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Fida M, Tande AJ. State-of-the-Art Metagenomic Sequencing and Its Role in the Diagnosis of Periprosthetic Joint Infections. Infect Dis Clin North Am 2024:S0891-5520(24)00062-X. [PMID: 39277504 DOI: 10.1016/j.idc.2024.07.011] [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: 09/17/2024]
Abstract
Metagenomic next-generation sequencing (mNGS) is increasingly being recognized as a valuable diagnostic tool for periprosthetic joint infections (PJIs). This study reviews the diagnostic utility of mNGS, highlighting its improved sensitivity in detecting pathogens, particularly in culture-negative and polymicrobial infections. However, the clinical application of this method is hindered by challenges such as the prevalence of host DNA, the necessity for extensive bioinformatic analysis, and the potential for contamination, which can lead to misinterpretation of results. As mNGS continues to evolve, it holds significant potential to improve the management of PJI and enhance the application of precision medicine in orthopedic infections.
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Affiliation(s)
- Madiha Fida
- Division of Public Health, Infectious Diseases and Occupational Medicine, Department of Medicine, Mayo Clinic, Rochester, MN, USA.
| | - Aaron J Tande
- Division of Public Health, Infectious Diseases and Occupational Medicine, Department of Medicine, Mayo Clinic, Rochester, MN, USA
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2
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Su LD, Chiu CY, Gaston D, Hogan CA, Miller S, Simon DW, Thakur KT, Yang S, Piantadosi A. Clinical Metagenomic Next-Generation Sequencing for Diagnosis of Central Nervous System Infections: Advances and Challenges. Mol Diagn Ther 2024; 28:513-523. [PMID: 38992308 DOI: 10.1007/s40291-024-00727-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2024] [Indexed: 07/13/2024]
Abstract
Central nervous system (CNS) infections carry a substantial burden of morbidity and mortality worldwide, and accurate and timely diagnosis is required to optimize management. Metagenomic next-generation sequencing (mNGS) has proven to be a valuable tool in detecting pathogens in patients with suspected CNS infection. By sequencing microbial nucleic acids present in a patient's cerebrospinal fluid, brain tissue, or samples collected outside of the CNS, such as plasma, mNGS can detect a wide range of pathogens, including rare, unexpected, and/or fastidious organisms. Furthermore, its target-agnostic approach allows for the identification of both known and novel pathogens. This is particularly useful in cases where conventional diagnostic methods fail to provide an answer. In addition, mNGS can detect multiple microorganisms simultaneously, which is crucial in cases of mixed infections without a clear predominant pathogen. Overall, clinical mNGS testing can help expedite the diagnostic process for CNS infections, guide appropriate management decisions, and ultimately improve clinical outcomes. However, there are key challenges surrounding its use that need to be considered to fully leverage its clinical impact. For example, only a few specialized laboratories offer clinical mNGS due to the complexity of both the laboratory methods and analysis pipelines. Clinicians interpreting mNGS results must be aware of both false negatives-as mNGS is a direct detection modality and requires a sufficient amount of microbial nucleic acid to be present in the sample tested-and false positives-as mNGS detects environmental microbes and their nucleic acids, despite best practices to minimize contamination. Additionally, current costs and turnaround times limit broader implementation of clinical mNGS. Finally, there is uncertainty regarding the best practices for clinical utilization of mNGS, and further work is needed to define the optimal patient population(s), syndrome(s), and time of testing to implement clinical mNGS.
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Affiliation(s)
- LingHui David Su
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
- The Consortium for Clinical Metagenomics in Infectious Diseases, Nashville, TN, USA
| | - Charles Y Chiu
- The Consortium for Clinical Metagenomics in Infectious Diseases, Nashville, TN, USA
- Department of Laboratory Medicine and Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, CA, USA
| | - David Gaston
- The Consortium for Clinical Metagenomics in Infectious Diseases, Nashville, TN, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Catherine A Hogan
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
- The Consortium for Clinical Metagenomics in Infectious Diseases, Nashville, TN, USA
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Steve Miller
- The Consortium for Clinical Metagenomics in Infectious Diseases, Nashville, TN, USA
- Delve Bio, Inc., San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Dennis W Simon
- The Consortium for Clinical Metagenomics in Infectious Diseases, Nashville, TN, USA
- Department of Pediatric Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kiran T Thakur
- The Consortium for Clinical Metagenomics in Infectious Diseases, Nashville, TN, USA
- Department of Neurology, Columbia University Irving Medical Center-New York Presbyterian Hospital, New York, NY, USA
| | - Shangxin Yang
- The Consortium for Clinical Metagenomics in Infectious Diseases, Nashville, TN, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Anne Piantadosi
- The Consortium for Clinical Metagenomics in Infectious Diseases, Nashville, TN, USA.
- Department of Pathology and Laboratory Medicine, and Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 101 Woodruff Circle, Atlanta, GA, USA.
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Ma R, Wang YM, Guan H, Zhang L, Zhang W, Chen LC. Pulmonary abscess caused by Streptococcus pseudopneumoniae in a child: A case report and review of literature. World J Radiol 2024; 16:362-370. [PMID: 39239243 PMCID: PMC11372553 DOI: 10.4329/wjr.v16.i8.362] [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: 04/30/2024] [Revised: 08/05/2024] [Accepted: 08/09/2024] [Indexed: 08/28/2024] Open
Abstract
BACKGROUND Lung abscess found on chest X-ray and computed tomography examinations is rare in infants and young children. Several pathogens can cause lung abscesses, with the most common pathogens being anaerobes, Streptococci and Staphylococcus aureus. Streptococcus pseudopneumoniae (S. pseudopneumoniae) is a member of the Streptococcaceae family, and is mainly isolated from respiratory tract specimens. There are currently no cases of lung abscess caused by S. pseudopneumoniae in the literature. CASE SUMMARY A 2-year-old boy was admitted to hospital due to persistent cough and fever. Lung computed tomography examination suggested the formation of a lung abscess. His diagnosis was not confirmed by testing for serum respiratory pathogens (6 items), respiratory pathogen nucleic acid (27 items), and laboratory culture. Finally, metagenomic next-generation sequencing of bronchoalveolar lavage fluid revealed the presence of S. pseudopneumoniae, confirming its role in causing the lung abscess. After receiving antibiotic treatment, reexamination with lung computed tomography showed that the abscess was resorbed and the patient's outcome was good. CONCLUSION This is the first report of a lung abscess in a child caused by S. pseudopneumoniae infection. Metagenomic next-generation sequencing of bronchoalveolar lavage fluid is helpful in achieving rapid and accurate pathogen identification.
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Affiliation(s)
- Ran Ma
- Department of Pediatrics, Shihezi University, Shihezi 832000, Xinjiang Uygur Autonomous Region, China
| | - Yan-Mei Wang
- Department of Pediatrics, The First Affiliated Hospital of Shihezi University, Shihezi 832000, Xinjiang Uygur Autonomous Region, China
| | - Hua Guan
- Department of Pediatrics, Corps Fourth Division Hospital, Yining 844500, Xinjiang Uygur Autonomous Region, China
| | - Li Zhang
- Department of Pediatrics, The First Affiliated Hospital of Shihezi University, Shihezi 832000, Xinjiang Uygur Autonomous Region, China
| | - Wei Zhang
- Department of Pediatrics, The First Affiliated Hospital of Shihezi University, Shihezi 832000, Xinjiang Uygur Autonomous Region, China
| | - Ling-Cai Chen
- Department of Pediatrics, Corps First Division Hospital, Aksu 842008, Xinjiang Uygur Autonomous Region, China
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Wang X, Xu H, Qin L, Wang H, Jiang Y, Liu H, Zhang M, Pang R, Wu W, Li W. Metagenomic next-generation sequencing of cerebrospinal fluid reveals etiological and microbiological features in patients with various central nervous system infections. FASEB J 2024; 38:e23812. [PMID: 39041354 DOI: 10.1096/fj.202400792r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/30/2024] [Accepted: 06/26/2024] [Indexed: 07/24/2024]
Abstract
The application of metagenomic next-generation sequencing (mNGS) in pathogens detection of cerebrospinal fluid (CSF) is limited because clinical, microbiological, and biological information are not well connected. We analyzed the 428 enrolled patients' clinical features, pathogens diagnostic efficiency of mNGS in CSF, microbial community structure and composition in CSF, and correlation of microbial and clinical biomarkers in CSF. General characteristics were unspecific but helpful in formulating a differential diagnosis. CSF mNGS has a higher detection rate (34.6%) compared to traditional methods (5.4%). mNGS detection rate was higher when the time from onset to CSF collection was ≤20 days, the CSF leukocytes count was >200 × 106/L, the CSF protein concentration was >1.3 g/L, or CSF glucose concentration was ≤2.5 mmol/L in non-postoperative bacterial CNS infections (CNSi). CSF was not strictly a sterile environment, and the potential pathogens may contribute to the dysbiosis of CSF microbiome. Furthermore, clinical biomarkers were significantly relevant to CNS pathogens. Clinical data are helpful in choosing a proper opportunity to obtain an accurate result of mNGS, and can speculate whether the mNGS results are correct or not. Our study is a pioneering study exploring the CSF microbiome in different CNSIs.
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Affiliation(s)
- Xiaojuan Wang
- Department of Neurology, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital, Henan University, Zhengzhou, China
| | - Huan Xu
- Vision Medicals Center for Infection Diseases, Guangzhou, China
| | - Lingzhi Qin
- Department of Neurology, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital, Henan University, Zhengzhou, China
| | - Huimin Wang
- Special Ward, Xinxiang Central Hospital, Xinxiang, China
| | - Yushu Jiang
- Department of Neurology, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital, Henan University, Zhengzhou, China
| | - Huiqin Liu
- Department of Neurology, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital, Henan University, Zhengzhou, China
| | - Milan Zhang
- Department of Neurology, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital, Henan University, Zhengzhou, China
| | - Rui Pang
- Department of Neurology, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital, Henan University, Zhengzhou, China
| | - Wencai Wu
- Vision Medicals Center for Infection Diseases, Guangzhou, China
| | - Wei Li
- Department of Neurology, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital, Henan University, Zhengzhou, China
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Cai X, Sun C, Zhong H, Cai Y, Cao M, Wang L, Sun W, Tao Y, Ma G, Huang B, Yan S, Zhong J, Wang J, Lu Y, Guan Y, Song M, Wang Y, Li Y, Su X. The value of metagenomic next-generation sequencing with different nucleic acid extracting methods of cell-free DNA or whole-cell DNA in the diagnosis of non-neutropenic pulmonary aspergillosis. Front Cell Infect Microbiol 2024; 14:1398190. [PMID: 39135636 PMCID: PMC11317373 DOI: 10.3389/fcimb.2024.1398190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 07/09/2024] [Indexed: 08/15/2024] Open
Abstract
Purpose Metagenomic next-generation sequencing(mNGS) is a novel molecular diagnostic technique. For nucleic acid extraction methods, both whole-cell DNA (wcDNA) and cell-free DNA (cfDNA) are widely applied with the sample of bronchoalveolar lavage fluid (BALF). We aim to evaluate the clinical value of mNGS with cfDNA and mNGS with wcDNA for the detection of BALF pathogens in non-neutropenic pulmonary aspergillosis. Methods mNGS with BALF-cfDNA, BALF-wcDNA and conventional microbiological tests (CMTs) were performed in suspected non-neutropenic pulmonary aspergillosis. The diagnostic value of different assays for pulmonary aspergillosis was compared. Results BALF-mNGS (cfDNA, wcDNA) outperformed CMTs in terms of microorganisms detection. Receiver operating characteristic (ROC) analysis indicated BALF-mNGS (cfDNA, wcDNA) was superior to culture and BALF-GM. Combination diagnosis of either positive for BALF-mNGS (cfDNA, wcDNA) or CMTs is more sensitive than CMTs alone in the diagnosis of pulmonary aspergillosis (BALF-cfDNA+CMTs/BALF-wcDNA+CMTs vs. CMTs: ROC analysis: 0.813 vs.0.66, P=0.0142/0.796 vs.0.66, P=0.0244; Sensitivity: 89.47% vs. 47.37%, P=0.008/84.21% vs. 47.37%, P=0.016). BALF-cfDNA showed a significantly greater reads per million (RPM) than BALF-wcDNA. The area under the ROC curve (AUC) for RPM of Aspergillus detected by BALF-cfDNA, used to predict "True positive" pulmonary aspergillosis patients, was 0.779, with a cut-off value greater than 4.5. Conclusion We propose that the incorporation of BALF-mNGS (cfDNA, wcDNA) with CMTs improves diagnostic precision in the identification of non-neutropenic pulmonary aspergillosis when compared to CMTs alone. BALF-cfDNA outperforms BALF-wcDNA in clinical value.
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Affiliation(s)
- Xiaomin Cai
- Department of Respiratory and Critical Care Medicine, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
- Department of Respiratory and Critical Medicine, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Chao Sun
- Department of Respiratory and Critical Medicine, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Huanhuan Zhong
- Department of Respiratory and Critical Medicine, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Suzhou University, Suzhou, China
| | - Yuchen Cai
- Department of Respiratory and Critical Medicine, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Min Cao
- Department of Respiratory and Critical Care Medicine, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Li Wang
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Wenkui Sun
- Department of Respiratory and Critical Care Medicine, Jiangsu Province Hospital, The First Affiliated of Nanjing Medical University, Nanjing, China
| | - Yujian Tao
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Yangzhou University, Yangzhou, China
| | - Guoer Ma
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Baoju Huang
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Shengmei Yan
- Department of Respiratory and Critical Medicine, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Jinjin Zhong
- Department of Respiratory and Critical Medicine, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Jiamei Wang
- Department of Respiratory and Critical Care Medicine, Jinling Hospital, Nanjing Medical University, Nanjing, China
| | - Yajie Lu
- Department of Respiratory and Critical Medicine, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Yuanlin Guan
- Department of Research and Development, Hugobiotech Co., Ltd., Beijing, China
| | - Mengyue Song
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Suzhou University, Suzhou, China
| | - Yujie Wang
- Department of Respiratory and Critical Medicine, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Yuanyuan Li
- Department of Respiratory and Critical Medicine, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Xin Su
- Department of Respiratory and Critical Care Medicine, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
- Department of Respiratory and Critical Medicine, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
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Li Z, Guo Z, Wu W, Tan L, Long Q, Xia H, Hu M. The effects of sequencing strategies on Metagenomic pathogen detection using bronchoalveolar lavage fluid samples. Heliyon 2024; 10:e33429. [PMID: 39027502 PMCID: PMC11255660 DOI: 10.1016/j.heliyon.2024.e33429] [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: 12/03/2023] [Revised: 06/17/2024] [Accepted: 06/21/2024] [Indexed: 07/20/2024] Open
Abstract
Objectives Metagenomic next-generation sequencing (mNGS) is a powerful tool for pathogen detection. The accuracy depends on both wet lab and dry lab procedures. The objective of our study was to assess the influence of read length and dataset size on pathogen detection. Methods In this study, 43 clinical BALF samples, which tested positive via clinical mNGS and were consistent with the diagnosis, were subjected to re-sequencing on the Illumina NovaSeq 6000 platform. The raw re-sequencing data, consisting of 100 million (M) paired-end 150 bp (PE150) reads, were divided into simulated datasets with eight different data sizes (5 M, 10 M, 15 M, 20 M, 30 M, 50 M, 75 M, 100 M) and five different read lengths (single-end 50 bp (SE50), SE75, SE100, PE100, and PE150). Both Kraken2 and IDseq bioinformatics pipelines were employed to analyze the previously diagnosed pathogens in the simulated data. Detection of pathogens was based on read counts ranging from 1 to 10 and RPM values ranging from 0.2 to 2. Results Our results revealed that increasing dataset sizes and read lengths can enhance the performance of mNGS in pathogen detection. However, a larger data sizes for mNGS require higher economic costs and longer turnaround time for data analysis. Our findings indicate 20 M reads being sufficient for SE75 mode to achieve high recall rates. Additionally, high nucleic acid loads in samples can lead to increased stability in pathogen detection efficiency, reducing the impact of sequencing strategies. The choice of bioinformatics pipelines had a significant impact on recall rates achieved in pathogen detection. Conclusions Increasing dataset sizes and read lengths can enhance the performance of mNGS in pathogen detection but increase the economic and time costs of sequencing and data analysis. Currently, the 20 M reads in SE75 mode may be the best sequencing option.
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Affiliation(s)
- Ziyang Li
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
- Center for Clinical Molecular Diagnostics, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Zhe Guo
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
- Center for Clinical Molecular Diagnostics, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Weimin Wu
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
- Center for Clinical Molecular Diagnostics, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Li Tan
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
- Center for Clinical Molecular Diagnostics, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Qichen Long
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
- Center for Clinical Molecular Diagnostics, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Han Xia
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Min Hu
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
- Center for Clinical Molecular Diagnostics, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
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Wei E, Niu J, Zhang M, Zhang Y, Yan K, Fang X, Ma W, Xie L, Jia P, Wang H. Metagenomic next-generation sequencing could play a pivotal role in validating the diagnosis of invasive mold disease of the central nervous system. Front Cell Infect Microbiol 2024; 14:1393242. [PMID: 38912204 PMCID: PMC11190073 DOI: 10.3389/fcimb.2024.1393242] [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: 02/28/2024] [Accepted: 05/10/2024] [Indexed: 06/25/2024] Open
Abstract
Background Invasive mold diseases of the central nervous (CNS IMD) system are exceedingly rare disorders, characterized by nonspecific clinical symptoms. This results in significant diagnostic challenges, often leading to delayed diagnosis and the risk of misdiagnosis for patients. Metagenomic Next-Generation Sequencing (mNGS) holds significant importance for the diagnosis of infectious diseases, especially in the rapid and accurate identification of rare and difficult-to-culture pathogens. Therefore, this study aims to explore the clinical characteristics of invasive mold disease of CNS IMD in children and assess the effectiveness of mNGS technology in diagnosing CNS IMD. Methods Three pediatric patients diagnosed with Invasive mold disease brain abscess and treated in the Pediatric Intensive Care Unit (PICU) of the First Affiliated Hospital of Zhengzhou University from January 2020 to December 2023 were selected for this study. Results Case 1, a 6-year-old girl, was admitted to the hospital with "acute liver failure." During her hospital stay, she developed fever, irritability, and seizures. CSF mNGS testing resulted in a negative outcome. Multiple brain abscesses were drained, and Aspergillus fumigatus was detected in pus culture and mNGS. The condition gradually improved after treatment with voriconazole combined with caspofungin. Case 2, a 3-year-old girl, was admitted with "acute B-lymphoblastic leukemia." During induction chemotherapy, she developed fever and seizures. Aspergillus fumigatus was detected in the intracranial abscess fluid by mNGS, and the condition gradually improved after treatment with voriconazole combined with caspofungin, followed by "right-sided brain abscess drainage surgery." Case 3, a 7-year-old girl, showed lethargy, fever, and right-sided limb weakness during the pending chemotherapy period for acute B-lymphoblastic leukemia. Rhizomucor miehei and Rhizomucor pusillus was detected in the cerebrospinal fluid by mNGS. The condition gradually improved after treatment with amphotericin B combined with posaconazole. After a six-month follow-up post-discharge, the three patients improved without residual neurological sequelae, and the primary diseases were in complete remission. Conclusion The clinical manifestations of CNS IMD lack specificity. Early mNGS can assist in identifying the pathogen, providing a basis for definitive diagnosis. Combined surgical treatment when necessary can help improve prognosis.
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Affiliation(s)
- Erhu Wei
- Department of Pediatrics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Zou YS, Cao ZL, Guo Y, Wang BB, Wang JL, Cheng R, Yang Y, Zhou XG. The application value of metagenomic next-generation sequencing technology in the diagnosis and treatment of neonatal infectious meningitis - a single center retrospective case-control study. Neurol Res 2024; 46:561-567. [PMID: 38563313 DOI: 10.1080/01616412.2024.2337523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 03/26/2024] [Indexed: 04/04/2024]
Abstract
OBJECTIVE This retrospective study was conducted to investigate the application value of metagenomics next generation sequencing (mNGS) technology in the diagnosis and treatment of neonatal infectious meningitis. METHODS From 1 January 2020 to 31 December 2022, 73 newborns suspected of infectious meningitis were hospitalized. After screening by inclusion and exclusion criteria, 69 newborns were subsequently included in the study, containing 27 cases with positive mNGS result and 42 cases with negative mNGS result. Furthermore, according to the diagnosis of meningitis, mNGS positive group and mNGS negative group were further divided into infectious meningitis with mNGS (+) group (n = 27) and infectious meningitis with mNGS (-) group (n = 26), respectively. RESULTS (1) Compared with cerebrospinal fluid (CSF) culture, mNGS has better diagnostic value [positive predictive value (PPV) = 100.00% (27/27), negative predictive value (NPV) = 38.10% (16/42), agreement rate = 62.32% (43/69), area under the curve (AUC) = 0.750, 95% confidence interval (CI): 0.636-0.864]. (2) There were significant differences in the onset age, age at first CSF test, CSF leukocyte count, CSF glucose, positive rate of CSF culture, blood leukocyte count, procalcitonin (PCT), C-reaction protein (CRP), age at first mNGS test and adjusting anti-infective medication in the comparison between infectious meningitis with mNGS (+) group and infectious meningitis with mNGS (-) group (p < 0.05). (3) mNGS could help improve the cure rate [crude odds ratio (OR) = 3.393, 95%CI: 1.072-10.737; adjusted OR = 15.580, 95%CI: 2.114-114.798]. CONCLUSION Compared with classic meningitis detection methods, mNGS has better PPV, NPV, agreement rate, and AUC. mNGS could help improve the cure rate.
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Affiliation(s)
- Yun-Su Zou
- Department of Neonates, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu, P.R. China
| | - Zhao-Lan Cao
- Department of Neonates, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu, P.R. China
| | - Yan Guo
- Department of Neonates, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu, P.R. China
| | - Bei-Bei Wang
- Department of Neonates, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu, P.R. China
| | - Jia-Li Wang
- Department of Neonates, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu, P.R. China
| | - Rui Cheng
- Department of Neonates, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu, P.R. China
| | - Yang Yang
- Department of Neonates, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu, P.R. China
| | - Xiao-Guang Zhou
- Department of Neonates, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu, P.R. China
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Liu Y, Ma Y. Clinical applications of metagenomics next-generation sequencing in infectious diseases. J Zhejiang Univ Sci B 2024; 25:471-484. [PMID: 38910493 PMCID: PMC11199093 DOI: 10.1631/jzus.b2300029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 06/06/2023] [Indexed: 05/23/2024]
Abstract
Infectious diseases are a great threat to human health. Rapid and accurate detection of pathogens is important in the diagnosis and treatment of infectious diseases. Metagenomics next-generation sequencing (mNGS) is an unbiased and comprehensive approach for detecting all RNA and DNA in a sample. With the development of sequencing and bioinformatics technologies, mNGS is moving from research to clinical application, which opens a new avenue for pathogen detection. Numerous studies have revealed good potential for the clinical application of mNGS in infectious diseases, especially in difficult-to-detect, rare, and novel pathogens. However, there are several hurdles in the clinical application of mNGS, such as: (1) lack of universal workflow validation and quality assurance; (2) insensitivity to high-host background and low-biomass samples; and (3) lack of standardized instructions for mass data analysis and report interpretation. Therefore, a complete understanding of this new technology will help promote the clinical application of mNGS to infectious diseases. This review briefly introduces the history of next-generation sequencing, mainstream sequencing platforms, and mNGS workflow, and discusses the clinical applications of mNGS to infectious diseases and its advantages and disadvantages.
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Affiliation(s)
- Ying Liu
- Department of Clinical Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua 321000, China
| | - Yongjun Ma
- Department of Clinical Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua 321000, China.
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Nurmukanova V, Matsvay A, Gordukova M, Shipulin G. Square the Circle: Diversity of Viral Pathogens Causing Neuro-Infectious Diseases. Viruses 2024; 16:787. [PMID: 38793668 PMCID: PMC11126052 DOI: 10.3390/v16050787] [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: 03/27/2024] [Revised: 05/08/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
Neuroinfections rank among the top ten leading causes of child mortality globally, even in high-income countries. The crucial determinants for successful treatment lie in the timing and swiftness of diagnosis. Although viruses constitute the majority of infectious neuropathologies, diagnosing and treating viral neuroinfections remains challenging. Despite technological advancements, the etiology of the disease remains undetermined in over half of cases. The identification of the pathogen becomes more difficult when the infection is caused by atypical pathogens or multiple pathogens simultaneously. Furthermore, the modern surge in global passenger traffic has led to an increase in cases of infections caused by pathogens not endemic to local areas. This review aims to systematize and summarize information on neuroinvasive viral pathogens, encompassing their geographic distribution and transmission routes. Emphasis is placed on rare pathogens and cases involving atypical pathogens, aiming to offer a comprehensive and structured catalog of viral agents with neurovirulence potential.
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Affiliation(s)
- Varvara Nurmukanova
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, 119121 Moscow, Russia
| | - Alina Matsvay
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, 119121 Moscow, Russia
| | - Maria Gordukova
- G. Speransky Children’s Hospital No. 9, 123317 Moscow, Russia
| | - German Shipulin
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, 119121 Moscow, Russia
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Cai S, Pan J, Wang S, Bao R, Zhou C, Gao X, Shiiya H, Hu B. Accurate etiological diagnosis of Mycoplasma hominis mediastinitis in immunocompetent patients using metagenomic next-generation sequencing: a case series and literature review. J Thorac Dis 2024; 16:2499-2509. [PMID: 38738251 PMCID: PMC11087618 DOI: 10.21037/jtd-24-286] [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: 02/22/2024] [Accepted: 04/07/2024] [Indexed: 05/14/2024]
Abstract
Background As a culture-independent method, metagenomic next-generation sequencing (mNGS) is widely used in microbiological diagnosis with advantages in identifying potential pathogens, guiding antibiotic therapy, and improving clinical prognosis, especially in culture-negative cases. Mycoplasma hominis (M. hominis) mediastinitis is a rare and severe disease for which etiological diagnosis is important but challenging. The application of mNGS in the etiological diagnosis of mediastinitis has seldom been studied. Methods By searching the electronic medical history retrieval system with "Mycoplasma hominis" and "mediastinitis", seven patients diagnosed with M. hominis mediastinitis were reviewed in Zhongshan Hospital, Fudan University, Shanghai from 9 December 2020 to 14 February 2023. Microbiological cultures and mNGS were conducted for blood, abscess, and/or mediastinal fluid. Adjustment of the antibiotic therapy due to mNGS was assessed. A literature review was conducted in the PubMed database beginning in 1970 for M. hominis infection and mediastinitis. Results For the seven patients, cultures of blood, abscess, and mediastinal fluid were negative whereas mNGS identified M. hominis in serum, abscess, and/or mediastinal fluid and was used to guide specific antibiotic therapy. The stringent mapped reads number of genera (SMRNG), stringent mapped reads number of species (SMRN), and coverage rate of M. hominis detection by mNGS were significantly higher in body fluid (abscess or mediastinal fluid) than in serum. All seven patients had underlying heart diseases and underwent previous cardiac surgery. The most common symptoms were fever and sternal pain. After detection of M. hominis, antibiotics were adjusted to quinolones or doxycycline except for one patient, whose diagnosis was clarified after death. Two patients died. Literature review since 1970 identified 30 cases of extra-genital infection caused by M. hominis. Including our seven new cases, 2 (5.4%) were neonates and 35 (94.6%) were adults. Thirty (81.1%) cases were postoperative infection and 15 (40.5%) had implanted devices. Five patients (13.5%) died. Conclusions mNGS might be a promising technology in the detection of fastidious pathogens such as M. hominis. Accurate etiological diagnosis by mNGS could guide antibiotic therapy and facilitate clinical management.
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Affiliation(s)
- Sishi Cai
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jue Pan
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Suzhen Wang
- Department of Microbiology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Rong Bao
- Department of Microbiology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chunmei Zhou
- Department of Microbiology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xiaodong Gao
- Department of Hospital Infection Management, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Haruhiko Shiiya
- Department of Thoracic Surgery, Hokkaido University Hospital, Sapporo, Japan
| | - Bijie Hu
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
- Department of Hospital Infection Management, Zhongshan Hospital, Fudan University, Shanghai, China
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12
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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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Zou H, Gao S, Liu X, Liu Y, Xiao Y, Li A, Jiang Y. Combination of metagenomic next-generation sequencing and conventional tests unraveled pathogen profiles in infected patients undergoing allogeneic hematopoietic stem cell transplantation in Jilin Province of China. Front Cell Infect Microbiol 2024; 14:1378112. [PMID: 38567023 PMCID: PMC10985322 DOI: 10.3389/fcimb.2024.1378112] [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: 01/29/2024] [Accepted: 03/06/2024] [Indexed: 04/04/2024] Open
Abstract
Background Infection is the main cause of death for patients after allogeneic hematopoietic stem cell transplantation (HSCT). However, pathogen profiles still have not been reported in detail due to their heterogeneity caused by geographic region. Objective To evaluate the performance of metagenomic next-generation sequencing (mNGS) and summarize regional pathogen profiles of infected patients after HSCT. Methods From February 2021 to August 2022, 64 patients, admitted to the Department of Hematology of The First Hospital of Jilin University for HSCT and diagnosed as suspected infections, were retrospectively enrolled. Results A total of 38 patients were diagnosed as having infections, including bloodstream (n =17), pulmonary (n =16), central nervous system (CNS) (n =4), and chest (n =1) infections. Human betaherpesvirus 5 (CMV) was the most common pathogen in both bloodstream (n =10) and pulmonary (n =8) infections, while CNS (n =2) and chest (n =1) infections were mainly caused by Human gammaherpesvirus 4 (EBV). For bloodstream infection, Mycobacterium tuberculosis complex (n =3), Staphylococcus epidermidis (n =1), and Candida tropicalis (n =1) were also diagnosed as causative pathogens. Furthermore, mNGS combined with conventional tests can identify more causative pathogens with high sensitivity of 82.9% (95% CI 70.4-95.3%), and the total coincidence rate can reach up to 76.7% (95% CI 64.1-89.4%). Conclusions Our findings emphasized the importance of mNGS in diagnosing, managing, and ruling out infections, and an era of more rapid, independent, and impartial diagnosis of infections after HSCT can be expected.
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Affiliation(s)
- Hongyan Zou
- Key Laboratory of Organ Regeneration & Transplantation of the Ministry of Education, Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, China
| | - Sujun Gao
- Department of Hematology, The First Hospital of Jilin University, Changchun, China
| | - Xiaoliang Liu
- Department of Hematology, The First Hospital of Jilin University, Changchun, China
| | - Yong Liu
- Key Laboratory of Organ Regeneration & Transplantation of the Ministry of Education, Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, China
| | - Yunping Xiao
- Key Laboratory of Organ Regeneration & Transplantation of the Ministry of Education, Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, China
| | - Ao Li
- Key Laboratory of Organ Regeneration & Transplantation of the Ministry of Education, Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, China
| | - Yanfang Jiang
- Key Laboratory of Organ Regeneration & Transplantation of the Ministry of Education, Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, 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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Yuan H, Ma X, Xu J, Han P, Rao G, Chen G, Zhang K, Yang R, Han C, Jiang M. Application of metagenomic next-generation sequencing in the clinical diagnosis of infectious diseases after allo-HSCT: a single-center analysis. BMC Infect Dis 2024; 24:279. [PMID: 38438967 PMCID: PMC10910774 DOI: 10.1186/s12879-024-09153-y] [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: 05/11/2023] [Accepted: 02/19/2024] [Indexed: 03/06/2024] Open
Abstract
BACKGROUND We investigated the value of metagenomic next-generation sequencing (mNGS) in diagnosing infectious diseases in patients receiving allogeneic hematopoietic stem cell transplantation (allo-HSCT). METHODS Fifty-four patients who had fever following allo-HSCT from October 2019 to February 2022 were enrolled. Conventional microbiological tests (CMTs) and mNGS, along with imaging and clinical manifestations, were used to diagnose infection following allo-HSCT. The clinical diagnostic value of mNGS was evaluated. RESULTS A total of 61 mNGS tests were performed, resulting in the diagnosis of 46 cases of infectious diseases. Among these cases, there were 22 cases of viral infection, 13 cases of fungal infection, and 11 cases of bacterial infection. Moreover, 27 cases (58.7%) were classified as bloodstream infections, 15 (32.6%) as respiratory infections, 2 (4.3%) as digestive system infections, and 2 (4.3%) as central nervous system infections. Additionally, there were 8 cases with non-infectious diseases (8/54, 14.81%), including 2 cases of interstitial pneumonia, 2 cases of bronchiolitis obliterans, 2 cases of engraftment syndrome, and 2 cases of acute graft-versus-host disease. The positive detection rates of mNGS and CMT were 88.9% and 33.3%, respectively, with significant differences (P < 0.001). The sensitivity of mNGS was 97.82%, the specificity was 25%, the positive predictive value was 93.75%, and the negative predictive value was 50%. Following treatment, 51 patients showed improvement, and 3 cases succumbed to multidrug-resistant bacterial infections. CONCLUSIONS mNGS plays an important role in the early clinical diagnosis of infectious diseases after allo-HSCT, which is not affected by immunosuppression status, empiric antibiotic therapy, and multi-microbial mixed infection.
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Affiliation(s)
- Hailong Yuan
- Hematology Center, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang Institute of Hematology, No.137 Liyushan South Road, Urumqi, 830054, China
| | - Xiaolu Ma
- Department of Hematology, Guangyuan Central Hospital, Guangyuan, Sichuan Province, China
| | - Jianli Xu
- Hematology Center, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang Institute of Hematology, No.137 Liyushan South Road, Urumqi, 830054, China
| | - Peng Han
- Genskey Medical Technology Co., Ltd, Beijing, China
| | - Guanhua Rao
- Genskey Medical Technology Co., Ltd, Beijing, China
| | - Gang Chen
- Hematology Center, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang Institute of Hematology, No.137 Liyushan South Road, Urumqi, 830054, China
| | - Kaile Zhang
- Hematology Center, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang Institute of Hematology, No.137 Liyushan South Road, Urumqi, 830054, China
| | - Ruixue Yang
- Hematology Center, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang Institute of Hematology, No.137 Liyushan South Road, Urumqi, 830054, China
| | - Chuixia Han
- Hematology Center, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang Institute of Hematology, No.137 Liyushan South Road, Urumqi, 830054, China
| | - Ming Jiang
- Hematology Center, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang Institute of Hematology, No.137 Liyushan South Road, Urumqi, 830054, China.
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Tian Y, Duan Y, Gao R, Gao W, Xu S, Wang S, Li F, Fang F, Su R, Chen Y, Xu N, Li W, Zhang L, Zhou JX. DIAGNOSTIC PERFORMANCE OF CENTRAL NERVOUS SYSTEM INFECTIONS IN PATIENTS WITH NEUROSURGICAL INTENSIVE CARE USING METAGENOMIC NEXT-GENERATION SEQUENCING: A PROSPECTIVE OBSERVATIONAL STUDY. Shock 2024; 61:375-381. [PMID: 38517267 DOI: 10.1097/shk.0000000000002320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Abstract
ABSTRACT Background. Identifying the causative pathogens of central nervous system infections (CNSIs) is crucial, but the low detection rate of traditional culture methods in cerebrospinal fluid (CSF) has made the pathogenic diagnosis of CNSIs a longstanding challenge. Patients with CNSIs after neurosurgery often overlap with inflammatory and bleeding. Metagenomic next-generation sequencing (mNGS) has shown some benefits in pathogen detection. This study aimed to investigate the diagnostic performance of mNGS in the etiological diagnosis of CNSIs in patients after neurosurgery. Methods. In this prospective observational study, we enrolled patients with suspected CNSIs after neurosurgical operations who were admitted to the intensive care unit of Beijing Tiantan Hospital. All enrolled patients' CSF was tested using mNGS and pathogen culture. According to comprehensive clinical diagnosis, the enrolled patients were divided into CNSIs group and non-CNSIs group to compare the diagnostic efficiency of mNGS and pathogen culture. Results. From December 2021 to March 2023, 139 patients were enrolled while 66 in CNSIs group and 73 in non-CNSIs. The mNGS exceeded culture in the variety and quantity of pathogens detected. The mNGS outperformed traditional pathogen culture in terms of positive percent agreement (63.63%), accuracy (82.01%), and negative predictive value (75.00%), with statistically significant differences ( P < 0.05) for traditional pathogen culture. The mNGS also detected bacterial spectrum and antimicrobial resistance genes. Conclusions. Metagenomics has the potential to assist in the diagnosis of patients with CNSIs who have a negative culture.
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Affiliation(s)
- Ying Tian
- Department of Critical Care Medicine, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yuqing Duan
- Department of Critical Care Medicine, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Ran Gao
- Department of Critical Care Medicine, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Wei Gao
- Department of Microbiology and Immunology, Peter Doherty Institute, University of Melbourne, Melbourne, Australia
| | - Shanshan Xu
- Department of Critical Care Medicine, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Shuya Wang
- Department of Critical Care Medicine, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Fangqiang Li
- Department of Clinical Diagnosis, Laboratory of Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | | | - Rui Su
- Department of Critical Care Medicine, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yuqing Chen
- Department of Critical Care Medicine, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Ningyuan Xu
- Department of Critical Care Medicine, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | | | - Linlin Zhang
- Department of Critical Care Medicine, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Jian-Xin Zhou
- Beijing Shijitan Hospital, Capital Medical University, Beijing, China
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Zhang H, Liang R, Zhu Y, Hu L, Xia H, Li J, Ye Y. Metagenomic next-generation sequencing of plasma cell-free DNA improves the early diagnosis of suspected infections. BMC Infect Dis 2024; 24:187. [PMID: 38347444 PMCID: PMC10863141 DOI: 10.1186/s12879-024-09043-3] [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: 07/20/2023] [Accepted: 01/22/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND Metagenomic next-generation sequencing (mNGS) could improve the diagnosed efficiency of pathogens in bloodstream infections or sepsis. Little is known about the clinical impact of mNGS test when used for the early diagnosis of suspected infections. Herein, our main objective was to assess the clinical efficacy of utilizing blood samples to perform mNGS for early diagnosis of suspected infections, as well as to evaluate its potential in guiding antimicrobial therapy decisions. METHODS In this study, 212 adult hospitalized patients who underwent blood mNGS test in the early stage of suspected infections were enrolled. Diagnostic efficacy of mNGS test and blood culture was compared, and the clinical impact of mNGS on clinical care was analyzed. RESULTS In our study, the total detection rate of blood mNGS was significantly higher than that of culture method (74.4% vs. 12.1%, P < 0.001) in the paired mNGS test and blood culture. Blood stream infection (107, 67.3%) comprised the largest component of all the diseases in our patients, and the detection rate of single blood sample subgroup was similar with that of multiple type of samples subgroup. Among the 187 patients complained with fever, there was no difference in the diagnostic efficacy of mNGS when blood specimens or additional other specimens were used in cases presenting only with fever. While, when patients had other symptoms except fever, the performance of mNGS was superior in cases with specimens of suspected infected sites and blood collected at the same time. Guided by mNGS results, therapeutic regimens for 70.3% cases (149/212) were changed, and the average hospitalized days were significantly shortened in cases with the earlier sampling time of admission. CONCLUSION In this study, we emphasized the importance of blood mNGS in early infectious patients with mild and non-specific symptoms. Blood mNGS can be used as a supplement to conventional laboratory examination, and should be performed as soon as possible to guide clinicians to perform appropriate anti-infection treatment timely and effectively. Additionally, combining the contemporaneous samples from suspected infection sites could improve disease diagnosis and prognoses. Further research needs to be better validated in large-scale clinical trials to optimize diagnostic protocol, and the cost-utility analysis should be performed.
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Affiliation(s)
- Hui Zhang
- Department of Infectious Diseases, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Ruobing Liang
- Department of Scientific Affaires, Hugobiotech Co., Ltd, Beijing, China
| | - Yunzhu Zhu
- Department of Infectious Diseases, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Lifen Hu
- Department of Infectious Diseases, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Han Xia
- Department of Scientific Affaires, Hugobiotech Co., Ltd, Beijing, China.
| | - Jiabin Li
- Department of Infectious Diseases, The First Affiliated Hospital of Anhui Medical University, Hefei, China.
- Institute of Bacterial Resistance, Anhui Medical University, Hefei, China.
- Anhui Center for Surveillance of Bacterial Resistance, Hefei, China.
| | - Ying Ye
- Department of Infectious Diseases, The First Affiliated Hospital of Anhui Medical University, Hefei, China.
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Zhang H, Zhou F, Liu X, Huang J. Clinical application of metagenomic next-generation sequencing in patients with different organ system infection: A retrospective observational study. Medicine (Baltimore) 2024; 103:e36745. [PMID: 38277518 PMCID: PMC10817116 DOI: 10.1097/md.0000000000036745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 11/30/2023] [Indexed: 01/28/2024] Open
Abstract
Microbiological identification is essential for appropriate treatment, but conventional methods are time-consuming and have a low sensitivity. In contrast, metagenomic next-generation sequencing (mNGS) is a culture-free and hypothesis-free technique that can detect a wide array of potential pathogens. This study aimed to reveal the overall diagnostic value of mNGS for infectious diseases of different organ systems and compare the sensitivity and specificity of mNGS with conventional methods. In a retrospective cohort study, 94 patients with mNGS results were enrolled, and clinical data were recorded and analyzed to compare the positive rate of mNGS with traditional methods including as smears, serological tests, and traditional PCR, etc. In this study, mNGS and culture were both positive in 12.77% cases and were both negative in 23.4% cases. There were positive results in 56 cases (54.26%) only by mNGS and 4 cases (4.26%) were positive only by culture. There were significant differences in sensitivity of pathogen detection between of ID and NID group for mNGS (χ2 = 10.461, P = .001)and conventional methods(χ2 = 7.963, P = .005). The positive predictive values and negative predictive values of diagnosing infectious disease by mNGS were 94.12% and 30.77%, respectively. mNGS increased the sensitivity rate by approximately 53.66% compared with that of culture (78.05% vs24.39%; χ2 = 47.248, P < .001) and decreased the specificity rate by 12.5% compared with that of culture (66.67% vs 100.0%; χ2 = 4.8, P = .028). mNGS can identify emerging or rare pathogen and further guide treatment regimens. mNGS has advantages in identifying overall pathogens and bacteria, however, there was no obvious advantage in identifying fungi, virus and tuberculosis. mNGS has higher specificity than conventional methods in identifying pathogens and advantages in detecting emerging or rare pathogens.
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Affiliation(s)
- Haiyan Zhang
- Department of General Practice, The Third Affiliated Hospital of Sun Yat-Sen University Lingnan Hospital, Guangzhou, Guangdong Province, People’s Republic of China
| | - Fengli Zhou
- Department of General Practice, The Third Affiliated Hospital of Sun Yat-Sen University Lingnan Hospital, Guangzhou, Guangdong Province, People’s Republic of China
| | - Xiaoyun Liu
- Department of General Practice, The Third Affiliated Hospital of Sun Yat-Sen University Lingnan Hospital, Guangzhou, Guangdong Province, People’s Republic of China
| | - Jiabao Huang
- Department of General Practice, The Third Affiliated Hospital of Sun Yat-Sen University Lingnan Hospital, Guangzhou, Guangdong Province, People’s Republic of China
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Xiao YH, Luo ZX, Wu HW, Xu DR, Zhao R. Metagenomic next-generation sequencing for the identification of infections caused by Gram-negative pathogens and the prediction of antimicrobial resistance. Lab Med 2024; 55:71-79. [PMID: 37253164 DOI: 10.1093/labmed/lmad039] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023] Open
Abstract
OBJECTIVE The aim of this study was to evaluate the efficacy of metagenomic next-generation sequencing (mNGS) for the identification of Gram-negative bacteria (GNB) infections and the prediction of antimicrobial resistance. METHODS A retrospective analysis was conducted on 182 patients with diagnosis of GNB infections who underwent mNGS and conventional microbiological tests (CMTs). RESULTS The detection rate of mNGS was 96.15%, higher than CMTs (45.05%) with a significant difference (χ 2 = 114.46, P < .01). The pathogen spectrum identified by mNGS was significantly wider than CMTs. Interestingly, the detection rate of mNGS was substantially higher than that of CMTs (70.33% vs 23.08%, P < .01) in patients with but not without antibiotic exposure. There was a significant positive correlation between mapped reads and pro-inflammatory cytokines (interleukin-6 and interleukin-8). However, mNGS failed to predict antimicrobial resistance in 5 of 12 patients compared to phenotype antimicrobial susceptibility testing results. CONCLUSIONS Metagenomic next-generation sequencing has a higher detection rate, a wider pathogen spectrum, and is less affected by prior antibiotic exposure than CMTs in identifying Gram-negative pathogens. The mapped reads may reflect a pro-inflammatory state in GNB-infected patients. Inferring actual resistance phenotypes from metagenomic data remains a great challenge.
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Affiliation(s)
- Yang-Hua Xiao
- Department of Clinical Laboratory, Medical Center of Burn Plastic and Wound Repair, The First Affiliated Hospital of Nanchang University, Nanchang, China
- School of Public Health, Nanchang University, Nanchang, China
| | - Zhao-Xia Luo
- School of Public Health, Nanchang University, Nanchang, China
| | - Hong-Wen Wu
- Department of Medical Instruments, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - De-Rong Xu
- Department of Clinical Laboratory, Medical Center of Burn Plastic and Wound Repair, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Rui Zhao
- Department of Clinical Laboratory, Medical Center of Burn Plastic and Wound Repair, The First Affiliated Hospital of Nanchang University, Nanchang, China
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Overbeek R, Leitl CJ, Stoll SE, Wetsch WA, Kammerer T, Mathes A, Böttiger BW, Seifert H, Hart D, Dusse F. The Value of Next-Generation Sequencing in Diagnosis and Therapy of Critically Ill Patients with Suspected Bloodstream Infections: A Retrospective Cohort Study. J Clin Med 2024; 13:306. [PMID: 38256440 PMCID: PMC10816005 DOI: 10.3390/jcm13020306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 12/30/2023] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
Bloodstream infection (BSI), a frequent cause of severe sepsis, is a life-threatening complication in critically ill patients and still associated with a high mortality rate. Rapid pathogen identification from blood is crucial for an early diagnosis and the treatment of patients with suspected BSI. For this purpose, novel diagnostic tools on the base of genetic analysis have emerged for clinical application. The aim of this study was to assess the diagnostic value of additional next-generation sequencing (NGS) pathogen test for patients with suspected BSI in a surgical ICU and its potential impact on antimicrobial therapy. In this retrospective single-centre study, clinical data and results from blood culture (BC) and NGS pathogen diagnostics were analysed for ICU patients with suspected BSI. Consecutive changes in antimicrobial therapy and diagnostic procedures were evaluated. Results: 41 cases with simultaneous NGS and BC sampling were assessed. NGS showed a statistically non-significant higher positivity rate than BC (NGS: 58.5% (24/41 samples) vs. BC: 21.9% (9/41); p = 0.056). NGS detected eight different potentially relevant bacterial species, one fungus and six different viruses, whereas BC detected four different bacterial species and one fungus. NGS results affected antimicrobial treatment in 7.3% of cases. Conclusions: NGS-based diagnostics have the potential to offer a higher positivity rate than conventional culture-based methods in patients with suspected BSI. Regarding the high cost, their impact on anti-infective therapy is currently limited. Larger randomized prospective clinical multicentre studies are required to assess the clinical benefit of this novel diagnostic technology.
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Affiliation(s)
- Remco Overbeek
- Department of Anaesthesiology and Intensive Care Medicine, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Christoph J. Leitl
- Department of Anaesthesiology and Intensive Care Medicine, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Sandra E. Stoll
- Department of Anaesthesiology and Intensive Care Medicine, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Wolfgang A. Wetsch
- Department of Anaesthesiology and Intensive Care Medicine, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Tobias Kammerer
- Department of Anaesthesiology and Intensive Care Medicine, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Alexander Mathes
- Department of Anaesthesiology and Intensive Care Medicine, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Bernd W. Böttiger
- Department of Anaesthesiology and Intensive Care Medicine, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Harald Seifert
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50935 Cologne, Germany
| | - Dominique Hart
- Department of Anaesthesiology and Intensive Care Medicine, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Fabian Dusse
- Department of Anaesthesiology and Intensive Care Medicine, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
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Cui M, Sun W, Xue Y, Yang J, Xu T. Hepatitis E virus and Klebsiella pneumoniae co-infection detected by metagenomics next-generation sequencing in a patient with central nervous system and bloodstream Infection: a case report. BMC Infect Dis 2024; 24:33. [PMID: 38166638 PMCID: PMC10763291 DOI: 10.1186/s12879-023-08850-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 11/27/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Hepatitis E virus (HEV) is the most common cause of acute viral hepatitis worldwide with major prevalence in the developing countries and can cause extrahepatic disease including the nervous system. Central nervous system infections caused by HEV are rare and caused by HEV together with other bacteria are even rarer. CASE PRESENTATION A 68-year-old man was admitted to the hospital due to a headache lasting for 6 days and a fever for 3 days. Lab tests showed significantly raised indicators of inflammation, cloudy cerebrospinal fluid, and liver dysfunction. Hepatitis E virus and Klebsiella pneumoniae were identified in the blood and cerebrospinal fluid using metagenomic next-generation sequencing. The patient received meropenem injection to treat K. pneumoniae infection, isoglycoside magnesium oxalate injection and polyene phosphatidylcholine injection for liver protection. After ten days of treatment, the patient improved and was discharged from the hospital. CONCLUSION Metagenomic next-generation sequencing, which can detect various types of microorganisms, is powerful for identifying complicated infections.
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Affiliation(s)
- Manman Cui
- Department of Infectious Diseases, the Third People's Hospital of Changzhou, Changzhou, China.
| | - Wei Sun
- Department of Infectious Diseases, the Third People's Hospital of Changzhou, Changzhou, China
| | - Yuan Xue
- Department of Science and Education, the Third People's Hospital of Changzhou, Changzhou, China
| | - Jiangnan Yang
- Department of Medicine, Dinfectome Inc, Nanjing, China
| | - Tianmin Xu
- Department of Infectious Diseases, the Third People's Hospital of Changzhou, Changzhou, China
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22
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Tian Y, Gao R, Wang Y, Zhou Y, Xu S, Duan Y, Lv W, Wang S, Hou M, Chen Y, Li F, Gao W, Zhang L, Zhou JX. Economic impact of metagenomic next-generation sequencing versus traditional bacterial culture for postoperative central nervous system infections using a decision analysis mode: study protocol for a randomized controlled trial. mSystems 2023; 8:e0058123. [PMID: 37937972 PMCID: PMC10734456 DOI: 10.1128/msystems.00581-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 09/26/2023] [Indexed: 11/09/2023] Open
Abstract
IMPORTANCE Diagnosing and treating postoperative central nervous system infections (PCNSIs) remains challenging due to the low detection rate and time-consuming nature of traditional methods for identifying microorganisms in cerebrospinal fluid. Metagenomic next-generation sequencing (mNGS) technology provides a rapid and comprehensive understanding of microbial composition in PCNSIs by swiftly sequencing and analyzing the microbial genome. The current study aimed to assess the economic impact of using mNGS versus traditional bacterial culture-directed PCNSIs diagnosis and therapy in post-neurosurgical patients from Beijing Tiantan Hospital. mNGS is a relatively expensive test item, and whether it has the corresponding health-economic significance in the clinical application of diagnosing intracranial infection has not been studied clearly. Therefore, the investigators hope to explore the clinical application value of mNGS detection in PCNSIs after neurosurgery.
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Affiliation(s)
- Ying Tian
- Department of Critical Care Medicine, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Ran Gao
- Department of Critical Care Medicine, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yumei Wang
- Department of Critical Care Medicine, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yimin Zhou
- Department of Critical Care Medicine, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Shanshan Xu
- Department of Critical Care Medicine, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yuqing Duan
- Department of Critical Care Medicine, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Wenyi Lv
- Department of Critical Care Medicine, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Shuya Wang
- Department of Critical Care Medicine, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Mengxue Hou
- Department of Critical Care Medicine, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yuqing Chen
- Department of Critical Care Medicine, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Fangqiang Li
- Department of Clinical Diagnosis, Laboratory of Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Wei Gao
- Department of Microbiology and Immunology, Peter Doherty Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Linlin Zhang
- Department of Critical Care Medicine, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Beijing Engineering Research Center of Digital Healthcare for Neurological Diseases, Beijing, China
| | - Jian-Xin Zhou
- Department of Critical Care Medicine, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Beijing Engineering Research Center of Digital Healthcare for Neurological Diseases, Beijing, China
- Beijing Shijitan Hospital, Capital Medical University, Beijing, China
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23
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Fu Z, Ai J, Zhang H, Cui P, Xu T, Zhang Y, Zhang Y, Wu H, Shen A, Lin K, Zhang M, Qiu C, Jiang N, Zhou Y, Zhang W. Pathogen quantitative efficacy of different spike-in internal controls and clinical application in central nervous system infection with metagenomic sequencing. Microbiol Spectr 2023; 11:e0113923. [PMID: 37982612 PMCID: PMC10714923 DOI: 10.1128/spectrum.01139-23] [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: 03/27/2023] [Accepted: 10/01/2023] [Indexed: 11/21/2023] Open
Abstract
IMPORTANCE Metagenomic next-generation sequencing (mNGS) has been used broadly for pathogens detection of infectious diseases. However, there is a lack of method for the absolute quantitation of pathogens by mNGS. We compared the quantitative efficiency of three mNGS internal controls (ICs) Thermus thermophilus, T1 phages, and artificial DNA sequence and developed the most applicable strategies for pathogen quantitation via mNGS in central nervous system infection. The IC application strategy we developed will enable mNGS analysis to assess the pathogen load simultaneously with the detection of pathogens, which should provide critical information for quick decision-making of treatment as well as clinical prognosis.
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Affiliation(s)
- Zhangfan Fu
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jingwen Ai
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Haocheng Zhang
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Peng Cui
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Tao Xu
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yumeng Zhang
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yi Zhang
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Honglong Wu
- BGI PathoGenesis Pharmaceutical Technology, BGI-Shenzhen, Shenzhen, China
| | - Ao Shen
- BGI PathoGenesis Pharmaceutical Technology, BGI-Shenzhen, Shenzhen, China
| | - Ke Lin
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Miaoqu Zhang
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chao Qiu
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ning Jiang
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yang Zhou
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wenhong Zhang
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Medical Molecular Virology (MOE/MOH), Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Huashen Institute of Microbes and Infections, Shanghai, China
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24
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Liu X, Wang J, Liu J, Li X, Guan Y, Qian S, Jia X. Cryptosporidiosis diagnosed using metagenomic next-generation sequencing in a healthy child admitted to pediatric intensive care unit: a case report. Front Cell Infect Microbiol 2023; 13:1269963. [PMID: 37965251 PMCID: PMC10641789 DOI: 10.3389/fcimb.2023.1269963] [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: 08/02/2023] [Accepted: 10/12/2023] [Indexed: 11/16/2023] Open
Abstract
Background Cryptosporidium infections in humans typically result in symptoms such as abdominal pain and diarrhea. When the diarrhea is severe, it can cause serious complications and even be life-threatening, especially in patients with compromised immune systems. Case presentation Here, we reported the use of metagenomic next-generation sequencing (mNGS) to assist in the diagnosis and treatment of a 10-year-old boy with severe Cryptosporidium infection. Despite the absence of any history of immunocompromise, the infection still resulted in severe symptoms, including shock, as well as damage to his pancreas and kidneys. The mNGS tests detected the presence of Cryptosporidium parvum when conventional methods failed. The patient received anti-parasite treatment along with supportive care to manage the condition. With disease surveillance based on regular clinical tests and sequential mNGS tests, the child recovered from the severe conditions. Conclusion Our study emphasized the importance of recognizing the potential severity of Cryptosporidium infection, even among individuals with normal immune systems. Timely diagnosis and ongoing monitoring are essential for patient prognosis.
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Affiliation(s)
- Xiaoyi Liu
- Pediatric Intensive Care Unit, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Jing Wang
- Department of Scientific Affairs, Hugobiotech Co., Ltd., Beijing, China
| | - Jun Liu
- Pediatric Intensive Care Unit, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Xuming Li
- Department of Scientific Affairs, Hugobiotech Co., Ltd., Beijing, China
| | - Yuanlin Guan
- Department of Scientific Affairs, Hugobiotech Co., Ltd., Beijing, China
| | - Suyun Qian
- Pediatric Intensive Care Unit, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Xinlei Jia
- Pediatric Intensive Care Unit, Beijing Children's Hospital, Capital Medical University, Beijing, China
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Shen H, Zhou H, Zhang F, Wang J, Wang R, Wang J. Case Report: Successful Treatment of Recurrent Candida Albicans Meningitis with Kimura's Disease Using Amphotericin B Colloidal Dispersion Combined with Fluconazole. Infect Drug Resist 2023; 16:6905-6909. [PMID: 37915503 PMCID: PMC10617790 DOI: 10.2147/idr.s416040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 10/13/2023] [Indexed: 11/03/2023] Open
Abstract
Background Candida albicans meningitis is a fungal infectious disease of the central nervous system that most often occurs in immunodeficient populations. Kimura's disease is an IgE-mediated inflammatory reactive disease that is a chronic immune disorder with predominantly lymph node, soft tissue, and salivary gland damage, the treatment of which is hormone-based. The combination of Kimura's disease with C. albicans meningitis is relatively uncommon. Herein, we report a case of C. albicans meningitis in combination with Kimura's disease. Case Presentation The case is a 26-year-old male with a medical history of Kimura, who presented with symptoms of dizziness, headache, and double vision. Lumbar puncture and cerebrospinal fluid examination revealed an increased white blood cell count. Further analysis through cerebrospinal fluid culture and metagenomic second-generation sequencing (mNGS) led to the final diagnosis of C. albicans meningitis. The patient was treated with fluconazole after the onset of C. albicans meningitis and had a good response. During the treatment, changes in the pathogen genome sequences were monitored dynamically using metagenomic next-generation sequencing. After 1 year, the patient had a recurrence of Candida meningitis. Treatment with fluconazole alone was ineffective, while antifungal treatment with amphotericin B colloidal dispersion was effective with no detectable renal injury. Conclusion Candida meningitis can occur in the context of Kimura disease. In patients with mild disease, the possibility of recurrence exists with fluconazole treatment alone, and the efficacy of amphotericin B colloidal dispersion combined with fluconazole is better than fluconazole alone in patients with a recurrence. No nephrotoxicity was observed during amphotericin B colloidal dispersion treatment. The mNGS allows dynamic monitoring of pathogen sequencing reads, and for Candida meningitis, there may be a mismatch between peak sequencing reads and disease during treatment, the basis for which is unclear.
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Affiliation(s)
- Huijun Shen
- Department of Neurology, The First Hospital, Shanxi Medical University, Taiyuan, Shanxi, People’s Republic of China
| | - Hong Zhou
- Graduate School of Shanxi Medical University, Taiyuan, Shanxi, People’s Republic of China
| | - Fang Zhang
- Department of Neurology, The First Hospital, Shanxi Medical University, Taiyuan, Shanxi, People’s Republic of China
| | - Jing Wang
- Department of Neurology, The First Hospital, Shanxi Medical University, Taiyuan, Shanxi, People’s Republic of China
| | - Rui Wang
- Department of Neurology, The First Hospital, Shanxi Medical University, Taiyuan, Shanxi, People’s Republic of China
| | - Jie Wang
- Department of Neurology, The First Hospital, Shanxi Medical University, Taiyuan, Shanxi, People’s Republic of China
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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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Shangguan L, Xue L, Shang J, Wang H. The application value of metagenomic next-generation sequencing in community-acquired purulent meningitis after antibiotic intervention. BMC Infect Dis 2023; 23:683. [PMID: 37828452 PMCID: PMC10571418 DOI: 10.1186/s12879-023-08672-4] [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: 06/03/2023] [Accepted: 10/05/2023] [Indexed: 10/14/2023] Open
Abstract
BACKGROUND Bacteria account for nearly one third of the causes of community-acquired central nervous system infections, and traditional diagnostic methods are based on culture results, which are time-consuming and have a low detection rate leading to delayed diagnosis and treatment. Since metagenomic next-generation sequencing (mNGS) has the advantages of high timeliness and only detecting microbial trace gene fragments, it has been used more widely in recent years. Based on this, we explored whether the application of cerebrospinal fluid (CSF) mNGS is advantageous in patients with community-acquired purulent meningitis, especially in people who have already used antibiotics. METHODS This was a retrospective study of 63 patients with community-acquired purulent meningitis admitted to the Department of Neurology of Shanxi Bethune Hospital from March 2018 to November 2022. Data were systematically collected and classified into CSF culture group, blood culture group and CSF mNGS group according to different detection methods, and the total detection rate of each method was calculated. Each group of patients was divided into two subgroups according to whether antibiotics were used before sampling. The detection rates of the three groups were compared within and between groups to explore whether mNGS has advantages over traditional methods and the influence of antibiotic use on detection rates of the three methods. RESULTS Among the 63 patients, the cases of CSF culture, blood culture and CSF mNGS were 56, 46, 44, respectively. The total detection rates of the three methods were 17.86%, 36.96%, 81.82%, with statistical differences (p < 0.05),suggesting that the detection rate of mNGS was higher than CSF culture (p < 0.05) and blood culture (p < 0.05),and the detection rate of blood culture higher than CSF culture (p < 0.05). Further grouping found that without antibiotics, the detection rates of CSF culture, blood culture and CSF mNGS were 28.57%, 56.25% and 88.89%, with statistical differences (p < 0.05), and the detection rate of CSF mNGS was higher than that of CSF culture (p < 0.05), but there was no statistical difference between CSF and blood culture (p > 0.05), nor between blood culture and CSF mNGS (p > 0.05). The detection rates of the three groups with antibiotics were 14.29%, 26.67% and 80.00%, with statistical differences (p < 0.05), and the detection rate of CSF mNGS was still higher than CSF culture (p < 0.05) and blood culture (p < 0.05). However, the detection rate of CSF mNGS also decreased after antibiotics were used for more than 3 days. CONCLUSIONS The detection rate of CSF mNGS in patients with purulent meningitis is higher than traditional methods, especially in patients who have been given antibiotics, but the detection rate will decrease with the extension of antibiotic use.
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Affiliation(s)
- Lijuan Shangguan
- Department of Neurology, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, 030032, China
- Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Lanping Xue
- Department of Neurology, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, 030032, China
- Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Jing Shang
- Department of Neurology, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, 030032, China
- Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Hailong Wang
- Department of Neurology, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, 030032, China.
- Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
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He T, Luo N, Kang J, Ling N, Zhang D. Use of metagenomic next-generation sequencing for diagnosis of peritonitis in end-stage liver disease. Int J Med Sci 2023; 20:1698-1704. [PMID: 37928876 PMCID: PMC10620865 DOI: 10.7150/ijms.89242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 09/28/2023] [Indexed: 11/07/2023] Open
Abstract
Background: Conventional methods are low in positive rates and time-consuming for ascites pathogen detection in patients with end-stage liver disease (ESLD). With many advantages, metagenomic next-generation sequencing (mNGS) may be a good alternative method. However, the related studies are still lacking. Methods: Ascites from 50 ESLD patients were sampled for pathogen detection using mNGS and conventional methods (culture and polymorphonuclear neutrophils detection) in this prospective observational study. Results: Forty-two samples were detected positive using mNGS. 29 strains of bacteria, 11 strains of fungi, and 9 strains of viruses were detected. 46% of patients were detected to be co-infected with 2 or more pathogens by mNGS. Moreover, mNGS showed similar and high positive rates in ESLD patients with different clinical characteristics. Compared to conventional methods, mNGS had higher positivity rates (84% vs. 20%, P<0.001), sensitivity (45.2% vs. 23.8%, P=0.039), broader pathogen spectrum, shorter detection time (24 hours vs. 3-7 days), but lower specificity (25% vs 100%, P = 0.010). Furthermore, compared to conventional methods, mNGS showed similar consistence with final diagnosis (42% vs. 36%, P=0.539). Conclusions: mNGS may be a good supplement for conventional methods and helpful to early etiological diagnosis of peritonitis, and thus improve ESLD patients' survival.
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Affiliation(s)
- Taiyu He
- Department of Infectious Diseases, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, the Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Ning Luo
- Department of Infectious Diseases, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, the Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Juan Kang
- Department of Infectious Diseases, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, the Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Ning Ling
- Department of Infectious Diseases, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, the Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Dazhi Zhang
- Department of Infectious Diseases, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, the Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
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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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He Y, Geng S, Mei Q, Zhang L, Yang T, Zhu C, Fan X, Wang Y, Tong F, Gao Y, Fang X, Bao R, Sheng X, Pan A. Diagnostic Value and Clinical Application of Metagenomic Next-Generation Sequencing for Infections in Critically Ill Patients. Infect Drug Resist 2023; 16:6309-6322. [PMID: 37780531 PMCID: PMC10541086 DOI: 10.2147/idr.s424802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 09/14/2023] [Indexed: 10/03/2023] Open
Abstract
Objective To evaluate the diagnostic value and clinical application of metagenomic next-generation sequencing (mNGS) for infections in critically ill patients. Methods Comparison of diagnostic performance of mNGS and conventional microbiological testing for pathogens was analyzed in 234 patients. The differences between immunocompetent and immunocompromised individuals in mNGS-guided anti-infective treatment adjustment were also analyzed. Results The sensitivity and specificity of mNGS for bacterial and fungal detection were 96.6% (95% confidence interval [CI], 93.5%-99.6%) and 83.1% (95% CI, 75.2%-91.1%), and 85.7% (95% CI, 71.9%-99.5%) and 93.2% (95% CI, 89.7%-96.7%), respectively. Overall, 152 viruses were detected by mNGS, but in which 28 viruses were considered causative agents. The proportion of mNGS-guided beneficial anti-infective therapy adjustments in the immunocompromised group was greater than in the immunocompetent group (48.5% vs 30.1%; P=0.008). In addition, mNGS-guided anti-infective regimens with peripheral blood and BALF specimens had the highest proportion (39.0%; 40.0%), but the proportion of patients not helpful due to peripheral blood mNGS was also as high as 22.0%. Conclusion mNGS might be a promising technology to provide precision medicine for critically ill patients with infection.
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Affiliation(s)
- Yuxi He
- Department of Intensive Care Unit, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
| | - Shike Geng
- Department of Intensive Care Unit, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
| | - Qing Mei
- Department of Intensive Care Unit, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
| | - Lei Zhang
- Department of Intensive Care Unit, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
| | - Tianjun Yang
- Department of Intensive Care Unit, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
| | - Chunyan Zhu
- Department of Intensive Care Unit, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
| | - Xiaoqin Fan
- Department of Intensive Care Unit, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
| | - Yinzhong Wang
- Department of Intensive Care Unit, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
| | - Fei Tong
- Department of Intensive Care Unit, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
| | - Yu Gao
- Department of Intensive Care Unit, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
| | - Xiaowei Fang
- Department of Intensive Care Unit, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
| | - Renren Bao
- Department of Intensive Care Unit, the Affiliated Provincial Hospital of Anhui Medical University, Hefei, Anhui, People’s Republic of China
| | - Ximei Sheng
- Department of Intensive Care Unit, the Training Center of Anhui Provincial Hospital, Wannan Medical College, Wuhu, Anhui, People’s Republic of China
| | - Aijun Pan
- Department of Intensive Care Unit, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
- Department of Intensive Care Unit, the Affiliated Provincial Hospital of Anhui Medical University, Hefei, Anhui, People’s Republic of China
- Department of Intensive Care Unit, the Training Center of Anhui Provincial Hospital, Wannan Medical College, Wuhu, Anhui, People’s Republic of China
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Yan Z, Wang Y, Zeng W, Xia R, Liu Y, Wu Z, Deng W, Zhu M, Xu J, Deng H, Miao Y. Microbiota of long-term indwelling hemodialysis catheters during renal transplantation perioperative period: a cross-sectional metagenomic microbial community analysis. Ren Fail 2023; 45:2256421. [PMID: 37724520 PMCID: PMC10512886 DOI: 10.1080/0886022x.2023.2256421] [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: 03/23/2023] [Accepted: 09/02/2023] [Indexed: 09/21/2023] Open
Abstract
Background: Catheter-related infection (CRI) is a major complication in patients undergoing hemodialysis. The lack of high-throughput research on catheter-related microbiota makes it difficult to predict the occurrence of CRI. Thus, this study aimed to delineate the microbial structure and diversity landscape of hemodialysis catheter tips among patients during the perioperative period of kidney transplantation (KTx) and provide insights into predicting the occurrence of CRI.Methods: Forty patients at the Department of Transplantation undergoing hemodialysis catheter removal were prospectively included. Samples, including catheter tip, catheter outlet skin swab, catheter blood, peripheral blood, oropharynx swab, and midstream urine, from the separate pre- and post-KTx groups were collected and analyzed using metagenomic next-generation sequencing (mNGS). All the catheter tips and blood samples were cultured conventionally.Results: The positive detection rates for bacteria using mNGS and traditional culture were 97.09% (200/206) and 2.65% (3/113), respectively. Low antibiotic-sensitivity biofilms with colonized bacteria were detected at the catheter tip. In asymptomatic patients, no statistically significant difference was observed in the catheter tip microbial composition and diversity between the pre- and post-KTx group. The catheter tip microbial composition and diversity were associated with fasting blood glucose levels. Microorganisms at the catheter tip most likely originated from catheter outlet skin and peripheral blood.Conclusions: The long-term colonization microbiota at the catheter tip is in a relatively stable state and is not readily influenced by KTx. It does not act as the source of infection in all CRIs, but could reflect hematogenous infection to some extent.
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Affiliation(s)
- Ziyan Yan
- Department of General Surgery & Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical University, Guangzhou, P.R. China
| | - Yuchen Wang
- Department of Transplantation, Nanfang Hospital, Southern Medical Univerisity, Guangzhou, P.R. China
| | - Wenli Zeng
- Department of Transplantation, Nanfang Hospital, Southern Medical Univerisity, Guangzhou, P.R. China
| | - Renfei Xia
- Department of Transplantation, Nanfang Hospital, Southern Medical Univerisity, Guangzhou, P.R. China
| | - Yanna Liu
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, P.R. China
| | - Zhouting Wu
- Department of Transplantation, Nanfang Hospital, Southern Medical Univerisity, Guangzhou, P.R. China
| | - Wenfeng Deng
- Department of Transplantation, Nanfang Hospital, Southern Medical Univerisity, Guangzhou, P.R. China
| | - Miao Zhu
- Department of Bioinformatics and System Development, Dinfectome Inc, Nanjing, P.R. China
| | - Jian Xu
- Department of Transplantation, Nanfang Hospital, Southern Medical Univerisity, Guangzhou, P.R. China
| | - Haijun Deng
- Department of General Surgery & Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical University, Guangzhou, P.R. China
| | - Yun Miao
- Department of Transplantation, Nanfang Hospital, Southern Medical Univerisity, Guangzhou, P.R. China
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Zhang X, Lin Y, Chen H, Hu J, Zhao H, Yang M, Han D. Diagnostic Performance of Metagenomic Next-Generation Sequencing in Central Nervous System Cryptococcosis Using Cerebrospinal Fluid. Infect Drug Resist 2023; 16:6175-6183. [PMID: 37724093 PMCID: PMC10505399 DOI: 10.2147/idr.s425463] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 09/01/2023] [Indexed: 09/20/2023] Open
Abstract
Purpose Metagenomic next-generation sequencing (mNGS) has been widely used to diagnose infectious diseases. However, there are few studies on its diagnostic performance in the central nervous system (CNS) cryptococcosis. This study examined the diagnostic efficacy of mNGS in identifying Cryptococcus spp. in cerebrospinal fluid (CSF) samples. Patients and Methods From March 2021 to March 2023, 290 patients with suspected CNS infection were recruited from the First Affiliated Hospital, School of Medicine, Zhejiang University, and 74 patients were ultimately included in the study. Lastly, 22 patients with CNS cryptococcosis were included. Of these patients, 25 CSF samples were enrolled. The diagnostic performance of conventional assays [including India ink, cryptococcal antigen (CrAg) testing, and culture] and mNGS was evaluated for CNS cryptococcosis. Results In the 25 samples collected, the coincidence rates of mNGS with India ink, CrAg, and culture were 64.0% (16/25), 80.0% (20/25), and 80.0% (20/25), respectively. Without antifungal drug exposure, the coincidence rates were increased to 66.7% (10/15), 100.0% (15/15), and 93.3% (14/15), respectively. The coincidence rates after antifungal therapy were all decreased to 60.0% (6/10), 50.0% (5/10), and 60.0% (6/10), respectively. Moreover, in the 25 samples, the sensitivity of mNGS reached 80.0%, and of India ink, CrAg testing, and culture were 68.0, 100.0, and 60.0%, respectively. The mNGS showed an excellent positive rate (100.0%) in the 15 samples collected without antifungal drug exposure, which was significantly higher than the antifungal drug-exposed group (n = 10) (50.0%) (P = 0.005). The reads of Cryptococcus spp. before antifungal therapy were significantly higher than after it (median, 25,915 vs 2, P = 0.008). Conclusion mNGS is an effective tool for diagnosing CNS cryptococcosis using CSF; however, its sensitivity decreases considerably in patients who have been effectively treated with antifungal drugs.
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Affiliation(s)
- Xuan Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People’s Republic of China
| | - Yaqing Lin
- Shulan (Hangzhou) Hospital Affiliated to Zhejiang Shuren University Shulan International Medical College, Hangzhou, Zhejiang, People’s Republic of China
| | - Huixin Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People’s Republic of China
| | - Jianhua Hu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People’s Republic of China
| | - Hong Zhao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People’s Republic of China
| | - Meifang Yang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People’s Republic of China
| | - Dongsheng Han
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People’s Republic of China
- Key Laboratory of Clinical in vitro Diagnostic Techniques of Zhejiang Province, Hangzhou, Zhejiang, People’s Republic of China
- Institute of Laboratory Medicine, Zhejiang University, Hangzhou, Zhejiang, People’s Republic of China
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Zhuang BB, Chen J, Zhang Q, Zhang GL, Shi SS. Diagnosis of pituitary abscess and treatment via transsphenoidal surgery: experience from 15 cases. Neurochirurgie 2023; 69:101478. [PMID: 37598621 DOI: 10.1016/j.neuchi.2023.101478] [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: 05/10/2023] [Revised: 08/01/2023] [Accepted: 08/01/2023] [Indexed: 08/22/2023]
Abstract
OBJECTIVE Pituitary abscess is an often misdiagnosed, rare clinical disorder. To improve diagnostic accuracy and the efficacy of surgical and antibiotic therapy for patients with pituitary abscess, herein, we retrospectively reviewed 15 patients who presented with pituitary abscesses from 2005 to 2022. DESIGN Retrospective study. PATIENTS Fifteen patients underwent transsphenoidal surgery and received antibiotic treatment. MEASUREMENTS Complete details regarding medical history, clinical manifestations, laboratory examinations, imaging studies, and treatment strategies were obtained for all patients. RESULTS Most patients presented with hypopituitarism and headaches, while some presented with fever, visual disturbances, and diabetes insipidus (DI). Abscesses showed significant annular enhancement post gadolinium injection. In most patients, pituitary abscess can be cured via microscopic or endoscopic drainage of the abscess followed by antibiotic treatment. Complete cure of pituitary abscess was observed in nine patients, with six cases of prolonged hypopituitarism and only one case of recurrence. Long-term hormone replacement therapy was effective in the postoperative management of hypopituitarism. CONCLUSIONS The typical manifestations of pituitary abscess include hypopituitarism and headaches; the presence of an enhanced ring at the edge of the mass on contrast-enhanced magnetic resonance images (MRI) is highly suggestive of pituitary abscess. We recommend antibiotic treatment for 4-6 weeks postoperatively, based on the results of bacterial cultures or metagenomic next-generation sequencing (mNGS).
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Affiliation(s)
- Bing-Bo Zhuang
- Department of Neurosurgery, Fujian Medical University Union Hospital, 29# Xinquan Road, Fuzhou, 350001, Fujian, China
| | - Jing Chen
- Department of Neurosurgery, Fujian Medical University Union Hospital, 29# Xinquan Road, Fuzhou, 350001, Fujian, China.
| | - Qiang Zhang
- Department of Neurosurgery, Fujian Medical University Union Hospital, 29# Xinquan Road, Fuzhou, 350001, Fujian, China
| | - Guo-Liang Zhang
- Department of Neurosurgery, Fujian Medical University Union Hospital, 29# Xinquan Road, Fuzhou, 350001, Fujian, China
| | - Song-Sheng Shi
- Department of Neurosurgery, Fujian Medical University Union Hospital, 29# Xinquan Road, Fuzhou, 350001, Fujian, China
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Yue Z, Zhi X, Bi L, Zhao L, Ji J. Treatment and prognostic risk factors for intracranial infection after craniocerebral surgery. Neurosurg Rev 2023; 46:199. [PMID: 37568062 DOI: 10.1007/s10143-023-02106-0] [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: 05/25/2023] [Revised: 07/27/2023] [Accepted: 08/01/2023] [Indexed: 08/13/2023]
Abstract
The objective of this study was to determine risk factors of pejorative evolution course in patients suffering from postoperative cranial infection. The data of patients who developed an intracranial infection after craniocerebral surgery in the neurosurgical intensive care unit of the First Affiliated Hospital of Nanjing Medical University in Nanjing, Jiangsu, China, from February 2018 to August 2019 were retrospectively analyzed. Logistic regression was used to analyze the factors influencing the prognosis of intracranial infection treatment. Sixty-four patients developed an infection after craniocerebral surgery, and 48 of them with negative CSF cultures received experimental anti-infectives. In 16 patients, cerebrospinal fluid culture showed pandrug-resistant pathogens, including 11 Acinetobacter baumannii (11), Klebsiella pneumoniae (3), Escherichia coli (1), and Candida glabrata (1). Nine patients received intraventricular or intrathecal injections of polymyxin B. The mean duration of infection treatment was 22.2 ± 9.9 days, and the clinical cure rate was 85.9% (55/64). Logistic multivariate regression analysis showed that inadequate CSF drainage (OR, 6.839; 95% CI, 1.130-41.383; P = 0.036) and infection with drug-resistant bacteria (OR, 24.241; 95% CI, 2.032-289.150; P = 0.012) were independent risk factors for postoperative intracranial infection. Intracranial infection with positive CSF culture and inadequate CSF drainage are factors contributing to the poor prognosis of intracranial infection. Moreover, early anti-infection treatment and adequate CSF drainage may improve patient outcomes. In particular, intraventricular or intrathecal injection of polymyxin B may be a safe and effective treatment strategy for MDR/XDR gram-negative bacilli infection.
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Affiliation(s)
- Zhen Yue
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xiaohui Zhi
- Department of Rehabilitation, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Liqing Bi
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Lin Zhao
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jing Ji
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China.
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Zhang C, Li Z, Wang M, Zhou J, Yu W, Liu H, Hu B, Wang S. High specificity of metagenomic next-generation sequencing using protected bronchial brushing sample in diagnosing pneumonia in children. Front Cell Infect Microbiol 2023; 13:1165432. [PMID: 37637461 PMCID: PMC10457156 DOI: 10.3389/fcimb.2023.1165432] [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: 02/14/2023] [Accepted: 07/21/2023] [Indexed: 08/29/2023] Open
Abstract
Background Lower respiratory tract infections are the leading cause of morbidity and mortality in children worldwide. Timely and accurate pathogen detection is crucial for proper clinical diagnosis and therapeutic strategies. The low detection efficiency of conventional methods and low specificity using respiratory samples seriously hindered the accurate detection of pathogens. Methods In this study, we retrospectively enrolled 1,032 children to evaluate the performance of metagenomics next-generation sequencing (mNGS) using bronchoalveolar lavage fluid (BALF) sample and protected bronchial brushing (BB) sample in diagnosing pneumonia in children. In addition, conventional tests (CTs) were also performed. Results The specificity of BB mNGS [67.3% (95% CI 58.6%-75.9%)] was significantly higher than that of BALF mNGS [38.5% (95% CI 12.0%-64.9%)]. The total coincidence rate of BB mNGS [77.6% (95% CI 74.8%-80.5%)] was slightly higher than that of BALF mNGS [76.5% (95% CI 68.8%-84.1%)] and CTs [38.5% (95% CI 35.2%-41.9%)]. During the epidemics of Mycoplasma pneumoniae, the detection rate of M. pneumoniae in the >6-year group (81.8%) was higher than that in the 3-6-year (78.9%) and <3-year groups (21.5%). The highest detection rates of bacteria, fungi, and viruses were found in the <3-year, >6-year, and 3-6-year groups, respectively. mNGS detection should be performed at the duration of 5-7 days after the start of continuous anti-microbial therapy or at the duration of 6-9 days from onset to mNGS test. Conclusions This is the first report to evaluate the performance of BB mNGS in diagnosing pulmonary infections in children on a large scale. Based on our findings, extensive application of BB mNGS could be expected.
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Affiliation(s)
- Chunyan Zhang
- Department of Microbiology Laboratory, Children’s Hospital Affiliated to Shandong University, Jinan, China
- Department of Clinical Microbiology, Shandong Provincial Clinical Research Center for Children’s Health and Disease, Jinan, China
| | - Zheng Li
- Department of Microbiology Laboratory, Children’s Hospital Affiliated to Shandong University, Jinan, China
- Department of Clinical Microbiology, Shandong Provincial Clinical Research Center for Children’s Health and Disease, Jinan, China
| | - Mengyuan Wang
- Department of Microbiology Laboratory, Children’s Hospital Affiliated to Shandong University, Jinan, China
- Department of Clinical Microbiology, Shandong Provincial Clinical Research Center for Children’s Health and Disease, Jinan, China
| | - Jiemin Zhou
- Department of Scientific Affairs, Vision Medicals Center for Infectious Diseases, Guangzhou, China
| | - Wenwen Yu
- Department of Microbiology Laboratory, Children’s Hospital Affiliated to Shandong University, Jinan, China
- Department of Clinical Microbiology, Shandong Provincial Clinical Research Center for Children’s Health and Disease, Jinan, China
| | - Huifang Liu
- Department of Scientific Affairs, Vision Medicals Center for Infectious Diseases, Guangzhou, China
| | - Bingxue Hu
- Department of Scientific Affairs, Vision Medicals Center for Infectious Diseases, Guangzhou, China
| | - Shifu Wang
- Department of Microbiology Laboratory, Children’s Hospital Affiliated to Shandong University, Jinan, China
- Department of Clinical Microbiology, Shandong Provincial Clinical Research Center for Children’s Health and Disease, Jinan, China
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Li S, Wang P, Tian S, Zhang J. Risk factors and cerebrospinal fluid indexes analysis of intracranial infection by Acinetobacter baumannii after neurosurgery. Heliyon 2023; 9:e18525. [PMID: 37576262 PMCID: PMC10412996 DOI: 10.1016/j.heliyon.2023.e18525] [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: 10/04/2022] [Revised: 07/13/2023] [Accepted: 07/20/2023] [Indexed: 08/15/2023] Open
Abstract
Background Intracranial infection by Acinetobacter baumannii (A. baumannii) after neurosurgery has always been a difficult problem for neurosurgeons. This study analyzed risk factors that discriminated A. baumannii from other bacteria causing intracranial infection after neurosurgery. It also examined the differences in the cerebrospinal fluid (CSF) indexes to explore their value in the early diagnosis of intracranial infection by A. baumannii. Methods We retrospectively reviewed ten years (January 2011 to May 2021) of postoperative central nervous system (CNS) infections in the First Hospital of China Medical University. According to the pathogen, CNS infections were divided into A. baumannii group and other species of bacteria group. We collected clinical and laboratory information of patients, and statistical analysis was performed with SPSS 26.0. Risk factors were screened by univariate analysis, and independent risk factors were screened by multiple logistic regression analysis. Finally, CSF-Pro, CSF-Glu, CSF-Cl, CSF-monocytes (%), CSF-multinucleated cells (%) levels, and CSF multinucleated cells%/monocytes% in the different groups were analyzed. Results A total of 155 patients were included, 62 cases (40%) of intracranial infection by A. baumannii and 93 cases (60%) by other species of bacteria. The analysis showed that indwelling nasogastric tubes (P<0.001, OR = 4.231), indwelling peripherally inserted central catheters (PICCs) (P = 0.041, OR = 2.765), and CSF drainage obstruction (P = 0.003, OR = 3.765) were independent risk factors for intracranial infection by A. baumannii after neurosurgery. Indwelling ventriculoperitoneal shunt (VPS) was a protective factor (P = 0.033, OR = 0.22). In addition, compared with other bacterial groups, the A. baumannii group had higher CSF-pro and CSF- multinucleated cells (%) levels and lower CSF-Glu and CSF- monocytes (%) levels, and the difference was statistically significant (P < 0.01). Conclusions Our results elucidate risk factors and differences in CSF indexes for intracranial infection by A. baumannii after neurosurgery that could be detected and prevented early to reduce mortality.
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Affiliation(s)
- Shige Li
- Department of Infectious Diseases, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Pan Wang
- Department of Infectious Diseases, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Sufei Tian
- Laboratory Department, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Jingping Zhang
- Department of Infectious Diseases, The First Hospital of China Medical University, Shenyang, Liaoning, China
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Zhu Y, Gan M, Ge M, Dong X, Yan G, Zhou Q, Yu H, Wang X, Cao Y, Lu G, Wu B, Zhou W. Diagnostic Performance and Clinical Impact of Metagenomic Next-Generation Sequencing for Pediatric Infectious Diseases. J Clin Microbiol 2023; 61:e0011523. [PMID: 37260394 PMCID: PMC10281092 DOI: 10.1128/jcm.00115-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 05/12/2023] [Indexed: 06/02/2023] Open
Abstract
Metagenomic next-generation sequencing (mNGS) has shown promise in the diagnosis of infectious diseases in adults, while its efficacy in pediatric infections remains uncertain. We performed a retrospective analysis of 1,493 mNGS samples from pediatric patients with blood, central nervous system, and lower respiratory tract infections. The positive percent agreement (PPA) and the negative percent agreement (NPA) of mNGS were compared to conventional microbiological tests (CMT) based on clinical diagnosis. The agreement of mNGS compared to CMT, as well as the clinical impact of mNGS, were valuated. Using the clinical diagnosis as a reference, mNGS demonstrated a significantly higher overall PPA compared to CMT (53.1% [95% CI = 49.7 to 56.6%] versus 25.8% [95% CI = 22.8 to 28.9%]), while maintaining a comparable overall NPA (93.2% [95% CI = 91.3 to 95.1%] versus 97.2% [95% CI = 95.9 to 98.4%]). In septic patients under 6 years of age or with immunosuppressive status, mNGS showed a higher PPA and a comparable NPA compared to CMT. The overall PPA and NPA of mNGS compared to CMT were 75.3 and 75.0%, respectively. The majority of cases of Streptococcus pneumoniae, Streptococcus agalactiae, Mycobacterium tuberculosis complex, and Pneumocystis jirovecii infections were identified by mNGS. A positive clinical impact of 14.0% (206/1,473), a negative impact of 0.8% (11/1,473), a nonimpact of 84.7% (1,248/1,473), and an unknown impact of 0.5% (8/1,473) were observed in the mNGS results. Notably, the positive impact was greater among immunosuppressed patients than among nonimmunosuppressed individuals (67/247, 27.1% versus 139/1,226, 11.3%; P < 0.001). mNGS is valuable for pathogen detection, diagnosis, and clinical management of infections among pediatric patients. mNGS was thus effective for the diagnosis of pediatric infections, which may guide clinical management. Patients with immunosuppressive conditions benefited more from mNGS testing.
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Affiliation(s)
- Yunqian Zhu
- Department of Neonatology, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, People’s Republic of China
| | - Mingyu Gan
- Center for Molecular Medicine, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, People’s Republic of China
- Key Laboratory of Birth Defects, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, People’s Republic of China
| | - Mengmeng Ge
- Department of Neonatology, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, People’s Republic of China
| | - Xinran Dong
- Center for Molecular Medicine, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, People’s Republic of China
- Key Laboratory of Birth Defects, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, People’s Republic of China
| | - Gangfeng Yan
- Department of Critical Care Medicine, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, People’s Republic of China
| | - Qinhua Zhou
- Department of Clinical Immunology, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, People’s Republic of China
| | - Hui Yu
- Department of Infectious Diseases, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, People’s Republic of China
| | - Xiaochuan Wang
- Department of Clinical Immunology, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, People’s Republic of China
| | - Yun Cao
- Department of Neonatology, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, People’s Republic of China
| | - Guoping Lu
- Department of Critical Care Medicine, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, People’s Republic of China
| | - Bingbing Wu
- Center for Molecular Medicine, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, People’s Republic of China
- Key Laboratory of Birth Defects, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, People’s Republic of China
| | - Wenhao Zhou
- Department of Neonatology, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, People’s Republic of China
- Center for Molecular Medicine, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, People’s Republic of China
- Key Laboratory of Birth Defects, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, People’s Republic of China
- Key Laboratory of Neonatal Diseases, Ministry of Health, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, People’s Republic of China
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Li M, Wang J, Yao Z, Liao H, Su S, Yang X, Xie M, Zheng Y. Metagenomic-based pathogen surveillance for children with severe pneumonia in pediatric intensive care unit. Front Public Health 2023; 11:1177069. [PMID: 37397737 PMCID: PMC10309210 DOI: 10.3389/fpubh.2023.1177069] [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: 03/01/2023] [Accepted: 05/26/2023] [Indexed: 07/04/2023] Open
Abstract
Background Pneumonia is a significant cause of morbidity and mortality in children. Metagenomic next-generation sequencing (mNGS) has the potential to assess the landscape of pathogens responsible for severe pulmonary infection. Methods Bronchoalveolar lavage fluid (BALF) samples of 262 children with suspected pulmonary infections were collected from April 2019 to October 2021 in the Pediatric Intensive Care Unit (PICU) of Guangdong Women and Children Hospital. Both mNGS and conventional tests were utilized for pathogen detection. Results A total of 80 underlying pathogens were identified using both mNGS and conventional tests. Respiratory syncytial virus (RSV), Staphylococcus aureus and rhinovirus were the most frequently detected pathogens in this cohort. The incidence rate of co-infection was high (58.96%, 148/251), with bacterial-viral agents most co-detected. RSV was the main pathogen in children younger than 6 months of age, and was also commonly found in older pediatric patients. Rhinovirus was prevalent in children older than 6 months. Adenovirus and Mycoplasma pneumoniae were more prevalent in children older than 3 years than in other age groups. Pneumocystis jirovecii was detected in nearly 15% of children younger than 6 months. Besides, influenza virus and adenovirus were rarely found in 2020 and 2021. Conclusions Our study highlights the importance of using advanced diagnostic techniques like mNGS to improve our understanding of the microbial epidemiology of severe pneumonia in pediatric patients.
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Affiliation(s)
- Meijin Li
- Department of Pediatric Intensive Care Unit, Guangdong Women and Children Hospital, Guangzhou, China
| | - Jing Wang
- Department of Scientific Affairs, Hugobiotech Co., Ltd., Beijing, China
| | - Zhongwei Yao
- Department of Pediatric Intensive Care Unit, Guangdong Women and Children Hospital, Guangzhou, China
| | - Hailing Liao
- Department of Pediatric Intensive Care Unit, Guangdong Women and Children Hospital, Guangzhou, China
| | - Shufen Su
- Department of Pediatric Intensive Care Unit, Guangdong Women and Children Hospital, Guangzhou, China
| | - Xuying Yang
- Department of Scientific Affairs, Hugobiotech Co., Ltd., Beijing, China
| | - Mingzhou Xie
- Department of Scientific Affairs, Hugobiotech Co., Ltd., Beijing, China
| | - Yinan Zheng
- Department of Pediatric Intensive Care Unit, Guangdong Women and Children Hospital, Guangzhou, China
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You H, Li W, Chen Q. Effect of Spontaneous Subarachnoid Hemorrhage on Cerebrospinal Fluid Indicators. Brain Sci 2023; 13:brainsci13050778. [PMID: 37239250 DOI: 10.3390/brainsci13050778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 04/22/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
The cerebrospinal fluid (CSF) analysis in ruptured aneurysms can be greatly affected by subarachnoid hemorrhage (SAH), making the diagnosis of intracranial infection more difficult after surgery. This study aimed to identify the reference value range of CSF in the pathological state following spontaneous SAH. A retrospective analysis of demographic and CSF data of all spontaneous SAH patients treated between January 2018 and January 2023 was conducted. A total of 101 valid CSF specimen data were collected for analysis. Our results indicate that in 95% of patients after spontaneous SAH, the leukocyte count in CSF was less than 880 × 106/L. Additionally, the proportion of neutrophils, lymphocytes, and monocytes did not exceed 75%, 75%, and 15%, respectively, in 95% of the population. Furthermore, in 95% of the specimens, the concentration of chloride, glucose, and protein was >115 mmol/L, >2.2 mmol/L, and <2.3 g/L, respectively. Compared to the normal reference values, the CSF indexes after spontaneous SAH showed significant changes, especially in the leukocyte count, chloride concentration, and glucose concentration. Using "white blood cell count < 880/mm3, glucose > 2.2 mmol/L, chloride > 115" as the reference values for SAH pathological status is more meaningful for reference purposes.
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Affiliation(s)
- Huichao You
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Wenqi Li
- Department of Ultrasound, Hubei No. 3 People's Hospital of Jianghan University, Wuhan 430033, China
| | - Qianxue Chen
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
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Liang Y, Feng Q, Wei K, Hou X, Song X, Li Y. Potential of metagenomic next-generation sequencing in detecting infections of ICU patients. Mol Cell Probes 2023; 68:101898. [PMID: 36764622 DOI: 10.1016/j.mcp.2023.101898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/31/2023] [Accepted: 02/03/2023] [Indexed: 02/12/2023]
Abstract
BACKGROUND Due to the limitations of traditional microbiological detection techniques in evaluating complicated infections in ICU patients, it is necessary to explore novel and effective methods to improve the clinical detection of ICU patients' infections. OBJECTIVE This study aimed to evaluate the efficiency and specificity of mNGS in screening pathogens in the blood, deep phlegm, urine, and other sample types of ICU patients exploring an effective method for infection detection. METHODS A total of 56 ICU patients with 131 samples were included in this study. The sample types included blood, deep phlegm, urine, drainage, anal swabs, and other types. Samples were analyzed by both conventional detection method and mNGS tests. The diagnosis efficiency and consistency of the two methods were compared. The distribution of the identified pathogens was analyzed. Moreover, the clinical features of patients with mNGS-positive or mNGS-negative results were compared. RESULTS The positive rate of mNGS was 81.7% (107/131) including 3.1% (4/131) weakly positive, while the positive rate of traditional detection was only 30.5%, including 29 strong positive results and 11 weak positive results. Additionally, there were 41 patients chose to adjust anti-infection strategies according to the results of mNGS, which significantly saved treatment costs. The mNGS-positive patients showed a shorter ICU hospitalization and higher intention to adjust anti-infection strategies than the mNGS-negative patients. CONCLUSION mNGS is of great potential for the pathogen detection of ICU patients, and has a higher detection rate than traditional detection methods. Further clinical application investigations can be carried out to expand the application of mNGS.
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Affiliation(s)
- Yanxu Liang
- Department of Critical Care Medicine, The Fifth Central Hospital of Tianjin, Tianjin, 300450, China
| | - Qingguo Feng
- Department of Critical Care Medicine, The Fifth Central Hospital of Tianjin, Tianjin, 300450, China.
| | - Kai Wei
- Department of Critical Care Medicine, The Fifth Central Hospital of Tianjin, Tianjin, 300450, China
| | - Xiaoming Hou
- Department of Critical Care Medicine, The Fifth Central Hospital of Tianjin, Tianjin, 300450, China
| | - Xiaotao Song
- Department of Critical Care Medicine, The Fifth Central Hospital of Tianjin, Tianjin, 300450, China
| | - Yuantao Li
- Department of Critical Care Medicine, The Fifth Central Hospital of Tianjin, Tianjin, 300450, China
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Diagnostic Role of mNGS in Polymicrobial Periprosthetic Joint Infection. J Clin Med 2023; 12:jcm12051838. [PMID: 36902625 PMCID: PMC10003677 DOI: 10.3390/jcm12051838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 02/02/2023] [Accepted: 02/21/2023] [Indexed: 03/03/2023] Open
Abstract
OBJECTIVES The purpose of this study was to explore the clinical value of metagenomic next-generation sequencing (mNGS) in the diagnosis of polymicrobial periprosthetic joint infection (PJI). METHODS Patients with complete data who underwent surgery at our hospital between July 2017 and January 2021 for suspected periprosthetic joint infection (PJI), according to the 2018 ICE diagnostic criteria, were enrolled, and all patients underwent microbial culture and mNGS detection, which were performed on the BGISEQ-500 platform. Microbial cultures were performed on two samples of synovial fluid, six samples of tissue, and two samples of prosthetic sonicate fluid for each patient. The mNGS was performed on 10 tissues, 64 synovial fluid samples, and 17 prosthetic sonicate fluid samples. The results of mNGS testing were based on the interpretation of mNGS results in the previous literature and the assertions of microbiologists and orthopedic surgeons. The diagnostic efficacy of mNGS in polymicrobial PJI was assessed by comparing the results of conventional microbial cultures and mNGS. RESULTS A total of 91 patients were finally enrolled in this study. The sensitivity, specificity, and accuracy of conventional culture for the diagnosis of PJI were 71.0%, 95.4%, and 76.9%, respectively. The sensitivity, specificity, and accuracy of mNGS for the diagnosis of PJI were 91.3%, 86.3%, and 90.1%, respectively. The sensitivity, specificity, and accuracy of conventional culture for the diagnosis of polymicrobial PJI were 57.1%, 100%, and 91.3%, respectively. mNGS had a sensitivity, specificity, and accuracy of 85.7%, 60.0%, and 65.2%, respectively, for the diagnosis of polymicrobial PJI. CONCLUSIONS mNGS can improve the diagnosis efficiency of polymicrobial PJI, and the combination of culture and mNGS is a promising method to diagnose polymicrobial PJI.
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Wei Y, Zhang T, Ma Y, Yan J, Zhan J, Zheng J, Xu Y. Clinical Evaluation of Metagenomic Next-Generation Sequencing for the detection of pathogens in BALF in severe community acquired pneumonia. Ital J Pediatr 2023; 49:25. [PMID: 36805803 PMCID: PMC9938609 DOI: 10.1186/s13052-023-01431-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 02/12/2023] [Indexed: 02/19/2023] Open
Abstract
BACKGROUND Rapid and accurate identification of pathogens is very important for the treatment of Severe community-acquired pneumonia (SCAP) in children. Metagenomic Next-generation sequencing (mNGS) has been applied in the detection of pathogenic bacteria in recent years, while the overall evaluation the application of SCAP in children is lacking. METHODS In our study, 84 cases of SCAP were enrolled. Bronchoalveolar lavage fluid (BALF) samples were analysed using mNGS; and sputum, blood, and BALF samples were analysed using conventional technology (CT). RESULTS Among the 84 children, 41 were boys, and 43 were girls, with an average age ranging from 2 months to 14 years. The pathogen detection rate of mNGS was higher than that of CT (83.3% [70/84] vs. 63.1% [53/84], P = 0.003). The mNGS was much greater than that of the CT in detecting Streptococcus pneumoniae (89.2% [25/29] vs. 44.8% [13/29], P = 0.001) and Haemophilus influenzae (91.7% [11/12] vs. 33.3% [4/12], P < 0.005). The mNGS also showed superior fungal detection performance compared with that of the CT (81.8% [9/11] vs. 18.2% [2/11], P = 0.004). The mNGS test can detect viruses, such as bocavirus, rhinovirus, and human metapneumovirus, which are not frequently recognised using CT. However, the mNGS detection rate was lower than that of the CT (52.4% [11/21] vs. 95.2% [20/21], P = 0.004) for Mycoplasma pneumoniae (MP). The detection rate of mNGS for mixed infection was greater than that of the CT, although statistical significance was not observed (26.3% [20/39] vs. 21.1% [16/39], P > 0.005). Treatment for 26 (31.0%) children was changed based on mNGS results, and their symptoms were reduced; nine patients had their antibiotic modified, five had antibiotics added, nine had their antifungal medication, and seven had their antiviral medication. CONCLUSION mNGS has unique advantages in the detection of SCAP pathogens in children, especially S. pneumoniae, H. influenzae, and fungi. However, the detection rate of MP using mNGS was lower than that of the CT. Additionally, mNGS can detect pathogens that are not generally covered by CT, which is extremely important for the modification of the treatment strategy.
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Affiliation(s)
- Yupeng Wei
- grid.265021.20000 0000 9792 1228Clinical School of Paediatrics, Tianjin Medical University, Tianjin, China ,grid.417022.20000 0004 1772 3918Department of Respiratory Medicine, Tianjin Children’s Hospital (Tianjin University Children’s Hospital), Tianjin, China ,grid.410626.70000 0004 1798 9265Department of Neonatology, Tianjin Central Hospital of Gynecology Obstetrics, Tianjin, China
| | - Tongqiang Zhang
- grid.265021.20000 0000 9792 1228Clinical School of Paediatrics, Tianjin Medical University, Tianjin, China ,grid.417022.20000 0004 1772 3918Department of Respiratory Medicine, Tianjin Children’s Hospital (Tianjin University Children’s Hospital), Tianjin, China
| | - Yuting Ma
- grid.265021.20000 0000 9792 1228Clinical School of Paediatrics, Tianjin Medical University, Tianjin, China ,grid.417022.20000 0004 1772 3918Department of Infection, Tianjin Children’s Hospital (Tianjin University Children’s Hospital), Tianjin, China
| | - Jisi Yan
- grid.265021.20000 0000 9792 1228Clinical School of Paediatrics, Tianjin Medical University, Tianjin, China ,grid.417022.20000 0004 1772 3918Department of Respiratory Medicine, Tianjin Children’s Hospital (Tianjin University Children’s Hospital), Tianjin, China ,grid.410626.70000 0004 1798 9265Department of Neonatology, Tianjin Central Hospital of Gynecology Obstetrics, Tianjin, China
| | - Jianghua Zhan
- Department of Pediatric Surgery, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China.
| | - Jun Zheng
- Department of Neonatology, Tianjin Central Hospital of Gynecology Obstetrics, Tianjin, China.
| | - Yongsheng Xu
- Department of Respiratory Medicine, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China.
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Lin K, Zhang HC, Zhang Y, Zhou Y, Fu ZF, Wang HY, Zhao YH, Qiu C, Fan MX, Song JY, Ai JW, Zhang WH. Clinical application and drug-use-guidance value of metagenomic next-generation sequencing in central nervous system infection. Am J Transl Res 2023; 15:47-62. [PMID: 36777850 PMCID: PMC9908477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 08/11/2022] [Indexed: 02/14/2023]
Abstract
OBJECTIVE Timely and precise etiology diagnosis is crucial for optimized medication regimens and better prognosis in central nervous system infections (CNS infections). We aimed to analyze the impact of mNGS tests on the management of patients with CNS infections. METHODS We conducted a single-center retrospective cohort study to analyze the value of mNGS in clinical applications. Three hundred sixty-nine patients with a CNS infection diagnosis were enrolled, and their clinical data were collected. CDI and DDI were defined in our study to describe the intensity of drug use in different groups. We used LOH and mRS to evaluate if the application of mNGS can benefit CNS infected patients. RESULTS mNGS reported a 91.67% sensitivity in culture-positive patients and an 88.24% specificity compared with the final diagnoses. Patients who participated with the mNGS test had less drug use, both total (58.77 vs. 81.18) and daily (22.6 vs. 28.12, P < 0.1, McNemar) intensity of drug use, and length of hospitalization (23.14 vs. 24.29). Patients with a consciousness grading 1 and 3 had a decrease in CDI (Grade 1, 86.49 vs. 173.37; Grade 3, 48.18 vs. 68.21), DDI (Grade 1, 1.52 vs. 2.72; Grade 3, 2.3 vs. 2.45), and LOH (Grade 1, 32 vs. 40; Grade 3, 21 vs. 23) with the application of mNGS. Patients infected with bacteria in the CNS had a reduced CDI, DDI, and LOH in the mNGS group. This was compared with the TraE group that had 49% of patients altered medication plans, and 24.7% of patients reduced drug intensity four days after mNGS reports. This was because of the reduction of drug types. CONCLUSION mNGS showed its high sensitivity and specificity characteristics. mNGS may assist clinicians with more rational medication regimens and reduce the drug intensity for patients. The primary way of achieving this is to reduce the variety of drugs, especially for severe patients and bacterial infections. mNGS has the ability of improving the prognosis of CNS infected patients.
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Affiliation(s)
- Ke Lin
- Department of Infectious Disease of Huashan Hospital, National Medical Center for Infectious Diseases and Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Fudan University Shanghai 200040, China
| | - Hao-Cheng Zhang
- Department of Infectious Disease of Huashan Hospital, National Medical Center for Infectious Diseases and Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Fudan University Shanghai 200040, China
| | - Yi Zhang
- Department of Infectious Disease of Huashan Hospital, National Medical Center for Infectious Diseases and Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Fudan University Shanghai 200040, China
| | - Yang Zhou
- Department of Infectious Disease of Huashan Hospital, National Medical Center for Infectious Diseases and Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Fudan University Shanghai 200040, China
| | - Zhang-Fan Fu
- Department of Infectious Disease of Huashan Hospital, National Medical Center for Infectious Diseases and Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Fudan University Shanghai 200040, China
| | - Hong-Yu Wang
- Department of Infectious Disease of Huashan Hospital, National Medical Center for Infectious Diseases and Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Fudan University Shanghai 200040, China
| | - Yuan-Han Zhao
- Department of Infectious Disease of Huashan Hospital, National Medical Center for Infectious Diseases and Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Fudan University Shanghai 200040, China
| | - Chao Qiu
- Department of Infectious Disease of Huashan Hospital, National Medical Center for Infectious Diseases and Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Fudan University Shanghai 200040, China.,Key Laboratory of Medical Molecular Virology (MOE/MOH) and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University Shanghai 200032, China
| | - Ming-Xiang Fan
- Department of Urology, Tongji Hospital, School of Medicine, Tongji University Shanghai 200065, China
| | - Jie-Yu Song
- Department of Infectious Disease of Huashan Hospital, National Medical Center for Infectious Diseases and Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Fudan University Shanghai 200040, China
| | - Jing-Wen Ai
- Department of Infectious Disease of Huashan Hospital, National Medical Center for Infectious Diseases and Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Fudan University Shanghai 200040, China
| | - Wen-Hong Zhang
- Department of Infectious Disease of Huashan Hospital, National Medical Center for Infectious Diseases and Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Fudan University Shanghai 200040, China.,Key Laboratory of Medical Molecular Virology (MOE/MOH) and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University Shanghai 200032, China.,State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University Shanghai 200438, China.,National Clinical Research Centre for Aging & Medicine, Huashan Hospital, Fudan University Shanghai 200040, China
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Lin K, Zhao Y, Xu B, Yu S, Fu Z, Zhang Y, Wang H, Song J, Fan M, Zhou Y, Ai J, Qiu C, Zhang H, Zhang W. Clinical Diagnostic Performance of Droplet Digital PCR for Suspected Bloodstream Infections. Microbiol Spectr 2023; 11:e0137822. [PMID: 36602351 PMCID: PMC9927361 DOI: 10.1128/spectrum.01378-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 11/01/2022] [Indexed: 01/06/2023] Open
Abstract
Accurate and timely etiological diagnosis is crucial for bloodstream infections (BSIs) due to their high disability and mortality. We conducted a single-center prospective cohort study to compare the digital droplet PCR (ddPCR) assay with traditional blood culture. A total of 169 blood samples from 122 patients with suspected BSIs were collected, mostly from the department of infectious diseases, the emergency department, and the intensive care units, and the clinical data were also recorded. Nucleic acid was extracted from the blood samples, and a 5-fluorescent-channel droplet digital PCR assay was performed and then fed back with the pathogen and its copies. In BSI patients, ddPCR reported an overall 85.71% (12/14) (95% confidence interval [CI], 56.15 to 97.48%) sensitivity, 100% (7/7) (95% CI, 56.09 to 100.00%) and 71.43% (5/7) (95% CI, 30.26 to 94.89%) sensitivity in patients without empirical treatment and in empirically treated patients, respectively. Compared to traditional blood culture, the overall detection rate of ddPCR was significantly higher, 11.27% (16/142) (95% CI, 6.78 to 17.93%) versus 30.28% (43/142) (95% CI, 23.01 to 38.64%), and the extra detection rate of ddPCR was 19.01% (27/142) (95% CI, 13.11 to 26.63%). Of the ddPCR-positive culture-negative cases, 74.19% (23/31) (95% CI, 55.07 to 87.46%) were consistent with the final clinical diagnosis, including 10 bacteria and fungi. The detection rate of ddPCR was significantly higher in patients with white blood cell (WBC) counts of >10 · 109/L, C-reactive protein (CRP) of >70 mg/L, or procalcitonin (PCT) of >0.9 ng/L. Pathogen loads detected by ddPCR are correlated with WBC, CRP, and especially, PCT levels, precisely and rapidly reflecting clinical disease progression. ddPCR has an important guiding value for the clinical use of antibiotics to achieve the best pathogen coverage and the antibacterial effect. Collectively, ddPCR showed a great diagnostic performance in BSIs and had an overall higher detection rate than blood culture. In addition, ddPCR could be used to dynamically monitor the disease progression and provide medication guidance on antibiotic use. IMPORTANCE ddPCR is a promising method to address the current challenges of BSI diagnosis and precise treatment, as it is highly efficient in DNA detection. It shortens the identification of BSI-related pathogens from several days of traditional bacterial culture to 4 to 5 h. It is extremely sensitive and more tolerant to PCR inhibitors, which may facilitate the amplification and enable the detection of a meager amount of DNA fragments in detecting BSI-related pathogens and drug-resistant genes. It can identify almost 20 pathogens in one reaction, which reduces the usage of clinical blood samples to no more than 2 mL. Additionally, dynamic monitoring, assessment of pathogens, and antibiotic resistance genes in patients could be used to guide timely and precise adjustment of antimicrobial prescription. The short turnaround time of ddPCR may have the potential to guide antimicrobial treatment in the very early stage of sepsis and reduce the mortality and disability rate of sepsis.
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Affiliation(s)
- Ke Lin
- Department of Infectious Disease of Huashan Hospital, National Medical Center for Infectious Diseases and Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Fudan University, Shanghai, China
| | - Yuanhan Zhao
- Department of Infectious Disease of Huashan Hospital, National Medical Center for Infectious Diseases and Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Fudan University, Shanghai, China
| | - Bin Xu
- Department of Infectious Disease of Huashan Hospital, National Medical Center for Infectious Diseases and Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Fudan University, Shanghai, China
| | - Shenglei Yu
- Department of Infectious Disease of Huashan Hospital, National Medical Center for Infectious Diseases and Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Fudan University, Shanghai, China
| | - Zhangfan Fu
- Department of Infectious Disease of Huashan Hospital, National Medical Center for Infectious Diseases and Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Fudan University, Shanghai, China
| | - Yi Zhang
- Department of Infectious Disease of Huashan Hospital, National Medical Center for Infectious Diseases and Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Fudan University, Shanghai, China
| | - Hongyu Wang
- Department of Infectious Disease of Huashan Hospital, National Medical Center for Infectious Diseases and Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Fudan University, Shanghai, China
| | - Jieyu Song
- Department of Infectious Disease of Huashan Hospital, National Medical Center for Infectious Diseases and Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Fudan University, Shanghai, China
| | - Mingxiang Fan
- Department of Infectious Disease of Huashan Hospital, National Medical Center for Infectious Diseases and Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Fudan University, Shanghai, China
| | - Yang Zhou
- Department of Infectious Disease of Huashan Hospital, National Medical Center for Infectious Diseases and Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Fudan University, Shanghai, China
| | - Jingwen Ai
- Department of Infectious Disease of Huashan Hospital, National Medical Center for Infectious Diseases and Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Fudan University, Shanghai, China
| | - Chao Qiu
- Department of Infectious Disease of Huashan Hospital, National Medical Center for Infectious Diseases and Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Fudan University, Shanghai, China
| | - Haocheng Zhang
- Department of Infectious Disease of Huashan Hospital, National Medical Center for Infectious Diseases and Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Fudan University, Shanghai, China
| | - Wenhong Zhang
- Department of Infectious Disease of Huashan Hospital, National Medical Center for Infectious Diseases and Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Fudan University, Shanghai, China
- Key Laboratory of Medical Molecular Virology (MOE/MOH) and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China
- National Clinical Research Centre for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China
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Li X, Yang L, Li D, Yang X, Wang Z, Chen M, Wu F, Dou X, Niu M, Qi H, Deng T, Xia H, Wang D. Diagnosis of Neurological Infections in Pediatric Patients from Cell-Free DNA Specimens by Using Metagenomic Next-Generation Sequencing. Microbiol Spectr 2023; 11:e0253022. [PMID: 36651744 PMCID: PMC9927296 DOI: 10.1128/spectrum.02530-22] [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: 07/03/2022] [Accepted: 12/19/2022] [Indexed: 01/19/2023] Open
Abstract
Central nervous system (CNS) infections can cause significant morbidity and mortality, especially in children. Rapid and accurate pathogenic detection in suspected CNS infections is essential for disease control at the early stage of infection. To evaluate the performance of metagenomic next-generation sequencing (mNGS) of cell-free DNA (cfDNA) in cerebrospinal fluid (CSF) in pediatric patients, we retrospectively analyzed the efficiency of cfDNA mNGS in children with CNS infections (n = 257) or noninfectious neurological disorders (n = 81). The CSF samples of 124 random subjects were used to evaluate the accuracy between mNGS of cfDNA and whole-cell DNA (wcDNA). In total, cfDNA mNGS detected a wide range of microbes with a detection rate of 71.0%, and the sensitivity and total coincidence rate with clinical diagnosis reached 68.9% and 67.5%, respectively. Compared with wcDNA mNGS, cfDNA mNGS had a higher efficacy in detecting viruses (66 versus 13) and Mycobacterium (7 versus 1), with significantly higher reads per million. The dominant causative pathogens were bacteria and viruses in CNS infections, but these presented with different pathogen spectra in different age categories. The best timing for the mNGS test ranged from 1 to 6 days after the start of anti-infection therapy, and the earlier mNGS started, the better was identification of bacterial CNS infections. This study emphasized that cfDNA mNGS had overall superiority to conventional methods on causative pathogen detection in pediatric CNS infections, and it was even better than wcDNA mNGS. Furthermore, research needs to be better validated in large-scale clinical trials to improve the clinical applications of cfDNA mNGS. IMPORTANCE Our study emphasized that cfDNA mNGS had overall superiority to conventional methods on causative pathogen detection in CNS-infected children, and it was even better than wcDNA mNGS. cfDNA mNGS detected a wide range of pathogens with a high total coincidence rate (67.5%) against clinical diagnosis. The best timing for cfDNA mNGS detection ranged from 1 to 6 days, rather than 0 days, after the start of empirical anti-infection therapy. The earlier mNGS started, the better the identifications of bacterial CNS infections. To the best of our knowledge, this research is the first report evaluating the clinical utility of mNGS with different methods (cfDNA versus wcDNA) of extracting DNA from CSF specimens in diagnosing pediatric CNS infections. Meanwhile, this is the largest cohort study that has evaluated the performance of mNGS using cfDNA from CSF specimens in pediatric patients with CNS infections.
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Affiliation(s)
- Xia Li
- Department of Pediatric Neurology, Xi’an Children’s hospital, Xi’an City, Shaanxi Province, China
| | - Le Yang
- Department of Pediatric Neurology, Xi’an Children’s hospital, Xi’an City, Shaanxi Province, China
| | - Dongjing Li
- Department of Pediatric Neurology, Xi’an Children’s hospital, Xi’an City, Shaanxi Province, China
| | - Xuying Yang
- Department of Scientific Affaires, Hugobiotech Co., Ltd., Beijing, China
| | - Zhijing Wang
- Department of Pediatric Neurology, Xi’an Children’s hospital, Xi’an City, Shaanxi Province, China
| | - Mengyi Chen
- Department of Pediatric Neurology, Xi’an Children’s hospital, Xi’an City, Shaanxi Province, China
| | - Fang Wu
- Department of Pediatric Neurology, Xi’an Children’s hospital, Xi’an City, Shaanxi Province, China
| | - Xiangjun Dou
- Department of Pediatric Neurology, Xi’an Children’s hospital, Xi’an City, Shaanxi Province, China
| | - Mengmeng Niu
- Department of Pediatric Neurology, Xi’an Children’s hospital, Xi’an City, Shaanxi Province, China
| | - HongYan Qi
- Department of Pediatric Neurology, Xi’an Children’s hospital, Xi’an City, Shaanxi Province, China
| | - Ting Deng
- Department of Pediatric Neurology, Xi’an Children’s hospital, Xi’an City, Shaanxi Province, China
| | - Han Xia
- Department of Scientific Affaires, Hugobiotech Co., Ltd., Beijing, China
| | - Dong Wang
- Department of Pediatric Neurology, Xi’an Children’s hospital, Xi’an City, Shaanxi Province, China
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Wang G, Long J, Zhuang Y, Leng X, Zhang Y, Liu L, Fu J, Chen Y, Li C, Zhou Y, Huang B, Feng C. Application of metagenomic next-generation sequencing in the detection of pathogens in spinal infections. Spine J 2023; 23:859-867. [PMID: 36773890 DOI: 10.1016/j.spinee.2023.02.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 01/19/2023] [Accepted: 02/03/2023] [Indexed: 02/13/2023]
Abstract
BACKGROUND CONTEXT The precise diagnosis and treatment of spinal infections (SI) remains challenging for spine surgeons. Identifying the pathogens of SI through metagenomic next-generation sequencing (mNGS) may be a key approach to addressing this challenge. PURPOSE To evaluate the accuracy and applicability of mNGS in determining the etiology of SI. STUDY DESIGN Diagnostic test study. PATIENT SAMPLE Twenty-five patients who had a clinical suspicion of SI and underwent mNGS testing. OUTCOME MEASURES The specificity, sensitivity, and time cost of mNGS and bacterial culture were compared. Clinical outcomes were assessed using the numeric rating scale (NRS) score, Oswestry Disability Index (ODI), and the Japanese Orthopedic Association (JOA) score. Demographic data and laboratory results (blood cell count (WBC), erythrocyte sedimentation rate (ESR), neutrophil percentage (NEUT%), and C-reactive protein level (CRP) were also evaluated. METHODS In this retrospective study, samples were obtained from 25 eligible patients via surgery or CT-guided puncture and subjected to histopathological examination, bacterial culture, and mNGS. The sensitivity and specificity of the bacterial cultures and mNGS were calculated with respect to the histopathological results as a reference. Postoperative antibiotics or antituberculosis drugs were administered on the basis of mNGS results, combined with clinical manifestations, imaging examination, and histopathology. The changes of clinical outcomes and laboratory results after treatment were observed. RESULTS Of the 25 patients, 21 had a positive pathology, of which 10 showed a tuberculous pathology, and the remaining 11 showed a nontuberculous inflammatory pathology. The sensitivity of mNGS was higher than that of the bacterial culture. However, the difference in specificity between bacterial culture and mNGS was not significant. Moreover, the time needed to perform mNGS was significantly lower than that of bacterial culture and pathology. All patients were followed up for more than three months, and CRP and NEUT% significantly decreased by three months after treatment. There was no significant difference in WBC and ESR. The ODI, NRS and JOA scores were significantly improved after treatment. CONCLUSION Metagenomic next-generation sequencing technology can play an important role in the detection of pathogens in SI and should be further investigated and applied in future studies.
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Affiliation(s)
- Guanzhong Wang
- Department of Orthopedics Southwest Hospital, Army Medical University, Gaotanyan St No.30, Chongqing 400038, People's Republic of China
| | - Jiang Long
- Department of Orthopedics Xinqiao Hospital, Army Medical University, 183 Xinqiao Main St Shapingba, Chongqing 400037, People's Republic of China
| | - Yong Zhuang
- Department of Orthopedics, Affiliated Hospital of Guizhou Medical University, 28 Guiyi St Yunyan District, Guiyang 550004, People's Republic of China
| | - Xue Leng
- Department of Orthopedics Xinqiao Hospital, Army Medical University, 183 Xinqiao Main St Shapingba, Chongqing 400037, People's Republic of China
| | - Yaqing Zhang
- Department of Orthopedics Xinqiao Hospital, Army Medical University, 183 Xinqiao Main St Shapingba, Chongqing 400037, People's Republic of China
| | - Libangxi Liu
- Department of Orthopedics Xinqiao Hospital, Army Medical University, 183 Xinqiao Main St Shapingba, Chongqing 400037, People's Republic of China
| | - Jiawei Fu
- Department of Orthopedics Xinqiao Hospital, Army Medical University, 183 Xinqiao Main St Shapingba, Chongqing 400037, People's Republic of China
| | - Yu Chen
- Department of Orthopedics Xinqiao Hospital, Army Medical University, 183 Xinqiao Main St Shapingba, Chongqing 400037, People's Republic of China
| | - Changqing Li
- Department of Orthopedics Xinqiao Hospital, Army Medical University, 183 Xinqiao Main St Shapingba, Chongqing 400037, People's Republic of China
| | - Yue Zhou
- Department of Orthopedics Xinqiao Hospital, Army Medical University, 183 Xinqiao Main St Shapingba, Chongqing 400037, People's Republic of China
| | - Bo Huang
- Department of Orthopedics Xinqiao Hospital, Army Medical University, 183 Xinqiao Main St Shapingba, Chongqing 400037, People's Republic of China
| | - Chencheng Feng
- Department of Orthopedics Xinqiao Hospital, Army Medical University, 183 Xinqiao Main St Shapingba, Chongqing 400037, People's Republic of China.
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Piao S, Bao Y, Yang L, Zhang Y, Hu B, Li H, Geng D, Li Y. Brain MRI features of anti-N-methyl-D-aspartate (anti-NMDA) receptor encephalitis secondary to central nervous system infection in adult patients. Acta Radiol 2023; 64:760-768. [PMID: 35532900 DOI: 10.1177/02841851221091443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND Anti-N-methyl-D-aspartate receptor (anti-NMDAR) encephalitis secondary to central nervous system (CNS) infection is a unique subtype of the autoimmune-mediated disease, of which the imaging features are unclear. PURPOSE To compare the brain magnetic resonance imaging (MRI) features between the anti-NMDAR encephalitis secondary to CNS infection and that without initial infection. MATERIAL AND METHODS A total of 70 adult patients with anti-NMDAR encephalitis were retrospectively enrolled (24 in the post-infection group, 46 in the non-infection-related group). Their clinical and imaging features (lesion distribution, lesion shape, enhancement pattern, brain atrophy) were reviewed and summarized. Lesion distributions were compared between the two groups on lesion probability maps. RESULTS The patients with normal brain MRI scans in the post-infection group were less than those in the non-infection related group (29% vs. 63%; P = 0.0113). Among the 24 patients in the post-infection group, visible lesions were shown at the anti-NMDAR encephalitis onset in 17 patients; lesion distribution was more diffuse than the non-infection-related group, showing higher lesion peak probabilities in the bilateral hippocampus, frontal lobe, temporal lobe, insula, and cingulate. The lesions with contrast enhancement were also more common in the post-infection group than the non-infection-related group (7/13 vs. 2/10). Brain atrophy was observed in eight patients in the post-infection group and three in the non-infection-related group. CONCLUSION Anti-NMDAR encephalitis secondary to CNS infection has its imaging features-extensive lesion distribution, leptomeningeal enhancement, early atrophy, and necrosis-that could deepen the understanding of the pathophysiology and manifestation of the autoimmune encephalitis besides the classic type.
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Affiliation(s)
- Sirong Piao
- Department of Radiology, Huashan Hospital, 535039Fudan University, Shanghai, PR China
| | - Yifang Bao
- Department of Radiology, Huashan Hospital, 535039Fudan University, Shanghai, PR China.,Institute of Functional and Molecular Medical Imaging, Fudan University, Shanghai, PR China
| | - Liqin Yang
- Department of Radiology, Huashan Hospital, 535039Fudan University, Shanghai, PR China.,Institute of Functional and Molecular Medical Imaging, Fudan University, Shanghai, PR China
| | - Yi Zhang
- Department of Infectious Disease, Huashan Hospital, 159397Fudan University, Shanghai, PR China
| | - Bin Hu
- Department of Radiology, Huashan Hospital, 535039Fudan University, Shanghai, PR China.,Institute of Functional and Molecular Medical Imaging, Fudan University, Shanghai, PR China
| | - Haiqing Li
- Department of Radiology, Huashan Hospital, 535039Fudan University, Shanghai, PR China.,Institute of Functional and Molecular Medical Imaging, Fudan University, Shanghai, PR China
| | - Daoying Geng
- Department of Radiology, Huashan Hospital, 535039Fudan University, Shanghai, PR China
| | - Yuxin Li
- Department of Radiology, Huashan Hospital, 535039Fudan University, Shanghai, PR China
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Liang S, Wang Z, Wu P, Chen Z, Yang X, Li Y, Ren X, Zhang D, Ge Z. Risk Factors and Outcomes of Central Nervous System Infection After Spinal Surgery: A Retrospective Cohort Study. World Neurosurg 2023; 170:e170-e179. [PMID: 36328166 DOI: 10.1016/j.wneu.2022.10.098] [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: 09/12/2022] [Revised: 10/24/2022] [Accepted: 10/25/2022] [Indexed: 11/06/2022]
Abstract
OBJECTIVE To investigate the risk factor associated with central nervous system infection, a rare and dire complication after spinal surgery. METHODS Univariate and multivariate logistic regression analyses were performed to screen for the independent risk factors. According to the different administration methods of antibiotics, patients were divided into intravenous and intrathecal groups. The differences in time needed for body temperature, white blood cells (WBC), and C-reactive protein (CRP) to return to normal and the time of antibiotic application were compared between the 2 groups. In addition, the differences in WBC, neutrophil ratio, CRP, procalcitonin in blood, and WBC in cerebrospinal fluid were compared before intrathecal injection, after the first one, and the last one. The incidence of complications in the 2 groups was observed. RESULTS Dural tears, laminectomy, and operation time >3 hours were identified as independent risk factors. The time needed for body temperature, WBC, and CRP to return to normal and the antibiotic application time were significantly different between the 2 groups (all P < 0.05). Before and after the first intrathecal injection and after the last intrathecal injection, the differences in WBCs, neutrophil ratios, CRP, procalcitonin in blood, and cerebrospinal fluid-WBC were statistically significant in overall and pairwise comparisons (P < 0.05). Complications occurred in 2 and 14 cases, respectively. CONCLUSIONS The independent risk factors for central nervous system infection after spinal surgery were a dural tear, laminectomy, and operation time > 3 hours. Combined intravenous and intrathecal injections of antibiotics led to a better effect than intravenous injection alone; however, this approach was associated with more complications.
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Affiliation(s)
- Simin Liang
- Department of Orthopaedics, General Hospital of Ningxia Medical University, Yinchuan City of Ningxia, China
| | - Zhiqiang Wang
- Department of Orthopaedics, General Hospital of Ningxia Medical University, Yinchuan City of Ningxia, China
| | - Peng Wu
- Department of Orthopaedics, General Hospital of Ningxia Medical University, Yinchuan City of Ningxia, China
| | - Zhen Chen
- Department of Orthopaedics, General Hospital of Ningxia Medical University, Yinchuan City of Ningxia, China
| | - Xiaoyan Yang
- Medical Laboratory Center, General Hospital of Ningxia Medical University, Yinchuan City of Ningxia, China
| | - Ying Li
- Medical Record Room, General Hospital of Ningxia Medical University, Yinchuan City of Ningxia, China
| | - Xiaolu Ren
- Department of Radiology, General Hospital of Ningxia Medical University, Yinchuan City of Ningxia, China
| | - Danmei Zhang
- Department of Nosocomial Infection, General Hospital of Ningxia Medical University, Yinchuan City of Ningxia, China
| | - Zhaohui Ge
- Department of Orthopaedics, General Hospital of Ningxia Medical University, Yinchuan City of Ningxia, China.
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Borroni D, Bonzano C, Sánchez-González JM, Rachwani-Anil R, Zamorano-Martín F, Pereza-Nieves J, Traverso CE, García Lorente M, Rodríguez-Calvo-de-Mora M, Esposito A, Godin F, Rocha-de-Lossada C. Shotgun metagenomic sequencing in culture negative microbial keratitis. Eur J Ophthalmol 2023:11206721221149077. [PMID: 36617769 DOI: 10.1177/11206721221149077] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
PURPOSE To evaluate the microbiota of culture negative Corneal Impression Membrane (CIM) microbial keratitis samples with the use of shotgun metagenomics analysis. METHODS DNA of microbial keratitis samples were collected with CIM and extracted using the MasterPure™ Complete DNA and RNA Purification Kit (Epicentre). DNA was fragmented by sonication into fragments of 300 to 400 base pairs (bp) using Bioruptor® (Diagenode, Belgium) and then used as a template for library preparation. DNA libraries were sequenced on Illumina® HiSeq2500. The resulting reads were quality controlled, trimmed and mapped against the human reference genome. The unmapped reads were taxonomically classified using the Kraken software. RESULTS 18 microbial keratitis samples were included in the study. Brevundimonas diminuta was found in 5 samples while 6 samples showed the presence of viral infections. Cutibacterium acnes, Staphylococcus aureus, Moraxella lacunata and Pseudomonas alcaligenes were also identified as the presumed putative cause of the infection in 7 samples. CONCLUSIONS Shotgun sequencing can be used as a diagnostic tool in microbial keratitis samples. This diagnostic method expands the available tests to diagnose eye infections and could be clinically significant in culture negative samples.
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Affiliation(s)
- Davide Borroni
- Department of Ophthalmology, Riga Stradins University, Riga, Latvia
| | - Chiara Bonzano
- DiNOGMI, University of Genoa and IRCCS San Martino Polyclinic Hospital, Genoa, Italy
| | | | | | | | | | - Carlo Enrico Traverso
- DiNOGMI, University of Genoa and IRCCS San Martino Polyclinic Hospital, Genoa, Italy
| | | | | | - Alfonso Esposito
- 18470International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Fernando Godin
- Department of Ophthalmology, Universidad El Bosque, Bogotá, Colombia
| | - Carlos Rocha-de-Lossada
- Qvision, Opththalmology Department, VITHAS Almería Hospital, Almería, Spain.,Ophthalmology Department, VITHAS Málaga, Málaga, Spain.,Hospital Regional Universitario de Málaga, Plaza del Hospital Civil, Málaga, Spain.,Departamento de Cirugía, Universidad de Sevilla, Área de Oftalmología, Doctor Fedriani, Seville, Spain
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50
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Feng L, Chen J, Luo Q, Su M, Chen P, Lai R, Shen C, Zhou H, Wang H, Sun X, Chen L, Xia H, Feng H. mNGS facilitates the accurate diagnosis and antibiotic treatment of suspicious critical CNS infection in real practice: A retrospective study. Open Life Sci 2023; 18:20220578. [PMID: 36879645 PMCID: PMC9985444 DOI: 10.1515/biol-2022-0578] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 01/16/2023] [Accepted: 01/23/2023] [Indexed: 03/06/2023] Open
Abstract
Whether metagenomic next-generation sequencing (mNGS) could benefit patients with suspected severe central nervous system (CNS) infection in terms of diagnosis and antibiotic treatment remains unknown. We retrospectively analyzed 79 patients with suspected CNS infection and undertook mNGS. The value of mNGS was investigated in terms of identification of pathogen and guidance for the adjustment of antibiotic treatment. The relationship between the time of initiating mNGS since onset and the Glasgow Outcome Scale (GOS) score after 90-day follow-up were analyzed. Fifty out of 79 cases with suspicious severe CNS infection were finally diagnosed. Despite previous routine laboratory tests, mNGS further promoted the accurate identification of pathogens in 23 cases (47.9%). The sensitivity, specificity, and accuracy of mNGS test in this study were 84.0, 79.3, and 82.3%, respectively. Furthermore, mNGS facilitated the adjustment of empirical antibiotic treatments in 38 cases (48.1%). The time of taking mNGS since onset had an insignificant weak positive correlation with GOS after 90-day follow-up (r = -0.73, P = 0.08). mNGS facilitated the accurate identification of pathogens in suspicious severe CNS infections and promoted the accurate antibiotic therapy even empirical antibiotics were administrated. It should be taken as early as possible to improve the clinical outcome of patients with suspicious severe CNS infection.
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Affiliation(s)
- Li Feng
- Department of Neurology, Neurological Intensive Care Unit, The First Affiliated Hospital, Sun Yat-Sen University; Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases; National Key Clinical Department and Key Discipline of Neurology, No. 58 Zhongshan 2nd Road, Guangzhou, 510080, China
| | - Jiaxin Chen
- Department of Neurology, Neurological Intensive Care Unit, The First Affiliated Hospital, Sun Yat-Sen University; Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases; National Key Clinical Department and Key Discipline of Neurology, No. 58 Zhongshan 2nd Road, Guangzhou, 510080, China
| | - Qiuyan Luo
- Department of Neurology, Neurological Intensive Care Unit, The First Affiliated Hospital, Sun Yat-Sen University; Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases; National Key Clinical Department and Key Discipline of Neurology, No. 58 Zhongshan 2nd Road, Guangzhou, 510080, China
| | - Miao Su
- Department of Neurology, Neurological Intensive Care Unit, The First Affiliated Hospital, Sun Yat-Sen University; Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases; National Key Clinical Department and Key Discipline of Neurology, No. 58 Zhongshan 2nd Road, Guangzhou, 510080, China
| | - Peisong Chen
- Department of Laboratory Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Rong Lai
- Department of Neurology, Neurological Intensive Care Unit, The First Affiliated Hospital, Sun Yat-Sen University; Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases; National Key Clinical Department and Key Discipline of Neurology, No. 58 Zhongshan 2nd Road, Guangzhou, 510080, China
| | - Cunzhou Shen
- Department of Neurology, Neurological Intensive Care Unit, The First Affiliated Hospital, Sun Yat-Sen University; Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases; National Key Clinical Department and Key Discipline of Neurology, No. 58 Zhongshan 2nd Road, Guangzhou, 510080, China
| | - Hongyan Zhou
- Department of Neurology, Neurological Intensive Care Unit, The First Affiliated Hospital, Sun Yat-Sen University; Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases; National Key Clinical Department and Key Discipline of Neurology, No. 58 Zhongshan 2nd Road, Guangzhou, 510080, China
| | - Haiyan Wang
- Department of Neurology, Neurological Intensive Care Unit, The First Affiliated Hospital, Sun Yat-Sen University; Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases; National Key Clinical Department and Key Discipline of Neurology, No. 58 Zhongshan 2nd Road, Guangzhou, 510080, China
| | - Xunsha Sun
- Department of Neurology, Neurological Intensive Care Unit, The First Affiliated Hospital, Sun Yat-Sen University; Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases; National Key Clinical Department and Key Discipline of Neurology, No. 58 Zhongshan 2nd Road, Guangzhou, 510080, China
| | - Ling Chen
- Department of Neurology, Neurological Intensive Care Unit, The First Affiliated Hospital, Sun Yat-Sen University; Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases; National Key Clinical Department and Key Discipline of Neurology, No. 58 Zhongshan 2nd Road, Guangzhou, 510080, China
| | - Han Xia
- Department of Scientific Affairs, Hugobiotech Co., Ltd., Beijing 100176, China
| | - Huiyu Feng
- Department of Neurology, Neurological Intensive Care Unit, The First Affiliated Hospital, Sun Yat-Sen University; Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases; National Key Clinical Department and Key Discipline of Neurology, No. 58 Zhongshan 2nd Road, Guangzhou, 510080, China
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