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Jiang L, Liang TW, Al-Odaini N, Hu Y, Huang M, Wei L, Li XY, Pan KS, Zheng DY, Jiang ZW, Wei G, Cao CW. Metagenomic Next-Generation Sequencing as an Effective Diagnostic Tool for Talaromycosis in HIV-Negative Patients. Mycopathologia 2024; 189:63. [PMID: 38985209 DOI: 10.1007/s11046-024-00866-x] [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: 02/04/2024] [Accepted: 06/05/2024] [Indexed: 07/11/2024]
Abstract
The diagnosis of Talaromyces marneffei infection in HIV-negative patients remains challenging. There is an urgent need for rapid and convenient methods to diagnose this complicated disease. The aim of this study was to evaluate the diagnostic efficiency of metagenomic next-generation sequencing (mNGS) for talaromycosis in non-HIV-infected patients by comparing mNGS with traditional microbial culture. In total, 66 samples from 57 patients were analyzed via both mNGS and microbial culture. The ROC curve showed a sensitivity for mNGS of 97.22%, which was greater than that of microbial culture (61.11%). Samples from the respiratory tract, infectious skin lesions, and lymph nodes are recommended as routine samples for talaromycosis detection via mNGS. Furthermore, mNGS significantly reduced the diagnostic time compared to microbial culture. Overall, our study demonstrated that mNGS is a promising tool for rapid and accurate pathogenic detection in HIV-negative patients with talaromycosis.
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Affiliation(s)
- Li Jiang
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
- Fangchenggang Wanqing Institute of Mycosis Prevention and Control, Fangchenggang, China
| | - Tian-Wei Liang
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
- Fangchenggang Wanqing Institute of Mycosis Prevention and Control, Fangchenggang, China
| | - Najwa Al-Odaini
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
- Fangchenggang Wanqing Institute of Mycosis Prevention and Control, Fangchenggang, China
| | - Yuan Hu
- Richardson Medical Fungal Laboratory, Guangzhou Centre for Fungal Diagnostics and Research, Guangzhou, China
| | - Minli Huang
- Department of Ophthalmology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Lili Wei
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
- Fangchenggang Wanqing Institute of Mycosis Prevention and Control, Fangchenggang, China
| | - Xiu-Ying Li
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
- Fangchenggang Wanqing Institute of Mycosis Prevention and Control, Fangchenggang, China
| | - Kai-Su Pan
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
- Fangchenggang Wanqing Institute of Mycosis Prevention and Control, Fangchenggang, China
| | - Dong-Yan Zheng
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
- Fangchenggang Wanqing Institute of Mycosis Prevention and Control, Fangchenggang, China
| | - Zhi-Wen Jiang
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
- Fangchenggang Wanqing Institute of Mycosis Prevention and Control, Fangchenggang, China
| | - Gao Wei
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China.
- Fangchenggang Wanqing Institute of Mycosis Prevention and Control, Fangchenggang, China.
| | - Cun-Wei Cao
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China.
- Fangchenggang Wanqing Institute of Mycosis Prevention and Control, Fangchenggang, China.
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Pham D, Sivalingam V, Tang HM, Montgomery JM, Chen SCA, Halliday CL. Molecular Diagnostics for Invasive Fungal Diseases: Current and Future Approaches. J Fungi (Basel) 2024; 10:447. [PMID: 39057332 PMCID: PMC11278267 DOI: 10.3390/jof10070447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 06/21/2024] [Accepted: 06/24/2024] [Indexed: 07/28/2024] Open
Abstract
Invasive fungal diseases (IFDs) comprise a growing healthcare burden, especially given the expanding population of immunocompromised hosts. Early diagnosis of IFDs is required to optimise therapy with antifungals, especially in the setting of rising rates of antifungal resistance. Molecular techniques including nucleic acid amplification tests and whole genome sequencing have potential to offer utility in overcoming limitations with traditional phenotypic testing. However, standardisation of methodology and interpretations of these assays is an ongoing undertaking. The utility of targeted Aspergillus detection has been well-defined, with progress in investigations into the role of targeted assays for Candida, Pneumocystis, Cryptococcus, the Mucorales and endemic mycoses. Likewise, whilst broad-range polymerase chain reaction assays have been in use for some time, pathology stewardship and optimising diagnostic yield is a continuing exercise. As costs decrease, there is also now increased access and experience with whole genome sequencing, including metagenomic sequencing, which offers unparalleled resolution especially in the investigations of potential outbreaks. However, their role in routine diagnostic use remains uncommon and standardisation of techniques and workflow are required for wider implementation.
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Affiliation(s)
- David Pham
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia; (D.P.)
| | - Varsha Sivalingam
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia; (D.P.)
| | - Helen M. Tang
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia; (D.P.)
| | - James M. Montgomery
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia; (D.P.)
| | - Sharon C.-A. Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia; (D.P.)
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
- Sydney Infectious Diseases Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | - Catriona L. Halliday
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia; (D.P.)
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Xing F, Deng C, Luo Z, Zou S, Liu M, Ye H, Sun L, Tsang CC, Lo SKF, Lau SKP, Woo PCY. Rapid Diagnosis of Pneumocystis jirovecii Pneumonia and Respiratory Tract Colonization by Next-Generation Sequencing. Mycopathologia 2024; 189:38. [PMID: 38704795 PMCID: PMC11070382 DOI: 10.1007/s11046-024-00849-y] [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: 01/05/2024] [Accepted: 03/30/2024] [Indexed: 05/07/2024]
Abstract
OBJECTIVES To describe the epidemiology of Pneumocystis jirovecii pneumonia and colonization diagnosed by next-generation sequencing (NGS) and explore the usefulness of the number of P. jirovecii sequence reads for the diagnosis of P. jirovecii pneumonia. METHODS We examined the NGS results for P. jirovecii in respiratory samples collected from patients and analysed their clinical, radiological and microbiological characteristics. RESULTS Among 285 respiratory samples collected over a 12-month period (January to December 2022), P. jirovecii sequences were detected in 56 samples from 53 patients. Fifty (94.3%) of the 53 patients were HIV-negative. Following our case definitions, 37 (69.8%) and 16 (30.2%) of the 53 patients had P. jirovecii infection and colonization respectively. P. jirovecii infection was associated with presence of underlying disease with immunosuppression (94.6% vs 18.8%, P < 0.05), positive serum 1,3-β-D-glucan (41.2% vs 0%, P < 0.01) and higher number of P. jirovecii sequence reads (P < 0.005). In contrast, P. jirovecii colonization was associated with the male sex (93.8% vs 54.1%, P < 0.01), another definitive infectious disease diagnosis of the respiratory tract (43.8% vs 2.7%, P < 0.001) and higher survival (100% vs 67.6%, P < 0.01). Although P. jirovecii pneumonia was associated with higher number of P. jirovecii reads in respiratory samples, only a sensitivity of 82.14% and a specificity of 68.75% could be achieved. CONCLUSION Detection of P. jirovecii sequences in respiratory samples has to be interpreted discreetly. A combination of clinical, radiological and laboratory findings is still the most crucial in determining whether a particular case is genuine P. jirovecii pneumonia.
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Affiliation(s)
- Fanfan Xing
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Chaowen Deng
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Zhendong Luo
- Department of Radiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Shan Zou
- Department of Adult Intensive Care, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Min Liu
- Department of Respiratory Medicine, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Haiyan Ye
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Linlin Sun
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Chi-Ching Tsang
- School of Medical and Health Sciences, Tung Wah College, Homantin, Hong Kong, China
| | - Simon K F Lo
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Susanna K P Lau
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.
| | - Patrick C Y Woo
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.
- Doctoral Program in Translational Medicine and Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan.
- The iEGG and Animal Biotechnology Research Center, National Chung Hsing University, Taichung 402, Taiwan.
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Zhang X, Zhang L, Li Y, Wang N, Zhang Y. Clinical performance of metagenomic next-generation sequencing for diagnosis of invasive fungal disease after hematopoietic cell transplant. Front Cell Infect Microbiol 2024; 14:1210857. [PMID: 38590441 PMCID: PMC11000502 DOI: 10.3389/fcimb.2024.1210857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 03/04/2024] [Indexed: 04/10/2024] Open
Abstract
Background Timely diagnosis and appropriate antifungal therapy are critical for improving the prognosis of patients with invasive fungal disease (IFD) after hematopoietic stem cell transplantation (HSCT). We evaluated the performance of metagenomic next-generation sequencing (mNGS) and conventional microbiological testing (CMT), as well as the diagnosis, therapeutic management, and outcomes of IFD after HSCT. Methods We retrospectively studied 189 patients who underwent HSCT and were considered at risk for IFD. In total, 46 patients with IFD were enrolled in this study. The IFD consensus was followed for classifying IFD incidents. Results Forty-six patients were diagnosed with proven/probable (n = 12), possible (n = 27), and undefined (n = 7) IFD. Aspergillus was the most commonly detected fungal genus. Mucormycosis was found in 15 patients; two had Aspergillus, and one had Candida infections. Compared to CMT, mNGS significantly reduced the time required to identify pathogens (P = 0.0016). mNGS had a much higher sensitivity than CMT (84.78% vs. 36.96%; P < 0.0001). A total of 76.09% of patients received antifungal prophylaxis during fungal infections. All Pneumocystis infections occurred later than 100 days after transplantation. Among patients with Pneumocystis infection, 71.43% occurred following sulfonamide withdrawal, and subsequent treatment with sulfonamide alone or in combination with other drugs was effective. Based on the empirical antifungal treatment, the dosages, modes of administration, frequency of administration, or antifungal of 55.26% of the patients were changed according to the mNGS results. The 4-year overall survival rate of patients diagnosed with IFD after transplantation was 71.55% (95% CI, 55.18%-85.82%). Hypoproteinemia and corticosteroid use are independent risk factors for IFD. Conclusion mNGS, which has a high sensitivity and a short detection time, aids in the diagnosis and prognosis of pathogenic fungi. As a powerful technology, mNGS can influence treatment decisions in patients with IFD following HSCT.
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Affiliation(s)
- Xiaoying Zhang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Lingfeng Zhang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yun Li
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Na Wang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yicheng Zhang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Key Laboratory of Organ Transplantation, Ministry of Education, NHC Key Laboratory of Organ Transplantation, Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, China
- Immunotherapy Research Center for Hematologic Diseases of Hubei Province, Wuhan, Hubei, China
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Gudisa R, Harchand R, Rudramurthy SM. Nucleic-Acid-Based Molecular Fungal Diagnostics: A Way to a Better Future. Diagnostics (Basel) 2024; 14:520. [PMID: 38472992 DOI: 10.3390/diagnostics14050520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/20/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
The world has seen a tremendous increase in the number of fungal infections during the past two decades. Recently, the World Health Organisation released the pathogen priority list for fungal infections, signifying the importance of these infections in the fields of research and public health. Microbiology laboratories demand an upgrade in the diagnostic system to keep up with the increased burden of these infections. Diagnosis of fungal infections using conventional techniques has always faced limitations in terms of specificity, sensitivity, and turnaround time. Although these methods are the core pillars of the diagnosis, there is an increased need for molecular approaches. Molecular techniques have revolutionised the field of fungal diagnostics. The diverse array of molecular techniques, including techniques like Polymerase Chain Reaction (PCR), have emerged as a cornerstone in fungal diagnostics. Molecular techniques have transformed fungal diagnostics, providing powerful tools for the rapid and accurate identification of pathogens. As these technologies continue to evolve, their integration into routine clinical practice holds the promise of improving patient outcomes through timely and targeted antifungal interventions. This review will cover the molecular approaches involved in fungal diagnostics, moving from the basic techniques to the advanced-level nucleic-acid-based molecular approaches providing a high throughput and decreased turnaround time for the diagnosis of serious fungal infections.
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Affiliation(s)
- Rajendra Gudisa
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Ritika Harchand
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Shivaprakash M Rudramurthy
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh 160012, India
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Nafea AM, Wang Y, Wang D, Salama AM, Aziz MA, Xu S, Tong Y. Application of next-generation sequencing to identify different pathogens. Front Microbiol 2024; 14:1329330. [PMID: 38348304 PMCID: PMC10859930 DOI: 10.3389/fmicb.2023.1329330] [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: 10/28/2023] [Accepted: 12/18/2023] [Indexed: 02/15/2024] Open
Abstract
Early and precise detection and identification of various pathogens are essential for epidemiological monitoring, disease management, and reducing the prevalence of clinical infectious diseases. Traditional pathogen detection techniques, which include mass spectrometry, biochemical tests, molecular testing, and culture-based methods, are limited in application and are time-consuming. Next generation sequencing (NGS) has emerged as an essential technology for identifying pathogens. NGS is a cutting-edge sequencing method with high throughput that can create massive volumes of sequences with a broad application prospects in the field of pathogen identification and diagnosis. In this review, we introduce NGS technology in detail, summarizes the application of NGS in that identification of different pathogens, including bacteria, fungi, and viruses, and analyze the challenges and outlook for using NGS to identify clinical pathogens. Thus, this work provides a theoretical basis for NGS studies and provides evidence to support the application of NGS in distinguishing various clinical pathogens.
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Affiliation(s)
- Aljuboori M. Nafea
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
- College of Medicine, Department of Microbiology, Ibn Sina University of Medical and Pharmaceutical Science, Baghdad, Iraq
| | - Yuer Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Duanyang Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Ahmed M. Salama
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing, China
- Medical Laboratory at Sharkia Health Directorate, Ministry of Health, Sharkia, Egypt
| | - Manal A. Aziz
- College of Medicine, Department of Microbiology, Ibn Sina University of Medical and Pharmaceutical Science, Baghdad, Iraq
| | - Shan Xu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
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Overbeek R, Leitl CJ, Stoll SE, Wetsch WA, Kammerer T, Mathes A, Böttiger BW, Seifert H, Hart D, Dusse F. The Value of Next-Generation Sequencing in Diagnosis and Therapy of Critically Ill Patients with Suspected Bloodstream Infections: A Retrospective Cohort Study. J Clin Med 2024; 13:306. [PMID: 38256440 PMCID: PMC10816005 DOI: 10.3390/jcm13020306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 12/30/2023] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
Bloodstream infection (BSI), a frequent cause of severe sepsis, is a life-threatening complication in critically ill patients and still associated with a high mortality rate. Rapid pathogen identification from blood is crucial for an early diagnosis and the treatment of patients with suspected BSI. For this purpose, novel diagnostic tools on the base of genetic analysis have emerged for clinical application. The aim of this study was to assess the diagnostic value of additional next-generation sequencing (NGS) pathogen test for patients with suspected BSI in a surgical ICU and its potential impact on antimicrobial therapy. In this retrospective single-centre study, clinical data and results from blood culture (BC) and NGS pathogen diagnostics were analysed for ICU patients with suspected BSI. Consecutive changes in antimicrobial therapy and diagnostic procedures were evaluated. Results: 41 cases with simultaneous NGS and BC sampling were assessed. NGS showed a statistically non-significant higher positivity rate than BC (NGS: 58.5% (24/41 samples) vs. BC: 21.9% (9/41); p = 0.056). NGS detected eight different potentially relevant bacterial species, one fungus and six different viruses, whereas BC detected four different bacterial species and one fungus. NGS results affected antimicrobial treatment in 7.3% of cases. Conclusions: NGS-based diagnostics have the potential to offer a higher positivity rate than conventional culture-based methods in patients with suspected BSI. Regarding the high cost, their impact on anti-infective therapy is currently limited. Larger randomized prospective clinical multicentre studies are required to assess the clinical benefit of this novel diagnostic technology.
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Affiliation(s)
- Remco Overbeek
- Department of Anaesthesiology and Intensive Care Medicine, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Christoph J. Leitl
- Department of Anaesthesiology and Intensive Care Medicine, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Sandra E. Stoll
- Department of Anaesthesiology and Intensive Care Medicine, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Wolfgang A. Wetsch
- Department of Anaesthesiology and Intensive Care Medicine, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Tobias Kammerer
- Department of Anaesthesiology and Intensive Care Medicine, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Alexander Mathes
- Department of Anaesthesiology and Intensive Care Medicine, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Bernd W. Böttiger
- Department of Anaesthesiology and Intensive Care Medicine, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Harald Seifert
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50935 Cologne, Germany
| | - Dominique Hart
- Department of Anaesthesiology and Intensive Care Medicine, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Fabian Dusse
- Department of Anaesthesiology and Intensive Care Medicine, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
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Shi Y, Peng JM, Hu XY, Yang QW, Wang Y. Metagenomic next-generation sequencing for detecting Aspergillosis pneumonia in immunocompromised patients: a retrospective study. Front Cell Infect Microbiol 2023; 13:1209724. [PMID: 38188627 PMCID: PMC10770824 DOI: 10.3389/fcimb.2023.1209724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 12/07/2023] [Indexed: 01/09/2024] Open
Abstract
Purpose The identification of Aspergillus by metagenomic next-generation sequencing (mNGS) remains a challenging task due to the difficulty of nucleic acid extraction. The objective of this study was to determine whether mNGS could provide an accurate and efficient method for detecting invasive pulmonary aspergillosis (IPA) in immunocompromised patients (ICP). Methods A total of 133 ICP admitted to the ICU between January 2020 and September 2022 were enrolled in the study, of which 46 were diagnosed with IPA and 87 were non-IPA cases. The bronchoalveolar lavage fluid (BALF) was analyzed for the presence of Aspergillosis and other co-pathogens using mNGS, and its diagnostic performance was compared to conventional microbial tests (CMTs) that included smear, cultures, serum and BALF galactomannan (GM) test. Clinical composite diagnosis was used as the reference standard. Results mNGS had a sensitivity, specificity, and accuracy of 82.6%, 97.7%, and 92.5%, respectively, in diagnosing IPA. These findings were comparable to those of the combination of multiple CMTs. Interestingly, the sensitivity of mNGS was superior to that of any single CMT method, as demonstrated by comparisons with smears (8.7%, P < 0.001), culture (39.1%, P < 0.001), serum GM (23.9%, P < 0.001) and BALF GM (69.6%, P = 0.031). mNGS was capable of accurately distinguish strains of Aspergillus genus, with a consistency of 77.8% with culture. Furthermore, mNGS also identified A. fumigatus, A. flavus, A. terrestris, A. oryzae and Mucor spp. in culture-negative cases. The sequencing reads of Aspergillus by mNGS exhibited extensive variation, ranging from 11 to1702. A positive correlation was observed between the optical density index of BALF GM and unique reads by mNGS (r = 0.607, P = 0.001) in BALF-GM positive patients. Notably, mNGS was able to diagnose 35 out of 37 cases with mixed infection, with P. jirovecii and cytomegalovirus being the most common co-pathogens. Conclusions mNGS presents a feasible and remarkably sensitive approach for detecting Aspergillus in ICP, thereby serving as a valuable adjunctive tool to CMT. Furthermore, mNGS's ability to accurately identify fungal species and co-pathogens can assist in guiding appropriate antimicrobial therapy.
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Affiliation(s)
- Yan Shi
- Department of Medical ICU, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Jin-Min Peng
- Department of Medical ICU, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Xiao-Yun Hu
- Department of Medical ICU, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Qi-Wen Yang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yao Wang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
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9
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Douglas AP, Stewart AG, Halliday CL, Chen SCA. Outbreaks of Fungal Infections in Hospitals: Epidemiology, Detection, and Management. J Fungi (Basel) 2023; 9:1059. [PMID: 37998865 PMCID: PMC10672668 DOI: 10.3390/jof9111059] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 10/17/2023] [Accepted: 10/26/2023] [Indexed: 11/25/2023] Open
Abstract
Nosocomial clusters of fungal infections, whilst uncommon, cannot be predicted and are associated with significant morbidity and mortality. Here, we review reports of nosocomial outbreaks of invasive fungal disease to glean insight into their epidemiology, risks for infection, methods employed in outbreak detection including genomic testing to confirm the outbreak, and approaches to clinical and infection control management. Both yeasts and filamentous fungi cause outbreaks, with each having general and specific risks. The early detection and confirmation of the outbreak are essential for diagnosis, treatment of affected patients, and termination of the outbreak. Environmental sampling, including the air in mould outbreaks, for the pathogen may be indicated. The genetic analysis of epidemiologically linked isolates is strongly recommended through a sufficiently discriminatory approach such as whole genome sequencing or a method that is acceptably discriminatory for that pathogen. An analysis of both linked isolates and epidemiologically unrelated strains is required to enable genetic similarity comparisons. The management of the outbreak encompasses input from a multi-disciplinary team with epidemiological investigation and infection control measures, including screening for additional cases, patient cohorting, and strict hygiene and cleaning procedures. Automated methods for fungal infection surveillance would greatly aid earlier outbreak detection and should be a focus of research.
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Affiliation(s)
- Abby P. Douglas
- National Centre for Infections in Cancer, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
- Department of Infectious Diseases, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC 3000, Australia
- Department of Infectious Diseases, Austin Health, Heidelberg, VIC 3084, Australia
| | - Adam G. Stewart
- Centre for Clinical Research, Faculty of Medicine, Royal Brisbane and Women’s Hospital Campus, The University of Queensland, Herston, QLD 4006, Australia;
| | - Catriona L. Halliday
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, Sydney, NSW 2145, Australia; (C.L.H.); (S.C.-A.C.)
| | - Sharon C.-A. Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, Sydney, NSW 2145, Australia; (C.L.H.); (S.C.-A.C.)
- Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2050, Australia
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Chen G, Ma N, Zhu D, Zhou H, Liang Q, Meng J, Shen Y, Liu H, Liu L, He Z, Qin Z. Accurate diagnosis of bronchopulmonary Talaromyces marneffei infection in an anti-IFN-γ autoantibodies positive patient assisted by endobronchial ultrasound-guided TBNA and mNGS: a case report. Front Cell Infect Microbiol 2023; 13:1186335. [PMID: 37860065 PMCID: PMC10583546 DOI: 10.3389/fcimb.2023.1186335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 09/18/2023] [Indexed: 10/21/2023] Open
Abstract
RATIONALE T. marneffei is opportunistic and dimorphic fungus, which can cause systemic mycosis in human beings. It's being difficult to obtain histopathological or microbiological evidence in T. marneffei infection. We reported a rare non-HIV case of T. marneffei infection of bronchopulmonary and mediastinal lymph nodes which was diagnosed by EBUS-TBNA combined with mNGS. The high titer of anti-IFN-γ autoantibodies in serum was probably the cause of T. marneffei infection,which has yet to be fully known. PATIENT CONCERNS A 56-year-old Chinese man presented with a 5-month history of intermittent low or high fever and dry cough, followed by fatigue, night sweating, and chest pain when coughing. A large hilar lesion in the left lung and multiple mediastinal lymph node enlargements were found on his chest CT scan. DIAGNOSES The patient received EBUS-TBNA of hilar tissue and lymph node biopsy for mNGS at the second Ultrasonic bronchoscopy. No fungal hyphae or spores were found in the histopathology. There were high sequencing reads of T. marneffei in samples of lymph node fluid and bronchogenesis tissue detected by mNGS. His plasma anti-IFN-γ autoantibodies level was positive with a high titer at 1:2500↑. INTERVENTION The patient went through atrial fibrillation at the first dose of amphotericin B liposomes and treated with voriconazole later. OUTCOMES His fever, cough and dyspnea quickly disappeared since the fourth day of treatment. After six months, there was not any focus in his chest CT scans. But his plasma anti-IFN-γ autoantibodies remained unchanged. LESSONS Complementing the traditional laboratory and bronchoscopy, mNGS combined with EBUS-TBNA facilitate rapid and precise diagnosis of bronchopulmonary mediastinal lymph nodes T. marneffei infection. Clinicians should be aware of anti-INF-γ autoantibodies in opportunistic infections of non-HIV patients.
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Affiliation(s)
- Guirong Chen
- Department of Pulmonary and Critical Care Medicine, The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Nan Ma
- Department of Pulmonary and Critical Care Medicine, The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Donglan Zhu
- Department of Pulmonary and Critical Care Medicine, The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Huaihai Zhou
- Department of Pulmonary and Critical Care Medicine, The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Qiumei Liang
- Department of Pulmonary and Critical Care Medicine, The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Jianfeng Meng
- Department of Pulmonary and Critical Care Medicine, The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Yin Shen
- Department of International Medicine, The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Hang Liu
- Department of Pulmonary and Critical Care Medicine, The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Liu Liu
- Department of International Medicine, The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Zhiyi He
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Zhiqiang Qin
- Department of Pulmonary Medicine, Foresea Life Insurance Guangxi Hospital, Nanning, China
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Yu L, Zhang B, Shi J, Wang M, Wan H. Osteoarticular infection caused by Talaromyces Marneffei and Salmonella in a person living with HIV: a case report. BMC Infect Dis 2023; 23:560. [PMID: 37641024 PMCID: PMC10463968 DOI: 10.1186/s12879-023-08554-9] [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: 02/16/2023] [Accepted: 08/22/2023] [Indexed: 08/31/2023] Open
Abstract
INTRODUCTION Talaromycosis is a common invasive fungal disease in patients with HIV. However, its association with bone destruction is unusual in AIDS patients with talaromycosis. CASE PRESENTATION This report covers the case of a 38-year-old male AIDS patient coinfected with Talaromyces marneffei and Salmonella. The case, which involved bone destruction, was identified via metagenomic next-generation sequencing (mNGS). Following treatment with a combination of amphotericin B and piperacillin-tazobactam, the patient's elbow motion noticeably improved. Imaging findings revealed that the progression of bony destruction had halted. CONCLUSION Bone damage due to Talaromyces marneffei infection is infrequent in HIV-positive patients. Therefore, healthcare professionals must be vigilant for potential bone lesions associated with this type of infection. Prompt diagnosis and antimicrobial treatment are crucial.
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Affiliation(s)
- Lele Yu
- Department II of Infectious Diseases, Affiliated Hangzhou Xixi Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Binhai Zhang
- Department II of Infectious Diseases, Affiliated Hangzhou Xixi Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jinchuan Shi
- Department II of Infectious Diseases, Affiliated Hangzhou Xixi Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Mengyan Wang
- Department II of Infectious Diseases, Affiliated Hangzhou Xixi Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hu Wan
- Department II of Infectious Diseases, Affiliated Hangzhou Xixi Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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Wang Y, Mo X, Zhang J, Yan Z, Fang Y, Deng W, Xu J, Peng J, Miao Y. Clinical features of Talaromyces marneffei infection in HIV-positive and HIV-negative individuals: A retrospective study in southern China. Med Mycol 2023; 61:myad083. [PMID: 37553136 DOI: 10.1093/mmy/myad083] [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: 04/27/2023] [Revised: 07/31/2023] [Accepted: 08/07/2023] [Indexed: 08/10/2023] Open
Abstract
Talaromyces marneffei (TSM) is a temperature-dependent dimorphic fungus endemic to Southeast Asia and southern China. As the number of people at risk of TSM infection continues to increase, the clinical manifestations are becoming increasingly complex, posing challenges for clinical management. In this study, we analyzed the medical records of 99 patients (71 human immunodeficiency virus [HIV]-positive and 28 HIV-negative) diagnosed with TSM infection from January 1, 2017, to December 31, 2022, in southern China and compared the clinical manifestations in HIV-positive and HIV-negative patients. Most patients (83/99, 84%) were male. The incidence of skin and soft tissue involvement (48% vs. 21%, P = .016); disseminated infection with blood circulation, hematopoietic, lymphatic, alimentary, or central nervous system involvement (69% vs. 36%, P = .002); and gastrointestinal bleeding (33% vs. 9%, P = .023) was higher in the HIV-positive group than the HIV-negative group. The HIV-positive group also had significantly higher alanine aminotransferase (ALT) levels (31 [26-42] vs. 14 [11-16] U/l, P < .001) and ALT/aspartate transaminase ratio (1.9 [1.5-2.2] vs. 1.3 [1.1-1.6], P = .006) than the HIV-negative group. The time to diagnosis (5.5 ± 1.1 vs. 5.1 ± 1.4 days, P = .103), antifungal regimen (P = .278), case fatality rate (20% vs. 21%, P = .849), and relapse/reinfection rate (11% vs. 19%, P = .576) did not differ significantly between the HIV-positive and HIV-negative groups. Poor antiretroviral therapy adherence (OR = 26.19, 95%CI 3.26-210.70, P = .002), advanced age (OR = 1.13, 95%CI 1.03-1.23, P = .010), and Epstein-Barr virus co-infection (OR = 37.13, 95%CI 3.03-455.64, P = .005) were independent risk factors for all-cause mortality from TSM infection in HIV-positive patients. Overall, the predominant infection sites, clinical manifestations, and complications of TSM infection differed by HIV status. However, with prompt diagnosis and appropriate treatment, HIV-positive patients with TSM infection can have similar outcomes to HIV-negative patients.
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Affiliation(s)
- Yuchen Wang
- Department of Transplantation, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Xichao Mo
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Jian Zhang
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Ziyan Yan
- Department of Transplantation, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Yiling Fang
- Department of Transplantation, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Wenfeng Deng
- Department of Transplantation, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Jian Xu
- Department of Transplantation, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Jie Peng
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Yun Miao
- Department of Transplantation, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
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Notario E, Visci G, Fosso B, Gissi C, Tanaskovic N, Rescigno M, Marzano M, Pesole G. Amplicon-Based Microbiome Profiling: From Second- to Third-Generation Sequencing for Higher Taxonomic Resolution. Genes (Basel) 2023; 14:1567. [PMID: 37628619 PMCID: PMC10454624 DOI: 10.3390/genes14081567] [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: 06/21/2023] [Revised: 07/25/2023] [Accepted: 07/27/2023] [Indexed: 08/27/2023] Open
Abstract
The 16S rRNA amplicon-based sequencing approach represents the most common and cost-effective strategy with great potential for microbiome profiling. The use of second-generation sequencing (NGS) technologies has led to protocols based on the amplification of one or a few hypervariable regions, impacting the outcome of the analysis. Nowadays, comparative studies are necessary to assess different amplicon-based approaches, including the full-locus sequencing currently feasible thanks to third-generation sequencing (TGS) technologies. This study compared three different methods to achieve the deepest microbiome taxonomic characterization: (a) the single-region approach, (b) the multiplex approach, covering several regions of the target gene/region, both based on NGS short reads, and (c) the full-length approach, which analyzes the whole length of the target gene thanks to TGS long reads. Analyses carried out on benchmark microbiome samples, with a known taxonomic composition, highlighted a different classification performance, strongly associated with the type of hypervariable regions and the coverage of the target gene. Indeed, the full-length approach showed the greatest discriminating power, up to species level, also on complex real samples. This study supports the transition from NGS to TGS for the study of the microbiome, even if experimental and bioinformatic improvements are still necessary.
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Affiliation(s)
- Elisabetta Notario
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, 70126 Bari, Italy; (E.N.); (B.F.); (C.G.)
| | - Grazia Visci
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, 70126 Bari, Italy;
| | - Bruno Fosso
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, 70126 Bari, Italy; (E.N.); (B.F.); (C.G.)
| | - Carmela Gissi
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, 70126 Bari, Italy; (E.N.); (B.F.); (C.G.)
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, 70126 Bari, Italy;
- CoNISMa, Consorzio Nazionale Interuniversitario per le Scienze del Mare, 00196 Roma, Italy
| | | | - Maria Rescigno
- IRCCS Humanitas Research Hospital, 20089 Rozzano, Italy;
- Department of Biomedical Sciences, Humanitas University, 20072 Pieve Emanuele, Italy
| | - Marinella Marzano
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, 70126 Bari, Italy;
| | - Graziano Pesole
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, 70126 Bari, Italy; (E.N.); (B.F.); (C.G.)
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, 70126 Bari, Italy;
- Consorzio Interuniversitario Biotecnologie, 34148 Trieste, Italy
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14
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Wernery U, Teng JLL, Ma Y, Kinne J, Yeung ML, Anas S, Lau SKP, Woo PCY. Usefulness of Next-Generation Sequencing in Excluding Bovine Leukemia Virus as a Cause of Adult Camel Leukosis in Dromedaries. Pathogens 2023; 12:995. [PMID: 37623955 PMCID: PMC10459180 DOI: 10.3390/pathogens12080995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/20/2023] [Accepted: 07/25/2023] [Indexed: 08/26/2023] Open
Abstract
Adult camel leukosis is an emerging hematological and neoplastic disease in dromedaries. It has been hypothesized that bovine leukemia virus (BLV) or its genetic variants may be associated with adult camel leukosis. In this study, we used next-generation sequencing (NGS) to detect all possible viruses in five lung samples from five dromedaries with histopathological evidence of adult camel leukosis and four tissue samples from two control dromedaries. A total throughput of 114.7 Gb was achieved, with an average of 12.7 Gb/sample. For each sample, all the pair-end 151-bp reads were filtered to remove rRNA sequences, bacterial genomes and redundant sequences, resulting in 1-7 Gb clean reads, of which <3% matched to viruses. The largest portion of these viral sequences was composed of bacterial phages. About 100-300 reads in each sample matched "multiple sclerosis-associated retrovirus", but manual analysis showed that they were only repetitive sequences commonly present in mammalian genomes. All viral reads were also extracted for analysis, confirming that no BLV or its genetic variants or any other virus was detected in the nine tissue samples. NGS is not only useful for detecting microorganisms associated with infectious diseases, but also important for excluding an infective cause in scenarios where such a possibility is suspected.
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Affiliation(s)
- Ulrich Wernery
- Central Veterinary Research Laboratory, Dubai, United Arab Emirates; (J.K.)
| | - Jade L. L. Teng
- Faculty of Dentistry, The University of Hong Kong, Hong Kong Special Administrative Region, China;
| | - Yuanchao Ma
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China; (Y.M.); (M.-L.Y.); (S.K.P.L.)
| | - Joerg Kinne
- Central Veterinary Research Laboratory, Dubai, United Arab Emirates; (J.K.)
| | - Man-Lung Yeung
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China; (Y.M.); (M.-L.Y.); (S.K.P.L.)
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen 518053, China
- Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Safna Anas
- Central Veterinary Research Laboratory, Dubai, United Arab Emirates; (J.K.)
| | - Susanna K. P. Lau
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China; (Y.M.); (M.-L.Y.); (S.K.P.L.)
| | - Patrick C. Y. Woo
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China; (Y.M.); (M.-L.Y.); (S.K.P.L.)
- Doctoral Program in Translational Medicine and Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan
- The iEGG and Animal Biotechnology Research Center, National Chung Hsing University, Taichung 402, Taiwan
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15
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Xing F, Xia Y, Lu Q, Lo SKF, Lau SKP, Woo PCY. Rapid diagnosis of fatal Nocardia kroppenstedtii bacteremic pneumonia and empyema thoracis by next-generation sequencing: a case report. Front Med (Lausanne) 2023; 10:1226126. [PMID: 37534314 PMCID: PMC10392123 DOI: 10.3389/fmed.2023.1226126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 06/27/2023] [Indexed: 08/04/2023] Open
Abstract
Nocardia species do not replicate as rapidly as other pyogenic bacteria and nocardial infections can be highly fatal, particularly in immunocompromised patients. Here, we present the first report of fatal Nocardia kroppenstedtii bacteremic pneumonia and empyema thoracis diagnosed by next-generation sequencing (NGS) using the Oxford Nanopore Technologies' MinION device. The bacterium was not identified by matrix-assisted laser desorption ionization-time of flight mass spectrometry. Due to its low equipment cost, short turn-around-time, and portable size, the Oxford Nanopore Technologies' MinION device is a useful platform for NGS in routine clinical microbiology laboratories.
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Affiliation(s)
- Fanfan Xing
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong—Shenzhen Hospital, Shenzhen, China
| | - Yao Xia
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Qianyun Lu
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong—Shenzhen Hospital, Shenzhen, China
| | - Simon K. F. Lo
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong—Shenzhen Hospital, Shenzhen, China
| | - Susanna K. P. Lau
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Patrick C. Y. Woo
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Doctoral Program in Translational Medicine and Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
- The iEGG and Animal Biotechnology Research Center, National Chung Hsing University, Taichung, Taiwan
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16
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Li X, Li Z, Ye J, Ye W. Diagnostic performance of metagenomic next-generation sequencing for Pneumocystis jirovecii pneumonia. BMC Infect Dis 2023; 23:455. [PMID: 37430211 PMCID: PMC10331973 DOI: 10.1186/s12879-023-08440-4] [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: 03/23/2023] [Accepted: 07/03/2023] [Indexed: 07/12/2023] Open
Abstract
OBJECTIVE Pneumocystis jirovecii pneumonia (PJP) can be a life-threatening opportunistic infection. We aimed to evaluate the diagnostic accuracy of metagenomic next-generation sequencing (mNGS) for PJP. METHODS A comprehensive electronic literature search of Web of Knowledge, PubMed, Cochrane Library, CNKI and Wanfang data was performed. Bivariate analysis was conducted to calculate the pooled sensitivity, specificity, diagnostic odds ratio (DOR), the area under the summary receiver operator characteristic (SROC) curve and the Q-point value (Q*). RESULTS The literature search resulted in 9 studies with a total of 1343 patients, including 418 cases diagnosed with PJP and 925 controls. The pooled sensitivity of mNGS for diagnosis of PJP was 0.974 [95% confidence interval (CI), 0.953-0.987]. The pooled specificity was 0.943 (95% CI, 0.926-0.957), the DOR was 431.58 (95% CI, 186.77-997.27), the area under the SROC curve was 0.987, and the Q* was 0.951. The I2 test indicated no heterogeneity between studies. The Deek funnel test suggested no potential publication bias. Subgroup analyses showed that the area under the SROC curve of mNGS for diagnosis of PJP in immunocompromised and non-HIV patients was 0.9852 and 0.979, respectively. CONCLUSIONS Current evidence indicates that mNGS exhibits excellent accuracy for the diagnosis of PJP. The mNGS is a promising tool for assessment of PJP in both immunocompromised and non-HIV patients.
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Affiliation(s)
- Xuefang Li
- Department of Infectious Diseases, Zhejiang Hospital, 1229 Gudun Road, Xihu District, Hangzhou, 310013, Zhejiang Province, People's Republic of China
| | - Zhijun Li
- Department of Respiratory Diseases, Zhejiang Hospital, 1229 Gudun Road, Xihu District, Hangzhou, 310013, Zhejiang Province, People's Republic of China
| | - Jian Ye
- Department of Respiratory Diseases, Zhejiang Hospital, 1229 Gudun Road, Xihu District, Hangzhou, 310013, Zhejiang Province, People's Republic of China
| | - Wu Ye
- Department of Respiratory Diseases, Zhejiang Hospital, 1229 Gudun Road, Xihu District, Hangzhou, 310013, Zhejiang Province, People's Republic of China.
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Zaongo SD, Zhang F, Chen Y. An Overview of Diagnostic and Management Strategies for Talaromycosis, an Underrated Disease. J Fungi (Basel) 2023; 9:647. [PMID: 37367583 DOI: 10.3390/jof9060647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 05/31/2023] [Accepted: 06/02/2023] [Indexed: 06/28/2023] Open
Abstract
Underrated and neglected, talaromycosis is a life-threatening fungal disease endemic to the tropical and subtropical regions of Asia. In China, it has been reported that talaromycosis mortality doubles from 24 to 50% when the diagnosis is delayed, and reaches 100% when the diagnosis is missed. Thus, the accurate diagnosis of talaromycosis is of utmost importance. Herein, in the first part of this article, we provide an extensive review of the diagnostic tools used thus far by physicians in the management of cases of talaromycosis. The challenges encountered and the perspectives which may aid in the discovery of more accurate and reliable diagnostic approaches are also discussed. In the second part of this review, we discuss the drugs used to prevent and treat T. marneffei infection. Alternative therapeutic options and potential drug resistance reported in the contemporary literature are also discussed. We aim to guide researchers towards the discovery of novel approaches to prevent, diagnose, and treat talaromycosis, and therefore improve the prognosis for those afflicted by this important disease.
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Affiliation(s)
- Silvere D Zaongo
- Department of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing 400036, China
| | - Fazhen Zhang
- Fifth Unit for Tuberculosis, Chongqing Public Health Medical Center, Chongqing 400036, China
| | - Yaokai Chen
- Department of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing 400036, China
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Kanaujia R, Singh S, Rudramurthy SM. Aspergillosis: an Update on Clinical Spectrum, Diagnostic Schemes, and Management. CURRENT FUNGAL INFECTION REPORTS 2023; 17:1-12. [PMID: 37360858 PMCID: PMC10157594 DOI: 10.1007/s12281-023-00461-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/18/2023] [Indexed: 06/28/2023]
Abstract
Purpose of Review This review gives an overview of the diseases caused by Aspergillus, including a description of the species involved and the infected clinical systems. We provide insight into the various diagnostic methods available for diagnosing aspergillosis, particularly invasive aspergillosis (IA), including the role of radiology, bronchoscopy, culture, and non-culture-based microbiological methods. We also discuss the available diagnostic algorithms for the different disease conditions. This review also summarizes the main aspects of managing infections due to Aspergillus spp., such as antifungal resistance, choice of antifungals, therapeutic drug monitoring, and new antifungal alternatives. Recent Findings The risk factors for this infection continue to evolve with the development of many biological agents that target the immune system and the increase of viral illnesses such as coronavirus disease. Due to the limitations of present mycological test methods, establishing a fast diagnosis is frequently difficult, and reports of developing antifungal resistance further complicate the management of aspergillosis. Many commercial assays, like AsperGenius®, MycAssay Aspergillus®, and MycoGENIE®, have the advantage of better species-level identification and concomitant resistance-associated mutations. Fosmanogepix, ibrexafungerp, rezafungin, and olorofim are newer antifungal agents in the pipeline exhibiting remarkable activity against Aspergillus spp. Summary The fungus Aspergillus is found ubiquitously around the world and can cause various infections, from harmless saprophytic colonization to severe IA. Understanding the diagnostic criteria to be used in different patient groups and the local epidemiological data and antifungal susceptibility profile is critical for optimal patient management.
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Affiliation(s)
- Rimjhim Kanaujia
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research PGIMER, Chandigarh, India
| | - Shreya Singh
- Department of Microbiology, Dr B R Ambedkar State Institute of Medical Sciences (AIMS), Mohali, Punjab India
| | - Shivaprakash M. Rudramurthy
- Mycology Division, Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research PGIMER, Chandigarh, India
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Wang F, Han R, Chen S. An Overlooked and Underrated Endemic Mycosis-Talaromycosis and the Pathogenic Fungus Talaromyces marneffei. Clin Microbiol Rev 2023; 36:e0005122. [PMID: 36648228 PMCID: PMC10035316 DOI: 10.1128/cmr.00051-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Talaromycosis is an invasive mycosis endemic in tropical and subtropical Asia and is caused by the pathogenic fungus Talaromyces marneffei. Approximately 17,300 cases of T. marneffei infection are diagnosed annually, and the reported mortality rate is extremely high (~1/3). Despite the devastating impact of talaromycosis on immunocompromised individuals, particularly HIV-positive persons, and the increase in reported occurrences in HIV-uninfected persons, diagnostic and therapeutic approaches for talaromycosis have received far too little attention worldwide. In 2021, scientists living in countries where talaromycosis is endemic raised a global demand for it to be recognized as a neglected tropical disease. Therefore, T. marneffei and the infectious disease induced by this fungus must be treated with concern. T. marneffei is a thermally dimorphic saprophytic fungus with a complicated mycological growth process that may produce various cell types in its life cycle, including conidia, hyphae, and yeast, all of which are associated with its pathogenicity. However, understanding of the pathogenic mechanism of T. marneffei has been limited until recently. To achieve a holistic view of T. marneffei and talaromycosis, the current knowledge about talaromycosis and research breakthroughs regarding T. marneffei growth biology are discussed in this review, along with the interaction of the fungus with environmental stimuli and the host immune response to fungal infection. Importantly, the future research directions required for understanding this serious infection and its causative pathogenic fungus are also emphasized to identify solutions that will alleviate the suffering of susceptible individuals worldwide.
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Affiliation(s)
- Fang Wang
- Intensive Care Unit, Biomedical Research Center, Shenzhen Institute of Translational Medicine, Health Science Center, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen, China
| | - RunHua Han
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Shi Chen
- Intensive Care Unit, Biomedical Research Center, Shenzhen Institute of Translational Medicine, Health Science Center, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen, China
- Department of Burn and Plastic Surgery, Biomedical Research Center, Shenzhen Institute of Translational Medicine, Health Science Center, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen, China
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Pulmonary Histoplasmosis: A Clinical Update. J Fungi (Basel) 2023; 9:jof9020236. [PMID: 36836350 PMCID: PMC9964986 DOI: 10.3390/jof9020236] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
Histoplasma capsulatum, the etiological agent for histoplasmosis, is a dimorphic fungus that grows as a mold in the environment and as a yeast in human tissues. The areas of highest endemicity lie within the Mississippi and Ohio River Valleys of North America and parts of Central and South America. The most common clinical presentations include pulmonary histoplasmosis, which can resemble community-acquired pneumonia, tuberculosis, sarcoidosis, or malignancy; however, certain patients can develop mediastinal involvement or progression to disseminated disease. Understanding the epidemiology, pathology, clinical presentation, and diagnostic testing performance is pivotal for a successful diagnosis. While most immunocompetent patients with mild acute or subacute pulmonary histoplasmosis should receive therapy, all immunocompromised patients and those with chronic pulmonary disease or progressive disseminated disease should also receive therapy. Liposomal amphotericin B is the agent of choice for severe or disseminated disease, and itraconazole is recommended in milder cases or as "step-down" therapy after initial improvement with amphotericin B. In this review, we discuss the current epidemiology, pathology, diagnosis, clinical presentations, and management of pulmonary histoplasmosis.
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21
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Peng L, Shi YB, Zheng L, Hu LQ, Weng XB. Clinical features of patients with talaromycosis marneffei and microbiological characteristics of the causative strains. J Clin Lab Anal 2022; 36:e24737. [PMID: 36268985 DOI: 10.1002/jcla.24737] [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: 07/21/2022] [Revised: 10/02/2022] [Accepted: 10/03/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Talaromyces marneffei (T. marneffei) is a temperature-dependent dimorphic fungus that is mainly prevalent in Southeast Asia and South China and often causes disseminated life-threatening infections. This study aimed to investigate the clinical features and improve the early diagnosis of talaromycosis marneffei in nonendemic areas. METHODS We retrospectively analyzed the medical records of six cases of T. marneffei infection. We describe the clinical manifestations, laboratory tests, and imaging manifestations of the six patients. RESULTS Talaromyces marneffei infection was confirmed by sputum culture, blood culture, tissue biopsy, and metagenomic next-generation sequencing (mNGS). In this study, there were five disseminated-type patients and two HIV patients. One patient died within 24 h, and the others demonstrated considerable improvement after definitive diagnosis. CONCLUSIONS Due to the lack of significant clinical presentations of talaromycosis marneffei, many cases may be easily misdiagnosed in nonendemic areas. It is particularly important to analyze the imaging manifestations and laboratory findings of infected patients. With the rapid development of molecular biology, mNGS may be a rapid and effective diagnostic method.
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Affiliation(s)
- Lei Peng
- School of Medicine, Ningbo University, Ningbo, China
| | - Yu-Bo Shi
- Department of Medical Laboratory, Ningbo First Hospital, Ningbo, China
| | - Lin Zheng
- Department of Medical Laboratory, The Affiliated Hospital of Medical School of Ningbo University, Ningbo, China
| | - Li-Qing Hu
- Department of Medical Laboratory, Ningbo First Hospital, Ningbo, China
| | - Xing-Bei Weng
- School of Medicine, Ningbo University, Ningbo, China.,Department of Medical Laboratory, Ningbo First Hospital, Ningbo, China
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22
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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: 12] [Impact Index Per Article: 6.0] [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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23
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Liu L, Sun B, Ying W, Liu D, Wang Y, Sun J, Wang W, Yang M, Hui X, Zhou Q, Hou J, Wang X. Rapid diagnosis of Talaromyces marneffei infection by metagenomic next-generation sequencing technology in a Chinese cohort of inborn errors of immunity. Front Cell Infect Microbiol 2022; 12:987692. [PMID: 36159645 PMCID: PMC9493038 DOI: 10.3389/fcimb.2022.987692] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/17/2022] [Indexed: 11/13/2022] Open
Abstract
Talaromyces marneffei (T. marneffei) is an opportunistic pathogen. Patients with inborn errors of immunity (IEI) have been increasingly diagnosed with T. marneffei in recent years. The disseminated infection of T. marneffei can be life-threatening without timely and effective antifungal therapy. Rapid and accurate pathogenic microbiological diagnosis is particularly critical for these patients. A total of 505 patients with IEI were admitted to our hospital between January 2019 and June 2022, among whom T. marneffei was detected in 6 patients by metagenomic next-generation sequencing (mNGS), and their clinical and immunological characteristics were summarized. We performed a systematic literature review on T. marneffei infections with published immunodeficiency-related gene mutations. All patients in our cohort were confirmed to have genetic mutations in IL12RB1, IFNGR1, STAT1, STAT3, and CD40LG. T. marneffei was detected in both the blood and lymph nodes of P1 with IL12RB1 mutations, and the clinical manifestations were serious and included recurrent fever, weight loss, severe anemia, splenomegaly and lymphadenopathy, all requiring long-term antifungal therapy. These six patients received antifungal treatment, which relieved symptoms and improved imaging findings. Five patients survived, while one patient died of sepsis after hematopoietic stem cell transplantation. The application of mNGS methods for pathogen detection in IEI patients and comparison with traditional diagnosis methods were investigated. Traditional diagnostic methods and mNGS tests were performed simultaneously in 232 patients with IEI. Compared to the traditional methods, the sensitivity and specificity of mNGS in diagnosing T. marneffei infection were 100% and 98.7%, respectively. The reporting time for T. marneffei detection was approximately 26 hours by mNGS, 3-14 days by culture, and 6-11 days by histopathology. T. marneffei infection was first reported in IEI patients with IL12RB1 gene mutation, which expanded the IEI lineage susceptible to T. marneffei. For IEI patients with T. marneffei infection, we highlight the application of mNGS in pathogenic detection. mNGS is recommended as a front-line diagnostic test for rapidly identifying pathogens in complex and severe infections.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Jia Hou
- *Correspondence: Jia Hou, ; Xiaochuan Wang,
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Clinical impact of next-generation sequencing on laboratory diagnosis of suspected culture-negative meningitis and encephalitis. J Infect 2022; 85:573-607. [PMID: 36037832 DOI: 10.1016/j.jinf.2022.08.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 08/22/2022] [Indexed: 10/31/2022]
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25
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Li W, Zhu H, Wen L, Quan M, Wang L. Application Value of Metagenomics Next-Generation Sequencing (mNGS) in Detection of Mucormycosis after Chemotherapy in Childhood Acute Leukemia. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2022; 2022:7366432. [PMID: 36034963 PMCID: PMC9417758 DOI: 10.1155/2022/7366432] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 07/15/2022] [Indexed: 11/18/2022]
Abstract
Objective To analyze the application of macrogenomics next-generation sequencing (mNGS) in the detection of postchemotherapy trichomoniasis cases in children with acute leukemia. Methods To retrospectively analyze the clinical data of 7 patients with acute leukemia combined with trichomoniasis after chemotherapy in the department of hematology and oncology of Hebei Children's Hospital, and to summarize the characteristics of their postchemotherapy clinical data, diagnostic and therapeutic processes, and outcomes. Results Among the 7 children, 6 cases had acute lymphoblastic leukemia and 1 case had acute myeloid leukemia. mNGS detected trichoderma infection, including 1 case of pulmonary cerebral type and 6 cases of pulmonary type. After treatment, 1 case died, 2 cases were cured, and 4 cases improved. Conclusion The clinical manifestations of trichomoniasis after combined chemotherapy in pediatric acute leukemia lack specificity. Early application of the mNGS assay is of great value.
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Affiliation(s)
- Wenzi Li
- Department of Hematology and Oncology, Hebei Province Children's Hospital, Shijiazhuang City 050031, Hebei Province, China
| | - Hua Zhu
- Hebei Province Children's Hospital Orthopedics Department, Shijiazhuang City 050031, Hebei Province, China
| | - Li Wen
- Department of Hematology and Oncology, Hebei Province Children's Hospital, Shijiazhuang City 050031, Hebei Province, China
| | - Meijie Quan
- Department of Hematology and Oncology, Hebei Province Children's Hospital, Shijiazhuang City 050031, Hebei Province, China
| | - Li Wang
- Department of Hematology and Oncology, Hebei Province Children's Hospital, Shijiazhuang City 050031, Hebei Province, China
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26
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Sun L, Zhang S, Yang Z, Yang F, Wang Z, Li H, Li Y, Sun T. Clinical Application and Influencing Factor Analysis of Metagenomic Next-Generation Sequencing (mNGS) in ICU Patients With Sepsis. Front Cell Infect Microbiol 2022; 12:905132. [PMID: 35909965 PMCID: PMC9326263 DOI: 10.3389/fcimb.2022.905132] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 06/17/2022] [Indexed: 12/03/2022] Open
Abstract
Objective To analyze the clinical application and related influencing factors of metagenomic next-generation sequencing (mNGS) in patients with sepsis in intensive care unit (ICU). Methods The study included 124 patients with severe sepsis admitted to the ICU in the First Affiliated Hospital of Zhengzhou University from June 2020 to September 2021. Two experienced clinicians took blood mNGS and routine blood cultures of patients meeting the sepsis diagnostic criteria within 24 hours after sepsis was considered, and collection the general clinical data. Results mNGS positive rate was higher than traditional blood culture (67.74% vs. 19.35%). APACHE II score [odds ratio (OR)=1.096], immune-related diseases (OR=6.544), and hypertension (OR=2.819) were considered as positive independent factors for mNGS or culture-positive. The sequence number of microorganisms and pathogen detection (mNGS) type had no effect on prognosis. Age (OR=1.016), female (OR=5.963), myoglobin (OR=1.005), and positive virus result (OR=8.531) were independent risk factors of sepsis mortality. Adjusting antibiotics according to mNGS results, there was no statistical difference in the prognosis of patients with sepsis. Conclusion mNGS has the advantages of rapid and high positive rate in the detection of pathogens in patients with severe sepsis. Patients with high APACHE II score, immune-related diseases, and hypertension are more likely to obtain positive mNGS results. The effect of adjusting antibiotics according to mNGS results on the prognosis of sepsis needs to be further evaluated.
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Affiliation(s)
- Limin Sun
- General Intensive Care Unit, Zhengzhou Key Laboratory of Sepsis, Henan Key Laboratory of Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shuguang Zhang
- General Intensive Care Unit, Zhengzhou Key Laboratory of Sepsis, Henan Key Laboratory of Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ziyue Yang
- General Intensive Care Unit, Zhengzhou Key Laboratory of Sepsis, Henan Key Laboratory of Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Fei Yang
- General Intensive Care Unit, Zhengzhou Key Laboratory of Sepsis, Henan Key Laboratory of Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhenhua Wang
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hongqiang Li
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yaoguang Li
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Gene Hospital of Henan Province, Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Tongwen Sun
- General Intensive Care Unit, Zhengzhou Key Laboratory of Sepsis, Henan Key Laboratory of Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Tongwen Sun,
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Comparison of Fungal Fluorescent Staining and ITS rDNA PCR-based Sequencing with Conventional Methods for Diagnosis of Onychomycosis. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2022. [DOI: 10.22207/jpam.16.2.62] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Accurate identification of fungal causes for onychomycosis is essential for proper treatment. Presently available laboratory methods show unreliable sensitivity; so there is a requirement for innovative detection techniques. The aim for this work was to assess the efficiencies of fluorescent staining and internal transcribed spacer (ITS) ribosomal DNA (rDNA) polymerase chain reaction (PCR)-based sequencing in comparison to conventional techniques for diagnosis of onychomycosis. Nail specimens obtained from 100 patients with clinically- diagnosed onychomycosis were analyzed. Nail scrapings or clippings were subjected to direct microscopic examination by KOH mount, culture by using Sabouraud’s dextrose agar and histopathological examination with periodic-acid Schiff (PAS). Collected specimens were subsequently examined by fluorescent staining and PCR-based sequencing (30 specimens only) to compare the feasibility, sensitivity and diagnostic accuracy for these two methods. The most frequently isolated fungi were yeasts (39/76: 51.3%), dermatophytes (24/76; 31.6%) and non-dermatophyte molds (NDMs) (13/76; 17.1%). Mixed mycotic infections were recovered from 6% of the collected nail specimens. The positive detection rates were significantly different between KOH examinations (52%), nail plate histology (55%), fungal culture (70%) and fluorescent staining (80%). Considering fungal culture as the gold standard, the most sensitive technique was PCR (100%) followed by fluorescent staining (89%), PAS staining (69%) while the least sensitive technique was KOH mount (53%). Fluorescence staining can be used as a rapid and high-yield technique for identification of fungi in the specimens. PCR-based sequencing was highly sensitive and faster compared to culture. Whenever possible, it enables species identification with higher adequacy.
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28
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Tiew PY, Thng KX, Chotirmall SH. Clinical Aspergillus Signatures in COPD and Bronchiectasis. J Fungi (Basel) 2022; 8:jof8050480. [PMID: 35628736 PMCID: PMC9146266 DOI: 10.3390/jof8050480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 04/30/2022] [Accepted: 05/03/2022] [Indexed: 12/21/2022] Open
Abstract
Pulmonary mycoses remain a global threat, causing significant morbidity and mortality. Patients with airways disease, including COPD and bronchiectasis, are at increased risks of pulmonary mycoses and its associated complications. Frequent use of antibiotics and corticosteroids coupled with impaired host defenses predispose patients to fungal colonization and airway persistence, which are associated with negative clinical consequences. Notably, Aspergillus species remain the best-studied fungal pathogen and induce a broad spectrum of clinical manifestations in COPD and bronchiectasis ranging from colonization and sensitization to more invasive disease. Next-generation sequencing (NGS) has gained prominence in the field of respiratory infection, and in some cases is beginning to act as a viable alternative to traditional culture. NGS has revolutionized our understanding of airway microbiota and in particular fungi. In this context, it permits the identification of the previously unculturable, fungal composition, and dynamic change within microbial communities of the airway, including potential roles in chronic respiratory disease. Furthermore, inter-kingdom microbial interactions, including fungi, in conjunction with host immunity have recently been shown to have important clinical roles in COPD and bronchiectasis. In this review, we provide an overview of clinical Aspergillus signatures in COPD and bronchiectasis and cover the current advances in the understanding of the mycobiome in these disease states. The challenges and limitations of NGS will be addressed.
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Affiliation(s)
- Pei Yee Tiew
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore 168753, Singapore;
- Duke-NUS Medical School, Singapore 169857, Singapore
| | - Kai Xian Thng
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore;
| | - Sanjay H. Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore;
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore 308433, Singapore
- Correspondence:
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29
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Wang D, Lai M, Song H, Zhang JY, Zhao FY, Liang J, Xu WQ, Tang YM, Xu XJ. Integration of Interleukin-6 Improves the Diagnostic Precision of Metagenomic Next-Generation Sequencing for Infection in Immunocompromised Children. Front Microbiol 2022; 13:819467. [PMID: 35391735 PMCID: PMC8982073 DOI: 10.3389/fmicb.2022.819467] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 01/24/2022] [Indexed: 11/13/2022] Open
Abstract
The performance of metagenomic next-generation sequencing (mNGS) in identifying pathogens in immunocompromised children was not very clear. The purpose of this study is to assess the performance of mNGS in this population and to investigate whether the integration of serum cytokines and mNGS assay could improve diagnostic accuracy. We retrospectively collected the clinical data of pediatric patients who suffered febrile diseases and underwent mNGS determination simultaneously in the department of hematology/oncology between January 2019 and March 2021. Specimens were sent for conventional microbiological test (CMT), mNGS, and serum cytokine measurement in parallel. A total of 258 episodes of febrile diseases were enrolled, mNGS was positive in 224 cases, while CMT was positive in 78 cases. mNGS and CMT were both positive in 70 (27.1%) cases and were both negative in 26 (10.1%) cases. There were 154 (59.7%) cases positive by mNGS only while 8 (3.1%) were positive by CMT only. It was common that two or more pathogens were simultaneously detected by mNGS in a single specimen, with only 61 tests identified a single organism. Whether the organisms reported by mNGS were the microbiological etiology of infection was evaluated. Of the 224 cases with positive mNGS results, 135 (58.4%), 30 (13.0%), and 59 (28.6%) were considered as "probable," "possible," and "unlikely," respectively. Patients with high IL-6 (≥ 390 pg/ml) were likely to be bacterial infection. Although mNGS reported mixed pathogens, 84.6% (33/39) and 83.3% (10/12) of patients presenting high IL-6 were confirmed as bacterial infection in the training and validation cohort, respectively. In conclusion, mNGS analysis demonstrates promising diagnostic potential in rapidly identifying clinically relevant pathogens. Given the detection of many clinically irrelevant organisms, the integration of IL-6 improves the precision of mNGS results interpretation.
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Affiliation(s)
- Di Wang
- Division/Center of Hematology-Oncology, The Children's Hospital of Zhejiang University School of Medicine, Hangzhou, China.,The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, Hangzhou, China
| | - Min Lai
- Division/Center of Hematology-Oncology, The Children's Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Hua Song
- Division/Center of Hematology-Oncology, The Children's Hospital of Zhejiang University School of Medicine, Hangzhou, China.,The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, Hangzhou, China
| | - Jing-Ying Zhang
- Division/Center of Hematology-Oncology, The Children's Hospital of Zhejiang University School of Medicine, Hangzhou, China.,The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, Hangzhou, China
| | - Fen-Ying Zhao
- Division/Center of Hematology-Oncology, The Children's Hospital of Zhejiang University School of Medicine, Hangzhou, China.,The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, Hangzhou, China
| | - Juan Liang
- Division/Center of Hematology-Oncology, The Children's Hospital of Zhejiang University School of Medicine, Hangzhou, China.,The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, Hangzhou, China
| | - Wei-Qun Xu
- Division/Center of Hematology-Oncology, The Children's Hospital of Zhejiang University School of Medicine, Hangzhou, China.,The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, Hangzhou, China
| | - Yong-Min Tang
- Division/Center of Hematology-Oncology, The Children's Hospital of Zhejiang University School of Medicine, Hangzhou, China.,The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, Hangzhou, China
| | - Xiao-Jun Xu
- Division/Center of Hematology-Oncology, The Children's Hospital of Zhejiang University School of Medicine, Hangzhou, China.,The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, Hangzhou, China
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30
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Sun H, Wang F, Zhang M, Xu X, Li M, Gao W, Wu X, Han H, Wang Q, Yao G, Lou Z, Xia H, Shi Y, Li Q. Diagnostic Value of Bronchoalveolar Lavage Fluid Metagenomic Next-Generation Sequencing in Pneumocystis jirovecii Pneumonia in Non-HIV Immunosuppressed Patients. Front Cell Infect Microbiol 2022; 12:872813. [PMID: 35463643 PMCID: PMC9024294 DOI: 10.3389/fcimb.2022.872813] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 03/14/2022] [Indexed: 11/13/2022] Open
Abstract
Introduction This study aims to assess the value of metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) in the diagnosis of Pneumocystis jirovecii pneumonia (PJP) and its mixed infection in non-human immunodeficiency virus (HIV) immunosuppressed patients. Methods A total of 198 non-HIV immunosuppressed patients with severe pneumonia were enrolled, including 77 PJP patients and 121 patients infected by other pathogens. BALF-mNGS and traditional detection methods were used. Results The positive detection rate of various pathogens of BALF-mNGS was higher than that of the conventional methods, especially for mixed pathogens. The sensitivity and specificity of BALF-mNGS for the diagnosis of PJP were 97.40% and 85.12%, respectively. Compared with traditional methods, the sensitivity of BALF-mNGS was significantly higher than that of blood fungal G (BG)/lactate dehydrogenase (LDH) and BALF-microscopy (p<0.05), and its specificity was significantly higher than that of BG/LDH (p<0.05). In addition, the average detection time of BALF-mNGS (32.76 ± 10.32 h) was also significantly shorter than conventional methods (p<0.01), especially for mixed infections that were common in non-HIV immunosuppressed patients. In patients only detected as positive by BALF-mNGS, the underlying diseases mainly manifested as hematological malignancies with agranulocytosis and within 8 months after hematopoietic stem cell or solid organ transplantation. Conclusions BALF-mNGS technology is faster, more sensitive, and more comprehensive in detecting P. jirovecii and its mixed infection in immunosuppressed patients.
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Affiliation(s)
- He Sun
- Department of Respiratory and Critical Care Medicine, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Feilong Wang
- Department of Respiratory and Critical Care Medicine, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Ming Zhang
- Department of Respiratory and Critical Care Medicine, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Xiaoyong Xu
- Department of Pulmonary and Critical Care Medicine (PCCM), The Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Miaomiao Li
- Department of Respiratory and Critical Medicine, The Fourth Affiliated Hospital, School of Medicine, Zhejiang University, Yiwu, China
| | - Wei Gao
- Department of Pulmonary and Critical Care Medicine (PCCM), Shenzhen People’s Hospital, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Xiaodong Wu
- Department of Respiratory and Critical Care Medicine, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Huize Han
- Department of Respiratory and Critical Care Medicine, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Qin Wang
- Department of Respiratory and Critical Care Medicine, Jinling Hospital, Clinical School of Nanjing, Nanjing, China
| | - Gehong Yao
- Department of Respiratory and Critical Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zheng Lou
- Department of Scientific Affairs, Hugobiotech, Beijing, China
| | - Han Xia
- Department of Scientific Affairs, Hugobiotech, Beijing, China
| | - Yi Shi
- Department of Respiratory and Critical Care Medicine, Jinling Hospital, Clinical School of Nanjing, Nanjing, China
| | - Qiang Li
- Department of Respiratory and Critical Care Medicine, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
- *Correspondence: Qiang Li,
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Xing F, Ye H, Deng C, Sun L, Yuan Y, Lu Q, Yang J, Lo SKF, Zhang R, Chen JHK, Chan JFW, Lau SKP, Woo PCY. Diverse and atypical manifestations of Q fever in a metropolitan city hospital: Emerging role of next-generation sequencing for laboratory diagnosis of Coxiella burnetii. PLoS Negl Trop Dis 2022; 16:e0010364. [PMID: 35442979 PMCID: PMC9060374 DOI: 10.1371/journal.pntd.0010364] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 05/02/2022] [Accepted: 03/28/2022] [Indexed: 11/19/2022] Open
Abstract
Although Q fever has been widely reported in the rural areas of China, there is a paucity of data on the epidemiology and clinical characteristics of this disease in large metropolitan cities. In this study, we profile the epidemiology and clinical manifestations of Q fever from a tertiary hospital in Shenzhen, a Southern Chinese metropolitan city with a large immigrant population from other parts of China. A total of 14 patients were confirmed to have Q fever during a nine-year-and-six-month period, five of whom were retrospectively diagnosed during case review or incidentally picked up because of another research project on unexplained fever without localizing features. Some patients had the typical exposure histories and clinical features, while a few other patients had rare manifestations of Q fever, including one with heart failure and diffuse intracapillary proliferative glomerulonephritis, a patient presenting with a spontaneous bacterial peritonitis-like syndrome, and another one with concomitant Q fever and brucellosis. Using a combination of clinical manifestation, inflammatory marker levels, echocardiographic findings and serological or molecular test results, nine, three and two patients were diagnosed to have acute, chronic and convalescent Q fever, respectively. Seven, five and two patients were diagnosed to have Q fever by serological test, nested real-time PCR and next-generation sequencing respectively. Diverse and atypical manifestations are associated with Q fever. The incidence of Q fever is likely to be underestimated. Next-generation sequencing is becoming an important diagnostic modality for culture-negative infections, particularly those that the physicians fail to recognize clinically, such as Q fever. We describe the epidemiology and clinical manifestations of Q fever from a tertiary hospital in Shenzhen, a Southern Chinese metropolitan city in China. A total of 14 patients were confirmed to have Q fever during this study period. Notably, five of them were retrospectively diagnosed during case review or incidentally picked up because of another research project on patients with unexplained fever. Interestingly, some patients had rare manifestations of Q fever, such as heart failure and diffuse intracapillary proliferative glomerulonephritis and spontaneous bacterial peritonitis. One patient had concomitant Q fever and brucellosis. Half of the patients were diagnosed by traditional serological test, while the other half by PCR or next-generation sequencing. Clinicians should have a high index of suspicion of Q fever because of its diverse and atypical manifestations. The incidence of Q fever is likely to be underestimated. Next-generation sequencing is becoming increasingly important for diagnosis of culture-negative infections.
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Affiliation(s)
- Fanfan Xing
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong—Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Haiyan Ye
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong—Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Chaowen Deng
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong—Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Linlin Sun
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong—Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Yanfei Yuan
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong—Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Qianyun Lu
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong—Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Jin Yang
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong—Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Simon K. F. Lo
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong—Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Ruiping Zhang
- Department of Pathology, The University of Hong Kong—Shenzhen Hospital, Shenzhen, Guangdong, China
| | | | - Jasper F. W. Chan
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong—Shenzhen Hospital, Shenzhen, Guangdong, China
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Susanna K. P Lau
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- * E-mail: (SKPL); (PCYW)
| | - Patrick C. Y. Woo
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- * E-mail: (SKPL); (PCYW)
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Xing F, Lo SKF, Ma Y, Ip JD, Chan WM, Zhou M, Gong M, Lau SKP, Woo PCY. Rapid Diagnosis of Mycobacterium marinum Infection by Next-Generation Sequencing: A Case Report. Front Med (Lausanne) 2022; 9:824122. [PMID: 35187006 PMCID: PMC8854760 DOI: 10.3389/fmed.2022.824122] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 01/12/2022] [Indexed: 11/13/2022] Open
Abstract
We present the first report of histology- and culture-proven Mycobacterium marinum infection diagnosed by next-generation sequencing (NGS). It took <2 days to make a microbiological diagnosis using the Oxford Nanopore Technologies' MinION device, compared to 20 days for the mycobacterium to be isolated from the tissue biopsy. NGS is particularly useful for culture-negative and slow-growing microorganism infections, such as mycobacterial, fungal and partially treated pyogenic bacterial infections. Due to its low equipment cost, short turn-around-time and portable size, the Oxford Nanopore Technologies' MinION device is a useful platform for NGS in routine clinical microbiology laboratories.
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Affiliation(s)
- Fanfan Xing
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong - Shenzhen Hospital, Shenzhen, China
| | - Simon K. F. Lo
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong - Shenzhen Hospital, Shenzhen, China
| | - Yuanchao Ma
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Jonathan Daniel Ip
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Wan-Mui Chan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Meixun Zhou
- Department of Pathology, The University of Hong Kong - Shenzhen Hospital, Shenzhen, China
| | - Miaozi Gong
- Department of Pathology, The University of Hong Kong - Shenzhen Hospital, Shenzhen, China
| | - Susanna K. P. Lau
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Patrick C. Y. Woo
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- *Correspondence: Patrick C. Y. Woo
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Kim SH, Vujanovic V. Early transcriptomic response of the mycoparasite Sphaerodes mycoparasitica to the mycotoxigenic Fusarium graminearum 3-ADON, the cause of Fusarium head blight. BIORESOUR BIOPROCESS 2022; 8:127. [PMID: 34993050 PMCID: PMC8683091 DOI: 10.1186/s40643-021-00479-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 12/06/2021] [Indexed: 11/18/2022] Open
Abstract
Mycoparasites are an assemblage of biotrophic and necrotrophic fungi that occur on plant pathogenic fungal hosts. Biotrophic mycoparasites are often overlooked in transcriptomic-based biocontrol studies. Sphaerodes mycoparasitica (S.m.) is a specific biotrophic mycoparasite of plant pathogenic Fusarium graminearum (F.g.), a devastating Fusarium head blight (FHB) disease in small-grain cereals. To understand the biotrophic mycoparasitism comprehensively, we performed Illumina RNA-Seq transcriptomic study on the fungus–fungus interaction in vitro. The aim is to identify the transcript-level mechanism related to the biotrophic S.m. mycoparasitism, particularly its ability to effectively control the F.g. 3-ADON chemotype. A shift in the transcriptomic profile of the mycoparasite was triggered in response to its interaction with F.g. during recognition (1.5 days) and colonization (3.5 days) steps. RNA-Seq analysis revealed ~ 30% of annotated transcripts with "function unknown". Further, 14 differentially expressed genes functionally linked to the biotrophic mycoparasitism were validated by quantitative real-time PCR (qPCR). The gene expression patterns of the filamentous haemagglutinin/adhesin/attachment factor as well as cell wall-degrading glucanases and chitinases were upregulated by host interaction. Besides, mycoparasitism-associated antioxidant resistance genes encoding ATP-binding cassette (ABC) transporter(s) and glutathione synthetase(s) were upregulated. However, the thioredoxin reductase was downregulated which infers that this antioxidant gene can be used as a resistance marker to assess S.m. antifungal and antimycotoxigenic activities. The interactive transcriptome of S. mycoparasitica provides new insights into specific mycoparasitism and will contribute to future research in controlling FHB.
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Affiliation(s)
- Seon Hwa Kim
- Department of Food and Bioproduct Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8 Canada
| | - Vladimir Vujanovic
- Department of Food and Bioproduct Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8 Canada
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Hoang MTV, Irinyi L, Hu Y, Schwessinger B, Meyer W. Long-Reads-Based Metagenomics in Clinical Diagnosis With a Special Focus on Fungal Infections. Front Microbiol 2022; 12:708550. [PMID: 35069461 PMCID: PMC8770865 DOI: 10.3389/fmicb.2021.708550] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 12/03/2021] [Indexed: 12/12/2022] Open
Abstract
Identification of the causative infectious agent is essential in the management of infectious diseases, with the ideal diagnostic method being rapid, accurate, and informative, while remaining cost-effective. Traditional diagnostic techniques rely on culturing and cell propagation to isolate and identify the causative pathogen. These techniques are limited by the ability and the time required to grow or propagate an agent in vitro and the facts that identification based on morphological traits are non-specific, insensitive, and reliant on technical expertise. The evolution of next-generation sequencing has revolutionized genomic studies to generate more data at a cheaper cost. These are divided into short- and long-read sequencing technologies, depending on the length of reads generated during sequencing runs. Long-read sequencing also called third-generation sequencing emerged commercially through the instruments released by Pacific Biosciences and Oxford Nanopore Technologies, although relying on different sequencing chemistries, with the first one being more accurate both platforms can generate ultra-long sequence reads. Long-read sequencing is capable of entirely spanning previously established genomic identification regions or potentially small whole genomes, drastically improving the accuracy of the identification of pathogens directly from clinical samples. Long-read sequencing may also provide additional important clinical information, such as antimicrobial resistance profiles and epidemiological data from a single sequencing run. While initial applications of long-read sequencing in clinical diagnosis showed that it could be a promising diagnostic technique, it also has highlighted the need for further optimization. In this review, we show the potential long-read sequencing has in clinical diagnosis of fungal infections and discuss the pros and cons of its implementation.
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Affiliation(s)
- Minh Thuy Vi Hoang
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Westmead, NSW, Australia
| | - Laszlo Irinyi
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Westmead, NSW, Australia
- Sydney Infectious Disease Institute, The University of Sydney, Sydney, NSW, Australia
| | - Yiheng Hu
- Research School of Biology, Australia National University, Canberra, ACT, Australia
| | | | - Wieland Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Westmead, NSW, Australia
- Sydney Infectious Disease Institute, The University of Sydney, Sydney, NSW, Australia
- Westmead Hospital (Research and Education Network), Westmead, NSW, Australia
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