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Buddle S, Forrest L, Akinsuyi N, Martin Bernal LM, Brooks T, Venturini C, Miller C, Brown JR, Storey N, Atkinson L, Best T, Roy S, Goldsworthy S, Castellano S, Simmonds P, Harvala H, Golubchik T, Williams R, Breuer J, Morfopoulou S, Torres Montaguth OE. Evaluating metagenomics and targeted approaches for diagnosis and surveillance of viruses. Genome Med 2024; 16:111. [PMID: 39252069 PMCID: PMC11382446 DOI: 10.1186/s13073-024-01380-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 08/30/2024] [Indexed: 09/11/2024] Open
Abstract
BACKGROUND Metagenomics is a powerful approach for the detection of unknown and novel pathogens. Workflows based on Illumina short-read sequencing are becoming established in diagnostic laboratories. However, high sequencing depth requirements, long turnaround times, and limited sensitivity hinder broader adoption. We investigated whether we could overcome these limitations using protocols based on untargeted sequencing with Oxford Nanopore Technologies (ONT), which offers real-time data acquisition and analysis, or a targeted panel approach, which allows the selective sequencing of known pathogens and could improve sensitivity. METHODS We evaluated detection of viruses with readily available untargeted metagenomic workflows using Illumina and ONT, and an Illumina-based enrichment approach using the Twist Bioscience Comprehensive Viral Research Panel (CVRP), which targets 3153 viruses. We tested samples consisting of a dilution series of a six-virus mock community in a human DNA/RNA background, designed to resemble clinical specimens with low microbial abundance and high host content. Protocols were designed to retain the host transcriptome, since this could help confirm the absence of infectious agents. We further compared the performance of commonly used taxonomic classifiers. RESULTS Capture with the Twist CVRP increased sensitivity by at least 10-100-fold over untargeted sequencing, making it suitable for the detection of low viral loads (60 genome copies per ml (gc/ml)), but additional methods may be needed in a diagnostic setting to detect untargeted organisms. While untargeted ONT had good sensitivity at high viral loads (60,000 gc/ml), at lower viral loads (600-6000 gc/ml), longer and more costly sequencing runs would be required to achieve sensitivities comparable to the untargeted Illumina protocol. Untargeted ONT provided better specificity than untargeted Illumina sequencing. However, the application of robust thresholds standardized results between taxonomic classifiers. Host gene expression analysis is optimal with untargeted Illumina sequencing but possible with both the CVRP and ONT. CONCLUSIONS Metagenomics has the potential to become standard-of-care in diagnostics and is a powerful tool for the discovery of emerging pathogens. Untargeted Illumina and ONT metagenomics and capture with the Twist CVRP have different advantages with respect to sensitivity, specificity, turnaround time and cost, and the optimal method will depend on the clinical context.
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Affiliation(s)
- Sarah Buddle
- Infection, Immunity and Inflammation Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Leysa Forrest
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Naomi Akinsuyi
- Infection, Immunity and Inflammation Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Luz Marina Martin Bernal
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Tony Brooks
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Cristina Venturini
- Infection, Immunity and Inflammation Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Charles Miller
- Department of Microbiology, Virology and Infection Prevention & Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Julianne R Brown
- Department of Microbiology, Virology and Infection Prevention & Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Nathaniel Storey
- Department of Microbiology, Virology and Infection Prevention & Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Laura Atkinson
- Department of Microbiology, Virology and Infection Prevention & Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Timothy Best
- Department of Microbiology, Virology and Infection Prevention & Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Sunando Roy
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Sian Goldsworthy
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Sergi Castellano
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Heli Harvala
- Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Division of Infection and Immunity, University College London, London, UK
- Microbiology Services, NHS Blood and Transplant, Colindale, UK
| | - Tanya Golubchik
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Sydney Infectious Diseases Institute, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | - Rachel Williams
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Judith Breuer
- Infection, Immunity and Inflammation Department, Great Ormond Street Institute of Child Health, University College London, London, UK.
- Department of Microbiology, Virology and Infection Prevention & Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK.
| | - Sofia Morfopoulou
- Infection, Immunity and Inflammation Department, Great Ormond Street Institute of Child Health, University College London, London, UK.
- Section for Paediatrics, Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK.
| | - Oscar Enrique Torres Montaguth
- Infection, Immunity and Inflammation Department, Great Ormond Street Institute of Child Health, University College London, London, UK.
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Chen J, Qin Z, Jia Z. The application status of sequencing technology in global respiratory infectious disease diagnosis. Infection 2024:10.1007/s15010-024-02360-4. [PMID: 39152290 DOI: 10.1007/s15010-024-02360-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 07/22/2024] [Indexed: 08/19/2024]
Abstract
Next-generation sequencing (NGS) has revolutionized clinical microbiology, particularly in diagnosing respiratory infectious diseases and conducting epidemiological investigations. This narrative review summarizes conventional methods for routine respiratory infection diagnosis, including culture, smear microscopy, immunological assays, image techniques as well as polymerase chain reaction(PCR). In contrast to conventional methods, there is a new detection technology, sequencing technology, and here we mainly focus on the next-generation sequencing NGS, especially metagenomic NGS(mNGS). NGS offers significant advantages over traditional methods. Firstly, mNGS eliminates assumptions about pathogens, leading to faster and more accurate results, thus reducing diagnostic time. Secondly, it allows unbiased identification of known and novel pathogens, offering broad-spectrum coverage. Thirdly, mNGS not only identifies pathogens but also characterizes microbiomes, analyzes human host responses, and detects resistance genes and virulence factors. It can complement targeted sequencing for bacterial and fungal classification. Unlike traditional methods affected by antibiotics, mNGS is less influenced due to the extended survival of pathogen DNA in plasma, broadening its applicability. However, barriers to full integration into clinical practice persist, primarily due to cost constraints and limitations in sensitivity and turnaround time. Despite these challenges, ongoing advancements aim to improve cost-effectiveness and efficiency, making NGS a cornerstone technology for global respiratory infection diagnosis.
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Affiliation(s)
- Jingyuan Chen
- Department of Global Health, School of Public Health, Peking University, Beijing, China
| | - Zhen Qin
- School of Public Health, Peking University, Beijing, China
| | - Zhongwei Jia
- Department of Global Health, School of Public Health, Peking University, Beijing, China.
- Center for Intelligent Public Health, Institute for Artificial Intelligence, Peking University, Beijing, China.
- Center for Drug Abuse Control and Prevention, National Institute of Health Data Science, Peking University, Beijing, China.
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Cao H, Chen Y, Ge L, Kwong JSW, Lai H, Hu F, Zhang R, Zhao H, Hu L, He R, Zheng W, Zhang J. An umbrella review of the diagnostic value of next-generation sequencing in infectious diseases. Int J Clin Pharm 2024; 46:780-794. [PMID: 38570474 DOI: 10.1007/s11096-024-01704-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 01/18/2024] [Indexed: 04/05/2024]
Abstract
BACKGROUND An increasing number of systematic reviews (SRs) have evaluated the diagnostic values of next-generation sequencing (NGS) in infectious diseases (IDs). AIM This umbrella analysis aimed to assess the potential risk of bias in existing SRs and to summarize the published diagnostic values of NGS in different IDs. METHOD We searched PubMed, Embase, and the Cochrane Library until September 2023 for SRs assessing the diagnostic validity of NGS for IDs. Two investigators independently determined review eligibility, extracted data, and evaluated reporting quality, risk of bias, methodological quality, and evidence certainty in the included SRs. RESULTS Eleven SRs were analyzed. Most SRs exhibited a moderate level of reporting quality, while a serious risk of bias was observed in all SRs. The diagnostic performance of NGS in detecting pneumocystis pneumonia and periprosthetic/prosthetic joint infection was notably robust, showing excellent sensitivity (pneumocystis pneumonia: 0.96, 95% CI 0.90-0.99, very low certainty; periprosthetic/prosthetic joint infection: 0.93, 95% CI 0.83-0.97, very low certainty) and specificity (pneumocystis pneumonia: 0.96, 95% CI 0.92-0.98, very low certainty; periprosthetic/prosthetic joint infection: 0.95, 95% CI 0.92-0.97, very low certainty). NGS exhibited high specificity for central nervous system infection, bacterial meningoencephalitis, and tuberculous meningitis. The sensitivity to these infectious diseases was moderate. NGS demonstrated moderate sensitivity and specificity for multiple infections and pulmonary infections. CONCLUSION This umbrella analysis indicates that NGS is a promising technique for diagnosing pneumocystis pneumonia and periprosthetic/prosthetic joint infection with excellent sensitivity and specificity. More high-quality original research and SRs are needed to verify the current findings.
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Affiliation(s)
- Hong Cao
- School of Pharmaceutical Sciences, Guizhou University, 2708 South of Huaxi Avenue Road, Guiyang, Guizhou Province, China
- Department of Pharmacy, Guizhou Provincial People's Hospital, No.83 Zhongshandong Road, Guiyang, Guizhou Province, China
| | - Yan Chen
- School of Pharmaceutical Sciences, Guizhou University, 2708 South of Huaxi Avenue Road, Guiyang, Guizhou Province, China
- Department of Pharmacy, Guizhou Provincial People's Hospital, No.83 Zhongshandong Road, Guiyang, Guizhou Province, China
| | - Long Ge
- Evidence-Based Social Science Research Center, School of Public Health, Lanzhou University, Lanzhou, China
- Key Laboratory of Evidence Based Medicine and Knowledge Translation of Gansu Province, No. 199, Donggang West Road, Chengguan District, Lanzhou City, Gansu Province, China
| | - Joey Sum-Wing Kwong
- Global Health Nursing, Graduate School of Nursing Science, St. Luke's International University, 10-1 Akashi-Cho, Chuo-Ku, Tokyo, 104-0044, Japan
| | - Honghao Lai
- Evidence-Based Social Science Research Center, School of Public Health, Lanzhou University, Lanzhou, China
- Key Laboratory of Evidence Based Medicine and Knowledge Translation of Gansu Province, No. 199, Donggang West Road, Chengguan District, Lanzhou City, Gansu Province, China
| | - Fangfang Hu
- Department of Laboratory, Guizhou Provincial People's Hospital, No.83 Zhongshandong Road, Guiyang, 550002, Guizhou Province, China
| | - Rui Zhang
- Department of Pharmacy, Guizhou Provincial People's Hospital, No.83 Zhongshandong Road, Guiyang, Guizhou Province, China
| | - Huaye Zhao
- Department of Pharmacy, Guizhou Provincial People's Hospital, No.83 Zhongshandong Road, Guiyang, Guizhou Province, China
| | - Linfang Hu
- Department of Pharmacy, Guizhou Provincial People's Hospital, No.83 Zhongshandong Road, Guiyang, Guizhou Province, China
| | - Rui He
- Experimental Cancer Medicine, Department of Laboratory Medicine, Karolinska Institute, Room 601, Novum PI 6, Hälsovägen 7, Huddinge, 14157, Stockholm, Sweden
| | - Wenyi Zheng
- Experimental Cancer Medicine, Department of Laboratory Medicine, Karolinska Institute, Room 601, Novum PI 6, Hälsovägen 7, Huddinge, 14157, Stockholm, Sweden
| | - Jiaxing Zhang
- Department of Pharmacy, Guizhou Provincial People's Hospital, No.83 Zhongshandong Road, Guiyang, Guizhou Province, China.
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Su L, Yu T, Zhang C, Huo P, Zhao Z. A prediction model for secondary invasive fungal infection among severe SARS-CoV-2 positive patients in ICU. Front Cell Infect Microbiol 2024; 14:1382720. [PMID: 39040601 PMCID: PMC11260608 DOI: 10.3389/fcimb.2024.1382720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 06/24/2024] [Indexed: 07/24/2024] Open
Abstract
Background The global COVID-19 pandemic has resulted in over seven million deaths, and IFI can further complicate the clinical course of COVID-19. Coinfection of COVID-19 and IFI (secondary IFI) pose significant threats not only to healthcare systems but also to patient lives. After the control measures for COVID-19 were lifted in China, we observed a substantial number of ICU patients developing COVID-19-associated IFI. This creates an urgent need for predictive assessment of COVID-19 patients in the ICU environment for early detection of suspected fungal infection cases. Methods This study is a single-center, retrospective research endeavor. We conducted a case-control study on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) positive patients. The cases consisted of patients who developed any secondary IFI during their ICU stay at Jilin University China-Japan Union Hospital in Changchun, Jilin Province, China, from December 1st, 2022, to August 31st, 2023. The control group consisted of SARS-CoV-2 positive patients without secondary IFI. Descriptive and comparative analyses were performed, and a logistic regression prediction model for secondary IFI in COVID-19 patients was established. Additionally, we observed an increased incidence of COVID-19-associated pulmonary aspergillosis (CAPA) during this pandemic. Therefore, we conducted a univariate subgroup analysis on top of IFI, using non-CAPA patients as the control subgroup. Results From multivariate analysis, the prediction model identified 6 factors that are significantly associated with IFI, including the use of broad-spectrum antibiotics for more than 2 weeks (aOR=4.14, 95% CI 2.03-8.67), fever (aOR=2.3, 95%CI 1.16-4.55), elevated log IL-6 levels (aOR=1.22, 95% CI 1.04-1.43) and prone position ventilation (aOR=2.38, 95%CI 1.15-4.97) as independent risk factors for COVID-19 secondary IFI. High BMI (BMI ≥ 28 kg/m2) (aOR=0.85, 95% CI 0.75-0.94) and the use of COVID-19 immunoglobulin (aOR=0.45, 95% CI 0.2-0.97) were identified as independent protective factors against COVID-19 secondary IFI. The Receiver Operating Curve (ROC) area under the curve (AUC) of this model was 0.81, indicating good classification. Conclusion We recommend paying special attention for the occurrence of secondary IFI in COVID-19 patients with low BMI (BMI < 28 kg/m2), elevated log IL-6 levels and fever. Additionally, during the treatment of COVID-19 patients, we emphasize the importance of minimizing the duration of broad-spectrum antibiotic use and highlight the potential of immunoglobulin application in reducing the incidence of IFI.
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Affiliation(s)
- Leilei Su
- Department of Critical Care Medicine, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Tong Yu
- Department of Epidemiology, University of Pittsburgh School of Public Health, Pittsburgh, PA, United States
| | - Chunmei Zhang
- Department of Critical Care Medicine, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Pengfei Huo
- Department of Critical Care Medicine, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Zhongyan Zhao
- Department of Critical Care Medicine, China-Japan Union Hospital of Jilin University, Changchun, China
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Hanin A, Zhang L, Huttner AJ, Plu I, Mathon B, Bielle F, Navarro V, Hirsch LJ, Hafler DA. Single-Cell Transcriptomic Analyses of Brain Parenchyma in Patients With New-Onset Refractory Status Epilepticus (NORSE). NEUROLOGY(R) NEUROIMMUNOLOGY & NEUROINFLAMMATION 2024; 11:e200259. [PMID: 38810181 PMCID: PMC11139018 DOI: 10.1212/nxi.0000000000200259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 03/25/2024] [Indexed: 05/31/2024]
Abstract
BACKGROUND AND OBJECTIVES New-onset refractory status epilepticus (NORSE) occurs in previously healthy children or adults, often followed by refractory epilepsy and poor outcomes. The mechanisms that transform a normal brain into an epileptic one capable of seizing for prolonged periods despite treatment remain unclear. Nonetheless, several pieces of evidence suggest that immune dysregulation could contribute to hyperexcitability and modulate NORSE sequelae. METHODS We used single-nucleus RNA sequencing to delineate the composition and phenotypic states of the CNS of 4 patients with NORSE, to better understand the relationship between hyperexcitability and immune disturbances. We compared them with 4 patients with chronic temporal lobe epilepsy (TLE) and 2 controls with no known neurologic disorder. RESULTS Patients with NORSE and TLE exhibited a significantly higher proportion of excitatory neurons compared with controls, with no discernible difference in inhibitory GABAergic neurons. When examining the ratio between excitatory neurons and GABAergic neurons for each patient individually, we observed a higher ratio in patients with acute NORSE or TLE compared with controls. Furthermore, a negative correlation was found between the ratio of excitatory to GABAergic neurons and the proportion of GABAergic neurons. The ratio between excitatory neurons and GABAergic neurons correlated with the proportion of resident or infiltrating macrophages, suggesting the influence of microglial reactivity on neuronal excitability. Both patients with NORSE and TLE exhibited increased expression of genes associated with microglia activation, phagocytic activity, and NLRP3 inflammasome activation. However, patients with NORSE had decreased expression of genes related to the downregulation of the inflammatory response, potentially explaining the severity of their presentation. Microglial activation in patients with NORSE also correlated with astrocyte reactivity, possibly leading to higher degrees of demyelination. DISCUSSION Our study sheds light on the complex cellular dynamics in NORSE, revealing the potential roles of microglia, infiltrating macrophages, and astrocytes in hyperexcitability and demyelination, offering potential avenues for future research targeting the identified pathways.
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Affiliation(s)
- Aurélie Hanin
- From the Departments of Neurology and Immunobiology (A.H., L.Z., D.A.H.); Comprehensive Epilepsy Center (A.H., L.J.H.), Department of Neurology, Yale University School of Medicine, New Haven, CT; Sorbonne Université (A.H., I.P., B.M., V.N.), Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP; AP-HP (A.H., V.N.), Epilepsy Unit and Clinical Neurophysiology Department, DMU Neurosciences, Hôpital de la Pitié-Salpêtrière, Paris, France; Department of Pathology (A.J.H.), Yale University School of Medicine, New Haven, CT; AP-HP (I.P., F.B.), Department of Neuropathology, DMU Neurosciences; AP-HP (B.M.), Department of Neurosurgery, Hôpital de la Pitié-Salpêtrière; and Center of Reference for Rare Epilepsies (V.N.), EpiCare, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Le Zhang
- From the Departments of Neurology and Immunobiology (A.H., L.Z., D.A.H.); Comprehensive Epilepsy Center (A.H., L.J.H.), Department of Neurology, Yale University School of Medicine, New Haven, CT; Sorbonne Université (A.H., I.P., B.M., V.N.), Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP; AP-HP (A.H., V.N.), Epilepsy Unit and Clinical Neurophysiology Department, DMU Neurosciences, Hôpital de la Pitié-Salpêtrière, Paris, France; Department of Pathology (A.J.H.), Yale University School of Medicine, New Haven, CT; AP-HP (I.P., F.B.), Department of Neuropathology, DMU Neurosciences; AP-HP (B.M.), Department of Neurosurgery, Hôpital de la Pitié-Salpêtrière; and Center of Reference for Rare Epilepsies (V.N.), EpiCare, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Anita J Huttner
- From the Departments of Neurology and Immunobiology (A.H., L.Z., D.A.H.); Comprehensive Epilepsy Center (A.H., L.J.H.), Department of Neurology, Yale University School of Medicine, New Haven, CT; Sorbonne Université (A.H., I.P., B.M., V.N.), Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP; AP-HP (A.H., V.N.), Epilepsy Unit and Clinical Neurophysiology Department, DMU Neurosciences, Hôpital de la Pitié-Salpêtrière, Paris, France; Department of Pathology (A.J.H.), Yale University School of Medicine, New Haven, CT; AP-HP (I.P., F.B.), Department of Neuropathology, DMU Neurosciences; AP-HP (B.M.), Department of Neurosurgery, Hôpital de la Pitié-Salpêtrière; and Center of Reference for Rare Epilepsies (V.N.), EpiCare, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Isabelle Plu
- From the Departments of Neurology and Immunobiology (A.H., L.Z., D.A.H.); Comprehensive Epilepsy Center (A.H., L.J.H.), Department of Neurology, Yale University School of Medicine, New Haven, CT; Sorbonne Université (A.H., I.P., B.M., V.N.), Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP; AP-HP (A.H., V.N.), Epilepsy Unit and Clinical Neurophysiology Department, DMU Neurosciences, Hôpital de la Pitié-Salpêtrière, Paris, France; Department of Pathology (A.J.H.), Yale University School of Medicine, New Haven, CT; AP-HP (I.P., F.B.), Department of Neuropathology, DMU Neurosciences; AP-HP (B.M.), Department of Neurosurgery, Hôpital de la Pitié-Salpêtrière; and Center of Reference for Rare Epilepsies (V.N.), EpiCare, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Bertrand Mathon
- From the Departments of Neurology and Immunobiology (A.H., L.Z., D.A.H.); Comprehensive Epilepsy Center (A.H., L.J.H.), Department of Neurology, Yale University School of Medicine, New Haven, CT; Sorbonne Université (A.H., I.P., B.M., V.N.), Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP; AP-HP (A.H., V.N.), Epilepsy Unit and Clinical Neurophysiology Department, DMU Neurosciences, Hôpital de la Pitié-Salpêtrière, Paris, France; Department of Pathology (A.J.H.), Yale University School of Medicine, New Haven, CT; AP-HP (I.P., F.B.), Department of Neuropathology, DMU Neurosciences; AP-HP (B.M.), Department of Neurosurgery, Hôpital de la Pitié-Salpêtrière; and Center of Reference for Rare Epilepsies (V.N.), EpiCare, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Franck Bielle
- From the Departments of Neurology and Immunobiology (A.H., L.Z., D.A.H.); Comprehensive Epilepsy Center (A.H., L.J.H.), Department of Neurology, Yale University School of Medicine, New Haven, CT; Sorbonne Université (A.H., I.P., B.M., V.N.), Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP; AP-HP (A.H., V.N.), Epilepsy Unit and Clinical Neurophysiology Department, DMU Neurosciences, Hôpital de la Pitié-Salpêtrière, Paris, France; Department of Pathology (A.J.H.), Yale University School of Medicine, New Haven, CT; AP-HP (I.P., F.B.), Department of Neuropathology, DMU Neurosciences; AP-HP (B.M.), Department of Neurosurgery, Hôpital de la Pitié-Salpêtrière; and Center of Reference for Rare Epilepsies (V.N.), EpiCare, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Vincent Navarro
- From the Departments of Neurology and Immunobiology (A.H., L.Z., D.A.H.); Comprehensive Epilepsy Center (A.H., L.J.H.), Department of Neurology, Yale University School of Medicine, New Haven, CT; Sorbonne Université (A.H., I.P., B.M., V.N.), Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP; AP-HP (A.H., V.N.), Epilepsy Unit and Clinical Neurophysiology Department, DMU Neurosciences, Hôpital de la Pitié-Salpêtrière, Paris, France; Department of Pathology (A.J.H.), Yale University School of Medicine, New Haven, CT; AP-HP (I.P., F.B.), Department of Neuropathology, DMU Neurosciences; AP-HP (B.M.), Department of Neurosurgery, Hôpital de la Pitié-Salpêtrière; and Center of Reference for Rare Epilepsies (V.N.), EpiCare, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Lawrence J Hirsch
- From the Departments of Neurology and Immunobiology (A.H., L.Z., D.A.H.); Comprehensive Epilepsy Center (A.H., L.J.H.), Department of Neurology, Yale University School of Medicine, New Haven, CT; Sorbonne Université (A.H., I.P., B.M., V.N.), Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP; AP-HP (A.H., V.N.), Epilepsy Unit and Clinical Neurophysiology Department, DMU Neurosciences, Hôpital de la Pitié-Salpêtrière, Paris, France; Department of Pathology (A.J.H.), Yale University School of Medicine, New Haven, CT; AP-HP (I.P., F.B.), Department of Neuropathology, DMU Neurosciences; AP-HP (B.M.), Department of Neurosurgery, Hôpital de la Pitié-Salpêtrière; and Center of Reference for Rare Epilepsies (V.N.), EpiCare, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - David A Hafler
- From the Departments of Neurology and Immunobiology (A.H., L.Z., D.A.H.); Comprehensive Epilepsy Center (A.H., L.J.H.), Department of Neurology, Yale University School of Medicine, New Haven, CT; Sorbonne Université (A.H., I.P., B.M., V.N.), Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP; AP-HP (A.H., V.N.), Epilepsy Unit and Clinical Neurophysiology Department, DMU Neurosciences, Hôpital de la Pitié-Salpêtrière, Paris, France; Department of Pathology (A.J.H.), Yale University School of Medicine, New Haven, CT; AP-HP (I.P., F.B.), Department of Neuropathology, DMU Neurosciences; AP-HP (B.M.), Department of Neurosurgery, Hôpital de la Pitié-Salpêtrière; and Center of Reference for Rare Epilepsies (V.N.), EpiCare, Hôpital de la Pitié-Salpêtrière, Paris, France
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Pan JL, Wu WJ, Zeng SY, Xu JH, Lu K. A Report of Two Cases of Meningoencephalitis Caused by Streptococcus intermedius. Infect Drug Resist 2024; 17:2189-2198. [PMID: 38835493 PMCID: PMC11149631 DOI: 10.2147/idr.s438615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 05/16/2024] [Indexed: 06/06/2024] Open
Abstract
Objective In this paper, we analyzed the clinical data of patients with meningoencephalitis caused by Streptococcus intermedius to understand better the clinical characteristics of the disease and recommend auxiliary diagnostic mode as well as treatment experience. Methods We reviewed the clinical data of two patients admitted to our department in 2019 with meningoencephalitis caused by S. intermedius. Results Two female patients were examined, one of whom had a history of radiotherapy for nasopharyngeal carcinoma while the other had no underlying disease. These two patients were admitted with symptoms of meningoencephalitis. Cerebrospinal fluid examinations revealed elevated levels of leukocytes and protein. After treatment with meropenem, the condition improved for a brief time, but then worsened with a decline in mental status and limb movement. Blood and cerebrospinal fluid cultures demonstrated the absence of pathogenic bacteria, while genome sequencing of cerebrospinal fluids revealed the presence of S. intermedius. Cranial magnetic resonance imaging revealed multiple cerebral abscesses (CAs). After coadministration of linezolid as an anti-infective, clinical symptoms gradually improved, and the CAs shrank on follow-up imaging. The condition exhibited a pattern of improvement-deterioration-improvement. Conclusion Meningoencephalitis caused by S. intermedius is complex and prone to fluctuation and formation of multiple CAs. The definitive clinical diagnosis of this disease can be aided by genome sequencing technology, and early clarification of the etiology combined with the use of potent antibiotics is effective.
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Affiliation(s)
- Jun-Li Pan
- Department of Neurology, Zhongshan City People's Hospital, Zhongshan, Guangdong province, 528403, People's Republic of China
| | - Wen-Jun Wu
- Department of Neurology, Zhongshan City People's Hospital, Zhongshan, Guangdong province, 528403, People's Republic of China
| | - Shu-Yan Zeng
- Department of MRI Room, Zhongshan City People's Hospital, Zhongshan, Guangdong province, 528403, People's Republic of China
| | - Jia-He Xu
- Department of Neurology, Zhongshan City People's Hospital, Zhongshan, Guangdong province, 528403, People's Republic of China
| | - Kui Lu
- Department of Neurology, Zhongshan City People's Hospital, Zhongshan, Guangdong province, 528403, People's Republic of China
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Wu Y, Wu J, Xu N, Lin M, Yue W, Chen Y, Zhang Q, Li H. Clinical application value of metagenome next-generation sequencing in pulmonary diffuse exudative lesions: a retrospective study. Front Cell Infect Microbiol 2024; 14:1367885. [PMID: 38784566 PMCID: PMC11113015 DOI: 10.3389/fcimb.2024.1367885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 04/09/2024] [Indexed: 05/25/2024] Open
Abstract
Objective This study aims to investigate the clinical application value of Metagenome Next-Generation Sequencing (mNGS) for pulmonary diffuse exudative lesions. Methods From January 1, 2014, to November 31, 2021, 136 cases with chest radiologic presentations of pulmonary diffuse exudative lesions admitted to Fujian Provincial Hospital were included in the study; of those, 77 patients underwent mNGS pathogen detection. Based on the pathogen detection outcomes and clinical diagnoses, patients were categorized into an infection group (IG) and a non-infection group (NIG). A comparison was made between the diagnostic efficacy of the mNGS technique and traditional culture methods. Meanwhile, 59 patients clinically identified as having infectious pulmonary diffuse exudative lesions but who did not receive mNGS testing were designated as the non-NGS infection group (non-IG). A retrospective cohort study was conducted on patients in both the IG and non-IG, with a 30-day all-cause mortality endpoint used for follow-up. Outcomes When compared to conventional culture methods, mNGS demonstrated an approximate 35% increase in sensitivity (80.0% vs 45.5%, P<0.001), without significant disparity in specificity (77.3% vs 95.5%, P=0.185). Under antibiotic exposure, the positivity rate detected by mNGS was notably higher than that by traditional culture methods, indicating that mNGS is less affected by exposure to antibiotics (P<0.05). Within 30 days, the all-cause mortality rate for patients in the IG versus the non-IG was 14.55% and 37.29%, respectively (P<0.05). Following a COX regression analysis to adjust for confounding factors, the analysis revealed that a CURB-65 score ≥3 points (HR=3.348, P=0.001) and existing cardiovascular disease (HR=2.473, P=0.026) were independent risk factors for these patients. Conversely, mNGS testing (HR=0.368, P=0.017) proved to be an independent protective factor. Conclusion mNGS technology makes it easier to pinpoint the cause of pulmonary diffuse infectious exudative lesions without much interference from antibiotics, helping doctors spot and diagnose these issues early on, thereby playing a key role in helping them decide the best treatment approach for patients. Such conclusions may have a bias, as the performance of traditional methods might be underestimated due to the absence of complete results from other conventional diagnostic techniques like serological testing and PCR.
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Affiliation(s)
- Yisong Wu
- Fujian Provincial Hospital, Shengli Clinical College of Fujian Medical University, Fuzhou, Fujian, China
| | - Jian Wu
- Fujian Provincial Hospital, Shengli Clinical College of Fujian Medical University, Fuzhou, Fujian, China
| | - Nengluan Xu
- Department of Infectious Diseases, Fujian Provincial Hospital, Shengli Clinical College of Fujian Medical University, Fuzhou, Fujian, China
| | - Ming Lin
- Fujian Provincial Hospital, Shengli Clinical College of Fujian Medical University, Fuzhou, Fujian, China
| | - Wenxiang Yue
- Fujian Provincial Hospital, Shengli Clinical College of Fujian Medical University, Fuzhou, Fujian, China
| | - Yusheng Chen
- Fujian Provincial Hospital, Shengli Clinical College of Fujian Medical University, Fuzhou, Fujian, China
| | - Qiongyao Zhang
- Fujian Provincial Key Laboratory of Medical Big Data Engineering, Fujian Provincial Hospital, Fuzhou, Fujian, China
| | - Hongru Li
- Department of Infectious Diseases, Fujian Provincial Hospital, Shengli Clinical College of Fujian Medical University, Fuzhou, Fujian, China
- Fujian Provincial Key Laboratory of Medical Big Data Engineering, Fujian Provincial Hospital, Fuzhou, Fujian, China
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Lu Y, Li S, Su Z, Luo C, Gu M, Yuan D, Qin BE, Dai K, Xia H, Chen Y, Peng F, Jiang Y. Presence of Epstein-Barr virus in cerebrospinal fluid is associated with increased mortality in HIV-negative cryptococcal meningitis. Med Mycol 2024; 62:myae052. [PMID: 38710585 DOI: 10.1093/mmy/myae052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 04/15/2024] [Accepted: 05/05/2024] [Indexed: 05/08/2024] Open
Abstract
Cryptococcus neoformans is the most common cause of fungal meningitis and is associated with a high mortality. The clinical significance of concurrent Epstein-Barr virus (EBV) in the cerebrospinal fluid (CSF) of human immunodeficiency virus (HIV)-negative patients with cryptococcal meningitis (CM) remains unclear. A retrospective cohort study was performed by analyzing CSF samples from 79 HIV-negative Chinese Han patients with confirmed CM. We identified CSF viral DNA in these patients by metagenomic next-generation sequencing (mNGS) and compared 10-week survival rates among those with and without EBV DNA in CSF. Of the 79 CSF samples tested, 44.3% (35/79) had detectable viral DNA in CSF, while 55.7% (44/79) were virus-negative. The most frequent viral pathogen was EBV, which was detected in 22.8% (18/79) patients. The median number of CSF-EBV DNA reads was 4 reads with a range from 1 to 149 reads. The 10-week mortality rates were 22.2% (4/18) in those with positive CSF-EBV and 2.3% (1/44) in those with negative CSF-virus (hazard ratio 8.20, 95% confidence interval [CI] 1.52-81.80; P = 0.014), which remained significant after a multivariate adjustment for the known risk factors of mortality (adjusted hazard ratio 8.15, 95% CI 1.14-92.87; P = 0.037). mNGS can identify viruses that coexist in CSF of HIV-negative patients with CM. EBV DNA is most commonly found together with C. neoformans in CSF and its presence is associated with increased mortality in HIV-negative CM patients.
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Affiliation(s)
- Yi Lu
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, PR China
- Department of Neurology, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong, PR China
| | - Shubo Li
- Department of Statistics, The Pennsylvania State University, State College, Pennsylvania, USA
| | - Zhihui Su
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, PR China
| | - Chongliang Luo
- Division of Public Health Sciences, Washington University School of Medicine in St. Louis, St Louis, Missouri, USA
| | - Meifeng Gu
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, PR China
| | - Dasen Yuan
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, PR China
| | - Bang-E Qin
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, PR China
| | - Kai Dai
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, PR China
| | - Han Xia
- Department of Scientific Affairs, Hugobiotech Co, Beijing, PR China
| | - Yong Chen
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Fuhua Peng
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, PR China
| | - Ying Jiang
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, PR China
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Meinhardt A, Reilly L, Kaliakatsos M, Abdel-Aziz K, Alsharidah S, Bodi I, Booth C, Chetty K, Evans J, Ferreras-Antolín L, Froude S, Galtrey CM, Guruprasad S, Hadden RD, Hassell J, Hyöty H, Kreins AY, Laiho JE, Lowe DM, Lunn MP, Mankad K, Struik S, Whittaker E, Worth A, Yong P, Zhang L, Breuer J, Kadambari S. Novel antivirals for severe enterovirus infection in immunocompromised hosts; A case series. J Infect 2024; 88:106142. [PMID: 38527653 DOI: 10.1016/j.jinf.2024.106142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 03/17/2024] [Accepted: 03/20/2024] [Indexed: 03/27/2024]
Affiliation(s)
- Andrea Meinhardt
- Department of Immunology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK; Department of Paediatric Haematology, Oncology and Immunodeficiencies, Justus, Liebig-University, Giessen, Germany.
| | - Liam Reilly
- Department of Immunology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK; Department of Paediatric Infectious Diseases and Immunology, Royal Hospital for Children, Glasgow, UK
| | - Marios Kaliakatsos
- Department of Neurology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Khaled Abdel-Aziz
- Department of Neurology, St George's University Hospital NHS Foundation Trust, London, UK
| | - Sondus Alsharidah
- Paediatric Immunology, Leeds Children`s Hospital, Leeds, UK; Paediatric Haematology-Oncology Stem Cell Transplant Department at NBK Children's Hospital, Kuwait
| | - Istvan Bodi
- Department of Neuropathology, Kings College Hospital NHS Foundation Trust, London, UK
| | - Claire Booth
- Department of Immunology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK; Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Kritika Chetty
- Department of Immunology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK; Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Jennifer Evans
- Paediatric Infectious Disease and Immunology, University Hospital of Wales, Cardiff, UK
| | - Laura Ferreras-Antolín
- Paediatric Infectious Disease and Immunology, St George's University Hospitals, NHS Foundation Trust, London, UK
| | - Susannah Froude
- Public Health Wales Microbiology, Public Health Wales NHS Trust, Cardiff, UK
| | - Clare M Galtrey
- Department of Neurology, St George's University Hospital NHS Foundation Trust, London, UK
| | - Suba Guruprasad
- Paediatric Infectious Disease and Immunology, St George's University Hospitals, NHS Foundation Trust, London, UK
| | - Robert D Hadden
- Department of Neurology, King's College Hospital, London, UK
| | - Jane Hassell
- Department of Neurology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Heikki Hyöty
- Faculty of Medicine and Health Technology, Tampere University, Finland; Fimlab Laboratories, Tampere, Finland
| | - Alexandra Y Kreins
- Department of Immunology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK; Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Jutta E Laiho
- Faculty of Medicine and Health Technology, Tampere University, Finland
| | - David M Lowe
- Institute of Immunity and Transplantation, University College London, London, UK
| | - Michael P Lunn
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Kshitij Mankad
- Department of Radiology, Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Siske Struik
- Paediatric Infectious Disease and Immunology, University Hospital of Wales, Cardiff, UK
| | - Elizabeth Whittaker
- Department of Paediatric Infectious Diseases, St Mary's Hospital, Imperial College NHS Healthcare Trust, London, UK; Department of Academic Paediatrics, Imperial College, 2nd Floor Wright-Fleming Building, London, UK
| | - Austen Worth
- Department of Immunology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Patrick Yong
- Department of Neurology, St George's University Hospital NHS Foundation Trust, London, UK
| | - Liqun Zhang
- Department of Neurology, St George's University Hospital NHS Foundation Trust, London, UK
| | - Judith Breuer
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, London, UK; Department of Infectious Diseases, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Seilesh Kadambari
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, London, UK; Department of Infectious Diseases, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
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10
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Yu Y, Zhuo B, Xu W, Li L, Jin X, Ji Y, Ge Y. Diagnosis of an immunocompetent adult with acute headache and fever as Epstein-Barr virus encephalitis by mNGS of cerebrospinal fluid. Diagn Microbiol Infect Dis 2024; 109:116213. [PMID: 38359677 DOI: 10.1016/j.diagmicrobio.2024.116213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 01/31/2024] [Accepted: 02/09/2024] [Indexed: 02/17/2024]
Abstract
Complicated case with fever or headache of unknown origin is currently one of the main challenges in clinical diagnosis. A retrospective analysis was conducted on a 27-year-old female patient hospitalized with headache and fever, and the pathogen species were ultimately determined by metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF). The culture results of CSF showed no bacterial or fungal growth. CSF cytology showed a significant increase in nucleated cells. Pathogenic index (corresponded to human gamma herpesvirus 4) of the microorganism after correcting for human background was 12846.77 with a host index (human resource) of 27822.48 by mNGS of CSF. The patient improved through antiviral treatment with ganciclovir. Epstein-Barr virus encephalitis is rare in immunocompetent adults, which can easily cause misdiagnosis and should be paid attention to. mNGS of CSF has significant advantages in the diagnosis of Epstein-Barr virus encephalitis.
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Affiliation(s)
- Yan Yu
- Center for Rehabilitation Medicine, Department of Ophthalmology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, 310014, China
| | - Bingqian Zhuo
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, 310014, China
| | - Wei Xu
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, 310014, China; School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 310053, China
| | - Lanhui Li
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 310053, China
| | - Xinyue Jin
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, 310014, China
| | - Youqi Ji
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 310053, China
| | - Yumei Ge
- Center for Rehabilitation Medicine, Department of Ophthalmology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, 310014, China; Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, 310014, China; School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 310053, China; Key Laboratory of Precision Medicine for Head and Neck Cancers of Zhejiang Province, Zhejiang Provincial People's Hospital, Hangzhou, Zhejiang, 310014, China.
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11
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Wang C, Pan M, Lin Q, Mofatteh M, Chen Y, Baizabal-Carvallo JF, Su F, Wang Z. Metagenomic next-generation sequencing assistance in identifying Mycobacterium avium meningoencephalitis: A case report and literature review. Heliyon 2024; 10:e28630. [PMID: 38596092 PMCID: PMC11002592 DOI: 10.1016/j.heliyon.2024.e28630] [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: 10/07/2023] [Revised: 03/14/2024] [Accepted: 03/21/2024] [Indexed: 04/11/2024] Open
Abstract
Nontuberculous mycobacteria associated intracranial infection is a rare disease that mainly occurs in HIV-infected patients. The disease has a poor prognosis. The authors report a case of non-tuberculous mycobacterial meningoencephalitis in a non-AIDS patient, but long history of poorly controlled type 2 diabetes mellitus. A 55-year-old, right-handed, male patient presented with an 8-day history of fever, episodes of severe headache with signs of meningeal irritation. MRI showed hyperintensities/contrast enhancement in the visual pathways, basal ganglia sellar region and leptomeninges. No etiological diagnosis was reached until metagenomic next-generation sequencing (mNGS) was used, showing the presence of Mycobacterium avium. The patient was cured with aggressive antimycobacterial therapy. The authors discuss the clinical manifestations and drug therapy of nontuberculous mycobacteria-related intracranial infections by reviewing relevant literature. As meningoencephalitis by Mycobacterium avium has a high mortality an early diagnosis and appropriate therapeutic interventions are warranted. For this reason, the use of mNGS can be helpful to avoid therapeutic delay.
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Affiliation(s)
- Changsheng Wang
- Key Specialty of Clinical Pharmacy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
| | - Mengqiu Pan
- Department of Neurology, GuangDong Sanjiu Brain Hospital, Guangzhou, China
| | - Qinjian Lin
- Department of Pharmacy, GuangDong Sanjiu Brain Hospital, Guangzhou, China
| | - Mohammad Mofatteh
- School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, United Kingdom
| | - Yimin Chen
- Department of Neurology and Advanced National Stroke Center, Foshan Sanshui District People's Hospital, Foshan, 528100, China
| | - José Fidel Baizabal-Carvallo
- Parkinson's Disease Center and Movement Disorders Clinic, Department of Neurology, Baylor College of Medicine, Houston, TX, USA
- Department of Sciences and Engineering, University of Guanajuato, León, Mexico
| | - Fanghua Su
- Department of Pharmacy, GuangDong Sanjiu Brain Hospital, Guangzhou, China
| | - Zhanhang Wang
- Department of Neurology, GuangDong Sanjiu Brain Hospital, Guangzhou, China
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12
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Yuan L, Chen Q, Zhu XY, Lai LM, Zhao R, Liu Y. Evaluation of clinical characteristics and risk factors associated with Chlamydia psittaci infection based on metagenomic next-generation sequencing. BMC Microbiol 2024; 24:86. [PMID: 38481150 PMCID: PMC10935969 DOI: 10.1186/s12866-024-03236-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 02/26/2024] [Indexed: 03/17/2024] Open
Abstract
INTRODUCTION Psittacosis is a zoonosis caused by Chlamydia psittaci, the clinical manifestations of Psittacosis range from mild illness to fulminant severe pneumonia with multiple organ failure. This study aimed to evaluate the clinical characteristics of Chlamydia psittaci infection diagnosed based on metagenomic next-generation sequencing(mNGS), as well as the risk factors affecting the progress of Chlamydia psittaci infection, in order to improve the effect of therapeutics. METHODS We retrospectively analyzed the clinical data of patients infected with chlamydia psittaci in the First Affiliated Hospital of Nanchang University from January 2021 to December 2021. The patient's past medical history, clinical manifestations, laboratory examinations, chest CT results, treatment status, and prognosis data were collected. we also investigated both the pathogenic profile characteristics and the lower respiratory tract microbiota of patients with Chlamydia psittaci pneumonia using mNGS. RESULTS All cases of Chlamydia psittaci in our research have been confirmed by mNGS. Among 46 cases of Chlamydia psittaci pneumonia, Poultry exposure was reported in 35 cases. In severe cases of Chlamydia psittaci pneumonia, Neutrophils, Procalcitonin (PCT), Lactate Dehydrogenase (LDH), Hydroxybutyrate Dehydrogenase (HBDH), Creatine Kinase Isoenzymes-B (CK-MB) and D-Dimer levels were remarkably higher than that of non-severe cases, except for lymphocytes (all P < 0.05). Chest CT scans showed Bilateral (77.8%), multiple lobar lungs (85.2%), pleural effusions (44.4%) involvement in those suffering from severe Chlamydia psittaci pneumonia, whereas its incidence was 0%, 21.1% and 10.5% in non-severe patients, respectively (P < 0.05). Multivariate analysis revealed that higher lymphocyte concentrations (OR 0.836, 95% CI 0.714-0.962, P = 0.041) were the only protective factor for survival. mNGS results indicated that 41.3% of patients (19/46) had suspected coinfections with a coinfection rate of 84.2% (16/19) in the severe group, much higher than that in the non severe group (p < 0.05). No significantly different profiles of lower respiratory tract microbiota diversity were found between non severe group and severe group. CONCLUSION A history of poultry exposure in patients can serve as an important basis for diagnosing Chlamydia psittaci pneumonia, and patients with severe Chlamydia psittaci pneumonia are more likely to develop elevated inflammatory biomarkers as well as elevated cardiac markers. Higher lymphocyte concentrations are protective factors associated with severe C. psittaci pneumonia. The higher proportion of patients with coinfections in our study supports the use of mNGS for comprehensive early detection of respiratory infections in patients with C. psittaci pneumonia.
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Affiliation(s)
- Lei Yuan
- Department of Clinical laboratory, The First Affiliated Hospital of Nanchang University of Nanchang University, Nanchang University, No.17, YongWaiZhengStreet, Nanchang, 330006, China
| | - Qiang Chen
- Department of Clinical laboratory, The First Affiliated Hospital of Nanchang University of Nanchang University, Nanchang University, No.17, YongWaiZhengStreet, Nanchang, 330006, China
| | - Xin Yu Zhu
- Department of Clinical laboratory, The First Affiliated Hospital of Nanchang University of Nanchang University, Nanchang University, No.17, YongWaiZhengStreet, Nanchang, 330006, China
| | - Lan Min Lai
- Department of Clinical laboratory, The First Affiliated Hospital of Nanchang University of Nanchang University, Nanchang University, No.17, YongWaiZhengStreet, Nanchang, 330006, China
| | - Rui Zhao
- Department of Clinical laboratory, The First Affiliated Hospital of Nanchang University of Nanchang University, Nanchang University, No.17, YongWaiZhengStreet, Nanchang, 330006, China.
| | - Yang Liu
- Department of Clinical laboratory, The First Affiliated Hospital of Nanchang University of Nanchang University, Nanchang University, No.17, YongWaiZhengStreet, Nanchang, 330006, China.
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13
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Tan J, Wu L, Zhan L, Sheng M, Tang Z, Xu J, Ma H. Optimal selection of specimens for metagenomic next-generation sequencing in diagnosing periprosthetic joint infections. Front Cell Infect Microbiol 2024; 14:1356804. [PMID: 38500507 PMCID: PMC10945027 DOI: 10.3389/fcimb.2024.1356804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 02/19/2024] [Indexed: 03/20/2024] Open
Abstract
Objective This study aimed to assess the diagnostic value of metagenomic next-generation sequencing (mNGS) across synovial fluid, prosthetic sonicate fluid, and periprosthetic tissues among patients with periprosthetic joint infection (PJI), intending to optimize specimen selection for mNGS in these patients. Methods This prospective study involved 61 patients undergoing revision arthroplasty between September 2021 and September 2022 at the First Affiliated Hospital of Zhengzhou University. Among them, 43 cases were diagnosed as PJI, and 18 as aseptic loosening (AL) based on the American Musculoskeletal Infection Society (MSIS) criteria. Preoperative or intraoperative synovial fluid, periprosthetic tissues, and prosthetic sonicate fluid were collected, each divided into two portions for mNGS and culture. Comparative analyses were conducted between the microbiological results and diagnostic efficacy derived from mNGS and culture tests. Furthermore, the variability in mNGS diagnostic efficacy for PJI across different specimen types was assessed. Results The sensitivity and specificity of mNGS diagnosis was 93% and 94.4% for all types of PJI specimens; the sensitivity and specificity of culture diagnosis was 72.1% and 100%, respectively. The diagnostic sensitivity of mNGS was significantly higher than that of culture (X2 = 6.541, P=0.011), with no statistically significant difference in specificity (X2 = 1.029, P=0.310). The sensitivity of the synovial fluid was 83.7% and the specificity was 94.4%; the sensitivity of the prosthetic sonicate fluid was 90.7% and the specificity was 94.4%; and the sensitivity of the periprosthetic tissue was 81.4% and the specificity was 100%. Notably, the mNGS of prosthetic sonicate fluid displayed a superior pathogen detection rate compared to other specimen types. Conclusion mNGS can function as a precise diagnostic tool for identifying pathogens in PJI patients using three types of specimens. Due to its superior ability in pathogen identification, prosthetic sonicate fluid can replace synovial fluid and periprosthetic tissue as the optimal sample choice for mNGS.
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Affiliation(s)
- Jun Tan
- Department of Mini-invasive Spinal Surgery, The Third People’s Hospital of Henan Province, Zhengzhou, Henan, China
| | - Lingxiao Wu
- Department of Orthopedic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Lijuan Zhan
- Department of Neurology, People’s Hospital of Zhengzhou, Zhengzhou, Henan, China
| | - Minkui Sheng
- Department of Mini-invasive Spinal Surgery, The Third People’s Hospital of Henan Province, Zhengzhou, Henan, China
| | - Zhongxin Tang
- Department of Mini-invasive Spinal Surgery, The Third People’s Hospital of Henan Province, Zhengzhou, Henan, China
- Department of Orthopedic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Jianzhong Xu
- Department of Orthopedic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Haijun Ma
- Department of Mini-invasive Spinal Surgery, The Third People’s Hospital of Henan Province, Zhengzhou, Henan, China
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Chen GJ, Chen XB, Rao WY, Pan XY, Li SY, Su ZQ. Airway necrosis and granulation tissue formation caused by Rhizopus oryzae leading to severe upper airway obstruction: a case report. Front Cell Infect Microbiol 2024; 14:1366472. [PMID: 38500502 PMCID: PMC10944989 DOI: 10.3389/fcimb.2024.1366472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 02/19/2024] [Indexed: 03/20/2024] Open
Abstract
Pulmonary Mucormycosis is a fatal infectious disease with high mortality rate. The occurrence of Mucormycosis is commonly related to the fungal virulence and the host's immunological defenses against pathogens. Mucormycosis infection and granulation tissue formation occurred in the upper airway was rarely reported. This patient was a 60-year-old male with diabetes mellitus, who was admitted to hospital due to progressive cough, sputum and dyspnea. High-resolution computed tomography (HRCT) and bronchoscopy revealed extensive tracheal mucosal necrosis, granulation tissue proliferation, and severe airway stenosis. The mucosal necrotic tissue was induced by the infection of Rhizopus Oryzae, confirmed by metagenomic next-generation sequencing (mNGS) in tissue biopsy. This patient was treated with the placement of a covered stent and local instillation of amphotericin B via bronchoscope. The tracheal mucosal necrosis was markedly alleviated, the symptoms of cough, shortness of breath, as well as exercise tolerance were significantly improved. The placement of airway stent and transbronchial microtube drip of amphotericin B could conduce to rapidly relieve the severe airway obstruction due to Mucormycosis infection.
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Affiliation(s)
- Geng-Jia Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
- Nanshan School of Medical, Guangzhou Medical University, Guangzhou, China
| | - Xiao-Bo Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Wan-Yuan Rao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xiao-Yi Pan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Shi-Yue Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Zhu-Quan Su
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
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15
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Lv Q, Cao Y, Wang J, Meng L, Wang G. Metagenomic Next-generation Sequencing May be a Tool for Timely Diagnosis of Seronegative and Primary Toxoplasma Infection After Allogeneic Hematopoietic Stem Cell Transplantation: A Case Report and Literature Review. Pediatr Infect Dis J 2024; 43:155-159. [PMID: 38190489 DOI: 10.1097/inf.0000000000004170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
We report a case of Toxoplasma gondii ( T. gondii ) antibody seronegativity in a 14-year-old boy with a primary infection of T. gondii after allogeneic hematopoietic stem cell transplantation for acute T-cell lymphoblastic leukemia who was rapidly diagnosed through metagenomic next-generation sequencing of peripheral blood as well as clinical manifestations. He was successfully cured with timely administration of trimethoprim-sulfamethoxazole due to early diagnosis.
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Affiliation(s)
- Qiuxia Lv
- From the Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
- Department of Hematology, The Peoples Hospital of Guangxi Zhuang Autonomous Region, Guangxi Academy of Medical Sciences, Nanning, People's Republic of China
| | - Yang Cao
- From the Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Jue Wang
- From the Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Li Meng
- From the Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Gaoxiang Wang
- From the Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
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16
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Liang W, Zhang Q, Qian Q, Wang M, Ding Y, Zhou J, Zhu Y, Jin Y, Chen X, Kong H, Song W, Lu X, Wu X, Xu X, Dai S, Sun W. Diagnostic strategy of metagenomic next-generation sequencing for gram negative bacteria in respiratory infections. Ann Clin Microbiol Antimicrob 2024; 23:10. [PMID: 38302964 PMCID: PMC10835912 DOI: 10.1186/s12941-024-00670-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 01/20/2024] [Indexed: 02/03/2024] Open
Abstract
OBJECTIVE This study aims to identify the most effective diagnostic method for distinguishing pathogenic and non-pathogenic Gram-negative bacteria (GNB) in suspected pneumonia cases using metagenomic next-generation sequencing (mNGS) on bronchoalveolar lavage fluid (BALF) samples. METHODS The effectiveness of mNGS was assessed on BALF samples collected from 583 patients, and the results were compared with those from microbiological culture and final clinical diagnosis. Three interpretational approaches were evaluated for diagnostic accuracy. RESULTS mNGS outperformed culture significantly. Among the interpretational approaches, Clinical Interpretation (CI) demonstrated the best diagnostic performance with a sensitivity of 87.3%, specificity of 100%, positive predictive value of 100%, and negative predictive value of 98.3%. CI's specificity was significantly higher than Simple Interpretation (SI) at 37.9%. Additionally, CI excluded some microorganisms identified as putative pathogens by SI, including Haemophilus parainfluenzae, Haemophilus parahaemolyticus, and Klebsiella aerogenes. CONCLUSION Proper interpretation of mNGS data is crucial for accurately diagnosing respiratory infections caused by GNB. CI is recommended for this purpose.
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Affiliation(s)
- Wenyan Liang
- Department of Respirology and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Qun Zhang
- Department of Respirology and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Qian Qian
- Jiangsu Health Vocational College, Nanjing, 211800, China
| | - Mingyue Wang
- Department of Respirology and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Yuchen Ding
- Department of Respirology and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Ji Zhou
- Department of Respirology and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Yi Zhu
- Department of Respirology and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Yu Jin
- Department of Respirology and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Xuesong Chen
- Department of Respirology and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Hui Kong
- Department of Respirology and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Wei Song
- Department of Respirology and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Xin Lu
- Department of Respiratory and Critical Care Medicine, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaodong Wu
- Department of Respiratory and Critical Care Medicine, Shanghai East Hospital, Tongji University, Shanghai, China
| | - Xiaoyong Xu
- Department of respiratory and critical care medicine, The Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210000, China
| | - Shanling Dai
- Department of Respirology and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Wenkui Sun
- Department of Respirology and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China.
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17
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Fellner A, White S, Rockwell E, Giandomenico D, Diaz MM, Weber DJ, Miller MB, Boyce RM. The clinical epidemiology, management, and outcomes of patients diagnosed with encephalitis in North Carolina, 2015-2020. J Clin Microbiol 2023; 61:e0073123. [PMID: 38014985 PMCID: PMC10729753 DOI: 10.1128/jcm.00731-23] [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: 06/09/2023] [Accepted: 10/12/2023] [Indexed: 11/29/2023] Open
Abstract
IMPORTANCE Despite the relatively high mortality and the difficulty in diagnosis, nearly one-third of patients hospitalized with a documented diagnosis of encephalitis did not undergo a lumbar puncture (LP). When an LP was performed, pathogen-specific testing was greatly underutilized. Infectious etiologies were most common, but over 40% of cases were idiopathic at discharge. These findings suggest that there is a substantial opportunity to improve the quality of care through more accurate and timely diagnosis.
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Affiliation(s)
- Anuva Fellner
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Samuel White
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Emmanuel Rockwell
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Dana Giandomenico
- Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Monica M. Diaz
- Department of Neurology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - David J. Weber
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Melissa B. Miller
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ross M. Boyce
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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18
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Li Z, Wang J, Xiu X, Shi Z, Zhang Q, Chen D. Evaluation of different diagnostic methods for spinal tuberculosis infection. BMC Infect Dis 2023; 23:695. [PMID: 37853312 PMCID: PMC10583401 DOI: 10.1186/s12879-023-08655-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 09/27/2023] [Indexed: 10/20/2023] Open
Abstract
BACKGROUND AND PURPOSE Tuberculosis (TB) is the most fatal infectious disease worldwide. Approximately 24.6% of tuberculosis cases are extrapulmonary and predominantly affect the spine. It is difficult to diagnose spinal TB (STB). We aimed to evaluate the diagnostic performance of the Mycobacteria Growth Indicator Tube (MGIT)-960 culture, T-SPOT.TB, Xpert Mycobacterium tuberculosis complex (MTB)/resistance to rifampin (RIF), and Metagenomic Next-Generation Sequencing (mNGS) to detect STB. METHODS We assessed 126 patients presumed to have STB using these four methods. The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were calculated using clinical diagnosis as a reference. RESULTS Of the patients, 41 were diagnosed with STB and 85 with non-STB. In the STB group, the sensitivity, specificity, PPV, and NPV of the MGIT-960 culture were 29.3% (12/41), 100% (85/85), 100% (12/12), and 74.6% (85/114), respectively. The sensitivity, specificity, PPV, and NPV of T-SPOT.TB were 92.7% (38/41), 82.4% (70/85), 58.5% (31/53), and 95.9% (70/73), respectively. The sensitivity, specificity, PPV, and NPV of the Xpert MTB/RIF assay were 53.7% (22/41), 100% (85/85), 100% (22/22), and 81.7% (85/104), respectively. The sensitivity, specificity, PPV, and NPV of mNGS were 39.0% (16/41), 98.8% (84/85), 94.1% (16/17), and 77.1% (84/109), respectively. The sensitivity, specificity, PPV, and NPV of mNGS + Xpert MTB/RIF were 73.2% (30/41), 100% (85/85), 96.8% (30/31), and 72.0% (85/118), respectively. The sensitivity, specificity, PPV, and NPV of the mNGS + T-spot assay were 97.6% (40/41), 100% (85/85), 67.9% (38/56), and 75.9% (85/113), respectively. Moreover, the sensitivity, specificity, PPV, and NPV of T-spot + Xpert MTB/RIF were 95.1% (39/41), 100% (85/85), 72.2% (39/54), and 81.0% (85/105), respectively. CONCLUSIONS T-SPOT.TB is the most effective method for diagnosing STB; however, Xpert MTB/RIF is more reliable and can detect RIF resistance. Clinicians can use mNGS to identify pathogens in patients with spinal infections; these pathogens appeared to be more meaningful in guiding the clinical management of patients in the non-STB group. The combination of Xpert MTB/RIF and mNGS can improve the early diagnosis rate and drug resistance detection, reduce the diagnostic cycle, and provide early targeted anti-TB treatment for patients with STB.
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Affiliation(s)
- Zhaoxin Li
- Shandong University of Traditional Chinese Medicine, Shandong, China
| | - Jin Wang
- Shandong University of Traditional Chinese Medicine, Shandong, China
| | - Xin Xiu
- Shandong University of Traditional Chinese Medicine, Shandong, China
| | - Zhenpeng Shi
- Shandong University of Traditional Chinese Medicine, Shandong, China
| | - Qiang Zhang
- Department of Orthopedics, Shandong Public Health Clinical Center, Shandong, China.
| | - Deqiang Chen
- Shandong University of Traditional Chinese Medicine, Shandong, China.
- Department of Spinal Orthopedics, Shandong Provincial Hospital of Traditional Chinese Medicine, Shandong, China.
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19
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Li XX, Niu CZ, Zhao YC, Fu GW, Zhao H, Huang MJ, Li J. Clinical application of metagenomic next-generation sequencing in non-immunocompromised patients with severe pneumonia supported by veno-venous extracorporeal membrane oxygenation. Front Cell Infect Microbiol 2023; 13:1269853. [PMID: 37900317 PMCID: PMC10613042 DOI: 10.3389/fcimb.2023.1269853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 09/20/2023] [Indexed: 10/31/2023] Open
Abstract
Objectives This study aims to explore the pathogen-detected effect of mNGS technology and its clinical application in non-immunocompromised patients with severe pneumonia supported by vv-ECMO. Methods A retrospective analysis was conducted on a cohort of 50 non-immunocompromised patients who received vv-ECMO support for severe pneumonia between January 2016 and December 2022. These patients were divided into two groups based on their discharge outcomes: the deterioration group (Group D), which included 31 cases, and the improvement group (Group I), consisting of 19 cases. Baseline characteristics and clinical data were collected and analyzed. Results Among the 50 patients enrolled, Group D exhibited a higher prevalence of male patients (80.6% vs. 52.6%, p < 0.05), more smokers (54.8% vs. 21.1%, p < 0.05), and were older than those in Group I (55.16 ± 16.34 years vs. 42.32 ± 19.65 years, p < 0.05). Out of the 64 samples subjected to mNGS detection, 55 (85.9%) yielded positive results, with a positivity rate of 83.7% (36/43) in Group D and 90.5% (19/21) in Group I. By contrast, the positive rate through traditional culture stood at 64.9% (74/114). Among the 54 samples that underwent both culture and mNGS testing, 23 (42.6%) displayed consistent pathogen identification, 13 (24.1%) exhibited partial consistency, and 18 (33.3%) showed complete inconsistency. Among the last cases with complete inconsistency, 14 (77.8%) were culture-negative, while two (11.1%) were mNGS-negative, and the remaining two (11.1%) presented mismatches. Remarkably, mNGS surpassed traditional culture in pathogen identification (65 strains vs. 23 strains). Within these 65 strains, 56 were found in Group D, 26 in Group I, and 17 were overlapping strains. Interestingly, a diverse array of G+ bacteria, fungi, viruses, and special pathogens were exclusive to Group D. Furthermore, Acinetobacter baumannii, Pseudomonas aeruginosa, and Klebsiella pneumoniae were more prevalent in Group D compared to Group I. Importantly, mNGS prompted antibiotic treatment adjustments in 26 patients (52.0%). Conclusions Compared with the conventional culture, mNGS demonstrated a higher positive rate, and emerges as a promising method for identifying mixed pathogens in non-immunodeficient patients with severe pneumonia supported by vv-ECMO. However, it is crucial to combine the interpretation of mNGS data with clinical information and traditional culture results for a comprehensive assessment.
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Affiliation(s)
- Xing-Xing Li
- Department of Extracorporeal Life Support Center, Department of Cardiac Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Cheng-Zhi Niu
- Information Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yang-Chao Zhao
- Department of Extracorporeal Life Support Center, Department of Cardiac Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Guo-Wei Fu
- Department of Extracorporeal Life Support Center, Department of Cardiac Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hui Zhao
- Department of Extracorporeal Life Support Center, Department of Cardiac Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ming-Jun Huang
- Department of Extracorporeal Life Support Center, Department of Cardiac Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jun Li
- Department of Extracorporeal Life Support Center, Department of Cardiac Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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20
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Kim HS, Kim SH, Song HS, Kwon YK, Park CK, Kim HR. Application of metagenomics for diagnosis of broilers displaying neurological symptoms. BMC Vet Res 2023; 19:190. [PMID: 37798783 PMCID: PMC10552438 DOI: 10.1186/s12917-023-03732-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 09/13/2023] [Indexed: 10/07/2023] Open
Abstract
BACKGROUND Thirty-two-day-old broiler chickens at a farm located in northwestern South Korea displayed adverse neurological symptoms including limping, lying down, and head shaking. Approximately 2.1% of chickens died or were culled due to severe symptoms. Five carcasses were submitted to the Avian Disease Division of the Animal and Plant Quarantine Agency (APQA) for disease diagnosis. RESULTS Broilers displayed severe pericarditis and perihepatitis associated with gross lesions. Broilers also displayed microscopic lesions in the cerebrum and in the granular layer of the cerebellum, which were associated with multifocal perivascular cuffing and purulent necrosis in the cerebrum, and severe meningitis with heterophil and lymphocyte infiltration. Staphylococcus spp. were identified in the liver and heart using bacteriological culture. PCR/RT-PCR assays revealed that broilers were negative for avian Clostridium botulinum, Newcastle disease virus, and avian encephalomyelitis virus. Bacterial and viral metagenomic analysis of brain sample further revealed the presence of Pseudomonas spp. and Marek's disease virus, which are known etiological agents of chicken meningoencephalitis. CONCLUSIONS This study reports a diagnostic analysis of gross and histopathological lesions from 32-day-old broilers displaying unique neurological symptoms that revealed the presence of the several neurological diseases including meningoencephalitis. The causative agents associated with meningoencephalitis of broilers that had not been identified by routine diagnostic methods could be diagnosed by metagenomics, which proves the usefulness of metagenomics as a diagnostic tool for unknown neurological diseases in broilers.
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Grants
- M-1543084-2023-25-01 Animal and Plant Quarantine Agency (APQA), Ministry of Agriculture, Food and Rural Affairs, the Republic of Korea.
- M-1543084-2023-25-01 Animal and Plant Quarantine Agency (APQA), Ministry of Agriculture, Food and Rural Affairs, the Republic of Korea.
- M-1543084-2023-25-01 Animal and Plant Quarantine Agency (APQA), Ministry of Agriculture, Food and Rural Affairs, the Republic of Korea.
- M-1543084-2023-25-01 Animal and Plant Quarantine Agency (APQA), Ministry of Agriculture, Food and Rural Affairs, the Republic of Korea.
- M-1543084-2023-25-01 Animal and Plant Quarantine Agency (APQA), Ministry of Agriculture, Food and Rural Affairs, the Republic of Korea.
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Affiliation(s)
- Hyeon-Su Kim
- Avian Disease Division, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon-si, 39660 Korea
- College of Veterinary Medicine & Animal Disease Intervention Center, Kyungpook National University, Daegu, 41566 Korea
| | - Si-Hyeon Kim
- Avian Disease Division, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon-si, 39660 Korea
- College of Veterinary Medicine & Animal Disease Intervention Center, Kyungpook National University, Daegu, 41566 Korea
| | - Hye-Soon Song
- Avian Disease Division, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon-si, 39660 Korea
| | - Yong-Kuk Kwon
- Avian Disease Division, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon-si, 39660 Korea
| | - Choi-Kyu Park
- College of Veterinary Medicine & Animal Disease Intervention Center, Kyungpook National University, Daegu, 41566 Korea
| | - Hye-Ryoung Kim
- Avian Disease Division, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon-si, 39660 Korea
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21
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Rocha-de-Lossada C, Mazzotta C, Gabrielli F, Papa FT, Gómez-Huertas C, García-López C, Urbinati F, Rachwani-Anil R, García-Lorente M, Sánchez-González JM, Rechichi M, Rubegni G, Borroni D. Ocular Surface Microbiota in Naïve Keratoconus: A Multicenter Validation Study. J Clin Med 2023; 12:6354. [PMID: 37834997 PMCID: PMC10573816 DOI: 10.3390/jcm12196354] [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: 09/10/2023] [Revised: 09/29/2023] [Accepted: 10/01/2023] [Indexed: 10/15/2023] Open
Abstract
In the field of Ophthalmology, the mNGS 16S rRNA sequencing method of studying the microbiota and ocular microbiome is gaining more and more weight in the scientific community. This study aims to characterize the ocular microbiota of patients diagnosed with keratoconus who have not undergone any prior surgical treatment using the mNGS 16S rRNA sequencing method. Samples of naïve keratoconus patients were collected with an eNAT with 1 mL of Liquid Amies Medium (Copan Brescia, Italy), and DNA was extracted and analyzed with 16S NGS. The microbiota analysis showed a relative abundance of microorganisms at the phylum level in each sample collected from 38 patients with KC and 167 healthy controls. A comparison between healthy control and keratoconus samples identified two genera unique to keratoconus, Pelomonas and Ralstonia. Our findings suggest that alterations in the microbiota may play a role in the complex scenario of KC development.
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Affiliation(s)
- Carlos Rocha-de-Lossada
- Eyemetagenomics Ltd., 71–75, Shelton Street, Covent Garden, London WC2H 9JQ, UK;
- Ophthalmology Department, QVision, Vithas Almería, 04120 Almeria, Spain
- Ophthalmology Department, Hospital Regional Universitario Málaga, 29010 Malaga, Spain; (F.U.); (M.G.-L.)
| | - Cosimo Mazzotta
- Siena Crosslinking Center, 53100 Siena, Italy;
- Departmental Ophthalmology Unit, USL Toscana Sud Est l, 53100 Siena, Italy
- Postgraduate Ophthalmology School, University of Siena, 53100 Siena, Italy;
| | - Federico Gabrielli
- Biolab SRL, Laboratorio di Genetica e Genomica Molecolare, Largo degli Aranci, 9, 63100 Ascoli Piceno, Italy; (F.G.); (F.T.P.)
| | - Filomena Tiziana Papa
- Biolab SRL, Laboratorio di Genetica e Genomica Molecolare, Largo degli Aranci, 9, 63100 Ascoli Piceno, Italy; (F.G.); (F.T.P.)
| | - Carmen Gómez-Huertas
- Department of Ophthalmology, Hospital Universitario Virgen de las Nieves, 18014 Granada, Spain; (C.G.-H.); (C.G.-L.)
| | - Celia García-López
- Department of Ophthalmology, Hospital Universitario Virgen de las Nieves, 18014 Granada, Spain; (C.G.-H.); (C.G.-L.)
| | - Facundo Urbinati
- Ophthalmology Department, Hospital Regional Universitario Málaga, 29010 Malaga, Spain; (F.U.); (M.G.-L.)
| | | | - María García-Lorente
- Ophthalmology Department, Hospital Regional Universitario Málaga, 29010 Malaga, Spain; (F.U.); (M.G.-L.)
| | | | - Miguel Rechichi
- Centro Polispecialistico Mediterraneo, 88050 Sellia Marina, Italy;
| | - Giovanni Rubegni
- Postgraduate Ophthalmology School, University of Siena, 53100 Siena, Italy;
| | - Davide Borroni
- Eyemetagenomics Ltd., 71–75, Shelton Street, Covent Garden, London WC2H 9JQ, UK;
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22
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Li D, Li H. The Clinical Characteristics, Diagnostic Methods, Treatment, and Outcomes of Listeria monocytogenes Meningoencephalitis: A Case Series Study from China. Infect Drug Resist 2023; 16:6375-6383. [PMID: 37789837 PMCID: PMC10543931 DOI: 10.2147/idr.s423568] [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: 05/30/2023] [Accepted: 09/14/2023] [Indexed: 10/05/2023] Open
Abstract
Background Listeria monocytogenes meningoencephalitis (LMM) is a rare but dangerous infection of the nervous system. This study intends to summarize and discuss the clinical features, diagnostic methods, treatment, and outcomes. Methods LMM patients treated in the First Affiliated Hospital of Zhengzhou University from June 2013 to December 2022 were retrospectively studied. The clinical data, magnetic resonance imaging (MRI), biochemical and hematological parameters, pathogen tests, treatments, and outcomes information were collected and summarized. Results Ten LMM patients were enrolled in this study. Three were female and seven were male, with a mean age of 54.5 years old. Seven (70%) of the patients had chronic conditions that either affected the liver (1 case), heart (1 case), or immune system (5 cases). The main clinical manifestations were fever (100%), headache, (60%), and disturbance of consciousness (60%). Out of the nine patients taken MRI, enhanced magnetic resonance imaging was observed with cerebral parenchyma and meningeal enhancement in 3 patients, whereas six patients showed non-specific abnormal signals and brain edema. Seven (70%) patients were positive for L. monocytogenes by bacterial culture and five patients were positive by further next-generation sequencing (NGS) test in CSF. All patients were treated with antibiotics based on antibiotic sensitivity tests or experience, with seven (70%) improved but three (30%) died within one month. Conclusion LMM patients have a high mortality rate. Considering the time and reliability of NGS reports, it would be better to identify L. monocytogenes infection in the CSF than bacterial culture. While, after diagnosis, giving timely and appropriate antibiotics would still be a challenge to achieve good outcomes.
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Affiliation(s)
- Dongrui Li
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou City, People’s Republic of China
| | - Hui Li
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou City, People’s Republic of China
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23
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Xiang ZB, Leng EL, Cao WF, Liu SM, Zhou YL, Luo CQ, Hu F, Wen A. A systematic review and meta-analysis of the diagnostic accuracy of metagenomic next-generation sequencing for diagnosing tuberculous meningitis. Front Immunol 2023; 14:1223675. [PMID: 37822937 PMCID: PMC10562686 DOI: 10.3389/fimmu.2023.1223675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 09/05/2023] [Indexed: 10/13/2023] Open
Abstract
Objective The utility of metagenomic next-generation sequencing (mNGS) in the diagnosis of tuberculous meningitis (TBM) remains uncertain. We performed a meta-analysis to comprehensively evaluate its diagnostic accuracy for the early diagnosis of TBM. Methods English (PubMed, Medline, Web of Science, Cochrane Library, and Embase) and Chinese (CNKI, Wanfang, and CBM) databases were searched for relevant studies assessing the diagnostic accuracy of mNGS for TBM. Review Manager was used to evaluate the quality of the included studies, and Stata was used to perform the statistical analysis. Results Of 495 relevant articles retrieved, eight studies involving 693 participants (348 with and 345 without TBM) met the inclusion criteria and were included in the meta-analysis. The pooled sensitivity, specificity, positive likelihood ratio, negative likelihood ratio, diagnostic odds ratio, and area under the summary receiver-operating characteristic curve of mNGS for diagnosing TBM were 62% (95% confidence interval [CI]: 0.46-0.76), 99% (95% CI: 0.94-1.00), 139.08 (95% CI: 8.54-2266), 0.38 (95% CI: 0.25-0.58), 364.89 (95% CI: 18.39-7239), and 0.97 (95% CI: 0.95-0.98), respectively. Conclusions mNGS showed good specificity but moderate sensitivity; therefore, a more sensitive test should be developed to assist in the diagnosis of TBM.
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Affiliation(s)
- Zheng-Bing Xiang
- Department of Neurology, Jiangxi Provincial People’s Hospital (The First Affiliated Hospital of Nanchang Medical College), Nanchang, Jiangxi, China
- Department of Neurology, Xiangya Hospital, Central South University, Jiangxi Hospital, National Regional Center for Neurological Diseases, Nanchang, Jiangxi, China
| | - Er-Ling Leng
- Department of Pediatrics, Jiangxi Provincial People’s Hospital (The First Affiliated Hospital of Nanchang Medical College), Nanchang, Jiangxi, China
| | - Wen-Feng Cao
- Department of Neurology, Jiangxi Provincial People’s Hospital (The First Affiliated Hospital of Nanchang Medical College), Nanchang, Jiangxi, China
- Department of Neurology, Xiangya Hospital, Central South University, Jiangxi Hospital, National Regional Center for Neurological Diseases, Nanchang, Jiangxi, China
| | - Shi-Min Liu
- Department of Neurology, Jiangxi Provincial People’s Hospital (The First Affiliated Hospital of Nanchang Medical College), Nanchang, Jiangxi, China
- Department of Neurology, Xiangya Hospital, Central South University, Jiangxi Hospital, National Regional Center for Neurological Diseases, Nanchang, Jiangxi, China
| | - Yong-Liang Zhou
- Department of Neurology, Jiangxi Provincial People’s Hospital (The First Affiliated Hospital of Nanchang Medical College), Nanchang, Jiangxi, China
- Department of Neurology, Xiangya Hospital, Central South University, Jiangxi Hospital, National Regional Center for Neurological Diseases, Nanchang, Jiangxi, China
| | - Chao-Qun Luo
- Department of Neurology, Jiangxi Provincial People’s Hospital (The First Affiliated Hospital of Nanchang Medical College), Nanchang, Jiangxi, China
- Department of Neurology, Xiangya Hospital, Central South University, Jiangxi Hospital, National Regional Center for Neurological Diseases, Nanchang, Jiangxi, China
| | - Fan Hu
- Department of Neurology, Jiangxi Provincial People’s Hospital (The First Affiliated Hospital of Nanchang Medical College), Nanchang, Jiangxi, China
- Department of Neurology, Xiangya Hospital, Central South University, Jiangxi Hospital, National Regional Center for Neurological Diseases, Nanchang, Jiangxi, China
| | - An Wen
- Department of Neurology, Jiangxi Provincial People’s Hospital (The First Affiliated Hospital of Nanchang Medical College), Nanchang, Jiangxi, China
- Department of Neurology, Xiangya Hospital, Central South University, Jiangxi Hospital, National Regional Center for Neurological Diseases, Nanchang, Jiangxi, China
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Sun Z, Liu J, Zhang M, Wang T, Huang S, Weiss ST, Liu YY. Removal of false positives in metagenomics-based taxonomy profiling via targeting Type IIB restriction sites. Nat Commun 2023; 14:5321. [PMID: 37658057 PMCID: PMC10474111 DOI: 10.1038/s41467-023-41099-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 08/22/2023] [Indexed: 09/03/2023] Open
Abstract
Accurate species identification and abundance estimation are critical for the interpretation of whole metagenome sequencing (WMS) data. Yet, existing metagenomic profilers suffer from false-positive identifications, which can account for more than 90% of total identified species. Here, by leveraging species-specific Type IIB restriction endonuclease digestion sites as reference instead of universal markers or whole microbial genomes, we present a metagenomic profiler, MAP2B (MetAgenomic Profiler based on type IIB restriction sites), to resolve those issues. We first illustrate the pitfalls of using relative abundance as the only feature in determining false positives. We then propose a feature set to distinguish false positives from true positives, and using simulated metagenomes from CAMI2, we establish a false-positive recognition model. By benchmarking the performance in metagenomic profiling using a simulation dataset with varying sequencing depth and species richness, we illustrate the superior performance of MAP2B over existing metagenomic profilers in species identification. We further test the performance of MAP2B using real WMS data from an ATCC mock community, confirming its superior precision against sequencing depth. Finally, by leveraging WMS data from an IBD cohort, we demonstrate the taxonomic features generated by MAP2B can better discriminate IBD and predict metabolomic profiles.
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Affiliation(s)
- Zheng Sun
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Jiang Liu
- Qingdao OE Biotechnology Company Limited, Qingdao, Shandong, China
| | - Meng Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China
| | - Tong Wang
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Shi Huang
- Faculty of Dentistry, The University of Hong Kong, Hong Kong, China
| | - Scott T Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Yang-Yu Liu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Center for Artificial Intelligence and Modeling, The Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, USA.
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Michel C, Martin C, Smeesters P, Goffard JC, Demuyser T, Hallin M. Next-generation sequencing: what are the needs in routine clinical microbiology? A survey among clinicians involved in infectious diseases practice. Front Med (Lausanne) 2023; 10:1225408. [PMID: 37671400 PMCID: PMC10475535 DOI: 10.3389/fmed.2023.1225408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 08/08/2023] [Indexed: 09/07/2023] Open
Abstract
Background The translation of Next-Generation Sequencing (NGS) from research to clinical microbiology is increasing rapidly, but its integration into routine clinical care struggles to catch-up. A challenge for clinical laboratories is that the substantial investments made in the required technologies and resources must meet both current and forthcoming needs. Methods To get a clinical perspective of these needs, we have sent a survey to infectious diseases clinicians of five hospitals, covering the following topics: NGS knowledge, expected syndromes and patients foreseen to benefit from NGS, and expected impact on antimicrobial prescription. Results According to clinicians, benefits of NGS are mostly expected in neurological and respiratory infections diagnostics. Conclusion A better dialog between microbiologists and clinicians about hopes and limits of NGS in microbiology may help identifying key investments needed for clinical laboratories, today and tomorrow.
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Affiliation(s)
- Charlotte Michel
- Department of Microbiology, LHUB-ULB, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Charlotte Martin
- Department of Infectious Diseases, Saint-Pierre University Hospital, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Pierre Smeesters
- Department of Pediatrics, University Hospital Brussels, Université libre de Bruxelles (ULB), Brussels, Belgium
- Department of Pediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Jean-Christophe Goffard
- Department of Internal Medicine, University Hospital Brussels, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Thomas Demuyser
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - Marie Hallin
- Centre for Environmental Health and Occupational Health, School of Public Health, University Hospital Brussels, Université libre de Bruxelles (ULB), Brussels, Belgium
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Fan G, Li S, Tian F, Yang L, Yi S, Chen S, Li C, Zhang R, He X, Ma X. RNA-sequencing-based detection of human viral pathogens in cerebrospinal fluid and serum samples from children with meningitis and encephalitis. Microb Genom 2023; 9:mgen001079. [PMID: 37531160 PMCID: PMC10483426 DOI: 10.1099/mgen.0.001079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 07/07/2023] [Indexed: 08/03/2023] Open
Abstract
Encephalitis and meningitis are notable global public health concerns, especially among infants or children. Metagenomic next-generation sequencing (mNGS) has greatly advanced our understanding of the viruses responsible for these diseases. However, the detection rate of the aetiology remains low. We conducted RNA sequencing and virome analysis on cerebrospinal fluid (CSF) and serum samples commonly used in the clinical diagnosis to detect viral pathogens. In total, 226 paired CSF and serum samples from 113 children with encephalitis and meningitis were enrolled. The results showed that the diversity of viruses was higher in CSF, with a total of 12 viral taxa detected, including one case each of herpesvirus, coronavirus and enterovirus, and six cases of adenovirus related to human diseases. In contrast, the Anelloviridae was the most abundant viral family detected in serum, and only a few samples contained human viral pathogens, including one case of enterovirus and two cases of adenovirus. The detection rate for human viral pathogens increases to 10.6 %(12/113) when both types of samples are used simultaneously, compared to CSF along 7.9 % (9/113) or serum alone 2.6 % (3/113). However, we did not detect these viruses simultaneously in paired samples from the same case. These results suggest that CSF samples still have irreplaceable advantages for using mNGS to detect viruses in patients with meningitis and encephalitis, and serum can supplement to improve the detection rate of viral encephalitis and meningitis. The findings of this study could help improve the etiological diagnosis, clinical management and prognosis of patients with meningitis and encephalitis in children.
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Affiliation(s)
- Guohao Fan
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing 102206, PR China
- The Third People’s Hospital of Shenzhen, Shenzheng 518112, PR China
| | - Sai Li
- Hunan Children’s Hospital, Changsha, Hunan, 410001, PR China
| | - Fengyu Tian
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing 102206, PR China
- Graduate School, Hebei Medical University, Shijiazhuang 050031, PR China
| | - Longgui Yang
- Hunan Children’s Hospital, Changsha, Hunan, 410001, PR China
| | - Suwu Yi
- Hunan Children’s Hospital, Changsha, Hunan, 410001, PR China
| | - Sitian Chen
- Hunan Children’s Hospital, Changsha, Hunan, 410001, PR China
| | - Chengyi Li
- Hunan Children’s Hospital, Changsha, Hunan, 410001, PR China
| | - Ruiqing Zhang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing 102206, PR China
| | - Xiaozhou He
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing 102206, PR China
| | - Xuejun Ma
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing 102206, PR China
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Hanin A, Cespedes J, Huttner A, Strelnikov D, Gopaul M, DiStasio M, Vezzani A, Hirsch LJ, Aronica E. Neuropathology of New-Onset Refractory Status Epilepticus (NORSE). J Neurol 2023:10.1007/s00415-023-11726-x. [PMID: 37079033 DOI: 10.1007/s00415-023-11726-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/11/2023] [Accepted: 04/12/2023] [Indexed: 04/21/2023]
Abstract
New-Onset Refractory Status Epilepticus (NORSE), including its subtype with a preceding febrile illness known as FIRES (Febrile Infection-Related Epilepsy Syndrome), is one of the most severe forms of status epilepticus. Despite an extensive workup (clinical evaluation, EEG, imaging, biological tests), the majority of NORSE cases remain unexplained (i.e., "cryptogenic NORSE"). Understanding the pathophysiological mechanisms underlying cryptogenic NORSE and the related long-term consequences is crucial to improve patient management and preventing secondary neuronal injury and drug-resistant post-NORSE epilepsy. Previously, neuropathological evaluations conducted on biopsies or autopsies have been found helpful for identifying the etiologies of some cases that were previously of unknown cause. Here, we summarize the findings of studies reporting neuropathology findings in patients with NORSE, including FIRES. We identified 64 cryptogenic cases and 66 neuropathology tissue samples, including 37 biopsies, 18 autopsies, and seven epilepsy surgeries (the type of tissue sample was not detailed for 4 cases). We describe the main neuropathology findings and place a particular emphasis on cases for which neuropathology findings helped establish a diagnosis or elucidate the pathophysiology of cryptogenic NORSE, or on described cases in which neuropathology findings supported the selection of specific treatments for patients with NORSE.
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Affiliation(s)
- Aurélie Hanin
- Department of Neurology and Immunobiology, Yale University School of Medicine, New Haven, CT, USA.
- Institut du Cerveau, Paris Brain Institute, ICM, Inserm, CNRS, AP-HP, Hôpital de La Pitié-Salpêtrière, Sorbonne Université, DMU Neurosciences 6, Paris, France.
- Epilepsy Unit and Department of Clinical Neurophysiology, AP-HP, Hôpital de La Pitié-Salpêtrière, DMU Neurosciences 6, Paris, France.
| | - Jorge Cespedes
- Comprehensive Epilepsy Center, Department of Neurology, Yale University School of Medicine, New Haven, CT, USA
- School of Medicine, Universidad Autonoma de Centro America, San Jose, Costa Rica
| | - Anita Huttner
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - David Strelnikov
- Comprehensive Epilepsy Center, Department of Neurology, Yale University School of Medicine, New Haven, CT, USA
| | - Margaret Gopaul
- Comprehensive Epilepsy Center, Department of Neurology, Yale University School of Medicine, New Haven, CT, USA
| | - Marcello DiStasio
- Department of Neurology and Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Annamaria Vezzani
- Department of Acute Brain Injury, Istituto di Recerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Lawrence J Hirsch
- Comprehensive Epilepsy Center, Department of Neurology, Yale University School of Medicine, New Haven, CT, USA
| | - Eleonora Aronica
- Department of (Neuro)Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Meibergdreef 9, 1105, Amsterdam, The Netherlands
- Stichting Epilepsie Instellingen Nederland (SEIN), Heemstede, The Netherlands
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Deng ZF, Tang YJ, Yan CY, Qin ZQ, Yu N, Zhong XB. Pulmonary nocardiosis with bloodstream infection diagnosed by metagenomic next-generation sequencing in a kidney transplant recipient: A case report. World J Clin Cases 2023; 11:1634-1641. [PMID: 36926398 PMCID: PMC10011981 DOI: 10.12998/wjcc.v11.i7.1634] [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: 12/17/2022] [Revised: 01/28/2023] [Accepted: 02/13/2023] [Indexed: 03/02/2023] Open
Abstract
BACKGROUND Pulmonary nocardiosis is difficult to diagnose by culture and other conventional testing, and is often associated with lethal disseminated infections. This difficulty poses a great challenge to the timeliness and accuracy of clinical detection, especially in susceptible immunosuppressed individuals. Metagenomic next-generation sequencing (mNGS) has transformed the conventional diagnosis pattern by providing a rapid and precise method to assess all microorganisms in a sample.
CASE SUMMARY A 45-year-old male was hospitalized for cough, chest tightness and fatigue for 3 consecutive days. He had received a kidney transplant 42 d prior to admission. No pathogens were detected at admission. Chest computed tomography showed nodules, streak shadows and fiber lesions in both lung lobes as well as right pleural effusion. Pulmonary tuberculosis with pleural effusion was highly suspected based on the symptoms, imaging and residence in a high tuberculosis-burden area. However, anti-tuberculosis treatment was ineffective, showing no improvement in computed tomography imaging. Pleural effusion and blood samples were subsequently sent for mNGS. The results indicated Nocardia farcinica as the major pathogen. After switching to sulphamethoxazole combined with minocycline for anti-nocardiosis treatment, the patient gradually improved and was finally discharged.
CONCLUSION A case of pulmonary nocardiosis with an accompanying bloodstream infection was diagnosed and promptly treated before the dissemination of the infection. This report emphasizes the value of mNGS in the diagnosis of nocardiosis. mNGS may be an effective method for facilitating early diagnosis and prompt treatment in infectious diseases, which overcomes the shortcomings of conventional testing.
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Affiliation(s)
- Zhen-Feng Deng
- Clinical Genome Center, Guangxi KingMed Diagnostics, Nanning 530007, Guangxi Zhuang Autonomous Region, China
| | - Yan-Jiao Tang
- Graduate School, Guangxi University of Chinese Medicine, Nanning 530001, Guangxi Zhuang Autonomous Region, China
| | - Chun-Yi Yan
- Department of Organ Transplantation, No. 923 Hospital of Chinese People's Liberation Army, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Zi-Qian Qin
- Clinical Genome Center, Guangxi KingMed Diagnostics, Nanning 530007, Guangxi Zhuang Autonomous Region, China
| | - Ning Yu
- Clinical Genome Center, Guangxi KingMed Diagnostics, Nanning 530007, Guangxi Zhuang Autonomous Region, China
| | - Xiong-Bo Zhong
- Department of Urology Surgery, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning 530011, Guangxi Zhuang Autonomous Region, China
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Wang C, Hu J, Gu Y, Wang X, Chen Y, Yuan W. Application of next-generation metagenomic sequencing in the diagnosis and treatment of acute spinal infections. Heliyon 2023; 9:e13951. [PMID: 36879954 PMCID: PMC9984843 DOI: 10.1016/j.heliyon.2023.e13951] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 02/24/2023] Open
Abstract
Objectives The purpose of this study was to verify the value of metagenomic next-generation sequencing (mNGS) in detecting the pathogens causing acute spinal infection by reviewing the results of mNGS in 114 patients. Methods A total of 114 patients were included from our hospital. Samples (tissue/blood) were sent for mNGS detection, and the remaining samples were sent to the microbiology laboratory for pathogen culture, smear, histopathological analysis, and other tests. Patients' medical records were reviewed to determine their rates of detection, time needed, guidance for antibiotic treatment and clinical outcomes. Results mNGS showed a satisfying diagnostic positive percent agreement of 84.91% (95% confidence interval (CI): 6.34%-96.7%), compared to 30.19% (95% CI: 21.85%-39.99%) for culture and 43.40% (95% CI: 31.39%-49.97%) for conventional methods (p < 0.0125), and mNGS was found positive in 46 culture and smear negative samples. The time required for pathogen identification using mNGS ranged from 29 h to 53 h, which showed an advantage over culture (90.88 ± 8.33 h; P < 0.05). mNGS also played an important role in optimizing antibiotic regimens in patients with negative results obtained using conventional methods. The treatment success rate (TSR) of patients using mNGS-guided antibiotic regimens (20/24, 83.33%) was significantly higher than that of patients using empirical antibiotics (13/23, 56.52%) (P < 0.0001). Conclusions mNGS shows promising potential in the pathogenic diagnosis of acute spinal infections and may enable clinicians to make more timely and effective adjustments to antibiotic regimens.
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Ibañez-Lligoña M, Colomer-Castell S, González-Sánchez A, Gregori J, Campos C, Garcia-Cehic D, Andrés C, Piñana M, Pumarola T, Rodríguez-Frias F, Antón A, Quer J. Bioinformatic Tools for NGS-Based Metagenomics to Improve the Clinical Diagnosis of Emerging, Re-Emerging and New Viruses. Viruses 2023; 15:v15020587. [PMID: 36851800 PMCID: PMC9965957 DOI: 10.3390/v15020587] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 02/24/2023] Open
Abstract
Epidemics and pandemics have occurred since the beginning of time, resulting in millions of deaths. Many such disease outbreaks are caused by viruses. Some viruses, particularly RNA viruses, are characterized by their high genetic variability, and this can affect certain phenotypic features: tropism, antigenicity, and susceptibility to antiviral drugs, vaccines, and the host immune response. The best strategy to face the emergence of new infectious genomes is prompt identification. However, currently available diagnostic tests are often limited for detecting new agents. High-throughput next-generation sequencing technologies based on metagenomics may be the solution to detect new infectious genomes and properly diagnose certain diseases. Metagenomic techniques enable the identification and characterization of disease-causing agents, but they require a large amount of genetic material and involve complex bioinformatic analyses. A wide variety of analytical tools can be used in the quality control and pre-processing of metagenomic data, filtering of untargeted sequences, assembly and quality control of reads, and taxonomic profiling of sequences to identify new viruses and ones that have been sequenced and uploaded to dedicated databases. Although there have been huge advances in the field of metagenomics, there is still a lack of consensus about which of the various approaches should be used for specific data analysis tasks. In this review, we provide some background on the study of viral infections, describe the contribution of metagenomics to this field, and place special emphasis on the bioinformatic tools (with their capabilities and limitations) available for use in metagenomic analyses of viral pathogens.
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Affiliation(s)
- Marta Ibañez-Lligoña
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain
- Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
| | - Sergi Colomer-Castell
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain
- Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
| | - Alejandra González-Sánchez
- Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - Josep Gregori
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - Carolina Campos
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain
- Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
| | - Damir Garcia-Cehic
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain
| | - Cristina Andrés
- Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - Maria Piñana
- Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - Tomàs Pumarola
- Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
- Microbiology Department, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
| | - Francisco Rodríguez-Frias
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain
- Department of Basic Sciences, Universitat Internacional de Catalunya, Sant Cugat del Vallès, 08195 Barcelona, Spain
| | - Andrés Antón
- Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
- Microbiology Department, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
| | - Josep Quer
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain
- Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
- Correspondence:
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Liu Y, Mo X, Feng Y, Willoughby RE, Weng X, Wang Y, Li X, Gao J, Tian J, Peng J. Metagenomic next-generation sequencing for the etiological diagnosis of rabies virus in cerebrospinal fluid. Front Med (Lausanne) 2023; 10:982290. [PMID: 36844226 PMCID: PMC9947348 DOI: 10.3389/fmed.2023.982290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 01/02/2023] [Indexed: 02/11/2023] Open
Abstract
Background Rabies is a highly fatal disease. Once symptoms develop, death usually occurs within days. Survivors were occasionally reported in the literatures. Ante-mortem diagnosis remains a challenge in most rabies endemic countries. A novel, accurate diagnostic assay is highly desirable. Methods We used metagenomic next-generation sequencing (mNGS) to examine the cerebrospinal fluid (CSF) samples of a 49-year-old patient with rabies and validated the results by TaqMan PCR and RT-PCR/Sanger sequencing. Results Metagenomic next-generation sequencing identified sequence reads uniquely aligned to the rabies virus (RABV). PCR confirmed the presence of the partial RABV N gene in the CSF. Phylogenetic analysis showed that the RABV grouped as an Asian clade, which is the most broadly distributed clade in China. Conclusion Metagenomic next-generation sequencing may be a useful screening tool for the etiological diagnosis of rabies, especially in the absence of timely rabies laboratory testing or in patients with no exposure history.
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Affiliation(s)
- Yong Liu
- Intensive Care Unit, Shenzhen Hospital, Southern Medical University, Shenzhen, Guangdong, China
| | - Xichao Mo
- Department of Infectious Diseases, Nanfang Hospital of Southern Medical University, Guangzhou, Guangdong, China
| | - Ye Feng
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin, China
| | - Rodney E. Willoughby
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, MI, United States
| | - Xing Weng
- Department of Infectious Disease, BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Yuyang Wang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin, China
| | - Xing Li
- Department of Infectious Disease, BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Junling Gao
- Centre of Buddhists Studies, The University of Hong Kong, Hong Kong, Hong Kong SAR, China,Department of Medicine, LKS Medical Faculty, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Jinfei Tian
- Intensive Care Unit, Shenzhen Hospital, Southern Medical University, Shenzhen, Guangdong, China
| | - Jie Peng
- Department of Infectious Diseases, Nanfang Hospital of Southern Medical University, Guangzhou, Guangdong, China,*Correspondence: Jie Peng,
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Meng LN, Li G, Yuan HX, Feng XC, Liu F, Zhang SL. Utility of metagenomics next-generation sequencing in the diagnosis and treatment of severe infectious diseases in the intensive care unit. Technol Health Care 2023; 31:1887-1899. [PMID: 37302051 DOI: 10.3233/thc-220856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
BACKGROUND Metagenomic next-generation sequencing (mNGS) is a new method that combines high-throughput sequencing and bioinformatics analysis. However, it has not become as popular due to the limited testing equipment and high costs and lack of family awareness with not much relevant intensive care unit (ICU) research data. OBJECTIVE To explore the clinical use and value of metagenomics next-generation sequencing (mNGS) in patients with sepsis in the ICU. METHODS We conducted a retrospective analysis of 102 patients with sepsis admitted to the ICU of Peking University International Hospital from January 2018 to January 2022. Based on whether mNGS was performed, the identified patients were divided into the observation group (n= 51) and the control group (n= 51), respectively. Routine laboratory tests, including routine blood test, C-reactive protein, procalcitonin, and culture of suspicious lesion specimens were performed in both groups within 2 hours after admission to the ICU, while mNGS tests were performed in the observation group. Patients in both groups were routinely given initial anti-infective, anti-shock, and organ support treatment. Antibiotic regimens were optimized in a timely manner according to the etiological results. Relevant clinical data were collected. RESULTS The testing cycle of mNGS was shorter than that of the conventional culture (30.79 ± 4.01 h vs. 85.38 ± 9.94 h, P< 0.001), while the positive rate of mNGS was higher than that of the conventional culture (82.35% vs. 45.1%, P< 0.05), with obvious superiority in the detection of viruses and fungus. There were significant differences in the optimal time of antibiotics (48 h vs.100 h) and length of ICU stay (11 d vs. 16 d) between the observation group and control group (P< 0.01) respectively, with no difference in 28-day mortality (33.3% vs. 41.2%, P> 0.05). CONCLUSION mNGS is useful in the detection of sepsis-causing pathogens in the ICU with the advantages of short testing time and high positive rate. There was no difference in the 28-day outcome between the two groups, which may be related to other confounding factors such as small sample size. Additional studies with extended sample size are needed.
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Yu L, Zhang Y, Qi X, Bai K, Zhang Z, Bu H. Next-generation sequencing for the diagnosis of Listeria monocytogenes meningoencephalitis: a case series of five consecutive patients. J Med Microbiol 2023; 72. [PMID: 36748504 DOI: 10.1099/jmm.0.001641] [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: 01/11/2023] Open
Abstract
Introduction. The prompt and specific diagnosis of Listeria monocytogenes meningoencephalitis (LMM) is challenging. Next-generation sequencing (NGS) of cerebrospinal fluid (CSF) is an emerging technique for diagnosing infrequent causative pathogens.Hypothesis/Gap statement. We hypothesized that NGS of CSF is an effective approach for diagnosing LMM.Aim. To evaluate the effectiveness of NGS, we present five cases of LMM diagnosed using NGS of the CSF.Methodology. Between August 2017 and 30 September 2020, we used NGS of the CSF to detect pathogens in patients with clinically suspected central nervous system infections. The clinical characteristics, laboratory tests, imaging findings and NGS results are reviewed.Results. Five patients were diagnosed with LMM using NGS of the CSF within 2 to 4 days, although the clinical manifestations, medical history and imaging findings varied strikingly. NGS of CSF showed sequence reads corresponding to L. monocytogenes species ranging from 118 to 1997 bp, genomic coverage of 0.29-5.96 %, relative abundance of 14.83-32.16 % and sequencing depth of 1.12 to 1.35. The prompt diagnosis resulted in targeted and effective treatment with the appropriate antibiotics, although two patients with the most severe cerebral parenchymal lesions showed little improvement.Conclusion. Our results demonstrate the power of NGS of CSF for the prompt diagnosis of LMM. NGS of CSF is an important complementary tool for identifying L. monocytogenes.
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Affiliation(s)
- Lili Yu
- Department of Neurology, the Second Hospital of Hebei Medical University, Shijiazhuang 050000, Hebei, PR China.,Key Laboratory of Neurology of Hebei Province, Shijiazhuang 050000, Hebei, PR China
| | - Yu Zhang
- Department of Neurology, the Second Hospital of Hebei Medical University, Shijiazhuang 050000, Hebei, PR China.,Key Laboratory of Neurology of Hebei Province, Shijiazhuang 050000, Hebei, PR China
| | - Xuejiao Qi
- Department of Neurology, the Second Hospital of Hebei Medical University, Shijiazhuang 050000, Hebei, PR China.,Key Laboratory of Neurology of Hebei Province, Shijiazhuang 050000, Hebei, PR China
| | - Kaixuan Bai
- Department of Neurology, the Second Hospital of Hebei Medical University, Shijiazhuang 050000, Hebei, PR China.,Key Laboratory of Neurology of Hebei Province, Shijiazhuang 050000, Hebei, PR China
| | - Zhenyuan Zhang
- Department of Neurology, the Second Hospital of Hebei Medical University, Shijiazhuang 050000, Hebei, PR China.,Key Laboratory of Neurology of Hebei Province, Shijiazhuang 050000, Hebei, PR China
| | - Hui Bu
- Department of Neurology, the Second Hospital of Hebei Medical University, Shijiazhuang 050000, Hebei, PR China.,Key Laboratory of Neurology of Hebei Province, Shijiazhuang 050000, Hebei, PR China
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Zhao X, Bai LP, Li BY, Yue ZZ, Zhao YC, Zhao XY. Comparison of mNGS and conventional culture in non-organ transplant critically ill patients supported by ECMO: a single-center study. Front Cell Infect Microbiol 2023; 13:1146088. [PMID: 37139490 PMCID: PMC10149872 DOI: 10.3389/fcimb.2023.1146088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 03/28/2023] [Indexed: 05/05/2023] Open
Abstract
Objectives Infection is one of the important causes of death in intensive care unit (ICU) patients. At present, there are few articles focused on the detailed analysis of pathogenic microorganisms detected in different therapy periods of critically ill patients supported by extracorporeal membrane oxygenation (ECMO). Methods From October 2020 to October 2022, ECMO-assisted patients who underwent multiple times of both metagenomic next-generation sequencing (mNGS) test and conventional culture were enrolled continuously in the First Affiliated Hospital of Zhengzhou University. The baseline data, laboratory test results, and pathogenic microorganisms detected by mNGS and traditional culture in different time periods were recorded and analyzed. Results In the present study, 62 patients were included finally. According to whether the patients survived at discharge, they were divided into the survivor group (n = 24) and the non-survivor group (n = 38). Then, according to the different types of ECMO support, they were divided into the veno-venous ECMO (VV ECMO) group (n = 43) and the veno-arterial ECMO (VA ECMO) group (n = 19). The summit period of specimens of traditional culture and mNGS detection of ECMO patients was 7 days after admission, and the largest number of specimens of surviving patients appeared after ECMO withdrawal. The total number of traditional culture specimens was 1,249, the positive rate was 30.4% (380/1,249), and the positive rate of mNGS was 79.6% (82/103). A total of 28 kinds of pathogenic microorganisms were cultured from conventional culture, and 58 kinds of pathogenic microorganisms were detected by mNGS, including Mycobacterium, Rickettsia, and Chlamydia psittaci. In conventional culture, the most frequent Gram-negative bacteria, Gram-positive bacteria, and fungi were Klebsiella pneumoniae, Corynebacterium striatum, and Candida glabrata, and those with the highest frequency of occurrence in mNGS detection were Acinetobacter baumannii, Enterococcus faecium, and Aspergillus flavus. Conclusions Throughout the whole treatment process, different kinds of suspicious biological specimens of high-infection-risk ICU patients supported by ECMO should undergo both mNGS detection and traditional culture early and repeatedly.
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Affiliation(s)
- Xi Zhao
- Department of Cardiology, Cardiovascular Center, Henan Key Laboratory of Hereditary Cardiovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Lin-Peng Bai
- Department of Cardiology, Cardiovascular Center, Henan Key Laboratory of Hereditary Cardiovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Bo-Yan Li
- Department of Cardiology, Cardiovascular Center, Henan Key Laboratory of Hereditary Cardiovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Zhen-Zhen Yue
- Department of Cardiology, Cardiovascular Center, Henan Key Laboratory of Hereditary Cardiovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yang-Chao Zhao
- Department of Cardiology, Cardiovascular Center, Henan Key Laboratory of Hereditary Cardiovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- *Correspondence: Yang-Chao Zhao, ; Xiao-Yan Zhao,
| | - Xiao-Yan Zhao
- Department of Extracorporeal Life Support Center, Department of Cardiac Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- *Correspondence: Yang-Chao Zhao, ; Xiao-Yan Zhao,
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Harris KA, Brown JR. Diagnostic yield of broad-range 16s rRNA gene PCR varies by sample type and is improved by the addition of qPCR panels targeting the most common causative organisms. J Med Microbiol 2022; 71. [PMID: 36748452 DOI: 10.1099/jmm.0.001633] [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: 12/24/2022] Open
Abstract
Introduction. Molecular techniques are used in the clinical microbiology laboratory to support culture-based diagnosis of infection and are particularly useful for detecting difficult to culture bacteria or following empirical antimicrobial treatment.Hypothesis/Gap Statement. Broad-range 16S rRNA PCR is a valuable tool that detects a wide range of bacterial species. Diagnostic yield is low for some sample types but can be improved with the addition of qPCR panels targeting common bacterial pathogens.Aim. To evaluate the performance of a broad-range 16S rRNA gene PCR and the additional diagnostic yield of targeted qPCR applied to specimens according to a local testing algorithm.Methodology. In total, 6130 primary clinical samples were collected as part of standard clinical practice from patients with suspected infection during a 17 month period. Overall, 5497 samples were tested by broad-range 16S rRNA gene PCR and a panel of targeted real-time qPCR assays were performed on selected samples according to a local testing algorithm. An additional 633 samples were tested by real-time qPCR only. The 16S rRNA gene PCR was performed using two assays targeting different regions of the 16S rRNA gene. Laboratory developed qPCR assays for seven common bacterial pathogens were also performed. Data was extracted retrospectively from Epic Beaker Laboratory Information Management System (LIMS).Results. Broad-range 16S rRNA gene PCR improves diagnostic yield in culture-negative samples and detects a large range of bacterial species. Streptococcus spp., Staphylococcus spp. and the Enterobacteriaceae family are detected the most frequently in samples with a single causative organism, but mixed samples frequently contained anaerobic species. The highest diagnostic yield was obtained from abscess, pus and empyema samples; 44.9 % were positive by 16S and 61 % were positive by the combined 16S and targeted qPCR testing algorithm. Samples with a particularly low diagnostic yield were blood, with 3.3 % of samples positive by 16S and CSF with 4.8 % of samples positive by 16S. The increased diagnostic yield of adding targeted qPCR is largest (~threefold) in these two sample types.Conclusion. Broad-range PCR is a powerful technique that can detect a very large range of bacterial pathogens but has limited diagnostic sensitivity. The data in this report supports a testing strategy that combines broad-range and targeted bacterial PCR assays for maximizing diagnosis of infection in culture-negative specimens. This is particularly justified for blood and CSF samples. Alternative approaches, such as metagenomic sequencing, are needed to provide the breadth of broad-range PCR and the sensitivity of targeted qPCR panels.
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Affiliation(s)
- Kathryn A Harris
- Microbiology, Virology and Infection Prevention & Control, Great Ormond Street Hospital NHS Foundation Trust, Great Ormond Street, London, WC1N 3JH, UK.,Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Julianne R Brown
- Microbiology, Virology and Infection Prevention & Control, Great Ormond Street Hospital NHS Foundation Trust, Great Ormond Street, London, WC1N 3JH, UK
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Zhao E, Wang D, Zhao Z, Xie L, He X, Huang P, Ouyang F, Wen G, Huang S, Guan Y. The value of next-generation sequencing for the diagnosis of Streptococcus suis meningitis. Rev Assoc Med Bras (1992) 2022; 68:1663-1667. [PMID: 36449790 PMCID: PMC9779970 DOI: 10.1590/1806-9282.20220632] [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: 04/25/2022] [Accepted: 07/06/2022] [Indexed: 12/23/2022] Open
Abstract
OBJECTIVE The aim of this study was to investigate the value of next-generation sequencing for the diagnosis of Streptococcus suis meningitis. METHODS Patients with meningitis in the Department of Neurology of the Hainan General Hospital were recruited and 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 the specific pathogenic bacteria in the patients. In the control group, we used the cerebrospinal fluid bacterial culture method to detect the specific pathogenic bacteria in the patients. RESULTS A total of 28 participants were recruited for this study, with 14 participants in each group. The results showed similarities in both the average age and average course of the disease between the two groups (p>0.05). The white blood cell count, percentage of neutrophils, and level of C-reactive protein in the next-generation sequencing group were significantly higher than those in the control group (p<0.05). There were similarities in both the temperature and intracranial pressure between the two groups (p>0.05). In the next-generation sequencing group, all patients (100%) were detected as having had the S. suis meningitis infection by next-generation sequencing, while only 6 (43%) patients in the control group had been detected as having the S. suis meningitis infection by cerebrospinal fluid bacterial culture. CONCLUSIONS The positive detection rate of S. suis by the next-generation sequencing method was significantly higher compared with using a cerebrospinal fluid bacterial culture. Therefore, the next-generation sequencing method is valuable for the diagnosis of S. suis meningitis and is worthy of clinical application.
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Affiliation(s)
- Eryi Zhao
- Hainan Medical University, Hainan General Hospital, Department of Neurology – Hainan, China.,Corresponding author: ;
| | - Daimei Wang
- Hainan Medical University, Hainan General Hospital, Department of Pharmacy – Hainan, China.,Corresponding author: ;
| | - Zhongyan Zhao
- Hainan Medical University, Hainan General Hospital, Department of Neurology – Hainan, China
| | - Ling Xie
- Hainan Medical University, Hainan General Hospital, Department of Neurology – Hainan, China
| | - Xiangying He
- Hainan Medical University, Hainan General Hospital, Department of Neurology – Hainan, China
| | - Peijian Huang
- Hainan Medical University, Hainan General Hospital, Department of Neurology – Hainan, China
| | - Feng Ouyang
- Hainan Medical University, Hainan General Hospital, Department of Neurology – Hainan, China
| | - Guoqiang Wen
- Hainan Medical University, Hainan General Hospital, Department of Neurology – Hainan, China
| | - Shixiong Huang
- Hainan Medical University, Hainan General Hospital, Department of Neurology – Hainan, China.,Corresponding author: ;
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Shi Y, Wu J, Liu T, Li Y, Liu Y, Gu Y, Qi Y. Analysis of Metagenomic Next-Generation Sequencing Results of 25 Pus Samples. Infect Drug Resist 2022; 15:6515-6524. [DOI: 10.2147/idr.s385925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 10/27/2022] [Indexed: 11/09/2022] Open
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Chen M, Lai Z, Cheng M, Liang T, Lin Z. Rare brain and pulmonary abscesses caused by oral pathogens started with acute gastroenteritis diagnosed by metagenome next-generation sequencing: A case report and literature review. Front Cell Infect Microbiol 2022; 12:949840. [PMID: 36250052 PMCID: PMC9561126 DOI: 10.3389/fcimb.2022.949840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 08/29/2022] [Indexed: 11/13/2022] Open
Abstract
Odontogenic brain and pulmonary abscesses are extremely rare infectious diseases. It is mainly caused by the upward or downward transmission of local infection or blood-borne spread. In recent years, with the wide application of some novel testing methods in clinical practice, the diagnosis of unexplained infections such as odontogenic abscesses in different organs has gradually become clear. We report a case of a 21-year-old male who was healthy and had not received any oral treatment before onset. He started with acute gastroenteritis-related symptoms, then developed meningitis-related symptoms seven days later with septic shock. No obvious abscess lesions were found on head computed tomography (CT) at admission, and the etiology was not clear by routine examination, which was very easy to misdiagnose as a serious infection caused by intestinal pathogens. But odontogenic pathogens were found both in his blood and cerebrospinal fluid through metagenomic next-generation sequencing (mNGS) analysis. Subsequently, rechecked imaging examination displayed multiple brain and pulmonary abscesses. Finally, it was diagnosed as an odontogenic brain and pulmonary abscess. After an extremely lengthy anti-infection course (13 weeks of intravenous antibiotics plus 2 weeks of oral antibiotics) and surgery, the patient was improved and discharged from the hospital. From this case, we could see that the development of new diagnostic technologies such as mNGS plays an important role in the early and confirmed diagnosis of diseases previously difficult to diagnose such as odontogenic polymicrobial infections and ultimately helps to improve the prognosis of these patients.
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Affiliation(s)
- Minhua Chen
- Emergency and Critical Care Center, Intensive Care Unit, Zhejiang Provincial People’s Hospital(Affiliated People’s Hospital, Hangzhou Medical College), Hangzhou, China
| | - Zhiyi Lai
- Intensive Care Unit, Ningbo Fourth Hospital (The Affiliated Xiangshan Hospital of Wenzhou Medical University), Ningbo, China
| | - Mingjun Cheng
- Intensive Care Unit, Chun’an First People’s Hospital (Chun’an Branch of Zhejiang Provincial People’s Hospital and Chun’an Hospital Affiliated to Hangzhou Medical College), Hangzhou, China
| | - Tianyu Liang
- Emergency and Critical Care Center, Intensive Care Unit, Zhejiang Provincial People’s Hospital(Affiliated People’s Hospital, Hangzhou Medical College), Hangzhou, China
- *Correspondence: Zongbin Lin, ; Tianyu Liang,
| | - Zongbin Lin
- Emergency and Critical Care Center, Intensive Care Unit, Zhejiang Provincial People’s Hospital(Affiliated People’s Hospital, Hangzhou Medical College), Hangzhou, China
- *Correspondence: Zongbin Lin, ; Tianyu Liang,
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Jiang S, Chen Y, Han S, Lv L, Li L. Next-Generation Sequencing Applications for the Study of Fungal Pathogens. Microorganisms 2022; 10:microorganisms10101882. [PMID: 36296159 PMCID: PMC9609632 DOI: 10.3390/microorganisms10101882] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/13/2022] [Accepted: 09/15/2022] [Indexed: 11/16/2022] Open
Abstract
Next-generation sequencing (NGS) has become a widely used technology in biological research. NGS applications for clinical pathogen detection have become vital technologies. It is increasingly common to perform fast, accurate, and specific detection of clinical specimens using NGS. Pathogenic fungi with high virulence and drug resistance cause life-threatening clinical infections. NGS has had a significant biotechnological impact on detecting bacteria and viruses but is not equally applicable to fungi. There is a particularly urgent clinical need to use NGS to help identify fungi causing infections and prevent negative impacts. This review summarizes current research on NGS applications for fungi and offers a visual method of fungal detection. With the development of NGS and solutions for overcoming sequencing limitations, we suggest clinicians test specimens as soon as possible when encountering infections of unknown cause, suspected infections in vital organs, or rapidly progressive disease.
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Affiliation(s)
- Shiman Jiang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou 310003, China
| | - Yanfei Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou 310003, China
| | - Shengyi Han
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou 310003, China
| | - Longxian Lv
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou 310003, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou 310003, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan 250021, China
- Correspondence: ; Tel.: +86-0571-8723-6458
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Zhu M, Wang Q, Wang M, Wang S, Gong Q, Zhang X, Chen L. Rare Hepatic Cryptococcosis Mimicked Metastatic Liver Cancer and Confirmed by Metagenomic Next-Generation Sequencing in an Immunocompetent Patient: A Case Report. Infect Drug Resist 2022; 15:5753-5758. [PMID: 36213767 PMCID: PMC9532262 DOI: 10.2147/idr.s381730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 09/23/2022] [Indexed: 11/25/2022] Open
Abstract
Background Cryptococcus neoformans (C. neoformans) is commonly presented in immunocompromised individuals and causes cryptococcosis mostly in the respiratory and/or central nervous system. Liver cryptococcosis is exceedingly rare and sometimes difficult to diagnose through conventional assays. Case Presentation The present study reports a rare case of liver cryptococcosis characterized by increased serum carbohydrate antigen 19–9 (CA19-9) level and intrahepatic multiple nodules without other symptoms in an immunocompetent woman. Her cancer family history and imaging examinations initially suspected metastatic liver malignancy. But no sign of the malignant tumor was found after endoscopy, 18-fluorine fluorodeoxyglucose positron emission tomography-computed tomography, and liver biopsy. The histopathology of the liver biopsy specimen indicated chronic inflammatory granuloma and then infectious diseases were suspected. However, traditional microbiologic testing failed to identify any potential pathogen. Eventually, metagenomic next-generation sequencing (mNGS) was applied to identify the definite diagnosis of liver cryptococcosis by acquiring the genome sequence of C. neoformans. Fortunately, after 6-month diagnostic anti-fungal therapy of fluconazole, the liver nodules effectively faded away and the serum CA19-9 level gradually regressed to the normal range. Conclusion We identified a rare case of hepatic cryptococcosis by mNGS in an immunocompetent patient. When conventional methods have difficulties in the diagnosis of a specific pathogen, mNGS has the advantage of early and accurate identification of potential pathogens from the specimen.
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Affiliation(s)
- Mingyu Zhu
- Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, People's Republic of China
| | - Qingling Wang
- Department of Infectious Disease, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Mianyang, People's Republic of China
| | - Mingjie Wang
- Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, People's Republic of China
| | - Shengyu Wang
- Department of Radiology, Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, People's Republic of China
| | - Qiming Gong
- Department of Infectious Disease, Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, People's Republic of China
| | - Xinxin Zhang
- Department of Infectious Disease, Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, People's Republic of China
| | - Li Chen
- Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, People's Republic of China
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Gao H, Wang J, Zhang S, Li T. A Case Report of Two Kala-Azar Cases in China Diagnosed by Metagenomic Next-Generation Sequencing. Front Microbiol 2022; 13:922894. [PMID: 36386640 PMCID: PMC9650497 DOI: 10.3389/fmicb.2022.922894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 06/20/2022] [Indexed: 12/03/2022] Open
Abstract
Background Leishmaniasis being a local disease, as kala-azar this particular form is a visceral form. It is transmitted by sandflies, and is a parasitic disease involving the reticuloendothelial system of mononuclear macrophages. Due to its poor prognosis and high fatality rate, the fatality rate of patients without effective treatment can exceed 95%. Thereby, early diagnosis and treatment can significantly improve its prognosis. The metagenomic next-generation sequencing (mNGS) has the advantage of being able to find pathogens that cannot be detected by traditional methods. More importantly, it can conduct nucleic acid detection of pathogens covering a wide range in a short time. For infectious diseases like kala-azar, which is clinically complicated and difficult, mNGS detection provides a basis for accurate etiological diagnosis. Case Report We report 2 cases of kala-azar in West China Hospital, Chengdu, China. The first case is a 47-year-old male patient who had recurrent fever for 4 months, accompanied by reduction of red blood cell, white blood cell, and blood platelet. He was detected by mNGS and clinically diagnosed as kala-azar (Leishmania detection), finally died of multiple organ failure. The second patient was a 15-year-old male who had fever for more than 10 days. He was detected by mNGS and clinically diagnosed as kala-azar (Leishmania detection). He recovered and discharged quickly after treatment with sodium stibogluconate. Conclusion Efforts should be made to improve early etiological diagnosis in order to improve patient prognosis. mNGS detection is beneficial to the diagnosis and treatment of infectious diseases with unknown causes in the early stage of emergency treatment.
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Affiliation(s)
- Hongguang Gao
- Department of Emergency Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Jing Wang
- Precision Medicine Center, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, China
| | - Shu Zhang
- Department of Emergency Medicine, West China Hospital, Sichuan University, Chengdu, China
- *Correspondence: Shu Zhang
| | - Tian Li
- School of Basic Medicine, Fourth Military Medical University, Xi'an, China
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Gao H, Wang J, Zhang S, Li T. A Case Report of Two Kala-azar Cases in China Diagnosed by Metagenomic Next-Generation Sequencing. Front Med (Lausanne) 2022; 9:922894. [PMID: 36111106 PMCID: PMC9469688 DOI: 10.3389/fmed.2022.922894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 06/20/2022] [Indexed: 12/04/2022] Open
Abstract
Background Leishmaniasis being a local disease, as kala-azar this particular form is a visceral form. It is transmitted by sandflies, and is a parasitic disease involving the reticuloendothelial system of mononuclear macrophages. Due to its poor prognosis and high fatality rate, the fatality rate of patients without effective treatment can exceed 95%. Thereby, early diagnosis and treatment can significantly improve its prognosis. The metagenomic next-generation sequencing (mNGS) has the advantage of being able to find pathogens that cannot be detected by traditional methods. More importantly, it can conduct nucleic acid detection of pathogens covering a wide range in a short time. For infectious diseases like kala-azar, which is clinically complicated and difficult, mNGS detection provides a basis for accurate etiological diagnosis. Case Report We report 2 cases of kala-azar in West China Hospital, Chengdu, China. The first case is a 47-year-old male patient who had recurrent fever for 4 months, accompanied by reduction of red blood cell, white blood cell, and blood platelet. He was detected by mNGS and clinically diagnosed as kala-azar (Leishmania detection), finally died of multiple organ failure. The second patient was a 15-year-old male who had fever for more than 10 days. He was detected by mNGS and clinically diagnosed as kala-azar (Leishmania detection). He recovered and discharged quickly after treatment with sodium stibogluconate. Conclusion Efforts should be made to improve early etiological diagnosis in order to improve patient prognosis. mNGS detection is beneficial to the diagnosis and treatment of infectious diseases with unknown causes in the early stage of emergency treatment.
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Affiliation(s)
- Hongguang Gao
- Department of Emergency Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Jing Wang
- Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, China
| | - Shu Zhang
- Department of Emergency Medicine, West China Hospital, Sichuan University, Chengdu, China
- *Correspondence: Shu Zhang
| | - Tian Li
- School of Basic Medicine, Fourth Military Medical University, Xi'an, China
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Inglis LK, Edwards RA. How Metagenomics Has Transformed Our Understanding of Bacteriophages in Microbiome Research. Microorganisms 2022; 10:microorganisms10081671. [PMID: 36014086 PMCID: PMC9415785 DOI: 10.3390/microorganisms10081671] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 08/15/2022] [Accepted: 08/16/2022] [Indexed: 11/16/2022] Open
Abstract
The microbiome is an essential part of most ecosystems. It was originally studied mostly through culturing but relatively few microbes can be cultured, so much of the microbiome was left unexplored. The emergence of metagenomic sequencing techniques changed that and allowed the study of microbiomes from all sorts of habitats. Metagenomic sequencing also allowed for a more thorough exploration of prophages, viruses that integrate into bacterial genomes, and how they benefit their hosts. One issue with using open-access metagenomic data is that sequences added to databases often have little to no metadata to work with, so finding enough sequences can be difficult. Many metagenomes have been manually curated but this is a time-consuming process and relies heavily on the uploader to be accurate and thorough when filling in metadata fields and the curators to be working with the same ontologies. Using algorithms to automatically sort metagenomes based on either the taxonomic profile or the functional profile may be a viable solution to the issues with manually curated metagenomes, but it requires that the algorithm is trained on carefully curated datasets and using the most informative profile possible in order to minimize errors.
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Yek C, Pacheco AR, Vanaerschot M, Bohl JA, Fahsbender E, Aranda-Díaz A, Lay S, Chea S, Oum MH, Lon C, Tato CM, Manning JE. Metagenomic Pathogen Sequencing in Resource-Scarce Settings: Lessons Learned and the Road Ahead. FRONTIERS IN EPIDEMIOLOGY 2022; 2:926695. [PMID: 36247976 PMCID: PMC9558322 DOI: 10.3389/fepid.2022.926695] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 07/29/2022] [Indexed: 06/16/2023]
Abstract
Metagenomic next-generation sequencing (mNGS) is the process of sequencing all genetic material in a biological sample. The technique is growing in popularity with myriad applications including outbreak investigation, biosurveillance, and pathogen detection in clinical samples. However, mNGS programs are costly to build and maintain, and additional obstacles faced by low- and middle-income countries (LMICs) may further widen global inequities in mNGS capacity. Over the past two decades, several important infectious disease outbreaks have highlighted the importance of establishing widespread sequencing capacity to support rapid disease detection and containment at the source. Using lessons learned from the COVID-19 pandemic, LMICs can leverage current momentum to design and build sustainable mNGS programs, which would form part of a global surveillance network crucial to the elimination of infectious diseases.
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Affiliation(s)
- Christina Yek
- Department of Critical Care Medicine, National Institutes of Health Clinical Center, Bethesda, MD, United States
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, Rockville, MD, United States
| | - Andrea R. Pacheco
- International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
| | | | - Jennifer A. Bohl
- Vaccine Immunology Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States
| | | | - Andrés Aranda-Díaz
- Chan Zuckerberg Initiative, Redwood City, CA, United States
- Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Sreyngim Lay
- International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
| | - Sophana Chea
- International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
| | - Meng Heng Oum
- International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
| | - Chanthap Lon
- International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
| | | | - Jessica E. Manning
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, Rockville, MD, United States
- International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
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Zhao YC, Ding YZ, Zhao X, Fu GW, Huang MJ, Li XX, Sun QQ, Kan YB, Li J, Wang SL, Ma WT, Xu QF, Liu QL, Li HB. Role and Clinical Application of Metagenomic Next-Generation Sequencing in Immunocompromised Patients With Acute Respiratory Failure During Veno-Venous Extracorporeal Membrane Oxygenation. Front Cell Infect Microbiol 2022; 12:877205. [PMID: 36034706 PMCID: PMC9414489 DOI: 10.3389/fcimb.2022.877205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/23/2022] [Indexed: 11/29/2022] Open
Abstract
Objectives There are few studies of metagenomic next-generation sequencing (mNGS) in immunocompromised patients assisted by veno-venous extracorporeal membrane oxygenation (vv-ECMO). The present study is aimed to investigate the pathogen-detected effect and clinical therapy value of mNGS technologies in immunocompromised patients assisted by vv-ECMO. Methods Our study retrospectively enrolled 46 immunocompromised patients supported by vv-ECMO from Jan 2017 to June 2021 at the First Affiliated Hospital of Zhengzhou University, respectively. Patients were divided into the deterioration group (Group D) (n = 31) and improvement group (Group I) (n = 15) according to their outcomes. Baseline characteristics and etiological data of patients during hospitalization of 2 groups were compared. The pathogens detected by mNGS and antibiotic regimens guided by mNGS in immunocompromised patients assisted by vv-ECMO were analyzed. Results Compared with Group I, the deterioration patients showed a higher percentage of chronic obstructive pulmonary disease (COPD) (32.3% vs. 6.7%, p < 0.01) and were significantly older (47.77 ± 16.72 years vs. 32 ± 15.05 years, p < 0.01). Within 48 h of being ECMO assisted, the consistency of the samples detected by traditional culture and mNGS at the same time was good (traditional culture vs. mNGS detection, the positive rate of bronchoalveolar lavage fluid (BALF) culture: 26.1% vs. 30.4%; the positive rate of blood sample culture: 12.2% vs. 12.2%, p > 0.05). However, mNGS detected far more pathogen species and strains than conventional culture (30 strains vs. 78 strains, p < 0.01); the most popular pathogen was Klebsiella pneumoniae. Parts of patients had their antibiotic treatment adjustments, and the improvement patients showed less usage of broad-spectrum antibiotics. Conclusions mNGS may play a relatively important role in detecting mixed pathogens and personalized antibiotic treatment in immunocompromised patients assisted by vv-ECMO.
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Affiliation(s)
- Yang-Chao Zhao
- Department of Extracorporeal Life Support Center, Department of Cardiac Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Yang-Chao Zhao,
| | - Yan-Zhong Ding
- Department of Cardiology, Cardiovascular Center, Henan Key Laboratory of Hereditary Cardiovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xi Zhao
- Department of Cardiology, Cardiovascular Center, Henan Key Laboratory of Hereditary Cardiovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Guo-Wei Fu
- Department of Extracorporeal Life Support Center, Department of Cardiac Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ming-Jun Huang
- Department of Extracorporeal Life Support Center, Department of Cardiac Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xing-Xing Li
- Department of Extracorporeal Life Support Center, Department of Cardiac Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qian-Qian Sun
- Department of Extracorporeal Life Support Center, Department of Cardiac Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ya-Bai Kan
- Department of Extracorporeal Life Support Center, Department of Cardiac Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jun Li
- Department of Extracorporeal Life Support Center, Department of Cardiac Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shi-Lei Wang
- Department of Respiration, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wen-Tao Ma
- Department of Respiration, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qin-Fu Xu
- Department of Respiration, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qi-Long Liu
- Department of Surgery ICU, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hong-Bin Li
- Department of Surgery ICU, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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朱 珊, 刘 瑛, 罗 海, 杨 明, 杨 良, 邓 文. [Application value of metagenomic next-generation sequencing for pathogen detection in childhood agranulocytosis with fever]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2022; 24:753-758. [PMID: 35894189 PMCID: PMC9336627 DOI: 10.7499/j.issn.1008-8830.2204038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 06/01/2022] [Indexed: 06/15/2023]
Abstract
OBJECTIVES To study the application value of metagenomic next-generation sequencing (mNGS) for pathogen detection in childhood agranulocytosis with fever. METHODS A retrospective analysis was performed on the mNGS results of pathogen detection of 116 children with agranulocytosis with fever who were treated from January 2020 to December 2021. Among these children, 38 children with negative mNGS results were enrolled as the negative group, and 78 children with positive results were divided into a bacteria group (n=22), a fungal group (n=23), and a viral group (n=31). Clinical data were compared between groups. RESULTS For the 116 children with agranulocytosis and fever, the median age was 8 years at diagnosis, the median turnaround time of mNGS results was 2 days, and the positive rate of mNGS testing was 67.2% (78/116). Compared with the negative group, the bacterial group had a higher procalcitonin level (P<0.05), the fungal group had higher level of C-reactive protein and positive rate of (1,3)-β-D glucan test/galactomannan test (P<0.05), and the fungal group had a longer duration of fever (P<0.05). Among the 22 positive microbial culture specimens, 9 (41%) were consistent with the mNGS results. Among the 17 positive blood culture specimens, 8 (47%) were consistent with the mNGS results. Treatment was adjusted for 28 children (36%) with the mNGS results, among whom 26 were cured and discharged. CONCLUSIONS The mNGS technique has a shorter turnaround time and a higher sensitivity for pathogen detection and can provide evidence for the pathogenic diagnosis of children with agranulocytosis and fever.
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Wang D, Wang W, Ding Y, Tang M, Zhang L, Chen J, You H. Metagenomic Next-Generation Sequencing Successfully Detects Pulmonary Infectious Pathogens in Children With Hematologic Malignancy. Front Cell Infect Microbiol 2022; 12:899028. [PMID: 35837477 PMCID: PMC9273861 DOI: 10.3389/fcimb.2022.899028] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 05/31/2022] [Indexed: 12/24/2022] Open
Abstract
Background Pulmonary infection is a leading cause of mortality in pediatric patients with hematologic malignancy (HM). In clinical settings, pulmonary pathogens are frequently undetectable, and empiric therapies may be costly, ineffective and lead to poor outcomes in this vulnerable population. Metagenomic next-generation sequencing (mNGS) enhances pathogen detection, but data on its application in pediatric patients with HM and pulmonary infections are scarce. Methods We retrospectively reviewed 55 pediatric patients with HM and pulmonary infection who were performed mNGS on bronchoalveolar lavage fluid from January 2020 to October 2021. The performances of mNGS methods and conventional microbiological methods in pathogenic diagnosis and subsequently antibiotic adjustment were investigated. Results A definite or probable microbial etiology of pulmonary infection was established for 50 of the 55 patients (90.9%) when mNGS was combined with conventional microbiological tests. The positive rate was 87.3% (48 of 55 patients) for mNGS versus 34.5% (19 of 55 patients) with conventional microbiological methods (P < 0.001). Bacteria, viruses and fungi were detected in 17/55 (30.9%), 25/55 (45.5%) and 19/55 (34.5%) cases using mNGS, respectively. Furthermore, 17 patients (30.9%) were identified as pulmonary mixed infections. Among the 50 pathogen-positive cases, 38% (19/50) were not completely pathogen-covered by empirical antibiotics and all of them were accordingly made an antibiotic adjustment. In the present study, the 30-day mortality rate was 7.3%. Conclusion mNGS is a valuable diagnostic tool to determine the etiology and appropriate treatment in pediatric patients with HM and pulmonary infection. In these vulnerable children with HM, pulmonary infections are life-threatening, so we recommend that mNGS should be considered as a front-line diagnostic test.
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Hou Y, Wang Y, Zhang Y, Yu H, Zhao Y, Yi A. Human Encephalitis Caused by Pseudorabies Virus in China: A Case Report and Systematic Review. Vector Borne Zoonotic Dis 2022; 22:391-396. [PMID: 35736787 DOI: 10.1089/vbz.2022.0002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Background: Pseudorabies virus (PRV) is a common pathogen found in pigs. The pathogenicity of PRV in humans is under researched and there are few confirmed cases of PRV infections in humans, which has led to a lack of clinical consensus. Methods: We presented a case of viral encephalitis caused by PRV in China. We performed a systematic review of the literature to investigate the clinical features and prognosis of PRV encephalitis and included 12 patients with PRV encephalitis. Results: All the patients had a history of direct or indirect contact with living pigs or pork before the onset of the disease, accompanied by prodromal symptoms, such as fever and headache. They presented with a series of lesions involving the central nervous system (CNS) and respiratory system, such as acute encephalitis syndrome, respiratory failure, retinitis, or endophthalmitis. Conclusions: The differential diagnosis of an acute attack of CNS infection should include PRV encephalitis, which should be diagnosed by a head magnetic resonance imaging (MRI), fundus examination, and cerebrospinal fluid next-generation sequencing. Intravenous immunoglobulin, glucocorticoid, antiviral, and symptomatic support treatment should be administered as early as possible to improve the prognosis.
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Affiliation(s)
- Yue Hou
- Department of Neurology, Hebei University of Engineering Clinical Medical College, Handan, China
| | - YouMing Wang
- Department of Neurology, Affiliated Hospital of Hebei University of Engineering, Handan, China
| | - Yao Zhang
- Department of Neurology, Affiliated Hospital of Hebei University of Engineering, Handan, China
| | - HuiDan Yu
- Department of Neurology, Affiliated Hospital of Hebei University of Engineering, Handan, China
| | - Yan Zhao
- Department of Neurology, Hebei University of Engineering Clinical Medical College, Handan, China
| | - AiFen Yi
- The Fifth People's Hospital of Anyang, Anyang, China
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Diagnostic accuracy of the metagenomic next-generation sequencing (mNGS) for detection of bacterial meningoencephalitis: a systematic review and meta-analysis. Eur J Clin Microbiol Infect Dis 2022; 41:881-891. [PMID: 35474146 DOI: 10.1007/s10096-022-04445-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 04/12/2022] [Indexed: 11/03/2022]
Abstract
The early diagnosis of bacterial meningoencephalitis (BM/E) is difficult, and delay in diagnosis can cause complications leading to neurological impairment/death. In cases of unexplained BM/E, the metagenomic NGS (mNGS) offers an advantage over conventional methods, especially when a rare pathogen is implicated or the patient is on antibiotics. This study aims to evaluate and compare the diagnostic efficacy of mNGS for the diagnosis of BM/E using cerebrospinal fluid (CSF) specimens versus a composite reference standard (CRS). The electronic databases (Embase, PubMed, and Web of Science) were searched up to 15 June 2021. Studies such as cohort, case-control, prospective, or retrospective studies that assessed the diagnostic efficacy of mNGS in suspected bacterial meningitis/encephalitis cases were included. Ten studies met the inclusion criteria, including three retrospective and seven prospective studies. The sensitivity of mNGS for diagnosis of BM/E from CSF samples ranged from 33 (95% CI: 13-62) to 98% (95% CI: 76-99). The specificity of mNGS ranged from 67 (95% CI: 55-78) to 98% (95% CI: 95-99). The estimated AUC (area under curve) by hierarchical summary receiver operating characteristic (HSROC) of the studies being analyzed was 0.912. The meta-regression analysis demonstrated that the different types of studies (single-center vs. multi-center) had an effect on the specificity of mNGS for BM/E compared with CRS (90% vs. 96%, meta-regression P < 0.05). The current analysis revealed moderate diagnostic accuracy of mNGS. This approach can be helpful, especially in cases of undiagnosed BM/E by identification of organism and subsequently accelerating the patient management.
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Zhang J, Luo J, Weng X, Zhu Y, Goyal G, Perna F, Espinoza-Gutarra M, Jiang L, Chen L, Mi JQ. A case report of the metagenomics next-generation sequencing for early detection of central nervous system mucormycosis with successful rescue in patient with recurrent chronic lymphocytic leukemia. ANNALS OF TRANSLATIONAL MEDICINE 2022; 10:722. [PMID: 35845522 PMCID: PMC9279813 DOI: 10.21037/atm-22-2533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 06/20/2022] [Indexed: 11/06/2022]
Abstract
Background Central nervous system (CNS) mucormycosis is insidious and difficult to diagnose. It progresses rapidly and causes high mortality. Rare cases have been reported during ibrutinib use, which have poor prognosis. Through this case, we share the experience of successful diagnosis and treatment. We also emphasize the importance of focusing on high-risk groups, early diagnosis and prompt management. Case Description In this case, a 52-year-old patient was diagnosed with chronic lymphocytic leukemia (CLL) for more than 5 years. He was in remission after rituximab plus fludarabine and cyclophosphamide (RFC) regimen, and relapsed in the fourth year. During the ibrutinib monotherapy, the patient presented with sudden headache. Cranial imaging examination revealed a definite right occipitoparietal lobe mass with extensive edema. A rapid diagnosis of mucormycosis infection was made using metagenomic next-generation sequencing (mNGS). The patient at that time didn't have neutropenia, but he had hypogammaglobulinemia. The infection was treated with amphotericin B cholesteryl sulfate complex, posaconazole, and interventional surgery, and the treatment was successful. At the same time, we considered the control of disease progression in this relapsed patient with, as well as to the drug interaction with posaconazole. We chose the next generation Bruton's tyrosine kinase (BTK) inhibitor zanubrutinib as the treatment, whose safety has been identified. As of the submission date, the patient has been followed up for nearly 1 year, and his disease is stable. Conclusions When new clinical problems arise in recurrent CLL patients, it is important to identify multiple factors, especially the insidious fungal infections. In particular, the immunocompromised patients should be concerned. CNS mucormycosis is extremely deadly, the early diagnosis will improve the prognosis. In clinical practice, the gold standard diagnosis of mucormycosis is difficult to obtain through pathology. In this case, mNGS was applied to quickly diagnose mucormycosis, enabling earlier treatment and ameliorating the prognosis. Thus, it will help us to early detect this group of people who may be potentially infected. Current guidelines do not recommend the prophylactic use of antifungal agents in treated CLL patients. However, in patients with prior severe infection or hypogammaglobulinemia, intravenous immunoglobulin is recommended to reduce the associated infection rate.
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Affiliation(s)
- Jiaojiao Zhang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jing Luo
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiangqin Weng
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yongmei Zhu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Gaurav Goyal
- Division of Hematology and Oncology, University of Alabama at Birmingham (UAB), Birmingham, Alabama, USA
| | - Fabiana Perna
- Division of Hematology/Oncology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Manuel Espinoza-Gutarra
- Division of Hematology/Oncology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Lu Jiang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jian-Qing Mi
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
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