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Li CX, Burrell R, Dale RC, Kesson A, Blyth CC, Clark JE, Crawford N, Jones CA, Britton PN, Holmes EC. Diagnosis and analysis of unexplained cases of childhood encephalitis in Australia using metatranscriptomic sequencing. J Gen Virol 2022; 103. [PMID: 35486523 DOI: 10.1099/jgv.0.001736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Encephalitis is most often caused by a variety of infectious agents identified through diagnostic tests utilizing cerebrospinal fluid. We investigated the clinical characteristics and potential aetiological agents of unexplained encephalitis through metagenomic sequencing of residual clinical samples from multiple tissue types and independent clinical review. Forty-three specimens were collected from 18 encephalitis cases with no cause identified by the Australian Childhood Encephalitis study. Samples were subjected to total RNA sequencing ('metatranscriptomics') to determine the presence and abundance of potential pathogens, and to describe the possible aetiologies of unexplained encephalitis. Using this protocol, we identified five RNA and two DNA viruses associated with human infection from both non-sterile and sterile sites, which were confirmed by PCR. These comprised two human rhinoviruses, two human seasonal coronaviruses, two polyomaviruses and one picobirnavirus. Human rhinovirus and seasonal coronaviruses may be responsible for five of the encephalitis cases. Immune-mediated encephalitis was considered likely in six cases and metatranscriptomics did not identify a possible pathogen in these cases. The aetiology remained unknown in nine cases. Our study emphasizes the importance of respiratory viruses in the aetiology of unexplained child encephalitis and suggests that non-central-nervous-system sampling in encephalitis clinical guidelines and protocols could improve the diagnostic yield.
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Affiliation(s)
- Ci-Xiu Li
- School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, NSW, Australia.,Sydney Institute for Infectious Diseases, Sydney Medical School, The University of Sydney, NSW, Australia
| | - Rebecca Burrell
- Sydney Institute for Infectious Diseases, Sydney Medical School, The University of Sydney, NSW, Australia.,The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Russell C Dale
- Kids Neuroscience Centre, Children's Hospital at Westmead Clinical School, Faculty of Medicine, University of Sydney, NSW, Australia
| | - Alison Kesson
- Sydney Institute for Infectious Diseases, Sydney Medical School, The University of Sydney, NSW, Australia.,The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Christopher C Blyth
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute and School of Medicine, University of Western Australia, Nedlands, WA, Australia.,Department of Infectious Diseases, Perth Children's Hospital, Nedlands, WA, Australia.,Department of Microbiology, PathWest Laboratory Medicine WA, QEII Medical Centre, Nedlands, WA, Australia
| | - Julia E Clark
- Infection Management, Queensland Children's Hospital, Brisbane, QLD, Australia.,School of Clinical Medicine, Childrens Health Queensland Clinical Unit, University of Queensland, QLD, Australia
| | - Nigel Crawford
- Murdoch Children's Research Institute, Royal Children's Hospital Flemington Road, Parkville, VIC 3052 Australia
| | - Cheryl A Jones
- Kids Research, Sydney Children's Hospitals Network (Westmead), Westmead, NSW, Australia.,Sydney Institute for Infectious Diseases, Sydney Medical School, The University of Sydney, NSW, Australia.,The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Philip N Britton
- Kids Research, Sydney Children's Hospitals Network (Westmead), Westmead, NSW, Australia.,Sydney Institute for Infectious Diseases, Sydney Medical School, The University of Sydney, NSW, Australia.,The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Edward C Holmes
- School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, NSW, Australia.,Sydney Institute for Infectious Diseases, Sydney Medical School, The University of Sydney, NSW, Australia
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Guo Y, Yang Y, Xu M, Shi G, Zhou J, Zhang J, Li H. Trends and Developments in the Detection of Pathogens in Central Nervous System Infections: A Bibliometric Study. Front Cell Infect Microbiol 2022; 12:856845. [PMID: 35573778 PMCID: PMC9100591 DOI: 10.3389/fcimb.2022.856845] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 03/29/2022] [Indexed: 11/22/2022] Open
Abstract
Introduction Rapid, sensitive, and specific laboratory assays are critical for the diagnosis and management of central nervous system (CNS) infections. The purpose of this study is to explore the intellectual landscape of research investigating methods for the detection of pathogens in patients with CNS infections and to identify the development trends and research frontier in this field. Methods A bibliometric study is conducted by analyzing literature retrieved from the Web of Science (WoS) Core Collection Database for the years 2000 to 2021. CiteSpace software is used for bibliometric analysis and network visualization, including co-citation analysis of references, co-occurrence analysis of keywords, and cooperation network analysis of authors, institutions, and countries/regions. Results A total of 2,282 publications are eventually screened, with an upward trend in the number of publications per year. The majority of papers are attributed to the disciplines of MICROBIOLOGY, INFECTIOUS DISEASES, IMMUNOLOGY, NEUROSCIENCES & NEUROLOGY, and VIROLOGY. The co-citation analysis of references shows that recent research has focused on the largest cluster “metagenomic next-generation sequencing”; the results of the analysis of the highest-cited publications and the citation burst of publications reveal that there is a strong interest stimulated in metagenomic next-generation sequencing. The co-occurrence analysis of keywords indicates that “infection”, “pathogen”, “diagnosis”, “gene”, “virus”, “polymerase chain reaction”, “cerebrospinal fluid”, “epidemiology”, and “metagenomic next-generation sequencing” are the main research priorities in the field of pathogen detection for CNS infections, and the keyword with the highest strength of burst is “metagenomic next-generation sequencing”. Collaborative network analysis reveals that the USA, the Centers for Disease Control and Prevention of USA, and XIN WANG and JENNIFER DIEN BARD are the most influential country, institution, and researchers, respectively. Conclusions Exploring more advanced laboratory assays to improve the diagnostic accuracy of pathogens is essential for CNS infection research. Metagenomic next-generation sequencing is emerging as a novel useful unbiased approach for diagnosing infectious diseases of the CNS.
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Affiliation(s)
- Yangyang Guo
- Intensive Care Unit, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yanlin Yang
- Intensive Care Unit, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Ming Xu
- Intensive Care Unit, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Guangzhi Shi
- Intensive Care Unit, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Jianxin Zhou
- Intensive Care Unit, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Jindong Zhang
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China
- *Correspondence: Jindong Zhang, ; Hongliang Li,
| | - Hongliang Li
- Intensive Care Unit, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- *Correspondence: Jindong Zhang, ; Hongliang Li,
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Zeng X, Wu J, Li X, Xiong W, Tang L, Li X, Zhuang J, Yu R, Chen J, Jian X, Lei L. Application of Metagenomic Next-Generation Sequencing in the Etiological Diagnosis of Infective Endocarditis During the Perioperative Period of Cardiac Surgery: A Prospective Cohort Study. Front Cardiovasc Med 2022; 9:811492. [PMID: 35369282 PMCID: PMC8965566 DOI: 10.3389/fcvm.2022.811492] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 02/01/2022] [Indexed: 12/13/2022] Open
Abstract
Objective The present study aimed to prospectively evaluate the role of metagenomic next-generation sequencing (mNGS) in the etiological diagnosis of patients with perioperative infective endocarditis (IE). Methods From May 1st, 2019 to December 31st, 2020, a total of 99 patients with IE were enrolled in the present study according to the modified Duke criteria, etiological, and pathological results. 11 non-IE patients undergoing heart valve surgery in the same period were selected as the control group. A blood culture test was performed immediately after admission, and the valves harvested operatively were examined by blood culture and mNGS. Results In the IE group, there were 29 cases (29.3%) with positive blood culture, 16 cases (16.2%) with positive valve culture, and 85 cases (85.9%) with positive valve mNGS. Compared to culture-based detection, mNGS achieved better performance with a sensitivity, specificity, area under the curve (AUC) of 0.859, 0.727, and 0.793, respectively. The combined approach using culture and mNGS further improved the diagnostic accuracy (sensitivity 89.9%, specificity 72.7%, AUC 0.813). Preoperative white blood cell (P = 0.029) and neutrophils (P = 0.046) were identified as independent factors affecting the detection rate of mNGS. In the mNGS-positive group, 95 strains of pathogens were found and 10 cases were identified with mixed infection. There were 72 gram-positive bacteria and 14 gram-negative bacteria. mNGS positive group displayed higher species richness than mNGS negative group with enrichment of Streptococcus sanguis, Streptococcus buccalis, and Streptococcus griseus. Proteobacteria and Actinomycetes were enriched in mNGS negative group. Notably, six patients showed disconcordant results between culture and mNGS. Rothia aeria was identified in the blood culture, valve culture, and valve mNGS in one patient. Bartonella Quintana and Coxiella burnetii, which were fastidious intracellular bacteria, were found in two blood and valve culture-negative cases. Conclusions mNGS outperformed the conventional culture method and displayed high accuracy in detecting pathogens in IE patients. This study provided support for the use of mNGS in the etiological diagnosis of IE.
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Affiliation(s)
- Xiaodong Zeng
- Department of Intensive Care Unit of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Jinlin Wu
- Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Xin Li
- Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Weiping Xiong
- Department of Intensive Care Unit of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Lili Tang
- Department of Intensive Care Unit of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Xueming Li
- Department of Intensive Care Unit of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Jian Zhuang
- Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of South China Structural Heart Disease, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangdong, China
| | | | - Jimei Chen
- Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of South China Structural Heart Disease, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangdong, China
| | - Xuhua Jian
- Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Liming Lei
- Department of Intensive Care Unit of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of South China Structural Heart Disease, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangdong, China
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Performance of Five Metagenomic Classifiers for Virus Pathogen Detection Using Respiratory Samples from a Clinical Cohort. Pathogens 2022; 11:pathogens11030340. [PMID: 35335664 PMCID: PMC8953373 DOI: 10.3390/pathogens11030340] [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: 01/21/2022] [Revised: 02/21/2022] [Accepted: 03/07/2022] [Indexed: 01/10/2023] Open
Abstract
Viral metagenomics is increasingly applied in clinical diagnostic settings for detection of pathogenic viruses. While several benchmarking studies have been published on the use of metagenomic classifiers for abundance and diversity profiling of bacterial populations, studies on the comparative performance of the classifiers for virus pathogen detection are scarce. In this study, metagenomic data sets (n = 88) from a clinical cohort of patients with respiratory complaints were used for comparison of the performance of five taxonomic classifiers: Centrifuge, Clark, Kaiju, Kraken2, and Genome Detective. A total of 1144 positive and negative PCR results for a total of 13 respiratory viruses were used as gold standard. Sensitivity and specificity of these classifiers ranged from 83 to 100% and 90 to 99%, respectively, and was dependent on the classification level and data pre-processing. Exclusion of human reads generally resulted in increased specificity. Normalization of read counts for genome length resulted in a minor effect on overall performance, however it negatively affected the detection of targets with read counts around detection level. Correlation of sequence read counts with PCR Ct-values varied per classifier, data pre-processing (R2 range 15.1–63.4%), and per virus, with outliers up to 3 log10 reads magnitude beyond the predicted read count for viruses with high sequence diversity. In this benchmarking study, sensitivity and specificity were within the ranges of use for diagnostic practice when the cut-off for defining a positive result was considered per classifier.
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55
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Zhao G, Deng X, Wu D, Cao R, Shao A, Zhou Y, Zhang T, Li G, He H, Lu J, Zhang L. Application of metagenomic sequencing toward rapid and sensitive diagnosis of goose avastrovirus infection in China. VETERINARY RESEARCH FORUM : AN INTERNATIONAL QUARTERLY JOURNAL 2022; 13:1-6. [PMID: 35601781 PMCID: PMC9094594 DOI: 10.30466/vrf.2020.116892.2776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 02/12/2020] [Indexed: 12/02/2022]
Abstract
The gosling gout, a newly emerged disease, has widely broken out in China since 2017. Typical signs for the disease include diarrhea, anorexia, depression, dehydration, emaciation and paralysis. At autopsy, uratosis was the main pathological change which could be found at kidney, pericardium, air sac, muscle and leg joint. In this study, gosling gout was firstly diagnosed by metagenomic analysis. Samples of kidney, Fabricius bursa, spleen and jejunum were collected and submitted to next-generation DNA sequencing. Our results demonstrated that goose avastrovirus was highly related with this disease. We confirmed the sequencing results by reverse transcription polymerase chain reaction method and artificial infection experiment and got consistent results. In summary, metagenomic sequencing method combined with traditional molecular identification was applied toward diagnosis of a novel gosling gout disease in China and revealed that goose avastrovirus was highly related with this disease. It has been proved to be a powerful tool for rapid and sensitive diagnosis of animal diseases, especially for some exceptional pathogens. In addition, host range, variation, molecular pathogenesis and potential zoonotic infection of this novel goose astrovirus need to be further studied.
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Affiliation(s)
- Guangwei Zhao
- Department of Veterinary Medicine, College of Veterinary Medicine, Southwest University, Chongqing China;
| | - Xinzhu Deng
- Department of Veterinary Medicine, College of Veterinary Medicine, Southwest University, Chongqing China;
| | - Di Wu
- Department of Veterinary Medicine, College of Veterinary Medicine, Southwest University, Chongqing China;
| | - Ruibing Cao
- Department of Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China;
| | - Aojun Shao
- Chongqing Sanjiezhongxin Bioengineering Co., Ltd, Chongqing, China.
| | - Yu Zhou
- Chongqing Sanjiezhongxin Bioengineering Co., Ltd, Chongqing, China.
| | - Tianqi Zhang
- Chongqing Sanjiezhongxin Bioengineering Co., Ltd, Chongqing, China.
| | - Ge Li
- Chongqing Sanjiezhongxin Bioengineering Co., Ltd, Chongqing, China.
| | - Hongzhang He
- Chongqing Sanjiezhongxin Bioengineering Co., Ltd, Chongqing, China.
| | - Jing Lu
- Department of Veterinary Medicine, College of Veterinary Medicine, Southwest University, Chongqing China;
| | - Liwu Zhang
- Chongqing Sanjiezhongxin Bioengineering Co., Ltd, Chongqing, China.,Correspondence: Liwu Zhang. PhD, Chongqing Sanjiezhongxin Bioengineering Co., Ltd, Chongqing, China. E-mail:
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56
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Chen Y, Wang Y, Liu X, Li W, Fu H, Liu X, Zhang X, Zhou X, Yang B, Yao J, Ma X, Han L, Li H, Zheng L. Comparative diagnostic utility of metagenomic next-generation sequencing, GeneXpert, modified Ziehl-Neelsen staining, and culture using cerebrospinal fluid for tuberculous meningitis: A multi-center, retrospective study in China. J Clin Lab Anal 2022; 36:e24307. [PMID: 35202495 PMCID: PMC8993600 DOI: 10.1002/jcla.24307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 01/12/2022] [Accepted: 02/12/2022] [Indexed: 12/03/2022] Open
Abstract
Background Early diagnosis of tuberculosis meningitis (TBM) remains a great challenge during clinical practice. The diagnostic efficacies of cerebrospinal fluid (CSF)‐based mycobacterial growth indicator tube (MGIT) culture, modified Ziehl–Neelsen (ZN) staining, Xpert MTB/RIF, and metagenomic next‐generation sequencing (mNGS) for TBM remained elusive. Methods A total of 216 adult patients with suspicious TBM were retrospectively enrolled in this multi‐cohort study. The diagnostic performances for MGIT, modified ZN staining, Xpert MTB/RIF, and mNGS using CSF samples were evaluated. Results Uniform clinical case definition classified 88 (40.7%) out of 216 patients as the definite TBM, 5 (2.3%) patients as probable TBM cases, and 24 (11.1%) patients as possible TBM cases. The sensitivities of MGIT, modified ZN staining, Xpert MTB/RIF, and mNGS for TBM diagnosis against consensus uniform case definition for definite TBM were 25.0%, 76.1%, 73.9%, and 84.1%, respectively. Negative predictive values (NPVs) were 66.0%, 85.9%, 84.8%, and 90.1%, respectively. The sensitivities of MGIT, modified ZN staining, Xpert MTB/RIF, and mNGS for TBM diagnosis against consensus uniform case definition for definite, probable, and possible TBM were 18.8%, 57.3%, 55.5%, and 63.2%, respectively. Negative predictive values (NPVs) were 51.0%, 66.4%, 65.6%, and 69.7%, respectively. mNGS combined with modified ZN stain and Xpert could cover TBM cases against a composite microbiological reference standard, yielding 100% specificity and 100% NPV. Conclusion Metagenomic next‐generation sequencing detected TBM with higher sensitivity than Xpert, ZN staining and MGIT culture, but mNGS cannot be used as a rule‐out test. mNGS combined with Xpert or modified ZN staining could enhance the sensitivity of diagnostic tests for TBM.
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Affiliation(s)
- Yuxin Chen
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Yuqing Wang
- Department of Respiratory Medicine, No. 4 People's Hospital of Qinghai Province, Xining, China
| | - Xiaojin Liu
- Department of Infectious Disease, Hebei Chest Hospital, Hebei, China
| | - Wen Li
- Department of Radiology, Hebei Chest Hospital, Hebei, China
| | - Hongyi Fu
- Department of Tuberculosis, Hebei Chest Hospital, Hebei, China
| | - Xinyan Liu
- Department of Oncology, Hebei Chest Hospital, Hebei, China
| | - Xun Zhang
- Department of Clinical Laboratory, Hebei Chest Hospital, Hebei, China
| | - Xueqin Zhou
- Department of Clinical Laboratory, Hebei Chest Hospital, Hebei, China
| | - Bingzhou Yang
- Department of Clinical Laboratory, Hebei Chest Hospital, Hebei, China
| | - Jie Yao
- Department of Respiratory Medicine, No. 4 People's Hospital of Qinghai Province, Xining, China
| | - Xiaolei Ma
- Department of Respiratory Medicine, No. 4 People's Hospital of Qinghai Province, Xining, China
| | - Lijun Han
- The Center of Tuberculous Meningitis Diagnosis and Treatment, The Infectious Disease Hospital of Changchun, Jilin, China
| | - Huan Li
- The Center of Tuberculous Meningitis Diagnosis and Treatment, The Infectious Disease Hospital of Changchun, Jilin, China
| | - Liheng Zheng
- Department of Clinical Laboratory, Hebei Chest Hospital, Hebei, China
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Zhu Y, Xu M, Ding C, Peng Z, Wang W, Sun B, Cheng J, Chen C, Chen W, Wei H, Hu Z. Metagenomic Next-Generation Sequencing vs. Traditional Microbiological Tests for Diagnosing Varicella-Zoster Virus Central Nervous System Infection. Front Public Health 2022; 9:738412. [PMID: 35127608 PMCID: PMC8814106 DOI: 10.3389/fpubh.2021.738412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 12/03/2021] [Indexed: 11/27/2022] Open
Abstract
Background Unbiased metagenomic next-generation sequencing (mNGS) detects pathogens in a target-independent manner. It is not well-understood whether mNGS has comparable sensitivity to target-dependent nucleic acid test for pathogen identification. Methods This study included 31 patients with chickenpox and neurological symptoms for screening of possible varicella-zoster virus (VZV) central nervous system (CNS) infection. Microbiological diagnosing of VZV cerebrospinal fluid (CSF) infection was performed on stored CSF samples using mNGS, quantitative and qualitative VZV-specific PCR assays, and VZV IgM antibodies test. Results The median age was 30.0 [interquartile range (IQR), 24.3–33.3] years. 51.6% of the patients were men. About 80.6% of the patients had normal CSF white blood cell counts (≤ 5 × 106/L). VZV IgM antibodies presented in 16.1% of the CSF samples, and nucleic acids were detectable in 16.1 and 9.7% using two different VZV-specific real-time PCR protocols. Intriguingly, maximal identification of VZV elements was achieved by CSF mNGS (p = 0.001 and p = 007; compared with qualitative PCR and VZV IgM antibody test, respectively), with sequence reads of VZV being reported in 51.6% (16/31) of the CSF samples. All VZV PCR positive samples were positive when analyzed by mNGS. Of note, human betaherpesvirus 6A with clinical significance was unexpectedly detected in one CSF sample. Conclusions Our study suggests that CSF mNGS may have higher sensitivity for VZV detection than CSF VZV PCR and antibody tests, and has the advantage of identifying unexpected pathogens.
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Affiliation(s)
- Yunqi Zhu
- Department of Infectious Disease, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Miaomiao Xu
- Department of Infectious Disease, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Chengyuan Ding
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zhihang Peng
- School of Public Health, Nanjing Medical University, Nanjing, China
| | - Weixiao Wang
- Department of Clinical Research Center, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Binghu Sun
- Department of Infectious Disease, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jian Cheng
- Department of Infectious Disease, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Chen Chen
- Department of Infectious Disease, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Wei Chen
- Department of Clinical Research Center, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Hongxia Wei
- Department of Infectious Disease, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
- Hongxia Wei
| | - Zhiliang Hu
- Department of Infectious Disease, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- *Correspondence: Zhiliang Hu
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Miao S, Lin Q, Li X, Zhao L, Pan Z. Possible association between viral infection and poor survival of the corneal graft after penetrating keratoplasty in patients with congenital corneal opacity: a cohort study. Br J Ophthalmol 2022; 107:763-768. [PMID: 35027353 DOI: 10.1136/bjophthalmol-2021-320031] [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: 07/06/2021] [Accepted: 01/03/2022] [Indexed: 11/03/2022]
Abstract
BACKGROUND Congenital corneal opacity (CCO) is a rare disorder. Penetrating keratoplasty (PK) is the main surgical option for CCO, but many factors affect graft survival. Therefore, this study aimed to perform a virological examination of CCO specimens after PK to explore the relationship between virological factors and graft survival after PK. METHODS This prospective study included consecutive patients (<6 months of age) diagnosed with CCO and treated with PK at Beijing Tongren Hospital from August 2017 to January 2018. Next-generation sequencing was used to detect viral DNA in the CCO specimens. The survival of the primary graft was analysed using the Kaplan-Meier method. RESULTS Overall, 24 eyes of 24 infants were treated with PK during the study period. The mean age at surgery was 4.8±1.1 months. Epstein-Barr virus DNA was detected in two specimens, varicella-zoster virus DNA in one specimen, herpes simplex virus DNA in three specimens and cytomegalovirus DNA in one specimen. In the virus-positive group, only one (14.3%) graft remained clear during follow-up. In contrast, in the virus-negative group (n=17), 13 (76.5%) grafts were still clear at the last follow-up. The mean survival of the grafts in the virus-positive group was significantly shorter than in the virus-negative group (11.0±9.8 months vs 27.1±7.7, p<0.001). CONCLUSION The presence of viral DNA in CCO specimens might be associated with poor graft survival after PK.
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Affiliation(s)
- Sen Miao
- Department of Ophthalmology, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Qi Lin
- Department of Ophthalmology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Xu Li
- Department of Ophthalmology, Beijing Ophthalmology and Visual Science Key laboratory, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical Unversity, Beijing, China
| | - Lu Zhao
- Department of Ophthalmology, Beijing Ophthalmology and Visual Science Key laboratory, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical Unversity, Beijing, China
| | - Zhiqiang Pan
- Department of Ophthalmology, Beijing Ophthalmology and Visual Science Key laboratory, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical Unversity, Beijing, China
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Mathon B, Favreau M, Degos V, Amelot A, Le Joncour A, Weiss N, Rohaut B, Le Guennec L, Boch AL, Carpentier A, Bielle F, Mokhtari K, Idbaih A, Touat M, Combes A, Demoule A, Shotar E, Navarro V, Raux M, Demeret S, Pineton De Chambrun M. Brain Biopsy for Neurological Diseases of Unknown Etiology in Critically Ill Patients: Feasibility, Safety, and Diagnostic Yield. Crit Care Med 2022; 50:e516-e525. [PMID: 34995211 DOI: 10.1097/ccm.0000000000005439] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVES Brain biopsy is a useful surgical procedure in the management of patients with suspected neoplastic lesions. Its role in neurologic diseases of unknown etiology remains controversial, especially in ICU patients. This study was undertaken to determine the feasibility, safety, and the diagnostic yield of brain biopsy in critically ill patients with neurologic diseases of unknown etiology. We also aimed to compare these endpoints to those of non-ICU patients who underwent a brain biopsy in the same clinical context. DESIGN Monocenter, retrospective, observational cohort study. SETTING A French tertiary center. PATIENTS All adult patients with neurologic diseases of unknown etiology under mechanical ventilation undergoing in-ICU brain biopsy between January 2008 and October 2020 were compared with a cohort of non-ICU patients. INTERVENTIONS None. MEASUREMENTS AND MAIN RESULTS Among the 2,207 brain-biopsied patients during the study period, 234 biopsies were performed for neurologic diseases of unknown etiology, including 29 who were mechanically ventilated and 205 who were not ICU patients. Specific histological diagnosis and final diagnosis rates were 62.1% and 75.9%, respectively, leading to therapeutic management modification in 62.1% of cases. Meningitis on prebiopsy cerebrospinal fluid analysis was the sole predictor of obtaining a final diagnosis (2.3 [1.4-3.8]; p = 0.02). ICU patients who experienced therapeutic management modification after the biopsy had longer survival (p = 0.03). The grade 1 to 4 (mild to severe) complication rates were: 24.1%, 3.5%, 0%, and 6.9%, respectively. Biopsy-related mortality was significantly higher in ICU patients compared with non-ICU patients (6.9% vs 0%; p = 0.02). Hematological malignancy was associated with biopsy-related mortality (1.5 [1.01-2.6]; p = 0.04). CONCLUSIONS Brain biopsy in critically ill patients with neurologic disease of unknown etiology is associated with high diagnostic yield, therapeutic modifications and postbiopsy survival advantage. Safety profile seems acceptable in most patients. The benefit/risk ratio of brain biopsy in this population should be carefully weighted.
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Affiliation(s)
- Bertrand Mathon
- Department of Neurosurgery, AP-HP, Sorbonne University, La Pitié-Salpêtrière Hospital, Paris, France. Paris Brain Institute, ICM, INSERM U 1127, CNRS UMR 7225, Sorbonne Université, UMRS 1127, Paris, France. Department of Neurosurgical Anesthesiology and Critical Care, AP-HP, Sorbonne University, La Pitié Salpêtrière Hospital, Paris, France. Department of Internal Medicine and Clinical Immunology, AP-HP, Sorbonne University, La Pitié Salpêtrière Hospital, Paris, France. Department of Neurology, Neuro-ICU, AP-HP, Sorbonne University, La Pitié-Salpêtrière Hospital, Paris, France. Brain Liver Pitié-Salpêtrière Study Group, INSERM UMR S 938, Centre de Recherche Saint-Antoine, Sorbonne University, Paris, France. Department of Neuropathology, AP-HP, Sorbonne University, La Pitié-Salpêtrière Hospital, Paris, France. Department of Neurology, Sorbonne University, DMU Neurosciences, AP-HP, La Pitié-Salpêtrière Hospital, Paris, France. Intensive Care Medicine Department, AP-HP, Sorbonne University, La Pitié-Salpêtrière Hospital, Paris, France. Intensive Care Medicine Department (R3S Department), AP-HP, Sorbonne University, La Pitié-Salpêtrière Hospital, Paris, France. INSERM, UMRS1158 Neurophysiologie Respiratoire Expérimentale et Clinique, Paris, France. Department of Neuroradiology, AP-HP, Sorbonne University, La Pitié-Salpêtrière Hospital, Paris, France. Department of Neurology, Epileptology Unit, AP-HP, Sorbonne University, La Pitié Salpêtrière Hospital, Paris, France. Department of Anesthesiology and Critical Care, AP-HP, Sorbonne University, La Pitié Salpêtrière Hospital, Paris, France. Department of Internal Medicine 2, AP-HP, Sorbonne University, La Pitié-Salpêtrière Hospital, Paris, France. INSERM, UMRS 1166-ICAN, Institute of Cardiometabolism and Nutrition, Paris, France
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Zhan L, Huang K, Xia W, Chen J, Wang L, Lu J, Wang J, Lin J, Wu W. The Diagnosis of Severe Fever with Thrombocytopenia Syndrome Using Metagenomic Next-Generation Sequencing: Case Report and Literature Review. Infect Drug Resist 2022; 15:83-89. [PMID: 35046673 PMCID: PMC8760998 DOI: 10.2147/idr.s345991] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 12/21/2021] [Indexed: 12/15/2022] Open
Abstract
Background Severe fever with thrombocytopenia syndrome (SFTS) is an infectious disease caused by a bunyaviridae virus. Its main clinical manifestation is fever with thrombocytopenia, which may be accompanied by other clinical symptoms. Here, we report a patient diagnosed with SFTS using metagenomic next‑generation sequencing (mNGS). Case Presentation A 56-year-old female patient was hospitalized with intermittent diarrhea and fever. She visited a local clinic for treatment, but instead of improving, the symptoms progressed to unconsciousness. Diagnosis Using mNGS, we isolated the bunyaviridae virus and several other pathogens from the patient’s blood samples to confirm the diagnosis. Interventions The patient was treated with symptomatic and supportive therapy, including intravenous human γ-globulin (20 g/d), platelet transfusion, platelet elevation (subcutaneous injection of recombinant human thrombopoietin, 15,000 IU), white blood cell elevation (subcutaneous injection of recombinant human granulocyte colony-stimulating factor, 200 ug, qd); and antibiotic (cefoperazone sodium and tazobactam sodium, 2 g, q8h), antiviral (ganciclovir, 250 mg, q12h), and antifungal therapy (voriconazole for injection, 0.2 g, q12h). After ten days of treatment, the patient’s condition gradually improved. Conclusion Compared to traditional detection methods, mNGS has many advantages. It can quickly identify the pathogen when the patient’s clinical manifestations are complex and difficult to diagnose, resulting in the formulation of an effective treatment.
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Affiliation(s)
- Liying Zhan
- Department of Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, People’s Republic of China
| | - Kai Huang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, People’s Republic of China
| | - Wenfang Xia
- Department of Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, People’s Republic of China
| | - Jingdi Chen
- Department of Orthopedics, The Airborne Military Hospital, Wuhan, Hubei, People’s Republic of China
| | - Lu Wang
- Department of Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, People’s Republic of China
| | - Jiaming Lu
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei, People’s Republic of China
| | - Jing Wang
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei, People’s Republic of China
| | - Jun Lin
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, People’s Republic of China
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei, People’s Republic of China
| | - Wei Wu
- Department of Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, People’s Republic of China
- Correspondence: Wei Wu; Jun Lin Email ;
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61
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Wu S, Hu W, Xiao W, Li Y, Huang Y, Zhang X. Metagenomic Next-Generation Sequencing Assists in the Diagnosis of Gardnerella vaginalis in Males with Pleural Effusion and Lung Infection: A Case Report and Literature Review. Infect Drug Resist 2021; 14:5253-5259. [PMID: 34908857 PMCID: PMC8665863 DOI: 10.2147/idr.s337248] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/25/2021] [Indexed: 01/16/2023] Open
Abstract
Gardnerella vaginalis is a pathogen responsible for bacterial vaginosis, which is commonly found in female vaginas and rarely causes infections outside the female genitalia. Here, we report the use of metagenomic next-generation sequencing (mNGS) to detect and confirm pulmonary infection and pleural effusion caused by G. vaginalis in a 47-year-old man. The patient's symptoms and imaging improved after 2 weeks of oral ornidazole, and he was cured after 3 months. Overall, the findings of this case demonstrate that mNGS is a useful tool for diagnosis of unexplained lung infections and pleural effusions. Its effectiveness in rapid and accurate etiological diagnosis and monitoring of diseases can allow detection of the etiology of difficult cases that return negative results after traditional cultures.
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Affiliation(s)
- Simin Wu
- Department of Respiratory Medicine, The First Affiliated Hospital of Yangtze University, Jingzhou, 434000, Hubei, People’s Republic of China
| | - Weihua Hu
- Department of Respiratory Medicine, The First Affiliated Hospital of Yangtze University, Jingzhou, 434000, Hubei, People’s Republic of China
| | - Wei Xiao
- Department of Respiratory Medicine, The First Affiliated Hospital of Yangtze University, Jingzhou, 434000, Hubei, People’s Republic of China
| | - Yongxia Li
- Department of Respiratory Medicine, The Second Affiliated Hospital of Kunming Medical University, Kunming, 650000, Yunnan, People’s Republic of China
| | - Yan Huang
- Department of Respiratory Medicine, The First Affiliated Hospital of Yangtze University, Jingzhou, 434000, Hubei, People’s Republic of China
| | - Xu Zhang
- Department of Respiratory Medicine, The First Affiliated Hospital of Yangtze University, Jingzhou, 434000, Hubei, People’s Republic of China
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Ungureanu A, van der Meer J, Bicvic A, Abbuehl L, Chiffi G, Jaques L, Suter-Riniker F, Leib SL, Bassetti CLA, Dietmann A. Meningitis, meningoencephalitis and encephalitis in Bern: an observational study of 258 patients. BMC Neurol 2021; 21:474. [PMID: 34872509 PMCID: PMC8647376 DOI: 10.1186/s12883-021-02502-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 11/25/2021] [Indexed: 12/05/2022] Open
Abstract
Background Depending on geographic location, causes of encephalitis, meningoencephalitis and meningitis vary substantially. We aimed to identify the most frequent causes, clinical presentation and long-term outcome of encephalitis, meningoencephalitis and meningitis cases treated in the Inselspital University Hospital Bern, Switzerland. Methods In this monocentric, observational study, we performed a retrospective review of clinical patient records for all patients treated within a 3-year period. Patients were contacted for a telephone follow-up interview and to fill out questionnaires, especially related to disturbances of sleep and wakefulness. Results We included 258 patients with the following conditions: encephalitis (18%), nonbacterial meningoencephalitis (42%), nonbacterial meningitis (27%) and bacterial meningoencephalitis/meningitis (13%). Herpes simplex virus (HSV) was the most common cause of encephalitis (18%); tick-borne encephalitis virus (TBEV) was the most common cause of nonbacterial meningoencephalitis (46%), enterovirus was the most common cause of nonbacterial meningitis (21%) and Streptococcus pneumoniae was the most common cause of bacterial meningoencephalitis/meningitis (49%). Overall, 35% patients remained without a known cause. After a median time of 16 months, 162 patients participated in the follow-up interview; 56% reported suffering from neurological long-term sequelae such as fatigue and/or excessive daytime sleepiness (34%), cognitive impairment and memory deficits (22%), headache (14%) and epileptic seizures (11%). Conclusions In the Bern region, Switzerland, TBEV was the overall most frequently detected infectious cause, with a clinical manifestation of meningoencephalitis in the majority of cases. Long-term neurological sequelae, most importantly cognitive impairment, fatigue and headache, were frequently self-reported not only in encephalitis and meningoencephalitis survivors but also in viral meningitis survivors up to 40 months after acute infection. Supplementary Information The online version contains supplementary material available at 10.1186/s12883-021-02502-3.
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Affiliation(s)
- Anamaria Ungureanu
- Department of Neurology, University Hopsital and University of Bern, Inselspital, Bern, Switzerland
| | - Julia van der Meer
- Department of Neurology, University Hopsital and University of Bern, Inselspital, Bern, Switzerland
| | - Antonela Bicvic
- Department of Neurology, University Hopsital and University of Bern, Inselspital, Bern, Switzerland
| | - Lena Abbuehl
- Department of Neurology, University Hopsital and University of Bern, Inselspital, Bern, Switzerland
| | - Gabriele Chiffi
- Institute for Infectious Disease, University of Bern, Bern, Switzerland
| | - Léonore Jaques
- Department of Neurology, University Hopsital and University of Bern, Inselspital, Bern, Switzerland
| | | | - Stephen L Leib
- Institute for Infectious Disease, University of Bern, Bern, Switzerland
| | - Claudio L A Bassetti
- Department of Neurology, University Hopsital and University of Bern, Inselspital, Bern, Switzerland
| | - Anelia Dietmann
- Department of Neurology, University Hopsital and University of Bern, Inselspital, Bern, Switzerland.
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Król L, Turkiewicz D, Nordborg K, Englund E, Stenberg L, Karlsson Lindsjö O, Lind Karlberg M, Pronk CJ. Astrovirus VA1/HMO encephalitis after allogeneic hematopoietic cell transplantation: Significant role of immune competence in virus control. Pediatr Blood Cancer 2021; 68:e29286. [PMID: 34411414 DOI: 10.1002/pbc.29286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/07/2021] [Accepted: 07/21/2021] [Indexed: 11/08/2022]
Affiliation(s)
- Ladislav Król
- Childhood Cancer Centre, Skåne University Hospital, Lund, Sweden
| | | | - Karin Nordborg
- Department of Pediatric Neurology, Skåne University Hospital, Lund, Sweden
| | - Elisabet Englund
- Department of Genetics and Pathology, Skåne University Hospital, Lund, Sweden
| | - Lars Stenberg
- Department of Medical Imaging and Physiology, Skåne University Hospital, Lund, Sweden
| | | | | | - Cornelis Jan Pronk
- Childhood Cancer Centre, Skåne University Hospital, Lund, Sweden.,Division of Molecular Hematology, Lund University, Lund, Sweden.,Wallenberg Center for Molecular Medicine, Lund University, Lund, Sweden
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Laboratory diagnosis of bacterial meningitis by direct detection, serotyping and Next Generation Sequencing: How 10 years of testing in New York State has evolved to improve laboratory diagnosis and public health. Mol Cell Probes 2021; 61:101786. [PMID: 34863914 DOI: 10.1016/j.mcp.2021.101786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 11/09/2021] [Accepted: 11/27/2021] [Indexed: 11/23/2022]
Abstract
Since 2005, the Wadsworth Center (WC) has provided molecular testing on cerebrospinal fluid (CSF) and whole blood specimens in close collaboration with epidemiologists in New York State and New York City. In this study, we analyzed 10 years of data to demonstrate the significant value of utilizing molecular methods to assess patient specimens for etiologic agents of bacterial meningitis. A comprehensive molecular testing algorithm to detect and serotype/serogroup bacterial agents known to cause bacterial meningitis (Neisseria meningitidis, Streptococcus pneumoniae, Haemophilus influenzae and Streptococcus agalactiae) has evolved, and retrospective specimen testing has been essential for each improvement. Over a ten-year span from 2010 to 2019 the WC received 831 specimens from 634 patients with suspected bacterial meningitis. Real-time PCR was positive for at least one of the agents in 223 (27%) specimens from 183 patients (29%). Of the 223 positives, 146 (66%) were further characterized by real-time PCR into serogroup/serotype. Additionally, examination of 131 paired specimens of CSF and whole blood from the same patients found better detection in CSF, but whole blood is a useful alternative for diagnosis when CSF is not available. For specimens initially PCR-negative, 16S rDNA Sanger sequencing was requested by the submitter for 146 cases resulting in the identification of bacterial agents in an additional 24 (16%) specimens. In a retrospective study, Next Generation Sequencing (NGS) was evaluated for the detection of pathogens in 53 previously tested PCR-negative CSF specimens and identified bacteria in 14 (26%) specimens. This molecular testing algorithm has provided clinicians a diagnosis when culture is negative with the potential to guide therapy. It has also aided public health in determining when antibiotic prophylaxis was needed, augmented surveillance data to yield a fuller picture of community prevalence, and highlighted gaps in the spectrum of agents that cause bacterial meningitis.
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65
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Carbo EC, Blankenspoor I, Goeman JJ, Kroes ACM, Claas ECJ, De Vries JJC. Viral metagenomic sequencing in the diagnosis of meningoencephalitis: a review of technical advances and diagnostic yield. Expert Rev Mol Diagn 2021; 21:1139-1146. [PMID: 34607520 DOI: 10.1080/14737159.2021.1985467] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Meningoencephalitis patients are often severely impaired and benefit from early etiological diagnosis, though many cases remain without identified cause. Metagenomics as pathogen agnostic approach can result in additional etiological findings; however, the exact diagnostic yield when used as a secondary test remains unknown. AREAS COVERED This review aims to highlight recent advances with regard to wet and dry lab methodologies of metagenomic testing and technical milestones that have been achieved. A selection of procedures currently applied in accredited diagnostic laboratories is described in more detail to illustrate best practices. Furthermore, a meta-analysis was performed to assess the additional diagnostic yield utilizing metagenomic sequencing in meningoencephalitis patients. Finally, the remaining challenges for successful widespread implementation of metagenomic sequencing for the diagnosis of meningoencephalitis are addressed in a future perspective. EXPERT OPINION The last decade has shown major advances in technical possibilities for using mNGS in diagnostic settings including cloud-based analysis. An additional advance may be the current established infrastructure of platforms for bioinformatic analysis of SARS-CoV-2, which may assist to pave the way for global use of clinical metagenomics.
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Affiliation(s)
- Ellen C Carbo
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ivar Blankenspoor
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jelle J Goeman
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Aloys C M Kroes
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Eric C J Claas
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jutte J C De Vries
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
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66
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Zhang B, Zhou J, Gui R, Li Z, Zu Y, Wang J, Yu F, Zhang Y, Zhao H, Ji Z, Song Y. Metagenomic Next Generation Sequencing in the Detection of Pathogens in Cerebrospinal Fluid of Patients After Alternative Donor Transplantation: A Feasibility Analysis. Front Cell Infect Microbiol 2021; 11:720132. [PMID: 34595132 PMCID: PMC8476959 DOI: 10.3389/fcimb.2021.720132] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/20/2021] [Indexed: 11/19/2022] Open
Abstract
Central nervous system (CNS) complications can occur in 9%–15% of patients after allogeneic hematopoietic stem cell transplantation (allo-HSCT). The clinical manifestations of the CNS complications are non-specific, with most of them being disturbances of consciousness, convulsions, headaches, fever, and epilepsy, making it difficult to infer the cause of the complications based on clinical manifestations. We retrospectively analyzed the sensitivity and feasibility of metagenomic next generation sequencing (mNGS) in the diagnosis of CNS infections after allo-HSCT. Lumbar punctures were performed on 20 patients with CNS symptoms after receiving alternative donor HSCT(AD-HSCT) at the Affiliated Cancer Hospital of Zhengzhou University from February 2019 to December 2020, and their cerebrospinal fluid (CSF) was collected. The mNGS technique was used to detect pathogens in the CSF. Routine CSF testing, biochemical analyses, G experiments, GM experiments, ink staining, acid-fast staining, and bacterial cultures were carried out, and quantitative PCR (qPCR) tests were used to detect cytomegalovirus (CMV), Epstein-Barr virus (EBV), BK polyomavirus (BKPyV), and human alphaherpesvirus (HHV). A total of 29 tests were performed with 21 of them being positive. Of the five negative patients, three were diagnosed with a posterior reversible encephalopathy syndrome, one as having transplantation-associated thrombotic microangiopathy, and one with transient seizure caused by hypertension. Fifteen patients tested positive, of which four had single infections and eleven had mixed infections. Five cases of fungal infections, six cases of bacterial infections, and 13 cases of viral infections were detected. Among the 13 cases of viral infections, ten cases were CMV(HHV-5); three were BKPyV; two were Torque teno virus (TTV); Two were HHV-1,two were EBV(HHV4), and one each of HpyV5 and HHV-6B. Thirteen patients tested positive for virus while the qPCR detection method of 6 identical specimens were below the minimum detection limit(<1×103 U/ml). The mNGS technique is highly sensitive, and it can be used to diagnose CNS infections after allo-HSCT.
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Affiliation(s)
- Binglei Zhang
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China.,Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China.,Henan Academy of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China.,Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Jian Zhou
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Ruirui Gui
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Zhen Li
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Yingling Zu
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Juan Wang
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Fengkuan Yu
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Yanli Zhang
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Huifang Zhao
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Zhenyu Ji
- Henan Academy of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Yongping Song
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
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Piantadosi A, Mukerji SS, Ye S, Leone MJ, Freimark LM, Park D, Adams G, Lemieux J, Kanjilal S, Solomon IH, Ahmed AA, Goldstein R, Ganesh V, Ostrem B, Cummins KC, Thon JM, Kinsella CM, Rosenberg E, Frosch MP, Goldberg MB, Cho TA, Sabeti P. Enhanced Virus Detection and Metagenomic Sequencing in Patients with Meningitis and Encephalitis. mBio 2021; 12:e0114321. [PMID: 34465023 PMCID: PMC8406231 DOI: 10.1128/mbio.01143-21] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 07/02/2021] [Indexed: 01/21/2023] Open
Abstract
Meningitis and encephalitis are leading causes of central nervous system (CNS) disease and often result in severe neurological compromise or death. Traditional diagnostic workflows largely rely on pathogen-specific tests, sometimes over days to weeks, whereas metagenomic next-generation sequencing (mNGS) profiles all nucleic acid in a sample. In this single-center, prospective study, 68 hospitalized patients with known (n = 44) or suspected (n = 24) CNS infections underwent mNGS from RNA and DNA to identify potential pathogens and also targeted sequencing of viruses using hybrid capture. Using a computational metagenomic classification pipeline based on KrakenUniq and BLAST, we detected pathogen nucleic acid in cerebrospinal fluid (CSF) from 22 subjects, 3 of whom had no clinical diagnosis by routine workup. Among subjects diagnosed with infection by serology and/or peripheral samples, we demonstrated the utility of mNGS to detect pathogen nucleic acid in CSF, importantly for the Ixodes scapularis tick-borne pathogens Powassan virus, Borrelia burgdorferi, and Anaplasma phagocytophilum. We also evaluated two methods to enhance the detection of viral nucleic acid, hybrid capture and methylated DNA depletion. Hybrid capture nearly universally increased viral read recovery. Although results for methylated DNA depletion were mixed, it allowed the detection of varicella-zoster virus DNA in two samples that were negative by standard mNGS. Overall, mNGS is a promising approach that can test for multiple pathogens simultaneously, with efficacy similar to that of pathogen-specific tests, and can uncover geographically relevant infectious CNS disease, such as tick-borne infections in New England. With further laboratory and computational enhancements, mNGS may become a mainstay of workup for encephalitis and meningitis. IMPORTANCE Meningitis and encephalitis are leading global causes of central nervous system (CNS) disability and mortality. Current diagnostic workflows remain inefficient, requiring costly pathogen-specific assays and sometimes invasive surgical procedures. Despite intensive diagnostic efforts, 40 to 60% of people with meningitis or encephalitis have no clear cause of CNS disease identified. As diagnostic uncertainty often leads to costly inappropriate therapies, the need for novel pathogen detection methods is paramount. Metagenomic next-generation sequencing (mNGS) offers the unique opportunity to circumvent these challenges using unbiased laboratory and computational methods. Here, we performed comprehensive mNGS from 68 prospectively enrolled patients with known (n = 44) or suspected (n = 24) CNS viral infection from a single center in New England and evaluated enhanced methods to improve the detection of CNS pathogens, including those not traditionally identified in the CNS by nucleic acid detection. Overall, our work helps elucidate how mNGS can become integrated into the diagnostic toolkit for CNS infections.
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Affiliation(s)
- Anne Piantadosi
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Emory University School of Medicine, Atlanta, Georgia, USA
| | - Shibani S. Mukerji
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Simon Ye
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard-MIT Program of Health Sciences and Technology, Cambridge, Massachusetts, USA
| | - Michael J. Leone
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Lisa M. Freimark
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Daniel Park
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Gordon Adams
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Jacob Lemieux
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Sanjat Kanjilal
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Isaac H. Solomon
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Asim A. Ahmed
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Pediatrics, Harvard Medical School, Children’s Hospital, Boston, Massachusetts, USA
| | - Robert Goldstein
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Vijay Ganesh
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Neurology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Bridget Ostrem
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Kaelyn C. Cummins
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Jesse M. Thon
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Cormac M. Kinsella
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Eric Rosenberg
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Matthew P. Frosch
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Marcia B. Goldberg
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Tracey A. Cho
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- University of Iowa, Department of Neurology, Iowa City, Iowa, USA
| | - Pardis Sabeti
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
- Department of Immunology and Infectious Disease, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
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Feng C, Feng J, Wang Z, Pedersen C, Wang X, Saleem H, Domier L, Marzano SYL. Identification of the Viral Determinant of Hypovirulence and Host Range in Sclerotiniaceae of a Genomovirus Reconstructed from the Plant Metagenome. J Virol 2021; 95:e0026421. [PMID: 34132570 PMCID: PMC8354332 DOI: 10.1128/jvi.00264-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 06/09/2021] [Indexed: 12/14/2022] Open
Abstract
Uncharacterized viral genomes that encode circular replication-associated proteins of single-stranded DNA viruses have been discovered by metagenomics/metatranscriptomics approaches. Some of these novel viruses are classified in the newly formed family Genomoviridae. Here, we determined the host range of a novel genomovirus, SlaGemV-1, through the transfection of Sclerotinia sclerotiorum with infectious clones. Inoculating with the rescued virions, we further transfected Botrytis cinerea and Monilinia fructicola, two economically important members of the family Sclerotiniaceae, and Fusarium oxysporum. SlaGemV-1 causes hypovirulence in S. sclerotiorum, B. cinerea, and M. fructicola. SlaGemV-1 also replicates in Spodoptera frugiperda insect cells but not in Caenorhabditis elegans or plants. By expressing viral genes separately through site-specific integration, the replication protein alone was sufficient to cause debilitation. Our study is the first to demonstrate the reconstruction of a metagenomically discovered genomovirus without known hosts with the potential of inducing hypovirulence, and the infectious clone allows for studying mechanisms of genomovirus-host interactions that are conserved across genera. IMPORTANCE Little is known about the exact host range of widespread genomoviruses. The genome of soybean leaf-associated gemygorvirus-1 (SlaGemV-1) was originally assembled from a metagenomic/metatranscriptomic study without known hosts. Here, we rescued SlaGemV-1 and found that it could infect three important plant-pathogenic fungi and fall armyworm (S. frugiperda Sf9) insect cells but not a model nematode, C. elegans, or model plant species. Most importantly, SlaGemV-1 shows promise for inducing hypovirulence of the tested fungal species in the family Sclerotiniaceae, including Sclerotinia sclerotiorum, Botrytis cinerea, and Monilinia fructicola. The viral determinant of hypovirulence was further identified as replication initiation protein. As a proof of concept, we demonstrate that viromes discovered in plant metagenomes can be a valuable genetic resource when novel viruses are rescued and characterized for their host range.
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Affiliation(s)
- Chenchen Feng
- Department of Horticulture, Agronomy, and Plant Sciences, South Dakota State University, Brookings, South Dakota, USA
| | - Jiuhuan Feng
- Department of Horticulture, Agronomy, and Plant Sciences, South Dakota State University, Brookings, South Dakota, USA
| | - Ziyi Wang
- Department of Horticulture, Agronomy, and Plant Sciences, South Dakota State University, Brookings, South Dakota, USA
| | - Connor Pedersen
- Department of Biology and Microbiology, South Dakota State University, Brookings, South Dakota, USA
| | - Xiuqing Wang
- Department of Biology and Microbiology, South Dakota State University, Brookings, South Dakota, USA
| | - Huma Saleem
- Department of Biology and Microbiology, South Dakota State University, Brookings, South Dakota, USA
| | - Leslie Domier
- United States Department of Agriculture/Agricultural Research Service, Urbana, Illinois, USA
| | - Shin-Yi Lee Marzano
- Department of Horticulture, Agronomy, and Plant Sciences, South Dakota State University, Brookings, South Dakota, USA
- Department of Biology and Microbiology, South Dakota State University, Brookings, South Dakota, USA
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69
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Zhao E, Wang D, Li N, Huang S, Zhao Z, Hu S, He X, Wen G. Clinical study on the diagnosis of porcine streptococcal meningitis with negative blood and cerebrospinal fluid culture by next-generation sequencing. Eur J Med Res 2021; 26:85. [PMID: 34344456 PMCID: PMC8330088 DOI: 10.1186/s40001-021-00554-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 07/15/2021] [Indexed: 11/21/2022] Open
Abstract
Background Streptococcus suis (Ss) is a Gram-positive and anaerobic zoonotic pathogen that is susceptible to all populations and can cause meningitis, septicemia, endocarditis and arthritis in humans. Methods In this study, patients with meningitis who were admitted to our hospital with negative blood and cerebrospinal fluid culture were divided into a next-generation sequencing group and a control group. In the next-generation sequencing group, we used the next-generation sequencing method to detect pathogenic bacteria in the patients’ cerebrospinal fluid. In the control group, we used blood and cerebrospinal fluid bacterial culture method to detect pathogenic bacteria in the patients' cerebrospinal fluid. The detection rates of pathogenic bacteria in the cerebrospinal fluid of the two groups were compared and analyzed. Results A total of 18 patients were included in this study, including 8 patients in the next-generation sequencing group and 10 patients in the control group. The mean age (P = 0.613) and mean disease duration (P = 0.294) were similar in both groups. Patients in the next-generation sequencing group had a leukocyte count of 13.13 ± 4.79 × 109, a neutrophil percentage of 83.39 ± 10.36%, and a C-reactive protein level of 134.95 ± 107.69 mg/L. Patients in the control group had a temperature of 38.32 ± 1.07, a leukocyte count of 8.00 ± 2.99 × 109, and a neutrophil percentage of 74.61 ± 8.89%, and C-reactive protein level was 4.75 ± 6.8 mg/L. The statistical results showed that the leukocytes (P = 0.013) and C-reactive protein levels (P = 0.001) were significantly higher in the patients of the next-generation sequencing group than in the control group. No statistically significant differences were seen in body temperature and neutrophil percentage between the two groups (P > 0.05). The incidence of intracranial pressure and meningeal irritation signs were similar in the two groups (P > 0.05). The detection rate of Streptococcus suis in the cerebrospinal fluid of patients in the next-generation sequencing group was 100%, and the detection rate of Streptococcus suis in the cerebrospinal fluid of the control group was 0%. Conclusion The detection rate of Streptococcus suis infection in cerebrospinal fluid by next-generation sequencing was significantly higher than that by blood and cerebrospinal fluid bacterial culture. Therefore, the diagnosis of porcine streptococcal meningitis by next-generation sequencing method is worthy of clinical promotion and application.
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Affiliation(s)
- Eryi Zhao
- Department of Neurology, Hainan General Hospital, Hainan Affilicated Hospital of Hainan Medical University, Haikou, 570311, Hainan, China
| | - Daimei Wang
- Department of Pharmacy, Hainan General Hospital, Hainan Affilicated Hospital of Hainan Medical University, Haikou, 570311, Hainan, China
| | - Na Li
- Department of Pharmacy, Qianjiang Central Hospital of Chongqing, No. 63 of Road 9, Chengxi Street, Qianjiang District, Chongqing, 409099, China.
| | - Shixiong Huang
- Department of Neurology, Hainan General Hospital, Hainan Affilicated Hospital of Hainan Medical University, Haikou, 570311, Hainan, China
| | - Zhongyan Zhao
- Department of Neurology, Hainan General Hospital, Hainan Affilicated Hospital of Hainan Medical University, Haikou, 570311, Hainan, China
| | - Shijun Hu
- Department of Neurology, Hainan General Hospital, Hainan Affilicated Hospital of Hainan Medical University, Haikou, 570311, Hainan, China
| | - Xiangying He
- Department of Neurology, Hainan General Hospital, Hainan Affilicated Hospital of Hainan Medical University, Haikou, 570311, Hainan, China
| | - Guoqiang Wen
- Department of Neurology, Hainan General Hospital, Hainan Affilicated Hospital of Hainan Medical University, Haikou, 570311, Hainan, China
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de Vries JJ, Brown JR, Fischer N, Sidorov IA, Morfopoulou S, Huang J, Munnink BBO, Sayiner A, Bulgurcu A, Rodriguez C, Gricourt G, Keyaerts E, Beller L, Bachofen C, Kubacki J, Cordey S, Laubscher F, Schmitz D, Beer M, Hoeper D, Huber M, Kufner V, Zaheri M, Lebrand A, Papa A, van Boheemen S, Kroes AC, Breuer J, Lopez-Labrador FX, Claas EC. Benchmark of thirteen bioinformatic pipelines for metagenomic virus diagnostics using datasets from clinical samples. J Clin Virol 2021; 141:104908. [PMID: 34273858 PMCID: PMC7615111 DOI: 10.1016/j.jcv.2021.104908] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 05/18/2021] [Accepted: 06/30/2021] [Indexed: 12/22/2022]
Abstract
INTRODUCTION Metagenomic sequencing is increasingly being used in clinical settings for difficult to diagnose cases. The performance of viral metagenomic protocols relies to a large extent on the bioinformatic analysis. In this study, the European Society for Clinical Virology (ESCV) Network on NGS (ENNGS) initiated a benchmark of metagenomic pipelines currently used in clinical virological laboratories. METHODS Metagenomic datasets from 13 clinical samples from patients with encephalitis or viral respiratory infections characterized by PCR were selected. The datasets were analyzed with 13 different pipelines currently used in virological diagnostic laboratories of participating ENNGS members. The pipelines and classification tools were: Centrifuge, DAMIAN, DIAMOND, DNASTAR, FEVIR, Genome Detective, Jovian, MetaMIC, MetaMix, One Codex, RIEMS, VirMet, and Taxonomer. Performance, characteristics, clinical use, and user-friendliness of these pipelines were analyzed. RESULTS Overall, viral pathogens with high loads were detected by all the evaluated metagenomic pipelines. In contrast, lower abundance pathogens and mixed infections were only detected by 3/13 pipelines, namely DNASTAR, FEVIR, and MetaMix. Overall sensitivity ranged from 80% (10/13) to 100% (13/13 datasets). Overall positive predictive value ranged from 71-100%. The majority of the pipelines classified sequences based on nucleotide similarity (8/13), only a minority used amino acid similarity, and 6 of the 13 pipelines assembled sequences de novo. No clear differences in performance were detected that correlated with these classification approaches. Read counts of target viruses varied between the pipelines over a range of 2-3 log, indicating differences in limit of detection. CONCLUSION A wide variety of viral metagenomic pipelines is currently used in the participating clinical diagnostic laboratories. Detection of low abundant viral pathogens and mixed infections remains a challenge, implicating the need for standardization and validation of metagenomic analysis for clinical diagnostic use. Future studies should address the selective effects due to the choice of different reference viral databases.
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Affiliation(s)
- Jutte J.C. de Vries
- Clinical Microbiological Laboratory, department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Julianne R. Brown
- Microbiology, Virology and Infection Prevention & Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Nicole Fischer
- University Medical Center Hamburg-Eppendorf, UKE Institute for Medical Microbiology, Virology and Hygiene, Germany
| | - Igor A. Sidorov
- Clinical Microbiological Laboratory, department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Sofia Morfopoulou
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Jiabin Huang
- University Medical Center Hamburg-Eppendorf, UKE Institute for Medical Microbiology, Virology and Hygiene, Germany
| | | | - Arzu Sayiner
- Dokuz Eylul University, Medical Faculty, Izmir, Turkey
| | | | | | | | - Els Keyaerts
- Laboratory of Clinical and Epidemiological Virology (Rega Institute), KU Leuven, Belgium
| | - Leen Beller
- Laboratory of Clinical and Epidemiological Virology (Rega Institute), KU Leuven, Belgium
| | | | - Jakub Kubacki
- Institute of Virology, University of Zurich, Switzerland
| | - Samuel Cordey
- Laboratory of Virology, University Hospitals of Geneva, Geneva, Switzerland
| | - Florian Laubscher
- Laboratory of Virology, University Hospitals of Geneva, Geneva, Switzerland
| | - Dennis Schmitz
- RIVM National Institute for Public Health and Environment, Bilthoven, the Netherlands
| | - Martin Beer
- Friedrich-Loeffler-Institute, Institute of Diagnostic Virology, Greifswald, Germany
| | - Dirk Hoeper
- Friedrich-Loeffler-Institute, Institute of Diagnostic Virology, Greifswald, Germany
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Switzerland
| | - Verena Kufner
- Institute of Medical Virology, University of Zurich, Switzerland
| | - Maryam Zaheri
- Institute of Medical Virology, University of Zurich, Switzerland
| | | | - Anna Papa
- Department of Microbiology, Medical School, Aristotle University of Thessaloniki, Greece
| | | | - Aloys C.M. Kroes
- Clinical Microbiological Laboratory, department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Judith Breuer
- Microbiology, Virology and Infection Prevention & Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - F. Xavier Lopez-Labrador
- Virology Laboratory, Genomics and Health Area, Center for Public Health Research (FISABIO-Public Health), Generalitat Valenciana and Microbiology & Ecology Department, University of Valencia, Spain
- CIBERESP, Instituto de Salud Carlos III, Spain
| | - Eric C.J. Claas
- Clinical Microbiological Laboratory, department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
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Shi Y, Chen J, Shi X, Hu J, Li H, Li X, Wang Y, Wu B. A case of chlamydia psittaci caused severe pneumonia and meningitis diagnosed by metagenome next-generation sequencing and clinical analysis: a case report and literature review. BMC Infect Dis 2021; 21:621. [PMID: 34193063 PMCID: PMC8243071 DOI: 10.1186/s12879-021-06205-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 05/18/2021] [Indexed: 12/19/2022] Open
Abstract
Background Psittacosis, which is also known as parrot fever, is Chlamydia psittaci (C. psittaci) caused infectious disease. The clinical manifestations vary from asymptomatic infection to severe atypical pneumonia or even fatal meningitis. Early recognition of psittacosis is difficult because of its nonspecific clinical manifestations. Culture and gene probe techniques for C. psittaci are not available for routine clinical use, which makes the diagnosis difficult too. Although psittacosis has increasingly been recognized and reported in recent years, cure of severe pneumonia complicated with meningitis, with etiologic diagnosis aided by the use of metagenomic next-generation sequencing (mNGS), is still uncommon. So, it is necessary to report and review such potentially fatal case. Case presentation This report describes a 54-year-old woman with C. psittaci caused severe atypical pneumonia and meningitis. She presented with symptoms of fever, dry cough and dyspnea, accompanied by prominent headache. Her condition deteriorated rapidly to respiratory failure and lethargy under the treatment of empirical antibacterial agents, and was treated with invasive mechanical ventilation soon. She denied contact with birds, poultry or horses, but unbiased mNGS of both the bronchoalveolar lavage fluid (BALF) and the cerebrospinal fluid (CSF) identified sequence reads corresponding to C. psittaci infection, and there was no sequence read corresponding to other probable pathogens. Combined use of targeted antimicrobial agents of tetracyclines, macrolides and fluoroquinolones was carried out, and the patient’s condition improved and she was discharged home 28 days later. Her status returned close to premorbid condition on day 60 of follow-up. Conclusions When clinicians come across a patient with atypical pneumonia accompanied by symptoms of meningitis, psittacosis should be taken into consideration. mNGS is a promising detection method in such condition and is recommended. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-021-06205-5.
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Affiliation(s)
- Yunfeng Shi
- Medical Intensive Care Unit, Department of Respiratory and Critical Care Medicine, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China.,Institute of Respiratory Diseases, Sun Yat-Sen University, Guangzhou, China
| | - Junxian Chen
- Medical Intensive Care Unit, Department of Respiratory and Critical Care Medicine, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China.,Institute of Respiratory Diseases, Sun Yat-Sen University, Guangzhou, China
| | - Xiaohan Shi
- Medical Intensive Care Unit, Department of Respiratory and Critical Care Medicine, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China. .,Institute of Respiratory Diseases, Sun Yat-Sen University, Guangzhou, China.
| | - Jiajia Hu
- Medical Intensive Care Unit, Department of Respiratory and Critical Care Medicine, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China.,Institute of Respiratory Diseases, Sun Yat-Sen University, Guangzhou, China
| | - Hongtao Li
- Medical Intensive Care Unit, Department of Respiratory and Critical Care Medicine, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China.,Institute of Respiratory Diseases, Sun Yat-Sen University, Guangzhou, China
| | - Xiaojie Li
- Department of Laboratory Medicine, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China
| | - Yanhong Wang
- Medical Intensive Care Unit, Department of Respiratory and Critical Care Medicine, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China.,Institute of Respiratory Diseases, Sun Yat-Sen University, Guangzhou, China
| | - Benquan Wu
- Medical Intensive Care Unit, Department of Respiratory and Critical Care Medicine, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China. .,Institute of Respiratory Diseases, Sun Yat-Sen University, Guangzhou, China.
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72
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Chen B, Chen Z, Yang YS, Cai GL, Xu XJ, Guan HZ, Ren HT, Tuo HZ. Next-generation sequencing combined with serological tests based pathogen analysis for a neurocysticercosis patient with a 20-year history:a case report. BMC Neurol 2021; 21:236. [PMID: 34167488 PMCID: PMC8222500 DOI: 10.1186/s12883-021-02277-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 06/10/2021] [Indexed: 11/17/2022] Open
Abstract
Background Neurocysticercosis (NCC) is the most common helminthic infection of the central nervous system (CNS) caused by the larval stage of Taenia solium. Accurate and early diagnosis of NCC remains challenging due to its heterogeneous clinical manifestations, neuroimaging deficits, variable sensitivity, and specificity of serological tests. Next-generation sequencing (NGS)-based pathogen analysis in patient’s cerebrospinal fluid (CSF) with NCC infection has recently been reported indicating its diagnostic efficacy. In this case study, we report the diagnosis of a NCC patient with a symptomatic history of over 20 years using NGS analysis and further confirmation of the pathology by immunological tests. Case presentation This study reports the clinical imaging and immunological features of a patient with a recurrent headache for more than 20 years, which worsened gradually with the symptom of fever for more than 7 years and paroxysmal amaurosis for more than 1 year. By utilizing NGS technique, the pathogen was detected in patient’s CSF, and the presence of Taenia solium-DNA was confirmed by a positive immunological reaction to cysticercus IgG antibody in CSF and serum samples. The symptoms of the patient were alleviated, and the CSF condition was improved substantially after the anti-helminthic treatment. Conclusions This study suggests that combining CSF NGS with cysticercus IgG testing may be a highly promising approach for diagnosing the challenging cases of NCC. Further studies are needed to evaluate the parasitic DNA load in patients’ CSF for the diagnosis of disease severity, stage, and monitoring of therapeutic responses.
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Affiliation(s)
- Bin Chen
- Department of Neurology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Zheng Chen
- Department of Neurology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Yi-Shu Yang
- Department of Neurology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Gui-Lan Cai
- Department of Neurology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Xiao-Jiao Xu
- Department of Neurology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Hong-Zhi Guan
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hai-Tao Ren
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hou-Zhen Tuo
- Department of Neurology, Beijing Friendship Hospital, Capital Medical University, Beijing, China.
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Anh NT, Nhu LNT, Hong NTT, Phuc TM, Tam PTT, Huong DT, Anh TT, Deng X, Nghia HDT, Nguyen TT, Van Hung N, Thuan ND, Phuong PTH, Chau NVV, Baker S, Delwart E, Thwaites G, Van Tan L. Viral Metagenomic Analysis of Cerebrospinal Fluid from Patients with Acute Central Nervous System Infections of Unknown Origin, Vietnam. Emerg Infect Dis 2021; 27:205-213. [PMID: 33350920 PMCID: PMC7774551 DOI: 10.3201/eid2701.202723] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Central nervous system (CNS) infection is a serious neurologic condition, although the etiology remains unknown in >50% of patients. We used metagenomic next-generation sequencing to detect viruses in 204 cerebrospinal fluid (CSF) samples from patients with acute CNS infection who were enrolled from Vietnam hospitals during 2012–2016. We detected 8 viral species in 107/204 (52.4%) of CSF samples. After virus-specific PCR confirmation, the detection rate was lowered to 30/204 (14.7%). Enteroviruses were the most common viruses detected (n = 23), followed by hepatitis B virus (3), HIV (2), molluscum contagiosum virus (1), and gemycircularvirus (1). Analysis of enterovirus sequences revealed the predominance of echovirus 30 (9). Phylogenetically, the echovirus 30 strains belonged to genogroup V and VIIb. Our results expanded knowledge about the clinical burden of enterovirus in Vietnam and underscore the challenges of identifying a plausible viral pathogen in CSF of patients with CNS infections.
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74
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Regnault B, Evrard B, Plu I, Dacheux L, Troadec E, Cozette P, Chrétien D, Duchesne M, Jean-Michel V, Jamet A, Leruez M, Pérot P, Bourhy H, Eloit M, Seilhean D. First case of lethal encephalitis in Western Europe due to European bat lyssavirus type 1. Clin Infect Dis 2021; 74:461-466. [PMID: 33991184 DOI: 10.1093/cid/ciab443] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Inaccurate diagnosis of encephalitis is a major issue as immunosuppressive treatments can be deleterious in case of viral infection. The European bat lyssavirus type 1, a virus related to rabies virus, is endemic in European bats. No human case has yet been reported in Western Europe. A 59 year-old patient without specific past medical history died from encephalitis. A colony of bats lived in an outbuilding of his house. No diagnosis was made using standard procedures. METHODS We used a Next Generation Sequencing (NGS) based transcriptomic protocol to search for pathogens in autopsy samples (meninges and brain frontal lobe). Results were confirmed by PCR and by antibody testing in serum. Immunochemistry was used to characterize inflammatory cells and viral antigens in brain lesions. Cells and mice were inoculated with brain extracts for virus isolation. RESULTS The patient's brain lesions were severe and diffuse in white and gray matter. Perivascular inflammatory infiltrates were abundant and rich in plasma cells. NGS identified European bat lyssavirus type 1a in brain, which was confirmed by PCR. A high titer of neutralizing antibodies was found in serum. No viral antigen was detected and the virus could not be isolated by cell culture or by mouse inoculation. CONCLUSIONS The patient died from European bat lyssavirus type 1a infection. NGS was key to identifying this unexpected viral etiology in an epidemiological context that did not suggest rabies. People exposed to bats should be strongly advised to be vaccinated with rabies vaccines, which are effective against EBLV-1.
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Affiliation(s)
- Béatrice Regnault
- Pathogen Discovery Laboratory, Institut Pasteur, Paris, France.,The OIE Collaborating Center for the detection and identification in humans of emerging animal pathogens, Institut Pasteur, Paris, France)
| | - Bruno Evrard
- Medical-Surgical Intensive Care Unit, Dupuytren University Hospital, Limoges, France.,Inserm CIC 1435 and UMR 1092, Dupuytren Teaching Hospital, Limoges, France
| | - Isabelle Plu
- Sorbonne Université, Brain Institute (ICM; INSERM, UMRS 1127; CNRS, UMR 7225), Paris, France.,Département de Neuropathologie Raymond Escourolle, AP-HP-Sorbonne, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Laurent Dacheux
- Lyssavirus Epidemiology and Neuropathology Unit, National Reference Centre for Rabies, WHO Collaborative Centre for Reference and Research on Rabies, Institut Pasteur, Paris, France
| | - Eric Troadec
- Pathogen Discovery Laboratory, Institut Pasteur, Paris, France.,The OIE Collaborating Center for the detection and identification in humans of emerging animal pathogens, Institut Pasteur, Paris, France)
| | - Pascal Cozette
- Lyssavirus Epidemiology and Neuropathology Unit, National Reference Centre for Rabies, WHO Collaborative Centre for Reference and Research on Rabies, Institut Pasteur, Paris, France
| | - Delphine Chrétien
- Pathogen Discovery Laboratory, Institut Pasteur, Paris, France.,The OIE Collaborating Center for the detection and identification in humans of emerging animal pathogens, Institut Pasteur, Paris, France)
| | - Mathilde Duchesne
- Pathology Department, Dupuytren University Hospital, Limoges, France
| | | | - Anne Jamet
- Department of Clinical Microbiology, Necker Enfants-Malades Hospital, AP-HP, Centre Université de Paris, Paris, France
| | - Marianne Leruez
- Department of Clinical Microbiology, Necker Enfants-Malades Hospital, AP-HP, Centre Université de Paris, Paris, France
| | - Philippe Pérot
- Pathogen Discovery Laboratory, Institut Pasteur, Paris, France.,The OIE Collaborating Center for the detection and identification in humans of emerging animal pathogens, Institut Pasteur, Paris, France)
| | - Hervé Bourhy
- Lyssavirus Epidemiology and Neuropathology Unit, National Reference Centre for Rabies, WHO Collaborative Centre for Reference and Research on Rabies, Institut Pasteur, Paris, France
| | - Marc Eloit
- Pathogen Discovery Laboratory, Institut Pasteur, Paris, France.,The OIE Collaborating Center for the detection and identification in humans of emerging animal pathogens, Institut Pasteur, Paris, France).,Ecole Nationale Vétérinaire d'Alfort, Maisons-Alfort, France
| | - Danielle Seilhean
- Sorbonne Université, Brain Institute (ICM; INSERM, UMRS 1127; CNRS, UMR 7225), Paris, France.,Lyssavirus Epidemiology and Neuropathology Unit, National Reference Centre for Rabies, WHO Collaborative Centre for Reference and Research on Rabies, Institut Pasteur, Paris, France
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Mathon B, Pineton de Chambrun M, Bielle F, Amelot A, Le Joncour A. Encephalitis of Unknown Etiology? Not Until the Results of a Brain Biopsy! Clin Infect Dis 2021; 72:e432. [PMID: 32756947 DOI: 10.1093/cid/ciaa1093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Bertrand Mathon
- Department of Neurosurgery, Assistance Publique - Hôpitaux de Paris, La Pitié-Salpêtrière, Charles Foix University Hospital, Paris, France.,Sorbonne University, Université Pierre et Marie Curie University Paris, Paris, France.,Brain and Spine Institute (Institut du Cerveau et de la Moelle Epinière; INSERM, UMRS 1127; Centre national de la recherche scientifique, Unité Mixte de Recherche 7225), Paris, France
| | - Marc Pineton de Chambrun
- Sorbonne University, Université Pierre et Marie Curie University Paris, Paris, France.,Department of Internal Medicine 2, AP-HP, La Pitié-Salpêtrière, Charles Foix University Hospital, Paris, France.,Department of Intensive Care Medicine, AP-HP, La Pitié-Salpêtrière, Charles Foix University Hospital, Paris, France.,Sorbonne Université, Institut National de la santé et de la recherche médicale, UMRS_1166-Institute of Cardiometabolism and Nutrition, Institute of Cardiometabolism and Nutrition, Paris, France
| | - Franck Bielle
- Sorbonne University, Université Pierre et Marie Curie University Paris, Paris, France.,Brain and Spine Institute (Institut du Cerveau et de la Moelle Epinière; INSERM, UMRS 1127; Centre national de la recherche scientifique, Unité Mixte de Recherche 7225), Paris, France.,Department of Neuropathology, AP-HP, La Pitié-Salpêtrière, Charles Foix University Hospital, Paris, France
| | - Aymeric Amelot
- Department of Neurosurgery, Assistance Publique - Hôpitaux de Paris, La Pitié-Salpêtrière, Charles Foix University Hospital, Paris, France
| | - Alexandre Le Joncour
- Department of Internal Medicine and Clinical Immunology, AP-HP, La Pitié-Salpêtrière, Charles Foix University Hospital, Paris, France
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76
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Erdem G, Kaptsan I, Sharma H, Kumar A, Aylward SC, Kapoor A, Shimamura M. Cerebrospinal Fluid Analysis for Viruses by Metagenomic Next-Generation Sequencing in Pediatric Encephalitis: Not Yet Ready for Prime Time? J Child Neurol 2021; 36:350-356. [PMID: 33206020 DOI: 10.1177/0883073820972232] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND Metagenomic next-generation sequencing offers an unbiased approach to identifying viral pathogens in cerebrospinal fluid of patients with meningoencephalitis of unknown etiology. METHODS In an 11-month case series, we investigated the use of cerebrospinal fluid metagenomic next-generation sequencing to diagnose viral infections among pediatric hospitalized patients presenting with encephalitis or meningoencephalitis of unknown etiology. Cerebrospinal fluid from patients with known enterovirus meningitis were included as positive controls. Cerebrospinal fluid from patients with primary intracranial hypertension were included to serve as controls without known infections. RESULTS Cerebrospinal fluid metagenomic next-generation sequencing was performed for 37 patients. Among 27 patients with encephalitis or meningoencephalitis, 4 were later diagnosed with viral encephalitis, 6 had non-central nervous system infections with central nervous system manifestations, 6 had no positive diagnostic tests, and 11 were found to have a noninfectious diagnosis. Metagenomic next-generation sequencing identified West Nile virus (WNV) in the cerebrospinal fluid of 1 immunocompromised patient. Among the 4 patients with known enterovirus meningitis, metagenomic next-generation sequencing correctly identified enteroviruses and characterized the viral genotype. No viral sequences were detected in the cerebrospinal fluid of patients with primary intracranial hypertension. Metagenomic next-generation sequencing also identified sequences of nonpathogenic torque Teno virus in cerebrospinal fluid specimens from 13 patients. CONCLUSIONS Our results showed viral detection by cerebrospinal fluid metagenomic next-generation sequencing only in 1 immunocompromised patient and did not offer a diagnostic advantage over conventional testing. Viral phylogenetic characterization by metagenomic next-generation sequencing could be used in epidemiologic investigations of some viral pathogens, such as enteroviruses. The finding of torque Teno viruses in cerebrospinal fluid by metagenomic next-generation sequencing is of unknown significance but may merit further exploration for a possible association with noninfectious central nervous system disorders.
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Affiliation(s)
- Guliz Erdem
- Division of Infectious Diseases, Department of Pediatrics, 2650Nationwide Children's Hospital and The Ohio State University, Columbus, OH, USA
| | - Irina Kaptsan
- Center for Vaccines and Immunity, the Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Himanshu Sharma
- Center for Vaccines and Immunity, the Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Arvind Kumar
- Center for Vaccines and Immunity, the Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Shawn C Aylward
- Division of Neurology, Department of Pediatrics, 2650Nationwide Children's Hospital and The Ohio State University, Columbus, OH, USA
| | - Amit Kapoor
- Center for Vaccines and Immunity, the Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Masako Shimamura
- Division of Infectious Diseases, Department of Pediatrics, 2650Nationwide Children's Hospital and The Ohio State University, Columbus, OH, USA.,Center for Vaccines and Immunity, the Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
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77
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Peng JM, Du B, Qin HY, Wang Q, Shi Y. Metagenomic next-generation sequencing for the diagnosis of suspected pneumonia in immunocompromised patients. J Infect 2021; 82:22-27. [PMID: 33609588 DOI: 10.1016/j.jinf.2021.01.029] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 12/18/2020] [Accepted: 01/12/2021] [Indexed: 12/17/2022]
Abstract
OBJECTIVES To evaluate the potential of metagenomic next-generation sequencing (mNGS), compared with that of comprehensive conventional microbiological tests (CMTs), of bronchoalveolar lavage fluid (BALF) as a front-line diagnostic for immunocompromised patients with suspected pneumonia. METHODS Sixty critically ill immunocompromised patients undergoing both mNGS of BALF and CMTs for suspected pneumonia were retrospectively analysed. The diagnostic performance was compared between mNGS and CMTs, using the composite diagnosis as the reference standard. RESULTS Forty-nine patients were diagnosed with microbiologically confirmed pneumonia, with 55% having polymicrobial infections. There was no significant difference in the overall diagnostic accuracy between mNGS and CMTs (61.7% vs 76.7%; P = 0.11). mNGS and CMTs had comparable diagnostic accuracy for bacterial and viral infections. Although mNGS identified more viral pneumonia, it had a much lower diagnostic accuracy for fungal infections (76.7% vs 99.2%; P < 0.001), mainly due to the low sensitivity for invasive pulmonary aspergillosis (45.5% vs 100%; P < 0.001). CONCLUSION The overall diagnostic performance of BALF mNGS as a first-line diagnostic was similar to that of comprehensive CMTs, except in the case of a lack of consideration of potential pathogens or limited CMTs. The combination of mNGS and CMTs may be the best diagnostic strategy.
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Affiliation(s)
- Jin-Min Peng
- Department of Medical Intensive Care Unit, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Bin Du
- Department of Medical Intensive Care Unit, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Han-Yu Qin
- Department of Medical Intensive Care Unit, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Qian Wang
- Department of Rheumatology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China; National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID) , Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing 100730, China
| | - Yan Shi
- Department of Medical Intensive Care Unit, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China
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78
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Tsamis KI, Sakkas H, Giannakis A, Ryu HS, Gartzonika C, Nikas IP. Evaluating Infectious, Neoplastic, Immunological, and Degenerative Diseases of the Central Nervous System with Cerebrospinal Fluid-Based Next-Generation Sequencing. Mol Diagn Ther 2021; 25:207-229. [PMID: 33646562 PMCID: PMC7917176 DOI: 10.1007/s40291-021-00513-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2021] [Indexed: 12/24/2022]
Abstract
Cerebrospinal fluid (CSF) is a clear and paucicellular fluid that circulates within the ventricular system and the subarachnoid space of the central nervous system (CNS), and diverse CNS disorders can impact its composition, volume, and flow. As conventional CSF testing suffers from suboptimal sensitivity, this review aimed to evaluate the role of next-generation sequencing (NGS) in the work-up of infectious, neoplastic, neuroimmunological, and neurodegenerative CNS diseases. Metagenomic NGS showed improved sensitivity—compared to traditional methods—to detect bacterial, viral, parasitic, and fungal infections, while the overall performance was maximized in some studies when all diagnostic modalities were used. In patients with primary CNS cancer, NGS findings in the CSF were largely concordant with the molecular signatures derived from tissue-based molecular analysis; of interest, additional mutations were identified in the CSF in some glioma studies, reflecting intratumoral heterogeneity. In patients with metastasis to the CNS, NGS facilitated diagnosis, prognosis, therapeutic management, and monitoring, exhibiting higher sensitivity than neuroimaging, cytology, and plasma-based molecular analysis. Although evidence is still rudimentary, NGS could enhance the diagnosis and pathogenetic understanding of multiple sclerosis in addition to Alzheimer and Parkinson disease. To conclude, NGS has shown potential to aid the research, facilitate the diagnostic approach, and improve the management outcomes of all the aforementioned CNS diseases. However, to establish its role in clinical practice, the clinical validity and utility of each NGS protocol should be determined. Lastly, as most evidence has been derived from small and retrospective studies, results from randomized control trials could be of significant value.
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Affiliation(s)
- Konstantinos I Tsamis
- Department of Neurology, University Hospital of Ioannina, 45500, Ioannina, Greece. .,School of Medicine, European University Cyprus, 2404, Nicosia, Cyprus.
| | - Hercules Sakkas
- Microbiology Department, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110, Ioannina, Greece
| | - Alexandros Giannakis
- Department of Neurology, University Hospital of Ioannina, 45500, Ioannina, Greece
| | - Han Suk Ryu
- Department of Pathology, Seoul National University Hospital, Seoul, 03080, Korea
| | - Constantina Gartzonika
- Microbiology Department, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110, Ioannina, Greece
| | - Ilias P Nikas
- School of Medicine, European University Cyprus, 2404, Nicosia, Cyprus
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79
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Lyu HR, He XY, Hao HJ, Lu WY, Jin X, Zhao YJ, Zhao MF. Noninvasive tools based on immune biomarkers for the diagnosis of central nervous system graft- vs-host disease: Two case reports and a review of the literature. World J Clin Cases 2021; 9:1359-1366. [PMID: 33644203 PMCID: PMC7896680 DOI: 10.12998/wjcc.v9.i6.1359] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 12/09/2020] [Accepted: 12/16/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Central nervous system graft-vs-host disease (CNS-GVHD) is a rare cause of CNS disorders after allogeneic hematopoietic stem cell transplantation. Currently, establishing a diagnosis of CNS-GVHD is challenging because the diagnostic criteria and diagnostic methods are not well defined and many confounding factors need to be ruled out.
CASE SUMMARY Here, we present two patients with CNS-GVHD. Both patients with a history of acute GVHD or chronic GVHD developed neurological symptoms that could not be explained by other causes, and had abnormal cerebrospinal fluid (CSF) studies as determined by CSF and blood immune biomarker examinations, suggestive of suspected CNS-GVHD. Due to the lack of specific magnetic resonance imaging abnormalities and the rapid clinical deterioration of the patients, we did not attempt to perform a brain biopsy, but prompted the initiation of empirical immunosuppressive therapy. In view of the rapid and favorable response to local and systematic immunosuppressive treatment and the aforementioned neurologic manifestations together with CSF abnormalities and other negative findings, a final diagnosis of CNS-GVHD was made.
CONCLUSION CSF and blood immune biomarker examinations facilitated the diagnosis of CNS-GVHD, which are particularly suitable for patients who are critically ill and require urgent treatment and for those who are unsuitable for invasive diagnostic procedures.
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Affiliation(s)
- Hai-Rong Lyu
- Department of Hematology, Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin 300192, China
| | - Xiao-Yuan He
- Department of Hematology, Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin 300192, China
| | - Hong-Jun Hao
- Department of Neurology, Peking University First Hospital, Beijing 100034, China
| | - Wen-Yi Lu
- Department of Hematology, Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin 300192, China
| | - Xin Jin
- School of Medicine, Nankai University, Tianjin 300071, China
| | - Yu-Jiao Zhao
- Department of Radiology, Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin 300192, China
| | - Ming-Feng Zhao
- Department of Hematology, Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin 300192, China
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Abstract
PURPOSE OF REVIEW Neurological conditions associated with HIV/AIDS including central nervous system (CNS), opportunistic infections (OI), chronic conditions including HIV-associated neurocognitive disorder, and cerebrospinal fluid (CSF) viral escape remain major contributors to morbidity and mortality worldwide. CNS infections in HIV-infected patients are often challenging to diagnose by traditional microbiological testing, impacting treatment and outcome. RECENT FINDINGS Recent advances in diagnostic techniques, including metagenomic next-generation sequencing (mNGS), are changing the landscape of microbiological testing, mainly in resource-rich settings. Pathogen discovery techniques offer a hypothesis-free approach to diagnostic testing, yielding comprehensive analysis of microbial genetic material. Given the extent of genetic material produced, deep sequencing tools not only hold promise in the diagnosis of CNS infections but also in defining key pathogenic steps which have previously been unanswered. Significant challenges remain to implementing pathogen discovery techniques in routine clinical practice including cost, expertise and infrastructure needed including laboratory and bioinformatics support, and sample contamination risk. The use in resource-limited regions where the burden of CNS complications due to HIV/AIDS is highest remains poorly defined. Though, major opportunities utilizing pathogen discovery techniques exist to enhance surveillance and diagnosis and improve our understanding of mechanisms of neuroinvasion in CNS conditions associated with HIV.
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Affiliation(s)
- Kiran T Thakur
- Columbia University Irving Medical Center, New York, NY, USA. .,New York Presbyterian Hospital, New York, NY, USA.
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81
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Wu X, Yan G, Han S, Ye Y, Cheng X, Gong H, Yu H. Diagnosing Balamuthia mandrillaris encephalitis via next-generation sequencing in a 13-year-old girl. Emerg Microbes Infect 2021; 9:1379-1387. [PMID: 32552393 PMCID: PMC7473209 DOI: 10.1080/22221751.2020.1775130] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Balamuthia amoebic encephalitis has a subacute-to-chronic course and is almost invariably fatal owing to delayed diagnosis and a lack of effective therapy. Here, we report a 13-year-old girl with cutaneous lesions and multifocal granulomatous encephalitis. The patient underwent a series of tests and was suspected as having tuberculosis. She was treated with various empiric therapies without improvement. She was finally correctly diagnosed via next-generation sequencing of the cerebrospinal fluid. The patient deteriorated rapidly and died 2 months after being diagnosed with Balamuthia mandrillaris encephalitis. This study highlights the important clinical significance of next-generation sequencing, which provides better diagnostic testing for unexplained paediatric encephalitis, especially that caused by rare or emerging pathogens.
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Affiliation(s)
- Xia Wu
- Department of Infectious Diseases, Children's Hospital of Fudan University, Shanghai, People's Republic of China
| | - Gangfeng Yan
- Department of Pediatric Emergency Medicine and Critical Care Medicine, Children's Hospital of Fudan University, Shanghai, People's Republic of China
| | - Shuzhen Han
- Department of Infectious Diseases, Children's Hospital of Fudan University, Shanghai, People's Republic of China
| | - Yingzi Ye
- Department of Infectious Diseases, Children's Hospital of Fudan University, Shanghai, People's Republic of China
| | - Xunjia Cheng
- Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai, People's Republic of China
| | - Hairong Gong
- Department of Pediatric Emergency Medicine and Critical Care Medicine, Children's Hospital of Fudan University, Shanghai, People's Republic of China
| | - Hui Yu
- Department of Infectious Diseases, Children's Hospital of Fudan University, Shanghai, People's Republic of China
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82
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Fang X, Cai Y, Mei J, Huang Z, Zhang C, Yang B, Li W, Zhang W. Optimizing culture methods according to preoperative mNGS results can improve joint infection diagnosis. Bone Joint J 2021; 103-B:39-45. [PMID: 33380187 DOI: 10.1302/0301-620x.103b1.bjj-2020-0771.r2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
AIMS Metagenomic next-generation sequencing (mNGS) is useful in the diagnosis of infectious disease. However, while it is highly sensitive at identifying bacteria, it does not provide information on the sensitivity of the organisms to antibiotics. The purpose of this study was to determine whether the results of mNGS can be used to guide optimization of culture methods to improve the sensitivity of culture from intraoperative samples. METHODS Between July 2014 and October 2019, patients with suspected joint infection (JI) from whom synovial fluid (SF) was obtained preoperatively were enrolled. Preoperative aspirated SF was analyzed by conventional microbial culture and mNGS. In addition to samples taken for conventional microbial culture, some samples were taken for intraoperative culture to optimize the culture method according to the preoperative mNGS results. The demographic characteristics, medical history, laboratory examination, mNGS, and culture results of the patients were recorded, and the possibility of the optimized culture methods improving diagnostic efficiency was evaluated. RESULTS A total of 56 cases were included in this study. There were 35 cases of JI and 21 cases of non-joint infection (NJI). The sensitivity, specificity, and accuracy of intraoperative microbial culture after optimization of the culture method were 94.29%, 76.19%, and 87.5%, respectively, while those of the conventional microbial culture method were 60%, 80.95%, and 67.86%, respectively. CONCLUSION Preoperative aspirated SF detected via mNGS can provide more aetiological information than preoperative culture, which can guide the optimization and improve the sensitivity of intraoperative culture. Cite this article: Bone Joint J 2021;103-B(1):39-45.
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Affiliation(s)
- Xinyu Fang
- Department of Orthopedic Surgery, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Yuanqing Cai
- Department of Orthopedic Surgery, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Jian Mei
- Department of Orthopedic Surgery, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Zida Huang
- Department of Orthopedic Surgery, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Chaofan Zhang
- Department of Orthopedic Surgery, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Bin Yang
- Department of Laboratory Medicine, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Wenbo Li
- Department of Orthopedic Surgery, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Wenming Zhang
- Department of Orthopedic Surgery, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
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83
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Rezaei SJ, Mateen FJ. Encephalitis and meningitis in Western Africa: a scoping review of pathogens. Trop Med Int Health 2021; 26:388-396. [PMID: 33340211 DOI: 10.1111/tmi.13539] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
OBJECTIVE To give an overview of the recently reported literature on the aetiologies of meningitis and encephalitis in western sub-Saharan Africa. METHODS We conducted a scoping review following PRISMA guidance on published meningitis and encephalitis cases in the 16 countries of the United Nations-defined western sub-Saharan African region as identified in cohort studies, case series, and case reports, published 01/01/2000-08/01/2020, and available in four databases in August 2020 with an abstract in English, French or Italian. RESULTS There were 38 distinct pathogens identified from 91 cohort studies' data and 48 case reports or case series' data. In cohort-level data, the majority of cases were caused by Neisseria meningitidis (71.5%), Streptococcus pneumoniae (17.6%) and Haemophilus influenzae (7.3%). In case report- and case series-level data, 40.5% of patients were <18 years old, 28.6% were female, and 28.6% were known to be immunocompromised. The case fatality rate was 39.3%. The most commonly reported pathogens among immunocompetent patients were Salmonella species (13 cases) and Ebola virus (9 cases), and the most commonly reported pathogen among immunocompromised patients was Cryptococcus neoformans (18 cases). Most cohort cases (52.3%) derived from Niger followed by Burkina Faso (28.6%). Most cases from single reports or series were reported from Nigeria (21.4%), Mali (20.2%) and Burkina Faso (19.0%). CONCLUSIONS Given the small number of pathogens reported, our findings underscore the need to better screen, diagnose and monitor populations in western sub-Saharan Africa for additional CNS pathogens, including those posing significant outbreak risks.
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Affiliation(s)
- Shawheen J Rezaei
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Farrah J Mateen
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
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84
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Li N, Cai Q, Miao Q, Song Z, Fang Y, Hu B. High-Throughput Metagenomics for Identification of Pathogens in the Clinical Settings. SMALL METHODS 2021; 5:2000792. [PMID: 33614906 PMCID: PMC7883231 DOI: 10.1002/smtd.202000792] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/24/2020] [Indexed: 05/25/2023]
Abstract
The application of sequencing technology is shifting from research to clinical laboratories owing to rapid technological developments and substantially reduced costs. However, although thousands of microorganisms are known to infect humans, identification of the etiological agents for many diseases remains challenging as only a small proportion of pathogens are identifiable by the current diagnostic methods. These challenges are compounded by the emergence of new pathogens. Hence, metagenomic next-generation sequencing (mNGS), an agnostic, unbiased, and comprehensive method for detection, and taxonomic characterization of microorganisms, has become an attractive strategy. Although many studies, and cases reports, have confirmed the success of mNGS in improving the diagnosis, treatment, and tracking of infectious diseases, several hurdles must still be overcome. It is, therefore, imperative that practitioners and clinicians understand both the benefits and limitations of mNGS when applying it to clinical practice. Interestingly, the emerging third-generation sequencing technologies may partially offset the disadvantages of mNGS. In this review, mainly: a) the history of sequencing technology; b) various NGS technologies, common platforms, and workflows for clinical applications; c) the application of NGS in pathogen identification; d) the global expert consensus on NGS-related methods in clinical applications; and e) challenges associated with diagnostic metagenomics are described.
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Affiliation(s)
- Na Li
- Department of Infectious DiseasesZhongshan HospitalFudan UniversityShanghai200032China
| | - Qingqing Cai
- Genoxor Medical Science and Technology Inc.Zhejiang317317China
| | - Qing Miao
- Department of Infectious DiseasesZhongshan HospitalFudan UniversityShanghai200032China
| | - Zeshi Song
- Genoxor Medical Science and Technology Inc.Zhejiang317317China
| | - Yuan Fang
- Genoxor Medical Science and Technology Inc.Zhejiang317317China
| | - Bijie Hu
- Department of Infectious DiseasesZhongshan HospitalFudan UniversityShanghai200032China
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85
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Gabriel M, Hoeben BAW, Uhlving HH, Zajac-Spychala O, Lawitschka A, Bresters D, Ifversen M. A Review of Acute and Long-Term Neurological Complications Following Haematopoietic Stem Cell Transplant for Paediatric Acute Lymphoblastic Leukaemia. Front Pediatr 2021; 9:774853. [PMID: 35004543 PMCID: PMC8734594 DOI: 10.3389/fped.2021.774853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 12/02/2021] [Indexed: 12/02/2022] Open
Abstract
Despite advances in haematopoietic stem cell transplant (HSCT) techniques, the risk of serious side effects and complications still exists. Neurological complications, both acute and long term, are common following HSCT and contribute to significant morbidity and mortality. The aetiology of neurotoxicity includes infections and a wide variety of non-infectious causes such as drug toxicities, metabolic abnormalities, irradiation, vascular and immunologic events and the leukaemia itself. The majority of the literature on this subject is focussed on adults. The impact of the combination of neurotoxic drugs given before and during HSCT, radiotherapy and neurological complications on the developing and vulnerable paediatric and adolescent brain remains unclear. Moreover, the age-related sensitivity of the nervous system to toxic insults is still being investigated. In this article, we review current evidence regarding neurotoxicity following HSCT for acute lymphoblastic leukaemia in childhood. We focus on acute and long-term impacts. Understanding the aetiology and long-term sequelae of neurological complications in children is particularly important in the current era of immunotherapy for acute lymphoblastic leukaemia (such as chimeric antigen receptor T cells and bi-specific T-cell engager antibodies), which have well-known and common neurological side effects and may represent a future treatment modality for at least a fraction of HSCT-recipients.
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Affiliation(s)
- Melissa Gabriel
- Cancer Centre for Children, The Children's Hospital at Westmead, Sydney, NSW, Australia
| | - Bianca A W Hoeben
- Department of Radiation Oncology, University Medical Center Utrecht, Utrecht, Netherlands.,Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Hilde Hylland Uhlving
- Department of Pediatrics and Adolescent Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Olga Zajac-Spychala
- Department of Pediatric Oncology, Hematology and Transplantology, Poznan University of Medical Sciences, Poznań, Poland
| | - Anita Lawitschka
- Haematopoietic Stem Cell Transplant Unit, St. Anna Children's Hospital, Medical University Vienna, Vienna, Austria
| | - Dorine Bresters
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Marianne Ifversen
- Department of Pediatrics and Adolescent Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
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86
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Zhang X, Wu Z, Wang K. Diagnosis of Streptococcus suis Meningoencephalitis with metagenomic next-generation sequencing of the cerebrospinal fluid: a case report with literature review. BMC Infect Dis 2020; 20:884. [PMID: 33238913 PMCID: PMC7687824 DOI: 10.1186/s12879-020-05621-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 11/15/2020] [Indexed: 12/19/2022] Open
Abstract
Background Streptococcus suis meningoencephalitis is a zoonotic disease that mostly infects slaughterhouse workers. Rapid diagnosis of Streptococcus suis meningoencephalitis is critical for effective clinical management of this condition. However, the current diagnostic techniques are not effective for early diagnosis of this condition. To the best of our knowledge, the use of cerebrospinal fluid metagenomic next generation sequencing in the diagnosis of Streptococcus suis meningoencephalitis has been rarely reported. Case presentation Here, we report a case of Streptococcus suis meningoencephalitis in a 51-year-old female patient. The patient had a history of long-term contact with pork and had a three-centimeter-long wound on her left leg prior to disease onset. Conventional tests, including blood culture, gram staining and cerebrospinal fluid culture, did not reveal bacterial infection. However, Streptococcus suis was detected in cerebrospinal fluid using metagenomic next generation sequencing. Conclusions Metagenomic next generation sequencing is a promising approach for early diagnosis of central nervous system infections. This case report indicates that cases of clinical meningeal encephalitis of unknown cause can be diagnosed through this method.
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Affiliation(s)
- Xiaobo Zhang
- Department of Neurology, The First People's Hospital Of Changde City, 818 Renmin Road, Changde, 415000, Hunan Province, China.
| | - Zhaoping Wu
- Department of Neurology, Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan Province, China
| | - Kai Wang
- Department of Neurology, The First People's Hospital Of Changde City, 818 Renmin Road, Changde, 415000, Hunan Province, China
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87
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Grossegesse M, Hartkopf F, Nitsche A, Schaade L, Doellinger J, Muth T. Perspective on Proteomics for Virus Detection in Clinical Samples. J Proteome Res 2020; 19:4380-4388. [PMID: 33090795 PMCID: PMC7640980 DOI: 10.1021/acs.jproteome.0c00674] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Indexed: 12/29/2022]
Abstract
One of the most widely used methods to detect an acute viral infection in clinical specimens is diagnostic real-time polymerase chain reaction. However, because of the COVID-19 pandemic, mass-spectrometry-based proteomics is currently being discussed as a potential diagnostic method for viral infections. Because proteomics is not yet applied in routine virus diagnostics, here we discuss its potential to detect viral infections. Apart from theoretical considerations, the current status and technical limitations are considered. Finally, the challenges that have to be overcome to establish proteomics in routine virus diagnostics are highlighted.
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Affiliation(s)
- Marica Grossegesse
- Centre
for Biological Threats and Special Pathogens, Highly Pathogenic Viruses
(ZBS 1), Robert Koch Institute, Seestr. 10, Berlin 13353, Germany
| | - Felix Hartkopf
- Microbial
Genomics (NG 1), Robert Koch Institute, Berlin 13353, Germany
- Section
eScience (S.3), Federal Institute for Materials
Research and Testing, Unter den Eichen 87, Berlin 12205, Germany
| | - Andreas Nitsche
- Centre
for Biological Threats and Special Pathogens, Highly Pathogenic Viruses
(ZBS 1), Robert Koch Institute, Seestr. 10, Berlin 13353, Germany
| | - Lars Schaade
- Centre
for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin 13353, Germany
| | - Joerg Doellinger
- Centre
for Biological Threats and Special Pathogens, Proteomics and Spectroscopy
(ZBS 6), Robert Koch Institute, Berlin 13353, Germany
| | - Thilo Muth
- Section
eScience (S.3), Federal Institute for Materials
Research and Testing, Unter den Eichen 87, Berlin 12205, Germany
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88
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Bharucha T, Oeser C, Balloux F, Brown JR, Carbo EC, Charlett A, Chiu CY, Claas ECJ, de Goffau MC, de Vries JJC, Eloit M, Hopkins S, Huggett JF, MacCannell D, Morfopoulou S, Nath A, O'Sullivan DM, Reoma LB, Shaw LP, Sidorov I, Simner PJ, Van Tan L, Thomson EC, van Dorp L, Wilson MR, Breuer J, Field N. STROBE-metagenomics: a STROBE extension statement to guide the reporting of metagenomics studies. THE LANCET. INFECTIOUS DISEASES 2020; 20:e251-e260. [PMID: 32768390 PMCID: PMC7406238 DOI: 10.1016/s1473-3099(20)30199-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 03/09/2020] [Accepted: 03/12/2020] [Indexed: 02/07/2023]
Abstract
The term metagenomics refers to the use of sequencing methods to simultaneously identify genomic material from all organisms present in a sample, with the advantage of greater taxonomic resolution than culture or other methods. Applications include pathogen detection and discovery, species characterisation, antimicrobial resistance detection, virulence profiling, and study of the microbiome and microecological factors affecting health. However, metagenomics involves complex and multistep processes and there are important technical and methodological challenges that require careful consideration to support valid inference. We co-ordinated a multidisciplinary, international expert group to establish reporting guidelines that address specimen processing, nucleic acid extraction, sequencing platforms, bioinformatics considerations, quality assurance, limits of detection, power and sample size, confirmatory testing, causality criteria, cost, and ethical issues. The guidance recognises that metagenomics research requires pragmatism and caution in interpretation, and that this field is rapidly evolving.
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Affiliation(s)
- Tehmina Bharucha
- Department of Biochemistry, University of Oxford, Oxford, UK; Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos.
| | - Clarissa Oeser
- Centre for Molecular Epidemiology and Translational Research, University College London, London, UK
| | | | - Julianne R Brown
- Microbiology, Virology and Infection Prevention and Control, Great Ormond Street Hospital for Children, London, UK
| | - Ellen C Carbo
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Andre Charlett
- Statistics, Modelling and Economics Department, Public Health England, London, UK
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Eric C J Claas
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Marcus C de Goffau
- Wellcome Sanger Institute, Hinxton, UK; Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Jutte J C de Vries
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Marc Eloit
- Pathogen Discovery Laboratory, Institut Pasteur, Paris, France
| | - Susan Hopkins
- Healthcare-Associated Infection and Antimicrobial Resistance, Public Health England, London, UK; Infectious Diseases Unit, Royal Free Hospital, London, UK
| | - Jim F Huggett
- National Measurement Laboratory, LGC, Teddington, UK; School of Biosciences & Medicine, Faculty of Health & Medical Sciences, University of Surrey, Guildford, UK
| | - Duncan MacCannell
- Office of Advanced Molecular Detection, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Sofia Morfopoulou
- Division of Infection and Immunity, University College London, London, UK
| | - Avindra Nath
- Section of Infections of the Nervous System, National Institutes of Health, Bethesda, MD, USA
| | | | - Lauren B Reoma
- Section of Infections of the Nervous System, National Institutes of Health, Bethesda, MD, USA
| | - Liam P Shaw
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Igor Sidorov
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Patricia J Simner
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Le Van Tan
- Emerging Infections Group, Oxford University Clinical Research Unit, Ho Chi Minh city, Vietnam
| | - Emma C Thomson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, London, UK
| | - Michael R Wilson
- Weill Institute for Neurosciences and Department of Neurology, University of California, San Francisco, CA, USA
| | - Judith Breuer
- Division of Infection and Immunity, University College London, London, UK; Great Ormond Street Hospital for Children, London, UK
| | - Nigel Field
- Centre for Molecular Epidemiology and Translational Research, University College London, London, UK
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89
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Lan ZW, Xiao MJ, Guan YL, Zhan YJ, Tang XQ. Detection of Listeria monocytogenes in a patient with meningoencephalitis using next-generation sequencing: a case report. BMC Infect Dis 2020; 20:721. [PMID: 33004020 PMCID: PMC7528245 DOI: 10.1186/s12879-020-05447-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 09/23/2020] [Indexed: 12/19/2022] Open
Abstract
Background Listeria monocytogenes (L. monocytogenes) is a facultative intracellular bacterial pathogen which can invade different mammalian cells and reach to the central nervous system (CNS), leading to meningoencephalitis and brain abscesses. In the diagnosis of L. monocytogenes meningoencephalitis (LMM), the traditional test often reports negative owing to the antibiotic treatment or a low number of bacteria in the cerebrospinal fluid. To date, timely diagnosis and accurate treatment remains a challenge for patients with listeria infections. Case presentation We present the case of a 66-year-old woman whose clinical manifestations were suspected as tuberculous meningoencephalitis, but the case was finally properly diagnosed as LMM by next-generation sequencing (NGS). The patient was successfully treated using a combined antibacterial therapy, comprising ampicillin and trimethoprim-sulfamethoxazole. Conclusion To improve the sensitivity of LMM diagnosis, we used NGS for the detection of L. monocytogenes. Hence, the clinical utility of this approach can be very helpful since it provides quickly and trust results.
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Affiliation(s)
- Zi-Wei Lan
- The Second Xiangya Hospital, Central South University, No.139 Middle Renmin Road, Changsha, 410011, Hunan, China
| | - Min-Jia Xiao
- The Second Xiangya Hospital, Central South University, No.139 Middle Renmin Road, Changsha, 410011, Hunan, China
| | - Yuan-Lin Guan
- Hugobiotech Co., Ltd, No 1 Disheng East Road, Daxing District, Beijing, 100000, China
| | - Ya-Jing Zhan
- The Second Xiangya Hospital, Central South University, No.139 Middle Renmin Road, Changsha, 410011, Hunan, China.
| | - Xiang-Qi Tang
- The Second Xiangya Hospital, Central South University, No.139 Middle Renmin Road, Changsha, 410011, Hunan, China.
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90
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The clinical value of metagenomic next-generation sequencing in the microbiological diagnosis of skin and soft tissue infections. Int J Infect Dis 2020; 100:414-420. [PMID: 32898669 DOI: 10.1016/j.ijid.2020.09.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 07/31/2020] [Accepted: 09/02/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Metagenomic next-generation sequencing (mNGS), with its comprehensiveness, is widely applied in microbiological diagnosis. Etiological diagnosis is of paramount clinical importance in patients with skin and soft tissue infections (SSTIs). However, the clinical application of mNGS in SSTIs is relatively less studied. MATERIALS AND METHODS From April 1, 2017 to December 31, 2019, 96 SSTI cases were collected. The positive rates of pathogens detected by mNGS and culture were compared by analyzing tissue samples, pus, swabs, and/or interstitial fluids obtained from the infected parts. Modification of the antibiotic treatment strategy due to mNGS was also assessed. RESULTS The sensitivity of mNGS for detecting pathogens in SSTI cases was superior to that of culture testing (67.7% vs 35.4%; p < 0.01). Significantly higher identification rates for viruses (10.4% vs 0.0%; p < 0.01) and anaerobes (11.5% vs 1.0%; p < 0.01) were obtained with mNGS compared to culture. Of note, rare pathogens such as Vibrio vulnificus and Bartonella henselae were also detected by mNGS. Importantly, the proportion of multi-pathogen SSTIs detected by mNGS was higher than that of multi-pathogen SSTIs detected by culture (16.7% vs 6.3%; p = 0.035). The rate of targeted antibiotic treatment was significantly higher in mNGS-positive cases than in mNGS-negative cases (41.7% vs 3.8%; p < 0.01). In culture-negative and mNGS-positive cases, the improvement rate was higher than that in mNGS-negative cases, but this was not statistically significant (75.0% vs 73.1%; p = 0.864). CONCLUSIONS mNGS is a promising tool for the etiological diagnosis of SSTIs, particularly in identifying viruses, anaerobes, and multi-pathogen infections. The application of mNGS testing in clinical practice could change antibiotic treatment strategies and partly benefit clinical outcomes.
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91
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Carbo EC, Buddingh EP, Karelioti E, Sidorov IA, Feltkamp MC, Borne PAVD, Verschuuren JJ, Kroes AC, Claas EC, de Vries JJ. Improved diagnosis of viral encephalitis in adult and pediatric hematological patients using viral metagenomics. J Clin Virol 2020; 130:104566. [DOI: 10.1016/j.jcv.2020.104566] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 07/23/2020] [Accepted: 07/28/2020] [Indexed: 02/06/2023]
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92
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Yi Z, Zhong J, Wu H, Li X, Chen Y, Chen H, Yang Y, Yu X. Balamuthia mandrillaris encephalitis in a child: case report and literature review. Diagn Microbiol Infect Dis 2020; 100:115180. [PMID: 33887622 DOI: 10.1016/j.diagmicrobio.2020.115180] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 08/12/2020] [Accepted: 08/13/2020] [Indexed: 11/16/2022]
Abstract
Balamuthia mandrillaris encephalitis is a rare disease with high mortality in the children. Due to the lack of specificity in clinical manifestations, laboratory tests, and neuroimaging, the diagnosis of the disease is difficult, especially the diagnosis of etiology. Currently, the evidence shows that the diagnosis of the disease depends on local brain biopsy or autopsy, and it is difficult to detect the pathogens by traditional etiological detection methods in blood and cerebrospinal fluid. We report a 9-year-old Chinese girl with B. mandrillaris encephalitis who was diagnosed with metagenomic next-generation sequencing (mNGS). The technology of mNGS can provide rapid, early etiological diagnosis without the need for a local brain biopsy, which can buy time for the early treatment of patients. We also provide a comprehensive literature review on this disease.
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Affiliation(s)
- Zhaoshi Yi
- Department of Pediatric Neurology, Jiangxi Children's Hospital&The Affiliated Children's Hospital of Nanchang University, Nanchang, China
| | - Jianmin Zhong
- Department of Pediatric Neurology, Jiangxi Children's Hospital&The Affiliated Children's Hospital of Nanchang University, Nanchang, China
| | - Huaping Wu
- Department of Pediatric Neurology, Jiangxi Children's Hospital&The Affiliated Children's Hospital of Nanchang University, Nanchang, China
| | - Xiaoyan Li
- Department of Pediatric Neurology, Jiangxi Children's Hospital&The Affiliated Children's Hospital of Nanchang University, Nanchang, China
| | - Yong Chen
- Department of Pediatric Neurology, Jiangxi Children's Hospital&The Affiliated Children's Hospital of Nanchang University, Nanchang, China
| | - Hui Chen
- Department of Pediatric Neurology, Jiangxi Children's Hospital&The Affiliated Children's Hospital of Nanchang University, Nanchang, China
| | - Yu Yang
- Department of Pediatric Endocrinology, Genetics and Metabolism, Jiangxi Children's Hospital&The Affiliated Children's Hospital of Nanchang University, Nanchang, China
| | - Xiongying Yu
- Department of Pediatric Neurology, Jiangxi Children's Hospital&The Affiliated Children's Hospital of Nanchang University, Nanchang, China.
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93
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Zhang C, Wang C, Chen F, Huang Z, Fang X, Li W, Yang B, Zhang W. Metagenomic Next-Generation Sequencing Technique Helps Identify Cryptococcal Infection in the Rib: A Report of 2 Cases and Review of the Literature. JBJS Case Connect 2020; 9:e0367. [PMID: 31821204 DOI: 10.2106/jbjs.cc.19.00367] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
CASE Two patients presented with pathological lytic bone lesions in the rib and associated soft tissue mass believed initially to represent soft tissue neoplasm. However, further consideration of infectious etiologies led to the identification of cryptococcal osteomyelitis. In one case, the microbiological culture was negative, but Cryptococcus neoformans was identified with the help of the metagenomic next-generation sequencing (mNGS) technique. Both patients received oral fluconazole-only treatment, and the infections were successfully eradicated. CONCLUSIONS The mNGS technique helps identify cryptococcal infection in the rib.
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Affiliation(s)
- Chaofan Zhang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Chaoxin Wang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Fei Chen
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Zida Huang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Xinyu Fang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Wenbo Li
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Bin Yang
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Wenming Zhang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
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94
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Manso CF, Bibby DF, Mohamed H, Brown DWG, Zuckerman M, Mbisa JL. Enhanced Detection of DNA Viruses in the Cerebrospinal Fluid of Encephalitis Patients Using Metagenomic Next-Generation Sequencing. Front Microbiol 2020; 11:1879. [PMID: 32903437 PMCID: PMC7435129 DOI: 10.3389/fmicb.2020.01879] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 07/16/2020] [Indexed: 12/16/2022] Open
Abstract
The long and expanding list of viral pathogens associated with causing encephalitis confounds current diagnostic procedures, and in up to 50% of cases, the etiology remains undetermined. Sequence-agnostic metagenomic next-generation sequencing (mNGS) obviates the need to specify targets in advance and thus has great potential in encephalitis diagnostics. However, the low relative abundance of viral nucleic acids in clinical specimens poses a significant challenge. Our protocol employs two novel techniques to selectively remove human material at two stages, significantly increasing the representation of viral material. Our bioinformatic workflow using open source protein- and nucleotide sequence-matching software balances sensitivity and specificity in diagnosing and characterizing any DNA viruses present. A panel of 12 cerebrospinal fluid (CSFs) from encephalitis cases was retrospectively interrogated by mNGS, with concordant results in seven of nine samples with a definitive DNA virus diagnosis, and a different herpesvirus was identified in the other two. In two samples with an inconclusive diagnosis, DNA viruses were detected and in a virus-negative sample, no viruses were detected. This assay has the potential to detect DNA virus infections in cases of encephalitis of unknown etiology and to improve the current screening tests by identifying new and emerging agents.
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Affiliation(s)
- Carmen F Manso
- Virus Reference Department, Public Health England, London, United Kingdom
| | - David F Bibby
- Virus Reference Department, Public Health England, London, United Kingdom
| | - Hodan Mohamed
- Virus Reference Department, Public Health England, London, United Kingdom
| | - David W G Brown
- Virus Reference Department, Public Health England, London, United Kingdom.,Laboratorio de Virus Respiratorios e do Sarampo, Instituto Oswaldo Cruz/Fiocruz, Rio de Janeiro, Brazil
| | - Mark Zuckerman
- South London Specialist Virology Centre, King's College Hospital NHS Foundation Trust, London, United Kingdom
| | - Jean L Mbisa
- Virus Reference Department, Public Health England, London, United Kingdom
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95
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A Comparative Study of the Adherent-Invasive Escherichia coli Population and Gut Microbiota of Healthy Vegans versus Omnivores. Microorganisms 2020; 8:microorganisms8081165. [PMID: 32751971 PMCID: PMC7465959 DOI: 10.3390/microorganisms8081165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/28/2020] [Accepted: 07/29/2020] [Indexed: 12/12/2022] Open
Abstract
Adherent-invasive Escherichia coli (AIEC) strains carry virulence genes (VGs) which are rarely found in strains other than E. coli. These strains are abundantly found in gut mucosa of patients with inflammatory bowel disease (IBD); however, it is not clear whether their prevalence in the gut is affected by the diet of the individual. Therefore, in this study, we compared the population structure of E. coli and the prevalence of AIEC as well as the composition of gut microbiota in fecal samples of healthy participants (n = 61) on either a vegan (n = 34) or omnivore (n = 27) diet to determine whether diet is associated with the presence of AIEC. From each participant, 28 colonies of E. coli were typed using Random Amplified Polymorphic DNA (RAPD)–PCR. A representative of each common type within an individual was tested for the presence of six AIEC-associated VGs. Whole genomic DNA of the gut microbiota was also analyzed for its diversity profiles, utilizing the V5-V6 region of the16S rRNA gene sequence. There were no significant differences in the abundance and diversity of E. coli between the two diet groups. The occurrence of AIEC-associated VGs was also similar among the two groups. However, the diversity of fecal microbiota in vegans was generally higher than omnivores, with Prevotella and Bacteroides dominant in both groups. Whilst 88 microbial taxa were present in both diet groups, 28 taxa were unique to vegans, compared to seven unique taxa in the omnivores. Our results indicate that a vegan diet may not affect the number and diversity of E. coli populations and AIEC prevalence compared to omnivores. The dominance of Prevotella and Bacteroides among omnivores might be accounted for the effect of diet in these groups.
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96
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Ramachandran PS, Wilson MR. Metagenomics for neurological infections - expanding our imagination. Nat Rev Neurol 2020; 16:547-556. [PMID: 32661342 PMCID: PMC7356134 DOI: 10.1038/s41582-020-0374-y] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/04/2020] [Indexed: 12/11/2022]
Abstract
Over the past two decades, the diagnosis rate for patients with encephalitis has remained poor despite advances in pathogen-specific testing such as PCR and antigen assays. Metagenomic next-generation sequencing (mNGS) of RNA and DNA extracted from cerebrospinal fluid and brain tissue now offers another strategy for diagnosing neurological infections. Given that mNGS simultaneously assays for a wide range of infectious agents in an unbiased manner, it can identify pathogens that were not part of a neurologist’s initial differential diagnosis either because of the rarity of the infection, because the microorganism has not been previously associated with a clinical phenotype or because it is a newly discovered organism. This Review discusses the technical advantages and pitfalls of cerebrospinal fluid mNGS in the context of patients with neuroinflammatory syndromes, including encephalitis, meningitis and myelitis. We also speculate on how mNGS testing potentially fits into current diagnostic testing algorithms given data on mNGS test performance, cost and turnaround time. Finally, the Review highlights future directions for mNGS technology and other hypothesis-free testing methodologies that are in development. This Review discusses the advantages and pitfalls of metagenomic next-generation sequencing (mNGS) in patients with encephalitis, meningitis and myelitis. The authors outline data on mNGS test performance, cost and turnaround time and highlight future directions for mNGS technology. Meningoencephalitis remains a challenging diagnosis owing to the multitude of possible infectious and autoimmune causes. Meningoencephalitis is associated with a high rate of morbidity and mortality and requires prompt diagnosis and treatment. Metagenomic next-generation sequencing (mNGS) is now a clinically validated test for neuroinfectious diseases that can aid clinicians with a timely diagnosis. mNGS can improve the detection of pathogens that were missed by clinicians or on standard direct testing. mNGS does not perform well when indirect tests are required to make the diagnosis (for example, serology), when infections are compartmentalized and for certain low abundance pathogens. The clinical context of the case is required when interpreting the results of mNGS.
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Affiliation(s)
- Prashanth S Ramachandran
- Weill Institute for Neurosciences, University of California, San Francisco, CA, USA.,Department of Neurology, University of California, San Francisco, CA, USA
| | - Michael R Wilson
- Weill Institute for Neurosciences, University of California, San Francisco, CA, USA. .,Department of Neurology, University of California, San Francisco, CA, USA.
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97
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Abstract
PURPOSE OF REVIEW Central nervous system (CNS) infections present an ongoing diagnostic challenge for clinicians, with an aetiological agent remaining unidentified in the majority of cases even in high-income settings. This review summarizes developments in a range of diagnostic methods published in the past 18 months. RECENT FINDINGS Several commercial assays exist for the detection of viral, bacterial and fungal pathogens using single multiplex PCR. Multicentre validation of the Biofire FilmArray panel illustrated high sensitivity for bacterial and fungal pathogens, but poor results for Cryptococcus species detection. The development of microarray cards for bacterial CNS pathogens shows promise but requires further validation. Few developments have been made in proteomics and transcriptomics, contrasted with significant increase in the use of metagenomic (or unbiased) sequencing. Novel viruses causing CNS infection have been described using this technique but contamination, cost, expertise and turnaround time requirements remain restrictive. Finally, the development of Gene Xpert and Ultra has revolutionized tuberculosis meningitis diagnostics with newly released recommendations for their use from the WHO. SUMMARY Progress has been made in the clinical validation and international recommendation of PCR-based tests for CNS infections. Sequencing techniques present the most dynamic field, although significant ongoing challenges persist.
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98
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Fan S, Yuan H, Liu L, Li H, Wang S, Zhao W, Wu Y, Wang P, Hu Y, Han J, Lyu Y, Zhang W, Chen P, Wu H, Gong Y, Ma Z, Li Y, Yu J, Qiao X, Li G, Zhao Y, Wang D, Ren H, Peng B, Cui L, Wang J, Guan H. Pseudorabies virus encephalitis in humans: a case series study. J Neurovirol 2020; 26:556-564. [PMID: 32572833 DOI: 10.1007/s13365-020-00855-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 03/21/2020] [Accepted: 05/14/2020] [Indexed: 12/13/2022]
Abstract
Pseudorabies virus (PRV) is known to cause severe encephalitis in juvenile pigs and various non-native hosts; recent evidences suggest that PRV might cause encephalitis in humans. In a multicenter cohort study in China, next-generation sequencing of cerebrospinal fluid (CSF) was performed to detect pathogens in all patients with clinically suspected central nervous system infections. This study involved all the patients whose CSF samples were positive for PRV-DNA; their clinical features were evaluated, and species-specific PCR and serological tests were sequentially applied for validation. Among the 472 patients tested from June 1, 2016, to December 1, 2018, six were positive for PRV-DNA, which were partially validated by PCR and serological tests. Additionally, we retrospectively examined another case with similar clinical and neuroimaging appearance and detected the presence of PRV-DNA. These patients had similar clinical manifestations, including a rapid progression of panencephalitis, and similar neuroimaging features of symmetric lesions in the basal ganglia and bilateral hemispheres. Six of the patients were engaged in occupations connected with swine production. PRV infection should be suspected in patients with rapidly progressive panencephalitis and characteristic neuroimaging features, especially with exposure to swine.
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MESH Headings
- Adult
- Animals
- Antibodies, Viral/cerebrospinal fluid
- Basal Ganglia/diagnostic imaging
- Basal Ganglia/pathology
- Basal Ganglia/virology
- Cerebrum/diagnostic imaging
- Cerebrum/pathology
- Cerebrum/virology
- China
- DNA, Viral/cerebrospinal fluid
- DNA, Viral/genetics
- Encephalitis, Viral/cerebrospinal fluid
- Encephalitis, Viral/diagnosis
- Encephalitis, Viral/pathology
- Encephalitis, Viral/virology
- Female
- Herpesvirus 1, Suid/genetics
- Herpesvirus 1, Suid/growth & development
- Herpesvirus 1, Suid/pathogenicity
- High-Throughput Nucleotide Sequencing
- Humans
- Magnetic Resonance Imaging
- Male
- Meat/virology
- Middle Aged
- Polymerase Chain Reaction
- Pseudorabies/cerebrospinal fluid
- Pseudorabies/diagnosis
- Pseudorabies/pathology
- Pseudorabies/virology
- Swine
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Affiliation(s)
- Siyuan Fan
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Hongxun Yuan
- Department of Intensive Care Unit, Peking University International Hospital, Beijing, China
| | - Lei Liu
- Department of Neurology, Beijing Tongren Hospital, Capital Medical University, Beijing, 100730, China
| | - Hongfang Li
- Department of Neurology, Affiliated Hospital of Jining Medical University, Jining, China
| | - Shengnan Wang
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Weili Zhao
- Department of Neurology, Affiliated Hospital of Chifeng University, Chifeng, China
| | - Yihan Wu
- Department of Neurology, Inner Mongolia People's Hospital, Hohhot, China
| | - Pei Wang
- Department of Neurology, Baoding No.1 Central Hospital, Baoding, China
| | - Yafang Hu
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jun Han
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yanli Lyu
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Wuchao Zhang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Peng Chen
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Honglong Wu
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Yanping Gong
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Zhenzi Ma
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Yongjun Li
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - JiaoJiao Yu
- Department of Intensive Care Unit, Peking University International Hospital, Beijing, China
| | - Xiaodong Qiao
- Department of Neurology, Affiliated Hospital of Chifeng University, Chifeng, China
| | - Guoli Li
- Department of Neurology, Affiliated Hospital of Chifeng University, Chifeng, China
| | - Yan Zhao
- Department of Neurology, Inner Mongolia People's Hospital, Hohhot, China
| | - Dexin Wang
- Department of Neurology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Haitao Ren
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Bin Peng
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Liying Cui
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Jiawei Wang
- Department of Neurology, Beijing Tongren Hospital, Capital Medical University, Beijing, 100730, China.
| | - Hongzhi Guan
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
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99
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Chen L, Xu Y, Liu C, Huang H, Zhong X, Ma C, Zhao H, Chen Y. Clinical features of aseptic meningitis with varicella zoster virus infection diagnosed by next-generation sequencing: case reports. BMC Infect Dis 2020; 20:435. [PMID: 32571239 PMCID: PMC7309994 DOI: 10.1186/s12879-020-05155-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 06/12/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The aseptic meningitis caused by varicella zoster virus (VZV) reactivation was less described in the literature, most of which were detected by means of polymerase chain reaction. The authors presented 4 adult immunocompetent patients with acute aseptic meningitis with VZV infection diagnosed by next-generation sequencing (NGS). CASE PRESENTATION Four patients were admitted to the hospital with headache and fever between March 2018 and August 2019. The median ages were 37 years (range 22-52 years). The median symptoms onset to clinic time was 3.5 days (range 3-6 days). Two patients had signs of meningeal irritation. Rash occurred after the meningitis symptoms in 1 patient (time from meningitis symptoms to rash, 2 days). No other sign or symptom was reported. The brain Magnetic resonance imaging and electroencephalography were normal in all patients. Cerebrospinal fluid (CSF) samples were obtained at a median of 4 days (range 3-7 days) from the meningitis symptoms onset. Opening pressure of lumbar puncture after admission were high in these cases (median 256 mm H2O; range 165-400 mm H2O). White blood cell counts and protein levels were significantly elevated in CSF samples (median 317 × 10^6/L, range 147-478 × 10^6/L; median 1.41 g/L, range 0.57-1.79 g/L). The cytology of CSF demonstrated a lymphocytic pleocytosis, and most multinuclear cells. The culture of CSF was negative for all 4 cases, while T-cell spot test was positive for 2 cases, who were administrated with anti-tuberculosis treatment for suspicious tuberculous meningitis. NGS of CSF (the Vision Medical Research Institute) detected specific sequences of VZV in the 4 cases within 72 h after admission. The inappropriate treatment were stopped while acyclovir were continued intravenously for 10-14 days. All patients recovered completely. CONCLUSIONS VZV is an infectious agent that causes aseptic meningitis in immunocompetent adults and could not be accompanied by skin manifestations. The NGS of CSF is a rapid detection for the identification and differentiation of meningitis in patients, which is of great importance for providing the rapid and accurate diagnosis and the targeted antimicrobial therapy for central nervous system infection.
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Affiliation(s)
- Lanlan Chen
- Department of Neurology, Northern Jiangsu People's Hospital, Medical College of Yangzhou University, Yangzhou, 225001, China
| | - Yao Xu
- Department of Neurology, Northern Jiangsu People's Hospital, Medical College of Yangzhou University, Yangzhou, 225001, China
| | - Chunfeng Liu
- Department of Neurology, the Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Hong Huang
- Vision Medical Co., Ltd, Guangzhou, 510670, China
| | - Xingxing Zhong
- Department of Neurology, Northern Jiangsu People's Hospital, Medical College of Yangzhou University, Yangzhou, 225001, China
| | - Cancan Ma
- Department of Neurology, Northern Jiangsu People's Hospital, Medical College of Yangzhou University, Yangzhou, 225001, China
| | - Haina Zhao
- Department of Neurology, Northern Jiangsu People's Hospital, Medical College of Yangzhou University, Yangzhou, 225001, China
| | - Yingzhu Chen
- Department of Neurology, Northern Jiangsu People's Hospital, Medical College of Yangzhou University, Yangzhou, 225001, China.
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100
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Zou Y, Guan H, Wu H, Bu H, Yan L, Zhu Y, He J. Angiostrongyliasis detected by next-generation sequencing in a ELISA-negative eosinophilic meningitis: A case report. Int J Infect Dis 2020; 97:177-179. [PMID: 32502661 DOI: 10.1016/j.ijid.2020.05.108] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/27/2020] [Accepted: 05/27/2020] [Indexed: 10/24/2022] Open
Abstract
Next-generation sequencing (NGS) is an emerging method with the potential of pan-pathogen screening. This study described a case of eosinophilic meningitis (EoM) with enzyme-linked immunosorbent assay (ELISA)-negative results for Angiostrongylus cantonensis (A. cantonensis), Trichinella spiralis and Paragonimus westermani and a positive identification of A. cantonensis by NGS in the cerebrospinal fluid.
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Affiliation(s)
- Yueli Zou
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Hongzhi Guan
- Department of Neurology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Honglong Wu
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Hui Bu
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Litian Yan
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Yifei Zhu
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, China.
| | - Junying He
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, China.
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