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Mourik K, Sidorov I, Carbo EC, van der Meer D, Boot A, Kroes ACM, Claas ECJ, Boers SA, de Vries JJC. Comparison of the performance of two targeted metagenomic virus capture probe-based methods using reference control materials and clinical samples. J Clin Microbiol 2024; 62:e0034524. [PMID: 38757981 DOI: 10.1128/jcm.00345-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 04/05/2024] [Indexed: 05/18/2024] Open
Abstract
Viral enrichment by probe hybridization has been reported to significantly increase the sensitivity of viral metagenomics. This study compares the analytical performance of two targeted metagenomic virus capture probe-based methods: (i) SeqCap EZ HyperCap by Roche (ViroCap) and (ii) Twist Comprehensive Viral Research Panel workflow, for diagnostic use. Sensitivity, specificity, and limit of detection were analyzed using 25 synthetic viral sequences spiked in increasing proportions of human background DNA, eight clinical samples, and American Type Culture Collection (ATCC) Virome Virus Mix. Sensitivity and specificity were 95% and higher for both methods using the synthetic and reference controls as gold standard. Combining thresholds for viral sequence read counts and genome coverage [respectively 500 reads per million (RPM) and 10% coverage] resulted in optimal prediction of true positive results. Limits of detection were approximately 50-500 copies/mL for both methods as determined by ddPCR. Increasing proportions of spike-in cell-free human background sequences up to 99.999% (50 ng/mL) did not negatively affect viral detection, suggesting effective capture of viral sequences. These data show analytical performances in ranges applicable to clinical samples, for both probe hybridization metagenomic approaches. This study supports further steps toward more widespread use of viral metagenomics for pathogen detection, in clinical and surveillance settings using low biomass samples. IMPORTANCE Viral metagenomics has been gradually applied for broad-spectrum pathogen detection of infectious diseases, surveillance of emerging diseases, and pathogen discovery. Viral enrichment by probe hybridization methods has been reported to significantly increase the sensitivity of viral metagenomics. During the past years, a specific hybridization panel distributed by Roche has been adopted in a broad range of different clinical and zoonotic settings. Recently, Twist Bioscience has released a new hybridization panel targeting human and animal viruses. This is the first report comparing the performance of viral metagenomic hybridization panels.
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Affiliation(s)
- Kees Mourik
- Department of Medical Microbiology, Leiden University Center for Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands
| | - Igor Sidorov
- Department of Medical Microbiology, Leiden University Center for Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands
| | - Ellen C Carbo
- Department of Medical Microbiology, Leiden University Center for Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands
| | | | | | - Aloysius C M Kroes
- Department of Medical Microbiology, Leiden University Center for Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands
| | - Eric C J Claas
- Department of Medical Microbiology, Leiden University Center for Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands
| | - Stefan A Boers
- Department of Medical Microbiology, Leiden University Center for Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands
| | - Jutte J C de Vries
- Department of Medical Microbiology, Leiden University Center for Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands
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Lin J, Zheng D, Tian D, Zheng P, Zhang H, Li C, Lei C, Shi F, Wang H. High Frequency of Autoantibodies in COVID-19 Patients with Central Nervous System Complications: a Multicenter Observational Study. Mol Neurobiol 2024:10.1007/s12035-024-04109-4. [PMID: 38507030 DOI: 10.1007/s12035-024-04109-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 03/08/2024] [Indexed: 03/22/2024]
Abstract
We present a panel of central nervous system (CNS) complications associated with coronavirus disease 2019 (COVID-19) and their clinical characteristics. We aim to investigate associations between neurological autoantibodies and COVID-19 patients with predominant CNS complications. In this retrospective multi-center study, we analyze neurologic complications associated with COVID-19 patients from Dec. 2022 to Feb. 2023 at four tertiary hospitals in China. CSF and/or serum in the enrolled patients were tested for autoantibodies using tissue-based assays (TBAs) and cell-based assays (CBAs). A total of 34 consecutive patients (median age was 40.5 years [range 15-83], 50% were female) were enrolled. CNS syndromes included encephalitis (n=15), encephalopathies (n=6), meningoencephalitis (n=3), ADEM (n=2), depression (n = 2), Alzheimer's disease (n=2), Parkinson disease (n=1), and central nervous system vasculitis (n=1). Twenty-eight specimens (of 44 tested; 11/27 [40.7%] CSF, 13/17 [76.5%] serums) were confirmed by TBAs to be autoantibodies positive. However, only a few autoantibodies (1 with MOG and 1 with NMDAR) were detected by CBAs assays. Twenty-four patients received immunotherapy. After a mean time of 7.26 months of follow-up, 75.8% (25/33) of patients had good outcome (mRS score ≤2). Although no significant difference was observed between the two groups, the proportion of positive CSF autoantibodies in the poor outcomes group was higher than that in the good outcomes group (57.1% vs 31.5%, P = 0.369). Autoantibodies were frequently observed in COVID-19-associated CNS complications. The identification of these autoantibody-positive COVID-19 cases is important as they respond favorably to immunotherapy.
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Affiliation(s)
- Jingfang Lin
- Department of Neurology, Guangzhou First People's Hospital, South China University of Technology, Guangzhou, China
| | - Dong Zheng
- Department of Neurology, The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China
| | - Decai Tian
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Pei Zheng
- Center for Neurological Diseases, China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Hongya Zhang
- Department of Neurology, Shenzhen University General Hospital, Shenzhen, China
| | - Chuo Li
- Department of Neurology, Eight People's Hospital of Guangzhou, Guangzhou, China
| | - Chunliang Lei
- Eight People's Hospital of Guangzhou, Guangzhou, China
| | - Fudong Shi
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Center for Neurological Diseases, China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Honghao Wang
- Department of Neurology, Guangzhou First People's Hospital, South China University of Technology, Guangzhou, China.
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Zhu N, Zhou D, Xiong W, Zhang X, Li S. Performance of mNGS in bronchoalveolar lavage fluid for the diagnosis of invasive pulmonary aspergillosis in non-neutropenic patients. Front Cell Infect Microbiol 2023; 13:1271853. [PMID: 38029249 PMCID: PMC10644336 DOI: 10.3389/fcimb.2023.1271853] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 10/03/2023] [Indexed: 12/01/2023] Open
Abstract
The diagnosis of invasive pulmonary aspergillosis (IPA) diseases in non-neutropenic patients remains challenging. It is essential to develop optimal non-invasive or minimally invasive detection methods for the rapid and reliable diagnosis of IPA. Metagenomic next-generation sequencing (mNGS) in bronchoalveolar lavage fluid (BALF) can be a valuable tool for identifying the microorganism. Our study aims to evaluate the performance of mNGS in BALF in suspected IPA patients and compare it with other detection tests, including serum/BALF galactomannan antigen (GM) and traditional microbiological tests (BALF fungal culture and smear and lung biopsy histopathology). Ninety-four patients with suspicion of IPA were finally enrolled in our study. Thirty-nine patients were diagnosed with IPA, and 55 patients were non-IPA. There was significance between the IPA and non-IPA groups, such as BALF GM (P < 0.001), history of glucocorticoid use (P = 0.004), and pulmonary comorbidities (P = 0.002), as well as no significance of the other demographic data including age, sex, BMI, history of cigarette, blood GM assay, T-SPOT.TB, and NEUT#/LYMPH#. The sensitivity of the BALF mNGS was 92.31%, which was higher than that of the traditional tests or the GM assays. The specificity of BALF mNGS was 92.73%, which was relatively similar to that of the traditional tests. The AUC of BALF mNGS was 0.925, which presented an excellent performance compared with other traditional tests or GM assays. Our study demonstrated the important role of BALF detection by the mNGS platform for pathogen identification in IPA patients with non-neutropenic states, which may provide an optimal way to diagnose suspected IPA disease.
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Affiliation(s)
| | | | | | | | - Shengqing Li
- Department of Pulmonary and Critical Care Medicine, Huashan Hospital, Fudan University, Shanghai, China
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He S, Wei J, Feng J, Liu D, Wang N, Chen L, Xiong Y. The application of metagenomic next-generation sequencing in pathogen diagnosis: a bibliometric analysis based on Web of Science. Front Cell Infect Microbiol 2023; 13:1112229. [PMID: 37600953 PMCID: PMC10434771 DOI: 10.3389/fcimb.2023.1112229] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 07/18/2023] [Indexed: 08/22/2023] Open
Abstract
Background Infectious disease is a large burden on public health globally. Metagenomic next-generation sequencing (mNGS) has become popular as a new tool for pathogen diagnosis with numerous advantages compared to conventional methods. Recently, research on mNGS increases yearly. However, no bibliometric analysis has systematically presented the full spectrum of this research field. Therefore, we reviewed all the publications associated with this topic and performed this study to analyze the comprehensive status and future hotspots of mNGS for infectious disease diagnosis. Methods The literature was searched in the Web of Science Core Collection and screened without year or language restrictions, and the characteristics of the studies were also identified. The outcomes included publication years, study types, journals, countries, authorship, institutions, frontiers, and hotspots with trends. Statistical analysis and visualization were conducted using VOSviewer (version 1.6.16) and CiteSpace (version 6.1. R3). Results In total, 325 studies were included in the analysis after screening. Studies were published between 2009 and 2022 with a significantly increasing number from 1 to 118. Most of the studies were original articles and case reports. Frontiers in Cellular and Infection Microbiology and Clinical Infectious Disease were the most commonly cited and co-cited journals. Institutions and researchers from China contributed the most to this field, followed by those from the USA. The hotspots and frontiers of these studies are pneumonia, tuberculosis, and central nervous system infections. Conclusion This study determined that mNGS is a hot topic in the diagnosis of infectious diseases with development trends and provides insights into researchers, institutions, hotspots and frontiers in mNGS, which can offer references to related researchers and future research.
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Affiliation(s)
- Sike He
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Jingwen Wei
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Jiaming Feng
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Dan Liu
- Department of Periodical Press, West China Hospital, Sichuan University, Chengdu, China
| | - Neng Wang
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Liyu Chen
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Ying Xiong
- Department of Periodical Press, West China Hospital, Sichuan University, Chengdu, China
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Piantadosi A, Shariatzadeh N, Bombin A, Arkun K, Alexandrescu S, Kleinschmidt-DeMasters BK, Solomon IH. Double-stranded RNA immunohistochemistry as a screening tool for viral encephalitis. Am J Clin Pathol 2023; 160:210-219. [PMID: 37141170 PMCID: PMC10392367 DOI: 10.1093/ajcp/aqad039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 03/17/2023] [Indexed: 05/05/2023] Open
Abstract
OBJECTIVES Viral infections of the central nervous system can be challenging to diagnose because of the wide range of causative agents and nonspecific histologic features. We sought to determine whether detection of double-stranded RNA (dsRNA), produced during active RNA and DNA viral infections, could be used to select cases for metagenomic next-generation sequencing (mNGS) from formalin-fixed, paraffin-embedded brain tissue. METHODS Eight commercially available anti-dsRNA antibodies were optimized for immunohistochemistry (IHC) and the top antibody tested in a series of cases with confirmed viral infections (n = 34) and cases with inflammatory brain lesions of unclear etiology (n = 62). RESULTS Among known positives, anti-dsRNA IHC produced a strong cytoplasmic or nuclear staining pattern for Powassan virus, West Nile virus, rabies virus, JC polyoma virus, and adenovirus while failing to detect Eastern equine encephalitis virus, Jamestown Canyon virus, or any herpesvirus. All the unknown cases were negative by anti-dsRNA IHC, while mNGS detected rare viral reads (0.3-1.3 reads per million total reads) in 2 cases (3%), with only 1 having potential clinical significance. CONCLUSIONS Anti-dsRNA IHC can effectively identify a subset of clinically relevant viral infections but not all. The absence of staining should not exclude cases from mNGS if sufficient clinical and histologic suspicion exists.
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Affiliation(s)
- Anne Piantadosi
- Department of Pathology and Laboratory Medicine and Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA, US
| | - Nima Shariatzadeh
- Department of Pathology and Laboratory Medicine and Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA, US
| | - Andrei Bombin
- Department of Pathology and Laboratory Medicine and Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA, US
| | - Knarik Arkun
- Department of Pathology and Laboratory Medicine, Tufts University School of Medicine, Boston, MA, US
| | - Sanda Alexandrescu
- Department of Pathology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, US
| | | | - Isaac H Solomon
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, US
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Feng L, Chen J, Luo Q, Su M, Chen P, Lai R, Shen C, Zhou H, Wang H, Sun X, Chen L, Xia H, Feng H. mNGS facilitates the accurate diagnosis and antibiotic treatment of suspicious critical CNS infection in real practice: A retrospective study. Open Life Sci 2023; 18:20220578. [PMID: 36879645 PMCID: PMC9985444 DOI: 10.1515/biol-2022-0578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 01/16/2023] [Accepted: 01/23/2023] [Indexed: 03/06/2023] Open
Abstract
Whether metagenomic next-generation sequencing (mNGS) could benefit patients with suspected severe central nervous system (CNS) infection in terms of diagnosis and antibiotic treatment remains unknown. We retrospectively analyzed 79 patients with suspected CNS infection and undertook mNGS. The value of mNGS was investigated in terms of identification of pathogen and guidance for the adjustment of antibiotic treatment. The relationship between the time of initiating mNGS since onset and the Glasgow Outcome Scale (GOS) score after 90-day follow-up were analyzed. Fifty out of 79 cases with suspicious severe CNS infection were finally diagnosed. Despite previous routine laboratory tests, mNGS further promoted the accurate identification of pathogens in 23 cases (47.9%). The sensitivity, specificity, and accuracy of mNGS test in this study were 84.0, 79.3, and 82.3%, respectively. Furthermore, mNGS facilitated the adjustment of empirical antibiotic treatments in 38 cases (48.1%). The time of taking mNGS since onset had an insignificant weak positive correlation with GOS after 90-day follow-up (r = -0.73, P = 0.08). mNGS facilitated the accurate identification of pathogens in suspicious severe CNS infections and promoted the accurate antibiotic therapy even empirical antibiotics were administrated. It should be taken as early as possible to improve the clinical outcome of patients with suspicious severe CNS infection.
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Affiliation(s)
- Li Feng
- Department of Neurology, Neurological Intensive Care Unit, The First Affiliated Hospital, Sun Yat-Sen University; Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases; National Key Clinical Department and Key Discipline of Neurology, No. 58 Zhongshan 2nd Road, Guangzhou, 510080, China
| | - Jiaxin Chen
- Department of Neurology, Neurological Intensive Care Unit, The First Affiliated Hospital, Sun Yat-Sen University; Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases; National Key Clinical Department and Key Discipline of Neurology, No. 58 Zhongshan 2nd Road, Guangzhou, 510080, China
| | - Qiuyan Luo
- Department of Neurology, Neurological Intensive Care Unit, The First Affiliated Hospital, Sun Yat-Sen University; Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases; National Key Clinical Department and Key Discipline of Neurology, No. 58 Zhongshan 2nd Road, Guangzhou, 510080, China
| | - Miao Su
- Department of Neurology, Neurological Intensive Care Unit, The First Affiliated Hospital, Sun Yat-Sen University; Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases; National Key Clinical Department and Key Discipline of Neurology, No. 58 Zhongshan 2nd Road, Guangzhou, 510080, China
| | - Peisong Chen
- Department of Laboratory Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Rong Lai
- Department of Neurology, Neurological Intensive Care Unit, The First Affiliated Hospital, Sun Yat-Sen University; Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases; National Key Clinical Department and Key Discipline of Neurology, No. 58 Zhongshan 2nd Road, Guangzhou, 510080, China
| | - Cunzhou Shen
- Department of Neurology, Neurological Intensive Care Unit, The First Affiliated Hospital, Sun Yat-Sen University; Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases; National Key Clinical Department and Key Discipline of Neurology, No. 58 Zhongshan 2nd Road, Guangzhou, 510080, China
| | - Hongyan Zhou
- Department of Neurology, Neurological Intensive Care Unit, The First Affiliated Hospital, Sun Yat-Sen University; Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases; National Key Clinical Department and Key Discipline of Neurology, No. 58 Zhongshan 2nd Road, Guangzhou, 510080, China
| | - Haiyan Wang
- Department of Neurology, Neurological Intensive Care Unit, The First Affiliated Hospital, Sun Yat-Sen University; Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases; National Key Clinical Department and Key Discipline of Neurology, No. 58 Zhongshan 2nd Road, Guangzhou, 510080, China
| | - Xunsha Sun
- Department of Neurology, Neurological Intensive Care Unit, The First Affiliated Hospital, Sun Yat-Sen University; Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases; National Key Clinical Department and Key Discipline of Neurology, No. 58 Zhongshan 2nd Road, Guangzhou, 510080, China
| | - Ling Chen
- Department of Neurology, Neurological Intensive Care Unit, The First Affiliated Hospital, Sun Yat-Sen University; Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases; National Key Clinical Department and Key Discipline of Neurology, No. 58 Zhongshan 2nd Road, Guangzhou, 510080, China
| | - Han Xia
- Department of Scientific Affairs, Hugobiotech Co., Ltd., Beijing 100176, China
| | - Huiyu Feng
- Department of Neurology, Neurological Intensive Care Unit, The First Affiliated Hospital, Sun Yat-Sen University; Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases; National Key Clinical Department and Key Discipline of Neurology, No. 58 Zhongshan 2nd Road, Guangzhou, 510080, China
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[Value of metagenomic next-generation sequencing in children with hemophagocytic syndrome with central nervous system involvement]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2022; 24:1226-1230. [PMID: 36398548 PMCID: PMC9678067 DOI: 10.7499/j.issn.1008-8830.2206118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
OBJECTIVES To study the value of metagenomic next-generation sequencing (mNGS) in detecting intracranial Epstein-Barr virus (EBV) infection in children with hemophagocytic syndrome (HPS) with central nervous system involvement. METHODS A retrospective analysis was performed for the cerebrospinal fluid mNGS results of 30 HPS children with central nervous system involvement, which were compared with the results of cerebrospinal fluid EBV-DNA detection and serum EBV antibody profile. The change in serum EBV-DNA copy number after treatment was used to evaluate the efficacy of targeted therapy. RESULTS The positive rate of EBV in cerebrospinal fluid determined by mNGS was significantly higher than that of EBV-DNA in cerebrospinal fluid (100% vs 10%, P<0.001) and had no significant difference from the positive rate of serum EBV antibody profile (100% vs 93%, P>0.05). The median number of sequences determined by mNGS was 2 400, and serum EBV-DNA copy number before treatment was moderately positively correlated with the number of EBV sequences (rs=0.693, P<0.001). The multiple linear regression analysis showed that the number of sequences determined by mNGS in cerebrospinal fluid increased with the increase in serum EBV-DNA copy number before treatment (P<0.05). CONCLUSIONS EBV-associated HPS often results in EBV-infected viral encephalitis, and mNGS can significantly increase the detection rate of EBV in cerebrospinal fluid, which may help with clinical diagnosis.
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Morsli M, Lavigne JP, Drancourt M. Direct Metagenomic Diagnosis of Community-Acquired Meningitis: State of the Art. Front Microbiol 2022; 13:926240. [PMID: 35865915 PMCID: PMC9294516 DOI: 10.3389/fmicb.2022.926240] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
Current routine diagnosis of community-acquired meningitis (CAM) by multiplex real-time polymerase chain reaction (RT-PCR) is limited in the number of tested pathogens and their full characterisation, requiring additional in vitro investigations to disclose genotype and antimicrobial susceptibility. We reviewed 51 studies published through December 2021 reporting metagenomic next generation sequencing (mNGS) directly applied to the cerebrospinal fluid (CSF). This approach, potentially circumventing the above-mentioned limitations, indicated 1,248 investigated patients, and 617 patients dually investigated by routine diagnosis and mNGS, in whom 116 microbes were detected, including 50 by mNGS only, nine by routine methods only, and 57 by both routine methods and mNGS. Of 217 discordant CSF findings, 103 CSF samples were documented by mNGS only, 87 CSF samples by routine methods only, and 27 CSF samples in which the pathogen identified by mNGS was different than that found using routine methods. Overall, mNGS allowed for diagnosis and genomic surveillance of CAM causative pathogens in real-time, with a cost which is competitive with current routine multiplex RT-PCR. mNGS could be implemented at point-of-care (POC) laboratories as a part of routine investigations to improve the diagnosis and molecular epidemiology of CAM, particularly in the event of failure of routine assays.
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Affiliation(s)
- Madjid Morsli
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Jean Philippe Lavigne
- VBIC, INSERM U1047, Université de Montpellier, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, Nîmes, France
| | - Michel Drancourt
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- Laboratoire de Microbiologie, Assistance Publique-Hôpitaux de Marseille, IHU Méditerranée Infection, Marseille, France
- *Correspondence: Michel Drancourt,
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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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