response in SOT recipients. RESULTS Liver, lung, heart or kidney transplant recipients have common as well as different risk factors to the development of IA, thus each category needs a separate evaluation. Diagnosis of IA in SOT recipients requires a high degree of awareness, because established diagnostic tools may not provide the same sensitivity and specificity observed in the neutropenic population. IA treatment relies primarily on mold-active triazoles, but potential interactions with immunosuppressants and other concomitant therapies need special attention. CONCLUSIONS Criteria to assess response have not been sufficiently evaluated in the SOT population and CT lesion dynamics, and serologic markers may be influenced by the underlying disease and type and severity of immunosuppression. There is a need for well-orchestrated efforts to study IA diagnosis and management in SOT recipients and to develop comprehensive guidelines for this population.
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Affiliation(s)
- Dionysios Neofytos
- Service des Maladies Infectieuses, Hôpitaux Universitaires de Genève, Rue Gabrielle-Perret-Gentil 4, Geneva, Switzerland.
| | - Carolina Garcia-Vidal
- Servicio de Enfermedades Infecciosas, Hospital Clínic de Barcelona-IDIBAPS, Universitat de Barcelona, FungiCLINIC Research group (AGAUR), Barcelona, Spain
| | - Frédéric Lamoth
- Infectious Diseases Service, Department of Medicine, Lausanne University Hospital, 1011, Lausanne, Switzerland
- Department of Laboratories, Institute of Microbiology, Lausanne University Hospital, Lausanne, Switzerland
| | - Christoph Lichtenstern
- Department of Anaesthesiology, Heidelberg University Hospital, Im Neuenheimer Feld 110, Heidelberg, Germany
| | - Alessandro Perrella
- VII Department of Infectious Disease and Immunology, Hospital D. Cotugno, Naples, Italy
- CLSE-Liver Transplant Unit, Hospital A. Cardarelli, Naples, Italy
| | - Jörg Janne Vehreschild
- Medical Department II, Hematology and Oncology, University Hospital of Frankfurt, Frankfurt, Germany
- Department I for Internal Medicine, University Hospital of Cologne, Cologne, Germany
- German Centre for Infection Research, partner site Bonn-Cologne, University of Cologne, Cologne, Germany
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14
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Recent Advances and Novel Approaches in Laboratory-Based Diagnostic Mycology. J Fungi (Basel) 2021; 7:jof7010041. [PMID: 33440757 PMCID: PMC7827937 DOI: 10.3390/jof7010041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 12/31/2020] [Accepted: 01/01/2021] [Indexed: 12/16/2022] Open
Abstract
What was once just culture and microscopy the field of diagnostic mycology has significantly advanced in recent years and continues to incorporate novel assays and strategies to meet the changes in clinical demand. The emergence of widespread resistance to antifungal therapy has led to the development of a range of molecular tests that target mutations associated with phenotypic resistance, to complement classical susceptibility testing and initial applications of next-generation sequencing are being described. Lateral flow assays provide rapid results, with simplicity allowing the test to be performed outside specialist centres, potentially as point-of-care tests. Mycology has responded positively to an ever-diversifying patient population by rapidly identifying risk and developing diagnostic strategies to improve patient management. Nowadays, the diagnostic repertoire of the mycology laboratory employs classical, molecular and serological tests and should be keen to embrace diagnostic advancements that can improve diagnosis in this notoriously difficult field.
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15
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Verweij PE, Lucas JA, Arendrup MC, Bowyer P, Brinkmann AJ, Denning DW, Dyer PS, Fisher MC, Geenen PL, Gisi U, Hermann D, Hoogendijk A, Kiers E, Lagrou K, Melchers WJ, Rhodes J, Rietveld AG, Schoustra SE, Stenzel K, Zwaan BJ, Fraaije BA. The one health problem of azole resistance in Aspergillus fumigatus: current insights and future research agenda. FUNGAL BIOL REV 2020. [DOI: 10.1016/j.fbr.2020.10.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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16
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Khanina A, Douglas AP, Thursky KA. Implementation of Effective Antifungal Stewardship in Cancer Patients—A Review of Current Evidence. CURRENT FUNGAL INFECTION REPORTS 2020. [DOI: 10.1007/s12281-020-00408-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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17
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Emerging Microbiology Diagnostics for Transplant Infections: On the Cusp of a Paradigm Shift. Transplantation 2020; 104:1358-1384. [PMID: 31972701 DOI: 10.1097/tp.0000000000003123] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In light of the heightened risk for infection associated with solid organ and hematopoietic stem cell transplantation, rapid and accurate microbiology diagnostics are essential to the practice of transplant clinicians, including infectious diseases specialists. In the last decade, diagnostic microbiology has seen a shift toward culture-independent techniques including single-target and multiplexed molecular testing, mass-spectrometry, and magnetic resonance-based methods which have together greatly expanded the array of pathogens identified, increased processing speed and throughput, allowed for detection of resistance determinants, and ultimately improved the outcomes of infected transplant recipients. More recently, a newer generation of diagnostics with immense potential has emerged, including multiplexed molecular panels directly applicable to blood and blood culture specimens, next-generation metagenomics, and gas chromatography mass spectrometry. Though these methods have some recognized drawbacks, many have already demonstrated improved sensitivity and a positive impact on clinical outcomes in transplant and immunocompromised patients.
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18
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Hunter ES, Page ID, Richardson MD, Denning DW. Evaluation of the LDBio Aspergillus ICT lateral flow assay for serodiagnosis of allergic bronchopulmonary aspergillosis. PLoS One 2020; 15:e0238855. [PMID: 32976540 PMCID: PMC7518618 DOI: 10.1371/journal.pone.0238855] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 08/25/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Early recognition and diagnosis of allergic bronchopulmonary aspergillosis (ABPA) is critical to improve patient symptoms, and antifungal therapy may prevent or delay progression of bronchiectasis and development of chronic pulmonary aspergillosis. OBJECTIVE A recently commercialized lateral flow assay (Aspergillus ICT) (LDBio Diagnostics, Lyons, France) detects Aspergillus-specific antibodies in <30 minutes, requiring minimal laboratory equipment. We evaluated this assay for diagnosis of ABPA compared to diseased (asthma and/or bronchiectasis) controls. METHODS ABPA and control sera collected at the National Aspergillosis Centre (Manchester, UK) and/or from the Manchester Allergy, Respiratory and Thoracic Surgery research biobank were evaluated using the Aspergillus ICT assay. Results were read both visually and digitally (using a lateral flow reader). Serological Aspergillus-specific IgG and IgE, and total IgE titres were measured by ImmunoCAP. RESULTS For 106 cases of ABPA versus all diseased controls, sensitivity and specificity for the Aspergillus ICT were 90.6% and 87.2%, respectively. Sensitivity for 'proven' ABPA alone (n = 96) was 89.8%, and 94.4% for 'presumed' ABPA (n = 18). 'Asthma only' controls (no bronchiectasis) and 'bronchiectasis controls' exhibited 91.4% and 81.7% specificity, respectively. Comparison of Aspergillus ICT result with Aspergillus-specific IgG and IgE titres showed no evident immunoglobulin isotype bias. Digital measurements displayed no correlation between ImmunoCAP Aspergillus-specific IgE level and ICT test line intensity. CONCLUSIONS The Aspergillus ICT assay exhibits good sensitivity for ABPA serological screening. It is easy to perform and interpret, using minimal equipment and resources; and provides a valuable simple screening resource to rapidly distinguish more serious respiratory conditions from Aspergillus sensitization alone.
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Affiliation(s)
- Elizabeth Stucky Hunter
- Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, United Kingdom
| | - Iain D. Page
- Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, United Kingdom
- North Manchester General Hospital, Pennine Acute Hospitals NHS Trust, Manchester, United Kingdom
| | - Malcolm D. Richardson
- Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, United Kingdom
- Mycology Reference Centre Manchester, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - David W. Denning
- Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, United Kingdom
- National Aspergillosis Centre, Manchester University NHS Foundation Trust, Manchester, United Kingdom
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19
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Donnelly JP, Chen SC, Kauffman CA, Steinbach WJ, Baddley JW, Verweij PE, Clancy CJ, Wingard JR, Lockhart SR, Groll AH, Sorrell TC, Bassetti M, Akan H, Alexander BD, Andes D, Azoulay E, Bialek R, Bradsher RW, Bretagne S, Calandra T, Caliendo AM, Castagnola E, Cruciani M, Cuenca-Estrella M, Decker CF, Desai SR, Fisher B, Harrison T, Heussel CP, Jensen HE, Kibbler CC, Kontoyiannis DP, Kullberg BJ, Lagrou K, Lamoth F, Lehrnbecher T, Loeffler J, Lortholary O, Maertens J, Marchetti O, Marr KA, Masur H, Meis JF, Morrisey CO, Nucci M, Ostrosky-Zeichner L, Pagano L, Patterson TF, Perfect JR, Racil Z, Roilides E, Ruhnke M, Prokop CS, Shoham S, Slavin MA, Stevens DA, Thompson GR, Vazquez JA, Viscoli C, Walsh TJ, Warris A, Wheat LJ, White PL, Zaoutis TE, Pappas PG. 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. Clin Infect Dis 2020; 71:1367-1376. [PMID: 31802125 PMCID: PMC7486838 DOI: 10.1093/cid/ciz1008] [Citation(s) in RCA: 1393] [Impact Index Per Article: 348.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 10/08/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Invasive fungal diseases (IFDs) remain important causes of morbidity and mortality. The consensus definitions of the Infectious Diseases Group of the European Organization for Research and Treatment of Cancer and the Mycoses Study Group have been of immense value to researchers who conduct clinical trials of antifungals, assess diagnostic tests, and undertake epidemiologic studies. However, their utility has not extended beyond patients with cancer or recipients of stem cell or solid organ transplants. With newer diagnostic techniques available, it was clear that an update of these definitions was essential. METHODS To achieve this, 10 working groups looked closely at imaging, laboratory diagnosis, and special populations at risk of IFD. A final version of the manuscript was agreed upon after the groups' findings were presented at a scientific symposium and after a 3-month period for public comment. There were several rounds of discussion before a final version of the manuscript was approved. RESULTS There is no change in the classifications of "proven," "probable," and "possible" IFD, although the definition of "probable" has been expanded and the scope of the category "possible" has been diminished. The category of proven IFD can apply to any patient, regardless of whether the patient is immunocompromised. The probable and possible categories are proposed for immunocompromised patients only, except for endemic mycoses. CONCLUSIONS These updated definitions of IFDs should prove applicable in clinical, diagnostic, and epidemiologic research of a broader range of patients at high-risk.
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Affiliation(s)
| | - Sharon C Chen
- Centre for Infectious Diseases and Microbiology, Laboratory Services, Institute of Clinical Pathology and Medical Research, Westmead Hospital, University of Sydney, Sydney, Australia
| | - Carol A Kauffman
- Division of Infectious Diseases, University of Michigan, VA Ann Arbor Healthcare System, Ann Arbor, Michigan, USA
| | - William J Steinbach
- Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
| | - John W Baddley
- Department of Medicine, Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Paul E Verweij
- Center of Expertise in Mycology Radboudumc/CWZ, Nijmegen, The Netherlands
| | | | - John R Wingard
- Department of Medicine, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Shawn R Lockhart
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Andreas H Groll
- Infectious Disease Research Program, Center for Bone Marrow Transplantation and Department of Pediatric Hematology and Oncology University Children’s Hospital, Münster, Germany
| | - Tania C Sorrell
- University of Sydney, Marie Bashir Institute for Infectious Diseases & Biosecurity, University of Sydney School of Medicine Faculty of Medicine and Health, Westmead Institute for Centre for Infectious Diseases and Microbiology, Western Sydney Local Health District, Sydney, Australia
| | - Matteo Bassetti
- Infectious Disease Clinic, Department of Medicine University of Udine and Department of Health Sciences, DISSAL, University of Genoa, Genoa, Italy
| | - Hamdi Akan
- Ankara University, Faculty of Medicine, Cebeci Campus, Hematology Clinical Research Unit, Ankara, Turkey
| | - Barbara D Alexander
- Department of Medicine and Division of Infectious Diseases, Duke University Medical Center, Durham, North Carolina, USA
| | - David Andes
- Division of Infectious Diseases, Departments of Medicine, Microbiology and Immunology School of Medicine and Public Health and School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA
| | - Elie Azoulay
- Médicine Intensive et Réanimation Hôpital Saint-Louis, APHP, Université Paris Diderot, Paris, France
| | - Ralf Bialek
- Molecular Diagnostics of Infectious Diseases, Microbiology, LADR Zentrallabor Dr. Kramer & Kollegen, Geesthacht, Germany
| | - Robert W Bradsher
- Division of Infectious Diseases, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Stephane Bretagne
- Institut Pasteur, Molecular Mycology Unit, CNRS UMR2000, Mycology Laboratory, Saint-Louis Hospital, Assistance Publique-Hôpitaux de Paris, Université de Paris, Paris, France
| | - Thierry Calandra
- Infectious Diseases Service, Department of Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Angela M Caliendo
- Department of Medicine, Alpert Warren Medical School of Brown University, Providence, Rhode Island, USA
| | - Elio Castagnola
- Infectious Diseases Unit, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Mario Cruciani
- Infectious Diseases Unit, G. Fracastoro Hospital, San Bonifacio, Verona, Italy
| | | | - Catherine F Decker
- Infectious Diseases Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Sujal R Desai
- National Heart & Lung Institute, Imperial College London, the Royal Brompton & Harefield NHS Foundation Trust, London, UK
| | - Brian Fisher
- Pediatric Infectious Diseases Division at the Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Thomas Harrison
- Centre for Global Health, Institute for Infection and Immunity, St Georges University of London, London, UK
| | - Claus Peter Heussel
- Diagnostic and Interventional Radiology, University Hospital Heidelberg, Translational Lung Research Center and Diagnostic and Interventional Radiology with Nuclear Medicine, Thoraxklinik Heidelberg, Heidelberg, Germany
| | - Henrik E Jensen
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Bart-Jan Kullberg
- Radboud Center for Infectious Diseases and Department of Medicine, Radboudumc, Nijmegen, The Netherlands
| | - Katrien Lagrou
- Department of Microbiology, Immunology and Transplantation and Department of Laboratory Medicine and National Reference Centre for Mycosis, University Hospitals Leuven, Leuven, Belgium
| | - Frédéric Lamoth
- Infectious Diseases Service, Department of Medicine and Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Thomas Lehrnbecher
- Pediatric Hematology and Oncology, Hospital for Children and Adolescents, University of Frankfurt, Frankfurt, Germany
| | - Jurgen Loeffler
- Molecular Biology and Infection, Medical Hospital II, WÜ4i, University Hospital Würzburg, Würzburg, Germany
| | - Olivier Lortholary
- Paris University, Necker Pasteur Center for Infectious Diseases and Tropical Medicine, IHU Imagine & Institut Pasteur, Molecular Mycology Unit, CNRS UMR 2000, Paris, France
| | - Johan Maertens
- Department of Hematology, University Hospitals Leuven, Leuven, Belgium
- Department of Microbiology, Immunology and Transplantation, K.U. Leuven, Leuven, Belgium
| | - Oscar Marchetti
- Infectious Diseases Service, Department of Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Kieren A Marr
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins University School
| | - Henry Masur
- Critical Care Medicine Department NIH-Clinical Center, Bethesda, Maryland, USA
| | - Jacques F Meis
- Department of Medical Microbiology and Infectious Diseases and Centre of Expertise in Mycology Radboudumc/Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
| | | | - Marcio Nucci
- Department of Internal Medicine, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Livio Pagano
- Istituto di Ematologia, Università Cattolica S. Cuore, Rome, Italy
| | - Thomas F Patterson
- UT Health San Antonio and South Texas Veterans Health Care System, San Antonio, Texas, USA
| | - John R Perfect
- Department of Medicine and Division of Infectious Diseases, Duke University Medical Center, Durham, North Carolina, USA
| | - Zdenek Racil
- Department of Internal Medicine–Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Emmanuel Roilides
- Infectious Diseases Unit, 3rd Department of Pediatrics, Faculty of Medicine, Aristotle University School of Health Sciences, Hippokration General Hospital, Thessaloniki, Greece
| | - Marcus Ruhnke
- Department of Hematology & Oncology, Lukas Hospital, Buende, Germany
| | - Cornelia Schaefer Prokop
- Meander Medical Center Amersfoort and Radiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Shmuel Shoham
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins University School
| | - Monica A Slavin
- Department of Infectious Diseases, Peter MacCallum Cancer Center and the National Centre for Infections in Cancer, The University of Melbourne, Melbourne, Victoria, Australia
| | - David A Stevens
- Division of Infectious Diseases and Geographic Medicine, Stanford University Medical School, Stanford, California
- California Institute for Medical Research, San Jose, California, USA
| | - George R Thompson
- Department of Internal Medicine, Division of Infectious Diseases, University of California Davis Medical Center, Sacramento, California, USA
| | - Jose A Vazquez
- Division of Infectious Diseases, Medical College of Georgia/Augusta University, Augusta, Georgia, USA
| | - Claudio Viscoli
- Division of Infectious Disease, University of Genova and San Martino University Hospital, Genova, Italy
| | - Thomas J Walsh
- Weill Cornell Medicine of Cornell University, Departments of Medicine, Pediatrics, Microbiology & Immunology, New York, New York, USA
| | - Adilia Warris
- MRC Centre for Medical Mycology at the University of Aberdeen, Aberdeen, UK
| | | | - P Lewis White
- Public Health Wales Mycology Reference Laboratory, University Hospital of Wales, Heath Park, Cardiff, UK
| | - Theoklis E Zaoutis
- Perelman School of Medicine at the University of Pennsylvania, Children’s Hospital of Philadelphia and Roberts Center for Pediatric Research, Philadelphia, Pennsylvania, USA
| | - Peter G Pappas
- Department of Medicine, Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, Alabama, USA
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20
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High-Frequency Direct Detection of Triazole Resistance in Aspergillus fumigatus from Patients with Chronic Pulmonary Fungal Diseases in India. J Fungi (Basel) 2020; 6:jof6020067. [PMID: 32443672 PMCID: PMC7345705 DOI: 10.3390/jof6020067] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/13/2020] [Accepted: 05/15/2020] [Indexed: 12/18/2022] Open
Abstract
Aspergillosis due to azole-resistant Aspergillus fumigatus is a worldwide problem with major therapeutic implications. In patients with invasive aspergillosis, a low yield of fungal cultures results in underestimation of azole resistance. To detect azole resistance in A. fumigatus, we applied the AsperGenius® Resistance multiplex real-time polymerase chain reaction (PCR) assay to detect TR34/L98H, and TR46/T289A/Y121F mutations and the AsperGenius® G54/M220 RUO PCR assay to detect G54/M220 mutations directly in bronchoalveolar lavage (BAL) samples of 160 patients with chronic respiratory diseases in Delhi, India. Only 23% of samples were culture-positive compared to 83% positivity by A. fumigatus species PCR highlighting concerns about the low yield of cultures. Notably, 25% of BAL samples (33/160 patients) had azole resistance-associated mutation by direct detection using PCR assay. Detection of resistance-associated mutations was found mainly in 59% and 43% patients with chronic pulmonary aspergillosis (CPA) and allergic bronchopulmonary aspergillosis (ABPA), respectively. Overall, a G54 mutation, conferring itraconazole resistance, was the predominant finding in 87.5% and 67% of patients with CPA and ABPA, respectively. In culture-negative, PCR-positive samples, we detected azole-resistant mutations in 34% of BAL samples. Azole resistance in chronic Aspergillus diseases remains undiagnosed, warranting standardization of respiratory culture and inclusion of rapid techniques to detect resistance markers directly in respiratory samples.
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Posch W, Wilflingseder D, Lass-Flörl C. Immunotherapy as an Antifungal Strategy in Immune Compromised Hosts. CURRENT CLINICAL MICROBIOLOGY REPORTS 2020. [DOI: 10.1007/s40588-020-00141-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Abstract
Purpose of Review
IFIs cause high morbidity and mortality in the immunocompromised host worldwide. Although highly effective, conventional antifungal chemotherapy faces new challenges due to late diagnosis and increasing numbers of drug-resistant fungal strains. Thus, antifungal immunotherapy represents a viable treatment option, and recent advances in the field are summarized in this review.
Recent Findings
Antifungal immunotherapies include application of immune cells as well as the administration of cytokines, growth factors, and antibodies. Novel strategies to treat IFIs in the immunocompromised host target intracellular signaling pathways using SMTs such as checkpoint inhibitors.
Summary
Studies using cytokines or chemokines exerted a potential adjuvant role to conventional antifungal therapy, but issues on toxicity for some agents have to be resolved. Cell-based immunotherapies are very labor-intense and costly, but NK cell transfer and CAR T cell therapy provide exciting strategies to combat IFIs. Antibody-mediated protection and checkpoint inhibition are additional novel immunotherapeutic approaches.
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Dailey PJ, Elbeik T, Holodniy M. Companion and complementary diagnostics for infectious diseases. Expert Rev Mol Diagn 2020; 20:619-636. [PMID: 32031431 DOI: 10.1080/14737159.2020.1724784] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Companion diagnostics (CDx) are important in oncology therapeutic decision-making, but specific regulatory-approved CDx for infectious disease treatment are officially lacking. While not approved as CDx, several ID diagnostics are used as CDx. The diagnostics community, manufacturers, and regulatory agencies have made major efforts to ensure that diagnostics for new antimicrobials are available at or near release of new agents. AREAS COVERED This review highlights the status of Complementary and companion diagnostic (c/CDx) in the infectious disease literature, with a focus on genotypic antimicrobial resistance testing against pathogens as a class of diagnostic tests. EXPERT OPINION CRISPR, sepsis markers, and narrow spectrum antimicrobials, in addition to current and emerging technologies, present opportunities for infectious disease c/CDx. Challenges include slow guideline revision, high costs for regulatory approval, lengthy buy in by agencies, discordant pharmaceutical/diagnostic partnerships, and higher treatment costs. The number of patients and available medications used to treat different infectious diseases is well suited to support competing diagnostic tests. However, newer approaches to treatment (for example, narrow spectrum antibiotics), may be well suited for a small number of patients, i.e. a niche market in support of a CDx. The current emphasis is rapid and point-of-care (POC) diagnostic platforms as well as changes in treatment.
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Affiliation(s)
- Peter J Dailey
- School of Public Health, University of California, Berkeley , Berkeley, CA, USA.,The Foundation for Innovative New Diagnostics (FIND) , Geneva, Switzerland
| | - Tarek Elbeik
- VA Palo Alto Health Care System, Department of Veterans Affairs , Palo Alto, CA, USA
| | - Mark Holodniy
- VA Palo Alto Health Care System, Department of Veterans Affairs , Palo Alto, CA, USA.,Division of Infectious Diseases and Geographic Medicine, Stanford University , Stanford, CA, USA
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Egger M, Jenks JD, Hoenigl M, Prattes J. Blood Aspergillus PCR: The Good, the Bad, and the Ugly. J Fungi (Basel) 2020; 6:jof6010018. [PMID: 32012787 PMCID: PMC7151127 DOI: 10.3390/jof6010018] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 01/17/2020] [Accepted: 01/20/2020] [Indexed: 12/11/2022] Open
Abstract
Invasive Aspergillosis (IA) is one of the most common invasive fungal diseases and is accompanied by high morbidity and mortality. In order to maximize patient outcomes and survival, early and rapid diagnosis has been shown to be pivotal. Hence, diagnostic tools aiding and improving the diagnostic process are ambitiously searched for. In this context, polymerase chain reaction (PCR) may represent a potential candidate. Its additional value and benefits in diagnosis have been demonstrated and are scientifically established. Nevertheless, standardized and widespread usage is sparse because several factors influence diagnostic quality and need to be considered in order to optimize diagnostic performance and outcome. In the following review, the current role of PCR in the diagnosis of IA is explored, with special focus on the strengths and limitations of PCR in different settings.
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Affiliation(s)
- Matthias Egger
- Section of Infectious Diseases and Tropical Medicine, Medical University of Graz, 8036 Graz, Austria; (M.E.); (M.H.)
| | - Jeffrey D. Jenks
- Department of Medicine, University of California San Diego, San Diego, CA 92093, USA;
- Clinical and Translational Fungal Research Group, University of California San Diego, San Diego, CA 92093, USA
| | - Martin Hoenigl
- Section of Infectious Diseases and Tropical Medicine, Medical University of Graz, 8036 Graz, Austria; (M.E.); (M.H.)
- Department of Medicine, University of California San Diego, San Diego, CA 92093, USA;
- Clinical and Translational Fungal Research Group, University of California San Diego, San Diego, CA 92093, USA
| | - Juergen Prattes
- Section of Infectious Diseases and Tropical Medicine, Medical University of Graz, 8036 Graz, Austria; (M.E.); (M.H.)
- Correspondence: ; Tel.: +43-316-385-30046
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Evaluation of Commercially Available Real-Time Polymerase Chain Reaction Assays for the Diagnosis of Invasive Aspergillosis in Patients with Haematological Malignancies. Mycopathologia 2020; 185:269-277. [PMID: 31950340 DOI: 10.1007/s11046-020-00424-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 01/03/2020] [Indexed: 10/25/2022]
Abstract
Early diagnosis of invasive aspergillosis (IA) is a challenge. Non-specific clinical and radiologic findings, as well as difficulties in conventional diagnostic method application, may delay correct diagnosis. Nowadays, nucleic acid-based assays have reduced the need for conventional antigen detection and culture-based methods and provided new opportunities for patient care. Aspergillus PCR is now included in the latest European Cancer Research and Treatment Organization/Mycosis Study Group definition updates. We evaluated the performance of commercial real-time polymerase chain reaction (PCR) MycAssay Aspergillus PCR and Artus Aspergillus RG PCR assays and compared the results with galactomannan enzyme immunoassay. During 41 febrile neutropenic episodes, 168 serum samples were collected from 32 patients with haematological malignancies. IA diagnosis was established according to the revised guidelines of the European Organization for Research and Treatment of Cancer/Mycoses Study Group. Twenty-one probable episodes were identified. There were no proven IA cases in the study. In 20 episodes, patients did not fulfil the established criteria for the IA diagnosis. Artus Aspergillus RG PCR assay had a sensitivity of 47.6% and specificity of 100%, while those of MycAssay Aspergillus PCR were 61.9% and 100%, respectively. Two different PCR assays were used in this study. Although there are many studies that evaluated MycAssay Aspergillus PCR, data regarding Artus Aspergillus RG PCR assay are scarce. We found moderate sensitivity and high specificity in the diagnosis of IA in patients with haematological malignancy in both PCR methods. Our results demonstrated that commercial PCR assays can be applied for the early diagnosis and pre-emptive treatment of IA.
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Kidd SE, Chen SCA, Meyer W, Halliday CL. A New Age in Molecular Diagnostics for Invasive Fungal Disease: Are We Ready? Front Microbiol 2020; 10:2903. [PMID: 31993022 PMCID: PMC6971168 DOI: 10.3389/fmicb.2019.02903] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 12/02/2019] [Indexed: 12/18/2022] Open
Abstract
Invasive fungal diseases (IFDs) present an increasing global burden in immunocompromised and other seriously ill populations, including those caused by pathogens which are inherently resistant or less susceptible to antifungal drugs. Early diagnosis encompassing accurate detection and identification of the causative agent and of antifungal resistance is critical for optimum patient outcomes. Many molecular-based diagnostic approaches have good clinical utility although interpretation of results should be according to clinical context. Where an IFD is in the differential diagnosis, panfungal PCR assays allow the rapid detection/identification of fungal species directly from clinical specimens with good specificity; sensitivity is also high when hyphae are seen in the specimen including in paraffin-embedded tissue. Aspergillus PCR assays on blood fractions have good utility in the screening of high risk hematology patients with high negative predictive value (NPV) and positive predictive value (PPV) of 94 and 70%, respectively, when two positive PCR results are obtained. The standardization, and commercialization of Aspergillus PCR assays has now enabled direct comparison of results between laboratories with commercial assays also offering the simultaneous detection of common azole resistance mutations. Candida PCR assays are not as well standardized with the only FDA-approved commercial system (T2Candida) detecting only the five most common species; while the T2Candida outperforms blood culture in patients with candidemia, its role in routine Candida diagnostics is not well defined. There is growing use of Mucorales-specific PCR assays to detect selected genera in blood fractions. Quantitative real-time Pneumocystis jirovecii PCRs have replaced microscopy and immunofluorescent stains in many diagnostic laboratories although distinguishing infection may be problematic in non-HIV-infected patients. For species identification of isolates, DNA barcoding with dual loci (ITS and TEF1α) offer optimal accuracy while next generation sequencing (NGS) technologies offer highly discriminatory analysis of genetic diversity including for outbreak investigation and for drug resistance characterization. Advances in molecular technologies will further enhance routine fungal diagnostics.
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Affiliation(s)
- Sarah E. Kidd
- National Mycology Reference Centre, Microbiology and Infectious Diseases, South Australia Pathology, Adelaide, SA, Australia
| | - Sharon C.-A. Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR, New South Wales Health Pathology, Westmead Hospital, Westmead, NSW, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia
| | - Wieland Meyer
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia
- The Westmead Institute for Medical Research, Westmead, NSW, Australia
- Research and Education Network, Westmead Hospital, Westmead, NSW, Australia
| | - Catriona L. Halliday
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR, New South Wales Health Pathology, Westmead Hospital, Westmead, NSW, Australia
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van der Torre MH, Novak-Frazer L, Rautemaa-Richardson R. Detecting Azole-Antifungal Resistance in Aspergillus fumigatus by Pyrosequencing. J Fungi (Basel) 2020; 6:jof6010012. [PMID: 31936898 PMCID: PMC7151159 DOI: 10.3390/jof6010012] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/08/2020] [Accepted: 01/08/2020] [Indexed: 12/12/2022] Open
Abstract
Guidelines on the diagnosis and management of Aspergillus disease recommend a multi-test approach including CT scans, culture, fungal biomarker tests, microscopy and fungal PCR. The first-line treatment of confirmed invasive aspergillosis (IA) consists of drugs in the azole family; however, the emergence of azole-resistant isolates has negatively impacted the management of IA. Failure to detect azole-resistance dramatically increases the mortality rates of azole-treated patients. Despite drug susceptibility tests not being routinely performed currently, we suggest including resistance testing whilst diagnosing Aspergillus disease. Multiple tools, including DNA sequencing, are available to screen for drug-resistant Aspergillus in clinical samples. This is particularly beneficial as a large proportion of IA samples are culture negative, consequently impeding susceptibility testing through conventional methods. Pyrosequencing is a promising in-house DNA sequencing method that can rapidly screen for genetic hotspots associated with antifungal resistance. Pyrosequencing outperforms other susceptibility testing methods due to its fast turnaround time, accurate detection of polymorphisms within critical genes, including simultaneous detection of wild type and mutated sequences, and—most importantly—it is not limited to specific genes nor fungal species. Here we review current diagnostic methods and highlight the potential of pyrosequencing to aid in a diagnosis complete with a resistance profile to improve clinical outcomes.
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Affiliation(s)
- Mireille H. van der Torre
- Mycology Reference Centre, Excellence Centre of Medical Mycology (ECMM), Manchester University NHS Foundation Trust-Wythenshawe Hospital, Manchester M23 9LT, UK; (M.H.v.d.T.); (L.N.-F.)
| | - Lilyann Novak-Frazer
- Mycology Reference Centre, Excellence Centre of Medical Mycology (ECMM), Manchester University NHS Foundation Trust-Wythenshawe Hospital, Manchester M23 9LT, UK; (M.H.v.d.T.); (L.N.-F.)
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, NIHR Manchester Biomedical Research Centre (BRC) at the Manchester Academic Health Science Centre, The University of Manchester, Manchester M23 9LT, UK
| | - Riina Rautemaa-Richardson
- Mycology Reference Centre, Excellence Centre of Medical Mycology (ECMM), Manchester University NHS Foundation Trust-Wythenshawe Hospital, Manchester M23 9LT, UK; (M.H.v.d.T.); (L.N.-F.)
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, NIHR Manchester Biomedical Research Centre (BRC) at the Manchester Academic Health Science Centre, The University of Manchester, Manchester M23 9LT, UK
- Department of Infectious Diseases, Manchester University NHS Foundation Trust-Wythenshawe Hospital, Manchester M23 9LT, UK
- Correspondence: ; Tel.: +44-161-291-5941
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Linking calcium signaling and mitochondrial function in fungal drug resistance. Proc Natl Acad Sci U S A 2020; 117:1254-1256. [PMID: 31900354 DOI: 10.1073/pnas.1920497117] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
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del Rocío Reyes-Montes M, Duarte-Escalante E, Guadalupe Frías-De-León M, Obed Martínez-Herrera E, Acosta-Altamirano G. Molecular Diagnosis of Invasive Aspergillosis. Mol Med 2019. [DOI: 10.5772/intechopen.78694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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30
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White PL. Recent advances and novel approaches in laboratory-based diagnostic mycology. Med Mycol 2019; 57:S259-S266. [PMID: 31292661 DOI: 10.1093/mmy/myy159] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 11/29/2018] [Accepted: 12/20/2018] [Indexed: 12/12/2022] Open
Abstract
The field of diagnostic mycology represents much more than culture and microscopy and is rapidly embracing novel techniques and strategies to help overcome the limitations of conventional approaches. Commercial molecular assays increase the applicability of PCR testing and may identify markers of antifungal resistance, which are of great clinical concern. Lateral flow assays simplify testing and turn-around time, with potential for point of care testing, while proximity ligation assays embrace the sensitivity of molecular testing with the specificity of antibody detection. The first evidence of patient risk stratification is being described and together with the era of next generation sequencing represents an exciting time in mycology.
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Affiliation(s)
- P Lewis White
- Mycology Reference Laboratory, Public Health Wales, Microbiology Cardiff, Cardiff, United Kingdom
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Jenks JD, Spiess B, Buchheidt D, Hoenigl M. (New) Methods for Detection of Aspergillus fumigatus Resistance in Clinical Samples. CURRENT FUNGAL INFECTION REPORTS 2019; 13:129-136. [PMID: 31552129 PMCID: PMC6759225 DOI: 10.1007/s12281-019-00342-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
PURPOSE OF REVIEW The incidence of invasive aspergillosis has increased substantially over the past few decades, accompanied by a change in susceptibility patterns of Aspergillus fumigatus with increasing resistance observed against triazole antifungals, including voriconazole and isavuconazole, the most commonly used antifungal agents for the disease. Culture-based methods for determining triazole resistance are still the gold standard but are time consuming and lack sensitivity. We sought to provide an update on non-culture-based methods for detecting resistance patterns to Aspergillus. RECENT FINDINGS New molecular-based approaches for detecting triazole resistance to Aspergillus, real-time polymerase chain reaction (PCR) to detect mutations to the Cyp51A protein, have been developed which are able to detect most triazole-resistant A. fumigatus strains in patients with invasive aspergillosis. SUMMARY Over the last few years, a number of non-culture-based methods for molecular detection of Aspergillus triazole resistance have been developed that may overcome some of the limitations of culture. These molecular methods are therefore of high epidemiological and clinical relevance, mainly in immunocompromised patients with hematological malignancies, where culture has particularly limited sensitivity. These assays are now able to detect most triazole-resistant Aspergillus fumigatus strains. Given that resistance rates vary, clinical utility for these assays still depends on regional resistance patterns.
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Affiliation(s)
- Jeffrey D. Jenks
- Department of Medicine, University of California San Diego, San Diego, CA 92103, USA
| | - Birgit Spiess
- Department of Hematology and Oncology, Scientific Laboratory, University Hospital Mannheim, Heidelberg University, Pettenkoferstraße 22, 68169 Mannheim, Germany
| | - Dieter Buchheidt
- Department of Hematology and Oncology, Scientific Laboratory, University Hospital Mannheim, Heidelberg University, Pettenkoferstraße 22, 68169 Mannheim, Germany
| | - Martin Hoenigl
- Department of Medicine, University of California San Diego, San Diego, CA 92103, USA
- Section of Infectious Diseases and Tropical Medicine, Medical University of Graz, Graz, Austria
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A Novel Broad Allele-Specific TaqMan Real-Time PCR Method To Detect Triazole-Resistant Strains of Aspergillus fumigatus, Even with a Very Low Percentage of Triazole-Resistant Cells Mixed with Triazole-Susceptible Cells. J Clin Microbiol 2019; 57:JCM.00604-19. [PMID: 31315952 DOI: 10.1128/jcm.00604-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 07/08/2019] [Indexed: 11/20/2022] Open
Abstract
Invasive aspergillosis caused by triazole-resistant strains of Aspergillus fumigatus is a growing public health concern, as is the occurrence of mixed infections with triazole-resistant and -susceptible A. fumigatus strains. Therefore, it is crucial to develop robust methods to identify triazole-resistant strains of A. fumigatus, even in mixtures of triazole-resistant and -susceptible strains of A. fumigatus In this work, we developed a robust, highly selective, and broad-range allele-specific TaqMan real-time PCR platform consisting of 7 simultaneous assays that detect TR34 (a 34-bp tandem repeat in the promoter region), TR46, G54W (a change of G to W at position 54), G54R, L98H, Y121F, and M220I mutations in the cyp51A gene of A. fumigatus The method is based on the widely used TaqMan real-time PCR technology and combines allele-specific PCR with a blocking reagent (minor groove binder [MGB] oligonucleotide blocker) to suppress amplification of the wild-type cyp51A alleles. We used this method to detect triazole-resistant clinical strains of A. fumigatus with a variety of cyp51A gene mutations, as well as the triazole-resistant strains in mixtures of triazole-resistant and -susceptible strains of A. fumigatus The method had high efficiency and sensitivity (300 fg/well, corresponding to about 100 CFU per reaction mixture volume). It could promptly detect triazole resistance in a panel of 30 clinical strains of A. fumigatus within about 6 h. It could also detect cyp51A-associated resistance alleles, even in mixtures containing only 1% triazole-resistant A. fumigatus strains. These results suggest that this method is robustly able to detect cyp51A-associated resistance alleles even in mixtures of triazole-resistant and -susceptible strains of A. fumigatus and that it should have important clinical applications.
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Danion F, Rouzaud C, Duréault A, Poirée S, Bougnoux ME, Alanio A, Lanternier F, Lortholary O. Why are so many cases of invasive aspergillosis missed? Med Mycol 2019; 57:S94-S103. [PMID: 30816963 DOI: 10.1093/mmy/myy081] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 08/10/2018] [Indexed: 12/20/2022] Open
Abstract
Invasive aspergillosis (IA) incidence is increasing in several countries like France, and numerous cases are indeed missed and still only diagnosed at autopsy as evidenced by recently published data. Such missed diagnoses are obviously encountered when appropriate diagnostic tools are not available especially in low resource areas or when biologists have not been trained enough in medical mycology (i.e., microscopic examination and culture in most of those areas). Besides logistical issues, which are indeed critical, IA may not be recognized because clinicians failed to consider that risk factors are evolving with the IA burden now observed among patients with chronic lymphoid malignancies or receiving new biotherapies, with diabetes mellitus or liver cirrhosis and/or acute alcoholic hepatitis, with patients from the intensive care unit (ICU) and among patients with some predisposing primary immune deficiencies now reaching the adult's age. This is also the case for human immunodeficiency virus (HIV)-infected patients who failed to meet the classical definitions of IA. From the radiology perspective, new entities of IA have also emerged which absolutely need to be recognized especially bronchial-based-IA among allogeneic stem cell transplant recipients. Finally, from the laboratory side, contribution and limits of indirect blood biomarkers should be integrated to the clinical life in order not to miss IA cases. To conclude, several diagnostic tools should be combined and a constant dialog between laboratory and clinics is crucial to appropriately diagnose IA.
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Affiliation(s)
- François Danion
- Department of Infectious Diseases and Tropical Medicine, Necker-Pasteur Infectious Diseases Center, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Institut Imagine, Paris Descartes University, Paris, France.,Aspergillus Unit, Institut Pasteur, Paris, France
| | - Claire Rouzaud
- Department of Infectious Diseases and Tropical Medicine, Necker-Pasteur Infectious Diseases Center, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Institut Imagine, Paris Descartes University, Paris, France
| | - Amélie Duréault
- Department of Infectious Diseases and Tropical Medicine, Necker-Pasteur Infectious Diseases Center, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Institut Imagine, Paris Descartes University, Paris, France
| | - Sylvain Poirée
- Department of Radiology, Necker-Enfants Malades University Hospital, AP-HP, Paris Descartes University, Paris, France
| | - Marie-Elisabeth Bougnoux
- Department of Mycology, Necker-Enfants Malades University Hospital, AP-HP, Paris Descartes University, Paris, France
| | - Alexandre Alanio
- National Reference Center for Invasive Mycoses and Antifungals, Molecular Mycology Unit, Institut Pasteur, Paris, France.,Department of Mycology, Saint-Louis Hospital, AP-HP, Paris, France
| | - Fanny Lanternier
- Department of Infectious Diseases and Tropical Medicine, Necker-Pasteur Infectious Diseases Center, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Institut Imagine, Paris Descartes University, Paris, France.,National Reference Center for Invasive Mycoses and Antifungals, Molecular Mycology Unit, Institut Pasteur, Paris, France
| | - Olivier Lortholary
- Department of Infectious Diseases and Tropical Medicine, Necker-Pasteur Infectious Diseases Center, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Institut Imagine, Paris Descartes University, Paris, France.,National Reference Center for Invasive Mycoses and Antifungals, Molecular Mycology Unit, Institut Pasteur, Paris, France
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José P, Alvarez-Lerma F, Maseda E, Olaechea P, Pemán J, Soriano C, Zaragoza R. Invasive fungal infection in crtically ill patients: hurdles and next challenges. J Chemother 2019; 31:64-73. [PMID: 30761948 DOI: 10.1080/1120009x.2018.1557799] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A narrative review from a multidisciplinary task force of experts in critical care medicine and clinical mycology was carried out. The multi drug-resistant species Candida auris has emerged simultaneously on several continents, causing hospital outbreaks, especially in critically ill patients. Although there are not enough data to support the routine use of continuous antibiotic prophylaxis in patients subjected to extracorporeal membrane oxygenator, a clear increase of invasive fungal infection (IFI) has been described with the use of this device. Possible IFI treatment failures could be related with suboptimal antifungal concentrations despite dose adjustment. Invasive aspergillosis has become an important life-threating infection in intensive care unit related with new risk factors described. IFI remain important problem in critical patients due to the appearance of new risk factors, new species, and resistance increase. Multidisciplinary packages of measures designed to reduce IFI incidence and improve diagnostics tools may reduce the high mortality associated.
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Affiliation(s)
- Peral José
- a Intensive Care Unit , Hospital General Universitario Gregorio Marañón , Madrid , Spain
| | | | - Emilio Maseda
- c Surgical Intensive Care Unit , Hospital Universitario La Paz , Madrid , Spain
| | - Pedro Olaechea
- d Intensive Care Unit , Hospital Universitario de Galdákano- Usansolo , Galdakao , Spain
| | - Javier Pemán
- e Microbiology Department , Hospital Universitari i Politecnic La Fe , Valencia , Spain
| | - Cruz Soriano
- f Intensive Care Unit , Hospital Universitario Ramón y Cajal , Madrid , Spain
| | - Rafael Zaragoza
- g Intensive Care Unit , Hospital Universitario Dr. Peset , Valencia , Spain
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Lauruschkat CD, Einsele H, Loeffler J. Immunomodulation as a Therapy for Aspergillus Infection: Current Status and Future Perspectives. J Fungi (Basel) 2018; 4:jof4040137. [PMID: 30558125 PMCID: PMC6308942 DOI: 10.3390/jof4040137] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 12/09/2018] [Accepted: 12/10/2018] [Indexed: 12/30/2022] Open
Abstract
Invasive aspergillosis (IA) is the most serious life-threatening infectious complication of intensive remission induction chemotherapy and allogeneic stem cell transplantation in patients with a variety of hematological malignancies. Aspergillus fumigatus is the most commonly isolated species from cases of IA. Despite the various improvements that have been made with preventative strategies and the development of antifungal drugs, there is an urgent need for new therapeutic approaches that focus on strategies to boost the host’s immune response, since immunological recovery is recognized as being the major determinant of the outcome of IA. Here, we aim to summarize current knowledge about a broad variety of immunotherapeutic approaches against IA, including therapies based on the transfer of distinct immune cell populations, and the administration of cytokines and antibodies.
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Affiliation(s)
- Chris D Lauruschkat
- Department of Internal Medicine II, University Hospital Wuerzburg, WÜ4i, Building C11, 97080 Wuerzburg, Germany.
| | - Hermann Einsele
- Department of Internal Medicine II, University Hospital Wuerzburg, WÜ4i, Building C11, 97080 Wuerzburg, Germany.
| | - Juergen Loeffler
- Department of Internal Medicine II, University Hospital Wuerzburg, WÜ4i, Building C11, 97080 Wuerzburg, Germany.
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36
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Abstract
Diagnosing fungal infections poses a number of unique problems, including a decline in expertise needed for identifying fungi, and a reduced number of instruments and assays specific for fungal identification compared to that of bacteria and viruses.These problems are exacerbated by the fact that patients with fungal infections are often immunosuppressed, which predisposes to infections from both commonly and rarely seen fungi. In this review, we discuss current and future molecular technologies used for fungal identification, and some of the problems associated with development and implementation of these technologies in today’s clinical microbiology laboratories. Diagnosing fungal infections poses a number of unique problems. In this Review, Wickes and Wiederhold discuss molecular technologies used for fungal identification, and the problems associated with their development and implementation in today’s clinical microbiology laboratories.
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37
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Farmakiotis D, Le A, Weiss Z, Ismail N, Kubiak DW, Koo S. False positive bronchoalveolar lavage galactomannan: Effect of host and cut-off value. Mycoses 2018; 62:204-213. [PMID: 30387195 DOI: 10.1111/myc.12867] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 10/28/2018] [Indexed: 12/21/2022]
Abstract
OBJECTIVES Bronchoalveolar lavage galactomannan (BAL-GM) is a mycological criterion for diagnosis of probable invasive aspergillosis (IA) per European Organization for Research and Treatment of Cancer/Mycoses Study Group (EORT-MSG) consensus criteria, but its real-world positive predictive value (PPV) has not been well-studied. Our aim was to estimate the PPV of BAL-GM in a contemporary cohort of patients with positive BAL-GM. METHODS We identified consecutive patients with ≥1 positive BAL-GM value (index ≥ 0.5) at Brigham and Women's Hospital from 11/2009 to 3/2016. We classified patients as having no, possible, probable, or proven IA, excluding BAL-GM as mycological criterion. RESULTS We studied 134 patients: 54% had hematologic malignancy (HM), and 10% were solid organ transplant (SOT) recipients. A total of 42% of positive (≥0.5) BAL-GM results were falsely positive (PPV 58%). The number of probable IA cases was increased by 23% using positive BAL-GM as mycologic criterion alone. PPV was higher in patients with HM or SOT (P < 0.001) and with use of higher thresholds for positivity (BAL-GM ≥ 1 vs 1-0.8 vs 0.8-0.5: P = 0.002). CONCLUSIONS 42% of positive BAL-GM values were falsely positive. We propose a critical reassessment of BAL-GM cutoff values in different patient populations. Accurate noninvasive tests for diagnosis of IA are urgently needed.
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Affiliation(s)
- Dimitrios Farmakiotis
- Division of Infectious Diseases, Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, Rhode Island
| | - Audrey Le
- Department of Internal Medicine, Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, Rhode Island
| | - Zoe Weiss
- Department of Internal Medicine, Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, Rhode Island
| | - Nour Ismail
- Brigham and Women's Hospital, Rhode Island Hospital, Division of Infectious Diseases, Harvard Medical School, Boston, Massachusetts
| | - David W Kubiak
- Brigham and Women's Hospital, Rhode Island Hospital, Division of Infectious Diseases, Harvard Medical School, Boston, Massachusetts
| | - Sophia Koo
- Brigham and Women's Hospital, Rhode Island Hospital, Division of Infectious Diseases, Harvard Medical School, Boston, Massachusetts
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38
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de Groot T, Hagen F, Vreuls W, Verweij PE, Chowdhary A, Meis JF. Genotyping of Aspergillus fumigatus in Formalin-Fixed Paraffin-Embedded Tissues and Serum Samples From Patients With Invasive Aspergillosis. Front Cell Infect Microbiol 2018; 8:377. [PMID: 30406050 PMCID: PMC6206585 DOI: 10.3389/fcimb.2018.00377] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/05/2018] [Indexed: 12/15/2022] Open
Abstract
Invasive aspergillosis (IA) is a deep tissue infection with a high mortality occurring mostly in immunocompromised patients. To investigate the pathology of patients with IA it may be important to determine the genotype of the invasive isolate of Aspergillus, however available tissues for study are often formalin fixed paraffin embedded (FFPE). Although DNA has been successfully isolated from such tissues for species identification, genotyping of Aspergillus species on such tissues has not yet been performed. In this study we aimed to determine the genotype of Aspergillus fumigatus in FFPE tissue and serum samples from five patients with invasive aspergillosis using nine highly polymorphic short tandem repeat (STRAf) loci. FFPE lung and bronchial biopsies from all patients were successfully typed. By comparing the latter result with non-FFPE materials from non-sterile samples such as sputum, bronchoalveolar lavage and lung abscess, we found identical genotypes within three patients, while the two other patients had a dominant genotype shared among all sample types. Genotyping of serum samples was successful in two serum samples with galactomannan ratios of 4 and 5.6, but failed in serum samples with galactomannan levels <0.5. In addition, testing a subset of these materials with the AsperGenius multiplex qPCR assay, we did not find azole resistance mutations. With this STRAf assay, A. fumigatus from FFPE tissue and serum was successfully genotyped, allowing retrospective examination of A. fumigatus in culture negative patients with IA.
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Affiliation(s)
- Theun de Groot
- Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital, Nijmegen, Netherlands
| | - Ferry Hagen
- Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital, Nijmegen, Netherlands.,Department of Medical Mycology, Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands
| | - Willem Vreuls
- Department of Clinical Pathology, Canisius Wilhelmina Hospital, Nijmegen, Netherlands
| | - Paul E Verweij
- Centre of Expertise in Mycology Radboudumc/CWZ, Nijmegen, Netherlands.,Department of Medical Microbiology, Radboudumc, Nijmegen1, Netherlands
| | - Anuradha Chowdhary
- Department of Medical Mycology, Vallabhbhai Patel Chest Institute, University of Delhi, New Delhi, India
| | - Jacques F Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital, Nijmegen, Netherlands.,Centre of Expertise in Mycology Radboudumc/CWZ, Nijmegen, Netherlands.,Department of Medical Microbiology, Radboudumc, Nijmegen1, Netherlands
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39
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Beardsley J, Halliday CL, Chen SCA, Sorrell TC. Responding to the emergence of antifungal drug resistance: perspectives from the bench and the bedside. Future Microbiol 2018; 13:1175-1191. [PMID: 30113223 PMCID: PMC6190174 DOI: 10.2217/fmb-2018-0059] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 05/01/2018] [Indexed: 12/15/2022] Open
Abstract
The incidence of serious fungal infections is increasing rapidly, and yet the rate of new drugs becoming available to treat them is slow. The limited therapeutic armamentarium is a challenge for clinicians, because the available drugs are often toxic, expensive, difficult to administer, ineffective or a combination of all four. Given this setting, the emergence of resistance is especially concerning, and a review of the topic is timely. Here we discuss antifungal drug resistance in Candida spp. and Aspergillus spp. with reference to the most commonly used first-line antifungal agents - azoles and echinocandins. We review the resistance mechanisms of the leading pathogens, how resistance can be identified in the diagnostic lab and the clinical implications of resistance once detected.
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Affiliation(s)
- Justin Beardsley
- Marie Bashir Institute for Infectious Diseases & Biosecurity, University of Sydney & Westmead Institute for Medical Research, Westmead, NSW, Australia
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Catriona L Halliday
- The Center for Infectious Diseases & Microbiology Laboratory Services, ICPMR Pathology West, New South Wales Health Pathology, Westmead, NSW, Australia
| | - Sharon C-A Chen
- Marie Bashir Institute for Infectious Diseases & Biosecurity, University of Sydney & Westmead Institute for Medical Research, Westmead, NSW, Australia
- The Center for Infectious Diseases & Microbiology Laboratory Services, ICPMR Pathology West, New South Wales Health Pathology, Westmead, NSW, Australia
| | - Tania C Sorrell
- Marie Bashir Institute for Infectious Diseases & Biosecurity, University of Sydney & Westmead Institute for Medical Research, Westmead, NSW, Australia
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40
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Rath PM, Steinmann J. Overview of Commercially Available PCR Assays for the Detection of Aspergillus spp. DNA in Patient Samples. Front Microbiol 2018; 9:740. [PMID: 29740403 PMCID: PMC5928133 DOI: 10.3389/fmicb.2018.00740] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 03/29/2018] [Indexed: 12/31/2022] Open
Abstract
Invasive aspergillosis (IA) is a life-threatening infection in immunocompromised patients. Early diagnosis is essential to improve survival. Since the 1990s, attempts for PCR-based diagnosis of IA were made. Progress in the standardization of methods enabled the development of commercially available Aspergillus PCR assays in the last few years. Up to now, the clinical value of only a few commercial assays was investigated more extensively in large cohort studies. Most often, respiratory secretions such as bronchoalveolar lavage (BAL) were investigated, but some studies also included serum samples from high-risk patients. The data indicate that Aspergillus PCR, most likely in combination with galactomannan detection, has the potential for early and reliable diagnosis of IA including azole resistance markers. With the broad implementation of this technique in routine diagnosis and incorporation into patient care pathways, it is conceivable that an improvement in management of IA and subsequently patient outcome could occur.
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Affiliation(s)
- Peter-Michael Rath
- Institute of Medical Microbiology, Essen University Hospital, University of Duisburg-Essen, Essen, Germany
| | - Joerg Steinmann
- Institute of Medical Microbiology, Essen University Hospital, University of Duisburg-Essen, Essen, Germany.,Institute of Clinical Hygiene, Medical Microbiology and Infectiology, Paracelsus Medical University, Klinikum Nuernberg, Nuremberg, Germany
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41
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Otašević S, Momčilović S, Stojanović NM, Skvarč M, Rajković K, Arsić-Arsenijević V. Non-culture based assays for the detection of fungal pathogens. J Mycol Med 2018; 28:236-248. [PMID: 29605542 PMCID: PMC7110445 DOI: 10.1016/j.mycmed.2018.03.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 03/05/2018] [Accepted: 03/05/2018] [Indexed: 01/05/2023]
Abstract
Traditional, culture based methods for the diagnosis of fungal infections are still considered as gold standard, but they are time consuming and low sensitive. Therefore, in order to overcome the limitations, many researchers have focused on the development of new immunological and molecular based rapid assays that could enable early diagnosis of infection and accurate identification of fungal pathogens causing superficial and invasive infection. In this brief review, we highlighted the advantages and disadvantages of conventional diagnostic methods and possibility of non-culture based assays in diagnosis of superficial fungal infections and presented the overview on currently available immunochromatographic assays as well as availability of biomarkers detection by immunodiagnostic procedures in prompt and accurate diagnosis of invasive fungal infections. In addition, we presented diagnostic efficiency of currently available molecular panels and researches in this area.
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Affiliation(s)
- S Otašević
- Center of Microbiology and Parasitology, Public Health Institute Niš, Serbia, boulevard Zorana Djindjica 50, 18000 Niš, Serbia; Department of Microbiology and Immunology, Faculty of Medicine, University of Niš, Serbia, boulevard Zorana Djindjica 81, 18000 Niš, Serbia.
| | - S Momčilović
- Department of Microbiology and Immunology, Faculty of Medicine, University of Niš, Serbia, boulevard Zorana Djindjica 81, 18000 Niš, Serbia
| | - N M Stojanović
- Faculty of Medicine, University of Niš, Serbia, boulevard Zorana Djindjica 81, 18000 Niš, Serbia
| | - M Skvarč
- University of Ljubljana, Faculty of Medicine, Institute of Microbiology and Immunology, Zaloska 4, Ljubljana, Slovenia
| | - K Rajković
- High Chemical and Technological School for Professional Studies, Kosančićeva 36, 37000 Kruševac, Serbia
| | - V Arsić-Arsenijević
- Department for Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Serbia, Dr Subotića 1, 11000 Belgrade, Serbia
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42
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Postina P, Skladny J, Boch T, Cornely OA, Hamprecht A, Rath PM, Steinmann J, Bader O, Miethke T, Dietz A, Merker N, Hofmann WK, Buchheidt D, Spiess B. Comparison of Two Molecular Assays for Detection and Characterization of Aspergillus fumigatus Triazole Resistance and Cyp51A Mutations in Clinical Isolates and Primary Clinical Samples of Immunocompromised Patients. Front Microbiol 2018; 9:555. [PMID: 29662479 PMCID: PMC5890139 DOI: 10.3389/fmicb.2018.00555] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 03/12/2018] [Indexed: 11/23/2022] Open
Abstract
In hematological patients, the incidence of invasive aspergillosis (IA) caused by azole resistant Aspergillus fumigatus (ARAf) is rising. As the diagnosis of IA is rarely based on positive culture in this group of patients, molecular detection of resistance mutations directly from clinical samples is crucial. In addition to the in-house azole resistance ARAf polymerase chain reaction (PCR) assays detecting the frequent mutation combinations TR34/L98H, TR46/Y121F/T289A, and M220 in the Aspergillus fumigatus (A. fumigatus) Cyp51A gene by subsequent DNA sequence analysis, we investigated in parallel the commercially available AsperGenius® real time PCR system in detecting the Cyp51A alterations TR34/L98H and Y121F/T289A directly from 52 clinical samples (15 biopsies, 22 bronchoalveolar lavage (BAL), 15 cerebrospinal fluid (CSF) samples) and ARAf isolates (n = 3) of immunocompromised patients. We analyzed DNA aliquots and compared both methods concerning amplification and detection of Aspergillus DNA and Cyp51A alterations. As positive control for the feasibility of our novel Y121F and T289A PCR assays, we used two A. fumigatus isolates with the TR46/Y121F/T289A mutation combination isolated from hematological patients with known Cyp51A alterations and a lung biopsy sample of a patient with acute myeloid leukemia (AML). The rate of positive ARAf PCR results plus successful sequencing using the ARAf PCR assays was 61% in biopsies, 29% in CSF, 67% in BAL samples and 100% in isolates. In comparison the amount of positive PCRs using the AsperGenius® assays was 47% in biopsies, 42% in CSF, 59% in BAL samples and 100% in isolates. Altogether 17 Cyp51A alterations were detected using our ARAf PCRs plus DNA sequencing and therefrom 10 alterations also by the AsperGenius® system. The comparative evaluation of our data revealed that our conventional PCR assays are more sensitive in detecting ARAf in BAL and biopsy samples, whereby differences were not significant. The advantage of the AsperGenius® system is the time saving aspect. We consider non-culture based molecular detection of Aspergillus triazole resistance to be of high epidemiological and clinical relevance in patients with hematological malignancies.
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Affiliation(s)
- Patricia Postina
- Department of Hematology and Oncology, University Hospital Mannheim, Heidelberg University, Mannheim, Germany
| | - Julian Skladny
- Department of Hematology and Oncology, University Hospital Mannheim, Heidelberg University, Mannheim, Germany
| | - Tobias Boch
- Department of Hematology and Oncology, University Hospital Mannheim, Heidelberg University, Mannheim, Germany
| | - Oliver A Cornely
- Department I of Internal Medicine, University Hospital of Cologne, Cologne, Germany.,Clinical Trials Centre Cologne, ZKS Köln and Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases, University of Cologne, Cologne, Germany
| | - Axel Hamprecht
- Institute of Medical Microbiology, Immunology and Hygiene, University Hospital of Cologne, Cologne, Germany
| | - Peter-Michael Rath
- Institute of Medical Microbiology, University Hospital Essen, Essen, Germany
| | - Jörg Steinmann
- Institute of Clinical Hygiene, Medical Microbiology and Clinical Infectiology, Paracelsus Medical University, Nuremberg, Germany
| | - Oliver Bader
- Institute for Medical Microbiology, University Medical Center Göttingen, Göttingen, Germany
| | - Thomas Miethke
- Institute of Medical Microbiology and Hygiene, University Hospital Mannheim, Heidelberg University, Mannheim, Germany
| | - Anne Dietz
- Institute of Medical Microbiology and Hygiene, University Hospital Mannheim, Heidelberg University, Mannheim, Germany
| | - Natalia Merker
- Department of Hematology and Oncology, University Hospital Mannheim, Heidelberg University, Mannheim, Germany
| | - Wolf-Karsten Hofmann
- Department of Hematology and Oncology, University Hospital Mannheim, Heidelberg University, Mannheim, Germany
| | - Dieter Buchheidt
- Department of Hematology and Oncology, University Hospital Mannheim, Heidelberg University, Mannheim, Germany
| | - Birgit Spiess
- Department of Hematology and Oncology, University Hospital Mannheim, Heidelberg University, Mannheim, Germany
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43
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Buil JB, Zoll J, Verweij PE, Melchers WJG. Molecular Detection of Azole-Resistant Aspergillus fumigatus in Clinical Samples. Front Microbiol 2018; 9:515. [PMID: 29619020 PMCID: PMC5871680 DOI: 10.3389/fmicb.2018.00515] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 03/06/2018] [Indexed: 12/11/2022] Open
Abstract
Aspergillus diseases are often caused by Aspergillus fumigatus. Azoles are the mainstay of therapy, but the management of aspergillosis is hampered by the emergence of azole resistance. Rapid detection of azole resistance might benefit treatment outcome by early treatment modifications. However, the yield of fungal culture in invasive aspergillosis is low and susceptibility testing requires several days to be completed. To overcome the low yield of fungal cultures and slow detection of resistance, it is possible to use molecular tools directly on clinical specimens in order to rapidly detect molecular markers of azole resistance. Molecular tools to detect resistant markers in the Cyp51A gene can be expected to be less sensitive compared to molecular tools to detect Aspergillus DNA as the Cyp51A gene is a single copy gene and the target for Aspergillus DNA is often a multi-copy gene. In this mini-review, we summarize the current molecular tools for detection of azole-resistant A. fumigatus directly in clinical material. Several in-house PCR assays have been applied directly on clinical material. Furthermore, two assays are commercial available; the AsperGenius and MycoGENIE. The amplification of resistance markers was successful in 70–100% of samples that were positive for Aspergillus DNA in BAL samples using the AsperGenius assay. Despite using several samples per patient, amplification of resistance markers was only successful in 33–57% of patients with Aspergillus DNA in blood. Furthermore, several sequence based methods have been applied with the benefit of the ability to detect other Cyp51A gene alterations.
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Affiliation(s)
- Jochem B Buil
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, Netherlands.,Center of Expertise in Mycology Radboudumc/CWZ, Nijmegen, Netherlands
| | - Jan Zoll
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, Netherlands.,Center of Expertise in Mycology Radboudumc/CWZ, Nijmegen, Netherlands
| | - Paul E Verweij
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, Netherlands.,Center of Expertise in Mycology Radboudumc/CWZ, Nijmegen, Netherlands
| | - Willem J G Melchers
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, Netherlands.,Center of Expertise in Mycology Radboudumc/CWZ, Nijmegen, Netherlands
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44
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Morio F, Dannaoui E, Chouaki T, Cateau E, Malard O, Bonfils P, Page C, Dufour X, Cottrel C, Erwan T, Lavergne RA, Le Pape P. PCR-based detection of Aspergillus fumigatus and absence of azole resistance due to TR 34 /L98H in a french multicenter cohort of 137 patients with fungal rhinosinusitis. Mycoses 2017; 61:30-34. [PMID: 28922487 DOI: 10.1111/myc.12702] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 09/13/2017] [Accepted: 09/14/2017] [Indexed: 12/31/2022]
Abstract
Fungal rhinosinusitis (FRS) has a worldwide distribution, comprises distinct clinical entities but is mostly due to Aspergillus among which Aspergillus fumigatus plays a major role in European countries. Although, there is accumulating evidence for the emergence of environmentally acquired-azole resistance in A. fumigatus (such as TR34 /L98H) in various clinical settings, there is few data for patients with FRS. In this study, we aimed to investigate the prevalence of A. fumigatus azole resistance due to TR34 /L98H in a multicentre cohort of patients with FRS. One hundred and thirty-seven patients with FRS admitted between 2002 and 2016 at four French medical centres were retrospectively enrolled. Clinical and mycological findings were collected. Aspergillus fumigatus and the TR34 /L98H alteration conferring azole resistance were investigated directly from clinical samples using the commercial CE-IVD marked MycoGENIE® A. fumigatus real-time PCR assay. Fungal ball was the more frequent clinical form (n = 118). Despite the presence of fungal hyphae at direct microscopic examination, mycological cultures remained negative for 83 out of the 137 patients (60.6%). The PCR assay proved to be useful allowing the identification of A. fumigatus and etiological diagnosis in 106 patients (77.4%) compared with 44 patients (32.1%) when using culture as the reference method. Importantly, neither TR34 nor L98H alterations were evidenced.
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Affiliation(s)
- Florent Morio
- Laboratoire de Parasitologie-Mycologie, Institut de Biologie, CHU Nantes, Nantes, France.,Département de Parasitologie et Mycologie Médicale, EA1155 IICiMed, Institut de Recherche en Santé 2, Université de Nantes, Nantes Atlantique Universités, Nantes, France
| | - Eric Dannaoui
- Dynamyc Research Group, UPEC, EnvA, UPE, Créteil, Paris, France.,Faculté de Médecine, APHP, Hôpital Européen Georges Pompidou, Unité de Parasitologie-Mycologie, Service de Microbiologie, Université Paris-Descartes, Paris, France
| | - Taieb Chouaki
- Laboratoire de Parasitologie-Mycologie, CHU Amiens, Amiens, France.,EA 4666, CAP-Santé (FED 4231), Amiens, France
| | - Estelle Cateau
- Laboratoire de Parasitologie-Mycologie, CHU Poitiers, Poitiers, France.,Ecologie et Biologie des Interactions, UMR CNRS 7267, Equipe Microbiologie de l'Eau, Université de Poitiers, Poitiers, France
| | - Olivier Malard
- Service d'ORL et de chirurgie cervicofaciale, CHU Nantes, Nantes, France
| | - Pierre Bonfils
- Service d'ORL et de chirurgie cervicofaciale, Hôpital Européen Georges Pompidou, Paris, France
| | - Cyril Page
- Service d'ORL et de chirurgie cervicofaciale, CHU Amiens, Amiens, France
| | - Xavier Dufour
- Service d'ORL et de chirurgie cervicofaciale, CHU Poitiers, Poitiers, France
| | - Claire Cottrel
- Département de Parasitologie et Mycologie Médicale, EA1155 IICiMed, Institut de Recherche en Santé 2, Université de Nantes, Nantes Atlantique Universités, Nantes, France
| | - Tamic Erwan
- Département de Parasitologie et Mycologie Médicale, EA1155 IICiMed, Institut de Recherche en Santé 2, Université de Nantes, Nantes Atlantique Universités, Nantes, France
| | - Rose-Anne Lavergne
- Laboratoire de Parasitologie-Mycologie, Institut de Biologie, CHU Nantes, Nantes, France.,Département de Parasitologie et Mycologie Médicale, EA1155 IICiMed, Institut de Recherche en Santé 2, Université de Nantes, Nantes Atlantique Universités, Nantes, France
| | - Patrice Le Pape
- Laboratoire de Parasitologie-Mycologie, Institut de Biologie, CHU Nantes, Nantes, France.,Département de Parasitologie et Mycologie Médicale, EA1155 IICiMed, Institut de Recherche en Santé 2, Université de Nantes, Nantes Atlantique Universités, Nantes, France
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