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Liu Y, Qin S, Lan C, Huang Q, Zhang P, Cao W. Effectiveness of metagenomic next-generation sequencing in the diagnosis of infectious diseases: A systematic review and meta-analysis. Int J Infect Dis 2024; 142:106996. [PMID: 38458421 DOI: 10.1016/j.ijid.2024.106996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 02/25/2024] [Accepted: 03/02/2024] [Indexed: 03/10/2024] Open
Abstract
OBJECTIVES Early diagnosis of infectious diseases remains a challenge. This study assessed the diagnostic value of mNGS in infections and explored the effect of various factors on the accuracy of mNGS. METHODS An electronic article search of PubMed, Cochrane Library, and Embase was performed. A total of 85 papers were eligible for inclusion and analysis. Stata 12.0 was used for statistical calculation to evaluate the efficacy of mNGS for the diagnosis of infectious diseases. RESULTS The AUC of 85 studies was 0.88 (95%CI, 0.85-0.90). The AUC of the clinical comprehensive diagnosis and conventional test groups was 0.92 (95%CI, 0.89-0.94) and 0.82 (95%CI, 0.78-0.85), respectively. The results of subgroup analysis indicated that the PLR and NLR were 12.67 (95%CI, 6.01-26.70) and 0.05 (95%CI, 0.03-0.10), respectively, in arthrosis infections. The PLR was 24.41 (95%CI, 5.70-104.58) in central system infections and the NLR of immunocompromised patients was 0.08 (95%CI, 0.01-0.62). CONCLUSION mNGS demonstrated satisfactory diagnostic performance for infections, especially for bone and joint infections and central system infections. Moreover, mNGS also has a high value in the exclusion of infection in immunocompromised patients.
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Affiliation(s)
- Yusi Liu
- Department of Pharmacy, Shenzhen Luohu People's Hospital, Shenzhen, Guangdong, PR China
| | - Sibei Qin
- Department of Pharmacy, Shenzhen Luohu People's Hospital, Shenzhen, Guangdong, PR China
| | - Chunhai Lan
- Department of Orthopedic Surgery, Shenzhen Luohu People's Hospital, Shenzhen, Guangdong, PR China
| | - Qinmiao Huang
- Department of Respiratory, Shenzhen Luohu People's Hospital, Shenzhen, Guangdong, PR China
| | - Peng Zhang
- Department of Pharmacy, Shenzhen Luohu People's Hospital, Shenzhen, Guangdong, PR China
| | - Weiling Cao
- Department of Pharmacy, Shenzhen Luohu People's Hospital, Shenzhen, Guangdong, PR China.
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Yu Y, Zhuo B, Xu W, Li L, Jin X, Ji Y, Ge Y. Diagnosis of an immunocompetent adult with acute headache and fever as Epstein-Barr virus encephalitis by mNGS of cerebrospinal fluid. Diagn Microbiol Infect Dis 2024; 109:116213. [PMID: 38359677 DOI: 10.1016/j.diagmicrobio.2024.116213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 01/31/2024] [Accepted: 02/09/2024] [Indexed: 02/17/2024]
Abstract
Complicated case with fever or headache of unknown origin is currently one of the main challenges in clinical diagnosis. A retrospective analysis was conducted on a 27-year-old female patient hospitalized with headache and fever, and the pathogen species were ultimately determined by metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF). The culture results of CSF showed no bacterial or fungal growth. CSF cytology showed a significant increase in nucleated cells. Pathogenic index (corresponded to human gamma herpesvirus 4) of the microorganism after correcting for human background was 12846.77 with a host index (human resource) of 27822.48 by mNGS of CSF. The patient improved through antiviral treatment with ganciclovir. Epstein-Barr virus encephalitis is rare in immunocompetent adults, which can easily cause misdiagnosis and should be paid attention to. mNGS of CSF has significant advantages in the diagnosis of Epstein-Barr virus encephalitis.
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Affiliation(s)
- Yan Yu
- Center for Rehabilitation Medicine, Department of Ophthalmology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, 310014, China
| | - Bingqian Zhuo
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, 310014, China
| | - Wei Xu
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, 310014, China; School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 310053, China
| | - Lanhui Li
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 310053, China
| | - Xinyue Jin
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, 310014, China
| | - Youqi Ji
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 310053, China
| | - Yumei Ge
- Center for Rehabilitation Medicine, Department of Ophthalmology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, 310014, China; Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, 310014, China; School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 310053, China; Key Laboratory of Precision Medicine for Head and Neck Cancers of Zhejiang Province, Zhejiang Provincial People's Hospital, Hangzhou, Zhejiang, 310014, China.
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Li W, Wang S, Zheng D. Metagenomic next-generation sequencing for diagnosing severe leptospirosis in a patient suspected COVID-19: A case report. Diagn Microbiol Infect Dis 2024; 109:116288. [PMID: 38615598 DOI: 10.1016/j.diagmicrobio.2024.116288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 03/07/2024] [Accepted: 03/25/2024] [Indexed: 04/16/2024]
Abstract
Leptospirosis is a zoonotic and neglected waterborne disease caused by the pathogenic helical spirochetes. Early diagnosis of leptospirosis remains challenging due to non-specific symptoms and the limited availability of rapid point-of-care diagnostic tests. Herein, we present a case where a patient suspected of having COVID-19 was diagnosed with leptospirosis using metagenomic next-generation sequencing (mNGS). This case highlights the potential of mNGS to diagnose leptospirosis in the context of the COVID-19 pandemic.
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Affiliation(s)
- Weijia Li
- Department of Intensive Care Unit, Peking University Shenzhen Hospital, No. 1120, Lianhua Road, Futian District, Shenzhen 518000, China.
| | - Song Wang
- Dinfectome Inc., Nanjing, Jiangsu, China
| | - Dan Zheng
- Dinfectome Inc., Nanjing, Jiangsu, China
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Duan Y, Zhang X, Deng W, Wang S, Hu J, Wang X, Li W, Chen B. The first reported pulmonary nocardiosis caused by Nocardia gipuzkoensis resisted to TMP-SMZ in an immunocompetent patient. J Glob Antimicrob Resist 2024:S2213-7165(24)00031-6. [PMID: 38462073 DOI: 10.1016/j.jgar.2024.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 01/21/2024] [Accepted: 02/06/2024] [Indexed: 03/12/2024] Open
Abstract
BACKGROUND . Nocardia gipuzkoensis was first described as a novel and distinct species in 2020 by Imen Nouioui and pulmonary nocardiosis associated with Nocardia gipuzkoensis was once reported in two bronchiectasis patients. Noteworthy, both reported Nocardia gipuzkoensis cases showed sensitivity to Trimethoprim/Sulfamethoxazol (TMP-SMZ), which are usually recommended for empirical therapy. METHODS We reported the third case of Nocardia gipuzkoensis infection in a 16-year-old girl with chief complaints of cough, persistent chest and back pain. No underlying immuno-suppressive conditions and glucocorticoid use was revealed. Patchy lesions next to spine and located in the posterior basal segment of lower lobes of left lung were seen in thorax computed tomography (CT), but no pathogenic bacteria was detected according to routine laboratory testings. RESULTS Metagenomic next-generation sequencing (mNGS) combined with Whole Genome Sequencing (WGS) was used to classified our isolate from bronchoalveolar lavage fluid (BALF) as a Nocardia gipuzkoensis. It is worth mentioning that drug susceptibility testing of our isolate showed resistance to TMP-SMZ, which was never reported before. The patient improved remarkably both clinically and radiographically according to the treatment with Imipenem-cilastatin infusion alone. CONCLUSION mNGS and WGS showed excellent performance in identifying Nocardia genus to the species level and improving detection rate of Nocardia gipuzkoensis ignored by traditional culture. Different from previously reported cases, Nocardia gipuzkoensis infection case showed resistance to TMP-SMZ, which is an unprecedented finding and a crucial addition to our understanding of the antibacterial spectrum of Nocardia gipuzkoensis. The successful treatment with Imipenem-cilastatin infusion alone in this case is a testament to the importance of precise identification and tailored antibiotic therapy.
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Affiliation(s)
- Yishan Duan
- Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Xiaoxia Zhang
- Center of Infectious Diseases, West China Hospital of Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Wen Deng
- Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Suyan Wang
- Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Jinrui Hu
- Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Xiaohui Wang
- Center of Infectious Diseases, West China Hospital of Sichuan University, Chengdu 610041, Sichuan Province, China; Center for Infectious Diseases, Ya'an People's Hospital, Ya'an, Sichuan Province, China
| | - Weimin Li
- Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, Chengdu 610041, Sichuan Province, China; Precision Medicine Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Bojiang Chen
- Precision Medicine Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, China; Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, Chengdu 610041, Sichuan Province, China.
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Chen Z, Ye T, He Y, Pan A, Mei Q. Use of pus metagenomic next-generation sequencing for efficient identification of pathogens in patients with sepsis. Folia Microbiol (Praha) 2024:10.1007/s12223-024-01134-7. [PMID: 38341816 DOI: 10.1007/s12223-024-01134-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 01/12/2024] [Indexed: 02/13/2024]
Abstract
The positive detection rate of blood metagenomic next-generation sequencing (mNGS) was still too low to meet clinical needs, while pus from the site of primary infection may be advantageous for identification of pathogens. To assess the value of mNGS using pus in patients with sepsis, thirty-five samples were collected. Pathogen identification and mixed infection diagnosis obtained by use of mNGS or cultivation methods were compared. Fifty-three aerobic or facultative anaerobes, 59 obligate anaerobes and 7 fungi were identified by the two methods. mNGS increased the accuracy rate of diagnosing aerobic or facultative anaerobic infections from 44.4% to 94.4%; mNGS also increased the sensitivity of diagnosing obligate anaerobic infections from 52.9% to 100.0%; however, mNGS did not show any advantage in terms of fungal infections. Culture and mNGS identified 1 and 24 patients with mixed infection, respectively. For obligate anaerobes, source of microorganisms was analyzed. The odontogenic bacteria all caused empyema (n = 7) or skin and soft tissue infections (n = 5), whereas the gut-derived microbes all caused intra-abdominal infections (n = 7). We also compared the clinical characteristics of non-obligate anaerobic and obligate anaerobic infection groups. The SOFA score [9.0 (7.5, 14.3) vs. 5.0 (3.0, 8.0), P = 0.005], procalcitonin value [4.7 (1.8, 39.9) vs. 2.50 (0.7, 8.0), P = 0.035], the proportion of septic shock (66.7% vs. 35.3%, P = 0.044) and acute liver injury (66.7% vs. 23.5%, P = 0.018) in the non-obligate anaerobic infection group were significantly higher than those in the obligate anaerobic infection group. In patients with sepsis caused by purulent infection, mNGS using pus from the primary lesion may yield more valuable microbiological information.
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Affiliation(s)
- Zhendong Chen
- Department of Intensive Care Unit, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Tingting Ye
- Department of Cardiovascular Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Yuxi He
- Department of Intensive Care Unit, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Aijun Pan
- Department of Intensive Care Unit, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China.
- Department of Intensive Care Unit, The Affiliated Provincial Hospital of Anhui Medical University, Anhui, 230001, China.
- WanNan Medical College, Wuhu, 241002, Anhui, China.
| | - Qing Mei
- Department of Intensive Care Unit, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China.
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Jin Y, Lan W, Chen X, Liu W, Luo W, Chen S. A rare case of anti-DPPX encephalitis combined with neuroleptospirosis. BMC Neurol 2024; 24:34. [PMID: 38243162 PMCID: PMC10797929 DOI: 10.1186/s12883-024-03538-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 01/14/2024] [Indexed: 01/21/2024] Open
Abstract
BACKGROUND Neuroleptospirosis and anti-dipeptidyl-peptidase-like protein 6 (DPPX) encephalitis are both very rare and have only been reported in the form of respective case reports. There are no reports of anti-DPPX encephalitis combined with neuroleptospirosis in the literature. We reported the first case of neuroleptospirosis combined with elevated DPPX antibodies in serum and cerebrospinal fluid (CSF). CASE PRESENTATION A previously healthy 53-year-old Chinese male farmer with a history of drinking raw stream water and flood sewage exposure was brought to the hospital due to an acute onset of neuropsychiatric symptoms. No fever or meningeal irritation signs were detected on physical examination. Routine laboratory investigations, including infection indicators, leukocyte and protein in CSF, electroencephalogram and gadolinium-enhanced magnetic resonance imaging of the brain, all revealed normal. While metagenomic next-generation sequencing (mNGS) identified the DNA genome of Leptospira interrogans in the CSF. Anti-DPPX antibody was detected both in blood and in CSF. A diagnosis of neuroleptospirosis combined with autoimmune encephalitis associated with DPPX-Ab was eventually made. He resolved completely after adequate amount of penicillin combined with immunotherapy. CONCLUSION We highlight that in patients with acute or subacute behavioral changes, even in the absence of fever, if the most recent freshwater exposure is clear, physicians should pay attention to leptospirosis. Due to the low sensitivity of routine microscopy, culture, polymerase chain reaction and antibody testing, mNGS may have more advantages in diagnosing neuroleptospirosis. As autoimmune encephalitis can be triggered by various infections, neuroleptospirosis may be one of the causes of autoimmune encephalitis. Since neuronal antibody measurements themselves are not that common in neuroleptospirosis, future studies are needed to determine whether the detection of anti-DPPX antibodies is a rare event in leptospirosis. Early identification of autoimmune encephalitis and timely administration of immunotherapy may lead to a better outcome.
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Affiliation(s)
- Yong Jin
- Department of Neurology, Huizhou Central People's Hospital, No. 41, Eling North Road, Huizhou, Guangdong Province, 516001, China
| | - Wei Lan
- Department of Neurology, Huizhou Central People's Hospital, No. 41, Eling North Road, Huizhou, Guangdong Province, 516001, China
| | - Xiaodong Chen
- Department of Neurology, Huizhou Central People's Hospital, No. 41, Eling North Road, Huizhou, Guangdong Province, 516001, China
| | - Wu Liu
- Department of Neurology, Huizhou Central People's Hospital, No. 41, Eling North Road, Huizhou, Guangdong Province, 516001, China
| | - Weiliang Luo
- Department of Neurology, Huizhou Central People's Hospital, No. 41, Eling North Road, Huizhou, Guangdong Province, 516001, China.
| | - Suqin Chen
- Department of Neurology, Huizhou Central People's Hospital, No. 41, Eling North Road, Huizhou, Guangdong Province, 516001, China.
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Chen H, Zheng Y, Zhang X, Liu S, Yin Y, Guo Y, Wang X, Zhang Y, Zhao C, Gai W, Wang H. Clinical evaluation of cell-free and cellular metagenomic next-generation sequencing of infected body fluids. J Adv Res 2024; 55:119-129. [PMID: 36889461 PMCID: PMC10770109 DOI: 10.1016/j.jare.2023.02.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 02/14/2023] [Accepted: 02/26/2023] [Indexed: 03/08/2023] Open
Abstract
INTRODUCTION Previous studies have evaluated metagenomic next-generation sequencing (mNGS) of cell-free DNA (cfDNA) for pathogen detection in blood and body fluid samples. However, no study has assessed the diagnostic efficacy of mNGS using cellular DNA. OBJECTIVES This is the first study to systematically evaluate the efficacy of cfDNA and cellular DNA mNGS for pathogen detection. METHODS A panel of seven microorganisms was used to compare cfDNA and cellular DNA mNGS assays concerning limits of detection (LoD), linearity, robustness to interference, and precision. In total, 248 specimens were collected between December 2020 and December 2021. The medical records of all the patients were reviewed. These specimens were analysed using cfDNA and cellular DNA mNGS assays, and the mNGS results were confirmed using viral qPCR, 16S rRNA, and internal transcribed spacer (ITS) amplicon next-generation sequencing. RESULTS The LoD of cfDNA and cellular DNA mNGS was 9.3 to 149 genome equivalents (GE)/mL and 27 to 466 colony-forming units (CFU)/mL, respectively. The intra- and inter-assay reproducibility of cfDNA and cellular DNA mNGS was 100%. Clinical evaluation revealed that cfDNA mNGS was good at detecting the virus in blood samples (receiver operating characteristic (ROC) area under the curve (AUC), 0.9814). In contrast, the performance of cellular DNA mNGS was better than that of cfDNA mNGS in high host background samples. Overall, the diagnostic efficacy of cfDNA combined with cellular DNA mNGS (ROC AUC, 0.8583) was higher than that of cfDNA (ROC AUC, 0.8041) or cellular DNA alone (ROC AUC, 0.7545). CONCLUSION Overall, cfDNA mNGS is good for detecting viruses, and cellular DNA mNGS is suitable for high host background samples. The diagnostic efficacy was higher when cfDNA and cellular DNA mNGS were combined.
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Affiliation(s)
- Hongbin Chen
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Yafeng Zheng
- WillingMed Technology (Beijing) Co., Ltd, Beijing, China
| | - Xiaoyang Zhang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Si Liu
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Yuyao Yin
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Yifan Guo
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Xiaojuan Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Yawei Zhang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Chunjiang Zhao
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Wei Gai
- WillingMed Technology (Beijing) Co., Ltd, Beijing, China.
| | - Hui Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China.
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Tian C, Yan H, Tang P, Shi J, Liang M, Wan Y, Li W, Sun X, Qin C. Pelvic infection caused by periodontitis: A case report. Case Rep Womens Health 2023; 40:e00563. [PMID: 38046237 PMCID: PMC10690538 DOI: 10.1016/j.crwh.2023.e00563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 12/05/2023] Open
Abstract
Oral bacteria in patients with periodontitis can disseminate into the bloodstream via broken oral epithelial cells, causing odontogenic maxillofacial infections, brain abscesses and endocarditis. However, pelvic infection caused by periodontitis is rare. The case of a 48-year-old woman with a long history of recurrent periodontal infections, who complained of abdominal distention and pain for 14 days after dental implantation, is reported here. Pelvic ultrasound and magnetic resonance imaging signaled multiple inflammatory encapsulated effusions in the posterior uterus, which were removed by laparoscopic surgery and tested with metagenomic next-generation sequencing (mNGS). Through mNGS, numerous oral pathogens, including Filifactor alocis, were identified in the pelvic effusions. The patient was subsequently diagnosed with a pelvic infection originating from periodontitis, and recovered after undergoing surgery and targeted antibacterial treatment. Thus, the possibility of extrabuccal complications in patients with a history of periodontitis or invasive oral procedures merits closer attention.
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Affiliation(s)
- Cuihong Tian
- Clinical Research Center, Luohu Clinical College of Shantou University Medical College, Shenzhen, Guangdong 518001, China
- Clinical Research Center, First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, China
- Department of Cardiology, First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, China
- Center for Precision Health, Edith Cowan University, Perth, WA 6027, Australia
| | - Hongle Yan
- Department of Cardiology, First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Ping Tang
- Department of General Practice, Luohu Clinical College of Shantou University Medical College, Shenzhen, Guangdong 518001, China
| | - Jinqiu Shi
- Department of Obstetrics and Gynecology, Luohu Clinical College of Shantou University Medical College, Shenzhen, Guangdong 518001, China
| | - Maolian Liang
- Department of Obstetrics and Gynecology, Luohu Clinical College of Shantou University Medical College, Shenzhen, Guangdong 518001, China
| | - Yanyan Wan
- Department of Science and Education, Luohu Clinical College of Shantou University Medical College, Shenzhen, Guangdong 518001, China
| | - Weiping Li
- Department of Cardiology, First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, China
- Department of Information, First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Xizhuo Sun
- Department of Oncology Immunology, Luohu Hospital Group, Shenzhen, Guangdong 518001, China
| | - Chenglu Qin
- Department of Obstetrics and Gynecology, Luohu Clinical College of Shantou University Medical College, Shenzhen, Guangdong 518001, China
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Xu L, Huang X, Hou J, Ji P. Metagenomic next-generation sequencing (mNGS)-assisted diagnosis of a case with infective endocarditis caused by Bartonella species. Asian J Surg 2023; 46:4966-4967. [PMID: 37596226 DOI: 10.1016/j.asjsur.2023.06.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 06/07/2023] [Indexed: 08/20/2023] Open
Affiliation(s)
- Le Xu
- Department of Anesthesiology, West China Hospital, Sichuan University, No. 37 Guoxue Xiang, Chengdu, 610041, Sichuan, China
| | - XiaoYing Huang
- Department of Critical Care Medicine, West China Hospital, Sichuan University, No.37 Guoxue Xiang, Chengdu, 610041, Sichuan, China
| | - Jianglong Hou
- Department of Cardiovascular Surgery, West China Hospital, Sichuan University, No.37 Guoxue Xiang, Chengdu, 610041, Sichuan, China.
| | - Peng Ji
- Department of Critical Care Medicine, West China Hospital, Sichuan University, No.37 Guoxue Xiang, Chengdu, 610041, Sichuan, China.
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Wang Y, Chen T, Zhang S, Zhang L, Li Q, Lv Q, Kong D, Jiang H, Ren Y, Jiang Y, Li Y, Huang W, Liu P. Clinical evaluation of metagenomic next-generation sequencing in unbiased pathogen diagnosis of urinary tract infection. J Transl Med 2023; 21:762. [PMID: 37891586 PMCID: PMC10612365 DOI: 10.1186/s12967-023-04562-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND Early availability of pathogen identification in urinary tract infections (UTIs) has critical importance in disease management. Metagenomic next-generation sequencing (mNGS) has the potential to transform how acute and serious infections are diagnosed by offering unbiased and culture-free pathogen detection. However, clinical experience with application of the mNGS test is relatively limited. METHODS We therefore established a MinION-based mNGS pathogens diagnostic platform and evaluated its potential for clinical implementation in UTIs with clinical samples. 213 urine samples from patients with suspected UTIs were included and subjected to mNGS testing using the MinION platform. mNGS results were compared to the gold standard of clinical culture and composite standard of combining clinical testing, confirmatory qPCR testing, and clinical adjudication by doctors. RESULTS The mNGS exhibited a sensitivity of 81.4% and a specificity of 92.3%, along with a positive predictive value of 96.6%, a negative predictive value of 64.9%, and an overall accuracy of 84.4%, all of which were determined based on the gold standard of routine culture results. When assessed against the composite standard, the sensitivity and specificity both increased to 89.9% and 100%, respectively, while the accuracy rose to 92.4%. Notably, the positive predictive value and negative predictive value also saw improvements, reaching 100% and 76.8%, respectively. Moreover, this diagnostic platform successfully identified dsDNA viruses. Among the 65 culture-negative samples, the viral detection rate reached 33.8% (22/65) and was subsequently validated through qPCR. Furthermore, the automatic bioinformatics pipeline we developed enabled one-click analysis from data to results, leading to a significant reduction in diagnosis time. CONCLUSION These results demonstrate that the pathogen detection performance of mNGS is sufficient for diagnostic testing in clinical settings. As the method is generally unbiased, it can improve diagnostic testing of UTIs and other microbial infections.
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Affiliation(s)
- Ye Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Ting Chen
- Department of Critical Care Medicine, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Shengwei Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Lei Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Qian Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Qingyu Lv
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Decong Kong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Hua Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Yuhao Ren
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Yongqiang Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Yan Li
- Department of Critical Care Medicine, The Fifth Medical Center of PLA General Hospital, Beijing, China.
| | - Wenhua Huang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China.
| | - Peng Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China.
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Shangguan L, Xue L, Shang J, Wang H. The application value of metagenomic next-generation sequencing in community-acquired purulent meningitis after antibiotic intervention. BMC Infect Dis 2023; 23:683. [PMID: 37828452 PMCID: PMC10571418 DOI: 10.1186/s12879-023-08672-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 10/05/2023] [Indexed: 10/14/2023] Open
Abstract
BACKGROUND Bacteria account for nearly one third of the causes of community-acquired central nervous system infections, and traditional diagnostic methods are based on culture results, which are time-consuming and have a low detection rate leading to delayed diagnosis and treatment. Since metagenomic next-generation sequencing (mNGS) has the advantages of high timeliness and only detecting microbial trace gene fragments, it has been used more widely in recent years. Based on this, we explored whether the application of cerebrospinal fluid (CSF) mNGS is advantageous in patients with community-acquired purulent meningitis, especially in people who have already used antibiotics. METHODS This was a retrospective study of 63 patients with community-acquired purulent meningitis admitted to the Department of Neurology of Shanxi Bethune Hospital from March 2018 to November 2022. Data were systematically collected and classified into CSF culture group, blood culture group and CSF mNGS group according to different detection methods, and the total detection rate of each method was calculated. Each group of patients was divided into two subgroups according to whether antibiotics were used before sampling. The detection rates of the three groups were compared within and between groups to explore whether mNGS has advantages over traditional methods and the influence of antibiotic use on detection rates of the three methods. RESULTS Among the 63 patients, the cases of CSF culture, blood culture and CSF mNGS were 56, 46, 44, respectively. The total detection rates of the three methods were 17.86%, 36.96%, 81.82%, with statistical differences (p < 0.05),suggesting that the detection rate of mNGS was higher than CSF culture (p < 0.05) and blood culture (p < 0.05),and the detection rate of blood culture higher than CSF culture (p < 0.05). Further grouping found that without antibiotics, the detection rates of CSF culture, blood culture and CSF mNGS were 28.57%, 56.25% and 88.89%, with statistical differences (p < 0.05), and the detection rate of CSF mNGS was higher than that of CSF culture (p < 0.05), but there was no statistical difference between CSF and blood culture (p > 0.05), nor between blood culture and CSF mNGS (p > 0.05). The detection rates of the three groups with antibiotics were 14.29%, 26.67% and 80.00%, with statistical differences (p < 0.05), and the detection rate of CSF mNGS was still higher than CSF culture (p < 0.05) and blood culture (p < 0.05). However, the detection rate of CSF mNGS also decreased after antibiotics were used for more than 3 days. CONCLUSIONS The detection rate of CSF mNGS in patients with purulent meningitis is higher than traditional methods, especially in patients who have been given antibiotics, but the detection rate will decrease with the extension of antibiotic use.
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Affiliation(s)
- Lijuan Shangguan
- Department of Neurology, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, 030032, China
- Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Lanping Xue
- Department of Neurology, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, 030032, China
- Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Jing Shang
- Department of Neurology, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, 030032, China
- Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Hailong Wang
- Department of Neurology, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, 030032, China.
- Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
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12
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Xiao ST, Zhang HQ, Wang YX. Isolated neural arch tuberculosis with tuberculomas: case report. Skeletal Radiol 2023:10.1007/s00256-023-04450-0. [PMID: 37712982 DOI: 10.1007/s00256-023-04450-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 08/12/2023] [Accepted: 08/26/2023] [Indexed: 09/16/2023]
Abstract
We reported a case of atypical spinal tuberculosis on the posterior elements of lumbar spine in a 52-year-old female. It was easy to be misdiagnosed as spinal tumor due to its imaging characteristics. We performed puncture biopsy to initially consider tuberculosis, and then the patient was accepted surgical treatment. The intraoperative removed specimen was sent to pathological examination, microbial culture, Xpert MTB/RIF and metagenomic next-generation sequencing (mNGS) and then the diagnosis of neural arch tuberculosis was confirmed. After operation, the patient obtained stable effect by anti-tuberculosis drug treatment. In a word, the uncommon case had an important reference significance for the diagnosis of atypical spine tuberculosis and differentiation from spinal tumors. It is critical to make right preliminary diagnosis by appropriate examination as it determined the next diagnosis and treatment in special and rare clinical cases.
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Affiliation(s)
- Shun-Tian Xiao
- Department of Spine Surgery and Orthopaedics, Xiangya Spinal Surgery Center, Xiangya Hospital of Central South University, Xiang Ya Road 87, Changsha, 410008, Hunan Province, China
- National Clinical Research Center for Geriatric Disorder, Xiangya Hospital of Central South University, Changsha, 410008, Hunan Province, China
| | - Hong-Qi Zhang
- Department of Spine Surgery and Orthopaedics, Xiangya Spinal Surgery Center, Xiangya Hospital of Central South University, Xiang Ya Road 87, Changsha, 410008, Hunan Province, China
- National Clinical Research Center for Geriatric Disorder, Xiangya Hospital of Central South University, Changsha, 410008, Hunan Province, China
| | - Yu-Xiang Wang
- Department of Spine Surgery and Orthopaedics, Xiangya Spinal Surgery Center, Xiangya Hospital of Central South University, Xiang Ya Road 87, Changsha, 410008, Hunan Province, China.
- National Clinical Research Center for Geriatric Disorder, Xiangya Hospital of Central South University, Changsha, 410008, Hunan Province, China.
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13
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Liu H, Xu H, Liu H, Zhao Z, Zhang X. Metagenomic next-generation sequencing in the diagnose of pulmonary infection with airway complications in a lung transplant recipient. Heliyon 2023; 9:e19611. [PMID: 37809439 PMCID: PMC10558871 DOI: 10.1016/j.heliyon.2023.e19611] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 10/10/2023] Open
Abstract
We reported a case of a 60-year-old male with fever, cough, expectoration, and chest distress after right lung transplanted. Blood examination showed elevated C-reaction protein (CRP), white blood cell (WBC), and ammonia. Computed tomography (CT) revealed patchy high-density shadows and few pleural effusions in the transplanted lung. Bronchoscopy illustrated anastomotic fistula, and pseudomembrane and mucus plugs around the right main bronchial anastomosis. Carbapenem-resistant Klebsiella pneumoniae, Ureaplasma urealyticum, and Aspergillus flavus was successively detected by metagenomic next-generation sequencing (mNGS). Targeted anti-microbial agents were administered and patient was successfully discharged. Unfortunately, a year later, patient died of respiratory failure due to recurrent pulmonary infections.
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Affiliation(s)
- Hongmei Liu
- Department of Respiratory and Critical Care Medicine, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, China
| | - Huan Xu
- Department of Scientific Affairs, Vision Medicals Center for Infection Diseases, Guangzhou, China
| | - Hui Liu
- Department of Respiratory and Critical Care Medicine, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, China
| | - Zhigang Zhao
- Department of Respiratory and Critical Care Medicine, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, China
| | - Xiaoju Zhang
- Department of Respiratory and Critical Care Medicine, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, China
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Shen Z, Wang Y, Bao A, Yang J, Sun X, Cai Y, Wan L, Huang C, Xu X, Niu J, Xia X, Shen C, Wei Y, Qiu H, Zhou K, Zhang M, Tong Y, Song X. Metagenomic Next-Generation Sequencing for Pathogens in Bronchoalveolar Lavage Fluid Improves the Survival of Patients with Pulmonary Complications After Allogeneic Hematopoietic Stem Cell Transplantation. Infect Dis Ther 2023; 12:2103-2115. [PMID: 37541984 PMCID: PMC10505113 DOI: 10.1007/s40121-023-00850-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 07/14/2023] [Indexed: 08/06/2023] Open
Abstract
INTRODUCTION Unbiased metagenomic next-generation sequencing (mNGS) has been used for infection diagnosis. In this study, we explored the clinical diagnosis value of mNGS for pulmonary complications after allogeneic hematopoietic stem cell transplantation (allo-HSCT). METHODS From August 2019 to June 2021, a prospective study was performed to comparatively analyze the pathogenic results of mNGS and conventional tests for bronchoalveolar lavage fluid (BALF) from 134 cases involving 101 patients with pulmonary complications after allo-HSCT. RESULTS More pathogens were identified by mNGS than with conventional tests (226 vs 120). For bacteria, the diagnostic sensitivity (P = 0.144) and specificity (P = 0.687) were similar between the two methods. For fungus except Pneumocystis jirovecii (PJ), conventional tests had a significantly higher sensitivity (P = 0.013) with a similarly high specificity (P = 0.109). The sensitivities for bacteria and fungi could be increased with the combination of the two methods. As for PJ, both the sensitivity (100%) and specificity (99.12%) of mNGS were very high. For viruses, the sensitivity of mNGS was significantly higher (P = 0.021) and the negative predictive value (NPV) was 95.74% (84.27-99.26%). Pulmonary infection complications accounted for 90.30% and bacterium was the most common pathogen whether in single infection (63.43%) or mixed infection (81.08%). The 6-month overall survival (OS) of 88.89% in the early group (mNGS ≤ 7 days) was significantly higher than that of 65.52% (HR 0.287, 95% CI 0.101-0.819, P = 0.006) in the late group (mNGS > 7 days). CONCLUSIONS mNGS for BALF could facilitate accurate and fast diagnosis for pulmonary complications. Early mNGS could improve the prognosis of patients with pulmonary complications after allo-HSCT. TRIAL REGISTRATION ClinicalTrials.gov identifier, NCT04051372.
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Affiliation(s)
- Zaihong Shen
- Department of Hematology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
- Department of Hematology, Taizhou First People's Hospital, Huangyan Hospital of Wenzhou Medical University, Taizhou City, 318020, Zhejiang Province, China
| | - Ying Wang
- Department of Hematology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Aihua Bao
- Department of Respiratory and Critical Care Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Jun Yang
- Department of Hematology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Xi Sun
- Department of Hematology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Yu Cai
- Department of Hematology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Liping Wan
- Department of Hematology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Chongmei Huang
- Department of Hematology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Xiaowei Xu
- Department of Hematology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Jiahua Niu
- Department of Hematology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Xinxin Xia
- Department of Hematology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Chang Shen
- Department of Hematology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Yu Wei
- Department of Hematology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Huiying Qiu
- Department of Hematology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Kun Zhou
- Department of Hematology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Min Zhang
- Department of Respiratory and Critical Care Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Yin Tong
- Department of Hematology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Xianmin Song
- Department of Hematology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China.
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Zhang X, Chen H, Han D, Wu W. Clinical usefulness of metagenomic next-generation sequencing for Rickettsia and Coxiella burnetii diagnosis. Eur J Clin Microbiol Infect Dis 2023; 42:681-689. [PMID: 36997767 PMCID: PMC10172222 DOI: 10.1007/s10096-023-04586-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 03/07/2023] [Indexed: 04/01/2023]
Abstract
Rickettsia and Coxiella burnetii are zoonotic tick-borne pathogens that cause febrile illnesses in humans. Metagenomic next-generation sequencing (mNGS) is a new technology used to diagnose infectious diseases. However, clinical experience with applying the test to rickettsioses and Q fever is relatively limited. Therefore, this study aimed to explore the diagnostic performance of mNGS in detecting Rickettsia and C. burnetii. We retrospectively studied patients with rickettsioses or Q fever between August 2021 and July 2022. Peripheral blood mNGS and polymerase chain reaction (PCR) were performed for all patients. Clinical data were retrieved for analysis. Thirteen patients were included in this study (eleven confirmed cases and two suspected cases). Signs and symptoms included fever (13, 100%), rash (7, 53.8%), muscle soreness (5, 38.5%), headache (4, 30.8%), skin eschar (3, 23.1%), and disturbance of consciousness (2, 15.4%). In addition, eight patients (61.6%) had thrombocytopenia, ten (76.9%) had liver function impairment, and two (15.4%) had renal function impairment. The results of mNGS revealed seven patients with R. japonica (53.8%), five with C. burneti (38.5%), two with R. heilongjiangensis (15.4%), and one with R. honei (7.7%). PCR results were positive in 11 patients (84.6%). After receiving doxycycline-based treatment, 12 (92.3%) patients returned to a normal temperature within 72 h. All patients were discharged in better health. Therefore, mNGS can help diagnose Rickettsia and C. burnetii and shorten the diagnosis time, especially for patients with atypical clinical manifestations and unclear epidemiologic evidence of a tick bite or exposure.
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Affiliation(s)
- Xuan Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Huixin Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Dongsheng Han
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Hangzhou, China.
- Institute of Laboratory Medicine, Zhejiang University, Hangzhou, China.
| | - Wei Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China.
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16
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Huang L, Xu S, Huang Z, Chen Y, Xu N, Xie B. Risk factors associated with Pneumocystis jirovecii pneumonia in non-HIV immunocompromised patients and co-pathogens analysis by metagenomic next-generation sequencing. BMC Pulm Med 2023; 23:72. [PMID: 36829171 PMCID: PMC9951498 DOI: 10.1186/s12890-022-02300-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 12/26/2022] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND Pneumocystis jirovecii pneumonia (PJP) is one of the most common opportunistic infections in immunocompromised patients. However, the accurate prediction of the development of PJP in non-HIV immunocompromised patients is still unclear. METHODS Non-HIV immunocompromised patients confirmed diagnosis of PJP by the clinical symptoms, chest computed tomography and etiological results of metagenomic next-generation sequencing (mNGS) were enrolled as observation group. Another group of matched non-HIV immunocompromised patients with non-PJP pneumonia were enrolled to control group. The risk factors for the development of PJP and the co-pathogens in the bronchoalveolar lavage fluid (BALF) detected by mNGS were analyzed. RESULTS: A total of 67 (33 PJP, 34 non-PJP) participants were enrolled from Fujian Provincial Hospital. The ages, males and underlying illnesses were not significantly different between the two groups. Compared to non-PJP patients, PJP patients were more tends to have the symptoms of fever and dyspnea. The LYM and ALB were significantly lower in PJP patients than in non-PJP patients. Conversely, LDH and serum BDG in PJP patients were significantly higher than in non-PJP controls. For immunological indicators, the levels of immunoglobulin A, G, M and complement C3, C4, the numbers of T, B, and NK cells, had no statistical difference between these two groups. Logistic multivariate analysis showed that concomitant use of corticosteroids and immunosuppressant (OR 14.146, P = 0.004) and the lymphocyte counts < 0.7 × 109/L (OR 6.882, P = 0.011) were risk factors for the development of PJP in non-HIV immunocompromised patients. 81.82% (27/33) and 64.71% (22/34) mixed infections were identified by mNGS in the PJP group and non-PJP group separately. CMV, EBV and Candida were the leading co-pathogens in PJP patients. The percentages of CMV and EBV identified by mNGS in PJP group were significantly higher than those in the control group(p < 0.005). CONCLUSIONS: Clinicians should pay close attention to the development of PJP in non-HIV immunocompromised patients who possess the risk factors of concomitant use of corticosteroids and immunosuppressant and the lymphocyte counts < 0.7 × 109/L. Prophylaxis for PJP cannot rely solely on CD4+ T counts in non-HIV immunocompromised patients. Whether CMV infection increases the risk of PJP remains to be further investigated.
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Affiliation(s)
- Liping Huang
- grid.256112.30000 0004 1797 9307Shengli Clinical Medical college of Fujian Medical University, Fuzhou, 350001 Fujian Province China ,grid.415108.90000 0004 1757 9178Department of Respiratory and Critical Care Medicine, Fujian Provincial Hospital, Fuzhou, 350001 Fujian Province China
| | - Shuyun Xu
- grid.256112.30000 0004 1797 9307Shengli Clinical Medical college of Fujian Medical University, Fuzhou, 350001 Fujian Province China
| | - Zhimin Huang
- grid.256112.30000 0004 1797 9307Shengli Clinical Medical college of Fujian Medical University, Fuzhou, 350001 Fujian Province China
| | - Yusheng Chen
- grid.256112.30000 0004 1797 9307Shengli Clinical Medical college of Fujian Medical University, Fuzhou, 350001 Fujian Province China ,grid.415108.90000 0004 1757 9178Department of Respiratory and Critical Care Medicine, Fujian Provincial Hospital, Fuzhou, 350001 Fujian Province China
| | - Nengluan Xu
- grid.256112.30000 0004 1797 9307Shengli Clinical Medical college of Fujian Medical University, Fuzhou, 350001 Fujian Province China ,grid.415108.90000 0004 1757 9178Department of Respiratory and Critical Care Medicine, Fujian Provincial Hospital, Fuzhou, 350001 Fujian Province China
| | - Baosong Xie
- Shengli Clinical Medical college of Fujian Medical University, Fuzhou, 350001, Fujian Province, China. .,Department of Respiratory and Critical Care Medicine, Fujian Provincial Hospital, Fuzhou, 350001, Fujian Province, China.
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Wei Y, Zhang T, Ma Y, Yan J, Zhan J, Zheng J, Xu Y. Clinical Evaluation of Metagenomic Next-Generation Sequencing for the detection of pathogens in BALF in severe community acquired pneumonia. Ital J Pediatr 2023; 49:25. [PMID: 36805803 PMCID: PMC9938609 DOI: 10.1186/s13052-023-01431-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 02/12/2023] [Indexed: 02/19/2023] Open
Abstract
BACKGROUND Rapid and accurate identification of pathogens is very important for the treatment of Severe community-acquired pneumonia (SCAP) in children. Metagenomic Next-generation sequencing (mNGS) has been applied in the detection of pathogenic bacteria in recent years, while the overall evaluation the application of SCAP in children is lacking. METHODS In our study, 84 cases of SCAP were enrolled. Bronchoalveolar lavage fluid (BALF) samples were analysed using mNGS; and sputum, blood, and BALF samples were analysed using conventional technology (CT). RESULTS Among the 84 children, 41 were boys, and 43 were girls, with an average age ranging from 2 months to 14 years. The pathogen detection rate of mNGS was higher than that of CT (83.3% [70/84] vs. 63.1% [53/84], P = 0.003). The mNGS was much greater than that of the CT in detecting Streptococcus pneumoniae (89.2% [25/29] vs. 44.8% [13/29], P = 0.001) and Haemophilus influenzae (91.7% [11/12] vs. 33.3% [4/12], P < 0.005). The mNGS also showed superior fungal detection performance compared with that of the CT (81.8% [9/11] vs. 18.2% [2/11], P = 0.004). The mNGS test can detect viruses, such as bocavirus, rhinovirus, and human metapneumovirus, which are not frequently recognised using CT. However, the mNGS detection rate was lower than that of the CT (52.4% [11/21] vs. 95.2% [20/21], P = 0.004) for Mycoplasma pneumoniae (MP). The detection rate of mNGS for mixed infection was greater than that of the CT, although statistical significance was not observed (26.3% [20/39] vs. 21.1% [16/39], P > 0.005). Treatment for 26 (31.0%) children was changed based on mNGS results, and their symptoms were reduced; nine patients had their antibiotic modified, five had antibiotics added, nine had their antifungal medication, and seven had their antiviral medication. CONCLUSION mNGS has unique advantages in the detection of SCAP pathogens in children, especially S. pneumoniae, H. influenzae, and fungi. However, the detection rate of MP using mNGS was lower than that of the CT. Additionally, mNGS can detect pathogens that are not generally covered by CT, which is extremely important for the modification of the treatment strategy.
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Affiliation(s)
- Yupeng Wei
- grid.265021.20000 0000 9792 1228Clinical School of Paediatrics, Tianjin Medical University, Tianjin, China ,grid.417022.20000 0004 1772 3918Department of Respiratory Medicine, Tianjin Children’s Hospital (Tianjin University Children’s Hospital), Tianjin, China ,grid.410626.70000 0004 1798 9265Department of Neonatology, Tianjin Central Hospital of Gynecology Obstetrics, Tianjin, China
| | - Tongqiang Zhang
- grid.265021.20000 0000 9792 1228Clinical School of Paediatrics, Tianjin Medical University, Tianjin, China ,grid.417022.20000 0004 1772 3918Department of Respiratory Medicine, Tianjin Children’s Hospital (Tianjin University Children’s Hospital), Tianjin, China
| | - Yuting Ma
- grid.265021.20000 0000 9792 1228Clinical School of Paediatrics, Tianjin Medical University, Tianjin, China ,grid.417022.20000 0004 1772 3918Department of Infection, Tianjin Children’s Hospital (Tianjin University Children’s Hospital), Tianjin, China
| | - Jisi Yan
- grid.265021.20000 0000 9792 1228Clinical School of Paediatrics, Tianjin Medical University, Tianjin, China ,grid.417022.20000 0004 1772 3918Department of Respiratory Medicine, Tianjin Children’s Hospital (Tianjin University Children’s Hospital), Tianjin, China ,grid.410626.70000 0004 1798 9265Department of Neonatology, Tianjin Central Hospital of Gynecology Obstetrics, Tianjin, China
| | - Jianghua Zhan
- Department of Pediatric Surgery, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China.
| | - Jun Zheng
- Department of Neonatology, Tianjin Central Hospital of Gynecology Obstetrics, Tianjin, China.
| | - Yongsheng Xu
- Department of Respiratory Medicine, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China.
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18
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Zhang Y, Zhou D, Xia H, Wang J, Yang H, Xu L, Huang K, Fang J. Metagenomic next-generation sequencing for detection of pathogens in children with hematological diseases complicated with infection. Mol Cell Probes 2023; 67:101889. [PMID: 36513243 DOI: 10.1016/j.mcp.2022.101889] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 12/02/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022]
Abstract
OBJECTIVE Infection is one of the most common causes of death in children with hematological diseases. Here, we aim to investigate the value of metagenomic next-generation sequencing (mNGS) in the detection of causative pathogens in children with hematological diseases. METHODS In this retrospective study, specimens from children with hematological diseases, who were admitted to Sun Yat-Sen University between June 2019 and September 2021, were collected for culture and mNGS. RESULTS A total of 67 pediatric patients were enrolled, and 96 specimens were collected. The positive rate of mNGS was significantly higher than that of culture (57.2% vs 12.5%, P < 0.01). The concordance (90.9%, 10/11) between the positive results of the two methods was high. mNGS detected more cases with Pneumocystis jeroveci, Aspergillus flavus, viruses, and some rare pathogens than culture. Mixed infections were detected by mNGS in 16 cases. Clinical anti-infective treatment was adjusted according to the results of mNGS, the conditions of most patients improved. CONCLUSION Compared to culture, mNGS shows great advantages in diagnosing bacterial, fungal, viral, and mixed infections in children with hematologic diseases, positively impacting clinical care. mNGS can be used as a complement to culture for pathogen detection.
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Affiliation(s)
- Yating Zhang
- Children's Medical Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, SunYat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Dunhua Zhou
- Children's Medical Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, SunYat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Han Xia
- Department of Scientific Affairs, Hugobiotech Co., Ltd., Beijing, 100176, China
| | - Jian Wang
- Children's Medical Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, SunYat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Huaqing Yang
- Children's Medical Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, SunYat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Luhong Xu
- Children's Medical Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, SunYat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Ke Huang
- Children's Medical Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, SunYat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Jianpei Fang
- Children's Medical Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, SunYat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.
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Tian J, Huang M, Chen L, Liu J. 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] [What about the content of this article? (0)] [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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20
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Yee R, Simner PJ. Next-Generation Sequencing Approaches to Predicting Antimicrobial Susceptibility Testing Results. Clin Lab Med 2022; 42:557-572. [PMID: 36368782 DOI: 10.1016/j.cll.2022.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Rebecca Yee
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Meyer B1-193, 600 North Wolfe Street, Baltimore, MD 21287-7093, USA
| | - Patricia J Simner
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Meyer B1-193, 600 North Wolfe Street, Baltimore, MD 21287-7093, USA.
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21
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Wei P, Wu L, Li Y, Shi J, Luo Y, Wu W, Feng J. Metagenomic next-generation sequencing for the detection of pathogenic microorganisms in patients with pulmonary infection. Am J Transl Res 2022; 14:6382-6388. [PMID: 36247251 PMCID: PMC9556471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 08/03/2022] [Indexed: 06/16/2023]
Abstract
OBJECTIVE To explore the clinical value of metagenomic next-generation sequencing (mNGS) in diagnosing pulmonary infectious diseases. METHODS A retrospective analysis was performed on 82 patients with pulmonary infection who were admitted to the Eighth Affiliated Hospital of Guangxi Medical University & Guigang City People's Hospital from January 2020 to December 2021. The pathogens were detected by mNGS and conventional methods (culture and PCR). Then, the type and number of detected pathogens, as well as the specificity and sensitivity, were compared between the two methods. In addition, the positive rates of bacteria, fungi, tubercle bacillus, and mixed infection in bronchoalveolar lavage fluid, sputum, pleural effusion, and blood detected by mNGS, and the advantage in required test time were evaluated. RESULTS More types and numbers of pathogens were detected by mNGS with a higher sensitivity but a lower specificity, as compared to the conventional detection methods (all P<0.05). The positive rates and integrity rates of bacteria, fungi, and tubercle bacillus detected by mNGS were higher than those by conventional methods (all P<0.05). Moreover, there was no difference in the overall sensitivity of mNGS among different sample types, but the sensitivities of mNGS in bronchoalveolar lavage fluid and sputum samples were significantly higher than those of conventional methods (both P<0.05). The average test time for mNGS was shorter than that of conventional methods. CONCLUSION mNGS can detect more types and numbers of pathogenic microorganisms, improve the detection sensitivity, and reduce the detection time in patients with pulmonary infection.
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Affiliation(s)
- Peng Wei
- Department of Pulmonary and Critical Care Medicine, The Eighth Affiliated Hospital of Guangxi Medical University & Guigang City People’s HospitalGuigang 537100, Guangxi Zhuang Autonomous Region, China
| | - Lijuan Wu
- Department of Ultrasound, The Eighth Affiliated Hospital of Guangxi Medical University & Guigang City People’s HospitalGuigang 537100, Guangxi Zhuang Autonomous Region, China
| | - Yu Li
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Guangxi Medical UniversityNanning 530007, Guangxi Zhuang Autonomous Region, China
| | - Jian’gang Shi
- Department of Clinical Laboratory, The Eighth Affiliated Hospital of Guangxi Medical University & Guigang City People’s HospitalGuigang 537100, Guangxi Zhuang Autonomous Region, China
| | - Yifeng Luo
- Department of Intensive Care Unit, The Eighth Affiliated Hospital of Guangxi Medical University & Guigang City People’s HospitalGuigang 537100, Guangxi Zhuang Autonomous Region, China
| | - Wenbin Wu
- Department of Pulmonary and Critical Care Medicine, The Eighth Affiliated Hospital of Guangxi Medical University & Guigang City People’s HospitalGuigang 537100, Guangxi Zhuang Autonomous Region, China
| | - Jiemei Feng
- Department of Pulmonary and Critical Care Medicine, The Eighth Affiliated Hospital of Guangxi Medical University & Guigang City People’s HospitalGuigang 537100, Guangxi Zhuang Autonomous Region, China
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22
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Hong D, Wang P, Zhang J, Li K, Ye B, Li G, Zhou J, Tong Z, Ke L, Shi S, Li W. Plasma metagenomic next-generation sequencing of microbial cell-free DNA detects pathogens in patients with suspected infected pancreatic necrosis. BMC Infect Dis 2022; 22:675. [PMID: 35931956 PMCID: PMC9356476 DOI: 10.1186/s12879-022-07662-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 07/30/2022] [Indexed: 11/17/2022] Open
Abstract
Background Infected pancreatic necrosis (IPN) is a life-threatening complication of acute pancreatitis (AP). Timely diagnosis of IPN could facilitate appropriate treatment, but there is a lack of reliable non-invasive screening tests. In this study, we aimed to evaluate the diagnostic value of plasma metagenomic next-generation sequencing (mNGS) based on circulating microbial cell-free DNA in patients with suspected IPN. Methods From October 2020 to October 2021, 44 suspected IPN patients who underwent plasma mNGS were reviewed. Confirmatory diagnosis of IPN within two weeks after the index blood sampling was considered the reference standard. The confirmation of IPN relied on the microbiological results of drains obtained from the necrotic collections. The distribution of the pathogens identified by plasma mNGS was analyzed. Positive percent agreement (PPA) and negative percent agreement (NPA) were evaluated based on the conformity between the overall mNGS results and culture results of IPN drains. In addition, the clinical outcomes were compared between mNGS positive and negative patients. Results Across all the study samples, thirteen species of bacteria and five species of fungi were detected by mNGS. The positivity rate of plasma mNGS was 54.55% (24/44). Of the 24 mNGS positive cases, twenty (83.33%, 95% CI, 68.42–98.24%) were consistent with the culture results of IPN drains. The PPA and NPA of plasma mNGS for IPN were 80.0% (20/25; 95% CI, 64.32–95.68%) and 89.47% (17/19; 95% CI, 75.67–100%), respectively. Compared with the mNGS negative group, patients in the positive group had more new-onset septic shock [12 (50.0%) vs. 4 (20.0%), p = 0.039]. Conclusion IPN relevant pathogens can be identified by plasma mNGS, potentially facilitating appropriate treatment. The clinical application of mNGS in this cohort appears feasible. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-022-07662-2.
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Affiliation(s)
- Donghuang Hong
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China.,Department of Critical Care Medicine, Fujian Provincial Hospital, No.134 East Street, Fuzhou, 350001, Fujian, China
| | - Peng Wang
- Center of Severe Acute Pancreatitis (CSAP), Department of Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, No. 305 Zhongshan East Road, Nanjing, 210002, Jiangsu, China
| | - Jingzhu Zhang
- Center of Severe Acute Pancreatitis (CSAP), Department of Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, No. 305 Zhongshan East Road, Nanjing, 210002, Jiangsu, China
| | - Kaiwei Li
- Center of Severe Acute Pancreatitis (CSAP), Department of Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, No. 305 Zhongshan East Road, Nanjing, 210002, Jiangsu, China
| | - Bo Ye
- Center of Severe Acute Pancreatitis (CSAP), Department of Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, No. 305 Zhongshan East Road, Nanjing, 210002, Jiangsu, China
| | - Gang Li
- Center of Severe Acute Pancreatitis (CSAP), Department of Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, No. 305 Zhongshan East Road, Nanjing, 210002, Jiangsu, China
| | - Jing Zhou
- Center of Severe Acute Pancreatitis (CSAP), Department of Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, No. 305 Zhongshan East Road, Nanjing, 210002, Jiangsu, China
| | - Zhihui Tong
- Center of Severe Acute Pancreatitis (CSAP), Department of Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, No. 305 Zhongshan East Road, Nanjing, 210002, Jiangsu, China
| | - Lu Ke
- Center of Severe Acute Pancreatitis (CSAP), Department of Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, No. 305 Zhongshan East Road, Nanjing, 210002, Jiangsu, China.,National Institute of Healthcare Data Science, Nanjing University, Nanjing, China
| | - Songjing Shi
- Department of Critical Care Medicine, Fujian Provincial Hospital, No.134 East Street, Fuzhou, 350001, Fujian, China.
| | - Weiqin Li
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China. .,Center of Severe Acute Pancreatitis (CSAP), Department of Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, No. 305 Zhongshan East Road, Nanjing, 210002, Jiangsu, China. .,National Institute of Healthcare Data Science, Nanjing University, Nanjing, China.
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Chen S, Kang Y, Li D, Li Z. Diagnostic performance of metagenomic next-generation sequencing for the detection of pathogens in bronchoalveolar lavage fluid in patients with pulmonary infections: Systematic review and meta-analysis. Int J Infect Dis 2022; 122:867-873. [PMID: 35907477 DOI: 10.1016/j.ijid.2022.07.054] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 07/04/2022] [Accepted: 07/21/2022] [Indexed: 10/16/2022] Open
Abstract
BACKGROUND The identification of pathogens in patients with pulmonary infection has always been a major challenge in medicine. Compared with sputum and throat swabs, bronchoalveolar lavage fluid (BALF) can better reflect the actual state in the lungs. However, there has not been a meta-analysis of the diagnostic efficacy of metagenomic next-generation sequencing (mNGS) in detecting pathogens in BALF from patients with pulmonary infections. METHODS Data sources were PubMed, Web of Science, Embase, and the China National Knowledge Infrastructure. The pooled sensitivity and specificity were estimated by using random-effects or fixed-effect models. Subgroup analysis was performed to reveal the effect of potential explanatory factors on the diagnostic performance measures. RESULTS The pooled sensitivity was 78% (95% confidence interval: 67-87%; I2 = 92%) and the pooled specificity was 77% (95% confidence interval: 64-94%; I2 = 74%) for mNGS. Subgroup analyses for the sensitivity of mNGS revealed that patients with pulmonary infections who were severely ill or immunocompromised significantly affected heterogeneity (P < 0.001). The positive detection rate of mNGS for pathogens in BALF of severely or immunocompromised pulmonary-infected patients was 92% (95% confidence interval: 78-100%). CONCLUSION mNGS has high diagnostic performance for BALF pathogens in patients with pulmonary infections, especially in critically ill or immunocompromised patients.
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Affiliation(s)
- Shenglin Chen
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping, Beijing 102206, China; School of Public Health, Shanxi Medical University, 56 Xinjiannanlu Street, Taiyuan 030001, Shanxi, People's Republic of China
| | - Yutong Kang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping, Beijing 102206, China
| | - Dan Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping, Beijing 102206, China
| | - Zhenjun Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping, Beijing 102206, China; School of Public Health, Shanxi Medical University, 56 Xinjiannanlu Street, Taiyuan 030001, Shanxi, People's Republic of China.
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Zhang J, Wang J, Gan J, Luo R, Chen X. The first case of Streptococcus intermedius brain abscess with hemophagocytic histiocytosis. BMC Infect Dis 2022; 22:627. [PMID: 35850669 PMCID: PMC9290246 DOI: 10.1186/s12879-022-07600-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 07/07/2022] [Indexed: 12/01/2022] Open
Abstract
Background Hemophagocytic lymphohistiocytosis (HLH) is a rare but potentially life-threatening immune syndrome associated with an excessive systemic inflammatory response. Viral infection caused HLH is the most common secondary HLH, but there are relatively few reports of HLH caused by bacterial infection. The present study is the first case of HLH caused by Streptococcus intermedia meningitis. Case presentation The patient is an 11-year-old and 9-month-old boy. The main symptoms are fever, headache, and vomiting. The imaging finding of the brain is cerebritis and brain abscess. The cerebrospinal fluid (CSF) routine test showed increased nucleated cells, but the smear and culture of CSF were negative. The metagenomics next-generation sequencing (mNGS) of CSF detected Streptococcus intermedius, and the body temperature of the children returned to normal after antibiotic treatment according to etiology. One week later, the child developed fever again, with Kawasaki disease-like manifestations. After high-dose immunoglobulin therapy, the body temperature returned to normal again. The routine blood test showed a progressive decrease in leukocytes and platelets, and bone marrow biopsy detected histiocytes phagocytosed blood cells. Then infection-associated hemophagocytic syndrome (IAHS) was diagnosed, high-dose methylprednisolone and sequential therapy were given and the patient’s recovery was encouraging. Conclusions Our case shows that HLH can also be secondary to Streptococcus intermediate infection, and early bone marrow biopsy is the golden standard for HLH diagnosis. mNGS can improve the detection sensitivity for pathogens when traditional pathogenic tests are negative. Conventional chemotherapy regimens may not be required for IAHS when high-dose glucocorticoids and immunoglobulin therapy are effective.
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Affiliation(s)
- Jia Zhang
- Department of Pediatrics, West China Second University Hospital, Sichuan University, No. 20, Section Three, South Renmin Road, Chengdu, 610041, China.,Key Laboratory of Obstetrics & Gynecologic and Pediatric Diseases and Birth Defects of the Ministry of Education, Sichuan University, Chengdu, Sichuan, China.,Key Laboratory of Development and Maternal and Child Diseases of Sichuan Province, Chengdu, 610041, China
| | - Jianjun Wang
- Department of Pediatrics, West China Second University Hospital, Sichuan University, No. 20, Section Three, South Renmin Road, Chengdu, 610041, China.,Key Laboratory of Obstetrics & Gynecologic and Pediatric Diseases and Birth Defects of the Ministry of Education, Sichuan University, Chengdu, Sichuan, China.,Key Laboratory of Development and Maternal and Child Diseases of Sichuan Province, Chengdu, 610041, China
| | - Jing Gan
- Department of Pediatrics, West China Second University Hospital, Sichuan University, No. 20, Section Three, South Renmin Road, Chengdu, 610041, China.,Key Laboratory of Obstetrics & Gynecologic and Pediatric Diseases and Birth Defects of the Ministry of Education, Sichuan University, Chengdu, Sichuan, China.,Key Laboratory of Development and Maternal and Child Diseases of Sichuan Province, Chengdu, 610041, China
| | - Rong Luo
- Department of Pediatrics, West China Second University Hospital, Sichuan University, No. 20, Section Three, South Renmin Road, Chengdu, 610041, China.,Key Laboratory of Obstetrics & Gynecologic and Pediatric Diseases and Birth Defects of the Ministry of Education, Sichuan University, Chengdu, Sichuan, China.,Key Laboratory of Development and Maternal and Child Diseases of Sichuan Province, Chengdu, 610041, China
| | - Xiaolu Chen
- Department of Pediatrics, West China Second University Hospital, Sichuan University, No. 20, Section Three, South Renmin Road, Chengdu, 610041, China. .,Key Laboratory of Obstetrics & Gynecologic and Pediatric Diseases and Birth Defects of the Ministry of Education, Sichuan University, Chengdu, Sichuan, China. .,Key Laboratory of Development and Maternal and Child Diseases of Sichuan Province, Chengdu, 610041, China.
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Su XH, Li WP, Liu JY, Wang YJ, Liu J, Xu XF, Yang L, Xia H, Jiang Y, Peng FH. Comparison of features and outcomes between HIV-negative patients with Cryptococcus gattii meningitis and Cryptococcus neoformans meningitis in South China. Mycoses 2022; 65:887-896. [PMID: 35793429 DOI: 10.1111/myc.13491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 06/16/2022] [Accepted: 06/23/2022] [Indexed: 11/28/2022]
Abstract
OBJECTIVES To compare the epidemiologic, clinical, laboratory, and imaging features, and outcomes in patients with Cryptococcus gattii meningitis (CGM) and Cryptococcus neoformans meningitis (CNM). METHODS We performed a retrospective study of HIV-negative patients with CGM and CNM (2015-2021) distinguished by metagenomic next-generation sequencing in cerebrospinal fluid in South China. RESULTS 81 patients (17 CGM, 64 CNM) were enrolled (72.8% male, median age 49 years, range 21-77 years), and CGM patients were younger (median, 43 vs 53 years, p = 0.005). Of 17 CGM, VGI and VGII accounted for 70.6% and 29.4%, respectively. CGM patients had less underlying diseases (7/17 [41.2%] vs 48/64 [75%], p=0.018) and focal neurologic deficit (3/17 [17.6%] vs 35/64 [54.7%], p = 0.022), had higher intracranial pressure (15/17 [88.2%] vs 25/64 [39.1%], p=0.002), more meningeal enhancement (14/17 [82.4%] vs 32/64 [50%], p = 0.034), less parenchymal involvement (median, 1 vs 3, p = 0.018), more lung cryptococcomas (6/12 [50%] vs 6/47 [12.8%], p = 0.014), faster CSF fungal clearance (p = 0.004), less complications (median, 1 vs 3, p < 0.001), and more favorable outcomes (16/17 [94.1%] vs 41/64 [64.1%], p =0.035). CONCLUSIONS This study demonstrated that species identification helps to guide therapy and predict outcomes.
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Affiliation(s)
- Xiao-Hong Su
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, P. R. China
| | - Wei-Peng Li
- Department of Neurology, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, Guangdong, P. R. China
| | - Jun-Yu Liu
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, P. R. China
| | - Yi-Jie Wang
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, P. R. China
| | - Jia Liu
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, P. R. China
| | - Xiao-Feng Xu
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, P. R. China
| | - Lu Yang
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, P. R. China
| | - Han Xia
- Department of Scientific Affairs, Hugobiotech Co., Ltd., Beijing, P. R. China
| | - Ying Jiang
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, P. R. China
| | - Fu-Hua Peng
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, P. R. China
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Lu H, Du Y, Pan T, Lou Z, Li H, Liao Y, Wang L. Gardnerella vaginalis purulent meningitis in an adolescent male: a case report. BMC Neurol 2022; 22:217. [PMID: 35690718 PMCID: PMC9188035 DOI: 10.1186/s12883-022-02733-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 05/27/2022] [Indexed: 11/16/2022] Open
Abstract
Background We report a rare case of Gardnerella vaginalis found in the cerebrospinal fluid of a young boy. Case presentation A 14-year-old boy was admitted to hospital with headache, vomiting, fever, drowsiness and positive meningeal irritation signs on examination. Cerebrospinal fluid (CSF) shows white blood cell and protein were elevated, and glucose was low. Traditional aerobic and anaerobic culture of CSF did not grow any organisms. However, metagenomic next-generation sequencing (mNGS) reveals G. vaginalis in his CSF. The patient was diagnosed with purulent meningitis, and treated with intravenous meropenem and linezolid for a week, followed by oral administration of amoxicillin for two weeks. He recovered without sequelae. Conclusions Purulent meningitis caused by Gardnerella vaginalis is extremely rare. Metagenomic next-generation sequencing of CSF should be highlighted for early diagnosis. With effective antibiotic treatment, the prognosis was excellent.
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Affiliation(s)
- Hongji Lu
- Department of Neurocritical Care, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China
| | - Yaming Du
- Department of Neurocritical Care, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China
| | - Tao Pan
- Department of Neurocritical Care, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China
| | - Zheng Lou
- Department of Scientific Affairs, Hugobiotech Co., Ltd., Beijing, People's Republic of China
| | - Huiping Li
- Department of Neurocritical Care, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China
| | - Yingdi Liao
- Department of Neurocritical Care, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China
| | - Lixin Wang
- Department of Neurocritical Care, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China.
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Lin X, Li YZ, Chen T, Min SH, Wang DF, Ding MM, Jiang G. Effects of wearing personal protective equipment during COVID-19 pandemic on composition and diversity of skin bacteria and fungi of medical workers. J Eur Acad Dermatol Venereol 2022; 36:1612-1622. [PMID: 35538594 PMCID: PMC9348071 DOI: 10.1111/jdv.18216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/21/2022] [Indexed: 01/08/2023]
Abstract
BACKGROUND During the COVID-19 pandemic, wearing PPE can induce skin damage such as erythema, pruritus, erosion, and ulceration among others. Although the skin microbiome is considered important for skin health, the change of the skin microbiome after wearing PPE remain unknown. OBJECTIVE The present study aimed to characterize the diversity and structure of bacterial and fungal flora on skin surfaces of healthcare workers wearing personal protective equipment (PPE) during the COVID-19 pandemic using metagenomic next-generation sequencing (mNGS). METHODS A total of 10 Chinese volunteers were recruited and the microbiome of their face, hand, and back were analyzed before and after wearing PPE. Moreover, VISIA was used to analyze skin features. RESULTS Results of alpha bacterial diversity showed that there was statistically significant decrease in alpha diversity indice in the skin samples from face, hand, and three sites after wearing PPE as compared with the indice in the skin samples before wearing PPE. Further, the results of evaluated alpha fungal diversity show that there was a statistically significant decrease in alpha diversity indices in the skin samples from hand after wearing PPE as compared with the indices in the skin samples before wearing PPE (P<0.05). Results of the current study found that the main bacteria on the face, hand, and back skin samples before wearing the PPE were Propionibacterium spp. (34.04%), Corynebacterium spp. (13.12%), and Staphylococcus spp. (38.07%). The main bacteria found on the skin samples after wearing the PPE were Staphylococcus spp. (31.23%), Xanthomonas spp. (26.21%), and Cutibacterium spp. (42.59%). The fungal community composition was similar in three skin sites before and after wearing PPE. CONCLUSION It was evident that wearing PPE may affect the skin microbiota, especially bacteria. Therefore, it was evident that the symbiotic microbiota may reflect the skin health of medical workers during the COVID-19 pandemic.
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Affiliation(s)
- X Lin
- Department of dermatology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Y Z Li
- Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - T Chen
- Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - S H Min
- Department of dermatology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - D F Wang
- Department of dermatology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - M M Ding
- Department of dermatology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - G Jiang
- Department of dermatology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
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Xing N, Zhao Z, Li Q, Dong Y, Li J, Zhang S. Ureaplasma parvum meningitis following atypical choroid plexus papilloma resection in an adult patient: a case report and literature review. BMC Infect Dis 2021; 21:1276. [PMID: 34930148 PMCID: PMC8690907 DOI: 10.1186/s12879-021-06975-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 12/13/2021] [Indexed: 11/30/2022] Open
Abstract
Background While Ureaplasma parvum has previously been linked to the incidence of chorioamnionitis, abortion, premature birth, and perinatal complications, there have only been rare reports of invasive infections of the central nervous system (CNS) in adults. Owing to its atypical presentation and the fact that it will yield sterile cultures using conventional techniques, diagnosing U. parvum meningitis can be challenging. Case presentation We describe a case of U. parvum meningitis detected in an adult patient following surgical brain tumor ablation. After operation, the patient experienced epilepsy, meningeal irritation, and fever with unconsciousness. Cerebrospinal fluid (CSF) analysis showed leukocytosis (484 * 106 /L), elevated protein levels (1.92 g/L), and decreased glucose concentrations (0.02 mmol/L). Evidence suggested that the patient was suffering from bacterial meningitis. However, no bacterial pathogens in either CSF or blood were detected by routine culture or serology. The symptoms did not improve with empirical antibiotics. Therefore, we performed metagenomic next-generation sequencing (mNGS) to identify the etiology of the meningitis. Ureaplasma parvum was detected by mNGS in CSF samples. To the best of our knowledge, this case is the first reported instance of U. parvum meningitis in an adult patient in Asian. After diagnosis, the patient underwent successful moxifloxacin treatment and recovered without complications. Conclusions As mNGS strategies can enable the simultaneous detection of a diverse array of microbes in a single analysis, they may represent a valuable means of diagnosing the pathogens responsible for CNS infections and other clinical conditions with atypical presentations.
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Affiliation(s)
- Na Xing
- Department of Endocrinology, The Fourth Hospital of Hebei Medical University, No. 12, Jiankang Road, Shijiazhuang, 050000, Hebei, People's Republic of China
| | - Zhenxiang Zhao
- Department of Neurosurgery, The Fourth Hospital of Hebei Medical University, No. 12, Jiankang Road, Shijiazhuang, 050000, Hebei, People's Republic of China.
| | - Qingjing Li
- Clinical Laboratory, The Fourth Hospital of Hebei Medical University, No. 12, Jiankang Road, Shijiazhuang, 050000, Hebei, People's Republic of China
| | - Yalan Dong
- Department of Neurosurgery, The Fourth Hospital of Hebei Medical University, No. 12, Jiankang Road, Shijiazhuang, 050000, Hebei, People's Republic of China
| | - Jianfeng Li
- Department of Neurosurgery, The Fourth Hospital of Hebei Medical University, No. 12, Jiankang Road, Shijiazhuang, 050000, Hebei, People's Republic of China
| | - Shuping Zhang
- Department of Oncology, The Seventh People's Hospital of Hebei Province, No. 389, Jungong Road, Dingzhou, 073000, Hebei, People's Republic of China
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Guo F, Kang L, Xu M. The application value of metagenomic next-generation sequencing in children with invasive pneumococcal disease. Transl Pediatr 2021; 10:3282-3290. [PMID: 35070842 PMCID: PMC8753463 DOI: 10.21037/tp-21-533] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/15/2021] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND A retrospective analysis was conducted to explore the sensitivity and specificity of metagenomic next-generation sequencing (mNGS) in blood, cerebrospinal fluid, and pleural effusion samples in children with invasive pneumococcal disease (IPD), and the impact of detection timing on prognosis and cost. METHODS Children with IPD admitted to Hebei Children's Hospital from 1 January 2017 to 1 March 2021 were allocated to 1 of 3 groups according to the clinical symptoms and lesions (Group 1: bacteremia; Group 2: meningitis; Group 3: pleurisy). Taking Alere BinaxNow® Streptococcus pneumoniae (S. pneumoniae) antigen detection and blood culture as the gold standard, receiver operating characteristic (ROC) was used to establish the diagnostic value of mNGS. RESULTS A total of 96 cases were enrolled in the study, comprising Group 1 (n=65), Group 2 (n=17), and Group 3 (n=14). The positive rate of mNGS test was 62.5% (n=60), and the total coincidence rate was 75.0%. Delayed mNGS was found to have no significant effect on the 30-day survival rate; however, the species-specific read number (SSRN) of S. pneumoniae detected by mNGS in the early stage of the disease was higher, and it could significantly reduce the hospitalization days and costs (P<0.05). CONCLUSIONS The sensitivity and specificity of mNGS are high in the identification of S. pneumoniae in blood, cerebrospinal fluid, and pleural effusion samples, and the SSRN of S. pneumoniae is related to the interval from onset to sample collection. Early mNGS detection has no significant effect on the 30-day survival rate among children with IPD, but it can reduce hospitalization costs and duration.
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Affiliation(s)
- Fang Guo
- Department of Infection, Hebei Children's Hospital, Affiliated to Hebei Medical University, Shijiazhuang, China
| | - Lei Kang
- Department of Pediatric Intensive Care Unit, Hebei Children's Hospital, Affiliated to Hebei Medical University, Shijiazhuang, China
| | - Meixian Xu
- Department of Pediatric Intensive Care Unit, Hebei Children's Hospital, Affiliated to Hebei Medical University, Shijiazhuang, China
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Cai S, Yang Y, Pan J, Miao Q, Jin W, Ma Y, Zhou C, Gao X, Wang C, Hu B. The clinical value of valve metagenomic next-generation sequencing when applied to the etiological diagnosis of infective endocarditis. Ann Transl Med 2021; 9:1490. [PMID: 34805352 PMCID: PMC8573444 DOI: 10.21037/atm-21-2488] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/04/2021] [Indexed: 12/22/2022]
Abstract
Background Metagenomic next-generation sequencing (mNGS) is widely applied in the etiological diagnosis of infectious diseases. However, the clinical practice of mNGS in infective endocarditis (IE) is relatively less studied. This research aimed to assess the etiological diagnostic value of valve mNGS in IE. Methods We retrospectively analyzed 49 IE patients who underwent cardiac valve surgery in Zhongshan Hospital, Fudan University, Shanghai from 1 June 2018 to 30 November 2020. Among these IE patients, 28 were culture positive and 21 were culture negative. The culture results of the culture-positive IE patients were set as gold standard to assess the sensitivity and specificity of valve mNGS in the etiological diagnosis of IE. We studied the positive detection rate of pathogens by valve mNGS among the culture-negative IE patients. During the same period, we also collected the resected valves of 8 patients with non-infective valvular diseases for mNGS as negative controls. Results The valve mNGS results of the culture-positive IE patients were the exact same as their culture results. Both the sensitivity and specificity of valve mNGS were 100%. The positive detection rate of pathogens by valve mNGS was 100% among the culture-negative IE patients. The stringent mapped reads number of genera (SMRNG), relative abundance of genera, stringent mapped reads number of species (SMRN), relative abundance of species, and coverage rate of valve mNGS results were significantly higher in culture-positive IE participants than in culture-negative IE participants. The valve mNGS results of the 8 participants with non-infective valvular diseases were all negative. Conclusions Valve mNGS is a promising technology for the etiological diagnosis of IE, especially culture-negative IE, and it may be used to guide precise antibiotic treatment after surgery.
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Affiliation(s)
- Sishi Cai
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Ye Yang
- Department of Cardiac Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jue Pan
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Qing Miao
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Wenting Jin
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yuyan Ma
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chunmei Zhou
- Department of Microbiology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xiaodong Gao
- Department of Hospital Infection Management, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chunsheng Wang
- Department of Cardiac Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Bijie Hu
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China.,Department of Hospital Infection Management, Zhongshan Hospital, Fudan University, Shanghai, China
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Mao Y, Li X, Lou H, Shang X, Mai Y, Yang L, Peng F, Fu X. Detection of Coccidioides posadasii in a patient with meningitis using metagenomic next-generation sequencing: a case report. BMC Infect Dis 2021; 21:968. [PMID: 34535093 PMCID: PMC8447723 DOI: 10.1186/s12879-021-06661-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 09/06/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Coccidioidomycosis is a systemic infection caused by dimorphic fungi Coccidioides spp. endemic to Southwestern United States and Central and South America. A history of residence and travel in these areas is essential for the diagnostic of coccidioidomycosis, which has highly variable symptoms ranging from asymptomatic to severe, disseminated infection, and even death. Immunocompromised patients of coccidioidomycosis experience a high risk of dissemination, chronic infection, and mortality. Meningitis is one of the most deleterious coccidioidomycosis and can cause various life-threatening complications. CASE PRESENTATION Here we report a case of Coccidioides posadasii meningitis in a 49-year-old female who returned to China after one and a half years residence in Los Angeles, USA. The repeated routine cultures using CSF for bacteria or fungi were all negative. To hunt for an infectious etiology, the state-of-the-art technology metagenomic next-generation sequencing (mNGS) was then utilized, suggesting Coccidioides posadasii. Organizational pathological examination and polymerase-chain-reaction (PCR) results subsequently confirmed the mNGS detection. CONCLUSION To our knowledge, cases for coccidioidal meningitis have been rarely reported in China. While global travelling may spread this disease across continents and make the diagnosis more difficult. mNGS can detect almost all known pathogens with high sensitivity and specificity, especially for uncommon pathogen, such as Coccidioides posadasii in China.
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Affiliation(s)
- Yuqiao Mao
- Department of Infectious Diseases, Guangzhou Panyu Central Hospital, Guangzhou, China
| | - Xia Li
- Department of Infectious Diseases, Guangzhou Panyu Central Hospital, Guangzhou, China
| | - Haibo Lou
- Department of Infectious Diseases, Guangzhou Panyu Central Hospital, Guangzhou, China
| | - Xiaoyu Shang
- Department of Infectious Diseases, Guangzhou Panyu Central Hospital, Guangzhou, China
| | - Yanjun Mai
- Department of Infectious Diseases, Guangzhou Panyu Central Hospital, Guangzhou, China
| | - Lan Yang
- Department of Bioinformatics, Hugobiotech Co., Ltd., Beijing, China
| | - Fuhua Peng
- Department of Neurology, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China.
| | - Xihua Fu
- Department of Infectious Diseases, Guangzhou Panyu Central Hospital, Guangzhou, China.
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Xie G, Zhao B, Wang X, Bao L, Xu Y, Ren X, Ji J, He T, Zhao H. Exploring the Clinical Utility of Metagenomic Next-Generation Sequencing in the Diagnosis of Pulmonary Infection. Infect Dis Ther 2021; 10:1419-1435. [PMID: 34117999 PMCID: PMC8322361 DOI: 10.1007/s40121-021-00476-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 05/28/2021] [Indexed: 11/29/2022] Open
Abstract
INTRODUCTION We aimed to explore the real-world clinical application value and challenges of metagenomic next-generation sequencing (mNGS) for pulmonary infection diagnosis. METHODS We retrospectively reviewed the results of mNGS and conventional tests from 140 hospitalized patients with suspected pulmonary infections from January 2019 to December 2020. The sample types included bronchoalveolar lavage fluid, lung tissue by transbronchial lung biopsy, pleural effusion, blood, and bronchial sputum. Apart from the mNGS reports that our patients received, an extra comprehensive and thorough literature search was conducted. RESULTS Significant differences were noticed in the positive detection rates of pathogens between mNGS and conventional diagnostic testing (115/140, 82.14% vs 50/140, 35.71%, P < 0.05). The percentage of mNGS-positive patients was significantly higher than that of conventional testing-positive patients with regard to bacterial detection (P < 0.01), but no significant differences were found with regard to fungal detection (P = 0.67). Significant statistical differences were found between mixed infection cases (15, 22.70%) and single infection cases (4, 7.84%) in terms of diabetes (P = 0.03). The most frequent pattern of mixed infection was bacteria and fungi mixed infection (40, 40/89 = 44.94%), followed by bacteria mixed infection (29, 29/89 = 32.58%). The sensitivity of mNGS in pulmonary infection diagnosis was much higher than that of conventional test (89.17% vs 50.00%; P < 0.01), but the specificity was the opposite (75.00% vs 81.82%; P > 0.05). CONCLUSION mNGS is a valuable tool for the detection of pulmonary infections, especially mixed pulmonary infections. The most common combinations we found were bacterial-fungal coinfection and bacterial-bacterial coinfection. Still, there are many challenges in the clinical application of mNGS in the diagnosis of pulmonary infections. There is still a lot of work to be done in interpreting the mNGS reports, because both clinical judgment and literature analysis strategy need to be refined.
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Affiliation(s)
- Guijuan Xie
- Department of Respiratory, The Affiliated Wuxi Second People's Hospital of Nanjing Medical University, Wuxi, China.,Affiliated Wuxi Clinical College of Nantong University, Wuxi, China
| | - Bo Zhao
- Affiliated Wuxi Clinical College of Nantong University, Wuxi, China.,Department of Gastroenterology, The Affiliated Wuxi Second People's Hospital of Nanjing Medical University, Wuxi, China
| | - Xun Wang
- Department of Respiratory, The Affiliated Wuxi Second People's Hospital of Nanjing Medical University, Wuxi, China.,Affiliated Wuxi Clinical College of Nantong University, Wuxi, China
| | - Liang Bao
- Department of Respiratory, The Affiliated Wuxi Second People's Hospital of Nanjing Medical University, Wuxi, China.,Affiliated Wuxi Clinical College of Nantong University, Wuxi, China
| | - Yiming Xu
- Department of Respiratory, The Affiliated Wuxi Second People's Hospital of Nanjing Medical University, Wuxi, China.,Affiliated Wuxi Clinical College of Nantong University, Wuxi, China
| | - Xian Ren
- Department of Respiratory, The Affiliated Wuxi Second People's Hospital of Nanjing Medical University, Wuxi, China.,Affiliated Wuxi Clinical College of Nantong University, Wuxi, China
| | - Jiali Ji
- Department of Respiratory, The Affiliated Wuxi Second People's Hospital of Nanjing Medical University, Wuxi, China.,Affiliated Wuxi Clinical College of Nantong University, Wuxi, China
| | - Ting He
- Department of Respiratory, The Affiliated Wuxi Second People's Hospital of Nanjing Medical University, Wuxi, China.,Affiliated Wuxi Clinical College of Nantong University, Wuxi, China
| | - Hongqing Zhao
- Department of Respiratory, The Affiliated Wuxi Second People's Hospital of Nanjing Medical University, Wuxi, China. .,Affiliated Wuxi Clinical College of Nantong University, Wuxi, China.
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Chen Y, Yan X, Li N, Zhang Q, Lv Y, Ruan T. Metagenomic next-generation sequencing of radial ultrasound bronchoscopy-guided "cocktail" specimens as an efficient method for the diagnosis of focal pulmonary infections: a randomised study. Ann Palliat Med 2021; 10:2080-2088. [PMID: 33725766 DOI: 10.21037/apm-20-2578] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 02/04/2021] [Indexed: 11/06/2022]
Abstract
BACKGROUND To investigate the value of metagenomic next-generation sequencing (mNGS) in the diagnosis of focal pulmonary infections by using radial ultrasound bronchoscopic "cocktail" specimens. METHODS From March 2019 to May 2020, 90 patients with focal pulmonary infections [locatable by a radial probe endobronchial ultrasound (RP-EBUS)] treated by the Department of Respiratory and Critical Care Medicine at the Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital (Suzhou, China) were randomly allocated to the "cocktail" group, transbronchial brushing (TBBr) group or bronchoalveolar lavage fluid (BALF) group; 30 patients were assigned to each group. Using the extracted material, the diagnostic efficacy of the mNGS test for pathogen detection was compared across the three groups, and the effect of an antibiotic treatment on detection rate was assessed. RESULTS The sensitivity of mNGS analysis in cocktail group, TBBr group and BALF group was 90% (27/30), 66.7 (20/30) and 50% (15/30), respectively. The analysis of the sensitivity of the positive test, the detection rate of multiple pathogens, and the effect of antibiotics on the detection rate by mMGS indicated that the "cocktail" group was significantly higher number of samples positive for pathogens than the TBBr group (P<0.05), and the TBBr group was significantly higher number of samples positive for pathogens than the BALF group (P<0.05). CONCLUSIONS "Cocktail" specimens had high sensitivity in the identification of focal pathogens, and the use of antibiotics had little effect on the results of the mNGS analysis. These clinically valuable results can be used in the diagnosis and treatment of patients with focal pulmonary infections.
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Affiliation(s)
- Ying Chen
- Department of Respiratory and Critical Care Medicine, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou, China
| | - Xiaopei Yan
- Department of Respiratory and Critical Care Medicine, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou, China
| | - Ning Li
- Department of Respiratory and Critical Care Medicine, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou, China
| | - Qin Zhang
- Department of Respiratory and Critical Care Medicine, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou, China
| | - Yantian Lv
- Department of Respiratory and Critical Care Medicine, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou, China.
| | - Ting Ruan
- Department of Respiratory and Critical Care Medicine, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou, China.
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Zhang W, Mo G, Yang J, Hu X, Huang H, Zhu J, Zhang P, Xia H, Xie L. Community structure of environmental microorganisms associated with COVID-19 affected patients. Aerobiologia (Bologna) 2021; 37:575-583. [PMID: 33967379 PMCID: PMC8093081 DOI: 10.1007/s10453-021-09708-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 04/23/2021] [Indexed: 06/12/2023]
Abstract
UNLABELLED To clarify the characteristics and distribution of hospital environmental microbiome associated with confirmed COVID-19 patients. Environmental samples with varying degrees of contamination which were associated with confirmed COVID-19 patients were collected, including 13 aerosol samples collected near eight patients in different wards, five swabs from one patient's skin and his personal belongings, and two swabs from the surface of positive pressure respiratory protective hood and the face shield from a physician who had close contact with one patient. Metagenomic next-generation sequencing (mNGS) was used to analyze the composition of the microbiome. One of the aerosol samples (near patient 4) was detected positive for COVID-19, and others were all negative. The environmental samples collected in different wards possessed protean compositions and community structures, the dominant genera including Pseudomonas, Corynebacterium, Neisseria, Staphylococcus, Acinetobacter, and Cutibacterium. Top 10 of genera accounted for more than 76.72%. Genera abundance and proportion of human microbes and pathogens radiated outward from the patient, while the percentage of environmental microbes increased. The abundance of the pathogenic microorganism of medical supplies is significantly higher than other surface samples. The microbial compositions of the aerosol collected samples nearby the patients were mostly similar to those from the surfaces of the patient's skin and personal belongings, but the abundance varied greatly. The positive rate of COVID-19 RNA detected from aerosol around patients in general wards was quite low. The ward environment was predominantly inhabited by species closely related to admitted patients. The spread of hospital microorganisms via aerosol was influenced by the patients' activity. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10453-021-09708-5.
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Affiliation(s)
- Weihua Zhang
- College of Pulmonary and Critical Care Medicine, Chinese PLA General Hospital, Beijing, 100853 China
| | - Guoxin Mo
- College of Pulmonary and Critical Care Medicine, Chinese PLA General Hospital, Beijing, 100853 China
| | - Jie Yang
- Hugobiotech Co. Ltd, Beijing, 100000 China
| | - Xingshuo Hu
- College of Pulmonary and Critical Care Medicine, Chinese PLA General Hospital, Beijing, 100853 China
| | - Hujie Huang
- Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Shanghai, 201800 China
- Shanghai Lasensor Photoelectric Technology Co., Ltd, Shanghai, 201800 China
| | - Jing Zhu
- Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Shanghai, 201800 China
- Shanghai Lasensor Photoelectric Technology Co., Ltd, Shanghai, 201800 China
| | - Pei Zhang
- Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Shanghai, 201800 China
- Shanghai Lasensor Photoelectric Technology Co., Ltd, Shanghai, 201800 China
| | - Han Xia
- Hugobiotech Co. Ltd, Beijing, 100000 China
| | - Lixin Xie
- College of Pulmonary and Critical Care Medicine, Chinese PLA General Hospital, Beijing, 100853 China
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Xie D, Xu W, You J, Yuan X, Li M, Bi X, Zhang K, Li H, Xian Y. Clinical descriptive analysis of severe Pneumocystis jirovecii pneumonia in renal transplantation recipients. Bioengineered 2021; 12:1264-1272. [PMID: 33896387 PMCID: PMC8806328 DOI: 10.1080/21655979.2021.1911203] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Pneumocystis jirovecii (P. jirovecii) pneumonia (PJP) is an opportunistic fungal infection after renal transplantation, which is always severe, difficult to diagnose, combined with multiple complications and have poor prognosis. We retrospectively analyzed clinical data, including risk factors, diagnosis, treatment and complications of seven clinical cases suffered with severe PJP after renal transplantation in our department in 2019. All the seven recipients were routinely prescribed with PJP prophylaxis after renal transplantation, and six of them suffered acute graft rejection before the infection. P. jirovecii sequence was identified in blood or broncho-alveolar lavage fluid (BALF) by the metagenomic next-generation sequencing (mNGS) in all patients. All the patients were improved with the therapy trimethoprim-sulfamethoxazole (TMP-SMX) combined with caspofungin for the PJP treatment, but suffered with complications including renal insufficiency, leukopenia, thrombocytopenia, gastrointestinal bleeding, mediastinalemphysema, pulmonary hemorrhage, and hemophagocytic syndrome and other severe infections. Taken together, mNGS is a powerful tool that could be used to diagnose PJP in renal transplantation recipients. And PJP prophylaxis should be prescribed during and after treatment for acute rejection. TMP-SMX is the first-line and effective drug for PJP treatment, but the complications are always life-threatening and lead to poor prognosis. We should pay attention to these life-threatening complications.
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Affiliation(s)
- Dan Xie
- Department of General Intensive Care Unit, Lingnan Hospital, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Wen Xu
- Department of General Intensive Care Unit, Lingnan Hospital, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Jingya You
- Department of General Intensive Care Unit, Lingnan Hospital, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Xiaofeng Yuan
- Department of General Intensive Care Unit, Lingnan Hospital, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Mingliang Li
- Department of General Intensive Care Unit, Lingnan Hospital, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Xiaogang Bi
- Department of General Intensive Care Unit, Lingnan Hospital, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Kouxing Zhang
- Department of General Intensive Care Unit, Lingnan Hospital, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Heng Li
- Department of Kidney Transplantation, Lingnan Hospital, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Ying Xian
- Department of General Intensive Care Unit, Lingnan Hospital, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
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Zhang Q, Li S, Zhou W, Zheng L, Ren Y, Dong L, Feng J, Cao J. Application of metagenomic next-generation sequencing (mNGS) combined with rapid on-site cytological evaluation (ROSCE) for the diagnosis of Chlamydia psittaci pneumonia. Int J Clin Exp Pathol 2021; 14:389-398. [PMID: 33936360 PMCID: PMC8085828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 02/07/2021] [Indexed: 06/12/2023]
Abstract
We evaluated the application of metagenomic next-generation sequencing (mNGS) combined with rapid on-site cytological evaluation (ROSCE) in the diagnosis of Chlamydia psittaci pneumonia, to provide a basis for an accurate diagnosis. Clinical data from three patients with C. psittaci pneumonia diagnosed by the combination of mNGS and ROSCE from June 2019 to June 2020 in the Department of Respiratory and Critical Care Medicine of Tianjin Medical University General Hospital were reviewed. Three patients with community-acquired pneumonia failed to respond to the initial treatment, and were finally diagnosed by bronchoscopic lung biopsy and alveolar lavage fluid (BALF) mNGS. According to the ROSCE cytologic characteristics, the scope of the lesions was narrowed to inflammatory lesions excluding tumor and other non-infectious lesions. Subsequently, mNGS results confirmed that the three patients were infected by C. psittaci, sequence numbers 2066, 126, and 1077, respectively. Two patients developed severe pneumonia and required organ function support. The other patient had recurrent high fever and severe headache, which significantly complicated clinical diagnosis and treatment. Eventually, the treatment plan was adjusted according to the mNGS results, resulting in gradual improvement of symptoms and satisfactory prognosis. mNGS combined with ROSCE is effective for the accurate diagnosis and treatment of C. psittaci pneumonia, having significant advantages in comparison with other detection methods, particularly in the cases of rare pathogens, mixed pathogen infections, and immunodeficient patients.
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Affiliation(s)
- Qian Zhang
- Department of Respiratory and Critical Care Medicine, Tianjin Medical University General Hospital Tianjin 300052, China
| | - Shuo Li
- Department of Respiratory and Critical Care Medicine, Tianjin Medical University General Hospital Tianjin 300052, China
| | - Wei Zhou
- Department of Respiratory and Critical Care Medicine, Tianjin Medical University General Hospital Tianjin 300052, China
| | - Liwen Zheng
- Department of Respiratory and Critical Care Medicine, Tianjin Medical University General Hospital Tianjin 300052, China
| | - Yi Ren
- Department of Respiratory and Critical Care Medicine, Tianjin Medical University General Hospital Tianjin 300052, China
| | - Lixia Dong
- Department of Respiratory and Critical Care Medicine, Tianjin Medical University General Hospital Tianjin 300052, China
| | - Jing Feng
- Department of Respiratory and Critical Care Medicine, Tianjin Medical University General Hospital Tianjin 300052, China
| | - Jie Cao
- Department of Respiratory and Critical Care Medicine, Tianjin Medical University General Hospital Tianjin 300052, China
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Zhan C, Chen L, Hu L. Neonatal Ureaplasma parvum meningitis complicated with subdural hematoma: a case report and literature review. BMC Infect Dis 2021; 21:268. [PMID: 33731039 PMCID: PMC7968305 DOI: 10.1186/s12879-021-05968-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/08/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Neonatal meningitis is a severe infectious disease of the central nervous system with high morbidity and mortality. Ureaplasma parvum is extremely rare in neonatal central nervous system infection. CASE PRESENTATION We herein report a case of U. parvum meningitis in a full-term neonate who presented with fever and seizure complicated with subdural hematoma. After hematoma evacuation, the seizure disappeared, though the fever remained. Cerebrospinal fluid (CSF) analysis showed inflammation with CSF pleocytosis (1135-1319 leukocytes/μl, mainly lymphocytes), elevated CSF protein levels (1.36-2.259 g/l) and decreased CSF glucose (0.45-1.21 mmol/l). However, no bacterial or viral pathogens in either CSF or blood were detected by routine culture or serology. Additionally, PCR for enteroviruses and herpes simplex virus was negative. Furthermore, the CSF findings did not improve with empirical antibiotics, and the baby experienced repeated fever. Thus, we performed metagenomic next-generation sequencing (mNGS) to identify the etiology of the infection. U. parvum was identified by mNGS in CSF samples and confirmed by culture incubation on mycoplasma identification medium. The patient's condition improved after treatment with erythromycin for approximately 5 weeks. CONCLUSIONS Considering the difficulty of etiological diagnosis in neonatal U. parvum meningitis, mNGS might offer a new strategy for diagnosing neurological infections.
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Affiliation(s)
- Canyang Zhan
- Departments of Neonatology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China.
| | - Lihua Chen
- Departments of Neonatology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Lingling Hu
- Departments of Neonatology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
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Wang Q, Wu B, Yang D, Yang C, Jin Z, Cao J, Feng J. Optimal specimen type for accurate diagnosis of infectious peripheral pulmonary lesions by mNGS. BMC Pulm Med 2020; 20:268. [PMID: 33059646 PMCID: PMC7566056 DOI: 10.1186/s12890-020-01298-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 09/21/2020] [Indexed: 12/30/2022] Open
Abstract
Background Reports on the application of metagenomic next-generation sequencing (mNGS) to the diagnosis of peripheral pulmonary lesions (PPLs) are scarce. There have been no studies investigating the optimal specimen type for mNGS. Methods We used mNGS to detect pathogens in matched transbronchial lung biopsy (TBLB), bronchoalveolar lavage fluid (BALF), and bronchial needle brushing (BB) specimens from 39 patients suspected of having infectious PPLs. We explored differences in microbial composition and diagnostic accuracy of mNGS for the 3 specimen types. Results mNGS was more sensitive than conventional culture for detection of bacteria and fungi in TBLB, BALF, and BB specimens, with no difference in the sensitivity of mNGS across the different specimen types. mNGS showed higher sensitivity for fungi or uncategorized pulmonary pathogens in TBLB+BALF+BB compared to TBLB but not BALF or BB specimens. There were no significant differences between the 3 specimen types in the relative abundance of pathogens, or between TBLB and BB specimens in the relative abundance of 6 common lower respiratory tract commensals. Conclusions mNGS has a higher sensitivity than the conventional culture method for detecting pathogens in TBLB, BALF, or BB specimens. mNGS of BB samples is a less invasive alternative to TBLB for the diagnosis of infectious PPLs.
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Affiliation(s)
- Qing Wang
- Department of Respiratory and Critical Care Medicine, Tianjin Medical University General Hospital, Tianjin, 300052, China.,Respiratory Department of Kunming Municipal First People's Hospital, Kunming, 650000, China
| | - Bo Wu
- Transplantation Center, Nanjing Medical University, Affiliated Wuxi People's Hospital, Wuxi, 214023, China
| | - Donglin Yang
- Hematopoietic Stem Cell Transplantation Center, Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300052, China
| | - Chao Yang
- Respiratory Department of Kunming Municipal First People's Hospital, Kunming, 650000, China
| | - Zhixian Jin
- Respiratory Department of Kunming Municipal First People's Hospital, Kunming, 650000, China.
| | - Jie Cao
- Department of Respiratory and Critical Care Medicine, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Jing Feng
- Department of Respiratory and Critical Care Medicine, Tianjin Medical University General Hospital, Tianjin, 300052, China.
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Jin W, Pan J, Miao Q, Ma Y, Zhang Y, Huang Y, Yao Y, Su Y, Wang Q, Wang M, Li B, Bao R, Gao X, Wu H, Hu B. Diagnostic accuracy of metagenomic next-generation sequencing for active tuberculosis in clinical practice at a tertiary general hospital. Ann Transl Med 2020; 8:1065. [PMID: 33145284 PMCID: PMC7575944 DOI: 10.21037/atm-20-2274] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background To evaluate the diagnostic accuracy of metagenomic next-generation sequencing (mNGS) for active tuberculosis (TB). Methods We retrospectively collected 820 samples at Zhongshan Hospital, Fudan University in Shanghai, China, between 1 April 2017 and 31 March 2018. They were classified into TB cases (125, 15.2%) and NOT TB cases (695, 84.8%) according to the clinical diagnosis. Specimens were evaluated by a regular clinical microbiological assay and mNGS performed in parallel. Results Sixty-one confirmed TB cases and 64 clinical TB cases were included. The overall sensitivity of mNGS was 49.6% [95% confidence interval (95% CI), 40.6–58.6%], and the specificity was 98.3% (95% CI, 96.9–99.1%), with peak sensitivities of 88.9% (95% CI, 50.7–99.4%) for lung tissue, 55.0% (95% CI, 32.0–76.2%) for bronchoalveolar lavage fluid (BALF), and 50.0% (95% CI, 32.8–67.2%) for serous fluids. The overall sensitivity of mNGS was superior to that of the culture assay (35.2%, 95% CI, 27.0–44.3), but no superior sensitivity for sputum was observed in mNGS compared with the culture assay (mNGS: 52.3%, 95% CI, 31.1–72.6%; culture: 60.9%, 95% CI, 38.8–79.5%). In clinical TB cases, mNGS detected additional positive results (40.6%, 26/64). mNGS reduced the turnaround time from 2–6 weeks to 32–36 hours. Conclusions mNGS may be a promising technology for the early auxiliary diagnosis of active TB, especially sputum-negative pulmonary TB (PTB) and tuberculous serous effusion.
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Affiliation(s)
- Wenting Jin
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jue Pan
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Qing Miao
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yuyan Ma
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yao Zhang
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yingnan Huang
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yumeng Yao
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yi Su
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Qingqing Wang
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Mengran Wang
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Bing Li
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Rong Bao
- Department of Microbiology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xiaodong Gao
- Department of Hospital Infection Management, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Honglong Wu
- Binhai Genomics Institute, Tianjin Translational Genomics Center, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Bijie Hu
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China.,Department of Hospital Infection Management, Zhongshan Hospital, Fudan University, Shanghai, China
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Liu N, Kan J, Yu N, Cao W, Cao J, Jiang E, Feng J. Application of metagenomic next-generation sequencing technology for difficult lung lesions in patients with haematological diseases. Transl Cancer Res 2020; 9:5245-5254. [PMID: 35117891 PMCID: PMC8798119 DOI: 10.21037/tcr-20-604] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 07/29/2020] [Indexed: 01/05/2023]
Abstract
BACKGROUND The purpose of this study was to evaluate the diagnostic value of combined virtual bronchoscopic navigation (Direct Path), radial endobronchial ultrasound with guide-sheath (EBUS), ultrathin bronchoscopy, rapid on-site evaluation of cytology (ROSE), and metagenomic next-generation sequencing (mNGS) for difficult lung lesions in patients with haematological diseases. METHODS In this study, lung specimens were obtained from patients with haematological diseases by transbronchial lung biopsy (TBLB) and bronchoalveolar lavage (BAL). The specimens were subjected to mNGS for sequencing of pathogenic microorganisms and sent to the laboratory for examination and pathological analysis. Additionally, the clinical data and pathogenic characteristics of the patients were analysed. The sensitivity and specificity of mNGS for sequencing pathogenic microorganisms were compared between TBLB and BAL specimens. RESULTS In this study, the diagnosis of infectious pneumonia mainly included cytomegalovirus pneumonia, Pneumocystis jirovecii pneumonia (PCP), pulmonary aspergillosis, and tuberculosis. Some patients had non-infectious pulmonary complications, and the clinical and therapeutic outcomes were diagnosed as graft-versus-host disease (GVHD), idiopathic pneumonia syndrome (IPS), and delayed pulmonary toxicity syndrome (DPTS). The sensitivity of mNGS for pathogenic microbes in lung tissue is better than that of alveolar lavage fluid, whereas compared with alveolar lavage fluid, its specificity is reduced. CONCLUSIONS The results of this study indicate that combined virtual bronchoscopic navigation (Direct Path), radial EBUS, ultrathin bronchoscopy, and ROSE of target control specimens reduce the risk of bleeding, and their combination with mNGS has high diagnostic value for difficult lung lesions in patients with haematological diseases, especially in the field of infection diagnosis. TBLB and BAL specimens have respective advantages in specificity and sensitivity for mNGS analysis.
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Affiliation(s)
- Nana Liu
- Department of Respiratory, Tianjin Medical University General Hospital, Tianjin, China.,Department of Critical Care Medicine, Tianjin Academy of Traditional Chinese Medicine Affiliated Hospital, Tianjin, China
| | - Jianying Kan
- Department of Critical Care Medicine, Tianjin Academy of Traditional Chinese Medicine Affiliated Hospital, Tianjin, China
| | - Naihao Yu
- Department of Critical Care Medicine, Tianjin Academy of Traditional Chinese Medicine Affiliated Hospital, Tianjin, China
| | - Wenbin Cao
- Haematopoietic Stem Cell Transplantation Center, Institute of Haematology and Blood Disease Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Jie Cao
- Department of Respiratory, Tianjin Medical University General Hospital, Tianjin, China
| | - Erlie Jiang
- Haematopoietic Stem Cell Transplantation Center, Institute of Haematology and Blood Disease Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Jing Feng
- Department of Respiratory, Tianjin Medical University General Hospital, Tianjin, China
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Zhang P, Chen Y, Li S, Li C, Zhang S, Zheng W, Chen Y, Ma J, Zhang X, Huang Y, Liu S. Metagenomic next-generation sequencing for the clinical diagnosis and prognosis of acute respiratory distress syndrome caused by severe pneumonia: a retrospective study. PeerJ 2020; 8:e9623. [PMID: 32821543 PMCID: PMC7395598 DOI: 10.7717/peerj.9623] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 07/07/2020] [Indexed: 12/25/2022] Open
Abstract
Background Metagenome next-generation sequencing (mNGS) is a valuable diagnostic tool that can be used for the identification of early pathogens of acute respiratory distress syndrome (ARDS) in severe pneumonia. Little is known about the use of this technology in clinical application and the evaluation of the prognostic value of ARDS. Methods We performed a retrospective cohort study of patients with ARDS caused by severe pneumonia. Samples were collected from patients in the intensive care unit (ICU) of Jiangmen Central Hospital from January 2018 to August 2019. The no-next generation sequencing (NGS) group was composed of patients given conventional microbiological tests to examine sputum, blood, or bronchoalveolar lavage fluid. The NGS group was composed of patients tested using mNGS and conventional microbiological tests. We evaluated the etiological diagnostic effect and clinical prognostic value of mNGS in patients with ARDS caused by severe pneumonia. Results The overall positive rate (91.1%) detected by the mNGS method was significantly higher than that of the culture method (62.2%, P = 0.001), and antibody plus polymerase chain reaction (28.9%, P < 0.001). Following adjustment of the treatment plan based on microbial testing results, the Acute Physiology and Chronic Health Evaluation-II (APACHE II) score of the NGS group was lower than that of the no-NGS group 7 days after treatment (P < 0.05). The 28-day mortality rate of the NGS group was significantly lower than that of the no-NGS group (P < 0.05). Longer ICU stay, higher APACHE II score and sequential organ failure assessment score were risk factors for the death of ARDS, and adjusting the medication regimen based on mNGS results was a protective factor. The detection of mNGS can significantly shorten the ICU stay of immunosuppressed patients (P < 0.01), shorten the ventilation time (P < 0.01), and reduce the ICU hospitalization cost (P < 0.05). Conclusions Metagenome next-generation sequencing is a valuable tool to determine the etiological value of ARDS caused by severe pneumonia to improve diagnostic accuracy and prognosis for this disease. For immunosuppressed patients, mNGS technology can be used in the early stage to provide more diagnostic evidence and guide medications.
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Affiliation(s)
- Peng Zhang
- Department of Respiratory Medicine, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, China.,Department of Critical Care Medicine, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, Guangdong, China
| | - Yan Chen
- BGI PathoGenesis Pharmaceutical Technology Co., Ltd, BGI-Shenzhen, Shenzhen, Guangdong, China.,BGI Wuhan Biotechnology, BGI-Shenzhen, Wuhan, Hubei, China
| | - Shuyun Li
- Department of Neurology, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, Guangdong, China
| | - Chaoliang Li
- Department of Critical Care Medicine, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, Guangdong, China
| | - Shuang Zhang
- Department of Critical Care Medicine, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, Guangdong, China
| | - Weihao Zheng
- Department of Critical Care Medicine, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, Guangdong, China
| | - Yantang Chen
- Department of Critical Care Medicine, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, Guangdong, China
| | - Jie Ma
- Department of Critical Care Medicine, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, Guangdong, China
| | - Xin Zhang
- Clinical Experimental Center, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, Guangdong, China
| | - Yanming Huang
- Department of Respiration Medicine, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, Guangdong, China
| | - Shengming Liu
- Department of Respiratory Medicine, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, China
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Li M, Yang F, Lu Y, Huang W. Identification of Enterococcus faecalis in a patient with urinary-tract infection based on metagenomic next-generation sequencing: a case report. BMC Infect Dis 2020; 20:467. [PMID: 32615925 PMCID: PMC7330266 DOI: 10.1186/s12879-020-05179-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 06/18/2020] [Indexed: 12/17/2022] Open
Abstract
Background Urinary tract infection (UTI) caused by various pathogenic microorganisms is ubiquitous in the parts of the urinary system such as kidney, ureter, bladder, and urethra. Currently, clinical detection of UTI is mainly focused on urine culture; however, the diagnostic value of urine culture remains limited due to the time-consuming procedure and low detection rate, especially in patients who have used antibiotics. Generally, treatment for UTI relies on empirical medication rather than pathogen diagnosis, which leads to the inappropriate use of antimicrobial agents and a significant increase in resistant strains. Comparatively, metagenomic next-generation sequencing (mNGS) is capable of overcoming the disadvantages of clinical culture, and identifying pathogens for further treatment. Case presentation A 33-year-old male patient was admitted to hospital with a high fever and chills. None of his autoimmune disease or thyroid function related indicators were positive, and he had no risk of endocarditis. His white blood cell count, C-reactive protein, procalcitonin, interleukin 6, and neutrophil proportion were markedly elevated. He was initially diagnosed as having an infection of unknown etiology. Since empirical treatment of Sulperazon and Metronidazole did not relieve his symptoms, both the blood and urine specimens were examined using traditional culture, serological testing, and mNGS assay. Traditional culture and serological testing produced negative results, while the mNGS assay revealed the presence of a potential pathogen, Enterococcus faecalis, in the urine specimen, which was further confirmed by both Sanger sequencing and qPCR analysis. A CT scan of the patient’s whole abdomen showed stones in the right kidney. Once targeted antibiotic therapy was administered, the patient recovered quickly. Conclusions Our case illustrated that mNGS, as a novel culture-independent approach, demonstrated the capability of rapid, sensitive, and accurate pathogen identification. Furthermore, this technology provides strong support for guiding clinicians to determine appropriate treatment.
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Affiliation(s)
- Manshi Li
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, 200032, China
| | - Fuhuo Yang
- Dinfectome Inc., Shanghai, 200120, China
| | - Yihan Lu
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, 200032, China. .,Ministry of Education Key Laboratory of Public Health Safety (Fudan University), Shanghai, 200032, China.
| | - Weifeng Huang
- Department of Intensive Care Medicine, The Sixth People's Hospital, Shanghai Jiao Tong University, Shanghai, 200233, China.
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Li Y, Sun B, Tang X, Liu YL, He HY, Li XY, Wang R, Guo F, Tong ZH. Application of metagenomic next-generation sequencing for bronchoalveolar lavage diagnostics in critically ill patients. Eur J Clin Microbiol Infect Dis 2019; 39:369-374. [PMID: 31813078 PMCID: PMC7102353 DOI: 10.1007/s10096-019-03734-5] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 10/02/2019] [Indexed: 11/30/2022]
Abstract
The purpose of this study was to assess the value of metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) for the diagnosis of severe respiratory diseases based on interpretation of sequencing results. BALF samples were harvested and used for mNGS as well as microbiological detection. Infectious bacteria or fungi were defined according to relative abundance and number of unique reads. We performed mNGS on 35 BALF samples from 32 patients. The positive rate reached 100% in the mNGS analysis of nine immunocompromised patients. Compared with the culture method, mNGS had a diagnostic sensitivity of 88.89% and a specificity of 74.07% with an agreement rate of 77.78% between these two methods. Compared with the smear method and PCR, mNGS had a diagnostic sensitivity of 77.78% and a specificity of 70.00%. In 13 cases, detection results were positive by mNGS but negative by culture/smear and PCR. The mNGS findings in 11/32 (34.4%) cases led to changes in treatment strategies. Linear regression analysis showed that diversity was significantly correlated with interval between disease onset and sampling. Dynamic changes in reads could indirectly reflect therapeutic effectiveness. BALF mNGS improves sensitivity of pathogen detection and provides guidance in clinical practice. Potential pathogens can be identified based on relative abundance and number of unique reads.
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Affiliation(s)
- Ying Li
- Department of Respiratory and Critical Care Medicine, Beijing Chao-Yang Hospital, Capital Medical University, Beijing Institute of Respiratory Medicine, No. 8 Gongtinan Road, Beijing, 100020, China
| | - Bing Sun
- Department of Respiratory and Critical Care Medicine, Beijing Chao-Yang Hospital, Capital Medical University, Beijing Institute of Respiratory Medicine, No. 8 Gongtinan Road, Beijing, 100020, China
| | - Xiao Tang
- Department of Respiratory and Critical Care Medicine, Beijing Chao-Yang Hospital, Capital Medical University, Beijing Institute of Respiratory Medicine, No. 8 Gongtinan Road, Beijing, 100020, China
| | - Ya-Lan Liu
- Department of Respiratory and Critical Care Medicine, Beijing Chao-Yang Hospital, Capital Medical University, Beijing Institute of Respiratory Medicine, No. 8 Gongtinan Road, Beijing, 100020, China
| | - Hang-Yong He
- Department of Respiratory and Critical Care Medicine, Beijing Chao-Yang Hospital, Capital Medical University, Beijing Institute of Respiratory Medicine, No. 8 Gongtinan Road, Beijing, 100020, China
| | - Xu-Yan Li
- Department of Respiratory and Critical Care Medicine, Beijing Chao-Yang Hospital, Capital Medical University, Beijing Institute of Respiratory Medicine, No. 8 Gongtinan Road, Beijing, 100020, China
| | - Rui Wang
- Department of Respiratory and Critical Care Medicine, Beijing Chao-Yang Hospital, Capital Medical University, Beijing Institute of Respiratory Medicine, No. 8 Gongtinan Road, Beijing, 100020, China
| | - Fei Guo
- Department of Respiratory and Critical Care Medicine, Beijing Chao-Yang Hospital, Capital Medical University, Beijing Institute of Respiratory Medicine, No. 8 Gongtinan Road, Beijing, 100020, China
| | - Zhao-Hui Tong
- Department of Respiratory and Critical Care Medicine, Beijing Chao-Yang Hospital, Capital Medical University, Beijing Institute of Respiratory Medicine, No. 8 Gongtinan Road, Beijing, 100020, China.
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Zhang XX, Guo LY, Liu LL, Shen A, Feng WY, Huang WH, Hu HL, Hu B, Guo X, Chen TM, Chen HY, Jiang YQ, Liu G. The diagnostic value of metagenomic next-generation sequencing for identifying Streptococcus pneumoniae in paediatric bacterial meningitis. BMC Infect Dis 2019; 19:495. [PMID: 31164085 PMCID: PMC6549306 DOI: 10.1186/s12879-019-4132-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 05/24/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND There is currently no research on the diagnostic value of metagenomic next-generation sequencing (mNGS) for a single pathogens in CSF. The aim of this study was to analyse the value of mNGS for identifying Streptococcus pneumoniae (S. pneumoniae) in paediatric bacterial meningitis. METHODS Bacterial meningitis (BM) cases from October 23, 2014, to December 31, 2016, and December 1, 2017, to July 31, 2018 at Beijing Children's Hospital were reviewed. Clinical features and pathogens were analysed. RESULTS We diagnosed 135 patients with BM in this study. A total of 43 S. pneumoniae were identified by combination methods. 26/135 (19.3%) patients had positive results in S. pneumoniae by blood and/or cerebrospinal fluid (CSF) culture. Alere BinaxNow®Streptococcus pneumoniae Antigen test was positive in 35/135(25.9%) cases. 32/135 (23.7%) S. pneumoniae were identified by mNGS. Six CSF samples were identified as S. pneumoniae only by mNGS technology. Taking culture as the gold standard, the sensitivity and specificity of mNGS for diagnosing S. pneumoniae meningitis were 73.1 and 88.1%, respectively. The positive predictive value (PPV) and negative predictive value (NPV) of diagnosing S. pneumoniae meningitis by mNGS were 59.4 and 93.2%, respectively. When comparison between mNGS and combined tests (culture and Alere BinaxNow®Streptococcus pneumoniae Antigen test), the sensitivity and specificity of mNGS for S. pneumoniae identification were 70.3 and 93.9%, the PPV and NPV in the identification of S. pneumoniae by mNGS were 81.4 and 89.3%, respectively. The difference in number of unique reads of S. pneumoniaein from CSF sample (< 14 days onset) and CSF sample (> 14 days from onset) was statistically significant (170.5 VS. 13, P = 0.019). The difference in the collected time of CSF for culture and mNGS was statistically significant (4 days VS. 14 days, P < 0.001). CONCLUSIONS mNGS has high sensitivity and specificity for S. pneumoniae identification. The pathogen load (number of unique reads) of S. pneumonia is related to the CSF collection time. mNGS was less affected than culture by the use of antibiotics before CSF collection.
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MESH Headings
- Adolescent
- Age Factors
- Antigens, Bacterial/analysis
- Antigens, Bacterial/blood
- Antigens, Bacterial/cerebrospinal fluid
- Antigens, Bacterial/genetics
- Child
- Child, Preschool
- Diagnostic Tests, Routine
- Female
- High-Throughput Nucleotide Sequencing
- Humans
- Infant
- Infant, Newborn
- Male
- Meningitis, Bacterial/blood
- Meningitis, Bacterial/cerebrospinal fluid
- Meningitis, Bacterial/diagnosis
- Meningitis, Bacterial/microbiology
- Metagenomics/methods
- Pediatrics/methods
- Polymerase Chain Reaction/methods
- Predictive Value of Tests
- Sensitivity and Specificity
- Streptococcus pneumoniae/genetics
- Streptococcus pneumoniae/isolation & purification
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Affiliation(s)
- Xi-Xi Zhang
- Key Laboratory of Major Diseases in Children, Ministry of Education, Department of Infectious Diseases, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, No. 56 Nan Lishi Road, Beijing, 100045, China
| | - Ling-Yun Guo
- Key Laboratory of Major Diseases in Children, Ministry of Education, Department of Infectious Diseases, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, No. 56 Nan Lishi Road, Beijing, 100045, China
| | - Lin-Lin Liu
- Key Laboratory of Major Diseases in Children, Ministry of Education, Department of Infectious Diseases, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, No. 56 Nan Lishi Road, Beijing, 100045, China
| | - Ao Shen
- Tianjin Medical Laboratory, BGI-Tianjin, Tianjin, China
| | - Wen-Ya Feng
- Key Laboratory of Major Diseases in Children, Ministry of Education, Department of Infectious Diseases, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, No. 56 Nan Lishi Road, Beijing, 100045, China
| | - Wen-Hua Huang
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Science, Beijing, 100071, China
| | - Hui-Li Hu
- Key Laboratory of Major Diseases in Children, Ministry of Education, Department of Infectious Diseases, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, No. 56 Nan Lishi Road, Beijing, 100045, China
| | - Bing Hu
- Key Laboratory of Major Diseases in Children, Ministry of Education, Department of Infectious Diseases, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, No. 56 Nan Lishi Road, Beijing, 100045, China
| | - Xin Guo
- Key Laboratory of Major Diseases in Children, Ministry of Education, Department of Infectious Diseases, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, No. 56 Nan Lishi Road, Beijing, 100045, China
| | - Tian-Ming Chen
- Key Laboratory of Major Diseases in Children, Ministry of Education, Department of Infectious Diseases, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, No. 56 Nan Lishi Road, Beijing, 100045, China
| | - He-Ying Chen
- Key Laboratory of Major Diseases in Children, Ministry of Education, Department of Infectious Diseases, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, No. 56 Nan Lishi Road, Beijing, 100045, China
| | - Yong-Qiang Jiang
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Science, Beijing, 100071, China
| | - Gang Liu
- Key Laboratory of Major Diseases in Children, Ministry of Education, Department of Infectious Diseases, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, No. 56 Nan Lishi Road, Beijing, 100045, China.
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