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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; 69:1003-1011. [PMID: 38341816 PMCID: PMC11379781 DOI: 10.1007/s12223-024-01134-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [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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Fu R, Xu J, Fan Z, Qu H, Jiang Y, Xiong W, Huang F, Xuan L, Xu N, Liu H, Wang Z, Sun J, Liu Q, Lin R. Metagenomic Next-generation Sequencing in the Diagnosis of Pulmonary Infections After Allogeneic Hematopoietic Stem Cell Transplantation. Transplant Cell Ther 2024:S2666-6367(24)00607-9. [PMID: 39197493 DOI: 10.1016/j.jtct.2024.08.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2024] [Revised: 07/27/2024] [Accepted: 08/19/2024] [Indexed: 09/01/2024]
Abstract
BACKGROUND Early and accurate identification of pathogens is still challenging in pulmonary infections after allogeneic hematopoietic stem cell transplantation (allo-HSCT). The clinical usefulness of metagenomic next-generation sequencing (mNGS) remains under discussion in diagnosis of pulmonary infections after allo-HSCT. METHODS This multi-center retrospective study was conducted to compare mNGS and conventional microbiological tests (CMTs) in investigating the pathogens of pulmonary infections in allo-HSCT recipients. A hundred and forty allo-HSCT recipients with suspected pulmonary infections who underwent bronchoscopy were included. mNGS and CMTs were performed in BALF. RESULTS Among 140 allo-HSCT recipients with suspected pulmonary infections, the positive rate of mNGS was 71.4% whereas the positive rate of CMTs was 55.0%. mNGS identified 182 pathogens included bacteria (n = 88), fungi (n = 35) and viruses (n = 59) while 106 pathogens were detected by CMTs included bacteria (n = 31), fungi (n = 24) and viruses (n = 51). Ninety-eight patients were finally diagnosed as pulmonary infections, including 22 bacterial infections, 7 fungal,18 viral, 48 mixed infections, and 3 with unknown pathogen. Mixed infections were identified in 50.5% of the patients with pulmonary infection. The sensitivity of mNGS and CMTs for diagnosing pulmonary infections were 88.8% and 69.4%, respectively (P=0.001) while the specificity were 81.0% and 85.7%, respectively (P = 0.688). CONCLUSIONS mNGS might be a promising technology for diagnosis of pulmonary infections in the recipients of allo-HSCT.
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Affiliation(s)
- Rong Fu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou, China
| | - Jun Xu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou, China
| | - Zhiping Fan
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou, China
| | - Hong Qu
- Guangzhou Panyu Central Hospital, Infection Medicine Research Institute of Panyu District, Guangzhou, China
| | | | - Wenjie Xiong
- Foresea Life Insurance Guangzhou General Hospital, Guangzhou, China
| | - Fen Huang
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou, China
| | - Li Xuan
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou, China
| | - Na Xu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou, China
| | - Hui Liu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou, China
| | - Zhixiang Wang
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou, China
| | - Jing Sun
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou, China
| | - Qifa Liu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou, China.
| | - Ren Lin
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou, China.
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Wang C, Yang S, Liu Q, Liu H, Jin S, Zheng J, Xiao X, Hou X, Li J, Ma S, Cui L. Application of Second-Generation Sequencing Technology in Lower Respiratory Tract Infection. J Clin Lab Anal 2024:e25090. [PMID: 39158216 DOI: 10.1002/jcla.25090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 04/16/2024] [Accepted: 07/29/2024] [Indexed: 08/20/2024] Open
Abstract
BACKGROUND Lower respiratory tract infection (LRTI) has long been an important threat to people's life and health, so the rapid diagnosis of LRTI is of great significance in clinical treatment. In recent years, the development of the sequencing technology provides a new direction for the rapid diagnosis of LRTI. In this review, the advantages and disadvantages of second-generation sequencing techniques represented by metagenomics next-generation sequencing (mNGS) and droplet digital polymerase chain reaction (ddPCR) in LRTI were reviewed. Furthermore, it offers insights into the future trajectory of this technology, highlighting its potential to revolutionise the field of respiratory infection diagnostics. OBJECTIVE This review summarises developments in mechanistic research of second-generation sequencing technology their relationship with clinical practice, providing insights for future research. METHODS Authors conducted a search on PubMed and Web of Science using the professional terms 'Lower respiratory tract infection' and 'droplet digital polymerase chain reaction' and 'metagenomics next generation sequencing'. The obtained literature was then roughly categorised based on their research content. Similar studies were grouped into the same sections, and further searches were conducted based on the keywords of each section. RESULTS Different studies discussed the application of second-generation sequencing technology in LRTI from different angles, including the detection of pathogens of LRTI by mNGS and ddPCR, the prediction ability of drug-resistant bacteria, and comparison with traditional methods. We try to analyse the advantages and disadvantages of the second-generation sequencing technology by combing the research results of mNGS and ddPCR. In addition, the development direction of the second-generation sequencing technology is prospected.
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Affiliation(s)
- Chong Wang
- Department of Laboratory Medicine, Peking University Third Hospital, Beijing, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Peking University Third Hospital, Beijing, China
| | - Shuo Yang
- Department of Laboratory Medicine, Peking University Third Hospital, Beijing, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Peking University Third Hospital, Beijing, China
| | - Qi Liu
- Department of Laboratory Medicine, Peking University Third Hospital, Beijing, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Peking University Third Hospital, Beijing, China
| | - Hongchao Liu
- Department of Laboratory Medicine, Peking University Third Hospital, Beijing, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Peking University Third Hospital, Beijing, China
| | - Shangjia Jin
- Department of Laboratory Medicine, Peking University Third Hospital, Beijing, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Peking University Third Hospital, Beijing, China
| | - Jiajia Zheng
- Department of Laboratory Medicine, Peking University Third Hospital, Beijing, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Peking University Third Hospital, Beijing, China
| | - Xiumei Xiao
- Department of Laboratory Medicine, Peking University Third Hospital, Beijing, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Peking University Third Hospital, Beijing, China
| | - Xin Hou
- Department of Laboratory Medicine, Peking University Third Hospital, Beijing, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Peking University Third Hospital, Beijing, China
| | - Jing Li
- Department of Laboratory Medicine, Peking University Third Hospital, Beijing, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Peking University Third Hospital, Beijing, China
| | - Sisi Ma
- Department of Laboratory Medicine, Peking University Third Hospital, Beijing, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Peking University Third Hospital, Beijing, China
| | - Liyan Cui
- Department of Laboratory Medicine, Peking University Third Hospital, Beijing, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Peking University Third Hospital, Beijing, China
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Zhang H, Lu M, Guo C, Wang L, Ye K, Zhao Q, Yang J, Yang L, Li T. Clinical impact of metagenomic next-generation sequencing of bronchoalveolar lavage fluids for the diagnosis of pulmonary infections in respiratory intensive care unit. Heliyon 2024; 10:e35287. [PMID: 39170112 PMCID: PMC11336462 DOI: 10.1016/j.heliyon.2024.e35287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 07/23/2024] [Accepted: 07/25/2024] [Indexed: 08/23/2024] Open
Abstract
Background The real-world clinical impact of mNGS on BALF in the respiratory intensive care unit (RICU) is not yet fully understood. Methods We investigated the clinical impact of mNGS on BALF samples obtained from 92 patients admitted to the RICU over a 2-year period. We utilized both mNGS and culture methods to evaluate the effectiveness of mNGS in diagnosing pulmonary infections. The clinical impact of mNGS were evaluated by the clinician committees. Results Among the 92 diagnosed patients, 78 cases (84.7 %) were determined to have infectious diseases caused by pathogenic microorganisms, and the bacterial infections constituted the most prevalent diagnostic category. For mixed infection, the most common type was the Pneumocystis jironecii and cytomegalovirus co-infection. The mNGS results had a positive impact on the clinical management of 43 cases (46.7 %). Moreover, 19 cases (44.2 %) of positive clinical impacts were solely based on new diagnoses made possible by mNGS results. These new diagnoses were particularly helpful for identifying rare pathogens, which could not be detected by conventional diagnostic methods. Conclusions The BALF mNGS has a positive real-world impact in RICU. Clinician committee play a critical role in ensuring the appropriate use of mNGS.
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Affiliation(s)
- Heng Zhang
- Department of Emergency, The First Medical Center, Chinese PLA General Hospital, Medical School of Chinese PLA, Beijing, 100853, China
| | - Ming Lu
- Laboratory Medicine Department, Tangshan Nanhu Hospital, Hebei, 063000, China
| | - Chaomin Guo
- Laboratory Medicine Department, The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Lifeng Wang
- Laboratory Medicine Department, The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Kun Ye
- Laboratory Medicine Department, The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Qiang Zhao
- Laboratory Medicine Department, The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Jiyong Yang
- Laboratory Medicine Department, The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Liuyang Yang
- Laboratory Medicine Department, The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Tanshi Li
- Department of Emergency, The First Medical Center, Chinese PLA General Hospital, Medical School of Chinese PLA, Beijing, 100853, China
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Chen S, Wen L, Ou J, Lai Y, Shen Y. Exploring the Application of Metagenomic Next-Generation Sequencing in the Diagnosis of Unexplained Pulmonary Infection. Int J Gen Med 2024; 17:2465-2474. [PMID: 38826507 PMCID: PMC11141768 DOI: 10.2147/ijgm.s459373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 05/16/2024] [Indexed: 06/04/2024] Open
Abstract
Background Pulmonary infections are significant global health burdens, and conventional diagnostic methods (culture and polymerase chain reaction), are often limited by slow results and low sensitivity. Metagenomic next-generation sequencing (mNGS) offers a rapid, comprehensive alternative for identifying diverse pathogens, including rare and mixed infections. Thus, we assessed the diagnostic performance of mNGS in pulmonary infections, compared the findings with those of traditional pathogen detection methods, and explored its potential to enhance clinical diagnostics and patient care. Methods We collected samples from 125 immunocompromised patients diagnosed with pulmonary infection at the Department of Respiratory Medicine of Shenzhen Longgang Central Hospital from March 2020 to July 2022. We compared the rate of pathogen positivity and pathogen distribution between conventional pathogen detection methods and mNGS using samples including sputum, blood, and bronchoalveolar lavage fluid. Results Among the 125 cases of unexplained pulmonary infection, 82 (65.6%) and 40 (32.0%) tested positive for pathogens using mNGS and routine culture, respectively (P < 0.05). Both methods of pathogen detection were positive in 28 (22.4%) cases (complete match, 9; complete mismatch, 13; partial match, 6). However, 43.2% of cases only tested positive using mNGS, 9.4% only tested positive using routine tests, and 24.8% tested negative using both methods. A viral infection was present in 55.2% of cases. The detection rate of mycobacteria using mNGS (12.8%) was higher than that using conventional pathogen detection methods (5.6%). Conclusion mNGS technology enhances pathogen detection in unexplained pulmonary infections, enabling targeted antimicrobial therapy and consequently helping to reduce broad-spectrum antibiotic use, aligning treatments more closely with the causative pathogens. Thus, mNGS offers significant clinical value by improving treatment efficacy and potentially reducing antibiotic resistance in pulmonary infection cases.
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Affiliation(s)
- Sida Chen
- Department of Respiratory, Shenzhen Longgang Central Hospital, Shenzhen, Guangdong, 518000, People’s Republic of China
| | - Ling Wen
- Department of Respiratory, Shenzhen Longgang Central Hospital, Shenzhen, Guangdong, 518000, People’s Republic of China
| | - Jintao Ou
- Department of Respiratory, Shenzhen Longgang Central Hospital, Shenzhen, Guangdong, 518000, People’s Republic of China
| | - Yuting Lai
- Department of Respiratory, Shenzhen Longgang Central Hospital, Shenzhen, Guangdong, 518000, People’s Republic of China
| | - Yan Shen
- Department of Respiratory, Shenzhen Longgang Central Hospital, Shenzhen, Guangdong, 518000, People’s Republic of China
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Liu Y, Ma Y. Clinical applications of metagenomics next-generation sequencing in infectious diseases. J Zhejiang Univ Sci B 2024; 25:471-484. [PMID: 38910493 PMCID: PMC11199093 DOI: 10.1631/jzus.b2300029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 06/06/2023] [Indexed: 05/23/2024]
Abstract
Infectious diseases are a great threat to human health. Rapid and accurate detection of pathogens is important in the diagnosis and treatment of infectious diseases. Metagenomics next-generation sequencing (mNGS) is an unbiased and comprehensive approach for detecting all RNA and DNA in a sample. With the development of sequencing and bioinformatics technologies, mNGS is moving from research to clinical application, which opens a new avenue for pathogen detection. Numerous studies have revealed good potential for the clinical application of mNGS in infectious diseases, especially in difficult-to-detect, rare, and novel pathogens. However, there are several hurdles in the clinical application of mNGS, such as: (1) lack of universal workflow validation and quality assurance; (2) insensitivity to high-host background and low-biomass samples; and (3) lack of standardized instructions for mass data analysis and report interpretation. Therefore, a complete understanding of this new technology will help promote the clinical application of mNGS to infectious diseases. This review briefly introduces the history of next-generation sequencing, mainstream sequencing platforms, and mNGS workflow, and discusses the clinical applications of mNGS to infectious diseases and its advantages and disadvantages.
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Affiliation(s)
- Ying Liu
- Department of Clinical Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua 321000, China
| | - Yongjun Ma
- Department of Clinical Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua 321000, China.
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Zheng YR, Chen XH, Chen Q, Cao H. Metagenomic Next-generation Sequencing for Pathogen Identification in Bronchoalveolar Lavage Fluid From Neonates Receiving Extracorporeal Membrane Oxygenation. Pediatr Infect Dis J 2024; 43:371-377. [PMID: 38306604 DOI: 10.1097/inf.0000000000004250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2024]
Abstract
BACKGROUND Neonates on extracorporeal membrane oxygenation (ECMO) are at high risk of infection. Rapid and accurate identification of pathogens is essential to improve the prognosis of children on ECMO. Metagenome next-generation sequencing (mNGS) has been used in recent years to detect pathogenic bacteria, but evidence for its use in neonates on ECMO is lacking. METHODS This retrospective study was conducted using an electronic medical record system. We analyzed the results of mNGS and conventional microbiological tests (CMTs) in bronchoalveolar lavage fluid of neonates receiving ECMO support with pulmonary infections in our hospital from July 2021 to January 2023. RESULTS We screened 18 ECMO-supported neonates with pneumonia for inclusion in the study. The median age of the included children was 2 (1-4) days, the median gestational age was 38.3 (33-40 +4 ) weeks, and the median weight was 3.3 (2.2-4.8) kg. The detection rate of mNGS was 77.8% (14/18), higher than the 44.4% (8/18) of CMT ( P = 0.04). A total of 20 pathogens were detected in mNGS, with the top 3 most common pathogens being Klebsiella pneumoniae , Acinetobacter baumannii and Escherichia coli . Mixed infections were found in 14 cases (77.8%), including 13 cases (72.2%) with mixed infections detected by mNGS and 7 cases (27.8%) with mixed infections detected by CMT. A total of 9 children underwent treatment changes based on mNGS results and all of them experienced relief of symptoms. CONCLUSION Compared with CMT, mNGS can detect pathogens earlier and more sensitively, and may play an important role in ECMO-supported neonatal pneumonia pathogen detection and optimization of antibiotic therapy.
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Affiliation(s)
- Yi-Rong Zheng
- From the Department of Cardiac Surgery, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Children's Hospital (Fujian Branch of Shanghai Children's Medical Center), Fuzhou, China
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Yuan L, Chen Q, Zhu XY, Lai LM, Zhao R, Liu Y. Evaluation of clinical characteristics and risk factors associated with Chlamydia psittaci infection based on metagenomic next-generation sequencing. BMC Microbiol 2024; 24:86. [PMID: 38481150 PMCID: PMC10935969 DOI: 10.1186/s12866-024-03236-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 02/26/2024] [Indexed: 03/17/2024] Open
Abstract
INTRODUCTION Psittacosis is a zoonosis caused by Chlamydia psittaci, the clinical manifestations of Psittacosis range from mild illness to fulminant severe pneumonia with multiple organ failure. This study aimed to evaluate the clinical characteristics of Chlamydia psittaci infection diagnosed based on metagenomic next-generation sequencing(mNGS), as well as the risk factors affecting the progress of Chlamydia psittaci infection, in order to improve the effect of therapeutics. METHODS We retrospectively analyzed the clinical data of patients infected with chlamydia psittaci in the First Affiliated Hospital of Nanchang University from January 2021 to December 2021. The patient's past medical history, clinical manifestations, laboratory examinations, chest CT results, treatment status, and prognosis data were collected. we also investigated both the pathogenic profile characteristics and the lower respiratory tract microbiota of patients with Chlamydia psittaci pneumonia using mNGS. RESULTS All cases of Chlamydia psittaci in our research have been confirmed by mNGS. Among 46 cases of Chlamydia psittaci pneumonia, Poultry exposure was reported in 35 cases. In severe cases of Chlamydia psittaci pneumonia, Neutrophils, Procalcitonin (PCT), Lactate Dehydrogenase (LDH), Hydroxybutyrate Dehydrogenase (HBDH), Creatine Kinase Isoenzymes-B (CK-MB) and D-Dimer levels were remarkably higher than that of non-severe cases, except for lymphocytes (all P < 0.05). Chest CT scans showed Bilateral (77.8%), multiple lobar lungs (85.2%), pleural effusions (44.4%) involvement in those suffering from severe Chlamydia psittaci pneumonia, whereas its incidence was 0%, 21.1% and 10.5% in non-severe patients, respectively (P < 0.05). Multivariate analysis revealed that higher lymphocyte concentrations (OR 0.836, 95% CI 0.714-0.962, P = 0.041) were the only protective factor for survival. mNGS results indicated that 41.3% of patients (19/46) had suspected coinfections with a coinfection rate of 84.2% (16/19) in the severe group, much higher than that in the non severe group (p < 0.05). No significantly different profiles of lower respiratory tract microbiota diversity were found between non severe group and severe group. CONCLUSION A history of poultry exposure in patients can serve as an important basis for diagnosing Chlamydia psittaci pneumonia, and patients with severe Chlamydia psittaci pneumonia are more likely to develop elevated inflammatory biomarkers as well as elevated cardiac markers. Higher lymphocyte concentrations are protective factors associated with severe C. psittaci pneumonia. The higher proportion of patients with coinfections in our study supports the use of mNGS for comprehensive early detection of respiratory infections in patients with C. psittaci pneumonia.
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Affiliation(s)
- Lei Yuan
- Department of Clinical laboratory, The First Affiliated Hospital of Nanchang University of Nanchang University, Nanchang University, No.17, YongWaiZhengStreet, Nanchang, 330006, China
| | - Qiang Chen
- Department of Clinical laboratory, The First Affiliated Hospital of Nanchang University of Nanchang University, Nanchang University, No.17, YongWaiZhengStreet, Nanchang, 330006, China
| | - Xin Yu Zhu
- Department of Clinical laboratory, The First Affiliated Hospital of Nanchang University of Nanchang University, Nanchang University, No.17, YongWaiZhengStreet, Nanchang, 330006, China
| | - Lan Min Lai
- Department of Clinical laboratory, The First Affiliated Hospital of Nanchang University of Nanchang University, Nanchang University, No.17, YongWaiZhengStreet, Nanchang, 330006, China
| | - Rui Zhao
- Department of Clinical laboratory, The First Affiliated Hospital of Nanchang University of Nanchang University, Nanchang University, No.17, YongWaiZhengStreet, Nanchang, 330006, China.
| | - Yang Liu
- Department of Clinical laboratory, The First Affiliated Hospital of Nanchang University of Nanchang University, Nanchang University, No.17, YongWaiZhengStreet, Nanchang, 330006, China.
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Guo Q, Xiao Y, Zhang S. Metagenomic next generation sequencing of bronchoalveolar lavage samples for the diagnosis of lower respiratory tract infections: A systematic review and meta-analysis. Heliyon 2024; 10:e23188. [PMID: 38148812 PMCID: PMC10750151 DOI: 10.1016/j.heliyon.2023.e23188] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 10/07/2023] [Accepted: 11/29/2023] [Indexed: 12/28/2023] Open
Abstract
Background Lower respiratory tract infections (LRTI)are known to be diagnosed late or inaccurately. This has fueled the unscrupulous use of antibiotics, as they are often used empirically and clinically, leading to antibiotic abuse and multidrug resistance in patients. Metagenomic next-generation sequencing (mNGS), now widely used in clinical studies, could be a potential intervention to revolutionize microbiology by rapidly identifying unknown species. Methods This review and meta-analysis were conducted on eligible studies with respect to metagenomic sequencing on clinical LRTI diagnostics up to May 01, 2022. QUADAS-2 was employed to assess the methodological bias as well as applicability. After that, a meta-analysis was conducted to analyze the accuracy of mNGS, compared with the composite reference standard (CRS), among the enrolled studies. Results This work collected 1248 samples in 13/21 qualified articles to factor in the accuracy of the diagnostic test. Typically, methods like molecular testing, culture, composite measures, and clinical decision-making were adopted as the reference criteria. With regard to Bronchoalveolar Lavage Samples, their sensitivity was 89% (82-93%) while their specificity was 90% (66-98%), with obvious heterogeneities in these two factors as demonstrated by different studies. The summary receiver operating characteristic (SROC) curve was plotted for mNGS as a function of LRTI, and the area under the curve (AUC) was 0.94. A Funnel plot with a p-value greater than 0.05 indicated the absence of publication bias. Positive and negative likelihood ratios (PLR and NLR) were >10 and > 0.1, respectively. In this pre-test probability-post-probability-likelihood ratio relationship graph, the values were Prior prob (%) = 20, Post-prob-Pos (%) = 77 and Post-prob-Neg (%) = 4. Conclusion The AUC value of SROC suggested a high accuracy of mNGS in diagnosis, with no publication bias and high reliability. The application of mNGS exhibits notable diagnostic efficacy in discerning pathogens present in bronchoalveolar lavage fluid (BALF) among patients afflicted with LRTI. However, mNGS is more meaningful for the definitive diagnosis of the disease rather than the exclusion of the disease. This post-test probability is significantly higher than the pre-test probability.
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Affiliation(s)
- Qiang Guo
- Department of Clinical Laboratory, Anhui Provincial Children’s Hospital, Hefei, 230000, Anhui, China
| | - Yang Xiao
- School of Anesthesiology, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Shihai Zhang
- Department of Clinical Laboratory, Anhui Provincial Children’s Hospital, Hefei, 230000, Anhui, China
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Shi Y, Peng JM, Hu XY, Yang QW, Wang Y. Metagenomic next-generation sequencing for detecting Aspergillosis pneumonia in immunocompromised patients: a retrospective study. Front Cell Infect Microbiol 2023; 13:1209724. [PMID: 38188627 PMCID: PMC10770824 DOI: 10.3389/fcimb.2023.1209724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 12/07/2023] [Indexed: 01/09/2024] Open
Abstract
Purpose The identification of Aspergillus by metagenomic next-generation sequencing (mNGS) remains a challenging task due to the difficulty of nucleic acid extraction. The objective of this study was to determine whether mNGS could provide an accurate and efficient method for detecting invasive pulmonary aspergillosis (IPA) in immunocompromised patients (ICP). Methods A total of 133 ICP admitted to the ICU between January 2020 and September 2022 were enrolled in the study, of which 46 were diagnosed with IPA and 87 were non-IPA cases. The bronchoalveolar lavage fluid (BALF) was analyzed for the presence of Aspergillosis and other co-pathogens using mNGS, and its diagnostic performance was compared to conventional microbial tests (CMTs) that included smear, cultures, serum and BALF galactomannan (GM) test. Clinical composite diagnosis was used as the reference standard. Results mNGS had a sensitivity, specificity, and accuracy of 82.6%, 97.7%, and 92.5%, respectively, in diagnosing IPA. These findings were comparable to those of the combination of multiple CMTs. Interestingly, the sensitivity of mNGS was superior to that of any single CMT method, as demonstrated by comparisons with smears (8.7%, P < 0.001), culture (39.1%, P < 0.001), serum GM (23.9%, P < 0.001) and BALF GM (69.6%, P = 0.031). mNGS was capable of accurately distinguish strains of Aspergillus genus, with a consistency of 77.8% with culture. Furthermore, mNGS also identified A. fumigatus, A. flavus, A. terrestris, A. oryzae and Mucor spp. in culture-negative cases. The sequencing reads of Aspergillus by mNGS exhibited extensive variation, ranging from 11 to1702. A positive correlation was observed between the optical density index of BALF GM and unique reads by mNGS (r = 0.607, P = 0.001) in BALF-GM positive patients. Notably, mNGS was able to diagnose 35 out of 37 cases with mixed infection, with P. jirovecii and cytomegalovirus being the most common co-pathogens. Conclusions mNGS presents a feasible and remarkably sensitive approach for detecting Aspergillus in ICP, thereby serving as a valuable adjunctive tool to CMT. Furthermore, mNGS's ability to accurately identify fungal species and co-pathogens can assist in guiding appropriate antimicrobial therapy.
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Affiliation(s)
- Yan Shi
- Department of Medical ICU, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Jin-Min Peng
- Department of Medical ICU, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Xiao-Yun Hu
- Department of Medical ICU, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Qi-Wen Yang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yao Wang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
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11
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Kahl LJ, Stremmel N, Esparza-Mora MA, Wheatley RM, MacLean RC, Ralser M. Interkingdom interactions between Pseudomonas aeruginosa and Candida albicans affect clinical outcomes and antimicrobial responses. Curr Opin Microbiol 2023; 75:102368. [PMID: 37677865 DOI: 10.1016/j.mib.2023.102368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/24/2023] [Accepted: 07/24/2023] [Indexed: 09/09/2023]
Abstract
Infections that involve interkingdom microbial communities, such as those between bacteria and yeast pathogens, are difficult to treat, associated with worse patient outcomes, and may be a source of antimicrobial resistance. In this review, we address co-occurrence and co-infections of Candida albicans and Pseudomonas aeruginosa, two pathogens that occupy multiple infection niches in the human body, especially in immunocompromised patients. The interaction between the pathogen species influences microbe-host interactions, the effectiveness of antimicrobials and even infection outcomes, and may thus require adapted treatment strategies. However, the molecular details of bacteria-fungal interactions both inside and outside the infection sites, are insufficiently characterised. We argue that comprehensively understanding the P. aeruginosa-C. albicans interaction network through integrated systems biology approaches will capture the highly dynamic and complex nature of these polymicrobial infections and lead to a more comprehensive understanding of clinical observations such as reshaped immune defences and low antimicrobial treatment efficacy.
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Affiliation(s)
- Lisa J Kahl
- Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany
| | - Nina Stremmel
- Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany
| | | | - Rachel M Wheatley
- University of Oxford, Department of Biology, Oxford OX1 3SZ, United Kingdom
| | - R Craig MacLean
- University of Oxford, Department of Biology, Oxford OX1 3SZ, United Kingdom
| | - Markus Ralser
- Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany; University of Oxford, The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, Oxford OX3 7BN, United Kingdom; Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany.
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12
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Pan X, Zhang Y, Chen G. The clinical utility of metagenomic next-generation sequencing for the diagnosis of central nervous system infectious diseases. Neurol Res 2023; 45:919-925. [PMID: 37615407 DOI: 10.1080/01616412.2023.2247299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 06/10/2023] [Indexed: 08/25/2023]
Abstract
BACKGROUND To evaluate the clinical utility of metagenomic next-generation sequencing (mNGS) for the diagnosis of central nervous system infections (CNSI). METHODS Cerebrospinal fluid (CSF) from 54 patients who were high-level clinical suspicion of CNSI was collected and sent for mNGS and conventional tests from January 2019 to March 2022. RESULTS Twenty out of 54 patients were diagnosed with CNSI and 34 non-CNSI. Among the 34 non-CNSI, one was false positive by mNGS. Among the 20 CNSI, 11 had presumed viral encephalitis and/or meningitis, 5 had presumed bacterial meningitis, 2 had presumed TMB, 1 had Crytococcus meningitis and 1 had neurosyphilis. The sensitivity of viral encephalitis and/or meningitis was 0.73 (8/11); 10 virus were detected; 9/10 was dsDNA; 1/10 was ssRNA. SSRN ranged from 1 to 13. The accuracy rate was 0.4, the accuracy rate was positively correlated with SSRN (r = 0.738, P = 0.015), SSRN ≥ 1, the accuracy rate was 0.4; SSRN ≥ 3, the accuracy rate was 0.66; SSRN ≥ 4, the accuracy rate was 0.75; SSRN ≥ 6, the accuracy rate was 1. The sensitivity of bacterial meningitis was 1. Seven kinds of bacteria were detected, among which 3/7 were gram positive, 3/7 were gram negative, and 1/7 was infected NTM (nontuberculous mycobacteria). The accuracy rate was 0.43 (3/7). The sensitivity of TBM was 0.66 (2/3), the accuracy rate was 1. The sensitivity of Crytococcus meningitis was 1, the accuracy rate was 0.5. PPV (positive predictive value) of mNGS was 0.94, NPV (negative predictive value) of mNGS was 0.89, specificity was 0.97 and sensitivity was 0.8. The AUG for CSF mNGS diagnosis of CNSI was 0.89 (95% CI = 0.78-0.99) Headache, meningeal irritation sign and image of meninges abnormal were correlated with the sensitivity of mNGS (r = 0.451, 0.313, 0.446; p = 0.001, 0.021, 0.001); CSF Glucose and CSF Chloride were negatively correlated with sensitivity of mNGS (r = -0.395, -0.462; p = 0.003, < 0.001). CONCLUSION mNGS is a detection means with high sensitivity, wide coverage and strong timeliness, which can help clinicians to identify the pathogen diagnosis quickly, conduct targeted anti-infection treatment early and reduce antibiotic abuse. The pathogen which causing low CSF Glucose, low CSF Chloride or meninges infections was more likely to be detected by mNGS. It may be related to growth and structural characteristics of the pathogen and blood-brain barrier damage.
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Affiliation(s)
- Xiaoying Pan
- Department of Neurology, The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yuefeng Zhang
- Department of Neurology, The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China
| | - Guohua Chen
- Department of Neurology, The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China
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13
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Guan Y, Yu C, Fei Y, Wang Q, Wang P, Zuo W, Wu H, Qi X, Shi Q. Case Report: Four cases of SARS-CoV-2-associated Guillain-Barré Syndrome with SARS-CoV-2-positive cerebrospinal fluid detected by metagenomic next-generation sequencing: a retrospective case series from China. Front Immunol 2023; 14:1258579. [PMID: 37701436 PMCID: PMC10493301 DOI: 10.3389/fimmu.2023.1258579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 08/14/2023] [Indexed: 09/14/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is often absent or at low levels in the cerebrospinal fluid (CSF) of patients with previous SARS-CoV-2-associated Guillain-Barré syndrome (GBS). This has led to speculation that SARS-CoV-2-associated GBS is more likely mediated by post-infectious immunity or a parainfection. This understanding has influenced the development of treatment regimens for SARS-CoV-2-associated GBS. This paper reports our experience with four Chinese patients with SARS-CoV-2-associated GBS who tested positive for SARS-CoV-2 RNA in the CSF. They developed symptoms of peripheral nerve damage 4-15 days after fever and confirmed SARS-CoV-2 infection, all of whom presented with progressive weakness of both lower limbs; three with autonomic nerve function impairment such as constipation and urination disorder; and one with polycranial neuritis and Miller-Fisher syndrome. Three patients were tested for anti-ganglioside antibodies, and one tested positive for GD1a-IgG. Four patients recovered well after treatment with anti-viral drugs combined with intravenous immunoglobulin. The present results showed that SARS-CoV-2 RNA can be detected via mNGS in the CSF of some patients with SARS-CoV-2-associated GBS, suggesting that SARS-CoV-2-associated GBS may have multiple pathogeneses.
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Affiliation(s)
- Yalin Guan
- Department of Neurology, Tianjin Huanhu Hospital, Tianjin, China
| | - Changshen Yu
- Department of Neurology, Tianjin Huanhu Hospital, Tianjin, China
| | - Yunhan Fei
- Department of Emergency, Tianjin Huanhu Hospital, Tianjin, China
| | - Qiushi Wang
- Infection Business Unit, Tianjin Novogene Med LAB Co., Ltd., Tianjin, China
- Infection Business Unit, Novogene Co., Ltd., Beijing, China
| | - Pan Wang
- Department of Neurology, Tianjin Huanhu Hospital, Tianjin, China
| | - Wenchao Zuo
- Department of Neurology, Tianjin Huanhu Hospital, Tianjin, China
| | - Hao Wu
- Department of Neurology, Tianjin Huanhu Hospital, Tianjin, China
| | - Xuemei Qi
- Department of Neurology, The second hospital of tianjin medical university, Tianjin, China
| | - Qiyun Shi
- Infection Business Unit, Tianjin Novogene Med LAB Co., Ltd., Tianjin, China
- Infection Business Unit, Novogene Co., Ltd., Beijing, China
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Fang W, Wu J, Cheng M, Zhu X, Du M, Chen C, Liao W, Zhi K, Pan W. Diagnosis of invasive fungal infections: challenges and recent developments. J Biomed Sci 2023; 30:42. [PMID: 37337179 DOI: 10.1186/s12929-023-00926-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/13/2023] [Indexed: 06/21/2023] Open
Abstract
BACKGROUND The global burden of invasive fungal infections (IFIs) has shown an upsurge in recent years due to the higher load of immunocompromised patients suffering from various diseases. The role of early and accurate diagnosis in the aggressive containment of the fungal infection at the initial stages becomes crucial thus, preventing the development of a life-threatening situation. With the changing demands of clinical mycology, the field of fungal diagnostics has evolved and come a long way from traditional methods of microscopy and culturing to more advanced non-culture-based tools. With the advent of more powerful approaches such as novel PCR assays, T2 Candida, microfluidic chip technology, next generation sequencing, new generation biosensors, nanotechnology-based tools, artificial intelligence-based models, the face of fungal diagnostics is constantly changing for the better. All these advances have been reviewed here giving the latest update to our readers in the most orderly flow. MAIN TEXT A detailed literature survey was conducted by the team followed by data collection, pertinent data extraction, in-depth analysis, and composing the various sub-sections and the final review. The review is unique in its kind as it discusses the advances in molecular methods; advances in serology-based methods; advances in biosensor technology; and advances in machine learning-based models, all under one roof. To the best of our knowledge, there has been no review covering all of these fields (especially biosensor technology and machine learning using artificial intelligence) with relevance to invasive fungal infections. CONCLUSION The review will undoubtedly assist in updating the scientific community's understanding of the most recent advancements that are on the horizon and that may be implemented as adjuncts to the traditional diagnostic algorithms.
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Affiliation(s)
- Wenjie Fang
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China
| | - Junqi Wu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
- Shanghai Engineering Research Center of Lung Transplantation, Shanghai, 200433, China
| | - Mingrong Cheng
- Department of Anorectal Surgery, The Third Affiliated Hospital of Guizhou Medical University, Guizhou, 558000, China
| | - Xinlin Zhu
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China
| | - Mingwei Du
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China
| | - Chang Chen
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
- Shanghai Engineering Research Center of Lung Transplantation, Shanghai, 200433, China
| | - Wanqing Liao
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China
| | - Kangkang Zhi
- Department of Vascular and Endovascular Surgery, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China.
| | - Weihua Pan
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China.
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15
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Bao R, Mei Q, Yang T, Zhang L, Zhu C, Fan X, Wang Y, Tong F, He Y, Fang X, Geng S, Yang Y, Sheng X, Pan A. Comparison of endotracheal aspirate and bronchoalveolar lavage fluid metagenomic next-generation sequencing in severe pneumonia: a nested, matched case-control study. BMC Infect Dis 2023; 23:389. [PMID: 37303052 DOI: 10.1186/s12879-023-08376-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 06/06/2023] [Indexed: 06/13/2023] Open
Abstract
OBJECTIVES To compare clinical outcomes in patients with severe pneumonia according to the diagnostic strategy used. METHODS In this retrospective, nested, case-control study, patients with severe pneumonia who had undergone endotracheal aspirate (ETA) metagenomic next-generation sequencing of (mNGS) testing (n = 53) were matched at a ratio of 1 to 2 (n = 106) by sex, age, underlying diseases, immune status, disease severity scores, and type of pneumonia with patients who had undergone bronchoalveolar lavage fluid (BALF) mNGS. The microbiological characteristics and patient's prognosis of the two groups were compared. RESULTS An overall comparison between the two groups showed no significant differences in bacterial, fungal, viral, or mixed infections. However, subgroup analysis of 18 patients who received paired ETA and BALF mNGS showed a complete agreement rate for the two specimens of 33.3%. There were more cases for whom targeted treatment was initiated (36.79% vs. 22.64%; P = 0.043) and fewer cases who received no clinical benefit after mNGS (5.66% vs. 15.09%; P = 0.048) in the BALF group. The pneumonia improvement rate in the BALF group was significantly higher than in the ETA group (73.58% vs. 87.74%, P = 0.024). However, there were no significant differences in ICU mortality or 28-day mortality. CONCLUSIONS We do not recommend using ETA mNGS as the first-choice method for analyzing airway pathogenic specimens from severe pneumonia patients.
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Affiliation(s)
- Renren Bao
- Department of Critical Care Medicine, The Affiliated Provincial Hospital of Anhui Medical University, Hefei, 230001, Anhui, China
| | - Qing Mei
- Department of Critical Care Medicine, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, 230001, Anhui, China.
| | - Tianjun Yang
- Department of Critical Care Medicine, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, 230001, Anhui, China
| | - Lei Zhang
- Department of Critical Care Medicine, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, 230001, Anhui, China
| | - Chunyan Zhu
- Department of Critical Care Medicine, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, 230001, Anhui, China
| | - Xiaoqin Fan
- Department of Critical Care Medicine, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, 230001, Anhui, China
| | - Yinzhong Wang
- Department of Critical Care Medicine, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, 230001, Anhui, China
| | - Fei Tong
- Department of Critical Care Medicine, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, 230001, Anhui, China
| | - Yuxi He
- Department of Critical Care Medicine, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, 230001, Anhui, China
| | - Xiaowei Fang
- Department of Critical Care Medicine, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, 230001, Anhui, China
| | - Shike Geng
- Department of Critical Care Medicine, The Affiliated Provincial Hospital of Anhui Medical University, Hefei, 230001, Anhui, China
| | - Yu Yang
- Department of Critical Care Medicine, The Affiliated Provincial Hospital of Anhui Medical University, Hefei, 230001, Anhui, China
| | - Ximei Sheng
- WanNan Medical College, Wuhu, 241002, Anhui, China
| | - Aijun Pan
- Department of Critical Care Medicine, The Affiliated Provincial Hospital of Anhui Medical University, Hefei, 230001, Anhui, China.
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Wu P, Weng H, Luo W, Zhan Y, Xiong L, Zhang H, Yan H. An improved Yolov5s based on transformer backbone network for detection and classification of bronchoalveolar lavage cells. Comput Struct Biotechnol J 2023; 21:2985-3001. [PMID: 37249972 PMCID: PMC10209489 DOI: 10.1016/j.csbj.2023.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/31/2023] Open
Abstract
Biological tissue information of the lung, such as cells and proteins, can be obtained from bronchoalveolar lavage fluid (BALF), through which it can be used as a complement to lung biopsy pathology. BALF cells can be confused with each other due to the similarity of their characteristics and differences in the way sections are handled or viewed. This poses a great challenge for cell detection. In this paper, An Improved Yolov5s Based on Transformer Backbone Network for Detection and Classification of BALF Cells is proposed, focusing on the detection of four types of cells in BALF: macrophages, lymphocytes, neutrophils and eosinophils. The network is mainly based on the Yolov5s network and uses Swin Transformer V2 technology in the backbone network to improve cell detection accuracy by obtaining global information; the C3Ghost module (a variant of the Convolutional Neural Network architecture) is used in the neck network to reduce the number of parameters during feature channel fusion and to improve feature expression performance. In addition, embedding intersection over union Loss (EIoU_Loss) was used as a bounding box regression loss function to speed up the bounding box regression rate, resulting in higher accuracy of the algorithm. The experiments showed that our model could achieve mAP of 81.29% and Recall of 80.47%. Compared to the original Yolov5s, the mAP has improved by 3.3% and Recall by 3.67%. We also compared it with Yolov7 and the newly launched Yolov8s. mAP improved by 0.02% and 2.36% over Yolov7 and Yolov8s respectively, while the FPS of our model was higher than both of them, achieving a balance of efficiency and accuracy, further demonstrating the superiority of our model.
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Affiliation(s)
- Puzhen Wu
- The Faculty of Architecture, Civil and Transportation Engineering, Beijing University of Technology, Beijing 100124, China
- Beijing-Dublin International College, Beijing University of Technology, Beijing 100124, China
| | - Han Weng
- Beijing-Dublin International College, Beijing University of Technology, Beijing 100124, China
| | - Wenting Luo
- Department of Pathophysiology, Medical College, Nanchang University, 461 Bayi Road, Nanchang 330006, China
| | - Yi Zhan
- Beijing-Dublin International College, Beijing University of Technology, Beijing 100124, China
| | - Lixia Xiong
- Department of Pathophysiology, Medical College, Nanchang University, 461 Bayi Road, Nanchang 330006, China
| | - Hongyan Zhang
- Department of Burn, The First Affiliated Hospital, Nanchang University, 17 Yongwaizheng Road, Nanschang 330066, China
| | - Hai Yan
- The Faculty of Architecture, Civil and Transportation Engineering, Beijing University of Technology, Beijing 100124, China
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Zhang S, Ou J, Tan Y, Yang B, Wu Y, Liu L. Metagenomic next-generation sequencing for pulmonary infections diagnosis in patients with diabetes. BMC Pulm Med 2023; 23:142. [PMID: 37106322 PMCID: PMC10141947 DOI: 10.1186/s12890-023-02441-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 04/17/2023] [Indexed: 04/29/2023] Open
Abstract
BACKGROUND Diabetes mellitus is a major cause of high mortality and poor prognosis in patients with pulmonary infections. However, limited data on the application of metagenomic next-generation sequencing (mNGS) are available for diabetic patients. This study aimed to evaluate the diagnostic performance of mNGS in diabetic patients with pulmonary infections. METHODS We retrospectively reviewed 184 hospitalized patients with pulmonary infections at Guizhou Provincial People's Hospital between January 2020 to October 2021. All patients were subjected to both mNGS analysis of bronchoalveolar lavage fluid (BALF) and conventional testing. Positive rate by mNGS and the consistency between mNGS and conventional testing results were evaluated for diabetic and non-diabetic patients. RESULTS A total of 184 patients with pulmonary infections were enrolled, including 43 diabetic patients and 141 non-diabetic patients. For diabetic patients, the microbial positive rate by mNGS was significantly higher than that detected by conventional testing methods, primarily driven by bacterial detection (microbes: 95.3% vs. 67.4%, P = 0.001; bacteria: 72.1% vs. 37.2%, P = 0.001). mNGS and traditional tests had similar positive rates with regard to fungal and viral detection in diabetic patients. Klebsiella pneumoniae was the most common pathogen identified by mNGS in patients with diabetes. Moreover, mNGS identified pathogens in 92.9% (13/14) of diabetic patients who were reported negative by conventional testing. No significant difference was found in the consistency of the two tests between diabetic and non-diabetic groups. CONCLUSIONS mNGS is superior to conventional microbiological tests for bacterial detection in diabetic patients with pulmonary infections. mNGS is a valuable tool for etiological diagnosis of pulmonary infections in diabetic patients.
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Affiliation(s)
- Siqin Zhang
- Department of Endocrinology and Metabolism, Guizhou Provincial People's Hospital, Guiyang, Guizhou, 550002, China
| | - Jing Ou
- School of Medicine, Zunyi Medical University, Zunyi, Guizhou, 563000, China
| | - Yuxue Tan
- School of Medicine, Zunyi Medical University, Zunyi, Guizhou, 563000, China
| | - Bin Yang
- Department of Central Laboratory, Guizhou Provincial People's Hospital, Guiyang, Guizhou, 550002, China
| | - Yaoyao Wu
- Department of Respiratory and Critical Medicine, Guizhou Provincial People's Hospital, No. 83, Zhongshan East Road, Guiyang, Guizhou, 550002, China
| | - Lin Liu
- Department of Respiratory and Critical Medicine, Guizhou Provincial People's Hospital, No. 83, Zhongshan East Road, Guiyang, Guizhou, 550002, China.
- NHC Key Laboratory of Pulmonary Immunological Diseases (Guizhou Provincial People's Hospital), Guiyang, Guizhou, 550002, China.
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Ventilator-Associated Pneumonia in Immunosuppressed Patients. Antibiotics (Basel) 2023; 12:antibiotics12020413. [PMID: 36830323 PMCID: PMC9952186 DOI: 10.3390/antibiotics12020413] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
Immunocompromised patients-including patients with cancer, hematological malignancies, solid organ transplants and individuals receiving immunosuppressive therapies for autoimmune diseases-account for an increasing proportion of critically-ill patients. While their prognosis has improved markedly in the last decades, they remain at increased risk of healthcare- and intensive care unit (ICU)-acquired infections. The most frequent of these are ventilator-associated lower respiratory tract infections (VA-LTRI), which include ventilator-associated pneumonia (VAP) and tracheobronchitis (VAT). Recent studies have shed light on some of the specific features of VAP and VAT in immunocompromised patients, which is the subject of this narrative review. Contrary to previous belief, the incidence of VAP and VAT might actually be lower in immunocompromised than non-immunocompromised patients. Further, the relationship between immunosuppression and the incidence of VAP and VAT related to multidrug-resistant (MDR) bacteria has also been challenged recently. Etiological diagnosis is essential to select the most appropriate treatment, and the role of invasive sampling, specifically bronchoscopy with bronchoalveolar lavage, as well as new molecular syndromic diagnostic tools will be discussed. While bacteria-especially gram negative bacteria-are the most commonly isolated pathogens in VAP and VAT, several opportunistic pathogens are a special concern among immunocompromised patients, and must be included in the diagnostic workup. Finally, the impact of immunosuppression on VAP and VAT outcomes will be examined in view of recent papers using improved statistical methodologies and treatment options-more specifically empirical antibiotic regimens-will be discussed in light of recent findings on the epidemiology of MDR bacteria in this population.
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Wei Y, Zhang T, Ma Y, Yan J, Zhan J, Zheng J, Xu Y. Clinical Evaluation of Metagenomic Next-Generation Sequencing for the detection of pathogens in BALF in severe community acquired pneumonia. Ital J Pediatr 2023; 49:25. [PMID: 36805803 PMCID: PMC9938609 DOI: 10.1186/s13052-023-01431-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 02/12/2023] [Indexed: 02/19/2023] Open
Abstract
BACKGROUND Rapid and accurate identification of pathogens is very important for the treatment of Severe community-acquired pneumonia (SCAP) in children. Metagenomic Next-generation sequencing (mNGS) has been applied in the detection of pathogenic bacteria in recent years, while the overall evaluation the application of SCAP in children is lacking. METHODS In our study, 84 cases of SCAP were enrolled. Bronchoalveolar lavage fluid (BALF) samples were analysed using mNGS; and sputum, blood, and BALF samples were analysed using conventional technology (CT). RESULTS Among the 84 children, 41 were boys, and 43 were girls, with an average age ranging from 2 months to 14 years. The pathogen detection rate of mNGS was higher than that of CT (83.3% [70/84] vs. 63.1% [53/84], P = 0.003). The mNGS was much greater than that of the CT in detecting Streptococcus pneumoniae (89.2% [25/29] vs. 44.8% [13/29], P = 0.001) and Haemophilus influenzae (91.7% [11/12] vs. 33.3% [4/12], P < 0.005). The mNGS also showed superior fungal detection performance compared with that of the CT (81.8% [9/11] vs. 18.2% [2/11], P = 0.004). The mNGS test can detect viruses, such as bocavirus, rhinovirus, and human metapneumovirus, which are not frequently recognised using CT. However, the mNGS detection rate was lower than that of the CT (52.4% [11/21] vs. 95.2% [20/21], P = 0.004) for Mycoplasma pneumoniae (MP). The detection rate of mNGS for mixed infection was greater than that of the CT, although statistical significance was not observed (26.3% [20/39] vs. 21.1% [16/39], P > 0.005). Treatment for 26 (31.0%) children was changed based on mNGS results, and their symptoms were reduced; nine patients had their antibiotic modified, five had antibiotics added, nine had their antifungal medication, and seven had their antiviral medication. CONCLUSION mNGS has unique advantages in the detection of SCAP pathogens in children, especially S. pneumoniae, H. influenzae, and fungi. However, the detection rate of MP using mNGS was lower than that of the CT. Additionally, mNGS can detect pathogens that are not generally covered by CT, which is extremely important for the modification of the treatment strategy.
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Affiliation(s)
- Yupeng Wei
- grid.265021.20000 0000 9792 1228Clinical School of Paediatrics, Tianjin Medical University, Tianjin, China ,grid.417022.20000 0004 1772 3918Department of Respiratory Medicine, Tianjin Children’s Hospital (Tianjin University Children’s Hospital), Tianjin, China ,grid.410626.70000 0004 1798 9265Department of Neonatology, Tianjin Central Hospital of Gynecology Obstetrics, Tianjin, China
| | - Tongqiang Zhang
- grid.265021.20000 0000 9792 1228Clinical School of Paediatrics, Tianjin Medical University, Tianjin, China ,grid.417022.20000 0004 1772 3918Department of Respiratory Medicine, Tianjin Children’s Hospital (Tianjin University Children’s Hospital), Tianjin, China
| | - Yuting Ma
- grid.265021.20000 0000 9792 1228Clinical School of Paediatrics, Tianjin Medical University, Tianjin, China ,grid.417022.20000 0004 1772 3918Department of Infection, Tianjin Children’s Hospital (Tianjin University Children’s Hospital), Tianjin, China
| | - Jisi Yan
- grid.265021.20000 0000 9792 1228Clinical School of Paediatrics, Tianjin Medical University, Tianjin, China ,grid.417022.20000 0004 1772 3918Department of Respiratory Medicine, Tianjin Children’s Hospital (Tianjin University Children’s Hospital), Tianjin, China ,grid.410626.70000 0004 1798 9265Department of Neonatology, Tianjin Central Hospital of Gynecology Obstetrics, Tianjin, China
| | - Jianghua Zhan
- Department of Pediatric Surgery, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China.
| | - Jun Zheng
- Department of Neonatology, Tianjin Central Hospital of Gynecology Obstetrics, Tianjin, China.
| | - Yongsheng Xu
- Department of Respiratory Medicine, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China.
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Wang L, Li S, Qin J, Tang T, Hong J, Tung TH, Xu C, Yu S, Qian J. Clinical Diagnosis Application of Metagenomic Next-Generation Sequencing of Plasma in Suspected Sepsis. Infect Drug Resist 2023; 16:891-901. [PMID: 36820080 PMCID: PMC9938705 DOI: 10.2147/idr.s395700] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 02/02/2023] [Indexed: 02/16/2023] Open
Abstract
Purpose We analyzed the clinical concordance of mNGS test results from blood samples and improved the clinical efficiency of mNGS in the diagnosis of suspected sepsis pathogens. Patients and Methods In this study, 99 samples of suspected blood flow infection were included for plasma mNGS, and the correlation between mNGS results and blood culture results, serum inflammatory indices, clinical symptoms and antibiotic treatment was analyzed, as well as the comparison with the detection rate of BALF pathogens, as well as the classification of different pathogens in the mNGS results were analyzed. Results The mNGS pathogen detection rate was higher than that of traditional blood culture (83.02% vs 35.82%). The rate of the mNGS results being consistent with the clinical diagnosis was also higher than that of traditional blood culture (58.49% vs 20.75%). This study shows that bacteria and fungi are the main pathogens in sepsis, and viral sepsis is very rare. In this study, 32% of sepsis patients were secondary to pneumonia. Compared with the pathogen detection rate using alveolar lavage fluid, the detection rate from plasma mNGS was 62.5%. Samples were also easy to sample, noninvasive, and more convenient for clinical application. Conclusion This study shows that compared with blood culture, the detection rate of mNGS pathogen that meets the diagnosis of sepsis is higher. We need a combination of multiple indicators to monitor the early diagnosis and treatment of sepsis.
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Affiliation(s)
- Lisha Wang
- Department of Laboratory Medicine, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, People’s Republic of China
| | - Shixiao Li
- Department of Laboratory Medicine, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, People’s Republic of China
| | - Jiajia Qin
- Department of Laboratory Medicine, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, People’s Republic of China
| | - Tianbin Tang
- Department of Laboratory Medicine, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, People’s Republic of China
| | - Jiawen Hong
- Department of Laboratory Medicine, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, People’s Republic of China
| | - Tao-Hsin Tung
- Evidence-Based Medicine Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, People’s Republic of China
| | - Chunyan Xu
- Department of Laboratory Medicine, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, People’s Republic of China
| | - Sufei Yu
- Department of Laboratory Medicine, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, People’s Republic of China,Correspondence: Sufei Yu; Jiao Qian, Email ;
| | - Jiao Qian
- Department of Laboratory Medicine, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, People’s Republic of China
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Qin C, Zhang S, Zhao Y, Ding X, Yang F, Zhao Y. Diagnostic value of metagenomic next-generation sequencing in sepsis and bloodstream infection. Front Cell Infect Microbiol 2023; 13:1117987. [PMID: 36844396 PMCID: PMC9950395 DOI: 10.3389/fcimb.2023.1117987] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 01/30/2023] [Indexed: 02/12/2023] Open
Abstract
Objective To evaluate the diagnostic value of metagenomic next-generation sequencing (mNGS) in sepsis and bloodstream infection (BSI). Methods A retrospective analysis of patients diagnosed with sepsis and BSI at the First Affiliated Hospital of Zhengzhou University from January 2020 to February 2022 was conducted. All the patients underwent blood culture and were divided into mNGS group and non-mNGS group according to whether mNGS was performed or not. The mNGS group was further divided into early group (< 1 day), intermediate group (1-3 days), and late group (> 3 days) according to the time of mNGS inspection. Results In 194 patients with sepsis and BSI, the positive rate of mNGS for identifying pathogens was significantly higher than that of blood culture (77.7% vs. 47.9%), and the detection period was shorter (1.41 ± 1.01 days vs. 4.82 ± 0.73 days); the difference was statistically significant (p < 0.05). The 28-day mortality rate of the mNGS group (n = 112) was significantly lower than that of the non-mNGS group (n = 82) (47.32% vs. 62.20%, p = 0.043). The total hospitalization time for the mNGS group was longer than that for the non-mNGS group (18 (9, 33) days vs. 13 (6, 23) days, p = 0.005). There was no significant difference in the ICU hospitalization time, mechanical ventilation time, vasoactive drug use time, and 90-day mortality between the two groups (p > 0.05). Sub-group analysis of patients in the mNGS group showed that the total hospitalization time and the ICU hospitalization time in the late group were longer than those in the early group (30 (18, 43) days vs. 10 (6, 26) days, 17 (6, 31) days vs. 6 (2, 10) days), and the ICU hospitalization time in the intermediate group was longer than that in the early group (6 (3, 15) days vs. 6 (2, 10) days); the differences were statistically significant (p < 0.05). The 28-day mortality rate of the early group was higher than that of the late group (70.21% vs. 30.00%), and the difference was statistically significant (p = 0.001). Conclusions mNGS has the advantages of a short detection period and a high positive rate in the diagnosis of pathogens causing BSI and, eventually, sepsis. Routine blood culture combined with mNGS can significantly reduce the mortality of septic patients with BSI. Early detection using mNGS can shorten the total hospitalization time and the ICU hospitalization time of patients with sepsis and BSI.
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Affiliation(s)
- Cuihong Qin
- General ICU, Henan Key Laboratory of Critical Care Medicine, Henan Engineering Research Center for Critical Care Medicine, Zhengzhou Key Laboratory of Sepsis, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shuguang Zhang
- General ICU, Henan Key Laboratory of Critical Care Medicine, Henan Engineering Research Center for Critical Care Medicine, Zhengzhou Key Laboratory of Sepsis, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yingying Zhao
- General ICU, Henan Key Laboratory of Critical Care Medicine, Henan Engineering Research Center for Critical Care Medicine, Zhengzhou Key Laboratory of Sepsis, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xianfei Ding
- General ICU, Henan Key Laboratory of Critical Care Medicine, Henan Engineering Research Center for Critical Care Medicine, Zhengzhou Key Laboratory of Sepsis, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Fei Yang
- General ICU, Henan Key Laboratory of Critical Care Medicine, Henan Engineering Research Center for Critical Care Medicine, Zhengzhou Key Laboratory of Sepsis, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yangchao Zhao
- Cardiopulmonary Support Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Yangchao Zhao,
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Li S, Qin J, Zhou P, Peng M, Qian J, Cai Y, Shi Q, Tung TH, Shen B, Yu S. The clinical significance of in-house metagenomic next-generation sequencing for bronchoalveolar lavage fluid diagnostics in patients with lower respiratory tract infections. Front Cell Infect Microbiol 2022; 12:961746. [PMID: 36590589 PMCID: PMC9801411 DOI: 10.3389/fcimb.2022.961746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 11/18/2022] [Indexed: 12/23/2022] Open
Abstract
Objective Metagenomic next-generation sequencing (mNGS) technology has the potential to detect a wide range of pathogenic microorganisms. However, reports on the diagnostic value and clinical significance of different platforms of mNGS for patients with lower respiratory tract infections (LRTIs) remain scarce. Methods A total of 306 patients with suspected LRTIs were enrolled from January 2019 to December 2021. The diagnostic performance of conventional methods and mNGS on bronchoalveolar lavage fluid (BALF) were compared. BALF mNGS was performed using a commercial and an in-house laboratory. The diagnostic value and the clinical implications of mNGS for LRTIs were analyzed for the different platforms. Results The positive rate of mNGS in the in-house group was higher than that in the commercial group (85.26% vs. 70.67%, p < 0.001). mNGS significantly increased the pathogen detection rate compared with conventional methods [from 70.67% vs. 22.67% (p < 0.001) to 85.26% vs. 30.77% (p < 0.001)]. The pathogens detected using mNGS included bacteria, fungi, viruses, and atypical pathogens. The in-house platform performed well on a wider spectrum of microbial distribution. Furthermore, it showed an advantage in detecting mixed pathogens in immunocompromised patients. Among the mNGS positive cases, 34 (32.0%) cases had their antibiotics adjusted in the commercial group, while 51 (38.3%) cases had a change of treatment in the in-house group. Moreover, the turnaround time of mNGS and the time from mNGS to discharge in the in-house group were significantly shorter than those in the commercial group. Conclusion In-house mNGS had a higher detection rate and can show a wider spectrum of pathogens, with potential benefits for the clinic by shortening the turnaround time and hospitalization, and it may be more suitable for clinical microbiology laboratories.
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Affiliation(s)
- Shixiao Li
- Department of Clinical Microbiology Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang, China
| | - Jiajia Qin
- Department of Clinical Microbiology Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang, China
| | - Peng Zhou
- Department of Pharmacy, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang, China
| | - Minfei Peng
- Department of Clinical Microbiology Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang, China
| | - Jiao Qian
- Department of Clinical Microbiology Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang, China
| | - Yingying Cai
- Department of Clinical Microbiology Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang, China
| | - Qingxin Shi
- Department of Clinical Microbiology Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang, China
| | - Tao-Hsin Tung
- Evidence-Based Medicine Center, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang, China
| | - Bo Shen
- Department of Clinical Microbiology Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang, China
| | - Sufei Yu
- Department of Clinical Microbiology Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang, China,*Correspondence: Sufei Yu,
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Diagnostic Value of Metagenomic Next-Generation Sequencing for Pneumonia in Immunocompromised Patients. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2022; 2022:5884568. [PMID: 36507192 PMCID: PMC9731749 DOI: 10.1155/2022/5884568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 11/21/2022] [Accepted: 11/23/2022] [Indexed: 12/05/2022]
Abstract
Introduction The diagnosis of pulmonary infection and the identification of pathogens are still clinical challenges in immunocompromised patients. Metagenomic next-generation sequencing (mNGS) has emerged as a promising infection diagnostic technique. However, its diagnostic value in immunocompromised patients needs further exploration. Purposes This study was to evaluate the diagnostic value of mNGS compared with comprehensive conventional pathogen tests (CTs) in the etiology of pneumonia in immunocompromised patients and immunocompetent patients. Methods We retrospectively reviewed 53 patients who were diagnosed with pneumonia from May 2019 to June 2021. There were 32 immunocompromised patients and 21 immunocompetent patients with pneumonia who received both mNGS and CTs. The diagnostic performance was compared between mNGS and CTs in immunocompromised patients, using the composite diagnosis as the reference standard. And, the diagnostic value of mNGS for mixed infections was further analyzed. Results Compared to immunocompetent patients, the most commonly pathogens, followed by Cytomegalovirus, Pneumocystis jirovecii and Klebsiella pneumoniae in immunocompromised patients. Furthermore, more mixed infections were diagnosed, and bacterial-fungal-virus coinfection was the most frequent combination (43.8%). mNGS can detect more types of pathogenic microorganisms than CTs in both groups (78.1% vs. 62.5%, P = 0.016and 57.1% vs. 42.9%, P = 0.048). The overall diagnostic positive rate of mNGS for pathogens was higher in immunocompromised patients (P = 0.002). In immunocompromised patients, a comparable diagnostic accuracy of mNGS and CTs was found for bacterial, fungal, and viral infections and coinfection. mNGS had a much higher sensitivity for bacterial infections (92.9% vs. 50%, P < 0.001) and coinfections (68.8% vs. 48.3%, P < 0.05), and it had no significant advantage in the detection of fungal infections, mainly due to the high sensitivity for Pneumocystis jirovecii in both groups. Conclusion mNGS is more valuable in immunocompromised patients and exhibits apparent advantages in detecting bacterial and mixed infections. It may be an alternative or complementary diagnostic method for the diagnosis of complicated infections in immunocompromised patients.
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Shi Y, Wu J, Liu T, Li Y, Liu Y, Gu Y, Qi Y. Analysis of Metagenomic Next-Generation Sequencing Results of 25 Pus Samples. Infect Drug Resist 2022; 15:6515-6524. [DOI: 10.2147/idr.s385925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 10/27/2022] [Indexed: 11/09/2022] Open
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Deng W, Xu H, Wu Y, Li J. Diagnostic value of bronchoalveolar lavage fluid metagenomic next-generation sequencing in pediatric pneumonia. Front Cell Infect Microbiol 2022; 12:950531. [PMID: 36389175 PMCID: PMC9648200 DOI: 10.3389/fcimb.2022.950531] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 09/26/2022] [Indexed: 07/25/2023] Open
Abstract
OBJECTIVES The aim of this study was to evaluate the diagnostic value of bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) versus conventional microbiological tests (CMTs) for pediatric pneumonia. METHODS This retrospective observational study enrolled 103 children who were diagnosed with pneumonia and hospitalized at Hubei Maternity and Child Health Care Hospital between 15 October 2020 and 15 February 2022. The pneumonia diagnosis was based on clinical manifestations, lung imaging, and microbiological tests. Pathogens in the lower respiratory tract were detected using CMTs and BALF mNGS (of DNA and RNA). The diagnostic performance of BALF mNGS was compared with that of CMTs. RESULTS In 96 patients, pathogens were identified by microbiological tests. The overall pathogen detection rate of mNGS was significantly higher than that of CMTs (91.3% vs. 59.2%, p = 0.000). The diagnostic performance of mNGS varied for different pathogens; however, its sensitivity and accuracy for diagnosing bacterial and viral infections were both higher than those of CMTs (p = 0.000). For the diagnosis of fungi, the sensitivity of mNGS (87.5%) was higher than that of CMTs (25%); however, its specificity and accuracy were lower than those of CMTs (p < 0.01). For the diagnosis of Mycoplasma pneumoniae, the specificity (98.8%) and accuracy (88.3%) of mNGS were high; however, its sensitivity (42.1%) was significantly lower than that of CMTs (100%) (p = 0.001). In 96 patients with definite pathogens, 52 cases (50.5%) were infected with a single pathogen, while 44 cases (42.7%) had polymicrobial infections. Virus-bacteria and virus-virus co-infections were the most common. Staphylococcus aureus, Haemophilus influenzae, rhinovirus, cytomegalovirus, parainfluenza virus, and fungi were more likely to be associated with polymicrobial infections. CONCLUSIONS BALF mNGS improved the detection rate of pediatric pneumonia, especially in mixed infections. The diagnostic performance of BALF mNGS varies according to pathogen type. mNGS can be used to supplement CMTs. A combination of mNGS and CMTs may be the best diagnostic strategy.
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Affiliation(s)
- Wenhua Deng
- Pediatric Respiratory Department, Maternal and Child Health Hospital of Hubei Province, Wuhan, China
| | - Huan Xu
- Department of Scientific Affairs, Vision Medicals Center for Infection Diseases, Guangzhou, China
| | - Yabin Wu
- Pediatric Respiratory Department, Maternal and Child Health Hospital of Hubei Province, Wuhan, China
| | - Jie Li
- Pediatric Respiratory Department, Maternal and Child Health Hospital of Hubei Province, Wuhan, China
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Wu D, Wang W, Xun Q, Wang H, Liu J, Zhong Z, Ouyang C, Yang Q. Metagenomic next-generation sequencing indicates more precise pathogens in patients with pulmonary infection: A retrospective study. Front Cell Infect Microbiol 2022; 12:977591. [PMID: 36275015 PMCID: PMC9585196 DOI: 10.3389/fcimb.2022.977591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 09/20/2022] [Indexed: 11/22/2022] Open
Abstract
Background Timely identification of causative pathogens is important for the diagnosis and treatment of pulmonary infections. Metagenomic next-generation sequencing (mNGS), a novel approach to pathogen detection, can directly sequence nucleic acids of specimens, providing a wide range of microbial profile. The purpose of this study was to evaluate the diagnostic performance of mNGS in the bronchoalveolar lavage fluid (BALF) of patients with suspected pulmonary infection. Methods From April 2019 to September 2021, 502 patients with suspected pneumonia, who underwent both mNGS of BALF and conventional microbiological tests (CMTs), were classified into different groups based on comorbidities. The diagnostic performances of mNGS and CMTs were compared. Comprehensive clinical analysis was used as the reference standard. Results The diagnostic accuracy and sensitivity of mNGS were 74.9% (95% confidence interval [CI], 71.7-78.7%) and 72.5% (95% CI, 68.2-76.8%) respectively, outperformed those of CMTs (36.9% diagnostic accuracy, 25.4% sensitivity). For most pathogens, the detection rate of mNGS was higher than that of CMTs. Polymicrobial infections most often occurred in immunocompromised patients (22.1%). Only 2.3% patients without underlying diseases developed polymicrobial infections. Additionally, the spectrums of pathogens also varied among the different groups. We found the positive predictive values (PPV) to be dependent upon both the pathogen of interest as well as the immunologic status of the patient (e.g., the PPV of Mycobacterium tuberculosis was 94.9% while the PPV of Pneumocystis jirovecii in immunocompetent individuals was 12.8%). This information can help physicians interpret mNGS results. Conclusion mNGS of BALF can greatly enhance the accuracy and detection rate of pathogens in patients with pulmonary infections. Moreover, the comorbidities and types of pathogens should be taken consideration when interpreting the results of mNGS.
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Affiliation(s)
- Dengfeng Wu
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Wei Wang
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Qiufen Xun
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Hongluan Wang
- Department of Respiratory and Critical Care Medicine, Jiangxi Provincial People’s Hospital, Nanchang, China
| | - Jiarong Liu
- Department of Nephrology Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Ziqing Zhong
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Chao Ouyang
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Qing Yang
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, China
- *Correspondence: Qing Yang,
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Liu L, Yuan M, Sun S, Wang J, Shi Y, Yu Y, Su X. The Performance of Metagenomic Next-Generation Sequence in the Diagnosis of Suspected Opportunistic Infections in Patients with Acquired Immunodeficiency Syndrome. Infect Drug Resist 2022; 15:5645-5653. [PMID: 36187731 PMCID: PMC9518679 DOI: 10.2147/idr.s378249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 08/29/2022] [Indexed: 11/23/2022] Open
Abstract
Background For acquired immunodeficiency syndrome (AIDS) patients with suspected opportunistic infections, the rapid and accurate identification of pathogens remains a challenge. Metagenomic next-generation sequencing (mNGS) has emerged as a pan-pathogen assay for infectious diseases diagnosis, but its guiding significance for diagnosis and antimicrobials treatment in AIDS patients with suspected opportunistic infections is still not well established. In this study, we compared the microbiological diagnostic value of mNGS with that of conventional microbiological tests (CMTs) in AIDS patients with suspected opportunistic infections. Methods From January 2018 to February 2021, a retrospective study was performed at four tertiary teaching hospitals in China and data of 86 AIDS patients with suspected opportunistic infections were collected. The pathogen detection performance of mNGS and CMTs were compared. Results Positive agreement between mNGS and clinical diagnosis was significantly higher than that of CMTs (65/86 (75.6%) vs 37/86 (43.0%)). In addition, mNGS identified more bacterial (25 vs 2), fungal (5 vs 3), viral (9 vs 2) organisms compared with CMTs. Mixed infection were detected in 34 patients by mNGS combined with CMTs. Viruses (94.1%, 32/34) and fungi (94.1%, 32/34) were commonly seen in the mixed infection cases. mNGS helped identify the pathogen or guide appropriate treatment in 49/86 (57%) patients. Meanwhile, CMTs also contributed in the decision of appropriate treatment in 28 patients. The successful de-escalation or discontinuation of treatment was supported in 37 patients with the help of mNGS. We observed a significant reduction in the number of patients being prescribed foscarnet (52.3% vs 23.26%, p < 0.001), moxifloxacin (34.9% vs 10.5%, p = 0.005), and levofloxacin (32.6% vs 14%, p = 0.001) before and after mNGS. Conclusion For AIDS patients with suspected opportunistic infections, mNGS can provide early, noninvasive, and rapid microbiological diagnosis. mNGS may lead to a more precise antimicrobial treatment and reduced the unreasonable use of antimicrobials.
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Affiliation(s)
- Li Liu
- Department of Respiratory and Critical Care Medicine, Jinling Hospital, The First School of Clinical Medicine, Southern Medical University, Nanjing, People’s Republic of China
- Department of Infectious Disease, Hunan Provincial People’s Hospital (The First Affiliated Hospital of Hunan Normal University), Changsha, Hunan Province, People’s Republic of China
| | - Mingjuan Yuan
- Department of Infectious Disease, The Central Hospital of Yueyang, Yueyang, Hunan Province, People’s Republic of China
| | - Siqing Sun
- Department of General Medicine, The Second Hospital of Nanjing, Nanjing Hospital of Nanjing University of Chinese Medicine, Nanjing, People’s Republic of China
| | - Jinrong Wang
- Department of Respiratory and Critical Care Medicine, Hengshui People’s hospital, Hengshui, Hebei Province, People’s Republic of China
| | - Yi Shi
- Department of Respiratory and Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, Nanjing, People’s Republic of China
| | - Yamin Yu
- Department of Nephrology, Ningxiang People’s Hospital, Changsha, Hunan Province, People’s Republic of China
| | - Xin Su
- Department of Respiratory and Critical Care Medicine, Jinling Hospital, The First School of Clinical Medicine, Southern Medical University, Nanjing, People’s Republic of China
- Department of Respiratory and Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, Nanjing, People’s Republic of China
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Zhang B, Gui R, Wang Q, Jiao X, Li Z, Wang J, Han L, Zhou L, Wang H, Wang X, Fan X, Lyu X, Song Y, Zhou J. Comparing the application of mNGS after combined pneumonia in hematologic patients receiving hematopoietic stem cell transplantation and chemotherapy: A retrospective analysis. Front Cell Infect Microbiol 2022; 12:969126. [PMID: 36211959 PMCID: PMC9532739 DOI: 10.3389/fcimb.2022.969126] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 08/31/2022] [Indexed: 11/13/2022] Open
Abstract
Rapid and accurate pathogen identification is essential for timely and effective treatment of pneumonia. Here, we describe the use of metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage (BALF) fluid to identify pathogens in patients with hematologic comorbid respiratory symptoms in a retrospective study with 84 patients. In the transplantation group, 8 cases (19.5%) and 47 cases (97.9%) were positive for BALF by conventional method detection and mNGS detection, respectively, and 6 cases (14.0%) and 41 cases (91.1%) in chemotherapy group, respectively. The detection rate of mNGS in both groups was significantly higher than that of conventional detection methods (all P<0.05). Pseudomonas aeruginosa and Streptococcus pneumoniae were the most common bacterial infections in the transplantation and chemotherapy groups, respectively. Aspergillus was the most common fungal infection in both groups. Human betaherpesvirus 5 (HHV-5), torque teno virus and human betaherpesvirus 7 (HHV-7) were the most common pathogen species in both groups. The most common type of infection in patients in the transplantation and chemotherapy groups was the mixed infection of bacteria-virus. Most patients in the transplantation group had mixed infections based on multiple viruses, with 42 cases of viral infections in the transplantation group and 30 cases of viral infections in the chemotherapy group, which were significantly higher in the transplantation group than in the chemotherapy group (χ2 = 5.766, P=0.016). and the mixed infection of virus-virus in the transplantation group was significantly higher than that in the chemotherapy group (27.1% vs 4.4%, P=0.003). The proportion of death due to pulmonary infection was significantly higher in the transplantation group than in the chemotherapy group (76.9% vs 16.7%, χ2 = 9.077, P=0.003). This study demonstrated the value of mNGS of BALF in improving the diagnosis and prognosis of hematologic comorbid pneumonia, helping patients to obtain timely and effective treatment, and giving guidance on the overall treatment plan for patients, with particular benefit for patients with hematologic chemotherapy comorbid pneumonia.
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Affiliation(s)
- Binglei Zhang
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
- School of Basic Medical Sciences, Academy of Medical Sciences, Henan Academy of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Ruirui Gui
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Qian Wang
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Xueli Jiao
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Zhen Li
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Juan Wang
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Lu Han
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Ling Zhou
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Huili Wang
- Department of Hematology, The Third People’s Hospital of Zhengzhou, Zhengzhou, China
| | - Xianjing Wang
- Department of Hematology, The Third People’s Hospital of Zhengzhou, Zhengzhou, China
| | - Xinxin Fan
- Department of Hematology, The Third People’s Hospital of Zhengzhou, Zhengzhou, China
| | - Xiaodong Lyu
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
- *Correspondence: Xiaodong Lyu, ; Yongping Song, ; Jian Zhou,
| | - Yongping Song
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
- *Correspondence: Xiaodong Lyu, ; Yongping Song, ; Jian Zhou,
| | - Jian Zhou
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
- *Correspondence: Xiaodong Lyu, ; Yongping Song, ; Jian Zhou,
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Cao XG, Zhou SS, Wang CY, Jin K, Meng HD. The diagnostic value of next-generation sequencing technology in sepsis. Front Cell Infect Microbiol 2022; 12:899508. [PMID: 36189371 PMCID: PMC9518011 DOI: 10.3389/fcimb.2022.899508] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 08/24/2022] [Indexed: 11/13/2022] Open
Abstract
ObjectiveThis study aims to assess the clinical utility of next-generation sequencing (NGS) in sepsis diagnosis.MethodsA prospective study was conducted on patients with a high suspicion of sepsis by unknown pathogens from January 2017 to December 2021. Blood samples were taken from patients to perform NGS, blood culture (BC), leucocyte (WBC), procalcitonin (PCT), creatinine (CREA), Albumin (ALB) and C-reactive protein (CRP) tests.ResultsThe feedback time for BC was 3~5 days for bacteria and 5~7 days for fungi, while the turnover time for NGS was only 24 h. The clinical diagnosis was considered the “gold standard”. 83 patients passed our inclusion criteria and were separated into two groups by clinical diagnosis. 62 met the clinical diagnosis criteria for sepsis and 21 were non-sepsis. The data from the two groups were retrospectively compared and analyzed. Of 62 sepsis in 83 patients, 8(9.64%) were diagnosed by both BC and NGS, 51 (61.45%) by NGS only, 1(1.20%) by BC and 2 (2.41%) by conventional testing only; PCT, CREA, CRP levels and the detection rate of NGS and BC were higher in the sepsis group than in the non-sepsis group, while ALB levels were lower (p<0.05). The logistic regression results in our study revealed that NGS and ALB were independent prediction factors for sepsis (p<0.05), the area under the receiver operating characteristic curve (AUC), sensitivity and specificity of NGS for diagnosing sepsis was 0.857, 95.16% and 76.19%, while ALB was 0.728, 58.06%, 80.95%, respectively. The combination’s sensitivity, specificity and AUC of NGS and ALB were 93.55%, 85.71% and 0.935, greater than that of Albumin or NGS only (both p<0.05).ConclusionNGS can effectively and quickly identify pathogens, thereby emerges as a promising technology for sepsis diagnosis. Combination of NGS and ALB can be used for early screening and is more powerful than NGS or ALB only.
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Affiliation(s)
- Xiao-guang Cao
- Department of Emergency Medical Center, the First Affiliated Hospital of University of Science and Technology of China (Anhui Provincial Hospital), Hefei, China
| | - Shu-sheng Zhou
- Department of Emergency Medical Center, the First Affiliated Hospital of University of Science and Technology of China (Anhui Provincial Hospital), Hefei, China
| | - Chun-yan Wang
- Department of Emergency Medical Center, the First Affiliated Hospital of University of Science and Technology of China (Anhui Provincial Hospital), Hefei, China
| | - Kui Jin
- Department of Emergency Medical Center, the First Affiliated Hospital of University of Science and Technology of China (Anhui Provincial Hospital), Hefei, China
| | - Hua-dong Meng
- Department of Emergency Intensive Care Unit (EICU), the third Affiliated Hospital of Anhui Medical University, (the First People’s Hospital of Hefei), Hefei, China
- *Correspondence: Hua-dong Meng,
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Jiao M, Ma X, Li Y, Wang H, Liu Y, Guo W, Lv J. Metagenomic next-generation sequencing provides prognostic warning by identifying mixed infections in nocardiosis. Front Cell Infect Microbiol 2022; 12:894678. [PMID: 36118026 PMCID: PMC9471186 DOI: 10.3389/fcimb.2022.894678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 08/16/2022] [Indexed: 11/23/2022] Open
Abstract
Nocardia is an opportunistic pathogen that mainly involves immunosuppressed patients and causes a high mortality rate. As an emerging approach to detect infectious pathogens, metagenomic next-generation sequencing (mNGS) was reported in the detection of Nocardia. However, there is no evidence demonstrating the effect of mNGS on the prognosis of Nocardia infection. In this retrospective study, we included 18 nocardiosis patients. Nocardia species were detected by mNGS from their clinical samples. All the patients were diagnosed with nocardiosis by clinical experts through a comprehensive evaluation. Of these 18 patients, fever is the most frequent initial symptom. Compared to traditional culture methods, mNGS provides a faster turnaround time (TAT) and higher sensitivity. Pulmonary nocardiosis was the most common clinical presentation in the study. mNGS detected 13 types of Nocardia species, of which Nocardia abscessus and Nocardia cyriacigeorgica were the most common species. The study’s most noteworthy discovery is that mNGS outperforms culture at detecting mixed infections (more than one pathogen detected in one clinical specimen, including bacteria, fungi, and excluding virus), and number of infectious species was an independent risk factor for nocardiosis patients’ prognostics after adjusting age, ICU days, gender and underlying diseases (adjusted HR = 1.47, 95% CI: 1.09-1.98, p = 0.011). As a result, we believe that by detecting mixed infections (more than one pathogenic species), mNGS can provide a clinical risk warning for the prognosis of nocardiosis.
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Affiliation(s)
- Mengfan Jiao
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Gene Hospital of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaoxu Ma
- Department of Respiration, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yaoguang Li
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Gene Hospital of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Huifen Wang
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Gene Hospital of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ying Liu
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Gene Hospital of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wenhu Guo
- R&D Center, Agene (Fuzhou) Medical Laboratory Co. Ltd., Fuzhou, China
| | - Jun Lv
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Jun Lv,
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Improving Suspected Pulmonary Infection Diagnosis by Bronchoalveolar Lavage Fluid Metagenomic Next-Generation Sequencing: a Multicenter Retrospective Study. Microbiol Spectr 2022; 10:e0247321. [PMID: 35943274 PMCID: PMC9431624 DOI: 10.1128/spectrum.02473-21] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Metagenomic next-generation sequencing (mNGS) has been gradually applied to clinical practice due to its unbiased characteristics of pathogen detection. However, its diagnostic performance and clinical value in suspected pulmonary infection need to be evaluated. We systematically reviewed the clinical data of 246 patients with suspected pulmonary infection from 4 medical institutions between January 2019 and September 2021. The diagnostic performances of mNGS and conventional testing (CT) were systematically analyzed based on bronchoalveolar lavage fluid (BALF). The impacts of mNGS and CT on diagnosis modification and treatment adjustment were also assessed. The positive rates of mNGS and CT were 47.97% and 23.17%, respectively. The sensitivity of mNGS was significantly higher than that of CT (53.49% versus 23.26%, P < 0.01), especially for infections of Mycobacterium tuberculosis (67.86% versus 17.86%, P < 0.01), atypical pathogens (100.00% versus 7.14%, P < 0.01), viruses (92.31% versus 7.69%, P < 0.01), and fungi (78.57% versus 39.29%, P < 0.01). The specificity of mNGS was superior to that of CT, with no statistical difference (90.32% versus 77.42%, P = 0.167). The positive predictive value (PPV) and negative predictive value (NPV) of mNGS were 97.46% and 21.88%, respectively. Diagnosis modification and treatment adjustment were conducted in 32 (32/246, 13.01%) and 23 (23/246, 9.35%) cases, respectively, according to mNGS results only. mNGS significantly improved the diagnosis of suspected pulmonary infection, especially infections of M.tuberculosis, atypical pathogens, viruses, and fungi, and it demonstrated the pathogen distribution of pulmonary infections. It is expected to be a promising microbiological detection and diagnostic method in clinical practice. IMPORTANCE Pulmonary infection is a heterogeneous and complex infectious disease with high morbidity and mortality worldwide. In clinical practice, a considerable proportion of the etiology of pulmonary infection is unclear, microbiological diagnosis being challenging. Metagenomic next-generation sequencing detects all nucleic acids in a sample in an unbiased manner, revealing the microbial community environment and organisms and improving the microbiological detection and diagnosis of infectious diseases in clinical settings. This study is the first multicenter, large-scale retrospective study based entirely on BALF for pathogen detection by mNGS, and it demonstrated the superior performance of mNGS for microbiological detection and diagnosis of suspected pulmonary infection, especially in infections of Mycobacterium tuberculosis, atypical pathogens, viruses, and fungi. It also demonstrated the pathogen distribution of pulmonary infections in the real world, guiding targeted treatment and improving clinical management and prognoses.
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Shi Y, Peng JM, Qin HY, Du B. Metagenomic next-generation sequencing: A promising tool for diagnosis and treatment of suspected pneumonia in rheumatic patients with acute respiratory failure: Retrospective cohort study. Front Cell Infect Microbiol 2022; 12:941930. [PMID: 35992169 PMCID: PMC9381725 DOI: 10.3389/fcimb.2022.941930] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/12/2022] [Indexed: 11/17/2022] Open
Abstract
Background The effectiveness of metagenomic next-generation sequencing (mNGS) in respiratory pathogen detection and clinical decision-making in critically rheumatic patients remains largely unexplored. Methods A single-center retrospective study of 58 rheumatic patients who were admitted to ICU due to suspected pneumonia with acute respiratory failure if they underwent both bronchoalveolar lavage fluid specimen mNGS and combined microbiological tests (CMTs) was conducted to compare their diagnostic performance, using clinical composite diagnosis as the gold standard. Treatment modifications based on mNGS results were also reviewed. Results Forty-three patients were diagnosed with microbiologically confirmed pneumonia and 15 were considered as a non-infectious disease. mNGS outperformed CMTs in the accurate diagnosis of infectious and non-infectious lung infiltration (98.1% [57/58] vs. 87.9% [51/58], P = 0.031). A total of 94 causative pathogens were defined by the gold standard and 27 patients had polymicrobial pneumonia. The sensitivity of pathogen detection and complete concordance with the gold standard by mNGS exceeded those by CMTs (92.6% [87/94] vs. 76.6% [72/94], P < 0.001 and 72.1% [31/43] vs. 51.2% [22/43], P = 0.004, respectively). Moreover, 22 pathogens were detected only by mNGS and confirmed by orthogonal test. Accordingly, the etiological diagnosis changed in 19 cases, and the empirical treatment improved in 14 cases, including 8 cases of rescue treatment and 11 of antibiotics de-escalation. At the pathogen-type level, both methods were comparable for bacteria, but mNGS was advantageous to identify viruses (accuracy: 100% vs. 81%, P = 0.004). For Pneumocystis jirovecii detection, mNGS improved the sensitivity compared with Gomori’s methenamine silver stain (91.7% vs. 4.2%, P < 0.001) and was higher than polymerase chain reaction (79.2%), but the difference was not significant (P = 0.289). In terms of Aspergillus, the better sensitivity with a combination of culture and galactomannan test than that with mNGS was found (100% vs. 66.7%, P = 0.033). Conclusions mNGS has an excellent accuracy in etiological diagnosis and pathogen detection of suspected pneumonia in critically rheumatic patients, which has potential significance for clinical decision-making. Its superiority to different types of pathogens depends on the comprehensiveness of CMTs.
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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: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [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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Utility of Metagenomic Next-Generation Sequencing for Etiological Diagnosis of Patients with Sepsis in Intensive Care Units. Microbiol Spectr 2022; 10:e0074622. [PMID: 35861525 PMCID: PMC9430677 DOI: 10.1128/spectrum.00746-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The performance of metagenomic next-generation sequencing (mNGS) was evaluated and compared with that of conventional culture testing in patients with sepsis. Prospective blood and bronchoalveolar lavage fluid (BALF) samples from 50 patients with sepsis were tested using cultures (bacterial, fungal, and viral) and mNGS of microbial DNA (blood and BALF) and RNA (BALF). mNGS had higher detection rates than blood culture (88.0% versus 26.0%, P < 0.001) and BALF culture (92.0% versus 76.0%, P = 0.054). RNA-based mNGS has increased the detection rate of several bacteria, fungi, and viruses, but not mycobacteria and Toxoplasma gondii. The number of multiple detections per specimen was higher in BALF (92.0%) than in blood (78.0%) samples, and the highest number of pathogens detected in a single specimen was 32. Among blood samples, compared to cultures, mNGS detected significantly more bacteria (P < 0.001), fungi (P = 0.012), and viruses (P < 0.001), whereas BALF mNGS had a higher detection rate for bacteria (P < 0.001) and viruses (P < 0.001). The percentage of mNGS-positive samples was significantly higher than that of culture-positive samples for several Gram-negative bacteria, some Gram-positive bacteria, and viruses, but not fungi. Mycobacteria had a higher detection rate by culture than by mNGS, but the difference was not significant due to the small sample size. The positive and negative agreements with 95% confidence intervals of mNGS and culture were 62.0% (50.4 to 72.7) and 96.8% (96.5 to 97.1), respectively. mNGS offers a sensitive diagnostic method for patients with sepsis and is promising for the detection of multipathogen infections. Clinical correlation is advised to interpret mNGS data due to the lack of unified diagnostic criteria. IMPORTANCE Delays in effective antimicrobial therapy have resulted in decreased survival rates among patients with sepsis. However, current culture-based diagnostic methods have low sensitivity because of concurrent antibiotic exposure and fastidious and atypical causative organisms. Among patients with sepsis, we showed that mNGS methods had higher positive rates than culture methods, especially for bacteria, viruses, and multipathogen infections, which are difficult to culture and detect in patients treated with antibiotics. RNA-based mNGS has increased the detection rate of several bacteria, fungi, and viruses, but not mycobacteria and Toxoplasma gondii. mNGS also showed a high negative percent agreement with cultures. However, the interpretation of mNGS data should be combined with clinical data and conventional methods considering the lack of unified diagnostic criteria.
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Guo W, Cui X, Wang Q, Wei Y, Guo Y, Zhang T, Zhan J. Clinical evaluation of metagenomic next-generation sequencing for detecting pathogens in bronchoalveolar lavage fluid collected from children with community-acquired pneumonia. Front Med (Lausanne) 2022; 9:952636. [PMID: 35911412 PMCID: PMC9334703 DOI: 10.3389/fmed.2022.952636] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 06/27/2022] [Indexed: 01/05/2023] Open
Abstract
This study is to evaluate the usefulness of pathogen detection using metagenomic next-generation sequencing (mNGS) on bronchoalveolar lavage fluid (BALF) specimens from children with community-acquired pneumonia (CAP). We retrospectively collected BALF specimens from 121 children with CAP at Tianjin Children's Hospital from February 2021 to December 2021. The diagnostic performances of mNGS and conventional tests (CT) (culture and targeted polymerase chain reaction tests) were compared, using composite diagnosis as the reference standard. The results of mNGS and CT were compared based on pathogenic and non-pathogenic organisms. Pathogen profiles and co-infections between the mild CAP and severe CAP groups were also analyzed. The overall positive coincidence rate was 86.78% (105/121) for mNGS and 66.94% (81/121) for CT. The proportion of patients diagnosed using mNGS plus CT increased to 99.18%. Among the patients, 17.36% were confirmed only by mNGS; Streptococcus pneumoniae accounted for 52.38% and 23.8% of the patients were co-infected. Moreover, Bordetella pertussis and Human bocavirus (HBoV) were detected only using mNGS. Mycoplasma pneumoniae, which was identified in 89 (73.55%) of 121 children with CAP, was the most frequent pathogen detected using mNGS. The infection rate of M. pneumoniae in the severe CAP group was significantly higher than that in the mild CAP group (P = 0.007). The symptoms of single bacterial infections (except for mycoplasma) were milder than those of mycoplasma infections. mNGS identified more bacterial infections when compared to the CT methods and was able to identify co-infections which were initially missed on CT. Additionally, it was able to identify pathogens that were beyond the scope of the CT methods. The mNGS method is a powerful supplement to clinical diagnostic tools in respiratory infections, as it can increase the precision of diagnosis and guide the use of antibiotics.
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Affiliation(s)
- Wei Guo
- Clinical School of Paediatrics, Tianjin Medical University, Tianjin, China
- Department of Respiratory Medicine, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China
| | - Xiaojian Cui
- Department of Clinical Lab, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China
| | - Qiushi Wang
- Infection Business Unit, Tianjin Novogene Med LAB Co., Ltd., Tianjin, China
| | - Yupeng Wei
- Department of Respiratory Medicine, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China
| | - Yanqing Guo
- Infection Business Unit, Tianjin Novogene Med LAB Co., Ltd., Tianjin, China
- *Correspondence: Yanqing Guo
| | - Tongqiang Zhang
- Clinical School of Paediatrics, Tianjin Medical University, Tianjin, China
- Department of Respiratory Medicine, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China
- Tongqiang Zhang
| | - Jianghua Zhan
- Clinical School of Paediatrics, Tianjin Medical University, Tianjin, China
- Department of Pediatric Surgery, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China
- Jianghua Zhan
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Zhao D, Guo L, Lian D, Gu Y, Yan X, Hu H, Yuan J. Diagnostic Value and Clinical Application of mNGS for Post-Liver Transplantation Infection: A Cross-Sectional Study With Case Reports. Front Microbiol 2022; 13:919363. [PMID: 35847093 PMCID: PMC9283086 DOI: 10.3389/fmicb.2022.919363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 05/24/2022] [Indexed: 02/05/2023] Open
Abstract
Liver transplantation is widely acknowledged as the only effective treatment for end-stage liver disease, and infection is reportedly an important cause of postoperative death. Clinical use of metagenomic next-generation sequencing (mNGS) to diagnose postoperative infection and successfully guide drug therapy remains rare. This study included patients with infectious complications after liver transplantation from July 2019 to December 2020 and was divided into three groups: pneumonia, unknown fever, and others (including hepatic failure, kidney failure, cirrhosis after LT, and other postoperative complications that predispose to infection). The mNGS sequencing was used to detect microorganisms, and the results were compared with traditional culture. We found that mNGS yielded improved sensitivity over culture (85.19 vs. 22.22%; p<0.0001) but lower specificity (35.71 vs. 89.28%; p<0.0001). Among the 48 kinds of pathogens detected, the Torque teno virus 22 (15/122) was the most common, followed by Primate erythroparvovirus 1 (13/122). The top four bacteria included Klebsiella pneumoniae (n = 8), Enterococcus faecium (n = 5), Stenotrophomonas maltophilia (n = 4), and Escherichia coli (n = 4). Aspergillus fumigatus was the most common fungus. The bronchoalveolar lavage fluid (BALF) exhibited the highest proportion of positive findings among sample types, with viral, fungal, and bacterial mixed infection being the most common (n = 6, 19.35%). Besides, using mNGS for early diagnosis of infection after liver transplantation may effectively prolong patient survival. This is the first study to explore the application value of mNGS and its comparison with traditional culture in pneumonia and other infections in post-liver transplantation patients. The simultaneous application of these two methods suggested that the Torque teno virus 22, Klebsiella pneumoniae, and the Aspergillus fumigatus are the most common pathogens of viruses, bacteria, and fungi after LT, suggesting that these pathogens may be associated with postoperative pathogen infection and patient prognosis. The mNGS technique showed distinct advantages in detecting mixed, viral, and parasitic infections in this patient population. Further studies are warranted to systematically elucidate the dynamic evolution and molecular characteristics of infection after liver transplantation.
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Affiliation(s)
- Dong Zhao
- Division of Liver Surgery and Organ Transplantation Center, Shenzhen Third People's Hospital, Second Affiliated Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Liping Guo
- Department for Infectious Diseases, Shenzhen Third People's Hospital, Second Affiliated Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Dongli Lian
- Department for Infectious Diseases, Shenzhen Third People's Hospital, Second Affiliated Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Yuchen Gu
- Department for Infectious Diseases, Shenzhen Third People's Hospital, Second Affiliated Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Xu Yan
- Division of Liver Surgery and Organ Transplantation Center, Shenzhen Third People's Hospital, Second Affiliated Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Hongxing Hu
- Department of Kidney Transplant, Shenzhen Third People's Hospital, Second Affiliated Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Jing Yuan
- Department for Infectious Diseases, Shenzhen Third People's Hospital, Second Affiliated Hospital, Southern University of Science and Technology, Shenzhen, China
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Yang T, Mei Q, Fang X, Zhu S, Wang Y, Li W, Pan A. Clinical Value of Metagenomics Next-Generation Sequencing in Bronchoalveolar Lavage Fluid for Patients with Severe Hospital-Acquired Pneumonia: A Nested Case–Control Study. Infect Drug Resist 2022; 15:1505-1514. [PMID: 35411157 PMCID: PMC8994607 DOI: 10.2147/idr.s356662] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 03/29/2022] [Indexed: 12/26/2022] Open
Abstract
Background Metagenomics next-generation sequencing (mNGS) is more efficient in identifying pathogens responsible for pneumonia. However, whether these patients ultimately benefit from this improvement remains unknown. Methods In this retrospective, nested, case–control study, patients with severe hospital-acquired pneumonia (HAP) who had undergone mNGS of bronchoalveolar lavage fluid while in our intensive care unit from March 2017 to December 2020 (n = 33) were matched in a ratio of 1 to 2 (n = 66) by sex, age, comorbidities, immune status, Acute Physiology and Chronic Health Evaluation II score, severity of pulmonary infection, and use of extracorporeal life support with patients who had undergone conventional microbiological testing only. The primary outcome was 90-day mortality; secondary outcomes being length of intensive care unit stay, duration of mechanical ventilation support, 7-day and 28-day mortality, and efficacy of treatment of pulmonary infection. Results In the CMT group, 17 patients (25.8%) had negative results, whereas only one (3.0%) had negative results in the mNGS group (P < 0.001). After receipt of microbiology results, antibiotics were altered in 23/33 patients (70.0%) in the mNGS group, but in only 29/66 (43.9%) in the CMT group (P = 0.016). Pulmonary infection-related findings improved in 20/33 patients (60.6%) in the mNGS group in the subsequent 7 days, but in only 25/66 (37.9%) in the CMT group (P = 0.032). However, the 28-day (33.3% vs 31.2%, P = 1.0) and 90-day (48.5% vs 45.5%, P = 0.78) mortality rates did not differ significantly between the two groups. These findings were supported by Cox-regression and Kaplan–Meier survival curve analyses. Conclusion mNGS is helpful in the treatment of severe HAP but does not improve medium or long-term survival rates, especially in patients with severe comorbidities.
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Affiliation(s)
- Tianjun Yang
- Department of Intensive Care Unit, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, Anhui Province, 230001, People’s Republic of China
- Department of Intensive Care Unit, The Affiliated Provincial Hospital of Anhui Medical University, Hefei, Anhui Province, 230001, People’s Republic of China
| | - Qing Mei
- Department of Intensive Care Unit, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, Anhui Province, 230001, People’s Republic of China
- Department of Intensive Care Unit, The Affiliated Provincial Hospital of Anhui Medical University, Hefei, Anhui Province, 230001, People’s Republic of China
| | - Xiaowei Fang
- Department of Intensive Care Unit, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, Anhui Province, 230001, People’s Republic of China
- Department of Intensive Care Unit, The Affiliated Provincial Hospital of Anhui Medical University, Hefei, Anhui Province, 230001, People’s Republic of China
| | - Shoujun Zhu
- Department of Intensive Care Unit, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, Anhui Province, 230001, People’s Republic of China
- Department of Intensive Care Unit, The Affiliated Provincial Hospital of Anhui Medical University, Hefei, Anhui Province, 230001, People’s Republic of China
| | - Yinzhong Wang
- Department of Intensive Care Unit, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, Anhui Province, 230001, People’s Republic of China
- Department of Intensive Care Unit, The Affiliated Provincial Hospital of Anhui Medical University, Hefei, Anhui Province, 230001, People’s Republic of China
| | - Wanli Li
- Department of Intensive Care Unit, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, Anhui Province, 230001, People’s Republic of China
- Department of Intensive Care Unit, The Affiliated Provincial Hospital of Anhui Medical University, Hefei, Anhui Province, 230001, People’s Republic of China
| | - Aijun Pan
- Department of Intensive Care Unit, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, Anhui Province, 230001, People’s Republic of China
- Department of Intensive Care Unit, The Affiliated Provincial Hospital of Anhui Medical University, Hefei, Anhui Province, 230001, People’s Republic of China
- Correspondence: Aijun Pan; Qing Mei, Department of Intensive Care Unit, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, No. 17, Lu Jiang Road, Hefei, Anhui Province, 230001, People’s Republic of China, Fax +86-551-62283114, Email ;
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Zhang J, Liu MH, Gao X, Dong C, Li YX. Vedolizumab-associated diffuse interstitial lung disease in patients with ulcerative colitis: A case report. World J Clin Cases 2022; 10:1716-1722. [PMID: 35211614 PMCID: PMC8855246 DOI: 10.12998/wjcc.v10.i5.1716] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/18/2021] [Accepted: 01/05/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Vedolizumab, a newer class of integrin antagonist biological agents, has been applied to treat patients with moderate-to-severe Crohn’s disease (CD) and ulcerative colitis (UC), especially for patients who are refractory to traditional therapies and tumor necrosis factor antagonists. However, some rare but life-threatening adverse effects warrant pharmacovigilance. We describe the first fatal case of vedolizumab-associated severe diffuse interstitial lung disease in China.
CASE SUMMARY We present a case of new-onset diffuse parenchymal lung disease developing under treatment with vedolizumab in a patient with UC. After two doses of vedolizumab, he developed persistent fever and progressively worsening dyspnea. Extensive workups, including bronchoalveolar lavage, transbronchial lung biopsy and metagenomic next-generation sequencing, identified no infectious causes, and other potential causes (such as tumors and cardiogenic pulmonary edema) were also excluded. As a result, a diagnosis of vedolizumab-related interstitial lung disease was established. Unfortunately, although corticosteroids and empiric antibiotics were administered, the patient eventually died of respiratory failure.
CONCLUSION Vedolizumab-related interstitial lung disease in patients with UC is rare but potentially lethal. Gastroenterologists and pulmonologists should be aware of vedolizumab-related adverse drug reactions.
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Affiliation(s)
- Jie Zhang
- Department of Pulmonary and Critical Care Medicine, First Affiliated Hospital of Dalian Medical University, Dalian 116011, Liaoning Province, China
| | - Mei-Hong Liu
- Department of Pulmonary and Critical Care Medicine, First Affiliated Hospital of Dalian Medical University, Dalian 116011, Liaoning Province, China
| | - Xue Gao
- Department of Pathology, First Affiliated Hospital of Dalian Medical University, Dalian 116011, Liaoning Province, China
| | - Chang Dong
- Department of Pulmonary and Critical Care Medicine, First Affiliated Hospital of Dalian Medical University, Dalian 116011, Liaoning Province, China
| | - Yan-Xia Li
- Department of Pulmonary and Critical Care Medicine, First Affiliated Hospital of Dalian Medical University, Dalian 116011, Liaoning Province, China
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Shao J, Hassouna A, Wang Y, Zhang R, Zhen L, Li R, Chen M, Liu C, Wang X, Zhang M, Wang P, Yuan S, Chen J, Lu J. Next-generation sequencing as an advanced supplementary tool for the diagnosis of pathogens in lower respiratory tract infections: An observational trial in Xi'an, China. Biomed Rep 2021; 16:14. [PMID: 35070298 PMCID: PMC8764650 DOI: 10.3892/br.2021.1497] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/07/2021] [Indexed: 11/06/2022] Open
Abstract
The application of next-generation sequencing (NGS) in routine clinical analysis is still limited. The significance of NGS in the identification of pathogens of lower respiratory tract infection should be assessed as part of routine clinical bacterial examinations and chest imaging results. In the present study, the alveolar lavage fluid samples of 30 patients (25 males and 5 females, aged 19-92 years old, with a median age of 62) were examined by routine bacterial culture and NGS, and the results of pathogen detection and identification were compared. Chest imaging showed consolidation in all 30 patients (100%), and pleural effusion in 13 of the 30 patients (43.33%). The routine bacterial culture of the lavage solution was only positive in 14 of the 30 patients (46.6%), and negative in 16 patients (53.33%). However, the positive rate of NGS test results of the lavage fluid was 100%. A total of 12 cases (40%) were completely consistent with the routine bacterial culture test, with 56 other pathogens of mixed infection detected, accounting for the short comings of the routine bacterial examination. Although NGS cannot distinguish between live and dead bacteria, it is still a useful detection technology for accurate diagnosis of clinical infectious diseases. It is worthy of adaptation in the clinic for more effective clinical management and treatment of the lower respiratory airway infection in addition to the routine bacterial culture testing.
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Affiliation(s)
- Jie Shao
- Norinco 521 Hospital, Xi'an, Shaanxi 710065, P.R. China
| | - Amira Hassouna
- School of Public Health and Interdisciplinary Studies, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland 0622, New Zealand
| | - Yaqin Wang
- Norinco 521 Hospital, Xi'an, Shaanxi 710065, P.R. China
| | - Ruirui Zhang
- Norinco 521 Hospital, Xi'an, Shaanxi 710065, P.R. China
| | - Lifang Zhen
- Norinco 521 Hospital, Xi'an, Shaanxi 710065, P.R. China
| | - Ruidan Li
- Norinco 521 Hospital, Xi'an, Shaanxi 710065, P.R. China
| | - Mingli Chen
- Norinco 521 Hospital, Xi'an, Shaanxi 710065, P.R. China
| | - Chengjie Liu
- Norinco 521 Hospital, Xi'an, Shaanxi 710065, P.R. China
| | - Xiangye Wang
- Norinco 521 Hospital, Xi'an, Shaanxi 710065, P.R. China
| | | | - Peng Wang
- Norinco 521 Hospital, Xi'an, Shaanxi 710065, P.R. China
| | - Shenghua Yuan
- Norinco 521 Hospital, Xi'an, Shaanxi 710065, P.R. China
| | - Jie Chen
- Guangzhou Sagene Biotech Co., Ltd., Guangzhou, Guangdong 510320, P.R. China
| | - Jun Lu
- School of Public Health and Interdisciplinary Studies, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland 0622, New Zealand
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Fromentin M, Ricard JD, Roux D. Lung Microbiome in Critically Ill Patients. Life (Basel) 2021; 12:life12010007. [PMID: 35054400 PMCID: PMC8778861 DOI: 10.3390/life12010007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/16/2021] [Accepted: 12/17/2021] [Indexed: 12/11/2022] Open
Abstract
The historical hypothesis of sterility of the lungs was invalidated over a decade ago when studies demonstrated the existence of sparse but very diverse bacterial populations in the normal lung and the association between pulmonary dysbiosis and chronic respiratory diseases. Under mechanical ventilation, dysbiosis occurs rapidly with a gradual decline in diversity over time and the progressive predominance of a bacterial pathogen (mainly Proteobacteria) when lung infection occurs. During acute respiratory distress syndrome, an enrichment in bacteria of intestinal origin, mainly Enterobacteriaceae, is observed. However, the role of this dysbiosis in the pathogenesis of ventilator-associated pneumonia and acute respiratory distress syndrome is not yet fully understood. The lack of exploration of other microbial populations, viruses (eukaryotes and prokaryotes) and fungi is a key issue. Further analysis of the interaction between these microbial kingdoms and a better understanding of the host−microbiome interaction are necessary to fully elucidate the role of the microbiome in the pathogenicity of acute diseases. The validation of a consensual and robust methodology in order to make the comparison of the different studies relevant is also required. Filling these different gaps should help develop preventive and therapeutic strategies for both acute respiratory distress syndrome and ventilator-associated pneumonia.
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Affiliation(s)
- Mélanie Fromentin
- Anesthesiology and Intensive Care Department, AP-HP, Hôpital Cochin, 75014 Paris, France;
- UMR1137 IAME, Université de Paris, INSERM, 75018 Paris, France;
| | - Jean-Damien Ricard
- UMR1137 IAME, Université de Paris, INSERM, 75018 Paris, France;
- Médecine Intensive Réanimation, AP-HP, Hôpital Louis Mourier, DMU ESPRIT, 92700 Colombes, France
| | - Damien Roux
- Médecine Intensive Réanimation, AP-HP, Hôpital Louis Mourier, DMU ESPRIT, 92700 Colombes, France
- Institut Necker-Enfants Malades, Université de Paris, INSERM U1151, CNRS UMR 8253, 75015 Paris, France
- Correspondence: ; Tel.: +33-1-47-60-63-29
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The Application of Metagenomic Next-Generation Sequencing in Detection of Pathogen in Bronchoalveolar Lavage Fluid and Sputum Samples of Patients with Pulmonary Infection. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2021; 2021:7238495. [PMID: 34790254 PMCID: PMC8592753 DOI: 10.1155/2021/7238495] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/12/2021] [Accepted: 10/23/2021] [Indexed: 11/17/2022]
Abstract
Objective To uncover the application value of metagenomic next-generation sequencing (mNGS) in the detection of pathogen in bronchoalveolar lavage fluid (BALF) and sputum samples. Methods Totally, 32 patients with pulmonary infection were included. Pathogens in BALF and sputum samples were tested simultaneously by routine microbial culture and mNGS. Main infected pathogens (bacteria, fungi, and viruses) and their distribution in BALF and sputum samples were analyzed. Moreover, the diagnostic performance of mNGS in paired BALF and sputum samples was assessed. Results The pathogen culture results were positive in 9 patients and negative in 13 patients. No statistical differences were recorded on the sensitivity (78.94% vs. 63.15%, p = 0.283) and specificity (62.50% vs. 75.00%, p = 0.375) of mNGS diagnosis in bacteria and fungus in two types of samples. As shown in mNGS detection, 10 patients' two samples were both positive, 13 patients' two samples were both negative, 7 patients were only positive in BALF samples, and 2 patients' sputum samples were positive. Main viruses mNGS detected were EB virus, human adenovirus 5, herpes simplex virus type 1, and human cytomegalovirus. Kappa consensus analysis indicated that mNGS showed significant consistency in detecting pathogens in two samples, no matter bacteria (p < 0.001), fungi (p = 0.026), or viruses (p = 0.008). Conclusion mNGS showed no statistical differences in sensitivity and specificity of pathogen detection in BALF and sputum samples. Under certain conditions, sputum samples might be more suitable for pathogen detection because of invasiveness of BALF samples.
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Wang S, Xia D, Wu J, Jia D, Li L, Xu S. Severe Pneumonia Caused by Infection With Tropheryma whipplei Complicated With Acinetobacter baumannii Infection: A Case Report Involving a Young Woman. Front Public Health 2021; 9:729595. [PMID: 34760862 PMCID: PMC8575073 DOI: 10.3389/fpubh.2021.729595] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 09/29/2021] [Indexed: 11/13/2022] Open
Abstract
Whipple's disease is a very rare systemic infectious disease, and very few cases have been reported. However, it can be fatal if not diagnosed and treated appropriately. The major clinical manifestations of this disease are usually digestive and nervous system symptoms. The majority of patients are male and between 40 and 50 years old. Although respiratory symptoms of this disease have rarely been reported, they pose a serious threat to the lives of the patients, especially when they progress to severe pneumonia. During admission to the hospital, Acinetobacter baumannii infection makes treatment more difficult. While most patients are middle-aged men, more attention should be given to the diagnosis and treatment of affected young women. To our knowledge, the case presented in the study is the first case of Tropheryma whipplei infection that resulted in severe pneumonia and was complicated by A. baumannii infection during treatment. We hope that our study can serve as a reference for the diagnosis and treatment of related cases in the future.
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Affiliation(s)
- Sheng Wang
- Department of Emergency, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Demeng Xia
- Department of Emergency, Changhai Hospital, Naval Medical University, Shanghai, China.,Health Clinic, Liberation Army Unit 91666, Zhoushan, China
| | - Jianghong Wu
- Department of Emergency, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Dandan Jia
- Department of Emergency, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Lei Li
- Department of Emergency, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Shuogui Xu
- Department of Emergency, Changhai Hospital, Naval Medical University, Shanghai, China
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Huang C, Chen H, Ding Y, Ma X, Zhu H, Zhang S, Du W, Summah HD, Shi G, Feng Y. A Microbial World: Could Metagenomic Next-Generation Sequencing Be Involved in Acute Respiratory Failure? Front Cell Infect Microbiol 2021; 11:738074. [PMID: 34671569 PMCID: PMC8522648 DOI: 10.3389/fcimb.2021.738074] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 09/10/2021] [Indexed: 11/13/2022] Open
Abstract
Background The usefulness of metagenomic next-generation sequencing (mNGS) in identifying pathogens is being investigated. We aimed to compare the power of microbial identification between mNGS and various methods in patients with acute respiratory failure. Methods We reviewed 130 patients with respiratory failure, and 184 specimens including blood, bronchoalveolar lavage fluid (BALF), sputum, pleural effusion, ascitic fluid, and urine were tested by mNGS and conventional methods (culture, PCR). We also enrolled 13 patients to evaluate the power of mNGS and pathogen targets NGS (ptNGS) in microbial identifications. Clinical features and microbes detected were analyzed. Results mNGS outperformed the conventional method in the positive detection rate of Mycobacterium tuberculosis (MTB) (OR, ∞; 95% CI, 1–∞; P < 0.05), bacteria (OR, 3.7; 95% CI, 2.4–5.8; P < 0.0001), fungi (OR, 4.37; 95% CI, 2.7–7.2; P < 0.0001), mycoplasma (OR, 10.5; 95% CI, 31.8–115; P = 0.005), and virus (OR, ∞; 95% CI, 180.7–∞; P < 0.0001). We showed that 20 patients (28 samples) were detected with Pneumocystis jirovecii (P. jirovecii) by mNGS, but not by the conventional method, and most of those patients were immunocompromised. Read numbers of Klebsiella pneumoniae (K. pneumoniae), Acinetobacter baumannii (A. baumannii), Pseudomonas aeruginosa (P. aeruginosa), P. jirovecii, cytomegalovirus (CMV), and Herpes simplex virus 1 (HSV1) in BALF were higher than those in other sample types, and the read number of Candida albicans (C. albicans) in blood was higher than that in BALF. We found that orotracheal intubation and type 2 diabetes mellitus (T2DM) were associated with a higher detection rate of bacteria and virus by mNGS, immunosuppression was associated with a higher detection rate of fungi and virus by mNGS, and inflammatory markers were associated with mNGS-positive detection rate of bacteria. In addition, we observed preliminary results of ptNGS. Conclusion mNGS outperformed the conventional method in the detection of MTB, bacteria, fungi, mycoplasma, and virus. Orotracheal intubation, T2DM, immunosuppression, and inflammatory markers were associated with a higher detection rate of bacteria, fungi, and virus by mNGS. In addition, ptNGS results were consistent with the detection of abundant bacteria, fungi, and mycoplasma in our specimens.
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Affiliation(s)
- Chunrong Huang
- Department of Respiratory and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Ruijin Hospital, Shanghai, China
| | - Hong Chen
- Department of Respiratory and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Ruijin Hospital, Shanghai, China
| | - Yongjie Ding
- Department of Respiratory and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Ruijin Hospital, Shanghai, China
| | - Xiaolong Ma
- Department of Respiratory and Critical Care Medicine, The First Hospital of Jiaxing, Jiaxing, China
| | - Haixing Zhu
- Department of Respiratory and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Ruijin Hospital, Shanghai, China
| | - Shengxiong Zhang
- Department of Respiratory and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Ruijin Hospital, Shanghai, China
| | - Wei Du
- Department of Respiratory and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Ruijin Hospital, Shanghai, China
| | - Hanssa Dwarka Summah
- Department of Respiratory and Critical Care Medicine, Poudre D'Or Chest Hospital, Rivière du Rempart, Mauritius
| | - Guochao Shi
- Department of Respiratory and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Ruijin Hospital, Shanghai, China
| | - Yun Feng
- Department of Respiratory and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Ruijin Hospital, Shanghai, China
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Zheng Y, Qiu X, Wang T, Zhang J. The Diagnostic Value of Metagenomic Next-Generation Sequencing in Lower Respiratory Tract Infection. Front Cell Infect Microbiol 2021; 11:694756. [PMID: 34568089 PMCID: PMC8458627 DOI: 10.3389/fcimb.2021.694756] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 08/24/2021] [Indexed: 01/04/2023] Open
Abstract
Lower respiratory tract infections are associated with high morbidity and mortality and significant clinical harm. Due to the limited ability of traditional pathogen detection methods, anti-infective therapy is mostly empirical. Therefore, it is difficult to adopt targeted drug therapy. In recent years, metagenomic next-generation sequencing (mNGS) technology has provided a promising means for pathogen-specific diagnosis and updated the diagnostic strategy for lower respiratory tract infections. This article reviews the diagnostic value of mNGS for lower respiratory tract infections, the impact of different sampling methods on the detection efficiency of mNGS, and current technical difficulties in the clinical application of mNGS.
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Affiliation(s)
- Yan Zheng
- Department of Respiratory and Critical Care, Beijing Tian Tan Hospital, Capital Medical University, Beijing, China
| | - Xiaojian Qiu
- Department of Respiratory and Critical Care, Beijing Tian Tan Hospital, Capital Medical University, Beijing, China
| | - Ting Wang
- Department of Respiratory and Critical Care, Beijing Tian Tan Hospital, Capital Medical University, Beijing, China
| | - Jie Zhang
- Department of Respiratory and Critical Care, Beijing Tian Tan Hospital, Capital Medical University, Beijing, China
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45
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Tsang CC, Teng JLL, Lau SKP, Woo PCY. Rapid Genomic Diagnosis of Fungal Infections in the Age of Next-Generation Sequencing. J Fungi (Basel) 2021; 7:jof7080636. [PMID: 34436175 PMCID: PMC8398552 DOI: 10.3390/jof7080636] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 07/27/2021] [Accepted: 07/30/2021] [Indexed: 11/16/2022] Open
Abstract
Next-generation sequencing (NGS) technologies have recently developed beyond the research realm and started to mature into clinical applications. Here, we review the current use of NGS for laboratory diagnosis of fungal infections. Since the first reported case in 2014, >300 cases of fungal infections diagnosed by NGS were described. Pneumocystis jirovecii is the predominant fungus reported, constituting ~25% of the fungi detected. In ~12.5% of the cases, more than one fungus was detected by NGS. For P. jirovecii infections diagnosed by NGS, all 91 patients suffered from pneumonia and only 1 was HIV-positive. This is very different from the general epidemiology of P. jirovecii infections, of which HIV infection is the most important risk factor. The epidemiology of Talaromyces marneffei infection diagnosed by NGS is also different from its general epidemiology, in that only 3/11 patients were HIV-positive. The major advantage of using NGS for laboratory diagnosis is that it can pick up all pathogens, particularly when initial microbiological investigations are unfruitful. When the cost of NGS is further reduced, expertise more widely available and other obstacles overcome, NGS would be a useful tool for laboratory diagnosis of fungal infections, particularly for difficult-to-grow fungi and cases with low fungal loads.
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46
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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: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [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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47
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Al-Omari B, McMeekin P, Allen AJ, Akram AR, Graziadio S, Suklan J, Jones WS, Lendrem BC, Winter A, Cullinan M, Gray J, Dhaliwal K, Walsh TS, Craven TH. Systematic review of studies investigating ventilator associated pneumonia diagnostics in intensive care. BMC Pulm Med 2021; 21:196. [PMID: 34107929 PMCID: PMC8189711 DOI: 10.1186/s12890-021-01560-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 06/02/2021] [Indexed: 02/06/2023] Open
Abstract
Background Ventilator-associated pneumonia (VAP) is an important diagnosis in critical care. VAP research is complicated by the lack of agreed diagnostic criteria and reference standard test criteria. Our aim was to review which reference standard tests are used to evaluate novel index tests for suspected VAP. Methods We conducted a comprehensive search using electronic databases and hand reference checks. The Cochrane Library, MEDLINE, CINHAL, EMBASE, and web of science were searched from 2008 until November 2018. All terms related to VAP diagnostics in the intensive treatment unit were used to conduct the search. We adopted a checklist from the critical appraisal skills programme checklist for diagnostic studies to assess the quality of the included studies. Results We identified 2441 records, of which 178 were selected for full-text review. Following methodological examination and quality assessment, 44 studies were included in narrative data synthesis. Thirty-two (72.7%) studies utilised a sole microbiological reference standard; the remaining 12 studies utilised a composite reference standard, nine of which included a mandatory microbiological criterion. Histopathological criteria were optional in four studies but mandatory in none. Conclusions Nearly all reference standards for VAP used in diagnostic test research required some microbiological confirmation of infection, with BAL culture being the most common reference standard used. Supplementary Information The online version contains supplementary material available at 10.1186/s12890-021-01560-0.
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Affiliation(s)
- Basem Al-Omari
- College of Medicine and Health Sciences, Khalifa University, PO Box 127788, Abu Dhabi, UAE. .,Translational Healthcare Technologies Group, Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK.
| | - Peter McMeekin
- School of Health and Life Science, University of Northumbria, Newcastle upon Tyne, UK
| | - A Joy Allen
- NIHR Newcastle In Vitro Diagnostics Co-operative, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Ahsan R Akram
- Translational Healthcare Technologies Group, Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Sara Graziadio
- NIHR Newcastle In Vitro Diagnostics Co-operative, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK.,York Health Economics Consortium, Enterprise House, Innovation Way, University of York, York, UK
| | - Jana Suklan
- NIHR Newcastle In Vitro Diagnostics Co-operative, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - William S Jones
- NIHR Newcastle In Vitro Diagnostics Co-operative, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - B Clare Lendrem
- NIHR Newcastle In Vitro Diagnostics Co-operative, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Amanda Winter
- NIHR Newcastle In Vitro Diagnostics Co-operative, The Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Milo Cullinan
- Laboratory Medicine, Newcastle-Upon-Tyne Hospitals Foundation Trust, Newcastle upon Tyne, UK
| | - Joanne Gray
- School of Health and Life Science, University of Northumbria, Newcastle upon Tyne, UK
| | - Kevin Dhaliwal
- Translational Healthcare Technologies Group, Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Timothy S Walsh
- Edinburgh Critical Care Research Group, University of Edinburgh, Edinburgh, UK
| | - Thomas H Craven
- Translational Healthcare Technologies Group, Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK.,Edinburgh Critical Care Research Group, University of Edinburgh, Edinburgh, UK
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48
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Li F, Wang Y, Zhang Y, Shi P, Cao L, Su L, Zhu Q, Wang L, Lu R, Tan W, Shen J. Etiology of Severe Pneumonia in Children in Alveolar Lavage Fluid Using a High-Throughput Gene Targeted Amplicon Sequencing Assay. Front Pediatr 2021; 9:659164. [PMID: 34249808 PMCID: PMC8267249 DOI: 10.3389/fped.2021.659164] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/26/2021] [Indexed: 12/18/2022] Open
Abstract
Objective: To evaluate the diagnostic value of a high-throughput gene targeted amplicon sequencing (TAS) assay for detecting pathogenic microorganisms in alveolar lavage fluid (ALF) from children with severe community-acquired pneumonia (SCAP). Methods: A retrospective study was performed on 48 frozen ALF samples from 47 severe pneumonia cases admitted to Children's Hospital of Fudan University from January 1, 2019, to March 31, 2019. All samples were tested by a multiplex PCR (Multi-PCR) assay and a TAS assay. The results of the TAS panels were parallel compared with Multi-PCR and Conventional Tests (CT) including culture, direct fluorescent antibody method (DFA), and singleplex polymerase chain reaction (PCR). Results: The proportion of pathogens detection by CT was 81.2% (39/48). The 8 common respiratory viruses including respiratory syncytial virus (RSV), adenovirus (ADV), influenza A virus (FLUA), influenza B virus (FLUB), parainfluenza virus 1-3 (PIV1-3), and human Metapneumovirus (hMPV) were found in 31.2% (15/48) of the 48 samples by DFA. With the criteria of CT results used as "Golden Standard" for determing of TAS results, the proportion of pathogens detection by TAS was 70.8% (34/48). The difference of proportion of pathogens detection between TAS and CT was not statistically significant (p = 0.232). The sensitivity and specificity of TAS for pathogens detection based on CT were 87.1% (95% CI, 71.77-95.18%) and 100.0% (95% CI, 62.88-100%), the positive predictive value (PPV) and negative predictive value (NPV) were 100.0% (95% CI, 87.35-100%) and 64.2% (95% CI, 35.62-86.02%), respectively. While Multi-PCR results were used as "Golden Standard," the total pathogens detection rate of TAS was 83.3% (40/48), which had a significant difference with that of Multi-PCR (p = 0.003). The sensitivity and PPV of TAS compared with Multi-PCR were 83.3% (95% CI, 69.23-92.03%) and 100.0% (95% CI, 89.08-100%), respectively. High rates of co-infection were proved by CT, Multi-PCR, and TAS. Mycoplasma pneumoniae (MP) and ADV were the two most frequently detected pathogens in all three assays. Conclusion: Compared with the CT and Multi-PCR methods, this TAS assay had a good performance in detecting bacteriological and viral pathogens from ALF. More research is needed to establish interpretation criteria based on TAS reads or analysis platforms.
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Affiliation(s)
- Fei Li
- Infectious Disease Department, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Yin Wang
- Clinical Trial Unit, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Yuhan Zhang
- Infectious Disease Department, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Peng Shi
- Statistics and Data Management Center, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Linfeng Cao
- Virology Department, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - LiYun Su
- Virology Department, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Qiguo Zhu
- Respiratory Department, Children's Hospital Xiamen Branch, Xiamen, China
| | - Libo Wang
- Respiratory Department, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Roujian Lu
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Wenjie Tan
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Jun Shen
- Infectious Disease Department, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
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