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Rafanomezantsoa LC, Sabourin E, Guennouni Sebbouh N, Sitterlé E, Ben Halima N, Raveloarisaona YS, Quesne G, Dannaoui E, Bougnoux ME. Agreement between two real-time commercial PCR kits and an in-house real-time PCR for diagnosis of mucormycosis. Microbiol Spectr 2024:e0358523. [PMID: 38916337 DOI: 10.1128/spectrum.03585-23] [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: 10/05/2023] [Accepted: 05/22/2024] [Indexed: 06/26/2024] Open
Abstract
Mucormycosis is a severe and emerging invasive fungal infection associated with high mortality rates. Early diagnosis is crucial for initiating specific antifungal treatment, with molecular tools currently representing the most efficient diagnostic approach. Presently, a standardized in-house real-time PCR method is widely employed for diagnosing mucormycosis. Our study aimed to evaluate the agreement for the Mucorales DNA detection between two commercial real-time PCR assays-the Fungiplex Mucorales Real-Time PCR Kit and the MycoGENIE Aspergillus-Mucorales spp. Real-Time PCR Kit-in comparison with the in-house PCR. We retrospectively analyzed 58 samples previously identified as positive for Mucorales using the in-house PCR. These samples, obtained from 22 patients with proven or probable mucormycosis, were tested with both commercial kits. Additionally, samples from 40 patients without mucormycosis served as negative controls. Our findings revealed that the MycoGENIE Kit demonstrated superior performance in detecting Mucorales DNA in samples identified as positive by the in-house PCR. Notably, we observed minimal variability in cycle threshold (CT) values when comparing the results of the MycoGENIE Kit with those of the in-house PCR, with an average difference of 1.8 cycles. In contrast, the Fungiplex Kit exhibited a larger discrepancy in CT values compared to the in-house PCR, with an average difference of 4.1 cycles. The MycoGENIE Kit exhibited very good agreement (kappa of 0.82) with the in-house PCR for detecting Mucorales DNA across various sample types. These findings are important for the choice of kits that could be used to diagnose mucormycosis in clinical microbiology laboratories. IMPORTANCE Early diagnosis of mucormycosis is crucial for initiating effective treatment. The detection of Mucorales DNA by PCR in serum has revolutionized the diagnosis of this infection. However, the use of in-house methods can be time consuming. The availability of a commercial kit eliminates the need for in-house assay development, reducing laboratory workload and ensuring consistent performance across different healthcare settings. Currently, there are several commercial assays available, but many have limited evaluation. In this study, we compared two commercial kits and found that the MycoGENIE Kit offers a promising alternative to the in-house method.
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Affiliation(s)
- Lovanirina Clémencia Rafanomezantsoa
- Université Paris Cité, Faculté de Médecine, APHP, Hôpital Necker Enfants-Malades, Hôpital Européen Georges Pompidou, Unité de Parasitologie-Mycologie, Service de Microbiologie, Paris, France
| | - Estelle Sabourin
- Université Paris Cité, Faculté de Médecine, APHP, Hôpital Necker Enfants-Malades, Hôpital Européen Georges Pompidou, Unité de Parasitologie-Mycologie, Service de Microbiologie, Paris, France
| | - Nadia Guennouni Sebbouh
- Université Paris Cité, Faculté de Médecine, APHP, Hôpital Necker Enfants-Malades, Hôpital Européen Georges Pompidou, Unité de Parasitologie-Mycologie, Service de Microbiologie, Paris, France
| | - Emilie Sitterlé
- Université Paris Cité, Faculté de Médecine, APHP, Hôpital Necker Enfants-Malades, Hôpital Européen Georges Pompidou, Unité de Parasitologie-Mycologie, Service de Microbiologie, Paris, France
| | - Nada Ben Halima
- Université Paris Cité, Faculté de Médecine, APHP, Hôpital Necker Enfants-Malades, Hôpital Européen Georges Pompidou, Unité de Parasitologie-Mycologie, Service de Microbiologie, Paris, France
| | - Yannick Sonjah Raveloarisaona
- Université Paris Cité, Faculté de Médecine, APHP, Hôpital Necker Enfants-Malades, Hôpital Européen Georges Pompidou, Unité de Parasitologie-Mycologie, Service de Microbiologie, Paris, France
| | - Gilles Quesne
- Université Paris Cité, Faculté de Médecine, APHP, Hôpital Necker Enfants-Malades, Hôpital Européen Georges Pompidou, Unité de Parasitologie-Mycologie, Service de Microbiologie, Paris, France
| | - Eric Dannaoui
- Université Paris Cité, Faculté de Médecine, APHP, Hôpital Necker Enfants-Malades, Hôpital Européen Georges Pompidou, Unité de Parasitologie-Mycologie, Service de Microbiologie, Paris, France
- Dynamyc Research Group, Paris Est Créteil University (UPEC, EnvA), Paris, France
| | - Marie-Elisabeth Bougnoux
- Université Paris Cité, Faculté de Médecine, APHP, Hôpital Necker Enfants-Malades, Hôpital Européen Georges Pompidou, Unité de Parasitologie-Mycologie, Service de Microbiologie, Paris, France
- Biologie et Pathogénicité fongiques, Département de Mycologie, Institut Pasteur, Paris, France
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Pandey M, Xess I, Sachdev J, Sharad N, Gupta S, Singh G, Yadav RK, Rana B, Raj S, Ahmad MN, Nityadarshini N, Baitha U, Soneja M, Shalimar, Prakash B, Sikka K, Mathur P, Jyotsna VP, Kumar R, Wig N, Gourav S, Biswas A, Thakar A. Utility of an in-house real-time PCR in whole blood samples as a minimally invasive method for early and accurate diagnosis of invasive mould infections. J Infect 2024; 88:106147. [PMID: 38555035 DOI: 10.1016/j.jinf.2024.106147] [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: 09/20/2023] [Revised: 03/11/2024] [Accepted: 03/24/2024] [Indexed: 04/02/2024]
Abstract
INTRODUCTION Invasive mould infections (IMIs) are a leading cause of death in patients with compromised immune systems. Proven invasive mould infection requires detection of a fungus by histopathological analysis of a biopsied specimen, sterile culture, or fungal DNA amplification by PCR in tissue. However, the clinical performance of a PCR assay on blood samples taken from patients suspected of invasive mould disease has not been fully evaluated, particularly for the differential diagnosis of invasive aspergillosis (IA) and invasive Mucormycosis (IM). OBJECTIVES To assess the diagnostic utility of our previously validated in-house real-time PCR in blood samples for diagnosis of invasive aspergillosis and mucormycosis in patients with suspected invasive mould infection. METHODS All patients with suspected invasive mould infection were prospectively enrolled from May 2021 to July 2021. Conventional fungal diagnosis was performed using tissue and respiratory samples. In-house PCR was performed on blood samples and its diagnostic performance evaluated. RESULTS A total of 158 cases of suspected invasive mould infection were enrolled in the study. The sensitivity and specificity of in-house PCR performed on blood samples was found to be 92.5% and 81.4% respectively for diagnosis of probable IA, and 65% and 84.62% respectively for diagnosis of proven and probable IM. It was also able to detect 3 out of 5 cases of possible IM where no other microbiological evidence of IM was obtained. CONCLUSIONS This assay could be helpful in minimally invasive diagnosis of IMIs for patients in whom invasive sampling is not feasible, especially as a preliminary or screening test. It can help in early diagnosis, anticipating conventional laboratory confirmation by days or weeks. Possible correlation between fungal load and mortality can help in initiating aggressive treatment for patients with high initial fungal load.
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Affiliation(s)
- Mragnayani Pandey
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Immaculata Xess
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi 110029, India.
| | - Janya Sachdev
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Neha Sharad
- Department of Lab medicine JPNATC, All India Institute of Medical Sciences, New Delhi, India
| | - Sonakshi Gupta
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Gagandeep Singh
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Renu Kumari Yadav
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Bhaskar Rana
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Stephen Raj
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - M Nizam Ahmad
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Neha Nityadarshini
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Upendra Baitha
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Manish Soneja
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Shalimar
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, India
| | - Bindu Prakash
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Kapil Sikka
- Department of ENT, All India Institute of Medical Sciences, New Delhi, India
| | - Purva Mathur
- Department of Lab medicine JPNATC, All India Institute of Medical Sciences, New Delhi, India
| | - Viveka P Jyotsna
- Department of Endocrinology, All India Institute of Medical Sciences, New Delhi, India
| | - Rakesh Kumar
- Department of ENT, All India Institute of Medical Sciences, New Delhi, India
| | - Naveet Wig
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Sudesh Gourav
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Ashutosh Biswas
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Alok Thakar
- Department of ENT, All India Institute of Medical Sciences, New Delhi, 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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Mori G, Diotallevi S, Farina F, Lolatto R, Galli L, Chiurlo M, Acerbis A, Xue E, Clerici D, Mastaglio S, Lupo Stanghellini MT, Ripa M, Corti C, Peccatori J, Puoti M, Bernardi M, Castagna A, Ciceri F, Greco R, Oltolini C. High-Risk Neutropenic Fever and Invasive Fungal Diseases in Patients with Hematological Malignancies. Microorganisms 2024; 12:117. [PMID: 38257945 PMCID: PMC10818361 DOI: 10.3390/microorganisms12010117] [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: 12/11/2023] [Revised: 12/30/2023] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
Invasive fungal diseases (IFDs) still represent a relevant cause of mortality in patients affected by hematological malignancies, especially acute myeloid leukaemia (AML) and myelodysplastic syndrome (MDS) undergoing remission induction chemotherapy, and in allogeneic hematopoietic stem cell transplantation (allo-HSCT) recipients. Mold-active antifungal prophylaxis (MAP) has been established as a standard of care. However, breakthrough IFDs (b-IFDs) have emerged as a significant issue, particularly invasive aspergillosis and non-Aspergillus invasive mold diseases. Here, we perform a narrative review, discussing the major advances of the last decade on prophylaxis, the diagnosis of and the treatment of IFDs in patients with high-risk neutropenic fever undergoing remission induction chemotherapy for AML/MDS and allo-HSCT. Then, we present our single-center retrospective experience on b-IFDs in 184 AML/MDS patients undergoing high-dose chemotherapy while receiving posaconazole (n = 153 induction treatments, n = 126 consolidation treatments, n = 60 salvage treatments). Six cases of probable/proven b-IFDs were recorded in six patients, with an overall incidence rate of 1.7% (6/339), which is in line with the literature focused on MAP with azoles. The incidence rates (IRs) of b-IFDs (95% confidence interval (95% CI), per 100 person years follow-up (PYFU)) were 5.04 (0.47, 14.45) in induction (n = 2), 3.25 (0.0013, 12.76) in consolidation (n = 1) and 18.38 (3.46, 45.06) in salvage chemotherapy (n = 3). Finally, we highlight the current challenges in the field of b-IFDs; these include the improvement of diagnoses, the expanding treatment landscape of AML with molecular targeted drugs (and related drug-drug interactions with azoles), evolving transplantation techniques (and their related impacts on IFDs' risk stratification), and new antifungals and their features (rezafungin and olorofim).
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Affiliation(s)
- Giovanni Mori
- Infectious Diseases Unit, Vita-Salute San Raffaele University, 20132 Milan, Italy; (G.M.)
- Infectious Diseases Unit, Ospedale Santa Chiara, 38122 Trento, Italy
| | - Sara Diotallevi
- Infectious Diseases Unit, IRCCS San Raffaele Scientific Institute, 20127 Milan, Italy
| | - Francesca Farina
- Haematology and Bone Marrow Transplant Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Riccardo Lolatto
- Infectious Diseases Unit, IRCCS San Raffaele Scientific Institute, 20127 Milan, Italy
| | - Laura Galli
- Infectious Diseases Unit, IRCCS San Raffaele Scientific Institute, 20127 Milan, Italy
| | - Matteo Chiurlo
- Infectious Diseases Unit, Vita-Salute San Raffaele University, 20132 Milan, Italy; (G.M.)
- Infectious Diseases Unit, IRCCS San Raffaele Scientific Institute, 20127 Milan, Italy
| | - Andrea Acerbis
- Infectious Diseases Unit, Vita-Salute San Raffaele University, 20132 Milan, Italy; (G.M.)
- Haematology and Bone Marrow Transplant Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Elisabetta Xue
- Haematology and Bone Marrow Transplant Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
- Centre for Immuno-Oncology, National Cancer Institute, Eliminate NIH, Bethesda, MD 20850, USA
| | - Daniela Clerici
- Haematology and Bone Marrow Transplant Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Sara Mastaglio
- Haematology and Bone Marrow Transplant Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | | | - Marco Ripa
- Infectious Diseases Unit, Vita-Salute San Raffaele University, 20132 Milan, Italy; (G.M.)
- Infectious Diseases Unit, IRCCS San Raffaele Scientific Institute, 20127 Milan, Italy
| | - Consuelo Corti
- Haematology and Bone Marrow Transplant Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Jacopo Peccatori
- Haematology and Bone Marrow Transplant Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Massimo Puoti
- Infectious Diseases Unit, ASST Grande Ospedale Metropolitano Niguarda, 20161 Milan, Italy
- Faculty of Medicine and Surgery, University of Milano-Bicocca, 20126 Milan, Italy
| | - Massimo Bernardi
- Haematology and Bone Marrow Transplant Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Antonella Castagna
- Infectious Diseases Unit, Vita-Salute San Raffaele University, 20132 Milan, Italy; (G.M.)
- Infectious Diseases Unit, IRCCS San Raffaele Scientific Institute, 20127 Milan, Italy
| | - Fabio Ciceri
- Infectious Diseases Unit, Vita-Salute San Raffaele University, 20132 Milan, Italy; (G.M.)
- Haematology and Bone Marrow Transplant Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Raffaella Greco
- Haematology and Bone Marrow Transplant Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Chiara Oltolini
- Infectious Diseases Unit, IRCCS San Raffaele Scientific Institute, 20127 Milan, Italy
- Infectious Diseases Unit, ASST Grande Ospedale Metropolitano Niguarda, 20161 Milan, Italy
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Hoenigl M, Egger M, Price J, Krause R, Prattes J, White PL. Metagenomic Next-Generation Sequencing of Plasma for Diagnosis of COVID-19-Associated Pulmonary Aspergillosis. J Clin Microbiol 2023; 61:e0185922. [PMID: 36809121 PMCID: PMC10035327 DOI: 10.1128/jcm.01859-22] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023] Open
Abstract
Timely diagnosis remains an unmet need in non-neutropenic patients at risk for aspergillosis, including those with COVID-19-associated pulmonary aspergillosis (CAPA), which in its early stages is characterized by tissue-invasive growth of the lungs with limited angioinvasion. Currently available mycological tests show limited sensitivity when testing blood specimens. Metagenomic next-generation sequencing (mNGS) to detect microbial cell-free DNA (mcfDNA) in plasma might overcome some of the limitations of conventional diagnostics. A two-center cohort study involving 114 COVID-19 intensive care unit patients evaluated the performance of plasma mcfDNA sequencing for the diagnosis of CAPA. Classification of CAPA was performed using the European Confederation for Medical Mycology (ECMM)/International Society for Human and Animal Mycoses (ISHAM) criteria. A total of 218 plasma samples were collected between April 2020 and June 2021 and tested for mcfDNA (Karius test). Only 6 patients were classified as probable CAPA, and 2 were classified as possible, while 106 patients did not fulfill CAPA criteria. The Karius test detected DNA of mold pathogens in 12 samples from 8 patients, including Aspergillus fumigatus in 10 samples from 6 patients. Mold pathogen DNA was detected in 5 of 6 (83% sensitivity) cases with probable CAPA (A. fumigatus in 8 samples from 4 patients and Rhizopus microsporus in 1 sample), while the test did not detect molds in 103 of 106 (97% specificity) cases without CAPA. The Karius test showed promising performance for diagnosis of CAPA when testing plasma, being highly specific. The test detected molds in all but one patient with probable CAPA, including cases where other mycological tests from blood resulted continuously negative, outlining the need for validation in larger studies.
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Affiliation(s)
- Martin Hoenigl
- Division of Infectious Diseases, Excellence Center for Medical Mycology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
- BioTechMed, Graz, Austria
| | - Matthias Egger
- Division of Infectious Diseases, Excellence Center for Medical Mycology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
- BioTechMed, Graz, Austria
| | - Jessica Price
- Public Health Wales, Microbiology Cardiff, University Hospital of Wales, Cardiff, United Kingdom
| | - Robert Krause
- Division of Infectious Diseases, Excellence Center for Medical Mycology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
- BioTechMed, Graz, Austria
| | - Juergen Prattes
- Division of Infectious Diseases, Excellence Center for Medical Mycology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
- University of Cologne, Cologne, Germany
- University Hospital of Cologne, Department 1 for Internal Medicine, Infectious Diseases, Excellence Center for Medical Mycology, Cologne, Germany
| | - P Lewis White
- Public Health Wales, Microbiology Cardiff, University Hospital of Wales, Cardiff, United Kingdom
- Division of Infection and Immunity, Center for Trials Research, Cardiff University, Cardiff, United Kingdom
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