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Rodrigues C, Singhal T. What is New in the Diagnosis of Childhood Tuberculosis? Indian J Pediatr 2024; 91:717-723. [PMID: 38163830 DOI: 10.1007/s12098-023-04992-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 12/08/2023] [Indexed: 01/03/2024]
Abstract
The fact that almost half of the 1 million cases of childhood tuberculosis (TB) globally remain undiagnosed jeopardizes the TB elimination goal. Fortunately, there are new advances in this field which have the potential to bridge this diagnostic gap. Advances in imaging include computer assisted interpretation of chest X-rays (CXRs), point of care ultrasound (POCUS) and faster and superior computed tomography/ magnetic resonance imaging (CT/ MRI) protocols. The urine lipoarabinomannan test has proved to be a good point of care test for diagnosing TB in Human immunodeficiency virus (HIV) infected children. Stool and nasopharyngeal aspirates are emerging as acceptable alternatives for gastric lavage and induced sputum for diagnosing intrathoracic tuberculosis. Xpert MTB/RIF Ultra has improved sensitivity compared to Xpert MTB/RIF for diagnosing both pulmonary/ extrapulmonary TB. Xpert XDR is another commercially available accurate point of care test for detecting resistance to drugs other than rifampicin in smear positive samples. Other molecular methods including new line probe assays, pyrosequencing, whole genome sequencing, and targeted next generation sequencing are extremely promising but not available commercially at present. The C-Tb skin test is an acceptable alternative to the tuberculin skin test and interferon gamma release assays for diagnosis of latent infection. There is an urgent need to incorporate some of these advances in the existing diagnostic algorithms of childhood TB.
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Affiliation(s)
- Camilla Rodrigues
- Department of Microbiology & Infection Prevention Control, Hinduja Hospital, Mahim, Mumbai, India
| | - Tanu Singhal
- Department of Pediatrics and Infectious Disease, Kokilaben Dhirubhai Ambani Hospital and Medical Research Institute, Mumbai, India.
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Yang L, Su J, Zhuo C. A case of intracranial infection caused by Aspergillus flavus originating from chronic otitis media. Med Mycol Case Rep 2024; 44:100637. [PMID: 38585188 PMCID: PMC10997898 DOI: 10.1016/j.mmcr.2024.100637] [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: 11/13/2023] [Revised: 02/18/2024] [Accepted: 02/22/2024] [Indexed: 04/09/2024] Open
Abstract
Central nervous system (CNS) aspergillosis is uncommon in immunocompetent patients. We present a 64-year-old man with chronic otitis media and uncontrolled diabetes. Aspergillus flavus was identified in cerebrospinal fluid via metagenomics next-generation sequencing technology. Initial voriconazole treatment offered limited relief, but personalized dosage adjustments, guided by drug concentration, led to remission. This case underscores the importance of diverse diagnostic approaches and tailored therapy for CNS Aspergillus infections.
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Affiliation(s)
- Ling Yang
- Department of Infection, The First Hospital of Guangzhou Medical University, Guangzhou, 510000, China
| | - Jiacun Su
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Chao Zhuo
- Department of Infection, The First Hospital of Guangzhou Medical University, Guangzhou, 510000, 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 2024:1-14. [PMID: 38772736 DOI: 10.1631/jzus.b2300029] [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: 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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Chen W, Liu G, Cui L, Tian F, Zhang J, Zhao J, Lv Y, Du J, Huan X, Wu Y, Zhang Y. Evaluation of metagenomic and pathogen-targeted next-generation sequencing for diagnosis of meningitis and encephalitis in adults: A multicenter prospective observational cohort study in China. J Infect 2024; 88:106143. [PMID: 38548243 DOI: 10.1016/j.jinf.2024.106143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 02/17/2024] [Accepted: 03/20/2024] [Indexed: 04/20/2024]
Abstract
BACKGROUND Next-generation sequencing (NGS) might aid in the identification of causal pathogens. However, the optimal approaches applied to cerebrospinal fluid (CSF) for detection are unclear, and studies evaluating the application of different NGS workflows for the diagnosis of intracranial infections are limited. METHODS In this multicenter, prospective observational cohort study, we described the diagnostic efficacy of pathogen-targeted NGS (ptNGS) and metagenomic NGS (mNGS) compared to that of composite microbiologic assays, for infectious meningitis/encephalitis (M/E). RESULTS In total, 152 patients diagnosed with clinically suspected M/E at four tertiary hospitals were enrolled; ptNGS and mNGS were used in parallel for pathogen detection in CSF. Among the 89 patients who were diagnosed with definite infectious M/E, 57 and 39 patients had causal microbial detection via ptNGS and mNGS, respectively. The overall accuracy of ptNGS was 65.1%, with a positive percent agreement (PPA) of 64% and a negative percent agreement (NPA) of 66.7%; and the overall accuracy of mNGS was 47.4%, with a PPA of 43.8% and an NPA of 52.4% after discrepancy analysis. There was a significant difference in the detection efficiency between these two methods both for PPA (sensitivity) and overall accuracy for pathogen detection (P < 0.05). CONCLUSIONS NGS tests have provided new information in addition to conventional microbiologic tests. ptNGS seems to have superior performance over mNGS for common causative pathogen detection in CSF for infectious M/E.
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Affiliation(s)
- Weibi Chen
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Gang Liu
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Lili Cui
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Fei Tian
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Jiatang Zhang
- Department of Neurology, the First Medical Center of People's Liberation Army General Hospital, Beijing, China
| | - Jiahua Zhao
- Department of Neurology, the First Medical Center of People's Liberation Army General Hospital, Beijing, China
| | - Ying Lv
- Department of Neurology & Psychiatry, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Jianxin Du
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China; Department of Neurosurgery, Beijing Fengtai Youanmen Hospital, Beijing, China
| | - Xinyu Huan
- Department of Neurosurgery, Beijing Fengtai Youanmen Hospital, Beijing, China
| | - Yingfeng Wu
- Department of Vascular Surgery, Xuanwu Hospital, Capital Medical University, Beijing, China.
| | - Yan Zhang
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China; Department of Sleep and Consciousness Disorders, Beijing Institute of Brain Disorders, Collaborative Innovation Center for Brain Disorders, Capital Medical University, Beijing, China.
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Guo SS, Fu G, Hu YW, Liu J, Wang YZ. Application of metagenomic next-generation sequencing technology in the etiological diagnosis of peritoneal dialysis-associated peritonitis. Open Life Sci 2024; 19:20220865. [PMID: 38681728 PMCID: PMC11049737 DOI: 10.1515/biol-2022-0865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 01/25/2024] [Accepted: 03/19/2024] [Indexed: 05/01/2024] Open
Abstract
Pathogens detected by metagenomic next-generation sequencing (mNGS) and the laboratory blood culture flask method were compared to understand the advantages and clinical significance of mNGS assays in the etiological diagnosis of peritoneal dialysis-associated peritonitis (PDAP). The study involved a total of 37 patients from the hospital's peritoneal dialysis centre, six of whom were patients with non-peritoneal dialysis-associated peritonitis. Peritoneal dialysis samples were collected from the 37 patients, who were divided into two groups. One group's samples were cultured using conventional blood culture flasks, and the other samples underwent pathogen testing using mNGS. The results showed that the positive rate of mNGS was 96.77%, while that of the blood culture flask method was 70.97% (p < 0.05). A total of 29 pathogens were detected by mNGS, namely 24 bacteria, one fungus, and four viruses. A total of 10 pathogens were detected using the bacterial blood culture method, namely nine bacteria and one fungus. The final judgment of the PDAP's causative pathogenic microorganism was made by combining the clinical condition, response to therapy, and the whole-genome sequencing findings. For mNGS, the sensitivity was 96.77%, the specificity was 83.33%, the positive predictive value was 96.77%, and the negative predictive value was 83.33%. For the blood culture flask method, the sensitivity was 70.97%, the specificity was 100%, the positive predictive value was 100%, and the negative predictive value was 0%. In conclusion, mNGS had a shorter detection time for diagnosing peritoneal dialysis-related peritonitis pathogens, with a higher positive rate than traditional bacterial cultures, providing significant advantages in diagnosing rare pathogens.
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Affiliation(s)
- Shan-Shan Guo
- The Nephrology Department, Beijing Haidian Hospital, Haidian District, Beijing100191, China
| | - Gang Fu
- The Nephrology Department, Beijing Haidian Hospital, Haidian District, Beijing100191, China
| | - Yan-Wei Hu
- The Nephrology Department, Beijing Haidian Hospital, Haidian District, Beijing100191, China
| | - Jing Liu
- The Nephrology Department, Beijing Haidian Hospital, Haidian District, Beijing100191, China
| | - Yu-Zhu Wang
- The Nephrology Department, Beijing Haidian Hospital, No. 29 Zhongguancun Street, Haidian District, Beijing100191, China
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Zhao W, Zhou Y, Hu Y, Luo W, Wang J, Zhu H, Xu Z. Predictors of mortality and poor outcome for patients with severe infectious encephalitis in the intensive care unit: a cross-sectional study. BMC Infect Dis 2024; 24:421. [PMID: 38644471 PMCID: PMC11034050 DOI: 10.1186/s12879-024-09312-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 04/10/2024] [Indexed: 04/23/2024] Open
Abstract
BACKGROUND There are few thorough studies assessing predictors of severe encephalitis, despite the poor prognosis and high mortality associated with severe encephalitis. The study aims to evaluate the clinical predictors of mortality and poor outcomes at hospital discharge in patients with severe infectious encephalitis in intensive care units. METHOD In two Chinese hospitals, a retrospective cohort study comprising 209 patients in intensive care units suffering from severe infectious encephalitis was carried out. Univariate and multivariate logistic regression analyses were used to identify the factors predicting mortality in all patients and poor outcomes in all survivors with severe infectious encephalitis. RESULTS In our cohort of 209 patients with severe encephalitis, 22 patients died, yielding a mortality rate of 10.5%. Cerebrospinal fluid pressure ≥ 400mmH2O (OR = 7.43), abnormal imaging (OR = 3.51), abnormal electroencephalogram (OR = 7.14), and number of rescues (OR = 1.12) were significantly associated with an increased risk of mortality in severe infectious encephalitis patients. Among the 187 survivors, 122 (65.2%) had favorable outcomes, defined as the modified Rankine Scale (mRS) score (0 ~ 3), and 65(34.8%) had poor outcomes (mRS scores 4 ~ 5). Age (OR = 1.02), number of rescues (OR = 1.43), and tubercular infection (OR = 10.77) were independent factors associated with poor outcomes at discharge in all survivors with severe infectious encephalitis. CONCLUSIONS Multiple clinical, radiologic, and electrophysiological variables are independent predictive indicators for mortality and poor outcomes in patients with severe encephalitis in intensive care units. Identifying these outcome predictors early in patients with severe encephalitis may enable the implementation of appropriate medical treatment and help reduce mortality rates.
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Affiliation(s)
- WenYan Zhao
- Department of Neuropsychology, Zhongnan Hospital of Wuhan University, Wuhan, People's Republic of China
| | - YuLiang Zhou
- Department of Neuropsychology, Zhongnan Hospital of Wuhan University, Wuhan, People's Republic of China
| | - YingYing Hu
- Department of Neuropsychology, Zhongnan Hospital of Wuhan University, Wuhan, People's Republic of China
| | - WenJing Luo
- Department of Neurology, General Hospital of Central Theater Command, Wuhan, People's Republic of China
| | - Jing Wang
- Department of Neuropsychology, Zhongnan Hospital of Wuhan University, Wuhan, People's Republic of China.
| | - Hong Zhu
- Department of Neuropsychology, Zhongnan Hospital of Wuhan University, Wuhan, People's Republic of China
| | - ZhiPeng Xu
- Department of Neuropsychology, Zhongnan Hospital of Wuhan University, Wuhan, People's Republic of China.
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Lee WJ, Tsai MH, Hsu JF, Chu SM, Chen CC, Yang PH, Huang HR, Chi MC, Lee CW, Ou-Yang MC. The Epidemiology, Management and Therapeutic Outcomes of Subdural Empyema in Neonates with Acute Bacterial Meningitis. Antibiotics (Basel) 2024; 13:377. [PMID: 38667053 PMCID: PMC11047628 DOI: 10.3390/antibiotics13040377] [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: 03/21/2024] [Revised: 04/18/2024] [Accepted: 04/19/2024] [Indexed: 04/29/2024] Open
Abstract
Background: Subdural empyema is one of the more serious complications of bacterial meningitis and therapeutic challenges to clinicians. We aimed to evaluate the clinical characteristics, treatment, and outcome of subdural empyema in neonates with bacterial meningitis. Methods: A retrospective cohort study was conducted in two medical centers in Taiwan that enrolled all cases of neonates with subdural empyema after bacterial meningitis between 2003 and 2020. Results: Subdural empyema was diagnosed in 27 of 153 (17.6%) neonates with acute bacterial meningitis compared with cases of meningitis without subdural empyema. The demographics and pathogen distributions were comparable between the study group and the controls, but neonates with subdural empyema were significantly more likely to have clinical manifestations of fever (85.2%) and seizure (81.5%) (both p values < 0.05). The cerebrospinal fluid results of neonates with subdural empyema showed significantly higher white blood cell counts, lower glucose levels and higher protein levels (p = 0.011, 0.003 and 0.006, respectively). Neonates with subdural empyema had a significantly higher rate of neurological complications, especially subdural effusions and periventricular leukomalacia. Although the final mortality rate was not increased in neonates with subdural empyema when compared with the controls, they were often treated much longer and had a high rate of long-term neurological sequelae. Conclusions: Subdural empyema is not uncommon in neonates with acute bacterial meningitis and was associated with a high risk of neurological complications, although it does not significantly increase the final mortality rate. Close monitoring of the occurrence of subdural empyema is required, and appropriate long-term antibiotic treatment after surgical intervention may lead to optimized outcomes.
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Affiliation(s)
- Wei-Ju Lee
- Division of Pediatric Emergency Medicine, Department of Pediatrics, Chang Gung Memorial Hospital, Chiayi 613, Taiwan;
- College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (M.-H.T.); (J.-F.H.); (S.-M.C.); (C.-C.C.); (P.-H.Y.); (H.-R.H.)
| | - Ming-Horng Tsai
- College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (M.-H.T.); (J.-F.H.); (S.-M.C.); (C.-C.C.); (P.-H.Y.); (H.-R.H.)
- Division of Neonatology and Pediatric Hematology/Oncology, Department of Pediatrics, Chang Gung Memorial Hospital, Yunlin 638, Taiwan
| | - Jen-Fu Hsu
- College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (M.-H.T.); (J.-F.H.); (S.-M.C.); (C.-C.C.); (P.-H.Y.); (H.-R.H.)
- Division of Pediatric Neonatology, Department of Pediatrics, Chang Gung Memorial Hospital, Kaohsiung 833, Taiwan
| | - Shih-Ming Chu
- College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (M.-H.T.); (J.-F.H.); (S.-M.C.); (C.-C.C.); (P.-H.Y.); (H.-R.H.)
- Division of Pediatric Neonatology, Department of Pediatrics, Chang Gung Memorial Hospital, Kaohsiung 833, Taiwan
| | - Chih-Chen Chen
- College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (M.-H.T.); (J.-F.H.); (S.-M.C.); (C.-C.C.); (P.-H.Y.); (H.-R.H.)
- Division of Pediatric Neonatology, Department of Pediatrics, Chang Gung Memorial Hospital, Kaohsiung 833, Taiwan
| | - Peng-Hong Yang
- College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (M.-H.T.); (J.-F.H.); (S.-M.C.); (C.-C.C.); (P.-H.Y.); (H.-R.H.)
- Department of Respiratory Care, Chang Gung University of Science and Technology, Chiayi 61363, Taiwan; (M.-C.C.); (C.-W.L.)
| | - Hsuan-Rong Huang
- College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (M.-H.T.); (J.-F.H.); (S.-M.C.); (C.-C.C.); (P.-H.Y.); (H.-R.H.)
- Division of Pediatric Neonatology, Department of Pediatrics, Chang Gung Memorial Hospital, Kaohsiung 833, Taiwan
| | - Miao-Ching Chi
- Department of Respiratory Care, Chang Gung University of Science and Technology, Chiayi 61363, Taiwan; (M.-C.C.); (C.-W.L.)
- Chronic Diseases and Health Promotion Research Center, Chang Gung University of Science and Technology, Chiayi 61363, Taiwan
| | - Chiang-Wen Lee
- Department of Respiratory Care, Chang Gung University of Science and Technology, Chiayi 61363, Taiwan; (M.-C.C.); (C.-W.L.)
- Chronic Diseases and Health Promotion Research Center, Chang Gung University of Science and Technology, Chiayi 61363, Taiwan
| | - Mei-Chen Ou-Yang
- College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (M.-H.T.); (J.-F.H.); (S.-M.C.); (C.-C.C.); (P.-H.Y.); (H.-R.H.)
- Division of Pediatric Neonatology, Department of Pediatrics, Chang Gung Memorial Hospital, Kaohsiung 833, Taiwan
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Lin L, Fang J, Li J, Tang Y, Xin T, Ouyang N, Cai W, Xie L, Lu S, Zhang J. Metagenomic Next-Generation Sequencing Contributes to the Early Diagnosis of Mixed Infections in Central Nervous System. Mycopathologia 2024; 189:34. [PMID: 38637353 DOI: 10.1007/s11046-024-00837-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 02/13/2024] [Indexed: 04/20/2024]
Abstract
Central nervous system (CNS) infections represent a challenge due to the complexities associated with their diagnosis and treatment, resulting in a high incidence rate and mortality. Here, we presented a case of CNS mixed infection involving Candida and human cytomegalovirus (HCMV), successfully diagnosed through macrogenomic next-generation sequencing (mNGS) in China. A comprehensive review and discussion of previously reported cases were also provided. Our study emphasizes the critical role of early pathogen identification facilitated by mNGS, underscoring its significance. Notably, the integration of mNGS with traditional methods significantly enhances the diagnostic accuracy of CNS infections. This integrated approach has the potential to provide valuable insights for clinical practice, facilitating early diagnosis, allowing for treatment adjustments, and ultimately, improving the prognosis for patients with CNS infections.
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Affiliation(s)
- Li Lin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Department of Dermatology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Junyue Fang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Cellular and Molecular Diagnostics Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Jiahao Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Department of Dermatology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Ying Tang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Department of Dermatology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Tengteng Xin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Department of Dermatology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Nengtai Ouyang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Cellular and Molecular Diagnostics Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Wenying Cai
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Department of Dermatology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Lisi Xie
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.
| | - Sha Lu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.
- Department of Dermatology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.
| | - Junmin Zhang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.
- Department of Dermatology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.
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10
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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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11
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Yuan L, Lai LM, Zhu X, Rui Z, Liu Y, Chen Q. Haemophilus aphrophilus and Eikenella corrodens Coinfection of Brain: An Unusual Case from China. Infect Drug Resist 2024; 17:1439-1445. [PMID: 38628241 PMCID: PMC11020326 DOI: 10.2147/idr.s458020] [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: 01/04/2024] [Accepted: 04/03/2024] [Indexed: 04/19/2024] Open
Abstract
Background The HACEK group comprises Haemophilus spp., Aggregatibacter actinomycetemcomitans, Cardiobacterium hominis, Eikenella corrodens, and Kingella kingae, are Gram-negative bacteria that are slow-growing and fastidious. These organisms are common causes of culture-negative endocarditis. However, brain abscesses caused by Haemophilus aphrophilus and E. corrodens have been rarely reported. The case we describe, which was promptly identified and successfully treated, will be meaningful for the diagnosis and treatment of such infectious diseases. Case Presentation Herein, we report a case of brain abscess in a young man who was infected with Haemophilus aphrophilus and E. corrodens. The patient was admitted to the hospital with sudden onset of vomiting, coma, and fever. Magnetic resonance imaging (MRI) of the brain and cerebrospinal fluid cell counts suggested cerebral abscess, he underwent drainage of the abscess and empirical antimicrobial therapy of meropenem (2 g every 8 hours) and linezolid (0.6 g every 12 hours) for more than 10 days without significant improvement. Metagenomic next-generation sequencing (mNGS) of drainage fluid and matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) detection for isolated bacteria from samples suggested the presence of H. aphrophilus and E. corrodens. After 7 weeks of ceftriaxone (2 g every 12 hours) and meropenem (2 g every 8 hours) intravenously, the patient was discharged with a normal temperature and brain MRI showed improvement of the lesion. Conclusion Similar cases reported in previous studies were always associated with bacterial blood dissemination after dental surgery or myocarditis; however, the patient in our case had no any associated risk factors. As far as we know, this is the only case of central nervous system infection caused by H. aphrophilus and E. corrodens that has utilized combined mNGS and MALDI-TOF MS in the diagnosis.
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Affiliation(s)
- Lei Yuan
- Department of Clinical laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, People’s Republic of China
| | - Lan Min Lai
- Department of Clinical laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, People’s Republic of China
| | - Xinyu Zhu
- Department of Clinical laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, People’s Republic of China
| | - Zhao Rui
- Department of Clinical laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, People’s Republic of China
| | - Yang Liu
- Department of Clinical laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, People’s Republic of China
| | - Qiang Chen
- Department of Clinical laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, People’s Republic of China
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12
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Lv T, Zhao Q, Liu J, Wang S, Wu W, Miao L, Zhan P, Chen X, Huang M, Ye M, Ou Q, Zhang Y. Utilizing metagenomic next-generation sequencing for pathogen detection and diagnosis in lower respiratory tract infections in real-world clinical practice. Infection 2024; 52:625-636. [PMID: 38368306 DOI: 10.1007/s15010-024-02185-1] [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: 07/13/2023] [Accepted: 01/12/2024] [Indexed: 02/19/2024]
Abstract
BACKGROUND Infectious etiologies of lower respiratory tract infections (LRTIs) by the conventional microbiology tests (CMTs) can be challenging. Metagenomic next-generation sequencing (mNGS) has great potential in clinical use for its comprehensiveness in identifying pathogens, particularly those difficult-to-culture organisms. METHODS We analyzed a total of 205 clinical samples from 201 patients with suspected LRTIs using mNGS in parallel with CMTs. mNGS results were used to guide treatment adjustments for patients who had negative CMT results. The efficacy of treatment was subsequently evaluated in these patients. RESULTS mNGS-detected microorganisms in 91.7% (188/205) of the clinical samples, whereas CMTs demonstrated a lower detection rate, identifying microorganisms in only 37.6% (77/205) of samples. Compared to CMT results, mNGS exhibited a detection sensitivity of 93.5% and 95.4% in all 205 clinical samples and 180 bronchoalveolar lavage fluid (BALF) samples, respectively. A total of 114 patients (114/201; 56.7%) showed negative CMT results, among which 92 received treatment adjustments guided by their positive mNGS results. Notably, 67.4% (62/92) of patients demonstrated effective treatment, while 25% (23/92) experienced a stabilized condition. Subgroup analysis of cancer patients revealed that 41.9% (13/31) exhibited an effective response to treatment, and 35.5% (11/31) maintained a stable condition following medication adjustments guided by mNGS. CONCLUSION mNGS demonstrated great potential in identifying microorganisms of clinical significance in LRTIs. The rapid turnaround time and reduced susceptibility to the impact of antimicrobial administration make mNGS a valuable supplementary tool for diagnosis and treatment decision-making for suspected LRTIs in clinical practice.
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Affiliation(s)
- Tangfeng Lv
- Department of Respiratory and Critical Care Medicine, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210002, Jiangsu, China
| | - Qi Zhao
- Department of Pulmonary and Critical Care Medicine, Nanjing Drum Tower Hospital, Nanjing, 210008, Jiangsu, China
| | - Jia Liu
- Dinfectome Inc., Nanjing, 210000, Jiangsu, China
| | - Song Wang
- Dinfectome Inc., Nanjing, 210000, Jiangsu, China
| | - Weiwei Wu
- Dinfectome Inc., Nanjing, 210000, Jiangsu, China
| | - Liyun Miao
- Department of Respiratory and Critical Care Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, Jiangsu, China
- Yancheng Branch of Nanjing Drum Tower Hospital, Yancheng, 224002, Jiangsu, China
| | - Ping Zhan
- Department of Respiratory and Critical Care Medicine, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210002, Jiangsu, China
| | - Xiaoli Chen
- Department of Respiratory and Critical Care Medicine, Jiangsu Provincial Hospital of Integrated Chinese and Western Medicine, 100 Cross Street, Hongshan Road, Nanjing, 210028, Jiangsu, China
| | - Manman Huang
- Dinfectome Inc., Nanjing, 210000, Jiangsu, China
| | - Mingxiang Ye
- Department of Respiratory and Critical Care Medicine, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210002, Jiangsu, China
| | - Qiuxiang Ou
- Dinfectome Inc., Nanjing, 210000, Jiangsu, China
| | - Yeqing Zhang
- Department of Respiratory and Critical Care Medicine, Jiangsu Provincial Hospital of Integrated Chinese and Western Medicine, 100 Cross Street, Hongshan Road, Nanjing, 210028, Jiangsu, China.
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13
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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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15
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Chen Y, Wang J, Niu T. Clinical and diagnostic values of metagenomic next-generation sequencing for infection in hematology patients: a systematic review and meta-analysis. BMC Infect Dis 2024; 24:167. [PMID: 38326763 PMCID: PMC10848439 DOI: 10.1186/s12879-024-09073-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 01/29/2024] [Indexed: 02/09/2024] Open
Abstract
OBJECTIVES This meta-analysis focused on systematically assessing the clinical value of mNGS for infection in hematology patients. METHODS We searched for studies that assessed the clinical value of mNGS for infection in hematology patients published in Embase, PubMed, Cochrane Library, Web of Science, and CNKI from inception to August 30, 2023. We compared the detection positive rate of pathogen for mNGS and conventional microbiological tests (CMTs). The diagnostic metrics, antibiotic adjustment rate and treatment effective rate were combined. RESULTS Twenty-two studies with 2325 patients were included. The positive rate of mNGS was higher than that of CMT (blood: 71.64% vs. 24.82%, P < 0.001; BALF: 89.86% vs. 20.78%, P < 0.001; mixed specimens: 82.02% vs. 28.12%, P < 0.001). The pooled sensitivity and specificity were 87% (95%CI: 81-91%) and 59% (95%CI: 43-72%), respectively. The reference standard/neutropenia and research type/reference standard may be sources of heterogeneity in sensitivity and specificity, respectively. The pooled antibiotic adjustment rate according to mNGS was 49.6% (95% CI: 41.8-57.4%), and the pooled effective rate was 80.9% (95% CI: 62.4-99.3%). CONCLUSION mNGS has high positive detection rates in hematology patients. mNGS can guide clinical antibiotic adjustments and improve prognosis, especially in China.
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Affiliation(s)
- Yuhui Chen
- Department of Hematology, West China Hospital, Sichuan University, Chengdu, China
| | - Jinjin Wang
- Department of Hematology, West China Hospital, Sichuan University, Chengdu, China
| | - Ting Niu
- Department of Hematology, West China Hospital, Sichuan University, Chengdu, China.
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16
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Guo Q, Xiao Y, Zhang S. Metagenomic next generation sequencing of bronchoalveolar lavage samples for the diagnosis of lower respiratory tract infections: A systematic review and meta-analysis. Heliyon 2024; 10:e23188. [PMID: 38148812 PMCID: PMC10750151 DOI: 10.1016/j.heliyon.2023.e23188] [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: 12/06/2022] [Revised: 10/07/2023] [Accepted: 11/29/2023] [Indexed: 12/28/2023] Open
Abstract
Background Lower respiratory tract infections (LRTI)are known to be diagnosed late or inaccurately. This has fueled the unscrupulous use of antibiotics, as they are often used empirically and clinically, leading to antibiotic abuse and multidrug resistance in patients. Metagenomic next-generation sequencing (mNGS), now widely used in clinical studies, could be a potential intervention to revolutionize microbiology by rapidly identifying unknown species. Methods This review and meta-analysis were conducted on eligible studies with respect to metagenomic sequencing on clinical LRTI diagnostics up to May 01, 2022. QUADAS-2 was employed to assess the methodological bias as well as applicability. After that, a meta-analysis was conducted to analyze the accuracy of mNGS, compared with the composite reference standard (CRS), among the enrolled studies. Results This work collected 1248 samples in 13/21 qualified articles to factor in the accuracy of the diagnostic test. Typically, methods like molecular testing, culture, composite measures, and clinical decision-making were adopted as the reference criteria. With regard to Bronchoalveolar Lavage Samples, their sensitivity was 89% (82-93%) while their specificity was 90% (66-98%), with obvious heterogeneities in these two factors as demonstrated by different studies. The summary receiver operating characteristic (SROC) curve was plotted for mNGS as a function of LRTI, and the area under the curve (AUC) was 0.94. A Funnel plot with a p-value greater than 0.05 indicated the absence of publication bias. Positive and negative likelihood ratios (PLR and NLR) were >10 and > 0.1, respectively. In this pre-test probability-post-probability-likelihood ratio relationship graph, the values were Prior prob (%) = 20, Post-prob-Pos (%) = 77 and Post-prob-Neg (%) = 4. Conclusion The AUC value of SROC suggested a high accuracy of mNGS in diagnosis, with no publication bias and high reliability. The application of mNGS exhibits notable diagnostic efficacy in discerning pathogens present in bronchoalveolar lavage fluid (BALF) among patients afflicted with LRTI. However, mNGS is more meaningful for the definitive diagnosis of the disease rather than the exclusion of the disease. This post-test probability is significantly higher than the pre-test probability.
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Affiliation(s)
- Qiang Guo
- Department of Clinical Laboratory, Anhui Provincial Children’s Hospital, Hefei, 230000, Anhui, China
| | - Yang Xiao
- School of Anesthesiology, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Shihai Zhang
- Department of Clinical Laboratory, Anhui Provincial Children’s Hospital, Hefei, 230000, Anhui, China
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Lu Y, Zhang Y, Lou Z, He X, Zhang Q, Zhang Q, Zhao S, Chen H, Zhu H, Song Z, Zhang R, Ma C, Liu D. Metagenomic next-generation sequencing of cell-free DNA for the identification of viruses causing central nervous system infections. Microbiol Spectr 2024; 12:e0226423. [PMID: 38095471 PMCID: PMC10783088 DOI: 10.1128/spectrum.02264-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 11/22/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE This study provides significant new data on the application of metagenomic next-generation sequencing (mNGS) to clinical diagnostics of central nervous system (CNS) viral infections, which can have high mortality rates and severe sequelae. Conventional diagnostic procedures for identifying viruses can be inefficient and rely on preconceived assumptions about the pathogen, making mNGS an appealing alternative. However, the effectiveness of mNGS is affected by the presence of human DNA contamination, which can be minimized by using cell-free DNA (cfDNA) instead of whole-cell DNA (wcDNA). This multi-center retrospective study of patients with suspected viral CNS infection found that mNGS using cfDNA had a significantly lower proportion of human DNA and higher sensitivity for detecting viruses than mNGS using wcDNA. Herpesviruses, particularly VZV, were found to be the most common DNA viruses in these patients. Overall, mNGS using cfDNA is a promising complementary diagnostic method for detecting CNS viral infections.
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Affiliation(s)
- Yuying Lu
- Department of Neurology, The Third Xiangya Hospital of Central South University, Changsha, China
- Key laboratory of Microbial Molecular Biology of Hunan Province, Hunan Provincial Center for Disease Control and Prevention, Changsha, China
| | - Ye Zhang
- Department of Scientific Affairs, Hugobiotech Co., Ltd., Beijing, China
| | - Zheng Lou
- Department of Scientific Affairs, Hugobiotech Co., Ltd., Beijing, China
| | - Xiaomin He
- Department of Scientific Affairs, Hugobiotech Co., Ltd., Beijing, China
| | - Qinghua Zhang
- Department of Neurology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Qingxia Zhang
- Department of Neurology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Shu Zhao
- Department of Neurology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Han Chen
- Department of Neurology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Haixia Zhu
- Department of Neurology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Zhi Song
- Department of Neurology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Ruxu Zhang
- Department of Neurology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Caiyu Ma
- Department of Neurology, The Third Xiangya Hospital of Central South University, Changsha, China
- Department of Neurology, The Affiliated Changsha Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Ding Liu
- Department of Neurology, The Third Xiangya Hospital of Central South University, Changsha, China
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Yang T, Cai Y, Zhu Y. Acute lymphoblastic leukemia with central nervous system Aspergillus infection: A case report and literature review. Exp Ther Med 2024; 27:46. [PMID: 38144920 PMCID: PMC10739171 DOI: 10.3892/etm.2023.12336] [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: 03/16/2023] [Accepted: 11/16/2023] [Indexed: 12/26/2023] Open
Abstract
Ubiquitous in nature, Aspergillus rarely invades the brain to induce infection in general. However, in clinical practice, some patients with hematological malignancies or immunosuppression may suffer from Aspergillus infection of the central nervous system, which arises most commonly as a result of hematogenous dissemination from a pulmonary focus or direct extension from the paranasal sinus infection. Treatment is clinically challenging and the mortality rate is relatively high. Recently, a case diagnosed with acute lymphocytic leukemia was admitted to the Department of Neurosurgery, The First People's Hospital of Huzhou (First Affiliated Hospital of Huzhou University, Huzhou, China). During chemotherapy, space-occupying lesions were observed in the right occipital lobe of the patient, and lesion progression was captured. After treatment with surgery, an analysis of specimens collected from the patient was performed and was suggestive of Aspergillus infection. Following the symptomatic therapy with voriconazole, the patient's disease prognosis was favorable. The focus of infection due to pulmonary aspergillosis or Aspergillus sinusitis was not detected in the patient and the focus was not a common site of hematogenous infection. In addition, the patient exhibited no obvious clinical symptoms. In view of the above observations, the possibility of hospital-acquired infection was considered, to which clinicians should be alert.
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Affiliation(s)
- Tao Yang
- Department of Neurosurgery, The First People's Hospital of Huzhou (First Affiliated Hospital of Huzhou University), Huzhou, Zhejiang 313000, P.R. China
| | - Yong Cai
- Department of Neurosurgery, The First People's Hospital of Huzhou (First Affiliated Hospital of Huzhou University), Huzhou, Zhejiang 313000, P.R. China
| | - Yaping Zhu
- Department of Pathology, The First People's Hospital of Huzhou (First Affiliated Hospital of Huzhou University), Huzhou, Zhejiang 313000, P.R. China
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Zhu N, Zhou D, Xiong W, Zhang X, Li S. Performance of mNGS in bronchoalveolar lavage fluid for the diagnosis of invasive pulmonary aspergillosis in non-neutropenic patients. Front Cell Infect Microbiol 2023; 13:1271853. [PMID: 38029249 PMCID: PMC10644336 DOI: 10.3389/fcimb.2023.1271853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 10/03/2023] [Indexed: 12/01/2023] Open
Abstract
The diagnosis of invasive pulmonary aspergillosis (IPA) diseases in non-neutropenic patients remains challenging. It is essential to develop optimal non-invasive or minimally invasive detection methods for the rapid and reliable diagnosis of IPA. Metagenomic next-generation sequencing (mNGS) in bronchoalveolar lavage fluid (BALF) can be a valuable tool for identifying the microorganism. Our study aims to evaluate the performance of mNGS in BALF in suspected IPA patients and compare it with other detection tests, including serum/BALF galactomannan antigen (GM) and traditional microbiological tests (BALF fungal culture and smear and lung biopsy histopathology). Ninety-four patients with suspicion of IPA were finally enrolled in our study. Thirty-nine patients were diagnosed with IPA, and 55 patients were non-IPA. There was significance between the IPA and non-IPA groups, such as BALF GM (P < 0.001), history of glucocorticoid use (P = 0.004), and pulmonary comorbidities (P = 0.002), as well as no significance of the other demographic data including age, sex, BMI, history of cigarette, blood GM assay, T-SPOT.TB, and NEUT#/LYMPH#. The sensitivity of the BALF mNGS was 92.31%, which was higher than that of the traditional tests or the GM assays. The specificity of BALF mNGS was 92.73%, which was relatively similar to that of the traditional tests. The AUC of BALF mNGS was 0.925, which presented an excellent performance compared with other traditional tests or GM assays. Our study demonstrated the important role of BALF detection by the mNGS platform for pathogen identification in IPA patients with non-neutropenic states, which may provide an optimal way to diagnose suspected IPA disease.
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Affiliation(s)
| | | | | | | | - Shengqing Li
- Department of Pulmonary and Critical Care Medicine, Huashan Hospital, Fudan University, Shanghai, China
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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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Shi Y, Zhang C, Pan S, Chen Y, Miao X, He G, Wu Y, Ye H, Weng C, Zhang H, Zhou W, Yang X, Liang C, Chen D, Hong L, Su F. The diagnosis of tuberculous meningitis: advancements in new technologies and machine learning algorithms. Front Microbiol 2023; 14:1290746. [PMID: 37942080 PMCID: PMC10628659 DOI: 10.3389/fmicb.2023.1290746] [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: 09/08/2023] [Accepted: 10/09/2023] [Indexed: 11/10/2023] Open
Abstract
Tuberculous meningitis (TBM) poses a diagnostic challenge, particularly impacting vulnerable populations such as infants and those with untreated HIV. Given the diagnostic intricacies of TBM, there's a pressing need for rapid and reliable diagnostic tools. This review scrutinizes the efficacy of up-and-coming technologies like machine learning in transforming TBM diagnostics and management. Advanced diagnostic technologies like targeted gene sequencing, real-time polymerase chain reaction (RT-PCR), miRNA assays, and metagenomic next-generation sequencing (mNGS) offer promising avenues for early TBM detection. The capabilities of these technologies are further augmented when paired with mass spectrometry, metabolomics, and proteomics, enriching the pool of disease-specific biomarkers. Machine learning algorithms, adept at sifting through voluminous datasets like medical imaging, genomic profiles, and patient histories, are increasingly revealing nuanced disease pathways, thereby elevating diagnostic accuracy and guiding treatment strategies. While these burgeoning technologies offer hope for more precise TBM diagnosis, hurdles remain in terms of their clinical implementation. Future endeavors should zero in on the validation of these tools through prospective studies, critically evaluating their limitations, and outlining protocols for seamless incorporation into established healthcare frameworks. Through this review, we aim to present an exhaustive snapshot of emerging diagnostic modalities in TBM, the current standing of machine learning in meningitis diagnostics, and the challenges and future prospects of converging these domains.
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Affiliation(s)
- Yi Shi
- Department of Infectious Diseases, Wenzhou Central Hospital, Wenzhou, China
- The First School of Medicine, Wenzhou Medical University, Wenzhou, China
| | - Chengxi Zhang
- School of Materials Science and Engineering, Shandong Jianzhu University, Jinan, China
| | - Shuo Pan
- The First School of Medicine, Wenzhou Medical University, Wenzhou, China
| | - Yi Chen
- The First School of Medicine, Wenzhou Medical University, Wenzhou, China
| | - Xingguo Miao
- Department of Infectious Diseases, Wenzhou Central Hospital, Wenzhou, China
- Department of Infectious Diseases, Wenzhou Sixth People’s Hospital, Wenzhou, China
- Wenzhou Key Laboratory of Diagnosis and Treatment of Emerging and Recurrent Infectious Diseases, Wenzhou, China
| | - Guoqiang He
- Postgraduate Training Base Alliance of Wenzhou Medical University, Wenzhou, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, China
| | - Yanchan Wu
- School of Electrical and Information Engineering, Quzhou University, Quzhou, China
| | - Hui Ye
- Department of Infectious Diseases, Wenzhou Central Hospital, Wenzhou, China
- Department of Infectious Diseases, Wenzhou Sixth People’s Hospital, Wenzhou, China
- Wenzhou Key Laboratory of Diagnosis and Treatment of Emerging and Recurrent Infectious Diseases, Wenzhou, China
| | - Chujun Weng
- The Fourth Affiliated Hospital Zhejiang University School of Medicine, Yiwu, China
| | - Huanhuan Zhang
- School and Hospital of Stomatology, Wenzhou Medical University, Wenzhou, China
| | - Wenya Zhou
- School and Hospital of Stomatology, Wenzhou Medical University, Wenzhou, China
| | - Xiaojie Yang
- Wenzhou Medical University Renji College, Wenzhou, China
| | - Chenglong Liang
- The First School of Medicine, Wenzhou Medical University, Wenzhou, China
| | - Dong Chen
- Wenzhou Key Laboratory of Diagnosis and Treatment of Emerging and Recurrent Infectious Diseases, Wenzhou, China
- Wenzhou Central Blood Station, Wenzhou, China
| | - Liang Hong
- Department of Infectious Diseases, The Third Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Feifei Su
- Department of Infectious Diseases, Wenzhou Central Hospital, Wenzhou, China
- Department of Infectious Diseases, Wenzhou Sixth People’s Hospital, Wenzhou, China
- Wenzhou Key Laboratory of Diagnosis and Treatment of Emerging and Recurrent Infectious Diseases, Wenzhou, China
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22
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Cao LJ, Zheng YM, Li F, Hao HJ, Gao F. Varicella-zoster virus meningitis with hypoglycorrhachia: A case report. World J Clin Cases 2023; 11:7101-7106. [PMID: 37946771 PMCID: PMC10631396 DOI: 10.12998/wjcc.v11.i29.7101] [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: 05/15/2023] [Revised: 07/16/2023] [Accepted: 08/03/2023] [Indexed: 10/13/2023] Open
Abstract
BACKGROUND Varicella-zoster virus (VZV) is a common viral infection, but meningitis is a rare complication of VZV infection. The cerebrospinal fluid glucose of viral meningitis is usually within the normal range, which is different from bacteria, fungi, and cancerous meningitis. This paper reports a case of VZV meningitis with hypoglycorrhachia and the relevant literature was reviewed. CASE SUMMARY We report a case of an immunocompetent 39-year-old male, presenting with severe headache and fevers, without meningeal signs or exanthem, found to have VZV meningitis by the metagenomic next-generation sequencing of cerebrospinal fluid. The cerebrospinal fluid analysis revealed hypoglycorrhachia (cerebrospinal fluid glucose of 2.16) and he was treated successfully with intravenous acyclovir. Our literature review identified only ten cases diagnosed with VZV meningitis with hypoglycorrhachia previously reported to date in the English literature whose cerebrospinal fluid glucose was from 1.6 to 2.7mmol/L, with a ratio of cerebrospinal fluid to serum glucose from 0.30 to 0.49. CONCLUSION Although rare, the cerebrospinal fluid of patients with VZV meningitis may have hypoglycorrhachia, which broadens the understanding of the disease.
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Affiliation(s)
- Li-Juan Cao
- Department of Neurology, Peking University First Hospital, Beijing 100034, China
- Department Acupuncture and Moxibustion, Huguosi Traditional Chinese Medicine Hospital Attached to Beijing Traditional Chinese Medicine University, Beijing 100034, China
| | - Yi-Ming Zheng
- Department of Neurology, Peking University First Hospital, Beijing 100034, China
| | - Fan Li
- Department of Neurology, Peking University First Hospital, Beijing 100034, China
| | - Hong-Jun Hao
- Department of Neurology, Peking University First Hospital, Beijing 100034, China
| | - Feng Gao
- Department of Neurology, Peking University First Hospital, Beijing 100034, China
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23
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Shaikh A, Rodrigues C. What's New in the Molecular Diagnosis of Childhood Tuberculosis? Pediatr Infect Dis J 2023; 42:e377-e379. [PMID: 37463349 DOI: 10.1097/inf.0000000000004044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Affiliation(s)
- Ambreen Shaikh
- From the Department of Laboratory Medicine, Section Tuberculosis, Foundation Medical Research, Worli, Mumbai, India
| | - Camilla Rodrigues
- Department of Laboratory Medicine, Section Microbiology, Hinduja Hospital, Mahim, Mumbai, India
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Pan X, Zhang Y, Chen G. The clinical utility of metagenomic next-generation sequencing for the diagnosis of central nervous system infectious diseases. Neurol Res 2023; 45:919-925. [PMID: 37615407 DOI: 10.1080/01616412.2023.2247299] [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: 12/14/2022] [Accepted: 06/10/2023] [Indexed: 08/25/2023]
Abstract
BACKGROUND To evaluate the clinical utility of metagenomic next-generation sequencing (mNGS) for the diagnosis of central nervous system infections (CNSI). METHODS Cerebrospinal fluid (CSF) from 54 patients who were high-level clinical suspicion of CNSI was collected and sent for mNGS and conventional tests from January 2019 to March 2022. RESULTS Twenty out of 54 patients were diagnosed with CNSI and 34 non-CNSI. Among the 34 non-CNSI, one was false positive by mNGS. Among the 20 CNSI, 11 had presumed viral encephalitis and/or meningitis, 5 had presumed bacterial meningitis, 2 had presumed TMB, 1 had Crytococcus meningitis and 1 had neurosyphilis. The sensitivity of viral encephalitis and/or meningitis was 0.73 (8/11); 10 virus were detected; 9/10 was dsDNA; 1/10 was ssRNA. SSRN ranged from 1 to 13. The accuracy rate was 0.4, the accuracy rate was positively correlated with SSRN (r = 0.738, P = 0.015), SSRN ≥ 1, the accuracy rate was 0.4; SSRN ≥ 3, the accuracy rate was 0.66; SSRN ≥ 4, the accuracy rate was 0.75; SSRN ≥ 6, the accuracy rate was 1. The sensitivity of bacterial meningitis was 1. Seven kinds of bacteria were detected, among which 3/7 were gram positive, 3/7 were gram negative, and 1/7 was infected NTM (nontuberculous mycobacteria). The accuracy rate was 0.43 (3/7). The sensitivity of TBM was 0.66 (2/3), the accuracy rate was 1. The sensitivity of Crytococcus meningitis was 1, the accuracy rate was 0.5. PPV (positive predictive value) of mNGS was 0.94, NPV (negative predictive value) of mNGS was 0.89, specificity was 0.97 and sensitivity was 0.8. The AUG for CSF mNGS diagnosis of CNSI was 0.89 (95% CI = 0.78-0.99) Headache, meningeal irritation sign and image of meninges abnormal were correlated with the sensitivity of mNGS (r = 0.451, 0.313, 0.446; p = 0.001, 0.021, 0.001); CSF Glucose and CSF Chloride were negatively correlated with sensitivity of mNGS (r = -0.395, -0.462; p = 0.003, < 0.001). CONCLUSION mNGS is a detection means with high sensitivity, wide coverage and strong timeliness, which can help clinicians to identify the pathogen diagnosis quickly, conduct targeted anti-infection treatment early and reduce antibiotic abuse. The pathogen which causing low CSF Glucose, low CSF Chloride or meninges infections was more likely to be detected by mNGS. It may be related to growth and structural characteristics of the pathogen and blood-brain barrier damage.
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Affiliation(s)
- Xiaoying Pan
- Department of Neurology, The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yuefeng Zhang
- Department of Neurology, The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China
| | - Guohua Chen
- Department of Neurology, The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China
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25
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Thy M, de Montmollin E, Bouadma L, Timsit JF, Sonneville R. Severe meningoencephalitis: epidemiology and outcomes. Curr Opin Crit Care 2023; 29:415-422. [PMID: 37641514 DOI: 10.1097/mcc.0000000000001087] [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: 08/31/2023]
Abstract
PURPOSE OF REVIEW This article aims to provide an updated review on the epidemiology and outcomes of severe meningoencephalitis. RECENT FINDINGS Meningoencephalitis is a critical medical condition characterized by inflammation in both the meninges and brain parenchyma. Bacterial, viral, or fungal infections are common causes, although noninfectious factors, such as autoimmune causes, can also contribute. In patients requiring intensive care, meningoencephalitis is associated with a severe prognosis, including mortality rates ranging from 11 to 25% and functional disability in 15-25% of survivors. Recent multicenter studies have identified several parameters linked to poor outcomes, including older age, immunocompromised status, focal neurologic signs, abnormal brain imaging, and delayed administration of antimicrobials. The use of new multiplex PCR techniques for diagnosis has generated debate based on recent data. Investigation is still needed to determine the effectiveness of adjunctive therapies, including seizure prophylaxis, and adjunctive steroids for nonbacterial causes. SUMMARY Recent multicenter studies have enhanced our understanding of the current epidemiology and outcomes of severe meningoencephalitis in adult patients.
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Affiliation(s)
- Michael Thy
- Department of Intensive Care Medicine
- Department of Infectious and Tropical Diseases, AP-HP, Bichat Hospital
- EA 7323 - Pharmacology and Therapeutic Evaluation in Children and Pregnant Women
| | - Etienne de Montmollin
- Department of Intensive Care Medicine
- INSERM UMR1137, IAME, Université de Paris Cité, Paris, France
| | - Lila Bouadma
- Department of Intensive Care Medicine
- INSERM UMR1137, IAME, Université de Paris Cité, Paris, France
| | - Jean-François Timsit
- Department of Intensive Care Medicine
- INSERM UMR1137, IAME, Université de Paris Cité, Paris, France
| | - Romain Sonneville
- Department of Intensive Care Medicine
- INSERM UMR1137, IAME, Université de Paris Cité, Paris, France
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26
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Li D, Li H. The Clinical Characteristics, Diagnostic Methods, Treatment, and Outcomes of Listeria monocytogenes Meningoencephalitis: A Case Series Study from China. Infect Drug Resist 2023; 16:6375-6383. [PMID: 37789837 PMCID: PMC10543931 DOI: 10.2147/idr.s423568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 09/14/2023] [Indexed: 10/05/2023] Open
Abstract
Background Listeria monocytogenes meningoencephalitis (LMM) is a rare but dangerous infection of the nervous system. This study intends to summarize and discuss the clinical features, diagnostic methods, treatment, and outcomes. Methods LMM patients treated in the First Affiliated Hospital of Zhengzhou University from June 2013 to December 2022 were retrospectively studied. The clinical data, magnetic resonance imaging (MRI), biochemical and hematological parameters, pathogen tests, treatments, and outcomes information were collected and summarized. Results Ten LMM patients were enrolled in this study. Three were female and seven were male, with a mean age of 54.5 years old. Seven (70%) of the patients had chronic conditions that either affected the liver (1 case), heart (1 case), or immune system (5 cases). The main clinical manifestations were fever (100%), headache, (60%), and disturbance of consciousness (60%). Out of the nine patients taken MRI, enhanced magnetic resonance imaging was observed with cerebral parenchyma and meningeal enhancement in 3 patients, whereas six patients showed non-specific abnormal signals and brain edema. Seven (70%) patients were positive for L. monocytogenes by bacterial culture and five patients were positive by further next-generation sequencing (NGS) test in CSF. All patients were treated with antibiotics based on antibiotic sensitivity tests or experience, with seven (70%) improved but three (30%) died within one month. Conclusion LMM patients have a high mortality rate. Considering the time and reliability of NGS reports, it would be better to identify L. monocytogenes infection in the CSF than bacterial culture. While, after diagnosis, giving timely and appropriate antibiotics would still be a challenge to achieve good outcomes.
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Affiliation(s)
- Dongrui Li
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou City, People’s Republic of China
| | - Hui Li
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou City, People’s Republic of China
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27
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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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Jia H, Liu H, Tu M, Wang Y, Wang X, Li J, Zhang G. Diagnostic efficacy of metagenomic next generation sequencing in bronchoalveolar lavage fluid for proven invasive pulmonary aspergillosis. Front Cell Infect Microbiol 2023; 13:1223576. [PMID: 37692168 PMCID: PMC10484620 DOI: 10.3389/fcimb.2023.1223576] [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: 05/16/2023] [Accepted: 08/02/2023] [Indexed: 09/12/2023] Open
Abstract
Objective To assess the diagnostic efficacy of metagenomic next generation sequencing (mNGS) for proven invasive pulmonary aspergillosis (IPA). Methods A total of 190 patients including 53 patients who had been diagnosed with proven IPA were retrospectively analyzed. Using the pathological results of tissue biopsy specimens as gold standard, we ploted the receiver operating characteristic (ROC) curve to determine the optimal cut-off value of mNGS species-specific read number (SSRN) of Aspergillus in bronchoalveolar lavage fluid (BALF)for IPA. Furthermore, we evaluated optimal cut-off value of mNGS SSRN in different populations. Results The optimal cut-off value of Aspergillus mNGS SSRN in BALF for IPA diagnosis was 2.5 for the whole suspected IPA population, and 1 and 4.5 for immunocompromised and diabetic patients, respectively. The accuracy of mNGS was 80.5%, 73.7% and 85.3% for the whole population, immunocompromised and diabetic patients, respectively. Conclusions The mNGS in BALF has a high diagnostic efficacy for proven IPA, superioring to Aspergillus culture in sputum and BALF and GM test in blood and BALF. However, the cut-off value of SSRN should be adjusted when in different population.
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Affiliation(s)
| | | | | | | | | | | | - Guojun Zhang
- Department of Pulmonary and Critical Care Medicine, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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29
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Li Y, Bian W, Wu S, Zhang J, Li D. Metagenomic next-generation sequencing for Mycobacterium tuberculosis complex detection: a meta-analysis. Front Public Health 2023; 11:1224993. [PMID: 37637815 PMCID: PMC10450767 DOI: 10.3389/fpubh.2023.1224993] [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: 05/18/2023] [Accepted: 07/24/2023] [Indexed: 08/29/2023] Open
Abstract
Objective Metagenomic next-generation sequencing (mNGS) has been gradually applied to the diagnosis of tuberculosis (TB) due to its rapid and highly sensitive characteristics. Despite numerous studies on this subject, their results vary significantly. Thus, the current meta-analysis was performed to assess the performance of the mNGS on tuberculosis. Methods PubMed, Embase, Web of Science, and The Cochrane Library were searched up to June 21, 2023. Studies utilizing the mNGS for tuberculosis detection were included. The risk of bias was assessed by QUADAS-2, and a meta-analysis was performed with STATA14.0 software. Results Seventeen studies comprising 3,205 specimens were included. The combined sensitivity and specificity of mNGS for clinical specimens were 0.69[0.58-0.79] and 1.00[0.99-1.00], respectively. Subgroup analysis identified sequencing platform, diagnostic criteria, study type, sample size, and sample types as potential sources of heterogeneity. Cerebrospinal Fluid (CSF) has a lower sensitivity of 0.58 (0.39-0.75). In a population with a 10% prevalence rate, the accuracy of sensitivity reached 94%. Conclusion Metagenomic next-generation sequencing technology exhibits high sensitivity and speed in diagnosing Mycobacterium tuberculosis. Its application in mono and mixed infections peoples shows promise, and mNGS is likely to be increasingly used to address challenges posed by Mycobacterium tuberculosis complexes in the future.
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Affiliation(s)
- Yulian Li
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Wentao Bian
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Shiping Wu
- Affiliated Hospital of North Sichuan Medical College, Nanchong, China
| | - Jie Zhang
- Department of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Dan Li
- School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
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Xu H, Chen P, Guo S, Shen X, Lu Y. Progress in etiological diagnosis of viral meningitis. Front Neurol 2023; 14:1193834. [PMID: 37583954 PMCID: PMC10423822 DOI: 10.3389/fneur.2023.1193834] [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] [Accepted: 06/05/2023] [Indexed: 08/17/2023] Open
Abstract
In recent years, with the rapid development of molecular biology techniques such as polymerase chain reaction and molecular biochip, the etiological diagnosis of viral encephalitis has a very big step forward. At present, the etiological examination of viral meningitis mainly includes virus isolation, serological detection and molecular biological nucleic acid detection. This article reviews the progress in etiological diagnosis of viral meningitis.
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Affiliation(s)
- Hongyan Xu
- Emergency Department, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Department of General Practice, The 900th Hospital of Joint Logistic Support Force, PLA, Fuzong Clinical College of Fujian Medical University, Fuzhou, Fujian, China
| | - Peng Chen
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China
| | - Shihan Guo
- Emergency Department, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xiaokai Shen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Yun Lu
- Emergency Department, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
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31
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Li HH, Zhou XM, Liu T, Wu R, Huang ZF, Sun CW, Liu ZA, Zheng SY, Lai W, Lou H, Xiong B. The clinical value of metagenomic next-generation sequencing for rapid microbial identification of chronic granulation wound infections. Arch Med Sci 2023; 19:1162-1167. [PMID: 37560730 PMCID: PMC10408008 DOI: 10.5114/aoms/166255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/16/2023] [Indexed: 08/11/2023] Open
Affiliation(s)
- Han-hua Li
- Department of Burns and Wound Repair Surgery, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Xiao-ming Zhou
- Department of Neurology, The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China
| | - Tao Liu
- Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Rongjie Wu
- Department of Orthopedics, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Shantou University Medical College, Shantou, China
| | - Zhi-feng Huang
- Department of Burns and Wound Repair Surgery, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Chuan-wei Sun
- Department of Burns and Wound Repair Surgery, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Zu-an Liu
- Department of Burns and Wound Repair Surgery, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Shao-yi Zheng
- Department of Burns and Wound Repair Surgery, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Wen Lai
- Department of Burns and Wound Repair Surgery, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Hongming Lou
- Department of Burns and Wound Repair Surgery, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Bing Xiong
- Department of Burns and Wound Repair Surgery, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
- Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Department of Burns and Wound Repair Surgery, Burns and Wound Repair Institute, Shenzhen People’s Hospital, Shenzhen, China Guangdong Provincial, China
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Ou-Yang MC, Tsai MH, Chu SM, Chen CC, Yang PH, Huang HR, Chang CM, Fu RH, Hsu JF. The Clinical Characteristics, Microbiology and Risk Factors for Adverse Outcomes in Neonates with Gram-Negative Bacillary Meningitis. Antibiotics (Basel) 2023; 12:1131. [PMID: 37508227 PMCID: PMC10376587 DOI: 10.3390/antibiotics12071131] [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: 05/14/2023] [Revised: 06/19/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
Background: We aimed to describe the clinical features of Gram-negative bacillary (GNB) meningitis in neonates and investigate the risk factors associated with final adverse outcomes of neonatal GNB meningitis. Methods: From 2003 to 2020, all neonates (aged ≤ 90 days old) with bacterial meningitis who were hospitalized in four tertiary-level neonatal intensive care units (NICUs) of two medical centers in Taiwan were enrolled. Neonates with GNB meningitis were compared with those with Streptococcus agalactiae (group B streptococcus, GBS) meningitis. Results: During the study period, a total of 153 neonates with bacterial meningitis were identified and enrolled. GNB and GBS accounted for 40.5% (n = 62) and 35.3% (n = 54) of all neonatal bacterial meningitis, respectively. In neonates with GNB meningitis, the final mortality rate was 6.5% (4 neonates died); 48 (77.4%) had neurological complications, and 26 (44.8%) of 58 survivors had neurological sequelae at discharge. Although the final outcomes were comparable between neonates with GNB meningitis and those with GBS meningitis, neonates with GNB meningitis were more likely to have more severe clinical manifestations initially and have ventriculomegaly at follow-up. After multivariate logistic regression analysis, neonates with seizure at onset, early onset sepsis, and requirement of surgical intervention for neurological complications were independently associated with final adverse outcomes. Conclusions: GNB meningitis was associated with a high risk of neurological complications and sequelae, although it did not significantly increase the final mortality rate. Close monitoring of the occurrence of neurological complications and advanced therapeutic strategies to optimize the outcomes are urgently needed in the future.
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Affiliation(s)
- Mei-Chen Ou-Yang
- Division of Pediatric Neonatology, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan 33382, Taiwan
- College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
| | - Ming-Horng Tsai
- College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
- Division of Neonatology and Pediatric Hematology/Oncology, Department of Pediatrics, Chang Gung Memorial Hospital, Yunlin 63812, Taiwan
| | - Shih-Ming Chu
- Division of Pediatric Neonatology, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan 33382, Taiwan
- College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
| | - Chih-Chen Chen
- Division of Pediatric Neonatology, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan 33382, Taiwan
- College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
| | - Peng-Hong Yang
- College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
- Division of Neonatology, Department of Pediatrics, Chang Gung Memorial Hospital, Chiayi 33382, Taiwan
| | - Hsuan-Rong Huang
- Division of Pediatric Neonatology, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan 33382, Taiwan
- College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
| | - Ching-Min Chang
- College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
- Division of Neonatology, Department of Pediatrics, Chang Gung Memorial Hospital, Chiayi 33382, Taiwan
| | - Ren-Huei Fu
- Division of Pediatric Neonatology, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan 33382, Taiwan
- College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
| | - Jen-Fu Hsu
- Division of Pediatric Neonatology, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan 33382, Taiwan
- College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
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Fang W, Wu J, Cheng M, Zhu X, Du M, Chen C, Liao W, Zhi K, Pan W. Diagnosis of invasive fungal infections: challenges and recent developments. J Biomed Sci 2023; 30:42. [PMID: 37337179 DOI: 10.1186/s12929-023-00926-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/13/2023] [Indexed: 06/21/2023] Open
Abstract
BACKGROUND The global burden of invasive fungal infections (IFIs) has shown an upsurge in recent years due to the higher load of immunocompromised patients suffering from various diseases. The role of early and accurate diagnosis in the aggressive containment of the fungal infection at the initial stages becomes crucial thus, preventing the development of a life-threatening situation. With the changing demands of clinical mycology, the field of fungal diagnostics has evolved and come a long way from traditional methods of microscopy and culturing to more advanced non-culture-based tools. With the advent of more powerful approaches such as novel PCR assays, T2 Candida, microfluidic chip technology, next generation sequencing, new generation biosensors, nanotechnology-based tools, artificial intelligence-based models, the face of fungal diagnostics is constantly changing for the better. All these advances have been reviewed here giving the latest update to our readers in the most orderly flow. MAIN TEXT A detailed literature survey was conducted by the team followed by data collection, pertinent data extraction, in-depth analysis, and composing the various sub-sections and the final review. The review is unique in its kind as it discusses the advances in molecular methods; advances in serology-based methods; advances in biosensor technology; and advances in machine learning-based models, all under one roof. To the best of our knowledge, there has been no review covering all of these fields (especially biosensor technology and machine learning using artificial intelligence) with relevance to invasive fungal infections. CONCLUSION The review will undoubtedly assist in updating the scientific community's understanding of the most recent advancements that are on the horizon and that may be implemented as adjuncts to the traditional diagnostic algorithms.
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Affiliation(s)
- Wenjie Fang
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China
| | - Junqi Wu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
- Shanghai Engineering Research Center of Lung Transplantation, Shanghai, 200433, China
| | - Mingrong Cheng
- Department of Anorectal Surgery, The Third Affiliated Hospital of Guizhou Medical University, Guizhou, 558000, China
| | - Xinlin Zhu
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China
| | - Mingwei Du
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China
| | - Chang Chen
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
- Shanghai Engineering Research Center of Lung Transplantation, Shanghai, 200433, China
| | - Wanqing Liao
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China
| | - Kangkang Zhi
- Department of Vascular and Endovascular Surgery, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China.
| | - Weihua Pan
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China.
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Pope CE, Whitlock KB, Hodor P, Limbrick DD, McDonald PJ, Hauptman J, Hoffman LR, Simon TD. A Refined, Controlled 16S rRNA Gene Sequencing Approach Reveals Limited Detection of Cerebrospinal Fluid Microbiota in Children with Bacterial Meningitis. Microbiol Spectr 2023; 11:e0036123. [PMID: 37140368 PMCID: PMC10269467 DOI: 10.1128/spectrum.00361-23] [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: 01/25/2023] [Accepted: 04/12/2023] [Indexed: 05/05/2023] Open
Abstract
Advances in both laboratory and computational components of high-throughput 16S amplicon sequencing (16S HTS) have markedly increased its sensitivity and specificity. Additionally, these refinements have better delineated the limits of sensitivity, and contributions of contamination to these limits, for 16S HTS that are particularly relevant for samples with low bacterial loads, such as human cerebrospinal fluid (CSF). The objectives of this work were to (i) optimize the performance of 16S HTS in CSF samples with low bacterial loads by defining and addressing potential sources of error, and (ii) perform refined 16S HTS on CSF samples from children diagnosed with bacterial meningitis and compare results with those from microbiological cultures. Several bench and computational approaches were taken to address potential sources of error for low bacterial load samples. We compared DNA yields and sequencing results after applying three different DNA extraction approaches to an artificially constructed mock-bacterial community. We also compared two postsequencing computational contaminant removal strategies, decontam R and full contaminant sequence removal. All three extraction techniques followed by decontam R yielded similar results for the mock community. We then applied these methods to 22 CSF samples from children diagnosed with meningitis, which has low bacterial loads relative to other clinical infection samples. The refined 16S HTS pipelines identified the cultured bacterial genus as the dominant organism for only 3 of these samples. We found that all three DNA extraction techniques followed by decontam R generated similar DNA yields for mock communities at the low bacterial loads representative of CSF samples. However, the limits of detection imposed by reagent contaminants and methodologic bias precluded the accurate detection of bacteria in CSF from children with culture-confirmed meningitis using these approaches, despite rigorous controls and sophisticated computational approaches. Although we did not find current DNA-based diagnostics to be useful for pediatric meningitis samples, the utility of these methods for CSF shunt infection remains undefined. Future advances in sample processing methods to minimize or eliminate contamination will be required to improve the sensitivity and specificity of these methods for pediatric meningitis. IMPORTANCE Advances in both laboratory and computational components of high-throughput 16S amplicon sequencing (16S HTS) have markedly increased its sensitivity and specificity. These refinements have better delineated the limits of sensitivity, and contributions of contamination to these limits, for 16S HTS that are particularly relevant for samples with low bacterial loads such as human cerebrospinal fluid (CSF). The objectives of this work were to (i) optimize the performance of 16S HTS in CSF samples by defining and addressing potential sources of error, and (ii) perform refined 16S HTS on CSF samples from children diagnosed with bacterial meningitis and compare results with those from microbiological cultures. We found that the limits of detection imposed by reagent contaminants and methodologic bias precluded the accurate detection of bacteria in CSF from children with culture-confirmed meningitis using these approaches, despite rigorous controls and sophisticated computational approaches.
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Affiliation(s)
- Christopher E. Pope
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | | | - Paul Hodor
- Seattle Children's Research Institute, Seattle, Washington, USA
| | - David D. Limbrick
- Department of Neurosurgery, Washington University in St. Louis, St. Louis, Missouri, USA
- St. Louis Children’s Hospital, St. Louis, Missouri, USA
| | - Patrick J. McDonald
- Division of Neurosurgery, University of British Columbia, Vancouver, British Columbia, Canada
- British Columbia Children’s Hospital, Vancouver, British Columbia, Canada
| | - Jason Hauptman
- Seattle Children's Research Institute, Seattle, Washington, USA
- Department of Neurosurgery, University of Washington, Seattle, Washington, USA
- Seattle Children's Hospital, Seattle, Washington, USA
| | - Lucas R. Hoffman
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
- Seattle Children's Research Institute, Seattle, Washington, USA
- Seattle Children's Hospital, Seattle, Washington, USA
| | - Tamara D. Simon
- Department of Pediatrics, University of Southern California, Los Angeles, California, USA
- The Saban Research Institute, Los Angeles, California, USA
- Children’s Hospital Los Angeles, Los Angeles, California, USA
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Qiu G, Zhu L, Chen S, Li N, Ye C, Zhuo S, Shen Y. High-throughput metagenomics analysis in early and precise diagnosis of eosinophilic meningoencephalitis complicated with respiratory failure: A case report. Medicine (Baltimore) 2023; 102:e33683. [PMID: 37171295 PMCID: PMC10174349 DOI: 10.1097/md.0000000000033683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/13/2023] Open
Abstract
RATIONALE Human infection with Angiostrongylus cantonensis is uncommon and has only been sporadically reported in the literature. Patients infected with A cantonensis usually have a delayed diagnosis and sometimes a poor prognosis. PATIENT CONCERNS A 70-year-old woman presented to the respiratory department with complaints of headache, chest pain, myalgia, fatigue, and anorexia for 7 days. DIAGNOSES Complete blood count showed eosinophilia. The serum was tested showing a positive finding of A cantonensis antibody. Cerebrospinal fluid was tested using high-throughput metagenomics analysis and 16 reads for A cantonensis were mapped. The patient was diagnosed with A cantonensis infection. INTERVENTIONS The patient received a 7-day course of albendazole and 4-day course of prednisone. OUTCOMES When discharged from the hospital, the patient still suffered from fatigue and poor memory. Aminotransferase levels were high due to albendazole's liver toxicity. In a post-discharge follow-up about 1 month later she had recovered completely both physically and mentally, and peripheral eosinophil count and aminotransferase levels were both normal. LESSONS Because the direct identification of parasites is difficult, high-throughput metagenomics analysis may provide a reliable alternative tool for the diagnoses of infection with A cantonensis. When albendazole is prescribed, caution must be taken with respect to its liver toxicity.
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Affiliation(s)
- Guoqing Qiu
- Respiratory Department, Longgang Central Hospital, Shenzhen, China
| | - Liqun Zhu
- Otolaryngological Department, South China Hospital of Shenzhen University, Shenzhen, China
| | - Sida Chen
- Respiratory Department, Longgang Central Hospital, Shenzhen, China
| | - Na Li
- Respiratory Department, Longgang Central Hospital, Shenzhen, China
| | - Chunxing Ye
- Respiratory Department, Longgang Central Hospital, Shenzhen, China
| | - Songming Zhuo
- Respiratory Department, Longgang Central Hospital, Shenzhen, China
| | - Yan Shen
- Respiratory Department, Longgang Central Hospital, Shenzhen, China
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Xie S, Lai Z, Xia H, Tang M, Lai J, Liu Q, Lu Z, He D, Qi J, Liu X. A case report of brainstem hemorrhage due to Rhizopus delemar-induced encephalitis diagnosed by metagenomic next-generation sequencing (mNGS). BMC Infect Dis 2023; 23:235. [PMID: 37069515 PMCID: PMC10107577 DOI: 10.1186/s12879-023-08192-1] [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: 01/13/2023] [Accepted: 03/23/2023] [Indexed: 04/19/2023] Open
Abstract
BACKGROUND Rhizopus delemar is an invasive fungal pathogen that can cause fatal mucormycosis in immunodeficient individuals. Encephalitis caused by R. delemar is rare and difficult to diagnose early. Clinical detection methods for R. delemar include blood fungal culture, direct microscopic examination, and histopathological examination, but the detection is often inadequate for clinical diagnosis and can easily lead to missed diagnosis with delayed treatment. CASE PRESENTATION We report a case of a 47-year-old male with brainstem hemorrhage caused by encephalitis due to R. delemar. The patient had a history of hypertension, type 2 diabetes, and irregular medication. No pathogens were detected in cerebrospinal fluid (CSF) and nasopharyngeal secretion cultures. R. delemar was identified by metagenomic next-generation sequencing (mNGS) in CSF, and in combination with the patient's clinical characteristics, encephalitis caused by R. delemar was diagnosed. Antibiotic treatment using amphotericin B liposome in combination with posaconazole was given immediately. However, due to progressive aggravation of the patient's symptoms, he later died due to brainstem hemorrhage after giving up treatment. CONCLUSIONS mNGS technique is a potential approach for the early diagnosis of infections, which can help clinicians provide appropriate antibiotic treatments, thus reducing the mortality and disability rate of patients.
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Affiliation(s)
- Shuhua Xie
- Department of Neurology, Ganzhou People's Hospital, Jiangxi, 341000, China
| | - Zhaohui Lai
- Department of Neurology, Ganzhou People's Hospital, Jiangxi, 341000, China
| | - Han Xia
- Department of Scientific Affairs, Hugobiotech Co., Ltd, Beijing, 100176, China
| | - Mingze Tang
- Department of Scientific Affairs, Hugobiotech Co., Ltd, Beijing, 100176, China
| | - Jinxing Lai
- Department of Neurology, Ganzhou People's Hospital, Jiangxi, 341000, China
| | - Qing Liu
- Department of Neurology, Ganzhou People's Hospital, Jiangxi, 341000, China
| | - Zhijuan Lu
- Department of Neurology, Ganzhou People's Hospital, Jiangxi, 341000, China
| | - Dehai He
- Department of Neurology, Ganzhou People's Hospital, Jiangxi, 341000, China
| | - Jiangli Qi
- Department of Neurology, Ganzhou People's Hospital, Jiangxi, 341000, China
| | - Xianghong Liu
- Department of Neurology, Ganzhou People's Hospital, Jiangxi, 341000, China.
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Venkatesan A, Habis R, Geocadin RG. Approach to acute encephalitis in the intensive care unit. Curr Opin Crit Care 2023; 29:89-98. [PMID: 36794940 DOI: 10.1097/mcc.0000000000001028] [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: 02/17/2023]
Abstract
PURPOSE OF REVIEW Recent years have seen a dramatic increase in the identification of autoimmune encephalitis (AE) and the emergence of new causes of infectious encephalitis (IE). However, management of these patients remains challenging, with many requiring care in intensive care units. Here, we describe recent advances in the diagnosis and management of acute encephalitis. RECENT FINDINGS Advances in the identification of clinical presentations, neuroimaging biomarkers, and electroencephalogram patterns have enabled more rapid diagnosis of encephalitis. Newer modalities such as meningitis/encephalitis multiplex PCR panels, metagenomic next-generation sequencing, and phage display-based assays are being evaluated in an effort to improve detection of autoantibodies and pathogens. Specific advances in the treatment of AE include establishment of a systematic approach to first-line therapies and the development of newer second-line modalities. The role of immunomodulation and its applications in IE are actively being investigated. In the ICU, particular attention to status epilepticus, cerebral edema, and dysautonomia may improve outcomes. SUMMARY Substantial diagnostic delays still occur, with many cases left without an identified etiology. Antiviral therapies remain scarce, and optimal treatment regimens for AE still need to be clarified. Nevertheless, our understanding of diagnostic and therapeutic approaches to encephalitis is rapidly evolving.
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Affiliation(s)
| | - Ralph Habis
- Johns Hopkins Encephalitis Center, Department of Neurology
| | - Romergryko G Geocadin
- Johns Hopkins Encephalitis Center, Department of Neurology
- Departments of Neurosurgery and Anaesthesia/Critical Care, Johns Hopkins University School of Medicine, Maryland, USA
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Xu J, Zhou P, Liu J, Zhao L, Fu H, Han Q, Wang L, Wu W, Ou Q, Ma Y, He J. Utilizing Metagenomic Next-Generation Sequencing (mNGS) for Rapid Pathogen Identification and to Inform Clinical Decision-Making: Results from a Large Real-World Cohort. Infect Dis Ther 2023; 12:1175-1187. [PMID: 36988865 PMCID: PMC10147866 DOI: 10.1007/s40121-023-00790-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/07/2023] [Indexed: 03/30/2023] Open
Abstract
INTRODUCTION Clinical metagenomic next-generation sequencing (mNGS) has proven to be a powerful diagnostic tool in pathogen detection. However, its clinical utility has not been thoroughly evaluated. METHODS In this single-center prospective study at the First Affiliated Hospital of Soochow University, a total of 228 samples from 215 patients suspected of having acute or chronic infections between June 2018 and December 2018 were studied. Samples that met the mNGS quality control (QC) criteria (N = 201) were simultaneously analyzed using conventional tests (CTs), including multiple clinical microbiological tests and real-time PCR (if applicable). RESULTS Pathogen detection results of mNGS in the 201 QC-passed samples were compared to CTs and exhibited a sensitivity of 98.8%, specificity of 38.5%, and accuracy of 87.1%. Specifically, 109 out of 160 (68.1%) CT+/mNGS+ samples exhibited concordant results at the species/genus level, 25 samples (15.6%) showed overlapping results, while the remaining 26 samples (16.3%) had discordant results between the CT and mNGS assays. In addition, mNGS could identify pathogens at the species level, whereas only the genera of some pathogens could be identified by CT. In this cohort, mNGS results were used to guide treatment plans in 24 out of 41 cases that had available follow-up information, and the symptoms were improved in over 70% (17/24) of them. CONCLUSION Our data demonstrated the analytic performance of our mNGS pipeline for pathogen detection using a large clinical cohort and strongly supports the notion that in clinical practice, mNGS represents a valuable supplementary tool to CTs to rapidly determine etiological factors of various types of infection and to guide treatment decision-making.
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Affiliation(s)
- Jie Xu
- Clinical Laboratory Center, The First Affiliated Hospital of Soochow University, Suzhou, 215031, China
| | - Peng Zhou
- Center of Translational Medicine and Clinical Laboratory, Dushu Lake Hospital Affiliated to Soochow University, Suzhou, 215028, China
| | - Jia Liu
- Dinfectome Inc., NanjingJiangsu, 210000, China
| | - Lina Zhao
- Department of Laboratory Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Hailong Fu
- Clinical Laboratory Center, The First Affiliated Hospital of Soochow University, Suzhou, 215031, China
| | - Qingzhen Han
- Center of Translational Medicine and Clinical Laboratory, Dushu Lake Hospital Affiliated to Soochow University, Suzhou, 215028, China
| | - Lin Wang
- Center of Translational Medicine and Clinical Laboratory, Dushu Lake Hospital Affiliated to Soochow University, Suzhou, 215028, China
| | - Weiwei Wu
- Dinfectome Inc., NanjingJiangsu, 210000, China
| | - Qiuxiang Ou
- Dinfectome Inc., NanjingJiangsu, 210000, China
| | - Yutong Ma
- Dinfectome Inc., NanjingJiangsu, 210000, China
| | - Jun He
- Clinical Laboratory Center, The First Affiliated Hospital of Soochow University, Suzhou, 215031, China.
- HLA Laboratory of Jiangsu Institute of Hematology, Collaborative Innovation Center of Hematology, The First Affiliated Hospital of Soochow University, 13/F (West), Hospital Comprehensive Building, No.899 Ping Hai Road, Suzhou, 215031, Jiangsu, 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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Pathogenic diagnosis of a patient with primary cervical intramedullary abscess by metagenomic next-generation sequencing: A case report. Asian J Surg 2023:S1015-9584(23)00033-7. [PMID: 36642550 DOI: 10.1016/j.asjsur.2022.12.145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 12/29/2022] [Indexed: 01/15/2023] Open
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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: 6] [Impact Index Per Article: 6.0] [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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Zhuang H, Xiang K, Gong S, Zhou Y, Chen J. Cerebral aspergillosis after heart-lung transplantation in a child: Case report with 3-year follow-up and literature review. Front Cardiovasc Med 2023; 9:1042631. [PMID: 36684597 PMCID: PMC9853382 DOI: 10.3389/fcvm.2022.1042631] [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: 09/12/2022] [Accepted: 12/13/2022] [Indexed: 01/08/2023] Open
Abstract
There are limited cases of heart-lung transplantation (HLT) in children worldwide owing to lack of donors, demanding surgical teamwork, and arduous post-operative management. Post-transplant management difficulties stem from the possible development of several post-operative complications, with infection being a common complication. Intracranial fungal infections are difficult to diagnose and prone to treatment delays because of their relatively insidious onset and atypical clinical presentation. Here, we present a case of a cerebral infection developed 3 months after HLT in a 10-year-old child, showing no positive results on conventional imaging or cerebrospinal fluid (CSF) examination and culture. On metagenomic next-generation sequencing of the cerebrospinal fluid, the causative organism was finally determined as Aspergillus. After administering 1-year anti-Aspergillus treatment, no recurrence of intracranial fungal infection was noted during the 3-year follow-up. This case illustrates the multifaceted diagnostic techniques for cerebral aspergillosis after HLT and shows the significance of dynamic monitoring of symptoms, such as headache, and of metagenomic sequencing results, trends in intracranial pressure and (1-3)-β-D-glucan levels for guiding diagnosis and treatment.
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Affiliation(s)
- Huanwei Zhuang
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, Changsha, China,Department of Cardiac Surgery, Haikou Affiliated Hospital of Central South University Xiangya School of Medicine, Haikou, China
| | - Kun Xiang
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Shuji Gong
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Yangang Zhou
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Jinlan Chen
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, Changsha, China,*Correspondence: Jinlan Chen,
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Feng L, Chen J, Luo Q, Su M, Chen P, Lai R, Shen C, Zhou H, Wang H, Sun X, Chen L, Xia H, Feng H. mNGS facilitates the accurate diagnosis and antibiotic treatment of suspicious critical CNS infection in real practice: A retrospective study. Open Life Sci 2023; 18:20220578. [PMID: 36879645 PMCID: PMC9985444 DOI: 10.1515/biol-2022-0578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 01/16/2023] [Accepted: 01/23/2023] [Indexed: 03/06/2023] Open
Abstract
Whether metagenomic next-generation sequencing (mNGS) could benefit patients with suspected severe central nervous system (CNS) infection in terms of diagnosis and antibiotic treatment remains unknown. We retrospectively analyzed 79 patients with suspected CNS infection and undertook mNGS. The value of mNGS was investigated in terms of identification of pathogen and guidance for the adjustment of antibiotic treatment. The relationship between the time of initiating mNGS since onset and the Glasgow Outcome Scale (GOS) score after 90-day follow-up were analyzed. Fifty out of 79 cases with suspicious severe CNS infection were finally diagnosed. Despite previous routine laboratory tests, mNGS further promoted the accurate identification of pathogens in 23 cases (47.9%). The sensitivity, specificity, and accuracy of mNGS test in this study were 84.0, 79.3, and 82.3%, respectively. Furthermore, mNGS facilitated the adjustment of empirical antibiotic treatments in 38 cases (48.1%). The time of taking mNGS since onset had an insignificant weak positive correlation with GOS after 90-day follow-up (r = -0.73, P = 0.08). mNGS facilitated the accurate identification of pathogens in suspicious severe CNS infections and promoted the accurate antibiotic therapy even empirical antibiotics were administrated. It should be taken as early as possible to improve the clinical outcome of patients with suspicious severe CNS infection.
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Affiliation(s)
- Li Feng
- Department of Neurology, Neurological Intensive Care Unit, The First Affiliated Hospital, Sun Yat-Sen University; Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases; National Key Clinical Department and Key Discipline of Neurology, No. 58 Zhongshan 2nd Road, Guangzhou, 510080, China
| | - Jiaxin Chen
- Department of Neurology, Neurological Intensive Care Unit, The First Affiliated Hospital, Sun Yat-Sen University; Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases; National Key Clinical Department and Key Discipline of Neurology, No. 58 Zhongshan 2nd Road, Guangzhou, 510080, China
| | - Qiuyan Luo
- Department of Neurology, Neurological Intensive Care Unit, The First Affiliated Hospital, Sun Yat-Sen University; Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases; National Key Clinical Department and Key Discipline of Neurology, No. 58 Zhongshan 2nd Road, Guangzhou, 510080, China
| | - Miao Su
- Department of Neurology, Neurological Intensive Care Unit, The First Affiliated Hospital, Sun Yat-Sen University; Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases; National Key Clinical Department and Key Discipline of Neurology, No. 58 Zhongshan 2nd Road, Guangzhou, 510080, China
| | - Peisong Chen
- Department of Laboratory Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Rong Lai
- Department of Neurology, Neurological Intensive Care Unit, The First Affiliated Hospital, Sun Yat-Sen University; Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases; National Key Clinical Department and Key Discipline of Neurology, No. 58 Zhongshan 2nd Road, Guangzhou, 510080, China
| | - Cunzhou Shen
- Department of Neurology, Neurological Intensive Care Unit, The First Affiliated Hospital, Sun Yat-Sen University; Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases; National Key Clinical Department and Key Discipline of Neurology, No. 58 Zhongshan 2nd Road, Guangzhou, 510080, China
| | - Hongyan Zhou
- Department of Neurology, Neurological Intensive Care Unit, The First Affiliated Hospital, Sun Yat-Sen University; Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases; National Key Clinical Department and Key Discipline of Neurology, No. 58 Zhongshan 2nd Road, Guangzhou, 510080, China
| | - Haiyan Wang
- Department of Neurology, Neurological Intensive Care Unit, The First Affiliated Hospital, Sun Yat-Sen University; Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases; National Key Clinical Department and Key Discipline of Neurology, No. 58 Zhongshan 2nd Road, Guangzhou, 510080, China
| | - Xunsha Sun
- Department of Neurology, Neurological Intensive Care Unit, The First Affiliated Hospital, Sun Yat-Sen University; Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases; National Key Clinical Department and Key Discipline of Neurology, No. 58 Zhongshan 2nd Road, Guangzhou, 510080, China
| | - Ling Chen
- Department of Neurology, Neurological Intensive Care Unit, The First Affiliated Hospital, Sun Yat-Sen University; Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases; National Key Clinical Department and Key Discipline of Neurology, No. 58 Zhongshan 2nd Road, Guangzhou, 510080, China
| | - Han Xia
- Department of Scientific Affairs, Hugobiotech Co., Ltd., Beijing 100176, China
| | - Huiyu Feng
- Department of Neurology, Neurological Intensive Care Unit, The First Affiliated Hospital, Sun Yat-Sen University; Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases; National Key Clinical Department and Key Discipline of Neurology, No. 58 Zhongshan 2nd Road, Guangzhou, 510080, China
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Wang YL, Guo XT, Zhu MY, Mao YC, Xu XB, Hua Y, Xu L, Jiang LH, Zhao CY, Zhang X, Sheng GX, Jiang PF, Yuan ZF, Gao F. Metagenomic next-generation sequencing and proteomics analysis in pediatric viral encephalitis and meningitis. Front Cell Infect Microbiol 2023; 13:1104858. [PMID: 37153144 PMCID: PMC10161730 DOI: 10.3389/fcimb.2023.1104858] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 03/22/2023] [Indexed: 05/09/2023] Open
Abstract
Introduction Early and accurate identification of pathogens is essential for improved outcomes in patients with viral encephalitis (VE) and/or viral meningitis (VM). Methods In our research, Metagenomic next-generation sequencing (mNGS) which can identify viral pathogens unbiasedly was performed on RNA and DNA to identify potential pathogens in cerebrospinal fluid (CSF) samples from 50 pediatric patients with suspected VEs and/or VMs. Then we performed proteomics analysis on the 14 HEV-positive CSF samples and another 12 CSF samples from health controls (HCs). A supervised partial least squaresdiscriminant analysis (PLS-DA) and orthogonal PLS-DA (O-PLS-DA) model was performed using proteomics data. Results Ten viruses in 48% patients were identified and the most common pathogen was human enterovirus (HEV) Echo18. 11 proteins overlapping between the top 20 DEPs in terms of P value and FC and the top 20 proteins in PLS-DA VIP lists were acquired. Discussion Our result showed mNGS has certain advantages on pathogens identification in VE and VM and our research established a foundation to identify diagnosis biomarker candidates of HEV-positive meningitis based on MS-based proteomics analysis, which could also contribute toward investigating the HEV-specific host response patterns.
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Affiliation(s)
- Yi-Long Wang
- Department of Neurology, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center For Child Health, Hangzhou, Zhejiang, China
| | - Xiao-Tong Guo
- Department of Neurology, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center For Child Health, Hangzhou, Zhejiang, China
| | - Meng-Ying Zhu
- Department of Neurology, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center For Child Health, Hangzhou, Zhejiang, China
| | - Yu-Chen Mao
- Department of Neurology, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center For Child Health, Hangzhou, Zhejiang, China
| | - Xue-Bin Xu
- Department of Neurology, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center For Child Health, Hangzhou, Zhejiang, China
| | - Yi Hua
- Department of Neurology, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center For Child Health, Hangzhou, Zhejiang, China
| | - Lu Xu
- Department of Neurology, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center For Child Health, Hangzhou, Zhejiang, China
| | - Li-Hua Jiang
- Department of Neurology, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center For Child Health, Hangzhou, Zhejiang, China
| | - Cong-Ying Zhao
- Department of Neurology, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center For Child Health, Hangzhou, Zhejiang, China
| | - Xin Zhang
- Department of Neurology, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center For Child Health, Hangzhou, Zhejiang, China
| | - Guo-Xia Sheng
- Department of Neurology, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center For Child Health, Hangzhou, Zhejiang, China
| | - Pei-Fang Jiang
- Department of Neurology, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center For Child Health, Hangzhou, Zhejiang, China
| | - Zhe-Feng Yuan
- Department of Neurology, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center For Child Health, Hangzhou, Zhejiang, China
| | - Feng Gao
- Department of Neurology, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center For Child Health, Hangzhou, Zhejiang, China
- *Correspondence: Feng Gao,
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Kinsella CM, Edridge AWD, van Zeggeren IE, Deijs M, van de Beek D, Brouwer MC, van der Hoek L. Bacterial ribosomal RNA detection in cerebrospinal fluid using a viromics approach. Fluids Barriers CNS 2022; 19:102. [PMID: 36550487 PMCID: PMC9773461 DOI: 10.1186/s12987-022-00400-5] [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: 09/22/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND In patients with central nervous system (CNS) infections identification of the causative pathogen is important for treatment. Metagenomic next-generation sequencing techniques are increasingly being applied to identify causes of CNS infections, as they can detect any pathogen nucleic acid sequences present. Viromic techniques that enrich samples for virus particles prior to sequencing may simultaneously enrich ribosomes from bacterial pathogens, which are similar in size to small viruses. METHODS We studied the performance of a viromic library preparation technique (VIDISCA) combined with low-depth IonTorrent sequencing (median ~ 25,000 reads per sample) for detection of ribosomal RNA from common pathogens, analyzing 89 cerebrospinal fluid samples from patients with culture proven bacterial meningitis. RESULTS Sensitivity and specificity to Streptococcus pneumoniae (n = 24) before and after optimizing threshold parameters were 79% and 52%, then 88% and 90%. Corresponding values for Neisseria meningitidis (n = 22) were 73% and 93%, then 67% and 100%, Listeria monocytogenes (n = 24) 21% and 100%, then 27% and 100%, and Haemophilus influenzae (n = 18) 56% and 100%, then 71% and 100%. A higher total sequencing depth, no antibiotic treatment prior to lumbar puncture, increased disease severity, and higher c-reactive protein levels were associated with pathogen detection. CONCLUSION We provide proof of principle that a viromic approach can be used to correctly identify bacterial ribosomal RNA in patients with bacterial meningitis. Further work should focus on increasing assay sensitivity, especially for problematic species (e.g. L. monocytogenes), as well as profiling additional pathogens. The technique is most suited to research settings and examination of idiopathic cases, rather than an acute clinical setting.
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Affiliation(s)
- Cormac M. Kinsella
- grid.7177.60000000084992262Amsterdam UMC, Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands ,Amsterdam Institute for Infection and Immunity, Postbus 22660, 1100 DD Amsterdam, The Netherlands
| | - Arthur W. D. Edridge
- grid.7177.60000000084992262Amsterdam UMC, Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands ,Amsterdam Institute for Infection and Immunity, Postbus 22660, 1100 DD Amsterdam, The Netherlands
| | - Ingeborg E. van Zeggeren
- grid.7177.60000000084992262Amsterdam UMC, Department of Neurology, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands ,grid.484519.5Amsterdam Neuroscience, Neuroinfection and Inflammation, Amsterdam, The Netherlands
| | - Martin Deijs
- grid.7177.60000000084992262Amsterdam UMC, Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands ,Amsterdam Institute for Infection and Immunity, Postbus 22660, 1100 DD Amsterdam, The Netherlands
| | - Diederik van de Beek
- grid.7177.60000000084992262Amsterdam UMC, Department of Neurology, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands ,grid.484519.5Amsterdam Neuroscience, Neuroinfection and Inflammation, Amsterdam, The Netherlands
| | - Matthijs C. Brouwer
- grid.7177.60000000084992262Amsterdam UMC, Department of Neurology, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands ,grid.484519.5Amsterdam Neuroscience, Neuroinfection and Inflammation, Amsterdam, The Netherlands
| | - Lia van der Hoek
- grid.7177.60000000084992262Amsterdam UMC, Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands ,Amsterdam Institute for Infection and Immunity, Postbus 22660, 1100 DD Amsterdam, The Netherlands
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Hu S, Liu T, Huang S, Liang H. Management of long-term cryptococcal meningitis neoformans in a surviving patient: A case report. Front Med (Lausanne) 2022; 9:1035201. [PMID: 36569160 PMCID: PMC9767947 DOI: 10.3389/fmed.2022.1035201] [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: 09/02/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022] Open
Abstract
Cryptococcal meningitis is a common fungal infection of the central nervous system with high mortality and disability rates. A prominent clinical manifestation is persistent and severe cranial hypertension, which is one of the most critical outcome determinants in patients with cryptococcal meningoencephalitis. Herein, we report and discuss a case of cryptococcal meningitis treated by an inadequate course of medical therapy and placement of a ventriculoperitoneal shunt in a patient who survived for more than 10 years.
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Liu J, Zhang Q, Dong YQ, Yin J, Qiu YQ. Diagnostic accuracy of metagenomic next-generation sequencing in diagnosing infectious diseases: a meta-analysis. Sci Rep 2022; 12:21032. [PMID: 36470909 PMCID: PMC9723114 DOI: 10.1038/s41598-022-25314-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
Many common pathogens are difficult or impossible to detect using conventional microbiological tests. However, the rapid and untargeted nature of metagenomic next-generation sequencing (mNGS) appears to be a promising alternative. To perform a systematic review and meta-analysis of evidence regarding the diagnostic accuracy of mNGS in patients with infectious diseases. An electronic literature search of Embase, PubMed and Scopus databases was performed. Quality was assessed using the Quality Assessment of Diagnostic Accuracy Studies-2 tool. Summary receiver operating characteristics (sROC) and the area under the curve (AUC) were calculated; A random-effects model was used in cases of heterogeneity. A total of 20 papers were eligible for inclusion and synthesis. The sensitivity and specificity of diagnostic mNGS were 75% and 68%, respectively. The AUC from the SROC was 85%, corresponding to excellent performance. mNGS demonstrated satisfactory diagnostic performance for infections and yielded an overall detection rate superior to conventional methods.
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Affiliation(s)
- Jian Liu
- grid.13402.340000 0004 1759 700XDepartment of Intensive Care Unit, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang China
| | - Qiao Zhang
- grid.13402.340000 0004 1759 700XDepartment of Clinical Pharmacy, Zhejiang Provincial Key Laboratory for Drug Evaluation and Clinical Research, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang China
| | - Yong-Quan Dong
- Department of Respiratory Disease, Yinzhou No.2 Hospital, Ningbo, Zhejiang China
| | - Jie Yin
- grid.9227.e0000000119573309Department of Colorectal Medicine, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang China
| | - Yun-Qing Qiu
- grid.13402.340000 0004 1759 700XDepartment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang China
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Zhaoyang S, Guowei S, Jing P, Yundong Z, Xinhua L, Muyun W, Xiaowei M, Lixin L, Xiaoying C. Clinical characteristics of the host DNA-removed metagenomic next-generation sequencing technology for detecting SARS-CoV-2, revealing host local immune signaling and assisting genomic epidemiology. Front Immunol 2022; 13:1016440. [PMID: 36458015 PMCID: PMC9705594 DOI: 10.3389/fimmu.2022.1016440] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 10/10/2022] [Indexed: 09/02/2023] Open
Abstract
BACKGROUND Metagenomic next-generation sequencing (mNGS) technology has been central in detecting infectious diseases and helping to simultaneously reveal the complex interplay between invaders and their hosts immune response characteristics. However, it needs to be rigorously assessed for clinical utility. The present study is the first to evaluate the clinical characteristics of the host DNA-removed mNGS technology for detecting SARS-CoV-2, revealing host local immune signaling and assisting genomic epidemiology. METHODS 46 swab specimens collected from COVID-19 patients were assayed by two approved commercial RT-qPCR kits and mNGS. The evolutionary tree of SARS-CoV-2 was plotted using FigTree directly from one sample. The workflow of removing the host and retaining the host was compared to investigate the influence of host DNA removal on the performances of mNGS. Functional enrichment analysis of DEGs and xCell score were used to explore the characteristics of host local immune signaling. RESULTS The detection rate of mNGS achieved 92.9% (26/28) for 28 samples with a Ct value ≤ 35 and 81.1% (30/37) for all 46 samples. The genome coverage of SARS-CoV-2 could reach up to 98.9% when the Ct value is about 20 in swab samples. Removing the host could enhance the sensitivity of mNGS for detecting SARS-CoV-2 from the swab sample but does not affect the species abundance of microbes RNA. Improving the sequencing depth did not show a positive effect on improving the detection sensitivity of SARS-CoV-2. Cell type enrichment scores found multiple immune cell types were differentially expressed between patients with high and low viral load. CONCLUSIONS The host DNA-removed mNGS has great potential utility and superior performance on comprehensive identification of SARS-CoV-2 and rapid traceability, revealing the microbiome's transcriptional profiles and host immune responses.
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Affiliation(s)
- Sun Zhaoyang
- Department of Laboratory Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Song Guowei
- Department of Laboratory Medicine, Shijiazhuang People’s Hospital, Shijiazhuang, China
| | - Pan Jing
- Department of Laboratory Medicine, Shijiazhuang People’s Hospital, Shijiazhuang, China
| | - Zhou Yundong
- Shanghai Medical Innovation Fusion Biomedical Research Center, Shanghai, China
| | - Lu Xinhua
- Department of Laboratory Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei Muyun
- Department of Laboratory Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ma Xiaowei
- Department of Laboratory Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li Lixin
- Department of Laboratory Medicine, Shijiazhuang People’s Hospital, Shijiazhuang, China
| | - Chen Xiaoying
- Department of Laboratory Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Feng W, Jiang X, Zhang R, Guo Z, Gao D. Diagnosis of an Acinetobacter pittii from a patient in China with a multiplex PCR-based targeted gene sequencing platform of the cerebrospinal fluid: A case report with literature review. Medicine (Baltimore) 2022; 101:e31130. [PMID: 36281177 PMCID: PMC9592278 DOI: 10.1097/md.0000000000031130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND The traditional diagnosis model has great challenges for the etiological diagnosis of the central nervous system (CNS) diseases with similar clinical manifestations, especially for the diagnosis of rare pathogens. It is very important to make rapid and accurate identification of pathogens for guiding clinical choices in administering countermeasures. CASE SUMMARY On August 22, 2020, a 49 years old Chinese male patient had a headache for two days, and then the computed tomography (CT) scan of the brain showed subarachnoid hemorrhage. Subsequently, he underwent twice craniotomy and about 3 weeks of hospitalization. Since September 20, the patient was in the local rehabilitation hospital for hyperbaric oxygen therapy for about three weeks. Then the patient developed acute purulent meningoencephalitis. In the absence of diagnosis of specific pathogenic bacteria, vancomycin (1 g every 12 hours), ceftazidime (2 g every 8 hours), mannitol dehydration (125 mL, every 8 hours), and sodium valproate (0.4 g tid) was used timely according to cerebrospinal fluid (CSF) examination and clinical manifestations. CSF smear and routine culture test were negative during hospitalization. We used the metagenomic next-generation sequencing (mNGS) analysis of CSF for quick and accurate diagnosis, which identified human herpesvirus type 4 (EBV), Corynebacterium corynebacterium, Achromobacter xylose oxidation, and Acinetobacter baumannii, But the mapping degree was not high. Then, we used the modified method-multiplex PCR-based targeted gene sequencing platform (ptNGS) to detect CSF samples and found that the sequences detected were Acinetobacter pittii (A. pittii) and Staphylococcus epidermidis. S. epidermidis might come from skin colonization during lumbar puncture, so it was excluded from the etiological diagnosis. Therefore, we highly suspected that A. pittii was the pathogen in this case. After about three weeks of hospitalization treatment, the patient's symptoms were relieved. CONCLUSION In conclusion, empirical medication before the identification of pathogens is very important. The ptNGS may be an effective method for the diagnosis of pathogens.
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Affiliation(s)
- Wenliang Feng
- Department of Critical Care Medicine, Fengtai Youanmen Hospital, Beijing, China
| | - Xuebin Jiang
- Intensive Care Unit, Renhe Hospital, Beijing, China
| | - Rujiang Zhang
- Department of Neurology, Yunnan St John’s Hospital, Yunnan, China
| | - Zhendong Guo
- Department of Science and Technology, Shanghai, China
| | - Daiquan Gao
- Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing, China
- *Correspondence: Daiquan Gao, Department of Neurology, Xuanwu Hospital of Capital Medical University, No. 45 Changchun Street, Xicheng District, Beijing 100053, China (e-mail: )
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Thy M, Gaudemer A, Vellieux G, Sonneville R. Critical care management of meningitis and encephalitis: an update. Curr Opin Crit Care 2022; 28:486-494. [PMID: 35975963 DOI: 10.1097/mcc.0000000000000980] [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: 11/25/2022]
Abstract
PURPOSE OF REVIEW Meningitis and encephalitis represent severe neurological syndromes associated with encephalopathy, seizures, focal deficits, and neurological sequelae in survivors. We update on the critical care management of adult patients with severe meningitis and encephalitis. RECENT FINDINGS Large multicenter studies conducted in the adult population improved current knowledge on the epidemiology and outcomes of patients with severe meningitis and encephalitis. An early multimodal diagnostic workup (including CSF analysis, brain MRI, EEG, and serum studies) is mandatory for diagnosis and prognostication in those patients.New diagnostic methods, including multiplex PCR and next-generation sequencing techniques, allow for a faster differential diagnosis of infectious causes that may require specific antimicrobial therapy. Autoimmune causes of encephalitis, which may require urgent immunotherapy, are also increasingly recognized in the ICU setting. Although observational data suggest that early combined immunotherapy is associated with better neurological outcomes in patients with autoimmune encephalitis, randomized clinical trials have yet to be performed. SUMMARY Our review highlights the importance of an early multimodal approach for diagnosing severe meningitis and encephalitis. Randomized clinical trials are needed to identify pharmacological interventions that may improve patients' outcomes.
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Affiliation(s)
- Michael Thy
- Department of Intensive Care Medicine, AP-HP, Hôpital Bichat - Claude Bernard
- Department of Infectious and Tropical Diseases, AP-HP, Bichat Hospital
- EA 7323 - Pharmacology and Therapeutic Evaluation in Children and Pregnant Women
| | - Augustin Gaudemer
- Department of Radiology, AP-HP, Bichat Hospital, Université de Paris Cité
| | - Geoffroy Vellieux
- Paris Brain Institute, ICM, Inserm, CNRS, Sorbonne Université
- Clinical Neurophysiology Department, Pitié-Salpêtrière Hospital
| | - Romain Sonneville
- Department of Intensive Care Medicine, AP-HP, Hôpital Bichat - Claude Bernard
- INSERM UMR1137, IAME, Université Paris Cité, Paris, France
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