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Su LD, Chiu CY, Gaston D, Hogan CA, Miller S, Simon DW, Thakur KT, Yang S, Piantadosi A. Clinical Metagenomic Next-Generation Sequencing for Diagnosis of Central Nervous System Infections: Advances and Challenges. Mol Diagn Ther 2024; 28:513-523. [PMID: 38992308 DOI: 10.1007/s40291-024-00727-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2024] [Indexed: 07/13/2024]
Abstract
Central nervous system (CNS) infections carry a substantial burden of morbidity and mortality worldwide, and accurate and timely diagnosis is required to optimize management. Metagenomic next-generation sequencing (mNGS) has proven to be a valuable tool in detecting pathogens in patients with suspected CNS infection. By sequencing microbial nucleic acids present in a patient's cerebrospinal fluid, brain tissue, or samples collected outside of the CNS, such as plasma, mNGS can detect a wide range of pathogens, including rare, unexpected, and/or fastidious organisms. Furthermore, its target-agnostic approach allows for the identification of both known and novel pathogens. This is particularly useful in cases where conventional diagnostic methods fail to provide an answer. In addition, mNGS can detect multiple microorganisms simultaneously, which is crucial in cases of mixed infections without a clear predominant pathogen. Overall, clinical mNGS testing can help expedite the diagnostic process for CNS infections, guide appropriate management decisions, and ultimately improve clinical outcomes. However, there are key challenges surrounding its use that need to be considered to fully leverage its clinical impact. For example, only a few specialized laboratories offer clinical mNGS due to the complexity of both the laboratory methods and analysis pipelines. Clinicians interpreting mNGS results must be aware of both false negatives-as mNGS is a direct detection modality and requires a sufficient amount of microbial nucleic acid to be present in the sample tested-and false positives-as mNGS detects environmental microbes and their nucleic acids, despite best practices to minimize contamination. Additionally, current costs and turnaround times limit broader implementation of clinical mNGS. Finally, there is uncertainty regarding the best practices for clinical utilization of mNGS, and further work is needed to define the optimal patient population(s), syndrome(s), and time of testing to implement clinical mNGS.
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Affiliation(s)
- LingHui David Su
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
- The Consortium for Clinical Metagenomics in Infectious Diseases, Nashville, TN, USA
| | - Charles Y Chiu
- The Consortium for Clinical Metagenomics in Infectious Diseases, Nashville, TN, USA
- Department of Laboratory Medicine and Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, CA, USA
| | - David Gaston
- The Consortium for Clinical Metagenomics in Infectious Diseases, Nashville, TN, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Catherine A Hogan
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
- The Consortium for Clinical Metagenomics in Infectious Diseases, Nashville, TN, USA
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Steve Miller
- The Consortium for Clinical Metagenomics in Infectious Diseases, Nashville, TN, USA
- Delve Bio, Inc., San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Dennis W Simon
- The Consortium for Clinical Metagenomics in Infectious Diseases, Nashville, TN, USA
- Department of Pediatric Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kiran T Thakur
- The Consortium for Clinical Metagenomics in Infectious Diseases, Nashville, TN, USA
- Department of Neurology, Columbia University Irving Medical Center-New York Presbyterian Hospital, New York, NY, USA
| | - Shangxin Yang
- The Consortium for Clinical Metagenomics in Infectious Diseases, Nashville, TN, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Anne Piantadosi
- The Consortium for Clinical Metagenomics in Infectious Diseases, Nashville, TN, USA.
- Department of Pathology and Laboratory Medicine, and Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 101 Woodruff Circle, Atlanta, GA, USA.
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Naik S, Kashyap D, Deep J, Darwish S, Cross J, Mansoor E, Garg VK, Honnavar P. Utilizing Next-Generation Sequencing: Advancements in the Diagnosis of Fungal Infections. Diagnostics (Basel) 2024; 14:1664. [PMID: 39125540 PMCID: PMC11311512 DOI: 10.3390/diagnostics14151664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/23/2024] [Accepted: 07/25/2024] [Indexed: 08/12/2024] Open
Abstract
Next-generation sequencing (NGS) has emerged as a promising tool for diagnosing fungal infections. It enables the identification of a wide range of fungal species and provides more accurate and rapid results than traditional diagnostic methods. NGS-based approaches involve the sequencing of DNA or RNA from clinical samples, which can be used to detect and identify fungal pathogens in complex clinical samples. The development of targeted gene panels and whole-genome sequencing has allowed for identifying genetic markers associated with antifungal drug resistance, enabling clinicians to tailor patient treatment options. NGS can also provide insights into the pathogenesis of fungal infections and aid in discovering novel drug targets. Although NGS has some limitations, such as cost and data analysis, it can potentially revolutionize the future diagnosis and treatment of fungal infections.
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Affiliation(s)
- Sheetal Naik
- Department of Physiology, American University of Antigua College of Medicine, St. Johns 1451, Antigua and Barbuda
| | - Dharambir Kashyap
- Brown Center for Immunotherapy, Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology and Oncology, School of Medicine, Indiana University, Indianapolis, IN 46202, USA
| | - Jashan Deep
- Basic Medical Science, American University of Antigua College of Medicine, St. Johns 1451, Antigua and Barbuda
| | - Saif Darwish
- Basic Medical Science, American University of Antigua College of Medicine, St. Johns 1451, Antigua and Barbuda
| | - Joseph Cross
- Department of Biochemistry, Cell Biology and Genetics; American University of Antigua College of Medicine, St. Johns 1451, Antigua and Barbuda
- Department of Microbial Pathogenesis and Immunology, Texas A & M University, College Station, TX 77843, USA
| | - Edmond Mansoor
- Department of Clinical Medicine; American University of Antigua College of Medicine, St. Johns 1451, Antigua and Barbuda
| | - Vivek Kumar Garg
- University Institute of Allied Health Sciences, Chandigarh University, Gharuan, Mohali 140413, Punjab, India
| | - Prasanna Honnavar
- Department of Microbiology and Immunology; American University of Antigua College of Medicine, St. Johns 1451, Antigua and Barbuda
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Sáenz V, Lizcano Salas AF, Gené J, Celis Ramírez AM. Fusarium and Neocosmospora: fungal priority pathogens in laboratory diagnosis. Crit Rev Microbiol 2024:1-14. [PMID: 38949272 DOI: 10.1080/1040841x.2024.2369693] [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: 10/12/2023] [Accepted: 06/11/2024] [Indexed: 07/02/2024]
Abstract
Fusarium and Neocosmospora are two fungal genera recently recognized in the list of fungal priority pathogens. They cause a wide range of diseases that affect humans, animals, and plants. In clinical laboratories, there is increasing concern about diagnosis due to limitations in sample collection and morphological identification. Despite the advances in molecular diagnosis, due to the cost, some countries cannot implement these methodologies. However, recent changes in taxonomy and intrinsic resistance to antifungals reveal the necessity of accurate species-level identification. In this review, we discuss the current phenotypic and molecular tools available for diagnosis in clinical laboratory settings and their advantages and disadvantages.
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Affiliation(s)
- Valeri Sáenz
- Grupo de Investigación Celular y Molecular de Microorganismos Patógenos (CeMoP), Departamento de Ciencias Biológicas, Universidad de Los Andes, Bogotá, Colombia
| | - Andrés Felipe Lizcano Salas
- Grupo de Investigación Celular y Molecular de Microorganismos Patógenos (CeMoP), Departamento de Ciencias Biológicas, Universidad de Los Andes, Bogotá, Colombia
| | - Josepa Gené
- Unitat de Micologia i Microbiologia Ambiental (MicroAmb), Facultat de Medicina i Ciències de la Salut i Institut d'Investigació Sanitària Pere Virgili (IISPV), Universitat Rovira i Virgili, Reus, Spain
| | - Adriana Marcela Celis Ramírez
- Grupo de Investigación Celular y Molecular de Microorganismos Patógenos (CeMoP), Departamento de Ciencias Biológicas, Universidad de Los Andes, Bogotá, Colombia
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Ocansey B, Erskine I, Okine L, Potakey D, Pappoe-Ashong P, Sraku I, Quayson S, Opintan J, Kosmidis C, Denning D. A diverse spectrum of mycoses histologically diagnosed in Ghana: Insights from a 10-year retrospective study. Med Mycol 2024; 62:myae015. [PMID: 38383897 PMCID: PMC10919345 DOI: 10.1093/mmy/myae015] [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: 12/22/2023] [Revised: 02/11/2024] [Accepted: 02/20/2024] [Indexed: 02/23/2024] Open
Abstract
In Ghana, most laboratory diagnoses of severe mycoses are based on histopathology findings due to inadequate availability of serology, culture, and molecular tests. The aim of this study was to evaluate the spectrum of mycoses diagnosed in Ghana. We retrospectively reviewed reports from 2012 to 2021 from three major pathology laboratories in Ghana to identify reports indicating the presence of fungal elements and diagnosis of a mycosis, then extracted demographic, clinical history, site of infection, stain(s), used and diagnosed mycosis details. Over the 10-year period, 107 cases were found. No apparent increasing and decreasing trend in the number of cases per year or in a period was observed. The age range of affected patients was from 4 to 86 years. Special stains for fungi were only used in 22 of 107 (20.6%) of cases. The most frequently affected site was the sino-nasal area (34%). Mycosis type was determined for 58 (54.2%) cases, comprising aspergillosis (21), candidiasis (14), dermatophytosis (6), mucormycosis (3), two cases each of chromoblastomycosis, histoplasmosis, eumycetoma, entomophthoromycosis, sporotrichosis, and Malassezia infection and a single case each of cryptococcosis and deep onychomycosis. Of the 53 (49.5%) cases with presumptive diagnosis data, only seven (13.2%) had a pre-biopsy suspicion of mycosis. There is a wide spectrum of mycoses in Ghana, including endemic mycoses not previously reported. Improving the use of special fungal stains could increase yield and mycoses identification. Laboratory diagnostic capacity needs enhancement to complement histopathology investigations with serology, culture, and molecular methods.
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Affiliation(s)
- Bright Ocansey
- Division of Evolution, Infection and Genomics, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9NT, UK
| | - Isaac Erskine
- Department of Pathology, Korle-Bu Teaching Hospital and University of Ghana Medical School, Korle-Bu, GA-221-1570, Ghana
| | - Leonard Okine
- Cellular Pathology Division, Ghana Standard Authority, Accra, GA-288-5605, Ghana
| | - Daniel Potakey
- Department of Pathology, Korle-Bu Teaching Hospital and University of Ghana Medical School, Korle-Bu, GA-221-1570, Ghana
| | - Prince Pappoe-Ashong
- Department of Medical Microbiology, University of Ghana Medical School, Korle-Bu, GA-270-4330, Ghana
| | - Isaac Sraku
- Department of Medical Microbiology, University of Ghana Medical School, Korle-Bu, GA-270-4330, Ghana
| | - Solomon Quayson
- Department of Pathology, Korle-Bu Teaching Hospital and University of Ghana Medical School, Korle-Bu, GA-221-1570, Ghana
| | - Japheth Opintan
- Department of Medical Microbiology, University of Ghana Medical School, Korle-Bu, GA-270-4330, Ghana
| | - Chris Kosmidis
- Division of Evolution, Infection and Genomics, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9NT, UK
- National Aspergillosis Centre, Manchester University NHS Foundation Trust, Manchester, M23 9LT, UK
| | - David Denning
- Division of Evolution, Infection and Genomics, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9NT, UK
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Baomo L, Guofen Z, Jie D, Liu X, Shuru C, Jing L. Disseminated cryptococcosis in a patient with idiopathic CD4 + T lymphocytopenia presenting as prostate and adrenal nodules: diagnosis from pathology and mNGS, a case report. BMC Infect Dis 2024; 24:26. [PMID: 38166809 PMCID: PMC10763445 DOI: 10.1186/s12879-023-08926-1] [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: 05/07/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024] Open
Abstract
Disseminated Cryptococcosis infection typically occurs in immunocompromised patients, often manifested as pneumonia or meningoencephalitis. Cases with involvement of either prostate or adrenal glands are less frequent. We describe a case of an immunocompromised 62-year-old man with new-found Idiopathic CD4 + T lymphocytopenia who presented with urinary irritation symptoms followed by headache. The patient was finally diagnosed as disseminated cryptococcosis of prostate, adrenal gland involvement with the help of combining histopathology of formalin-fixed, paraffin-embedded tissue with metagenomic next-generation sequencing technique to identify C neoformans sensu stricto in prostate, adrenal gland tissues. Clinicians should be aware of atypical presentations of cryptococcal disease. In this case of cryptococcosis in immunocompromised patients, we find that cryptococcosis can affect varied organs simultaneously and should be considered in the differential of infectious diseases. And mNGS technology helps to confirm the diagnosis.
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Affiliation(s)
- Liu Baomo
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Zeng Guofen
- Department of Infectious Diseases, Third Affiliated Hospital of Sun Yat-sen University, 510630, Guangzhou, China
| | - Dong Jie
- Department of Infectious Diseases, Zhuhai People's Hospital(Zhuhai Hospital affiliated with Jinan University), 519000, Zhuhai, China
| | - Xie Liu
- Department of Infectious Diseases, Shenzhen Longhua District People's Hospital, 518110, Shenzhen, China
| | - Chen Shuru
- Department of Infectious Diseases, Third Affiliated Hospital of Sun Yat-sen University, 510630, Guangzhou, China.
| | - Liu Jing
- Department of Infectious Diseases, Third Affiliated Hospital of Sun Yat-sen University, 510630, Guangzhou, China.
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Sun WW, Dong ZW, Zhou YM, Jin F, Liu HC, Fan L. Improving the identification and diagnostic efficiency of Metagenomic Next-Generation Sequencing for mycobacterial granuloma on postoperative formalin-fixed paraffin-embedded specimens. Microbes Infect 2023; 25:105185. [PMID: 37453490 DOI: 10.1016/j.micinf.2023.105185] [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: 01/22/2023] [Revised: 07/05/2023] [Accepted: 07/10/2023] [Indexed: 07/18/2023]
Abstract
OBJECTIVE Metagenomic Next-Generation Sequencing (mNGS) has been validated to have an important role in the diagnosis of mycobacterium infection. The study aimed to further explore the mycobacteria identification ability of mNGS on formalin-fixed paraffin-embedded(FFPE)tissues from postoperative specimens. METHODS Patients who underwent surgical biopsy or resection for clarifying the diagnosis and whose initial postoperative pathology indicated granulomatous lesions were included. Fresh tissues were sent for mycobacterium culture and Xpert MTB/RIF (Xpert) to establish the diagnosis. FFPE specimens were sent for mNGS and molecular pathology,the diagnostic values were compared between the two methods. RESULTS A total of 65 cases with definite diagnoses were finally included in the study. 31 cases were confirmed as mycobacterium granuloma using the fresh specimen etiology as diagnostic criteria. The overall sensitivity and specificity of mNGS on FFPE specimens in the diagnosis of mycobacterium granuloma were 100% and 88.24%, respectively. In 19 cases diagnosed as tuberculous granulomas, the sensitivity (100% vs47.37%) and negative predictive value (NPV, 100%vs 82.14%) of mNGS were both significantly higher than that of molecular pathology on the FFPE section(both p 0.00)while the positive predictive value (PPV) and specificity were not significantly different. In 12 cases diagnosed as Non-tuberculous mycobacterium (NTM)granuloma, the sensitivity of mNGS was also significantly higher than that of molecular pathology on FFPE section (100% vs 66.67%, p 0.00) while the specificity, PPV and NPV were all not significantly different. CONCLUSIONS The mNGS could be used for one-time detection of pathogens on FFPE sections with high sensitivity. It could be recommended as a supplementary method for the identification of pathogenic bacteria in the diagnosis of postoperative granuloma lesions.
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Affiliation(s)
- Wen-Wen Sun
- Shanghai Clinic and Research Center of Tuberculosis, Department of Tuberculosis, Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Zheng-Wei Dong
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yi-Ming Zhou
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Feng Jin
- Department of Thoracic Surgery, Shandong Key Laboratory of Infectious Respiratory Diseases, Shandong Public Health Clinical Center Affiliated to Shandong University, Jinan, China.
| | - Hong-Cheng Liu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China.
| | - Lin Fan
- Shanghai Clinic and Research Center of Tuberculosis, Department of Tuberculosis, Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China.
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McHardy IH, Barker B, Thompson GR. Review of Clinical and Laboratory Diagnostics for Coccidioidomycosis. J Clin Microbiol 2023; 61:e0158122. [PMID: 36883820 PMCID: PMC10204634 DOI: 10.1128/jcm.01581-22] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023] Open
Abstract
Coccidioidomycosis is a fungal disease associated with soil exposure that frequently goes undiagnosed due at least in part to its nonspecific presentation and the lack of clinical suspicion by health care providers. Currently available diagnostics for coccidioidomycosis offer qualitative results that can suffer from low specificity, while semiquantitative assays are labor-intensive and complex and can require multiple days to complete. Furthermore, significant confusion exists regarding the optimal diagnostic algorithms and appropriate usage of available diagnostic tests. This review aims to inform clinical laboratorians and treating clinicians about the current diagnostic landscape, appropriate diagnostic strategies, and future diagnostic directions for coccidioidomycosis, which is expected to become more prevalent due to increased migration into areas of endemicity and climate changes.
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Affiliation(s)
- Ian H. McHardy
- Scripps Medical Laboratory, Scripps Health, San Diego, California, USA
- University of California, Davis Center for Valley Fever, Sacramento, California, USA
| | - Bridget Barker
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - George R. Thompson
- Department of Internal Medicine, Division of Infectious Diseases, University of California, Davis Medical Center, Sacramento, California, USA
- University of California, Davis Center for Valley Fever, Sacramento, California, USA
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Kamau E, Yang S. Metagenomic Sequencing of Positive Blood Culture Fluid for Accurate Bacterial and Fungal Species Identification: A Pilot Study. Microorganisms 2023; 11:1259. [PMID: 37317232 DOI: 10.3390/microorganisms11051259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/27/2023] [Accepted: 05/09/2023] [Indexed: 06/16/2023] Open
Abstract
With blood stream infections (BSIs) representing a major cause of mortality and morbidity worldwide, blood cultures play a crucial role in diagnosis, but their clinical application is dampened by the long turn-around time and the detection of only culturable pathogens. In this study, we developed and validated a shotgun metagenomics next-generation sequencing (mNGS) test directly from positive blood culture fluid, allowing for the identification of fastidious or slow growing microorganisms more rapidly. The test was built based on previously validated next-generation sequencing tests, which rely on several key marker genes for bacterial and fungal identification. The new test utilizes an open-source metagenomics CZ-ID platform for the initial analysis to generate the most likely candidate species, which is then used as a reference genome for downstream, confirmatory analysis. This approach is innovative because it takes advantage of an open-source software's agnostic taxonomic calling capability while still relying on the more established and previously validated marker gene-based identification scheme, increasing the confidence in the final results. The test showed high accuracy (100%, 30/30) for both bacterial and fungal microorganisms. We further demonstrated its clinical utility especially for anaerobes and mycobacteria that are either fastidious, slow growing, or unusual. Although applicable in only limited settings, the Positive Blood Culture mNGS test provides an incremental improvement in solving the unmet clinical needs for the diagnosis of challenging BSIs.
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Affiliation(s)
- Edwin Kamau
- Department of Pathology and Laboratory Medicine, UCLA David Geffen School of Medicine, Los Angeles, CA 90095, USA
| | - Shangxin Yang
- Department of Pathology and Laboratory Medicine, UCLA David Geffen School of Medicine, Los Angeles, CA 90095, USA
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Trecourt A, Rabodonirina M, Mauduit C, Traverse-Glehen A, Devouassoux-Shisheboran M, Meyronet D, Dijoud F, Ginevra C, Chapey-Picq E, Josse E, Martins-Simoes P, Bentaher A, Dupont D, Miossec C, Persat F, Wallon M, Ferry T, Pham F, Simon B, Menotti J. Fungal Integrated Histomolecular Diagnosis Using Targeted Next-Generation Sequencing on Formalin-Fixed Paraffin-Embedded Tissues. J Clin Microbiol 2023; 61:e0152022. [PMID: 36809009 PMCID: PMC10035294 DOI: 10.1128/jcm.01520-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/30/2023] [Indexed: 02/23/2023] Open
Abstract
Histopathology is the gold standard for fungal infection (FI) diagnosis, but it does not provide a genus and/or species identification. The objective of the present study was to develop targeted next-generation sequencing (NGS) on formalin-fixed tissue samples (FTs) to achieve a fungal integrated histomolecular diagnosis. Nucleic acid extraction was optimized on a first group of 30 FTs with Aspergillus fumigatus or Mucorales infection by macrodissecting the microscopically identified fungal-rich area and comparing Qiagen and Promega extraction methods through DNA amplification by A. fumigatus and Mucorales primers. Targeted NGS was developed on a second group of 74 FTs using three primer pairs (ITS-3/ITS-4, MITS-2A/MITS-2B, and 28S-12-F/28S-13-R) and two databases (UNITE and RefSeq). A prior fungal identification of this group was established on fresh tissues. Targeted NGS and Sanger sequencing results on FTs were compared. To be valid, the molecular identifications had to be compatible with the histopathological analysis. In the first group, the Qiagen method yielded a better extraction efficiency than the Promega method (100% and 86.7% of positive PCRs, respectively). In the second group, targeted NGS allowed fungal identification in 82.4% (61/74) of FTs using all primer pairs, in 73% (54/74) using ITS-3/ITS-4, in 68.9% (51/74) using MITS-2A/MITS-2B, and in 23% (17/74) using 28S-12-F/28S-13-R. The sensitivity varied according to the database used (81% [60/74] using UNITE compared to 50% [37/74] using RefSeq [P = 0.000002]). The sensitivity of targeted NGS (82.4%) was higher than that of Sanger sequencing (45.9%; P < 0.00001). To conclude, fungal integrated histomolecular diagnosis using targeted NGS is suitable on FTs and improves fungal detection and identification.
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Affiliation(s)
- Alexis Trecourt
- Service de Pathologie Multi-Site—Site Sud, Hospices Civils de Lyon, Centre Hospitalier Lyon Sud, Lyon, France
- Faculté de Médecine Lyon-Sud Charles Mérieux, UR 3738–CICLY–Equipe Inflammation et Immunité de L’épithélium Respiratoire, Université Claude Bernard Lyon 1, Lyon, France
| | - Meja Rabodonirina
- Institut des Agents Infectieux, Service de Parasitologie et Mycologie Médicale, Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
- Faculté de Médecine Lyon Sud Charles Mérieux, Université Claude Bernard Lyon 1, Lyon, France
| | - Claire Mauduit
- Service de Pathologie Multi-Site—Site Sud, Hospices Civils de Lyon, Centre Hospitalier Lyon Sud, Lyon, France
- Faculté de Médecine Lyon Sud Charles Mérieux, Université Claude Bernard Lyon 1, Lyon, France
- Centre Méditerranéen de Médecine Moléculaire (C3M), Unité 1065, Institut National de la Santé et de la Recherche Médicale, Nice, France
| | - Alexandra Traverse-Glehen
- Service de Pathologie Multi-Site—Site Sud, Hospices Civils de Lyon, Centre Hospitalier Lyon Sud, Lyon, France
- Faculté de Médecine Lyon Sud Charles Mérieux, Université Claude Bernard Lyon 1, Lyon, France
- Faculté de Médecine Lyon Sud Charles Mérieux, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Université Claude Bernard Lyon 1, Lyon, France
| | - Mojgan Devouassoux-Shisheboran
- Service de Pathologie Multi-Site—Site Sud, Hospices Civils de Lyon, Centre Hospitalier Lyon Sud, Lyon, France
- Faculté de Médecine Lyon Est, Université Claude Bernard Lyon 1, Lyon, France
| | - David Meyronet
- Faculté de Médecine Lyon Est, Université Claude Bernard Lyon 1, Lyon, France
- Service de Pathologie Multi-site—Site Est, Hospices Civils de Lyon, Centre Hospitalier Lyon Est, Lyon, France
| | - Frédérique Dijoud
- Faculté de Médecine Lyon Est, Université Claude Bernard Lyon 1, Lyon, France
- Service de Pathologie Multi-site—Site Est, Hospices Civils de Lyon, Centre Hospitalier Lyon Est, Lyon, France
| | - Christophe Ginevra
- Institut des Agents Infectieux, Génomique Épidémiologique des Maladies Infectieuses (GENEPII), Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
- Institut des Agents Infectieux, Centre National de Référence des Légionelles, Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
| | - Emmanuelle Chapey-Picq
- Institut des Agents Infectieux, Service de Parasitologie et Mycologie Médicale, Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
- Faculté de Médecine Lyon Sud Charles Mérieux, Université Claude Bernard Lyon 1, Lyon, France
| | - Emilie Josse
- Institut des Agents Infectieux, Service de Parasitologie et Mycologie Médicale, Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
| | - Patricia Martins-Simoes
- Institut des Agents Infectieux, Génomique Épidémiologique des Maladies Infectieuses (GENEPII), Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
- Institut des Agents Infectieux, Centre National de Référence des Staphyloccoques, Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
| | - Abderrazzak Bentaher
- Faculté de Médecine Lyon-Sud Charles Mérieux, UR 3738–CICLY–Equipe Inflammation et Immunité de L’épithélium Respiratoire, Université Claude Bernard Lyon 1, Lyon, France
- Faculté de Médecine Lyon Sud Charles Mérieux, Université Claude Bernard Lyon 1, Lyon, France
| | - Damien Dupont
- Institut des Agents Infectieux, Service de Parasitologie et Mycologie Médicale, Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
- Faculté de Médecine Lyon Est, Université Claude Bernard Lyon 1, Lyon, France
| | - Charline Miossec
- Institut des Agents Infectieux, Service de Parasitologie et Mycologie Médicale, Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
| | - Florence Persat
- Faculté de Médecine Lyon-Sud Charles Mérieux, UR 3738–CICLY–Equipe Inflammation et Immunité de L’épithélium Respiratoire, Université Claude Bernard Lyon 1, Lyon, France
- Institut des Agents Infectieux, Service de Parasitologie et Mycologie Médicale, Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
- Faculté de Médecine Lyon Est, Université Claude Bernard Lyon 1, Lyon, France
| | - Martine Wallon
- Institut des Agents Infectieux, Service de Parasitologie et Mycologie Médicale, Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
- Faculté de Médecine Lyon Sud Charles Mérieux, Université Claude Bernard Lyon 1, Lyon, France
| | - Tristan Ferry
- Faculté de Médecine Lyon Est, Université Claude Bernard Lyon 1, Lyon, France
- Service de Maladies Infectieuses et Tropicales, Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
| | - Félix Pham
- Service de Dermatologie, Hospices Civils de Lyon, Centre Hospitalier Lyon Sud, Lyon, France
| | - Bruno Simon
- Institut des Agents Infectieux, Génomique Épidémiologique des Maladies Infectieuses (GENEPII), Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
- Institut des Agents Infectieux, Service de Virologie, Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
| | - Jean Menotti
- Faculté de Médecine Lyon-Sud Charles Mérieux, UR 3738–CICLY–Equipe Inflammation et Immunité de L’épithélium Respiratoire, Université Claude Bernard Lyon 1, Lyon, France
- Institut des Agents Infectieux, Service de Parasitologie et Mycologie Médicale, Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
- Faculté de Médecine Lyon Est, Université Claude Bernard Lyon 1, Lyon, France
- Institut des Agents Infectieux, Génomique Épidémiologique des Maladies Infectieuses (GENEPII), Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
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10
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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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11
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Jiang S, Chen Y, Han S, Lv L, Li L. Next-Generation Sequencing Applications for the Study of Fungal Pathogens. Microorganisms 2022; 10:microorganisms10101882. [PMID: 36296159 PMCID: PMC9609632 DOI: 10.3390/microorganisms10101882] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/13/2022] [Accepted: 09/15/2022] [Indexed: 11/16/2022] Open
Abstract
Next-generation sequencing (NGS) has become a widely used technology in biological research. NGS applications for clinical pathogen detection have become vital technologies. It is increasingly common to perform fast, accurate, and specific detection of clinical specimens using NGS. Pathogenic fungi with high virulence and drug resistance cause life-threatening clinical infections. NGS has had a significant biotechnological impact on detecting bacteria and viruses but is not equally applicable to fungi. There is a particularly urgent clinical need to use NGS to help identify fungi causing infections and prevent negative impacts. This review summarizes current research on NGS applications for fungi and offers a visual method of fungal detection. With the development of NGS and solutions for overcoming sequencing limitations, we suggest clinicians test specimens as soon as possible when encountering infections of unknown cause, suspected infections in vital organs, or rapidly progressive disease.
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Affiliation(s)
- Shiman Jiang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou 310003, China
| | - Yanfei Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou 310003, China
| | - Shengyi Han
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou 310003, China
| | - Longxian Lv
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou 310003, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou 310003, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan 250021, China
- Correspondence: ; Tel.: +86-0571-8723-6458
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12
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Hilt EE, Ferrieri P. Next Generation and Other Sequencing Technologies in Diagnostic Microbiology and Infectious Diseases. Genes (Basel) 2022; 13:genes13091566. [PMID: 36140733 PMCID: PMC9498426 DOI: 10.3390/genes13091566] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 12/03/2022] Open
Abstract
Next-generation sequencing (NGS) technologies have become increasingly available for use in the clinical microbiology diagnostic environment. There are three main applications of these technologies in the clinical microbiology laboratory: whole genome sequencing (WGS), targeted metagenomics sequencing and shotgun metagenomics sequencing. These applications are being utilized for initial identification of pathogenic organisms, the detection of antimicrobial resistance mechanisms and for epidemiologic tracking of organisms within and outside hospital systems. In this review, we analyze these three applications and provide a comprehensive summary of how these applications are currently being used in public health, basic research, and clinical microbiology laboratory environments. In the public health arena, WGS is being used to identify and epidemiologically track food borne outbreaks and disease surveillance. In clinical hospital systems, WGS is used to identify multi-drug-resistant nosocomial infections and track the transmission of these organisms. In addition, we examine how metagenomics sequencing approaches (targeted and shotgun) are being used to circumvent the traditional and biased microbiology culture methods to identify potential pathogens directly from specimens. We also expand on the important factors to consider when implementing these technologies, and what is possible for these technologies in infectious disease diagnosis in the next 5 years.
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13
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Tao R, Zhu P, Zhou Y, Li Q, Wan Z, Li R, Wang R. Altered skin fungal and bacterial community compositions in tinea capitis. Mycoses 2022; 65:834-840. [PMID: 35689543 DOI: 10.1111/myc.13480] [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: 03/30/2022] [Revised: 05/24/2022] [Accepted: 06/07/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND Tinea capitis is an infection of the scalp and hair shaft caused by dermatophytes that predominantly occurs in children. Skin fungal infections have been found to be associated with alterations in the overall bacterial and fungal communities. However, the scalp microbiome in tinea capitis have not been fully investigated. OBJECTIVES To investigate and compare the scalp bacterial and fungal microbiomes between children with tinea capitis and healthy children and between children and adults. METHODS Skin samples were collected from the scalp. Bacterial and fungal community compositions were analysed by amplification sequencing of the V3-V4 of 16S rDNA and ITS1-5F, respectively. RESULTS The predominant fungi detected using amplicon sequencing were consistent with the culture- or real-time PCR-positive pathogens in most samples. Children with tinea capitis had lower fungal and higher bacterial Shannon diversity than healthy children. A higher relative abundance of pathogenic fungi and significant alterations in the bacterial community in the lesional sites of tinea capitis than healthy scalps. Compared with adults, healthy children were characterised by higher Shannon diversities with significantly lower relative abundances of Malassezia and Cutibacterium and higher relative abundances of Candida and Streptococcus. CONCLUSIONS We demonstrated that tinea capitis was characterised by significant alterations in both fungal and bacterial communities and amplicon sequencing could be a complementary method for pathogen identification.
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Affiliation(s)
- Rong Tao
- Department of Dermatology, Peking University First Hospital, Beijing, China.,National Clinical Research Center for Skin and Immune Diseases, Beijing, China.,Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China.,NMPA Key Laboratory for Quality Control and Evaluation of Cosmetics, Beijing, China
| | - Peiqiu Zhu
- Department of Dermatology, Peking University First Hospital, Beijing, China.,National Clinical Research Center for Skin and Immune Diseases, Beijing, China.,Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China.,NMPA Key Laboratory for Quality Control and Evaluation of Cosmetics, Beijing, China
| | - Yabin Zhou
- Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Qian Li
- Children's Hospital Capital Institute of Pediatrics, Beijing, China
| | - Zhe Wan
- Department of Dermatology, Peking University First Hospital, Beijing, China.,National Clinical Research Center for Skin and Immune Diseases, Beijing, China.,Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China.,NMPA Key Laboratory for Quality Control and Evaluation of Cosmetics, Beijing, China
| | - Ruoyu Li
- Department of Dermatology, Peking University First Hospital, Beijing, China.,National Clinical Research Center for Skin and Immune Diseases, Beijing, China.,Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China.,NMPA Key Laboratory for Quality Control and Evaluation of Cosmetics, Beijing, China
| | - Ruojun Wang
- Department of Dermatology, Peking University First Hospital, Beijing, China.,National Clinical Research Center for Skin and Immune Diseases, Beijing, China.,Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China.,NMPA Key Laboratory for Quality Control and Evaluation of Cosmetics, Beijing, China
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14
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Kessel J, Hogardt M, Aspacher L, Wichelhaus TA, Gerkrath J, Rosenow E, Springer J, Rickerts V. Exclusion of Mucorales Co-Infection in a Patient with Aspergillus flavus Sinusitis by Fluorescence In Situ Hybridization (FISH). J Fungi (Basel) 2022; 8:jof8030306. [PMID: 35330308 PMCID: PMC8955397 DOI: 10.3390/jof8030306] [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] [Received: 02/22/2022] [Revised: 03/10/2022] [Accepted: 03/14/2022] [Indexed: 02/05/2023] Open
Abstract
Invasive fungal infections are associated with increased mortality in hematological patients. Despite considerable advances in antifungal therapy, the evaluation of suspected treatment failure is a common clinical challenge requiring extensive diagnostic testing to rule out potential causes, such as mixed infections. We present a 64-year-old patient with secondary AML, diabetes mellitus, febrile neutropenia, and sinusitis. While cultures from nasal tissue grew Aspergillus flavus, a microscopic examination of the tissue was suggestive of concomitant mucormycosis. However, fluorescence in situ hybridization (FISH) using specific probes targeting Aspergillus and Mucorales species ruled out mixed infection. This was confirmed by specific qPCR assays amplifying the DNA of Aspergillus, but not of Mucorales. These results provided a rational basis for step-down targeted therapy, i.e., the patient received posaconazole after seven days of calculated dual therapy with liposomal amphotericin B and posaconazole. Despite clinical response to the antifungal therapy, he died due to the progression of the underlying disease within two weeks after diagnosis of fungal infection. Molecular diagnostics applied to tissue blocks may reveal useful information on the etiology of invasive fungal infections, including challenging situations, such as with mixed infections. A thorough understanding of fungal etiology facilitates targeted therapy that may improve therapeutic success while limiting side effects.
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Affiliation(s)
- Johanna Kessel
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University, 60590 Frankfurt am Main, Germany
- Correspondence:
| | - Michael Hogardt
- Institute for Medical Microbiology and Infection Control, University Hospital Frankfurt, Goethe University, 60590 Frankfurt am Main, Germany; (M.H.); (T.A.W.)
| | - Lukas Aspacher
- Department of Internal Medicine, Hematology/Oncology, University Hospital Frankfurt, Goethe University, 60590 Frankfurt am Main, Germany;
| | - Thomas A. Wichelhaus
- Institute for Medical Microbiology and Infection Control, University Hospital Frankfurt, Goethe University, 60590 Frankfurt am Main, Germany; (M.H.); (T.A.W.)
| | - Jasmin Gerkrath
- Robert Koch Institute Berlin, FG16, Seestrasse 10, 13353 Berlin, Germany; (J.G.); (E.R.); (V.R.)
- Medizinische Klinik und Poliklinik II, Universitätsklinikum Würzburg, 97080 Wuerzburg, Germany;
| | - Emely Rosenow
- Robert Koch Institute Berlin, FG16, Seestrasse 10, 13353 Berlin, Germany; (J.G.); (E.R.); (V.R.)
| | - Jan Springer
- Medizinische Klinik und Poliklinik II, Universitätsklinikum Würzburg, 97080 Wuerzburg, Germany;
| | - Volker Rickerts
- Robert Koch Institute Berlin, FG16, Seestrasse 10, 13353 Berlin, Germany; (J.G.); (E.R.); (V.R.)
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15
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Ashraf MJ, Kord M, Morovati H, Ansari S, Shekarkhar G, Badali H, Pakshir K, Shamsizadeh F, Khademi B, Shishegar M, Ahmadikia K, Zomorodian K. Evaluating a semi-nested PCR to support histopathology reports of fungal rhinosinusitis in formalin-fixed paraffin-embedded tissue samples. J Clin Lab Anal 2022; 36:e24209. [PMID: 34997792 PMCID: PMC8841172 DOI: 10.1002/jcla.24209] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 11/17/2021] [Accepted: 12/17/2021] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Fungal rhinosinusitis (FRS) encompasses a various spectrum of diseases. Histopathology is the "reference method" for diagnosing FRS, but it cannot determine the genus and species. Moreover, in more than 50% of the histopathologically proven cases, the culture elicited no reliable results. This study was an attempt to evaluate the diagnostic efficiency of semi-nested polymerase chain reaction (PCR) from formalin-fixed paraffin-embedded (FFPE) functional endoscopic sinus surgery (FESS) in FRS patients. METHODS One hundred ten specimens were subjected to DNA extraction and histopathology examination. The amplification of the β-globin gene by conventional PCR was used to confirm the quality of extracted DNA. The semi-nested PCR was performed using ITS1, ITS2, and ITS4 primers during two steps. Sequencing the internal transcribed spacer region (ITS1-5.8S-ITS2) to identify causative agents was performed on PCR products. RESULTS Sixty-four out of 110 samples were positive by histopathology evidence, of which 56 samples (87.5%) were positive by PCR. Out of 46 negative samples by histopathological methods, five samples (10.9%) yielded positive results by PCR. Sensitivity, specificity, positive predictive value, and negative predictive value of the semi-nested PCR method were reported 87.5%, 89.2%, 92.7%, and 85.2%, respectively. The kappa factor between PCR and histopathological methods was 0.76, indicating substantial agreements between these two tests. CONCLUSION Due to the acceptable sensitivity and specificity of the present method, it might be used to diagnose fungal sinusitis infections along with microscopic techniques. This method is recommended to confirm the diagnose of suspected fungal sinusitis with negative histopathology results.
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Affiliation(s)
- Mohammad Javad Ashraf
- Department of Pathology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Kord
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hamid Morovati
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Saham Ansari
- Department of Medical Parasitology and Mycology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Golsa Shekarkhar
- Department of Pathology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hamid Badali
- Fungus Testing Laboratory, Department of Pathology and Laboratory Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA.,Invasive Fungi Research Center, Communicable Diseases Institute, Mazandaran University of Medical Sciences, Sari, Iran
| | - Kayvan Pakshir
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.,Basic Sciences in Infectious Diseases Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Forough Shamsizadeh
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Bijan Khademi
- Research Center of Otolaryngology Head and Neck Surgery, Shiraz University of Medical Sciences, Shiraz, Iran.,Department of Otolaryngology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mahmood Shishegar
- Research Center of Otolaryngology Head and Neck Surgery, Shiraz University of Medical Sciences, Shiraz, Iran.,Department of Otolaryngology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Kazem Ahmadikia
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Kamiar Zomorodian
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.,Basic Sciences in Infectious Diseases Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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16
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Current Insight into Culture-Dependent and Culture-Independent Methods in Discovering Ascomycetous Taxa. J Fungi (Basel) 2021; 7:jof7090703. [PMID: 34575741 PMCID: PMC8467358 DOI: 10.3390/jof7090703] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/22/2021] [Accepted: 08/23/2021] [Indexed: 01/08/2023] Open
Abstract
Culture techniques are vital in both traditional and modern fungal taxonomy. Establishing sexual-asexual links and synanamorphs, extracting DNA and secondary metabolites are mainly based on cultures. However, it is widely accepted that a large number of species are not sporulating in nature while others cannot be cultured. Recent ecological studies based on culture-independent methods revealed these unculturable taxa, i.e., dark taxa. Recent fungal diversity estimation studies suggested that environmental sequencing plays a vital role in discovering missing species. However, Sanger sequencing is still the main approach in determining DNA sequences in culturable species. In this paper, we summarize culture-based and culture-independent methods in the study of ascomycetous taxa. High-throughput sequencing of leaf endophytes, leaf litter fungi and fungi in aquatic environments is important to determine dark taxa. Nevertheless, currently, naming dark taxa is not recognized by the ICN, thus provisional naming of them is essential as suggested by several studies.
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17
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Tsang CC, Teng JLL, Lau SKP, Woo PCY. Rapid Genomic Diagnosis of Fungal Infections in the Age of Next-Generation Sequencing. J Fungi (Basel) 2021; 7:jof7080636. [PMID: 34436175 PMCID: PMC8398552 DOI: 10.3390/jof7080636] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 07/27/2021] [Accepted: 07/30/2021] [Indexed: 11/16/2022] Open
Abstract
Next-generation sequencing (NGS) technologies have recently developed beyond the research realm and started to mature into clinical applications. Here, we review the current use of NGS for laboratory diagnosis of fungal infections. Since the first reported case in 2014, >300 cases of fungal infections diagnosed by NGS were described. Pneumocystis jirovecii is the predominant fungus reported, constituting ~25% of the fungi detected. In ~12.5% of the cases, more than one fungus was detected by NGS. For P. jirovecii infections diagnosed by NGS, all 91 patients suffered from pneumonia and only 1 was HIV-positive. This is very different from the general epidemiology of P. jirovecii infections, of which HIV infection is the most important risk factor. The epidemiology of Talaromyces marneffei infection diagnosed by NGS is also different from its general epidemiology, in that only 3/11 patients were HIV-positive. The major advantage of using NGS for laboratory diagnosis is that it can pick up all pathogens, particularly when initial microbiological investigations are unfruitful. When the cost of NGS is further reduced, expertise more widely available and other obstacles overcome, NGS would be a useful tool for laboratory diagnosis of fungal infections, particularly for difficult-to-grow fungi and cases with low fungal loads.
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18
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Mariya T, Sato T, Fujibe Y, Ishido M, Shimada H, Kubo T, Nagai Y, Arai W, Tanaka SE, Ashikawa K, Sakuraba Y, Ishioka S, Yokota SI, Saito T. Next-generation sequencing of 16S rRNA for identification of invasive bacterial pathogens in a formalin-fixed paraffin-embedded placental specimen: a case report of perinatal fulminant Streptococcus pyogenes infection. Med Mol Morphol 2021; 54:374-379. [PMID: 34287707 DOI: 10.1007/s00795-021-00298-2] [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] [Received: 06/23/2021] [Accepted: 07/18/2021] [Indexed: 11/27/2022]
Abstract
Intrauterine infection is one of the most important causes of maternal death. In perinatal emergency, we often miss an opportunity to obtain culture specimens. In this study, we tried to examine whether we investigated whether bacteria causing infection can be detected from a formalin-fixed paraffin-embedded (FFPE) placental specimen. We examined the placenta from a maternal invasive infection that resulted in infectious abortion at 18 weeks of gestation. The case was diagnosed by acute fever and abdominal pain, and the patient was cured after 3 weeks of intensive antimicrobial treatment. Four Streptococcus pyogenes strains were isolated from vaginal fluid and blood cultures of the patient. All of the strain types were emm1/ST28. We amplified the V1-V2 region of 16S rRNA from an FFPE placental specimen and sequencing was performed using a next-generation sequencer (NGS). Taxonomic analysis was then performed for sequenced data. We succeeded in detecting causative pathogens from the FFPE placenta: 69.1% of the predominantly identified bacteria were S. pyogenes and other small populations of bacteria were detected. Our results revealed the utility of NGS for 16S rRNA analysis of an FFPE placenta. This method may reveal previous perinatal invasive infections of unknown origin retrospectively.
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Affiliation(s)
- Tasuku Mariya
- Department of Obstetrics and Gynecology, Sapporo Medical University School of Medicine, South 1 West 17, Chuo-ku, Sapporo, 060-8556, Japan.
| | - Toyotaka Sato
- Department of Microbiology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Yuya Fujibe
- Department of Obstetrics and Gynecology, Sapporo Medical University School of Medicine, South 1 West 17, Chuo-ku, Sapporo, 060-8556, Japan
| | - Manami Ishido
- Department of Obstetrics and Gynecology, Sapporo Medical University School of Medicine, South 1 West 17, Chuo-ku, Sapporo, 060-8556, Japan
| | - Hiroshi Shimada
- Department of Obstetrics and Gynecology, Sapporo Medical University School of Medicine, South 1 West 17, Chuo-ku, Sapporo, 060-8556, Japan
| | - Terufumi Kubo
- Department of Pathology 1st, Sapporo Medical University School of Medicine, Sapporo, Japan
| | | | | | | | | | | | - Shinichi Ishioka
- Department of Obstetrics and Gynecology, Sapporo Medical University School of Medicine, South 1 West 17, Chuo-ku, Sapporo, 060-8556, Japan
| | - Shin-Ichi Yokota
- Department of Microbiology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Tsuyoshi Saito
- Department of Obstetrics and Gynecology, Sapporo Medical University School of Medicine, South 1 West 17, Chuo-ku, Sapporo, 060-8556, Japan
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19
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Zhou H, Larkin PMK, Zhao D, Ma Q, Yao Y, Wu X, Wang J, Zhou X, Li Y, Wang G, Feng M, Wu L, Chen J, Zhou C, Hua X, Zhou J, Yang S, Yu Y. Clinical Impact of Metagenomic Next-Generation Sequencing of Bronchoalveolar Lavage in the Diagnosis and Management of Pneumonia: A Multicenter Prospective Observational Study. J Mol Diagn 2021; 23:1259-1268. [PMID: 34197923 DOI: 10.1016/j.jmoldx.2021.06.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/20/2021] [Accepted: 06/11/2021] [Indexed: 12/18/2022] Open
Abstract
Rapid and accurate pathogen identification is necessary for appropriate treatment of pneumonia. Here, we describe the use of shotgun metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage for pathogen identification in pneumonia in a large-scale multicenter prospective study with 159 patients enrolled. We compared the results of mNGS with standard methods including culture, staining, and targeted PCR, and evaluated the clinical impact of mNGS. A positive impact was defined by a definitive diagnosis made using the mNGS results, or change of management because of the mNGS results, leading to a favorable clinical outcome. Overall, mNGS identified more organisms than standard methods (117 versus 72), detected 17 pathogens that consistently were missed in all cases by standard methods, and had an overall positive clinical impact in 40.3% (64 of 159) of cases. mNGS was especially useful in identification of fastidious and atypical organisms causing pneumonia, contributing to detection of definitive pathogens in 45 (28.3%) cases in which standard results were either negative or insufficient. mNGS also helped reassure antibiotic de-escalation in 19 (11.9%) cases. Overall, mNGS led to a change of treatment in 59 (37.1%) cases, including antibiotic de-escalation in 40 (25.2%) cases. This study showed the significant value of mNGS of bronchoalveolar lavage for improving the diagnosis of pneumonia and contributing to better patient care.
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Affiliation(s)
- Hua Zhou
- Department of Respiratory Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Paige M K Larkin
- Department of Pathology and Laboratory Medicine, NorthShore University HealthSystem, Evanston, Illinois
| | - Dongdong Zhao
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Qiang Ma
- Department of Respiratory Diseases, Yuhang Second People's Hospital, Hangzhou, Zhejiang, China
| | - Yake Yao
- Department of Respiratory Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xiaohong Wu
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jiaoli Wang
- Department of Respiratory Diseases, Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - XiaoHu Zhou
- Department of Respiratory Diseases, The People's Hospital of Jiangshan, Quzhou, Zhejiang, China
| | - Yaqing Li
- Department of Respiratory Medicine, Zhejiang Provincial People's Hospital, Hangzhou, Zhejiang, China
| | - Gang Wang
- Department of Respiratory Diseases, Anji People's Hospital, Huzhou, Zhejiang, China
| | - Malong Feng
- Department of Respiratory Diseases, Fenghua People's Hospital of Ningbo, Ningbo, Zhejiang, China
| | - Lei Wu
- Department of Pulmonology and Endoscopy Center, The Children's Hospital, National Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jinyin Chen
- Department of Respiratory Diseases, Zhuji People's Hospital, Shaoxing, Zhejiang, China
| | - Changsheng Zhou
- Department of Respiratory Diseases, People's Hospital of Cangnan, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xiaoting Hua
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China; Department of Respiratory Diseases, Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Jianying Zhou
- Department of Respiratory Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Shangxin Yang
- Zhejiang-California International Nanosystems Institute, Zhejiang University, Hangzhou, Zhejiang, China; Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California.
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China; Department of Respiratory Diseases, Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang, China.
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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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Kattner S, Herbstreit F, Schmidt K, Stevens P, Grumaz S, Dubler S, Rath PM, Brenner T. Next-Generation Sequencing-Based Decision Support for Intensivists in Difficult-to-Diagnose Disease States: A Case Report of Invasive Cerebral Aspergillosis. A A Pract 2021; 15:e01447. [PMID: 33955856 DOI: 10.1213/xaa.0000000000001447] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Aspergillus spp. are widespread environmental pathogens that can induce invasive aspergillosis, especially in immunocompromised patients. An 86-year-old female patient presented with a rare case of invasive cerebral aspergillosis. The aspergilloma invaded the intracranial region originating from the ethmoidal sinus and the orbital apex. In contrast to routine diagnostic procedures, next-generation sequencing (NGS) was able to identify the fungal pathogen in the cerebrospinal fluid as well as in plasma samples, supporting the biopsy-based diagnosis of invasive cerebral aspergillosis. Therefore, NGS-based diagnostics may be of particular importance for difficult-to-diagnose disease states, when conventional diagnostic procedures fail.
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Affiliation(s)
- Simone Kattner
- From the Department of Anesthesiology and Intensive Care Medicine, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Frank Herbstreit
- From the Department of Anesthesiology and Intensive Care Medicine, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Karsten Schmidt
- From the Department of Anesthesiology and Intensive Care Medicine, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | | | | | - Simon Dubler
- From the Department of Anesthesiology and Intensive Care Medicine, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Peter-Michael Rath
- Institute of Medical Microbiology, Essen Center of Excellence in Clinical and Laboratory Mycology and Clinical Studies, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Thorsten Brenner
- From the Department of Anesthesiology and Intensive Care Medicine, University Hospital Essen, University Duisburg-Essen, Essen, Germany
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