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Pham D, Sivalingam V, Tang HM, Montgomery JM, Chen SCA, Halliday CL. Molecular Diagnostics for Invasive Fungal Diseases: Current and Future Approaches. J Fungi (Basel) 2024; 10:447. [PMID: 39057332 PMCID: PMC11278267 DOI: 10.3390/jof10070447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 06/21/2024] [Accepted: 06/24/2024] [Indexed: 07/28/2024] Open
Abstract
Invasive fungal diseases (IFDs) comprise a growing healthcare burden, especially given the expanding population of immunocompromised hosts. Early diagnosis of IFDs is required to optimise therapy with antifungals, especially in the setting of rising rates of antifungal resistance. Molecular techniques including nucleic acid amplification tests and whole genome sequencing have potential to offer utility in overcoming limitations with traditional phenotypic testing. However, standardisation of methodology and interpretations of these assays is an ongoing undertaking. The utility of targeted Aspergillus detection has been well-defined, with progress in investigations into the role of targeted assays for Candida, Pneumocystis, Cryptococcus, the Mucorales and endemic mycoses. Likewise, whilst broad-range polymerase chain reaction assays have been in use for some time, pathology stewardship and optimising diagnostic yield is a continuing exercise. As costs decrease, there is also now increased access and experience with whole genome sequencing, including metagenomic sequencing, which offers unparalleled resolution especially in the investigations of potential outbreaks. However, their role in routine diagnostic use remains uncommon and standardisation of techniques and workflow are required for wider implementation.
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Affiliation(s)
- David Pham
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia; (D.P.)
| | - Varsha Sivalingam
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia; (D.P.)
| | - Helen M. Tang
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia; (D.P.)
| | - James M. Montgomery
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia; (D.P.)
| | - Sharon C.-A. Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia; (D.P.)
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
- Sydney Infectious Diseases Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | - Catriona L. Halliday
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia; (D.P.)
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Lass-Flörl C. [Diagnostic approaches for invasive mycoses: what's hot?]. Dtsch Med Wochenschr 2024; 149:551-559. [PMID: 38657594 DOI: 10.1055/a-2133-4826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Invasive fungal infections are a significant cause of morbidity and mortality in immunocompromised patients. The primary and most frequent pathogens in Europe are Aspergillus and Candida species. However, other representatives such as Mucorales, Trichosporon, and Fusarium species are increasingly being identified. Confirming the diagnosis of an invasive mycosis is challenging; apart from imaging and clinical presentation, essential diagnostic elements include conventional fungal culture, microscopy, antibody/antigen detection tests, and molecular biology.
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Lamoth F, Kontoyiannis DP. PCR diagnostic platforms for non- Aspergillus mold infections: ready for routine implementation in the clinic? Expert Rev Mol Diagn 2024; 24:273-282. [PMID: 38501431 DOI: 10.1080/14737159.2024.2326474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 02/29/2024] [Indexed: 03/20/2024]
Abstract
INTRODUCTION While Aspergillus spp. remain the predominant cause of invasive mold infections, non-Aspergillus molds, such as the Mucorales or Fusarium spp., account for an increasing proportion of cases. The diagnosis of non-Aspergillus invasive mold infections (NAIMI) is challenging because of the low sensitivity and delay of conventional microbiological tests. Therefore, there is a particular interest to develop molecular tools for their early detection in blood or other clinical samples. AREAS COVERED This extensive review of the literature discusses the performance of Mucorales-specific PCR and other genus-specific or broad-range fungal PCR that can be used for the diagnosis of NAIMI in diverse clinical samples, with a focus on novel technologies. EXPERT OPINION PCR currently represents the most promising approach, combining good sensitivity/specificity and ability to detect NAIMI in clinical samples before diagnosis by conventional cultures and histopathology. Several PCR assays have been designed for the detection of Mucorales in particular, but also Fusarium spp. or Scedosporium/Lomentospora spp. Some commercial Mucorales PCRs are now available. While efforts are still needed for standardized protocols and the development of more rapid and simpler techniques, PCR is on the way to becoming an essential test for the early diagnosis of mucormycosis and possibly other NAIMIs.
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Affiliation(s)
- Frederic Lamoth
- Infectious Diseases Service, Department of Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- Institute of Microbiology, Department of Laboratory Medicine and Pathology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Dimitrios P Kontoyiannis
- Department of Infectious Diseases, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Gudisa R, Harchand R, Rudramurthy SM. Nucleic-Acid-Based Molecular Fungal Diagnostics: A Way to a Better Future. Diagnostics (Basel) 2024; 14:520. [PMID: 38472992 DOI: 10.3390/diagnostics14050520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/20/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
The world has seen a tremendous increase in the number of fungal infections during the past two decades. Recently, the World Health Organisation released the pathogen priority list for fungal infections, signifying the importance of these infections in the fields of research and public health. Microbiology laboratories demand an upgrade in the diagnostic system to keep up with the increased burden of these infections. Diagnosis of fungal infections using conventional techniques has always faced limitations in terms of specificity, sensitivity, and turnaround time. Although these methods are the core pillars of the diagnosis, there is an increased need for molecular approaches. Molecular techniques have revolutionised the field of fungal diagnostics. The diverse array of molecular techniques, including techniques like Polymerase Chain Reaction (PCR), have emerged as a cornerstone in fungal diagnostics. Molecular techniques have transformed fungal diagnostics, providing powerful tools for the rapid and accurate identification of pathogens. As these technologies continue to evolve, their integration into routine clinical practice holds the promise of improving patient outcomes through timely and targeted antifungal interventions. This review will cover the molecular approaches involved in fungal diagnostics, moving from the basic techniques to the advanced-level nucleic-acid-based molecular approaches providing a high throughput and decreased turnaround time for the diagnosis of serious fungal infections.
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Affiliation(s)
- Rajendra Gudisa
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Ritika Harchand
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Shivaprakash M Rudramurthy
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh 160012, India
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Aerts R, Feys S, Mercier T, Lagrou K. Microbiological Diagnosis of Pulmonary Aspergillus Infections. Semin Respir Crit Care Med 2024; 45:21-31. [PMID: 38228164 DOI: 10.1055/s-0043-1776777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
As microbiological tests play an important role in our diagnostic algorithms and clinical approach towards patients at-risk for pulmonary aspergillosis, a good knowledge of the diagnostic possibilities and especially their limitations is extremely important. In this review, we aim to reflect critically on the available microbiological diagnostic modalities for diagnosis of pulmonary aspergillosis and formulate some future prospects. Timely start of adequate antifungal treatment leads to a better patient outcome, but overuse of antifungals should be avoided. Current diagnostic possibilities are expanding, and are mainly driven by enzyme immunoassays and lateral flow device tests for the detection of Aspergillus antigens. Most of these tests are directed towards similar antigens, but new antibodies towards different targets are under development. For chronic forms of pulmonary aspergillosis, anti-Aspergillus IgG antibodies and precipitins remain the cornerstone. More studies on the possibilities and limitations of molecular testing including targeting resistance markers are ongoing. Also, metagenomic next-generation sequencing is expanding our future possibilities. It remains important to combine different test results and interpret them in the appropriate clinical context to improve performance. Test performances may differ according to the patient population and test results may be influenced by timing, the tested matrix, and prophylactic and empiric antifungal therapy. Despite the increasing armamentarium, a simple blood or urine test for the diagnosis of aspergillosis in all patient populations at-risk is still lacking. Research on diagnostic tools is broadening from a pathogen focus on biomarkers related to the patient and its immune system.
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Affiliation(s)
- Robina Aerts
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
- Department of Internal Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Simon Feys
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
- Medical Intensive Care Unit, University Hospitals Leuven, Leuven, Belgium
| | - Toine Mercier
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
- Department of Oncology-Hematology, AZ Sint-Maarten, Mechelen, Belgium
| | - Katrien Lagrou
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
- Department of Laboratory Medicine and National Reference Center for Mycosis, University Hospitals Leuven, Leuven, Belgium
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Price JS, Fallon M, Posso R, Backx M, White PL. An Evaluation of the OLM PneumID Real-Time Polymerase Chain Reaction to Aid in the Diagnosis of Pneumocystis Pneumonia. J Fungi (Basel) 2023; 9:1106. [PMID: 37998911 PMCID: PMC10672265 DOI: 10.3390/jof9111106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/17/2023] [Accepted: 11/13/2023] [Indexed: 11/25/2023] Open
Abstract
BACKGROUND The use of the PCR to aid in the diagnosis of Pneumocystis pneumonia (PcP) has demonstrated excellent clinical performance, as evidenced through various systematic reviews and meta-analyses, yet there are concerns over the interpretation of positive results due to the potential presence of Pneumocystis colonization of the airways. While this can be overcome by applying designated positivity thresholds to PCR testing, the shear number of assays described limits the development of a universal threshold. Commercial assays provide the opportunity to overcome this problem, provided satisfactory performance is determined through large-scale, multi-centre evaluations. METHODS Retrospective case/control and consecutive cohort performance evaluations of the OLM PneumID real-time PCR assay were performed on DNA eluates from a range of samples sent from patients where "in-house" PCR had been performed as part of routine diagnostic testing. The clinical performance of the PneumID assay was determined before including it in a diagnostic algorithm to provide the probability of PcP (dependent on diagnostic evidence). RESULTS After being used to test 317 patients (32 with PcP), the overall performance of the PneumID assay was found to be excellent (Sensitivity/Specificity: 96.9%/95.1%). False positivity could be removed by applying a threshold specific to sample type (<33.1 cycles for BAL fluid; <37.0 cycles for throat swabs), whereas considering any positive respiratory samples as significant generated 100% sensitivity, making absolute negativity sufficient to exclude PcP. Incorporating the PneumID assay into diagnostic algorithms alongside (1-3)-β-D-Glucan testing provided high probabilities of PcP (up to 85.2%) when both were positive and very low probabilities (<1%) when both were negative. CONCLUSIONS The OLM PneumID qPCR provides a commercial option for the accurate diagnosis of PcP, generating excellent sensitivity and specificity, particularly when testing respiratory specimens. The combination of PcP PCR with serum (1-3)-β-D-Glucan provides excellent clinical utility for diagnosing PcP.
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Affiliation(s)
| | | | | | | | - P. Lewis White
- Public Health Wales Mycology Reference Laboratory, PHW Microbiology Cardiff, University Hospital of Wales, Heath Park, Cardiff CF14 4XW, UK; (J.S.P.); (M.F.); (R.P.); (M.B.)
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Douglas AP, Stewart AG, Halliday CL, Chen SCA. Outbreaks of Fungal Infections in Hospitals: Epidemiology, Detection, and Management. J Fungi (Basel) 2023; 9:1059. [PMID: 37998865 PMCID: PMC10672668 DOI: 10.3390/jof9111059] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 10/17/2023] [Accepted: 10/26/2023] [Indexed: 11/25/2023] Open
Abstract
Nosocomial clusters of fungal infections, whilst uncommon, cannot be predicted and are associated with significant morbidity and mortality. Here, we review reports of nosocomial outbreaks of invasive fungal disease to glean insight into their epidemiology, risks for infection, methods employed in outbreak detection including genomic testing to confirm the outbreak, and approaches to clinical and infection control management. Both yeasts and filamentous fungi cause outbreaks, with each having general and specific risks. The early detection and confirmation of the outbreak are essential for diagnosis, treatment of affected patients, and termination of the outbreak. Environmental sampling, including the air in mould outbreaks, for the pathogen may be indicated. The genetic analysis of epidemiologically linked isolates is strongly recommended through a sufficiently discriminatory approach such as whole genome sequencing or a method that is acceptably discriminatory for that pathogen. An analysis of both linked isolates and epidemiologically unrelated strains is required to enable genetic similarity comparisons. The management of the outbreak encompasses input from a multi-disciplinary team with epidemiological investigation and infection control measures, including screening for additional cases, patient cohorting, and strict hygiene and cleaning procedures. Automated methods for fungal infection surveillance would greatly aid earlier outbreak detection and should be a focus of research.
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Affiliation(s)
- Abby P. Douglas
- National Centre for Infections in Cancer, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
- Department of Infectious Diseases, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC 3000, Australia
- Department of Infectious Diseases, Austin Health, Heidelberg, VIC 3084, Australia
| | - Adam G. Stewart
- Centre for Clinical Research, Faculty of Medicine, Royal Brisbane and Women’s Hospital Campus, The University of Queensland, Herston, QLD 4006, Australia;
| | - Catriona L. Halliday
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, Sydney, NSW 2145, Australia; (C.L.H.); (S.C.-A.C.)
| | - Sharon C.-A. Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, Sydney, NSW 2145, Australia; (C.L.H.); (S.C.-A.C.)
- Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2050, Australia
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Thompson GR, Jenks JD, Baddley JW, Lewis JS, Egger M, Schwartz IS, Boyer J, Patterson TF, Chen SCA, Pappas PG, Hoenigl M. Fungal Endocarditis: Pathophysiology, Epidemiology, Clinical Presentation, Diagnosis, and Management. Clin Microbiol Rev 2023; 36:e0001923. [PMID: 37439685 PMCID: PMC10512793 DOI: 10.1128/cmr.00019-23] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023] Open
Abstract
Fungal endocarditis accounts for 1% to 3% of all infective endocarditis cases, is associated with high morbidity and mortality (>70%), and presents numerous challenges during clinical care. Candida spp. are the most common causes of fungal endocarditis, implicated in over 50% of cases, followed by Aspergillus and Histoplasma spp. Important risk factors for fungal endocarditis include prosthetic valves, prior heart surgery, and injection drug use. The signs and symptoms of fungal endocarditis are nonspecific, and a high degree of clinical suspicion coupled with the judicious use of diagnostic tests is required for diagnosis. In addition to microbiological diagnostics (e.g., blood culture for Candida spp. or galactomannan testing and PCR for Aspergillus spp.), echocardiography remains critical for evaluation of potential infective endocarditis, although radionuclide imaging modalities such as 18F-fluorodeoxyglucose positron emission tomography/computed tomography are increasingly being used. A multimodal treatment approach is necessary: surgery is usually required and should be accompanied by long-term systemic antifungal therapy, such as echinocandin therapy for Candida endocarditis or voriconazole therapy for Aspergillus endocarditis.
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Affiliation(s)
- George R. Thompson
- Department of Internal Medicine, Division of Infectious Diseases, University of California-Davis Medical Center, Sacramento, California, USA
- Department of Medical Microbiology and Immunology, University of California-Davis, Davis, California, USA
| | - 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
| | - John W. Baddley
- Department of Medicine, Division of Infectious Diseases, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - James S. Lewis
- Department of Pharmacy, Oregon Health & Science University, Portland, Oregon, USA
| | - Matthias Egger
- Division of Infectious Diseases, ECMM Excellence Center for Medical Mycology, Department of Medicine, Medical University of Graz, Graz, Austria
| | - Ilan S. Schwartz
- Division of Infectious Diseases, Department of Medicine, Duke University, Durham, North Carolina, USA
| | - Johannes Boyer
- Division of Infectious Diseases, ECMM Excellence Center for Medical Mycology, Department of Medicine, Medical University of Graz, Graz, Austria
| | - Thomas F. Patterson
- Department of Medicine, Division of Infectious Diseases, The University of Texas Health Science Center, San Antonio, Texas, USA
| | - Sharon C.-A. Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Sydney, New South Wales, Australia
- Centre for Infectious Diseases and Microbiology, Westmead Hospital, The University of Sydney, Sydney, New South Wales, Australia
| | - Peter G. Pappas
- Department of Medicine Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Martin Hoenigl
- Division of Infectious Diseases, ECMM Excellence Center for Medical Mycology, Department of Medicine, Medical University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
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Stewart AG, Heney C, Paterson DL, Harris PNA, Edwards F, Laupland KB. Scedosporium species and Lomentospora prolificans fungaemia is uniformly fatal in patients with haematological malignancy. Intern Med J 2023; 53:1489-1491. [PMID: 37599232 DOI: 10.1111/imj.16198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 05/09/2023] [Indexed: 08/22/2023]
Abstract
Scedosporium and Lomentospora species are environmental moulds that are virulent in immunocompromised hosts and rarely cause bloodstream infection (BSI). Patients with Scedosporium and Lomentospora species BSI were identified by the state public laboratory service in Queensland, Australia, over a 20-year period. Twenty-two incident episodes occurred among 21 residents; one patient had a second episode 321 days following the first. Of these, 18 were Lomentospora prolificans, three were Scedosporium apiospermum complex and one was a nonspeciated Scedosporium species. Seventeen (81%) patients died during their index admission, and all-cause mortality at 30, 90 and 365 days was 73%, 82% and 91% respectively. All 20 patients with haematological malignancy died within 365 days of follow-up with a median time to death of 9 days (interquartile range, 6-20 days) following diagnoses of BSI.
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Affiliation(s)
- Adam G Stewart
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Royal Brisbane and Women's Hospital Campus, Brisbane, Queensland, Australia
- Department of Infectious Diseases, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
- Central Microbiology, Pathology Queensland, Brisbane, Queensland, Australia
| | - Claire Heney
- Central Microbiology, Pathology Queensland, Brisbane, Queensland, Australia
| | - David L Paterson
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Royal Brisbane and Women's Hospital Campus, Brisbane, Queensland, Australia
- Department of Infectious Diseases, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Patrick N A Harris
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Royal Brisbane and Women's Hospital Campus, Brisbane, Queensland, Australia
- Central Microbiology, Pathology Queensland, Brisbane, Queensland, Australia
| | - Felicity Edwards
- Queensland University of Technology, Brisbane, Queensland, Australia
| | - Kevin B Laupland
- Queensland University of Technology, Brisbane, Queensland, Australia
- Department of Intensive Care Services, Royal Brisbane and Women's Hospital, Brisbane, Queensland, 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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Arrieta AC, Lee A, Tran MT. Invasive Mold Infections in Children: Navigating Troubled Waters with a Broken Compass. Infect Dis Ther 2023:10.1007/s40121-023-00819-9. [PMID: 37209297 DOI: 10.1007/s40121-023-00819-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 05/03/2023] [Indexed: 05/22/2023] Open
Abstract
Incidence of invasive mold infections in children, while rare, is increasing as the population of high-risk patients expands, including premature infants, pediatric patients undergoing treatment for hematological malignancies, or recipients of allogeneic hematologic stem cell transplants. The infectious agents, including Aspergillus spp., Mucorales, and other molds, are especially difficult to treat and have serious morbidity and high mortality. Clinicians must maintain a high index of suspicion for invasive mold infections in at-risk patients. Diagnosis of invasive mold infections is complicated by difficulties isolating pathogens on culture, but progress is being made in immunological and molecular diagnostic technologies. Treatment in children is challenging; no randomized controlled trials exist. There is a growing body of data on treatment, specifically on safer antifungal agents, including indications for treatment, spectrum of coverage, pharmacokinetics for different ages, and pharmacodynamic targets associated with therapeutic success. However, pediatricians must often extrapolate from adult data. In this review, we aim to harmonize the existing body of literature on invasive mold infections in children, covering epidemiology, clinical presentations, diagnostic methods, and principles of management.
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Affiliation(s)
- Antonio C Arrieta
- Department of Infectious Diseases, Children's Hospital of Orange County, Orange, CA, USA
- Department of Pediatrics, University of California, Irvine, School of Medicine, Irvine, CA, USA
| | - Adam Lee
- Department of Infectious Diseases, Children's Hospital of Orange County, Orange, CA, USA.
| | - M Tuan Tran
- Department of Pharmacy, Children's Hospital of Orange County, Orange, CA, USA
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Luethy PM. Point-of-Care Testing for the Diagnosis of Fungal Infections. Clin Lab Med 2023; 43:209-220. [PMID: 37169443 DOI: 10.1016/j.cll.2023.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
Invasive fungal infections are increasing worldwide due to factors such as climate change and immunomodulating therapies. Unfortunately, the detection of these infections is limited due to the low sensitivity and long periods required for laboratory testing. Point-of-care testing could lead to more rapid diagnosis of these often devasting infections. However, there are currently no true point-of-care tests on the market for the detection of fungi. In this article, the current state of fungal antigen and molecular testing is reviewed, with commentary on the potential for development and use in the point-of-care setting.
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Knapp J, Lallemand S, Monnien F, Felix S, Courquet S, Umhang G, Millon L. Real-time multiplex PCR for human echinococcosis and differential diagnosis. Parasite 2023; 30:3. [PMID: 36700708 PMCID: PMC9886084 DOI: 10.1051/parasite/2023003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 01/06/2023] [Indexed: 01/27/2023] Open
Abstract
Molecular identification of rare human infectious pathogens appears to be one of the most relevant current methods for rapid diagnosis and management of patients. PCR techniques, in particular real-time quantitative PCR, are best suited for the detection of DNA from the pathogens, even at low concentrations. Echinococcosis infections are due to helminths of the Echinococcus genus, with closely related species involved in parasitic lesions affecting animals and, accidentally, humans. We developed a multiplex qPCR (MLX qPCR) assay allowing for the detection of four Echinococcus species involved in Europe in alveolar echinococcosis (AE) and cystic echinococcosis (CE) (Echinococcus multilocularis, E. granulosus sensu stricto, E. ortleppi, and E. canadensis), based on short mitochondrial targets. A collection of 81 fresh and formalin-fixed paraffin-embedded tissues (FFPE) of AE and CE lesions was assembled. The qPCR assays were performed in triplex for Echinococcus spp. detection, associated with a qPCR inhibitor control. A duplex qPCR was also designed to enable diagnosis of two other dead-end helminthiases (cysticercosis (Taenia solium), and toxocariasis (Toxocara cati and T. canis)). The sensitivity of the qPCR was assessed and ranged from 1 to 5 × 10-4 ng/μL (seven PCR assays positive), corresponding to 37-42 cycles for quantifiable DNA. The specificity was 100% for all the targets. This multiplex qPCR, adapted to low amounts of DNA can be implemented in the laboratory for the rapid molecular diagnosis of Echinococcosis species.
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Affiliation(s)
- Jenny Knapp
- Department of Parasitology-Mycology, National Reference Centre for Echinococcoses, University Hospital of Besançon 25030 Besançon France,UMR CNRS 6249 Laboratoire Chrono-environnement, University of Franche-Comté 16 Route de Gray 25030 Besançon France,Corresponding author:
| | - Séverine Lallemand
- UMR CNRS 6249 Laboratoire Chrono-environnement, University of Franche-Comté 16 Route de Gray 25030 Besançon France
| | - Franck Monnien
- Department of Pathology, University Hospital of Besançon 25030 Besançon France
| | - Sophie Felix
- Department of Pathology, University Hospital of Besançon 25030 Besançon France
| | - Sandra Courquet
- Department of Parasitology-Mycology, National Reference Centre for Echinococcoses, University Hospital of Besançon 25030 Besançon France,UMR CNRS 6249 Laboratoire Chrono-environnement, University of Franche-Comté 16 Route de Gray 25030 Besançon France
| | - Gérald Umhang
- ANSES Nancy laboratory for Rabies and Wildlife, National Reference Laboratory for Echinococcus spp., Wildlife Surveillance and Eco-epidemiology Unit, Technopole Agricole et Vétérinaire 54220 Malzéville France
| | - Laurence Millon
- Department of Parasitology-Mycology, National Reference Centre for Echinococcoses, University Hospital of Besançon 25030 Besançon France,UMR CNRS 6249 Laboratoire Chrono-environnement, University of Franche-Comté 16 Route de Gray 25030 Besançon France
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A Multiplex PCR and DNA-Sequencing Workflow on Serum for the Diagnosis and Species Identification for Invasive Aspergillosis and Mucormycosis. J Clin Microbiol 2023; 61:e0140922. [PMID: 36533925 PMCID: PMC9879116 DOI: 10.1128/jcm.01409-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
There has been significant increase in the use of molecular tools for the diagnosis of invasive aspergillosis (IA) and mucormycosis. However, their range of detection may be too limited as species diversity and coinfections are increasing. Here, we aimed to evaluate a molecular workflow based on a new multiplex PCR assay detecting the whole Aspergillus genus and the Mucorales order followed by a species-specific PCR or a DNA-sequencing approach for IA and/or mucormycosis diagnosis and species identification on serum. Performances of the MycoGENIE Aspergillus spp./Mucorales spp. duplex PCR kit were analyzed on a broad range of fungal strains and on sera from high-risk patients prospectively over a 12-month period. The kit allowed the detection of nine Aspergillus species and 10 Mucorales (eight genera) strains assessed. No cross-reactions between the two targets were observed. Sera from 744 patients were prospectively analyzed, including 35 IA, 16 mucormycosis, and four coinfections. Sensitivity varies from 85.7% (18/21) in probable/proven IA to 28.6% (4/14) in COVID-19-associated pulmonary aspergillosis. PCR-positive samples corresponded to 21 A. fumigatus, one A. flavus, and one A. nidulans infections. All the disseminated mucormycosis were positive in serum (14/14), including the four Aspergillus coinfections, but sensitivity fell to 33.3% (2/6) in localized forms. DNA sequencing allowed Mucorales identification in serum in 15 patients. Remarkably, the most frequent species identified was Rhizomucor pusillus (eight cases), whereas it is barely found in fungal culture. This molecular workflow is a promising approach to improve IA and mucormycosis diagnosis and epidemiology.
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Molecular Diagnosis of Endemic Mycoses. J Fungi (Basel) 2022; 9:jof9010059. [PMID: 36675880 PMCID: PMC9866865 DOI: 10.3390/jof9010059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/22/2022] [Accepted: 12/24/2022] [Indexed: 01/03/2023] Open
Abstract
Diagnosis of endemic mycoses is still challenging. The moderated availability of reliable diagnostic methods, the lack of clinical suspicion out of endemic areas and the limitations of conventional techniques result in a late diagnosis that, in turn, delays the implementation of the correct antifungal therapy. In recent years, molecular methods have emerged as promising tools for the rapid diagnosis of endemic mycoses. However, the absence of a consensus among laboratories and the reduced availability of commercial tests compromises the diagnostic effectiveness of these methods. In this review, we summarize the advantages and limitations of molecular methods for the diagnosis of endemic mycoses.
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Koc Ö, Kessler HH, Hoenigl M, Wagener J, Suerbaum S, Schubert S, Dichtl K. Performance of Multiplex PCR and β-1,3-D-Glucan Testing for the Diagnosis of Candidemia. J Fungi (Basel) 2022; 8:jof8090972. [PMID: 36135696 PMCID: PMC9504845 DOI: 10.3390/jof8090972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/05/2022] [Accepted: 09/15/2022] [Indexed: 11/28/2022] Open
Abstract
Bloodstream infections caused by Candida yeasts (candidemia) are associated with high morbidity and mortality. Diagnosis remains challenging, with the current gold standard—isolation from blood culture (BC)—being limited by low sensitivity and long turnaround time. This study evaluated the performance of two nonculture methods: PCR and β-1,3-D-glucan (BDG) testing. The sera of 103 patients with BC-proven candidemia and of 46 controls were analyzed with the Fungiplex Candida Real-Time PCR and the Wako β-Glucan Test. The BDG assay demonstrated higher sensitivity than the multiplex PCR (58% vs. 33%). This was particularly evident in ICU patients (60% vs. 28%) and in C. albicans candidemia (57% vs. 37%). The earlier prior to BC sampling the sera were obtained, the more the PCR sensitivity decreased (46% to 18% in the periods of 0−2 and 3−5 days before BC, respectively), while BDG testing was independent of the sampling date. No positive PCR results were obtained in sera sampled more than five days before BC. Specificities were 89% for BDG and 93% for PCR testing. In conclusion, BDG testing demonstrated several advantages over PCR testing for the diagnosis of candidemia, including higher sensitivity and earlier diagnosis. However, BC remains essential, as BDG does not allow for species differentiation.
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Affiliation(s)
- Özlem Koc
- Max von Pettenkofer-Institut für Hygiene und Medizinische Mikrobiologie, Medizinische Fakultät, LMU München, 80336 Munich, Germany
| | - Harald H. Kessler
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, 8010 Graz, Austria
| | - Martin Hoenigl
- Division of Infectious Diseases, Department of Internal Medicine, Medical University of Graz, 8010 Graz, Austria
| | - Johannes Wagener
- Microbiology Department, St. James’s Hospital, D08 RX0X Dublin, Ireland
- Department of Clinical Microbiology, School of Medicine, Trinity College Dublin, The University of Dublin, St. James’s Hospital Campus, D08 RX0X Dublin, Ireland
| | - Sebastian Suerbaum
- Max von Pettenkofer-Institut für Hygiene und Medizinische Mikrobiologie, Medizinische Fakultät, LMU München, 80336 Munich, Germany
| | - Sören Schubert
- Max von Pettenkofer-Institut für Hygiene und Medizinische Mikrobiologie, Medizinische Fakultät, LMU München, 80336 Munich, Germany
- Correspondence: (S.S.); (K.D.)
| | - Karl Dichtl
- Max von Pettenkofer-Institut für Hygiene und Medizinische Mikrobiologie, Medizinische Fakultät, LMU München, 80336 Munich, Germany
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, 8010 Graz, Austria
- Correspondence: (S.S.); (K.D.)
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An Evaluation of the OLM CandID Real-Time PCR to Aid in the Diagnosis of Invasive Candidiasis When Testing Serum Samples. J Fungi (Basel) 2022; 8:jof8090935. [PMID: 36135660 PMCID: PMC9505555 DOI: 10.3390/jof8090935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/23/2022] [Accepted: 09/01/2022] [Indexed: 11/17/2022] Open
Abstract
Background: Treatment for invasive candidiasis (IC) is time-critical, and culture-based tests can limit clinical utility. Nonculture-based methods such as Candida PCR represent a promising approach to improving patient management but require further evaluation to understand their optimal role and incorporation into clinical algorithms. This study determined the performance of the commercially available OLM CandID real-time PCR when testing serum and developed a diagnostic algorithm for IC. Methods: The study comprised a retrospective performance evaluation of the CandID real-time PCR assay when testing surplus serum (n = 83 patients, 38 with IC), followed by a prospective consecutive cohort evaluation (n = 103 patients, 24 with IC) post incorporation into routine service. A combined diagnostic algorithm, also including (1-3)-β-D-Glucan testing, was generated. Results: Prospective CandID testing generated a sensitivity/specificity of 88%/82%, respectively. Specificity was improved (>95%) when both PCR replicates were positive and/or the patient had multiple positive samples. When combining CandID with (1-3)-β-D-Glucan testing, the probability of IC when both were positive or negative was >69% or <1%, respectively. Conclusions: The CandID provides excellent performance and a rapid time-to-result using methods widely available in generic molecular diagnostic laboratories. By combining nonculture diagnostics, it may be possible to accurately confirm or exclude IC.
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de Carvalho JA, Monteiro RC, Hagen F, de Camargo ZP, Rodrigues AM. Trends in Molecular Diagnostics and Genotyping Tools Applied for Emerging Sporothrix Species. J Fungi (Basel) 2022; 8:jof8080809. [PMID: 36012797 PMCID: PMC9409836 DOI: 10.3390/jof8080809] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/22/2022] [Accepted: 07/25/2022] [Indexed: 11/23/2022] Open
Abstract
Sporotrichosis is the most important subcutaneous mycosis that affects humans and animals worldwide. The mycosis is caused after a traumatic inoculation of fungal propagules into the host and may follow an animal or environmental transmission route. The main culprits of sporotrichosis are thermodimorphic Sporothrix species embedded in a clinical clade, including S. brasiliensis, S. schenckii, S. globosa, and S. luriei. Although sporotrichosis occurs worldwide, the etiological agents are not evenly distributed, as exemplified by ongoing outbreaks in Brazil and China, caused by S. brasiliensis and S. globosa, respectively. The gold standard for diagnosing sporotrichosis has been the isolation of the fungus in vitro. However, with the advance in molecular techniques, molecular assays have complemented and gradually replaced the classical mycological tests to quickly and accurately detect and/or differentiate molecular siblings in Sporothrix. Nearly all techniques available for molecular diagnosis of sporotrichosis involve PCR amplification, which is currently moving towards detecting Sporothrix DNA directly from clinical samples in multiplex qPCR assays. From an epidemiological perspective, genotyping is key to tracing back sources of Sporothrix infections, detecting diversity in outbreak areas, and thus uncovering finer-scale epidemiological patterns. Over the past decades, molecular epidemiological studies have provided essential information to policymakers regarding outbreak management. From high-to-low throughput genotyping methods, MLSA, AFLP, SSR, RAPD, PCR-RFLP, and WGS are available to assess the transmission dynamics and sporotrichosis expansion. This review discusses the trends in the molecular diagnosis of sporotrichosis, genotyping techniques applied in molecular epidemiological studies, and perspectives for the near future.
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Affiliation(s)
- Jamile Ambrósio de Carvalho
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil; (J.A.d.C.); (R.C.M.); (Z.P.d.C.)
| | - Ruan Campos Monteiro
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil; (J.A.d.C.); (R.C.M.); (Z.P.d.C.)
| | - Ferry Hagen
- Department of Medical Mycology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands;
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Sciencepark 904, 1098 XH Amsterdam, The Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Zoilo Pires de Camargo
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil; (J.A.d.C.); (R.C.M.); (Z.P.d.C.)
- Department of Medicine, Discipline of Infectious Diseases, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil
| | - Anderson Messias Rodrigues
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil; (J.A.d.C.); (R.C.M.); (Z.P.d.C.)
- Department of Medicine, Discipline of Infectious Diseases, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil
- Correspondence: ; Tel.: +55-1155764551 (ext. 1540)
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