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Lin C, Bonsu AAFK, Li J, Ning C, Chen L, Zhu S, Zhong Q, Shen D, Huang G. Application of metagenomic next-generation sequencing for suspected infected pancreatic necrosis. Pancreatology 2022; 22:864-870. [PMID: 35864066 DOI: 10.1016/j.pan.2022.07.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 07/06/2022] [Accepted: 07/11/2022] [Indexed: 12/11/2022]
Abstract
BACKGROUND Metagenomic next-generation sequencing (mNGS) is increasingly used for the clinical diagnosis of infectious diseases, but there is a paucity of data regarding the application of mNGS in the early diagnosis of infected pancreatic necrosis (IPN). OBJECTIVE To investigate the clinical application value of mNGS in the pathogenic diagnosis of IPN. METHODS Forty-two patients with suspected IPN were prospectively and consecutively enrolled from August 2019 to August 2021. Blood samples were collected for mNGS and microbial culture simultaneously during fever (T ≥ 38.5 °C). For patients who had indications of surgical interventions, peri-pancreatic specimens were collected for mNGS and microbial culture simultaneously during the first surgical intervention to confirm IPN. The clinical performance of mNGS and microbial culture were compared. RESULTS A total of 21 patients (50.0%) were confirmed to have IPN during hospitalization. The sensitivity of blood mNGS was significantly higher than blood culture (95.2% vs. 23.8%, P < 0.001) in diagnosing IPN. The negative predictive value of blood mNGS was 90.0%. The turnaround time of mNGS was significantly shorter than that of microbial culture [(37.70 ± 1.44) vs. (115.23 ± 8.79) h, P < 0.01] and the average costs of mNGS accounted for 1.7% of the average total cost of hospitalization. The survival analysis demonstrates that the positive blood mNGS result was not associated with increased mortality (P = 0.119). CONCLUSIONS With more valuable diagnostic performance and shorter turnaround time, clinical mNGS represents a potential step forward in the early diagnosis of IPN.
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Affiliation(s)
- Chiayen Lin
- Department of Pancreatic Surgery, General Surgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan Province, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan Province, China
| | - Abdul Aziz F K Bonsu
- Department of Pancreatic Surgery, General Surgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan Province, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan Province, China
| | - Jiarong Li
- Department of Pancreatic Surgery, General Surgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan Province, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan Province, China
| | - Caihong Ning
- Department of Pancreatic Surgery, General Surgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan Province, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan Province, China
| | - Lu Chen
- Department of Pancreatic Surgery, General Surgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan Province, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan Province, China
| | - Shuai Zhu
- Department of Pancreatic Surgery, General Surgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan Province, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan Province, China
| | - Qiaoqing Zhong
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan Province, China; Department of Cardiovascular Medicine, Xiangya Hospital, Central South University, Changsha, 410008, Hunan Province, China
| | - Dingcheng Shen
- Department of Pancreatic Surgery, General Surgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan Province, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan Province, China.
| | - Gengwen Huang
- Department of Pancreatic Surgery, General Surgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan Province, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan Province, China.
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Zhang Y, Chen J, Yi X, Chen Z, Yao T, Tang Z, Zang G, Cao X, Lian X, Chen X. Evaluation of the metagenomic next-generation sequencing performance in pathogenic detection in patients with spinal infection. Front Cell Infect Microbiol 2022; 12:967584. [PMID: 36389162 PMCID: PMC9646980 DOI: 10.3389/fcimb.2022.967584] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 10/03/2022] [Indexed: 12/01/2023] Open
Abstract
Spinal infection is a rarely occurred pathology, whose diagnosis remains a major challenge due to the low sensitivity of culturing techniques. Metagenomic next-generation sequencing (mNGS) is a novel approach to identify the pathogenic organisms in infectious diseases. In this study, mNGS technology was adopted for pathogenic detection in spinal infection from the tissue and pus samples. Additionally, the diagnostic performance of mNGS for spinal infection was evaluated, by comparing it with that of the conventional microbial culture, with the histopathological results as the gold standard. Overall, 56 samples from 38 patients were enrolled for mNGS testing, and 69 samples were included for microbial culture. 30 patients (78.95%) were identified to be positive by the mNGS method, which was higher than that of microbial culture (17, 44.74%). The sensitivity and specificity of mNGS with pus samples were 84.2% and 100.0%, respectively, which outperformed those of microbial culture (42.1% and 100.0%). The pathogen identification results were applied to medication guidance, and all 38 patients experienced favorable outcomes at three months, followed-up post-treatment, without any adverse effects. These findings proved that mNGS was superior to microbial culture in pathogenic identification of the spinal infection, thereby showing great promise in guiding drug administration and improving clinical outcomes.
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Affiliation(s)
- Yi Zhang
- Department of Infectious Diseases, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Jinmei Chen
- Department of Infectious Diseases, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Xiaoli Yi
- Genoxor Medical Science and Technology Inc., Shanghai, China
| | - Zhiheng Chen
- Department of Orthopedics, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Ting Yao
- Department of Infectious Diseases, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Zhenghao Tang
- Department of Infectious Diseases, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Guoqing Zang
- Department of Infectious Diseases, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Xuejie Cao
- Genoxor Medical Science and Technology Inc., Shanghai, China
| | - Xiaofeng Lian
- Department of Orthopedics, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Xiaohua Chen
- Department of Infectious Diseases, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
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103
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Zhao M, Yue R, Wu X, Gao Z, He M, Pan L. The diagnostic value of metagenomic next-generation sequencing for identifying Pneumocystis jirovecii infection in non-HIV immunocompromised patients. Front Cell Infect Microbiol 2022; 12:1026739. [PMID: 36389151 PMCID: PMC9647189 DOI: 10.3389/fcimb.2022.1026739] [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: 08/24/2022] [Accepted: 10/10/2022] [Indexed: 11/25/2022] Open
Abstract
Background Pneumocystis jirovecii pneumonia (PJP) remains an important cause of morbidity and mortality in non-HIV immunocompromised patients especially in transplant recipients. But its diagnosis remains challenging due to the insuffificient performance of conventional methods for diagnosing Pneumocystis jirovecii(P. jirovecii) infection. Therefore, the auxiliary diagnostic function of metagenomics next-generation sequencing (mNGS) in clinical practice is worth of exploring. Method 34 non-HIV immunocompromised patients who were diagnosed as PJP by clinical manifestations, imaging findings, immune status of the host, and Methenamine silver staining were tested by mNGS from October 2018 to December 2020 in Sichuan Provincial People’s Hospital. The clinical performances of mNGS for P. jirovecii infection diagnosis were also evaluated with genome reads abundance and comparing with other traditional diagnostic methods. Results We diagnosed a total of 34 non-HIV PJP patients by the clinical composite diagnosis. Our data shows that, compared with the clinical microbiological test, the detection rate of mNGS for P. jirovecii in non-HIV infected PJP patients is significantly higher than that of Methenamine silver staining and serum 1-3-β-D-glucan. mNGS can be used as an auxiliary diagnostic tool to help diagnosis. The number of reads mapped to the genome of P. jirovecii and the duration of patients from onset to sampling collection were statistically significant between the two groups (Reads>100 and Reads ≤ 100) (8days vs. 23days, p=0.020). In addition, univariate analysis showed that C-reactive protein (15.8mg/L vs.79.56mg/L, p=0.016), lactate dehydrogenase (696U/l vs. 494U/l, p=0.030) and procalcitonin (0.09ng/ml vs. 0.59ng/ml, p=0.028) was also statistically significant between the two groups. Conclusions An effective detection rate was achieved in PJP patients using mNGS testing of bronchoalveolar lavage fluid (BALF) or blood. The study also confirmed that the abundance of reads of P. jirovecii is related to the interval between the onset and sample collection. And the inflammation status during simultaneous mNGS detection might determine the abundance of pathogens. Hence, we conclude that the mNGS strategy could benefit disease diagnosis as well as treatment when complicated clinical infections appeared.
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Affiliation(s)
- Mengyi Zhao
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, Chengdu, China
| | - Ruiming Yue
- Department of Critical Care Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, China
| | - Xiaoxiao Wu
- Department of Critical Care Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, China
| | - Zhan Gao
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, Chengdu, China
| | - Miao He
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, Chengdu, China
- *Correspondence: Miao He, ; Lingai Pan,
| | - Lingai Pan
- Department of Critical Care Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, China
- *Correspondence: Miao He, ; Lingai Pan,
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Bao XL, Tang N, Wang YZ. Severe Klebsiella pneumoniae pneumonia complicated by acute intra-abdominal multiple arterial thrombosis and bacterial embolism: A case report. World J Clin Cases 2022; 10:11101-11110. [PMID: 36338208 PMCID: PMC9631156 DOI: 10.12998/wjcc.v10.i30.11101] [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: 05/31/2022] [Revised: 07/22/2022] [Accepted: 09/12/2022] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Klebsiella pneumoniae (K. pneumoniae) is a clinically common Gram-negative bacillus that can cause community- and hospital-acquired infections and lead to pneumonia, liver abscesses, bloodstream infections, and other infectious diseases; however, severe pneumonia caused by hypervirulent K. pneumoniae (hvKp) complicated by acute intra-abdominal multiple arterial thrombosis and bacterial embolism is rarely seen in the clinical setting and has not been reported in the literature.
CASE SUMMARY A 51-year-old man was hospitalized with fever and dyspnea. Persistent mild pain in the middle and upper abdomen began at dawn on the 3rd day following admission and developed into persistent severe pain in the left upper abdomen 8 h later. Based on chest computed tomography (CT), bronchoscopy, bronchoalveolar lavage fluid metagenomic next-generation sequencing, abdominal aortic CT angiography (CTA), and culture of the superior mesenteric artery embolus, adult community-acquired severe hvKp pneumonia complicated by acute intra-abdominal multiple arterial thrombosis and bacterial embolism was diagnosed. Notably, he recovered and was discharged from the hospital after receiving effective meropenem anti-infection, endovascular contact thrombolytic, and systemic anticoagulant therapies and undergoing percutaneous thrombus aspiration. Ten days later, the patient returned to the hospital for abdominal CTA examination, which indicated blocked initial common pathway of the celiac trunk and superior mesenteric artery, and local stenosis. Therefore, celiac trunk artery stenting was performed in Chongqing Hospital, and postoperative recovery was good.
CONCLUSION We report a case of hvKp severe pneumonia complicated by acute intra-abdominal multiple arterial thrombosis and bacterial embolism and suggest that clinicians should consider the possibility of a Gram-negative bacillus infection and conduct effective pathogen detection in a timely fashion when managing patients with severe community-acquired pneumonia before obtaining bacteriologic and drug sensitivity results. At the same time, when patients have severe pulmonary infection complicated by severe abdominal pain, an acute mesenteric artery embolism should be considered to avoid delays in treatment.
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Affiliation(s)
- Xiao-Li Bao
- Department of Respiratory and Critical Care Medicine, Chongqing University Fuling Hospital, Chongqing 408000, China
| | - Nan Tang
- Department of Respiratory and Critical Care Medicine, Chongqing University Fuling Hospital, Chongqing 408000, China
| | - Yang-Zhong Wang
- Department of Respiratory and Critical Care Medicine, Chongqing University Fuling Hospital, Chongqing 408000, China
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Lu H, Ma L, Zhang H, Feng L, Yu Y, Zhao Y, Li L, Zhou Y, Song L, Li W, Zhao J, Liu L. The Comparison of Metagenomic Next-Generation Sequencing with Conventional Microbiological Tests for Identification of Pathogens and Antibiotic Resistance Genes in Infectious Diseases. Infect Drug Resist 2022; 15:6115-6128. [PMID: 36277249 PMCID: PMC9586124 DOI: 10.2147/idr.s370964] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 10/11/2022] [Indexed: 11/05/2022] Open
Abstract
Background Metagenomic next-generation sequencing (mNGS) has been widely studied, due to its ability of detecting all the microbial genetic information unbiasedly in a sample at one time and not relying on traditional culture. However, the application of mNGS in the diagnosis of clinical pathogens remains challenging. Methods From December 2019 to March 2021, 134 specimens including Broncho alveolar lavage fluid (BAFL), blood, sputum, cerebrospinal fluid (CSF), bile, pleural fluid, pus, were continuously collected in The First Hospital of Qinhuangdao, and their retrospective diagnoses were classified into infectious disease (128, 95.5%) and noninfectious disease (6, 4.5%). The pathogen-detection performance of mNGS was compared with conventional microbiological tests (CMT) and culture method. In addition, the antibiotic resistance genes (ARGs) and evolutionary relationship of common drug-resistant A. baumannii were also analyzed. Results Compared with CMT and culture methods, mNGS showed higher sensitivity in pathogen detection (74.2% vs 57.8%; P < 0.001 and 66.3% vs 31.7%; P < 0.001, respectively). Importantly, for cases that mNGS-positive only, 18 (35%) cases result in diagnosis modification, and 7 (23%) cases confirmed the clinical diagnosis. In 17 cases that A. baumannii were both detected in mNGS and culture, ade genes were the most frequently detected ARGs (from 13 cases), followed by sul2 and APH(3”)-Ib (both from 12 cases). High consistency was observed among these ARGs and the related phenotype (100% for ade genes, 91.6% for sul2 and APH(3”)-Ib). A. baumannii strains were classified into three groups, and most were well-clustered. It suggested those strains may be the epidemic strains. Conclusion In our study, mNGS had a higher sensitivity than CMT and culture method. And the result of ARGs frequency and cluster analysis of A. baumannii was of great significance to the anti-infective therapy.
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Affiliation(s)
- Hongzhi Lu
- Department of Infectious Diseases, First Hospital of Qinhuangdao, Qinhuangdao, Hebei, 066000, People’s Republic of China
| | - Li Ma
- Department of Infectious Diseases, First Hospital of Qinhuangdao, Qinhuangdao, Hebei, 066000, People’s Republic of China
| | - Hong Zhang
- Department of Infectious Diseases, First Hospital of Qinhuangdao, Qinhuangdao, Hebei, 066000, People’s Republic of China
| | - Li Feng
- Department of Infectious Diseases, First Hospital of Qinhuangdao, Qinhuangdao, Hebei, 066000, People’s Republic of China
| | - Ying Yu
- Department of Infectious Diseases, First Hospital of Qinhuangdao, Qinhuangdao, Hebei, 066000, People’s Republic of China
| | - Yihan Zhao
- Department of Infectious Diseases, First Hospital of Qinhuangdao, Qinhuangdao, Hebei, 066000, People’s Republic of China
| | - Li Li
- Department of Infectious Diseases, First Hospital of Qinhuangdao, Qinhuangdao, Hebei, 066000, People’s Republic of China
| | - Yujiao Zhou
- Department of Infectious Diseases, First Hospital of Qinhuangdao, Qinhuangdao, Hebei, 066000, People’s Republic of China
| | - Li Song
- Shanghai Biotecan Pharmaceuticals Co., Ltd, Shanghai, 201204, People’s Republic of China,Shanghai Zhangjiang Institute of Medical Innovation, Shanghai, 201204, People’s Republic of China
| | - Wushuang Li
- Shanghai Biotecan Pharmaceuticals Co., Ltd, Shanghai, 201204, People’s Republic of China,Shanghai Zhangjiang Institute of Medical Innovation, Shanghai, 201204, People’s Republic of China
| | - Jiangman Zhao
- Shanghai Biotecan Pharmaceuticals Co., Ltd, Shanghai, 201204, People’s Republic of China,Shanghai Zhangjiang Institute of Medical Innovation, Shanghai, 201204, People’s Republic of China
| | - Lanxiang Liu
- Medical Imaging Center, First Hospital of Qinhuangdao, Qinhuangdao, Hebei, 066000, People’s Republic of China,Correspondence: Lanxiang Liu, Department of Medical Imaging Center, First Hospital of Qinhuangdao, 258 Wenhua Road, Qinhuangdao, 066000, Hebei, People’s Republic of China, Email
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Su Y, Miao Q, Li N, Hu BJ, Pan J. Diagnostic accuracy of metagenomic next-generation sequencing for cryptococcosis in immunocompetent and immunocompromised patients. Front Cell Infect Microbiol 2022; 12:997256. [PMID: 36339336 PMCID: PMC9630913 DOI: 10.3389/fcimb.2022.997256] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 10/04/2022] [Indexed: 07/25/2023] Open
Abstract
OBJECTIVE To compare the diagnostic accuracy of metagenomic next-generation sequencing (mNGS) for cryptococcosis in patients with different immune statuses with that of conventional detection. METHODS A total of 1442 specimens including 71 specimens from patients with cryptococcosis were analyzed in the study. The chi square test was used to screen the sensitivity and specificity of different detection methods for different specimen types. One-way ANOVA was used to compare the mNGS results with age, CD4, lymphocytes, IFN, IL-6, IL-2 and serum antigen assay. RESULTS The sensitivity of mNGS was 44.29% in Cryptococcus infection cases. The positive rate of mNGS results for bronchoalveolar lavage fluid (BALF, 87.50%) from immunocompromised patients was higher than that of BALF from immunocompetent patients (40.00%, p=0.04). The sensitivity of the serum Cryptococcus capsular antigen assay was 80.00% in immunocompetent patients and 96.42% in immunocompromised patients (p = 0.049). A positive rate of detection of Cryptococcus from mNGS was higher when cryptococcal antigen ≥1:160 (p=0.022) in immunocompromised patients. A positive rate of detection of Cryptococcus from mNGS was higher when lymphocyte counts were lower in both immunocompetent patients(p=0.017) and in immunocompromised patients(p=0.029). CONCLUSIONS The sensitivity of mNGS is lower than that of serum cryptococcal antigen assay and histopathology in immunocompetent patients. However, BALF detection is recommend for immunocompromised patients compared with tissue and CSF. The positive mNGS result was correlated with lower lymphocyte counts, higher IL-2 and higher serum antigen assay in immunocompromised patients.
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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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Song T, Peng S, Zhou X, Jiang L, Zhang J. Case Report: Diagnosis of vertebral alveolar echinococcosis upon next-generation sequencing in a suspected tuberculosis. Front Surg 2022; 9:984640. [PMID: 36248358 PMCID: PMC9556986 DOI: 10.3389/fsurg.2022.984640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 09/13/2022] [Indexed: 11/17/2022] Open
Abstract
Introduction Alveolar echinococcosis (AE), caused by larval stages of Echinococcus multilocularis, is a rare zoonotic disease that mainly involves the liver. The diagnosis of extrahepatic AE is usually difficult. Here, we describe a rare case of vertebral alveolar echinococcosis with a suspected history of spinal tuberculosis, diagnosed by metagenomic next-generation sequencing (mNGS). Case Presentation A 44-year-old woman presented with repetitive neck and back pain, with a surgical history of suspected spinal tuberculosis. Magnetic resonance imaging (MRI) showed cystic masses in the craniocervical junction region and effusion around lumbar vertebrae. Multiple culture tests were performed to detect tuberculosis and other pathogens through puncture of the effusion and of cerebrospinal fluid, but the results were all negative. Finally, mNGS of the effusion fluid was performed and Echinococcus multilocularis were detected. The results were further confirmed by Sanger sequencing. Conclusion This case emphasizes a role of mNGS in the diagnosis of infectious diseases with unknown pathogen. As a newly emerged sensitive and accurate diagnostic strategy, mNGS provides clinicians an opportunity to clarify pathogens in complicated infectious cases, especially in patients with a history of multiple infections.
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Affiliation(s)
- Tiange Song
- Department of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Research Unit for Blindness Prevention of Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences, Chengdu, China
| | - Shengkun Peng
- Department of Radiology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Xiaoli Zhou
- Department of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Research Unit for Blindness Prevention of Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences, Chengdu, China
| | - Li Jiang
- Department of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Research Unit for Blindness Prevention of Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences, Chengdu, China
- Correspondence: Li Jiang Jie Zhang
| | - Jie Zhang
- Department of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Research Unit for Blindness Prevention of Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences, Chengdu, China
- Correspondence: Li Jiang Jie Zhang
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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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Kong M, Li W, Kong Q, Dong H, Han A, Jiang L. Application of metagenomic next-generation sequencing in cutaneous tuberculosis. Front Cell Infect Microbiol 2022; 12:942073. [PMID: 36211955 PMCID: PMC9539668 DOI: 10.3389/fcimb.2022.942073] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
Tuberculous infection in a skin wound is a rare but well-known condition. This study describes a child infected with tuberculosis after being wounded. Because of swelling and pain in his wrist tissue, he was admitted to the Affiliated Hospital of Jining Medical University of Shandong Province on 16 October 2021. His medical history only included a wound. He was discharged after debridement. The laboratory data were normal. Two months after surgery, his wound was still swollen and painful. Secretions from the wound were sent for metagenomic next-generation sequencing (mNGS), which revealed three reads related to the Mycobacterium tuberculosis complex group (MTBC). A diagnosis of cutaneous tuberculosis (TB) was made. The wound disappeared after anti-TB drugs were administered. This case demonstrates that, while TB presenting as a severe cutaneous wound is rare, it should be considered in the clinical diagnosis. Clinicians should also pay attention to extrapulmonary infection with MTBC in patients, particularly in some long-suffering patients, and identify the specific pathogen as soon as possible. mNGS could help to identify pathogens and facilitate early treatment, thereby improving the prognosis.
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Affiliation(s)
- Min Kong
- Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, China
- Medical Laboratory of Jining Medical University, Jining Medical University, Jining, China
| | - Wei Li
- Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, China
| | - Qingsheng Kong
- Medical Laboratory of Jining Medical University, Jining Medical University, Jining, China
| | - Haixin Dong
- Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, China
| | - Aizhong Han
- Medical Laboratory of Jining Medical University, Jining Medical University, Jining, China
| | - Liqing Jiang
- Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, China
- Medical Laboratory of Jining Medical University, Jining Medical University, Jining, China
- *Correspondence: Liqing Jiang,
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111
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Qu C, Chen Y, Ouyang Y, Huang W, Liu F, Yan L, Lu R, Zeng Y, Liu Z. Metagenomics next-generation sequencing for the diagnosis of central nervous system infection: A systematic review and meta-analysis. Front Neurol 2022; 13:989280. [PMID: 36203993 PMCID: PMC9530978 DOI: 10.3389/fneur.2022.989280] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 08/29/2022] [Indexed: 11/13/2022] Open
Abstract
Objective It is widely acknowledged that central nervous system (CNS) infection is a serious infectious disease accompanied by various complications. However, the accuracy of current detection methods is limited, leading to delayed diagnosis and treatment. In recent years, metagenomic next-generation sequencing (mNGS) has been increasingly adopted to improve the diagnostic yield. The present study sought to evaluate the value of mNGS in CNS infection diagnosis. Methods Following the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) 2022 guidelines, we searched relevant articles published in seven databases, including PubMed, Web of Science, and Cochrane Library, published from January 2014 to January 2022. High-quality articles related to mNGS applications in the CNS infection diagnosis were included. The comparison between mNGS and the gold standard of CNS infection, such as culture, PCR or serology, and microscopy, was conducted to obtain true positive (TP), true negative (TN), false positive (FP), and false negative (FN) values, which were extracted for sensitivity and specificity calculation. Results A total of 272 related studies were retrieved and strictly selected according to the inclusion and exclusion criteria. Finally, 12 studies were included for meta-analysis and the pooled sensitivity was 77% (95% CI: 70–82%, I2 = 39.69%) and specificity was 96% (95% CI: 93–98%, I2 = 72.07%). Although no significant heterogeneity in sensitivity was observed, a sub-group analysis was conducted based on the pathogen, region, age, and sample pretreatment method to ascertain potential confounders. The area under the curve (AUC) of the summary receiver operating characteristic curve (SROC) of mNGS for CNS infection was 0.91 (95% CI: 0.88–0.93). Besides, Deek's Funnel Plot Asymmetry Test indicated no publication bias in the included studies (Figure 3, p > 0.05). Conclusion Overall, mNGS exhibits good sensitivity and specificity for diagnosing CNS infection and diagnostic performance during clinical application by assisting in identifying the pathogen. However, the efficacy remains inconsistent, warranting subsequent studies for further performance improvement during its clinical application. Study registration number INPLASY202120002
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Affiliation(s)
- Chunrun Qu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- Xiangya School of Medicine, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Yu Chen
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Yuzhen Ouyang
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Weicheng Huang
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Fangkun Liu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Luzhe Yan
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Ruoyu Lu
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Yu Zeng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Yu Zeng
| | - Zhixiong Liu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Zhixiong Liu
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Wang Y, Hu X, Yang L, Chen C, Cheng H, Hu H, Liang W, Tong Y, Wang M, Wang H. Application of High-Throughput Sequencing Technology in the Pathogen Identification of Diverse Infectious Diseases in Nephrology Departments. Diagnostics (Basel) 2022; 12:diagnostics12092128. [PMID: 36140529 PMCID: PMC9497786 DOI: 10.3390/diagnostics12092128] [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: 07/07/2022] [Revised: 08/21/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
Objective: The purpose of this study was to explore the clinical applications of high-throughput sequencing (HTS) in the identification of pathogens in patients with urinary tract infection (UTI), peritoneal dialysis-associated peritonitis (PDAP), central venous catheter related blood infections (CRBIs), and lung infections in the nephrology department. Methods: Midstream urine samples from 112 patients with UTI, peritoneal fluid samples from 67 patients with PDAP, blood samples from 15 patients with CRBI, and sputum specimens from 53 patients with lung infection were collected. The HTS and ordinary culture methods were carried out in parallel to identify the pathogens in each sample. Pathogen detection positive rate and efficacy were compared between the two methods. Results: The pathogen positive detection rates of HTS in UTI, PDAP, CRBI, and lung infection were strikingly higher than those of the culture method (84.8% vs. 35.7, 71.6% vs. 23.9%, 75% vs. 46.7%, 84.9% vs. 5.7%, p < 0.05, respectively). HTS was superior to the culture method in the sensitivity of detecting bacteria, fungi, atypical pathogens, and mixed microorganisms in those infections. In patients who had empirically used antibiotics before the test being conducted, HTS still exhibited a considerably higher positive rate than the culture method (81.6% vs. 39.0%, 68.1% vs. 14.9%, 72.7% vs. 36.4%, 83.3% vs. 4.2%, p < 0.05, respectively). Conclusions: HTS is remarkably more efficient than the culture method in detecting pathogens in diverse infectious diseases in nephrology, and is particularly potential in identifying the pathogens that are unable to be identified by the common culture method, such as in cases of complex infection with specific pathogens or subclinical infection due to preemptive use of antibiotics.
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Affiliation(s)
- Yujuan Wang
- Department of Nephrology, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang District, Wuhan 430060, China
| | - Xiaoyi Hu
- Department of Nephrology, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang District, Wuhan 430060, China
| | - Lianhua Yang
- Department of Nephrology, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang District, Wuhan 430060, China
| | - Cheng Chen
- Department of Nephrology, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang District, Wuhan 430060, China
| | - Hui Cheng
- Department of Nephrology, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang District, Wuhan 430060, China
| | - Haiyun Hu
- Department of Nephrology, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang District, Wuhan 430060, China
| | - Wei Liang
- Department of Nephrology, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang District, Wuhan 430060, China
| | - Yongqing Tong
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang District, Wuhan 430060, China
| | - Ming Wang
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang District, Wuhan 430060, China
- Correspondence: (M.W.); (H.W.)
| | - Huiming Wang
- Department of Nephrology, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang District, Wuhan 430060, China
- Correspondence: (M.W.); (H.W.)
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Duan W, Yang Y, Zhao J, Yan T, Tian X. Application of metagenomic next-generation sequencing in the diagnosis and treatment of recurrent urinary tract infection in kidney transplant recipients. Front Public Health 2022; 10:901549. [PMID: 36072369 PMCID: PMC9441654 DOI: 10.3389/fpubh.2022.901549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 07/12/2022] [Indexed: 01/22/2023] Open
Abstract
Background Rapid and accurate pathogen diagnosis is an urgent unmet clinical need for recurrent urinary tract infection (RUTI) in kidney transplant recipients (KTRs). Metagenomic next-generation sequencing (mNGS) may offer another strategy for diagnosing uropathogens but remains to be studied. Methods Nineteen KTRs with RUTI were collected in this study. The uropathogens were detected and compared by mNGS and urine culture, respectively. Modifications of the anti-infection strategy were also assessed. Results Rich and diverse pathogens were revealed by mNGS. mNGS was significantly higher than culture in total positive rate (100.0% vs. 31.6%; p < 0.01) and in identification rates for bacteria (89.5% vs. 31.6%; p < 0.01), for viruses (57.9% vs. 0; p < 0.01), and for fungi (42.1% vs. 0; p < 0.01), respectively. mNGS identified a significantly higher proportion of mixed infections than culture (89.5% vs. 10.5%; p < 0.01). The anti-infection therapies were adjusted in two (33.3%) and 12 (76.9%) cases guided by culture and mNGS, respectively. Conclusion mNGS has more remarkable etiological diagnostic performance compared with urine culture for KTRs with RUTI to guide anti-infection strategies and, in turn, protect the graft.
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Affiliation(s)
- Wenjing Duan
- Department of the Clinical Research Center, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, China
| | - Yongguang Yang
- Department of the Clinical Research Center, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, China
| | - Jingge Zhao
- Department of the Clinical Research Center, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, China
| | - Tianzhong Yan
- Department of Urology, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, China,Tianzhong Yan
| | - Xiangyong Tian
- Department of Urology, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, China,*Correspondence: Xiangyong Tian
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Bhar A. The application of next generation sequencing technology in medical diagnostics: a perspective. PROCEEDINGS OF THE INDIAN NATIONAL SCIENCE ACADEMY 2022. [PMCID: PMC9395867 DOI: 10.1007/s43538-022-00098-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Rapid isolation, characterization, and identification are prerequisites of any successful medical intervention to infectious disease treatment. This is a real challenge to the scientific as well as a medical community to find out a proper and robust method of pathogen detection. Classical cultural, as well as biochemical test-based identification, has its own limitations to their time-consuming and ineffectiveness for closely related pathovars. Molecular diagnostics became a popular alternative to classical techniques for the past couple of decades but it required some prior information to detect the pathogen successfully. Recently, with the advent of next-generation sequencing (NGS) technology identification, and characterization of almost all the pathogenic bacteria become possible without any information a priori. Metagenomic next generation sequencing is another specialized type of NGS that is profoundly utilized in medical biotechnology and diagnostics now a days. Therefore, the present review is focused on a brief introduction to NGS technology, its application in medical microbiology, and possible future aspects for the development of medical sciences.
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Affiliation(s)
- Anirban Bhar
- Post Graduate Department of Botany, Ramakrishna Mission Vivekananda Centenary College, Rahara, Kolkata 700118 India
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115
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Wan J, Duan L, Chen Q, Wang L, Bai J, Hu J, Lu X, Zhang T, Song W, Yang D, Shan Y, Yan Z. Potential clinical impact of metagenomic next-generation sequencing of plasma for cervical spine injury with sepsis in intensive care unit: A retrospective study. Front Cell Infect Microbiol 2022; 12:948602. [PMID: 36017370 PMCID: PMC9397569 DOI: 10.3389/fcimb.2022.948602] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
Cervical spine injury (CSI) accounts for significant mortality in the intensive care unit (ICU), whereas sepsis remains one of the major causes of death in patients with CSI. However, there is no effective method to diagnose sepsis timely. The aim of this study is to investigate the effect of metagenomic next-generation sequencing (mNGS) on the pathogen features and the prognostic prediction of CSI patients with sepsis. A total of 27 blood samples from 17 included patients were tested by mNGS. Data of mNGS were compared with the conventional culture method. The Kaplan–Meier plots were used to visualize survival curves. A Cox proportional hazards model was used to identify independent prognostic factors for survival. Results showed that mNGS detected a wide spectrum of pathogens in CSI patients with sepsis, including 129 bacterial species, 8 viral species, and 51 fungal species. mNGS indicated 85.2% positive results, while the conventional culture method only showed 11.1% positive results in the blood samples. Further analyses revealed that mNGS had no prognostic effect on the septic CSI patients in ICU, whereas positive results of blood culture were closely correlated with an increased hazard ratio (HR) (HR 77.7067, 95%CI 2.860–2641.4595, p = 0.0155). Our results suggested that the mNGS application may provide evidence for clinicians to use antibiotics when a CSI case is diagnosed with sepsis.
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Affiliation(s)
- Jian Wan
- Department of Emergency and Critical Care Medicine, Shanghai Pudong New Area People’s Hospital, Shanghai, China
| | - Liwei Duan
- Department of Emergency and Critical Care Medicine, Shanghai Changzheng Hospital, Shanghai, China
| | - Qitong Chen
- Department of Emergency and Critical Care Medicine, Shanghai Changzheng Hospital, Shanghai, China
| | - Lv Wang
- Department of Emergency and Critical Care Medicine, Shanghai Changzheng Hospital, Shanghai, China
| | - Jinxia Bai
- Department of Emergency and Critical Care Medicine, Shanghai Pudong New Area People’s Hospital, Shanghai, China
| | - Jingyun Hu
- Central Lab, Shanghai Key Laboratory of Pathogenic Fungi Medical Testing, Shanghai Pudong New Area People’s Hospital, Shanghai, China
| | - Xinyuan Lu
- Department of Emergency and Critical Care Medicine, Shanghai Pudong New Area People’s Hospital, Shanghai, China
| | - Tao Zhang
- Department of Emergency and Critical Care Medicine, Shanghai Pudong New Area People’s Hospital, Shanghai, China
| | - Wei Song
- Department of Emergency and Critical Care Medicine, Shanghai Pudong New Area People’s Hospital, Shanghai, China
| | - Degang Yang
- Department of Infectious Diseases, Shanghai Skin Disease Hospital, Tongji University School of Medicine, Shanghai, China
- *Correspondence: Degang Yang, ; Yi Shan, ; Zhu Yan,
| | - Yi Shan
- Department of Emergency and Critical Care Medicine, Shanghai Changzheng Hospital, Shanghai, China
- *Correspondence: Degang Yang, ; Yi Shan, ; Zhu Yan,
| | - Zhu Yan
- Department of Emergency and Critical Care Medicine, Shanghai Changzheng Hospital, Shanghai, China
- *Correspondence: Degang Yang, ; Yi Shan, ; Zhu Yan,
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Su R, Yan H, Li N, Ding T, Li B, Xie Y, Gao C, Li X, Wang C. Application value of blood metagenomic next-generation sequencing in patients with connective tissue diseases. Front Immunol 2022; 13:939057. [PMID: 35979346 PMCID: PMC9376218 DOI: 10.3389/fimmu.2022.939057] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 06/27/2022] [Indexed: 12/05/2022] Open
Abstract
Objective This study aimed to analyze the application value of blood metagenomic next-generation sequencing (mNGS) in patients with connective tissue diseases (CTDs) to provide a reference for infection diagnosis and guidance for treatment. Methods A total of 126 CTD patients with suspected infections who were hospitalized in the Department of Rheumatology, the Second Hospital of Shanxi Medical University from January 2020 to December 2021 were enrolled in this study. We retrospectively reviewed the results of mNGS and conventional diagnostic tests (CDTs). Results Systemic lupus erythematosus (SLE) and polymyositis/dermatomyositis (DM/PM) had the highest incidence of infections. The positive pathogen detection rates of mNGS were higher than those of CDT. The virus infections are the most common type in CTD patients with single or mixed infection, especially Human gammaherpesvirus 4 (EBV), Human betaherpesvirus 5 (CMV), and Human alphaherpesvirus 1. The incidence of prokaryote and eukaryote infections is secondary to viruses. Bloodstream infections of rare pathogens such as Pneumocystis jirovecii should be of concern. Meanwhile, the most common mixed infection was bacterial–virus coinfection. Conclusion mNGS has incremental application value in patients with CTD suspected of co-infection. It has a high sensitivity, and a wide detection range for microorganisms in CTD patients. Furthermore, the high incidence of opportunistic virus infections in CTD patients should be of sufficient concern.
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Affiliation(s)
- Rui Su
- Department of Rheumatology, the Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Huanhuan Yan
- Department of Rheumatology, the Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Na Li
- Department of Rheumatology, the Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Tingting Ding
- Department of Rheumatology, the Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Baochen Li
- Department of Rheumatology, the Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Yuhuan Xie
- Department of Rheumatology, the Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Chong Gao
- Pathology, Joint Program in Transfusion Medicine, Brigham and Women’s Hospital/Children’s Hospital Boston, Harvard Medical School, Boston, MA, United States
| | - Xiaofeng Li
- Department of Rheumatology, the Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Caihong Wang
- Department of Rheumatology, the Second Hospital of Shanxi Medical University, Taiyuan, China
- *Correspondence: Caihong Wang,
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Liang M, Fan Y, Zhang D, Yang L, Wang X, Wang S, Xu J, Zhang J. Metagenomic next-generation sequencing for accurate diagnosis and management of lower respiratory tract infections. Int J Infect Dis 2022; 122:921-929. [PMID: 35908723 DOI: 10.1016/j.ijid.2022.07.060] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/07/2022] [Accepted: 07/23/2022] [Indexed: 11/24/2022] Open
Abstract
OBJECTIVES This study aimed to evaluate the clinical value of metagenomic next-generation sequencing (mNGS) in patients with suspected lower respiratory tract infections (LRTIs). METHODS This retrospective study reviewed patients with suspected LRTIs in Wuhan Union Hospital. Data including demographic, laboratory, and radiological profiles; treatment; and outcomes were recorded and analyzed. RESULTS mNGS identified pathogenic microbes in 100/140 (71.4%) patients, although 135 (96.4%) had received empiric antibiotic treatment before the mNGS tests. Single bacterial infection (35/100, 35%) was the most common type of infection in patients with positive mNGS results, followed by single fungal infection (14/100, 14%), bacterial-viral co-infection (14/100, 14%), single viral infection (12/100, 12%), bacterial-fungal co-infection (9/100, 9%), fungal-viral co-infection (9/100, 9%), and bacterial-fungal-viral co-infection (7/100, 7%). Moreover, compared with culture test, mNGS showed higher sensitivity (63/85, 74.1% vs. 22/85, 25.9% P=0.001) and lower processing time (24 h vs 48 h). Antibiotic treatment was adjusted or confirmed based on the mNGS results in 123 (87.9%) patients, including 5 (3.6%), 33 (23.6%) and 85 (60.7%) patients in whom treatment was downgraded, upgraded and unchanged, respectively, and almost all patients, regardless of escalation, de-escalation, or no change in treatment, showed significant improvement in clinical symptoms and inflammatory indicators. Additionally, 17 (12.1%) patients were referred to Wuhan Pulmonary Hospital for further treatment because of confirmed or suspected tuberculosis. CONCLUSIONS mNGS could be a promising technique for microbiological diagnosis and antibiotic management, potentially improving outcomes of patients.
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Affiliation(s)
- Mengyuan Liang
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical Collage, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei Province, 430022, China
| | - Yamin Fan
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical Collage, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei Province, 430022, China
| | - Dongmei Zhang
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical Collage, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei Province, 430022, China
| | - Lian Yang
- Department of Radiology, Union Hospital, Tongji Medical Collage, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei Province, 430022, China
| | - Xiaorong Wang
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical Collage, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei Province, 430022, China
| | - Sufei Wang
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical Collage, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei Province, 430022, China
| | - Juanjuan Xu
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical Collage, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei Province, 430022, China.
| | - Jianchu Zhang
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical Collage, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei Province, 430022, China.
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Xi Y, Zhou J, Lin Z, Liang W, Yang C, Liu D, Xu Y, Nong L, Chen S, Yu Y, He W, Zhang J, Zhang R, Liu X, Liu X, Sang L, Xu Y, Li Y. Patients with infectious diseases undergoing mechanical ventilation in the intensive care unit have better prognosis after receiving metagenomic next-generation sequencing assay. Int J Infect Dis 2022; 122:959-969. [PMID: 35908725 DOI: 10.1016/j.ijid.2022.07.062] [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: 02/15/2022] [Revised: 07/25/2022] [Accepted: 07/25/2022] [Indexed: 10/16/2022] Open
Abstract
OBJECTIVES To evaluate the relation between mNGS and the prognosis of patients with infectious diseases undergoing mechanical ventilation in the intensive care unit (ICU). DESIGN This is a single-center observational study, comparing non-randomly assigned diagnostic approaches. We analyzed the medical records of 228 patients with suspected infectious diseases undergoing mechanical ventilation in the ICU from March 2018 to May 2020. The concordance of pathogen results was also assessed for the results of mNGS, culture and PCR assays. RESULTS The 28-day mortality of the patients in the mNGS group was lower after the baseline difference correction (19.23% (20/104) vs. 29.03% (36/124) , p=0.039). Subgroup analysis showed that mNGS assay associates with improved 28-day mortality of non-immunosuppressive patients (14.06% vs. 29.82%, p=0.018) . Not performing mNGS assay, higher APACHE II score and hypertension are independent risk factors for 28-day mortality. The mNGS assay presented advantage in pathogen positivity (69.8% double positive and 25.0% mNGS positive only), and the concordance between thest two assays were 79.0%. CONCLUSIONS mNGS survey may be associated with a better prognosis as the reduction of 28-day mortality of patients with infectious diseases on mechanical ventilation in ICU. This technique presented advantage in pathogen positivity than traditional methods.
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Affiliation(s)
- Yin Xi
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Department of Pulmonary and Critical Care Medicine, 151 Yanjiang Road, Guangzhou, 510120, China
| | - Jing Zhou
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Department of Pulmonary and Critical Care Medicine, 151 Yanjiang Road, Guangzhou, 510120, China
| | - Zhimin Lin
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Department of Pulmonary and Critical Care Medicine, 151 Yanjiang Road, Guangzhou, 510120, China
| | - Weibo Liang
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Department of Pulmonary and Critical Care Medicine, 151 Yanjiang Road, Guangzhou, 510120, China
| | - Chun Yang
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Department of Pulmonary and Critical Care Medicine, 151 Yanjiang Road, Guangzhou, 510120, China
| | - Dongdong Liu
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Department of Pulmonary and Critical Care Medicine, 151 Yanjiang Road, Guangzhou, 510120, China
| | - Yonghao Xu
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Department of Pulmonary and Critical Care Medicine, 151 Yanjiang Road, Guangzhou, 510120, China
| | - Lingbo Nong
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Department of Pulmonary and Critical Care Medicine, 151 Yanjiang Road, Guangzhou, 510120, China
| | - Sibei Chen
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Department of Pulmonary and Critical Care Medicine, 151 Yanjiang Road, Guangzhou, 510120, China
| | - Yuheng Yu
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Department of Pulmonary and Critical Care Medicine, 151 Yanjiang Road, Guangzhou, 510120, China
| | - Weiqun He
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Department of Pulmonary and Critical Care Medicine, 151 Yanjiang Road, Guangzhou, 510120, China
| | - Jie Zhang
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Department of Pulmonary and Critical Care Medicine, 151 Yanjiang Road, Guangzhou, 510120, China
| | - Rong Zhang
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Department of Pulmonary and Critical Care Medicine, 151 Yanjiang Road, Guangzhou, 510120, China
| | - Xuesong Liu
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Department of Pulmonary and Critical Care Medicine, 151 Yanjiang Road, Guangzhou, 510120, China
| | - Xiaoqing Liu
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Department of Pulmonary and Critical Care Medicine, 151 Yanjiang Road, Guangzhou, 510120, China
| | - Ling Sang
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Department of Pulmonary and Critical Care Medicine, 151 Yanjiang Road, Guangzhou, 510120, China..
| | - Yuanda Xu
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Department of Pulmonary and Critical Care Medicine, 151 Yanjiang Road, Guangzhou, 510120, China..
| | - Yimin Li
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Department of Pulmonary and Critical Care Medicine, 151 Yanjiang Road, Guangzhou, 510120, China..
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Lou J, Wang B, Li J, Ni P, Jin Y, Chen S, Xi Y, Zhang R, Duan G. The CRISPR-Cas system as a tool for diagnosing and treating infectious diseases. Mol Biol Rep 2022; 49:11301-11311. [PMID: 35857175 PMCID: PMC9297709 DOI: 10.1007/s11033-022-07752-z] [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: 04/16/2022] [Revised: 06/12/2022] [Accepted: 06/28/2022] [Indexed: 10/26/2022]
Abstract
Emerging and relapsing infectious diseases pose a huge health threat to human health and a new challenge to global public health. Rapid, sensitive and simple diagnostic tools are keys to successful management of infectious patients and containment of disease transmission. In recent years, international research on Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-related proteins (Cas) has revolutionized our understanding of biology. The CRISPR-Cas system has the advantages of high specificity, high sensitivity, simple, rapid, low cost, and has begun to be used for molecular diagnosis and treatment of infectious diseases. In this paper, we described the biological principles, application fields and prospects of CRISPR-Cas system in the molecular diagnosis and treatment of infectious diseases, and compared it with existing molecular diagnosis methods, the advantages and disadvantages were summarized.
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Affiliation(s)
- Juan Lou
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Bin Wang
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Junwei Li
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Peng Ni
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Yuefei Jin
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Shuaiyin Chen
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Yuanlin Xi
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Rongguang Zhang
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China. .,International School of Public Health and One Health, The First Affiliated Hospital, Hainan Medical University, Haikou, China.
| | - Guangcai Duan
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China
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120
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Tan J, Liu Y, Ehnert S, Nüssler AK, Yu Y, Xu J, Chen T. The Effectiveness of Metagenomic Next-Generation Sequencing in the Diagnosis of Prosthetic Joint Infection: A Systematic Review and Meta-Analysis. Front Cell Infect Microbiol 2022; 12:875822. [PMID: 35755833 PMCID: PMC9226560 DOI: 10.3389/fcimb.2022.875822] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 05/11/2022] [Indexed: 12/02/2022] Open
Abstract
Background A prosthetic joint infection (PJI) is a devastating complication following total joint arthroplasties with poor prognosis. Identifying an accurate and prompt diagnostic method is particularly important for PJI. Recently, the diagnostic value of metagenomic next-generation sequencing (mNGS) in detecting PJI has attracted much attention, while the evidence of its accuracy is quite limited. Thus, this study aimed to evaluate the accuracy of mNGS for the diagnosis of PJI. Methods We summarized published studies to identify the potential diagnostic value of mNGS for PJI patients by searching online databases using keywords such as “prosthetic joint infection”, “PJI”, and “metagenomic sequencing”. Ten of 380 studies with 955 patients in total were included. The included studies provided sufficient data for the completion of 2-by-2 tables. We calculated the sensitivity, specificity, and area under the SROC curve (AUC) to evaluate mNGS for PJI diagnosis. Results We found that the pooled diagnostic sensitivity and specificity of mNGS for PJI were 0.93 (95% CI, 0.83 to 0.97) and 0.95 (95% CI, 0.92 to 0.97), respectively. Positive and negative likelihood ratios were 18.3 (95% CI, 10.9 to 30.6) and 0.07 (95% CI, 0.03 to 0.18), respectively. The area under the curve was 0.96 (95% CI, 0.93 to 0.97). Conclusion Metagenomic next-generation sequencing displays high accuracy in the diagnosis of PJI, especially for culture-negative cases.
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Affiliation(s)
- Jun Tan
- Department of Orthopedic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yang Liu
- Department of Clinical Sciences, Orthopedics, Faculty of Medicine, Lund University, Lund, Sweden
| | - Sabrina Ehnert
- Department of Trauma and Reconstructive Surgery, BG Trauma Center Tübingen, Siegfried Weller Institute for Trauma Research, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Andreas K Nüssler
- Department of Trauma and Reconstructive Surgery, BG Trauma Center Tübingen, Siegfried Weller Institute for Trauma Research, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Yang Yu
- Department of Orthopedic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jianzhong Xu
- Department of Orthopedic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Tao Chen
- Department of Orthopedic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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121
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Streptobacillus moniliformis Bacteremia in a Patient with Reactive Arthritis Without a Bite: A Case Report. Jundishapur J Microbiol 2022. [DOI: 10.5812/jjm-126419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Introduction: Clinically, rat bite fever (RBF) is a condition caused by Spirillum minus or Streptobacillus moniliformis infections, following rat or any rodent bite. In the absence of a rat bite, this condition cannot be accurately diagnosed. Here, we report the first case of RBF due to S. moniliformis but without a rat bite in China. Case Presentation: A 77-year-old woman with reactive arthritis was admitted to the hospital due to high fever. Initially, we suspected reactive arthritis with liver function deterioration. However, we isolated a bacterium which was confirmed to be S. moniliformis using Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Subsequently, the patient was given targeted anti-infective treatment, which completely resolved the symptoms. The patient was discharged upon fully recovery. Conclusions: Rat bite fever infection caused by S. moniliformis may occur without actual rodent bite. MALDI-TOF MS may be applied to determine the diagnosis of RBF. Difficulties in pathogen and clinical diagnosis highlight the need for discovering the complete exposure history and a greater understanding of this rare zoonotic infections.
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122
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Xu H, Hu X, Wang W, Chen H, Yu F, Zhang X, Zheng W, Han K. Clinical Application and Evaluation of Metagenomic Next-Generation Sequencing in Pulmonary Infection with Pleural Effusion. Infect Drug Resist 2022; 15:2813-2824. [PMID: 35677528 PMCID: PMC9167844 DOI: 10.2147/idr.s365757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 05/27/2022] [Indexed: 12/12/2022] Open
Affiliation(s)
- Huifen Xu
- Department of Respiratory and Critical Medicine, the Second Affiliated Hospital of Harbin Medical University, Heilongjiang, People’s Republic of China
| | - Xiaoman Hu
- Department of Respiratory and Critical Medicine, the Second Affiliated Hospital of Harbin Medical University, Heilongjiang, People’s Republic of China
| | - Wenyu Wang
- Department of Respiratory and Critical Medicine, the Second Affiliated Hospital of Harbin Medical University, Heilongjiang, People’s Republic of China
| | - Hong Chen
- Department of Respiratory and Critical Medicine, the Second Affiliated Hospital of Harbin Medical University, Heilongjiang, People’s Republic of China
| | - Fangfei Yu
- Department of Respiratory and Critical Medicine, the Second Affiliated Hospital of Harbin Medical University, Heilongjiang, People’s Republic of China
| | - Xiaofei Zhang
- Department of Respiratory and Critical Medicine, the Second Affiliated Hospital of Harbin Medical University, Heilongjiang, People’s Republic of China
| | - Weili Zheng
- Department of Respiratory and Critical Medicine, the Second Affiliated Hospital of Harbin Medical University, Heilongjiang, People’s Republic of China
| | - Kaiyu Han
- Department of Respiratory and Critical Medicine, the Second Affiliated Hospital of Harbin Medical University, Heilongjiang, People’s Republic of China
- Correspondence: Kaiyu Han, Tel +86-451-86605736, Email
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He Y, Fang K, Shi X, Yang D, Zhao L, Yu W, Zheng Y, Xu Y, Ma X, Chen L, Xie Y, Yu Y, Wang J, Gao Z. Enhanced DNA and RNA pathogen detection via metagenomic sequencing in patients with pneumonia. J Transl Med 2022; 20:195. [PMID: 35509078 PMCID: PMC9066823 DOI: 10.1186/s12967-022-03397-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 04/18/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Metagenomic next-generation sequencing (mNGS) is an important supplement to conventional tests for pathogen detections of pneumonia. However, mNGS pipelines were limited by irregularities, high proportion of host nucleic acids, and lack of RNA virus detection. Thus, a regulated pipeline based on mNGS for DNA and RNA pathogen detection of pneumonia is essential. METHODS We performed a retrospective study of 151 patients with pneumonia. Three conventional tests, culture, loop-mediated isothermal amplification (LAMP) and viral quantitative real-time polymerase chain reaction (qPCR) were conducted according to clinical needs, and all samples were detected using our optimized pipeline based on the mNGS (DNA and RNA) method. The performances of mNGS and three other tests were compared. Human DNA depletion was achieved respectively by MolYsis kit and pre-treatment using saponin and Turbo DNase. Three RNA library preparation methods were used to compare the detection performance of RNA viruses. RESULTS An optimized mNGS workflow was built, which had only 1-working-day turnaround time. The proportion of host DNA in the pre-treated samples decreased from 99 to 90% and microbiome reads achieved an approximately 20-fold enrichment compared with those without host removal. Meanwhile, saponin and Turbo DNase pre-treatment exhibited an advantage for DNA virus detection compared with MolYsis. Besides, our in-house RNA library preparation procedure showed a more robust RNA virus detection ability. Combining three conventional methods, 76 (76/151, 50.3%) cases had no clear causative pathogen, but 24 probable pathogens were successfully detected in 31 (31/76 = 40.8%) unclear cases using mNGS. The agreement of the mNGS with the culture, LAMP, and viral qPCR was 60%, 82%, and 80%, respectively. Compared with all conventional tests, mNGS had a sensitivity of 70.4%, a specificity of 72.7%, and an overall agreement of 71.5%. CONCLUSIONS A complete and effective mNGS workflow was built to provide timely DNA and RNA pathogen detection for pneumonia, which could effectively remove the host sequence, had a higher microbial detection rate and a broader spectrum of pathogens (especially for viruses and some pathogens that are difficult to culture). Despite the advantages, there are many challenges in the clinical application of mNGS, and the mNGS report should be interpreted with caution.
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Affiliation(s)
- Yukun He
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, 100044, China
| | - Kechi Fang
- CAS Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, 16 Lincui Road, Chaoyang District, Beijing, 100101, China.,Department of Psychology, University of Chinese Academy of Sciences, 19 A Yuquan Rd, Shijingshan District, Beijing, 100049, China
| | - Xing Shi
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, 100044, China
| | - Donghong Yang
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, 100044, China
| | - Lili Zhao
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, 100044, China
| | - Wenyi Yu
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, 100044, China
| | - Yali Zheng
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, 100044, China.,Department of Respiratory, Critical Care, and Sleep Medicine, Xiang'an Hospital of Xiamen University, Xiamen, 361101, China
| | - Yu Xu
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, 100044, China
| | - Xinqian Ma
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, 100044, China
| | - Li Chen
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, 100044, China
| | - Yu Xie
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, 100044, China
| | - Yan Yu
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, 100044, China
| | - Jing Wang
- CAS Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, 16 Lincui Road, Chaoyang District, Beijing, 100101, China. .,Department of Psychology, University of Chinese Academy of Sciences, 19 A Yuquan Rd, Shijingshan District, Beijing, 100049, China.
| | - Zhancheng Gao
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, 100044, China.
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Guo Y, Yang Y, Xu M, Shi G, Zhou J, Zhang J, Li H. Trends and Developments in the Detection of Pathogens in Central Nervous System Infections: A Bibliometric Study. Front Cell Infect Microbiol 2022; 12:856845. [PMID: 35573778 PMCID: PMC9100591 DOI: 10.3389/fcimb.2022.856845] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 03/29/2022] [Indexed: 11/22/2022] Open
Abstract
Introduction Rapid, sensitive, and specific laboratory assays are critical for the diagnosis and management of central nervous system (CNS) infections. The purpose of this study is to explore the intellectual landscape of research investigating methods for the detection of pathogens in patients with CNS infections and to identify the development trends and research frontier in this field. Methods A bibliometric study is conducted by analyzing literature retrieved from the Web of Science (WoS) Core Collection Database for the years 2000 to 2021. CiteSpace software is used for bibliometric analysis and network visualization, including co-citation analysis of references, co-occurrence analysis of keywords, and cooperation network analysis of authors, institutions, and countries/regions. Results A total of 2,282 publications are eventually screened, with an upward trend in the number of publications per year. The majority of papers are attributed to the disciplines of MICROBIOLOGY, INFECTIOUS DISEASES, IMMUNOLOGY, NEUROSCIENCES & NEUROLOGY, and VIROLOGY. The co-citation analysis of references shows that recent research has focused on the largest cluster “metagenomic next-generation sequencing”; the results of the analysis of the highest-cited publications and the citation burst of publications reveal that there is a strong interest stimulated in metagenomic next-generation sequencing. The co-occurrence analysis of keywords indicates that “infection”, “pathogen”, “diagnosis”, “gene”, “virus”, “polymerase chain reaction”, “cerebrospinal fluid”, “epidemiology”, and “metagenomic next-generation sequencing” are the main research priorities in the field of pathogen detection for CNS infections, and the keyword with the highest strength of burst is “metagenomic next-generation sequencing”. Collaborative network analysis reveals that the USA, the Centers for Disease Control and Prevention of USA, and XIN WANG and JENNIFER DIEN BARD are the most influential country, institution, and researchers, respectively. Conclusions Exploring more advanced laboratory assays to improve the diagnostic accuracy of pathogens is essential for CNS infection research. Metagenomic next-generation sequencing is emerging as a novel useful unbiased approach for diagnosing infectious diseases of the CNS.
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Affiliation(s)
- Yangyang Guo
- Intensive Care Unit, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yanlin Yang
- Intensive Care Unit, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Ming Xu
- Intensive Care Unit, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Guangzhi Shi
- Intensive Care Unit, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Jianxin Zhou
- Intensive Care Unit, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Jindong Zhang
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China
- *Correspondence: Jindong Zhang, ; Hongliang Li,
| | - Hongliang Li
- Intensive Care Unit, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- *Correspondence: Jindong Zhang, ; Hongliang Li,
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125
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Ma N, Chen M, Ding J, Wang F, Jin J, Fan S, Chen J. Recurrent Pneumonia With Tuberculosis and Candida Co-infection Diagnosed by Metagenomic Next-Generation Sequencing: A Case Report and Literature Review. Front Med (Lausanne) 2022; 9:755308. [PMID: 35462994 PMCID: PMC9026854 DOI: 10.3389/fmed.2022.755308] [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: 08/08/2021] [Accepted: 02/23/2022] [Indexed: 01/16/2023] Open
Abstract
An 82-year-old male patient was hospitalized in the Respiratory Department for “repeated cough and shortness of breath for 10 years, recurrence worsened for 1 month.” Later, he was transferred for further diagnosis and treatment, to the Infectious Disease Department for further hospitalization. Previously, the patient had repeatedly undergone tuberculosis-related examinations including bronchoscopy examinations. However, no evidence of Mycobacterium tuberculosis (MTB) infection was found. Early anti-infection treatments failed. Due to repeated symptoms, we performed bronchoscopy again and sent alveolar lavage fluid for the metagenomic next-generation sequencing (mNGS) test. Subsequently, MTB and Candida albicans were detected by mNGS. After antituberculosis and antifungal treatments, the symptoms were significantly relieved, and the chest CT showed resolution of the lung lesions. Therefore, we successfully diagnosed and treated a case of recurrent pneumonia with tuberculosis and Candida co-infection diagnosed by mNGS.
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Affiliation(s)
- Ning Ma
- Department of Infectious Diseases, Beilun District People’s Hospital, Ningbo, China
| | - Mei Chen
- Department of Infectious Diseases, Beilun District People’s Hospital, Ningbo, China
| | - Jingyi Ding
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Fang Wang
- Department of Hospital-Acquired Infection Control, Beilun District People’s Hospital, Ningbo, China
| | - Jingbo Jin
- Department of Infectious Diseases, Beilun District People’s Hospital, Ningbo, China
| | - Sitong Fan
- Department of Infectious Diseases, Beilun District People’s Hospital, Ningbo, China
| | - Jiajia Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- *Correspondence: Jiajia Chen,
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Xu J, Peng L, Zheng Z, Zhong W. Stone fragmentation urine culture as alternative role of stone culture in endourological urolithiasis management. World J Urol 2022; 40:1085-1086. [PMID: 33899134 DOI: 10.1007/s00345-021-03701-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 04/10/2021] [Indexed: 12/13/2022] Open
Affiliation(s)
- Jiandong Xu
- Urology, The First Affiliated Hospital of Guangzhou Medical University, Kangda Road 1, Haizhu District, Guangzhou, 510230, China
- Guangdong Key Laboratory of Urology, Guangzhou Institute of Urology, Guangzhou, China
- Guangzhou Institute of Urology, Guangzhou, China
| | - Linjie Peng
- Urology, The First Affiliated Hospital of Guangzhou Medical University, Kangda Road 1, Haizhu District, Guangzhou, 510230, China
- Guangdong Key Laboratory of Urology, Guangzhou Institute of Urology, Guangzhou, China
- Guangzhou Institute of Urology, Guangzhou, China
| | - Zexian Zheng
- Urology, The First Affiliated Hospital of Guangzhou Medical University, Kangda Road 1, Haizhu District, Guangzhou, 510230, China
- Guangdong Key Laboratory of Urology, Guangzhou Institute of Urology, Guangzhou, China
- Guangzhou Institute of Urology, Guangzhou, China
| | - Wen Zhong
- Urology, The First Affiliated Hospital of Guangzhou Medical University, Kangda Road 1, Haizhu District, Guangzhou, 510230, China.
- Guangdong Key Laboratory of Urology, Guangzhou Institute of Urology, Guangzhou, China.
- Guangzhou Institute of Urology, Guangzhou, China.
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Pan L, Wu F, Cai Q, Xu Z, Hu H, Tang T, Yue R, Hou Y, Zhang X, Fang Y, Huang X, Kang Y. Whole Genome Profiling of Lung Microbiome in Solid Organ Transplant Recipients Reveals Virus Involved Microecology May Worsen Prognosis. Front Cell Infect Microbiol 2022; 12:863399. [PMID: 35372133 PMCID: PMC8967177 DOI: 10.3389/fcimb.2022.863399] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 02/22/2022] [Indexed: 11/25/2022] Open
Abstract
Solid organ transplantation (SOT) is the final therapeutic option for recipients with end-stage organ failure, and its long-term success is limited by infections and chronic allograft dysfunction. Viral infection in SOT recipients is considered an important factor affecting prognosis. In this study, we retrospectively analyzed 43 cases of respiratory infections in SOT recipients using metagenomic next-generation sequencing (mNGS) for bronchoalveolar lavage fluid (BALF). At least one virus was detected in 26 (60.5%) recipients, while 17 (39.5%) were virus-negative. Among virus-positive recipients, cytomegalovirus (CMV) was detected in 14 (32.6%), Torque teno virus (TTV) was detected in 9 (20.9%), and other viruses were detected in 6 (14.0%). Prognostic analysis showed that the mortality of the virus-positive group was higher than that of the virus-negative group regardless whether it is the main cause of infection. Analysis of different types of viruses showed that the mortality of the CMV-positive group was significantly higher than that of the CMV-negative group, but no significant difference was observed in other type of virus groups. The diversity analysis of the lung microbiome showed that there was a significant difference between the virus-positive group and the negative group, in particular, the significant differences in microorganisms such as Pneumocystis jirovecii (PJP) and Moraxella osloensiswere detected. Moreover, in the presence of CMV, Pneumocystis jirovecii, Veillonella parvula, and other species showed dramatic changes in the lung of SOT patients, implying that high degree of co-infection between CMV and Pneumocystis jirovecii may occur. Taken together, our study shows that the presence of virus is associated with worse prognosis and dramatically altered lung microbiota in SOT recipients.
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Affiliation(s)
- Lingai Pan
- Department of Critical Care Medicine, West China Hospital, West China Clinical Medical School, Sichuan University, Chengdu, China
- Department of Critical Care Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Fengsheng Wu
- Genoxor Medical Science and Technology Inc., Zhejiang, China
| | - Qingqing Cai
- Genoxor Medical Science and Technology Inc., Zhejiang, China
| | - Zhuofei Xu
- Genoxor Medical Science and Technology Inc., Zhejiang, China
| | - Huan Hu
- Department of Critical Care Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Tian Tang
- Department of Critical Care Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Ruiming Yue
- Department of Critical Care Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Yifu Hou
- Department of Organ Transplant Center, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Xiaoqin Zhang
- Department of Critical Care Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Yuan Fang
- Genoxor Medical Science and Technology Inc., Zhejiang, China
| | - Xiaobo Huang
- Department of Critical Care Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
- *Correspondence: Yan Kang, ; Xiaobo Huang,
| | - Yan Kang
- Department of Critical Care Medicine, West China Hospital, West China Clinical Medical School, Sichuan University, Chengdu, China
- *Correspondence: Yan Kang, ; Xiaobo Huang,
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Yang J, Wu P, Liu X, Xia H, Lai Z. Autoimmune Encephalitis With Multiple Auto-Antibodies With Concomitant Human Herpesvirus-7 and Ovarian Teratoma: A Case Report. Front Med (Lausanne) 2022; 8:759559. [PMID: 35237615 PMCID: PMC8882612 DOI: 10.3389/fmed.2021.759559] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 12/30/2021] [Indexed: 11/13/2022] Open
Abstract
Infectious etiologies and tumors are common triggers of autoimmune encephalitis. We herein reported a rare case of autoimmune encephalitis with multiple autoantibodies in cerebrospinal fluid (CSF) and serum, with concomitant human herpesvirus 7 (HHV-7) infection and ovarian teratoma. A 36-year-old woman presented with mental and behavioral changes and gibberish for 13 days, followed by fever for 1 day. Her brain MRI indicated limbic encephalitis. Metagenomic next-generation sequencing (mNGS) of CSF revealed HHV-7. Antibody testing showed positive anti-N-methyl-D-aspartate receptor (NMDAR) and anti-α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) antibodies in CSF and serum. Ovarian teratoma was considered after pelvic MRI, which was then pathologically confirmed after laparoscopic ovariectomy. Her conditions improved after laparoscopic surgery, intravenous steroids, immunoglobulin, and rituximab therapy. Our findings suggested that the combination of multiple therapies including antiviral, immunotherapy, and resection of tumors were appropriate and improved the prognosis, when HHV-7 infection and ovarian teratoma were concomitant with multiple anti-neuronal antibodies of autoimmune encephalitis.
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Affiliation(s)
- Jianhua Yang
- Department of Neurology, The Affiliated Ganzhou Hospital of Nanchang University, Ganzhou, China
| | - Pengcheng Wu
- Department of Neurology, The Affiliated Ganzhou Hospital of Nanchang University, Ganzhou, China
| | - Xianghong Liu
- Department of Neurology, The Affiliated Ganzhou Hospital of Nanchang University, Ganzhou, China
| | - Han Xia
- Department of Scientific Affairs, Hugobiotech Co., Ltd., Beijing, China
| | - Zhaohui Lai
- Department of Neurology, The Affiliated Ganzhou Hospital of Nanchang University, Ganzhou, China
- *Correspondence: Zhaohui Lai
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Ju CR, Lian QY, Guan WJ, Chen A, Zhang JH, Xu X, Chen RC, Li SY, He JX. Metagenomic Next-Generation Sequencing for Diagnosing Infections in Lung Transplant Recipients: A Retrospective Study. Transpl Int 2022; 35:10265. [PMID: 35221789 PMCID: PMC8866178 DOI: 10.3389/ti.2022.10265] [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: 11/25/2021] [Accepted: 01/18/2022] [Indexed: 11/13/2022]
Abstract
Background: Accurate identification of pathogens is essential for the diagnosis and control of infections. We aimed to compare the diagnostic performance of metagenomic next-generation sequencing (mNGS) and conventional detection methods (CDM) in lung transplant recipients (LTRs).Methods: We retrospectively analyzed 107 LTRs with suspected infection of pulmonary, blood, central nervous system or chest wall between March 2018 and November 2020. Bronchoalveolar lavage fluid and other body fluids were subject to pathogen detection by both mNGS and CDM.Results: Of the 163 specimens, 84 (51.5%) tested positive for both mNGS and culture, 19 (11.7%) of which were completely consistent, 44 (27.0%) were partially congruent, and 21 (12.9%) were discordant (kappa = .215; p = .001). Compared with CDM, mNGS detected a higher diversity of pathogens. Moreover, the turn-around time was significantly shorter for mNGS compared with culture (2.7 ± .4 vs. 5.5 ± 1.6 days, p < .001). As an auxiliary method, treatment strategies were adjusted according to mNGS findings in 31 cases (29.0%), including eight patients with non-infectious diseases, who were finally cured.Conclusion: mNGS can identify pathogens with a shorter turn-around time and therefore provide a more accurate and timely diagnostic information to ascertaining pulmonary infections. mNGS might have a role in differentiating infectious from non-infectious lung diseases in LTRs.
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Affiliation(s)
- Chun-Rong Ju
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Qiao-Yan Lian
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wei-Jie Guan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Ao Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jian-Heng Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xin Xu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Department of Thoracic Surgery, Guangzhou Institute of Respiratory Disease, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Rong-Chang Chen
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Southern University of Science and Technology, Second Clinical Medical College of Jinan University, Shenzhen People’s Hospital, Shenzhen Institute of Respiratory Diseases, Shenzhen, China
| | - Shi-Yue Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- *Correspondence: Shi-Yue Li, ; Jian-Xing He,
| | - Jian-Xing He
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Department of Thoracic Surgery, Guangzhou Institute of Respiratory Disease, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- *Correspondence: Shi-Yue Li, ; Jian-Xing He,
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Song P, Chen S, Tan X, Gao Y, Fu J, You Z, Wang C, Zhao Q, Pang F. Metagenomic Analysis Identifying a Rare Leishmania Infection in an Adult With AIDS. Front Cell Infect Microbiol 2022; 11:764142. [PMID: 34976855 PMCID: PMC8714901 DOI: 10.3389/fcimb.2021.764142] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 11/23/2021] [Indexed: 11/13/2022] Open
Abstract
Leishmania belongs to a genus of the protozoan parasites that causes leishmaniasis, and includes cutaneous leishmaniasis (CL) and visceral leishmaniasis (VL). In this case, Leishmania amastigotes were found on cytomorphology examination of the bone marrow specimen, followed by 1,076 Leishmania donovani reads using metagenomic next generation sequencing (mNGS). Since being definitely diagnosed with VL/HIV coinfection, the patient was treated with liposomal amphotericin B as the parasite-resistant therapy and was discharged after clinical cure. But nearly a year later, on the mNGS follow-up, L. donovani was detected in the patient’s blood plasma specimen with 941 reads, suggesting that a relapse of leishmaniasis had occurred. These results indicate that leishmaniasis still exists in China and may represent a public health concern. This case could be helpful in the differential diagnosis of leishmaniasis, and for determining disease progression, prevention, and control of vectors and reservoir hosts.
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Affiliation(s)
- Pingping Song
- Department of Clinical Laboratory, Liaocheng People's Hospital, Liaocheng, China
| | - Shuai Chen
- Department of Clinical Laboratory, Liaocheng Third People's Hospital, Liaocheng, China
| | - Xiaoyu Tan
- Department of Clinical Laboratory, Liaocheng People's Hospital, Liaocheng, China
| | - Yanjun Gao
- Department of Clinical Laboratory, Liaocheng People's Hospital, Liaocheng, China
| | - Juanjuan Fu
- Department of Clinical Laboratory, Liaocheng People's Hospital, Liaocheng, China
| | - Zhiqing You
- Department of Clinical Laboratory, Liaocheng People's Hospital, Liaocheng, China
| | - Chengtan Wang
- Department of Clinical Laboratory, Liaocheng People's Hospital, Liaocheng, China
| | - Qigang Zhao
- Department of Clinical Laboratory, Liaocheng People's Hospital, Liaocheng, China
| | - Feng Pang
- Department of Clinical Laboratory, Liaocheng People's Hospital, Liaocheng, China
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Huge and ruptured amoebic liver abscess diagnosed by mNGS: A case report. JOURNAL OF INTENSIVE MEDICINE 2022; 2:127-129. [PMID: 36789188 PMCID: PMC9923956 DOI: 10.1016/j.jointm.2021.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/22/2021] [Accepted: 11/24/2021] [Indexed: 11/21/2022]
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Suminda GGD, Bhandari S, Won Y, Goutam U, Kanth Pulicherla K, Son YO, Ghosh M. High-throughput sequencing technologies in the detection of livestock pathogens, diagnosis, and zoonotic surveillance. Comput Struct Biotechnol J 2022; 20:5378-5392. [PMID: 36212529 PMCID: PMC9526013 DOI: 10.1016/j.csbj.2022.09.028] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 12/03/2022] Open
Abstract
Increasing globalization, agricultural intensification, urbanization, and climatic changes have resulted in a significant recent increase in emerging infectious zoonotic diseases. Zoonotic diseases are becoming more common, so innovative, effective, and integrative research is required to better understand their transmission, ecological implications, and dynamics at wildlife-human interfaces. High-throughput sequencing (HTS) methodologies have enormous potential for unraveling these contingencies and improving our understanding, but they are only now beginning to be realized in livestock research. This study investigates the current state of use of sequencing technologies in the detection of livestock pathogens such as bovine, dogs (Canis lupus familiaris), sheep (Ovis aries), pigs (Sus scrofa), horses (Equus caballus), chicken (Gallus gallus domesticus), and ducks (Anatidae) as well as how it can improve the monitoring and detection of zoonotic infections. We also described several high-throughput sequencing approaches for improved detection of known, unknown, and emerging infectious agents, resulting in better infectious disease diagnosis, as well as surveillance of zoonotic infectious diseases. In the coming years, the continued advancement of sequencing technologies will improve livestock research and hasten the development of various new genomic and technological studies on farm animals.
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Lai SY, Liu F, Chang L, Che GL, Yang QX, Jiang YM, Teng J. OUP accepted manuscript. Lab Med 2022; 53:e123-e125. [PMID: 35075476 DOI: 10.1093/labmed/lmab123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Shu-Yu Lai
- Department of Laboratory Medicine, West China Second University Hospital, and Key Laboratory of Obstetric and Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, Sichuan University, Chengdu, China
| | - Fang Liu
- Department of Laboratory Medicine, West China Second University Hospital, and Key Laboratory of Obstetric and Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, Sichuan University, Chengdu, China
| | - Li Chang
- Department of Laboratory Medicine, West China Second University Hospital, and Key Laboratory of Obstetric and Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, Sichuan University, Chengdu, China
| | - Guang-Lu Che
- Department of Laboratory Medicine, West China Second University Hospital, and Key Laboratory of Obstetric and Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, Sichuan University, Chengdu, China
| | - Qiu-Xia Yang
- Department of Laboratory Medicine, West China Second University Hospital, and Key Laboratory of Obstetric and Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, Sichuan University, Chengdu, China
| | - Yong-Mei Jiang
- Department of Laboratory Medicine, West China Second University Hospital, and Key Laboratory of Obstetric and Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, Sichuan University, Chengdu, China
| | - Jie Teng
- Department of Laboratory Medicine, West China Second University Hospital, and Key Laboratory of Obstetric and Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, Sichuan University, Chengdu, China
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134
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Xing N, Zhao Z, Li Q, Dong Y, Li J, Zhang S. Ureaplasma parvum meningitis following atypical choroid plexus papilloma resection in an adult patient: a case report and literature review. BMC Infect Dis 2021; 21:1276. [PMID: 34930148 PMCID: PMC8690907 DOI: 10.1186/s12879-021-06975-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 12/13/2021] [Indexed: 11/30/2022] Open
Abstract
Background While Ureaplasma parvum has previously been linked to the incidence of chorioamnionitis, abortion, premature birth, and perinatal complications, there have only been rare reports of invasive infections of the central nervous system (CNS) in adults. Owing to its atypical presentation and the fact that it will yield sterile cultures using conventional techniques, diagnosing U. parvum meningitis can be challenging. Case presentation We describe a case of U. parvum meningitis detected in an adult patient following surgical brain tumor ablation. After operation, the patient experienced epilepsy, meningeal irritation, and fever with unconsciousness. Cerebrospinal fluid (CSF) analysis showed leukocytosis (484 * 106 /L), elevated protein levels (1.92 g/L), and decreased glucose concentrations (0.02 mmol/L). Evidence suggested that the patient was suffering from bacterial meningitis. However, no bacterial pathogens in either CSF or blood were detected by routine culture or serology. The symptoms did not improve with empirical antibiotics. Therefore, we performed metagenomic next-generation sequencing (mNGS) to identify the etiology of the meningitis. Ureaplasma parvum was detected by mNGS in CSF samples. To the best of our knowledge, this case is the first reported instance of U. parvum meningitis in an adult patient in Asian. After diagnosis, the patient underwent successful moxifloxacin treatment and recovered without complications. Conclusions As mNGS strategies can enable the simultaneous detection of a diverse array of microbes in a single analysis, they may represent a valuable means of diagnosing the pathogens responsible for CNS infections and other clinical conditions with atypical presentations.
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Affiliation(s)
- Na Xing
- Department of Endocrinology, The Fourth Hospital of Hebei Medical University, No. 12, Jiankang Road, Shijiazhuang, 050000, Hebei, People's Republic of China
| | - Zhenxiang Zhao
- Department of Neurosurgery, The Fourth Hospital of Hebei Medical University, No. 12, Jiankang Road, Shijiazhuang, 050000, Hebei, People's Republic of China.
| | - Qingjing Li
- Clinical Laboratory, The Fourth Hospital of Hebei Medical University, No. 12, Jiankang Road, Shijiazhuang, 050000, Hebei, People's Republic of China
| | - Yalan Dong
- Department of Neurosurgery, The Fourth Hospital of Hebei Medical University, No. 12, Jiankang Road, Shijiazhuang, 050000, Hebei, People's Republic of China
| | - Jianfeng Li
- Department of Neurosurgery, The Fourth Hospital of Hebei Medical University, No. 12, Jiankang Road, Shijiazhuang, 050000, Hebei, People's Republic of China
| | - Shuping Zhang
- Department of Oncology, The Seventh People's Hospital of Hebei Province, No. 389, Jungong Road, Dingzhou, 073000, Hebei, People's Republic of China
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Chen L, Su Y, Xiong XZ. Rhizopus microsporus lung infection in an immunocompetent patient successfully treated with amphotericin B: A case report. World J Clin Cases 2021; 9:11108-11114. [PMID: 35047625 PMCID: PMC8678878 DOI: 10.12998/wjcc.v9.i35.11108] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/09/2021] [Accepted: 11/03/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Rhizopus microsporus (R. microsporus) lung infection is an invasive fungal disease with high mortality that is increasingly common in immunocompromised patients. However, it is very rare in immunocompetent patients. Here, we present the case of a 19-year-old girl who developed R. microsporus lung infection without any known immunodeficiency.
CASE SUMMARY The patient presented to our hospital because of hemoptysis and irritative cough without expectoration. She was first treated for community-acquired pneumonia until the detection of R. microsporus in bronchoalveolar lavage fluid by metagenomics next-generation sequencing (mNGS). After a combination therapy of intravenous inhalation and local airway perfusion of amphotericin B, she eventually recovered, with significant absorption of lung infections.
CONCLUSION Early diagnosis and treatment are very important for pulmonary mucormycosis. Compared to fungal culture, mNGS is a relatively precise and convenient method to obtain pathogenic results. A combination therapy of intravenous inhalation and local airway perfusion of amphotericin B may be a promising strategy for the treatment of pulmonary mucormycosis in the future.
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Affiliation(s)
- Long Chen
- Department of Respiratory and Critical Care Medicine, Union Hospital Affiliated to Tongji Medical College of Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, China
| | - Yuan Su
- Department of Respiratory and Critical Care Medicine, Union Hospital Affiliated to Tongji Medical College of Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, China
| | - Xian-Zhi Xiong
- Department of Respiratory and Critical Care Medicine, Union Hospital Affiliated to Tongji Medical College of Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, China
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136
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Lian QY, Chen A, Zhang JH, Guan WJ, Xu X, Wei B, Huang DX, He JX, Ju CR. High-throughput next-generation sequencing for identifying pathogens during early-stage post-lung transplantation. BMC Pulm Med 2021; 21:348. [PMID: 34742287 PMCID: PMC8572506 DOI: 10.1186/s12890-021-01723-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 10/31/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND High-throughput next-generation sequencing (HT-NGS) has the potential to detect a large variety of pathogens; however, the application of HT-NGS in lung transplant (LTx) recipients remains limited. We aimed to evaluate the value of HT-NGS for pathogen detection and diagnosis of pulmonary infection during early-stage post-lung transplantation. METHODS In this retrospective study, we enrolled 51 LTx recipients who underwent lung transplantation between January 2020 and December 2020. Bronchoalveolar lavage fluid (BALF) samples were collected for the detection of pathogens using both HT-NGS and conventional microbiological testing. The detection of pathogens and diagnostic performance of HT-NGS were compared with that of conventional methods. RESULTS HT-NGS provided a higher positive rate of pathogen detection than conventional microbiological testing (88.24% vs. 76.47%). The most common bacteria detected via HT-NGS during early-stage post-lung transplantation were Enterococcus, Staphylococcus, Pseudomonas and Klebsiella, while all fungi were Candida and all viruses were Herpesvirus. Uncommon pathogens, including Strongyloides, Legionella, and Mycobacterium abscesses were identified by HT-NGS. The sensitivity of HT-NGS for diagnosing pulmonary infection was significantly higher than that of conventional microbiological testing (97.14% vs. 68.57%; P < 0.001). For three LTx recipients, treatment regimens were adjusted according to the results of HT-NGS, leading to a complete recovery. CONCLUSION HT-NGS is a highly sensitive technique for pathogen detection, which may provide diagnostic advantages, especially in LTx recipients, contributing to the optimization of treatment regimens against pulmonary infection during early-stage post-lung transplantation.
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Affiliation(s)
- Qiao-Yan Lian
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Ao Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jian-Heng Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wei-Jie Guan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xin Xu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Bing Wei
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Dan-Xia Huang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jian-Xing He
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Chun-Rong Ju
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
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Jiang Z, Liu N, Wang L, Wu J, Guan X. Mining of a Clinical Database: The Interpretation of Intense Serial Procalcitonin in the Prediction for Bloodstream Infection. Front Med (Lausanne) 2021; 8:691793. [PMID: 34692716 PMCID: PMC8526537 DOI: 10.3389/fmed.2021.691793] [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: 04/07/2021] [Accepted: 09/02/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Procalcitonin (PCT) is a promising biomarker for predicting infection. Bloodstream infection (BSI) is usually a deteriorating stage of sepsis. The purpose of this study was to explore the predictive value of intense serial PCT assays for BSI in the intensive care unit (ICU). Methods: This study was a retrospective study based on a clinical database. We analyzed the data of critically ill patients from February 2016 to May 2020. The patients who received PCT assays and blood cultures (BCs) were classified into four groups according to the BCs: (i) BC negative, (ii) bacteria positive, (iii) fungi-positive, and (iv) combined-positive, and the patients with bacteremia were further subdivided into Gram+ and Gram- bacteremia. Results: The database included 11,219 patients. There were 3,593 patients who met the criteria for the analysis. The PCT concentration differed significantly across BC groups (p < 0.0001). The fluctuation of PCT significantly increased in the BC positive groups (p < 0.0001). According to the receiver operating characteristic (ROC), the optimum cutoff of the fluctuation of PCT was around 8 ng/ml for predicting BSI. Conclusion: Our study indicated that the fluctuation of PCT could be an indicator for screening BSI, but less accurate for Gram-positive infections. With a fluctuation of PCT less than 8 ng/ml, BSI should not be a rational cause for sepsis exacerbating.
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Affiliation(s)
- Zhiyi Jiang
- Department of Critical Care Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Ning Liu
- Department of Critical Care Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Luhao Wang
- Department of Critical Care Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Jianfeng Wu
- Department of Critical Care Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xiangdong Guan
- Department of Critical Care Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
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Zhu T, Cai QQ, Yu J, Liang XS. Metagenomic next-generation sequencing (mNGS) confirmed a critical case of severe fever with thrombocytopenia syndrome virus (SFTSV). Clin Chem Lab Med 2021; 60:e42-e45. [PMID: 34674414 DOI: 10.1515/cclm-2021-0791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 09/16/2021] [Indexed: 11/15/2022]
Affiliation(s)
- Tong Zhu
- Department of Infectious Disease, Shanghai Changhai Hospital, Navi Medical University, Shanghai, P.R. China
| | - Qing-Qing Cai
- Genoxor Medical Science and Technology Inc., Shanghai, P.R. China
| | - Jiao Yu
- Department of Infectious Disease, Shanghai Changhai Hospital, Navi Medical University, Shanghai, P.R. China
| | - Xue-Song Liang
- Department of Infectious Disease, Shanghai Changhai Hospital, Navi Medical University, Shanghai, P.R. China
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139
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Zhan Y, Xu T, He F, Guan WJ, Li Z, Li S, Xie M, Li X, Chen R, Cheng L, Zhong N, Ye F. Clinical Evaluation of a Metagenomics-Based Assay for Pneumonia Management. Front Microbiol 2021; 12:751073. [PMID: 34603275 PMCID: PMC8481773 DOI: 10.3389/fmicb.2021.751073] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 08/25/2021] [Indexed: 11/13/2022] Open
Abstract
Clinical value of metagenomic next-generation sequencing (mNGS) in pneumonia management is still controversial. A prospective study was conducted to evaluate the clinical impact of PneumoSeq in 57 immunocompetent (ICO) and 75 immunocompromised (ICH) pneumonia patients. The value of PneumoSeq for both etiological and clinical impact investigation in pneumonia was assessed. Among the 276 potential pathogens detected with PneumoSeq in our cohort, 251 (90.9%) were cross-validated. Clinical diagnoses of the causative pathogens were obtained for 97 patients, 90.7% of which were supported by PneumoSeq. Compared to conventional testing, PneumoSeq suggested potentially missed diagnoses in 16.7% of cases (22/132), involving 48 additional pathogenic microorganisms. In 58 (43.9%) cases, PneumoSeq data led to antimicrobial treatment de-escalation (n = 12 in ICO, n = 18 in ICH) and targeted treatment initiation (n = 7 in ICO, n = 21 in ICH). The PneumoSeq assay benefited the diagnosis and clinical management of both ICH and ICO pneumonia patients in real-world settings.
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Affiliation(s)
- Yangqing Zhan
- State Key Laboratory of Respiratory Disease, Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, National Clinical Research Center for Respiratory Disease, Guangzhou, China
| | - Teng Xu
- Vision Medicals Co., Ltd., Guangzhou, China.,Key Laboratory of Animal Gene Editing and Animal Cloning in Yunnan Province and College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Fusheng He
- Vision Medicals Co., Ltd., Guangzhou, China
| | - Wei-Jie Guan
- State Key Laboratory of Respiratory Disease, Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, National Clinical Research Center for Respiratory Disease, Guangzhou, China.,Department of Thoracic Surgery, Guangzhou Institute for Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhengtu Li
- State Key Laboratory of Respiratory Disease, Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, National Clinical Research Center for Respiratory Disease, Guangzhou, China
| | - Shaoqiang Li
- State Key Laboratory of Respiratory Disease, Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, National Clinical Research Center for Respiratory Disease, Guangzhou, China
| | | | - Xiaolei Li
- Vision Medicals Co., Ltd., Guangzhou, China
| | - Rongchang Chen
- State Key Laboratory of Respiratory Disease, Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, National Clinical Research Center for Respiratory Disease, Guangzhou, China.,Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Southern University of Science and Technology, Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen Institute of Respiratory Diseases, Shenzhen, China
| | - Linling Cheng
- State Key Laboratory of Respiratory Disease, Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, National Clinical Research Center for Respiratory Disease, Guangzhou, China
| | - Nanshan Zhong
- State Key Laboratory of Respiratory Disease, Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, National Clinical Research Center for Respiratory Disease, Guangzhou, China
| | - Feng Ye
- State Key Laboratory of Respiratory Disease, Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, National Clinical Research Center for Respiratory Disease, Guangzhou, China
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140
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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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141
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Giannini HM, Meyer NJ. Genetics of Acute Respiratory Distress Syndrome: Pathways to Precision. Crit Care Clin 2021; 37:817-834. [PMID: 34548135 DOI: 10.1016/j.ccc.2021.05.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Clinical risk factors alone fail to fully explain acute respiratory distress syndrome (ARDS) risk or ARDS death, suggesting that individual risk factors contribute. The goals of genomic ARDS studies include better mechanistic understanding, identifying dysregulated pathways that may be amenable to pharmacologic targeting, using genomic causal inference techniques to find measurable traits with meaning, and deconvoluting ARDS heterogeneity by proving reproducible subpopulations that may share a unique biology. This article discusses the latest advances in ARDS genomics, provides historical perspective, and highlights some of the ways that the coronavirus disease 2019 (COVID-19) pandemic is accelerating genomic ARDS research.
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Affiliation(s)
- Heather M Giannini
- University of Pennsylvania Perelman School of Medicine, 3400 Spruce Street, 5038 Gates Building, Philadelphia, PA 19104, USA
| | - Nuala J Meyer
- University of Pennsylvania Perelman School of Medicine, 3400 Spruce Street, 5038 Gates Building, Philadelphia, PA 19104, USA.
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142
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Ding L, Liu Y, Wu X, Wu M, Luo X, Ouyang H, Xia J, Liu X, Ding T. Pathogen Metagenomics Reveals Distinct Lung Microbiota Signatures Between Bacteriologically Confirmed and Negative Tuberculosis Patients. Front Cell Infect Microbiol 2021; 11:708827. [PMID: 34589441 PMCID: PMC8475726 DOI: 10.3389/fcimb.2021.708827] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/20/2021] [Indexed: 11/13/2022] Open
Abstract
Understanding the dynamics of lung microbiota in tuberculosis patients, especially those who cannot be confirmed bacteriologically in clinical practice, is imperative for accurate diagnosis and effective treatment. This study aims to characterize the distinct lung microbial features between bacteriologically confirmed and negative tuberculosis patients to understand the influence of microbiota on tuberculosis patients. We collected specimens of bronchoalveolar lavage fluid from 123 tuberculosis patients. Samples were subjected to metagenomic next-generation sequencing to reveal the lung microbial signatures. By combining conventional bacterial detection and metagenomic sequencing, 101/123 (82%) tuberculosis patients were bacteriologically confirmed. In addition to Mycobacterium tuberculosis, Staphylococcus aureus, Kluyveromyces lactis, and Pyricularia pennisetigena were also enriched in the bacteriological confirmation group. In contrast, Haemophilus parainfluenzae was enriched in the bacteriologically negative group. Besides, microbial interaction exhibits a different state between bacteriologically confirmed and negative tuberculosis patients. Mycobacterium tuberculosis was confirmed correlated with clinical characteristics such as albumin and chest cavities. Our study comprehensively demonstrates the correlation between unique features of lung microbial dynamics and the clinical characteristics of tuberculosis patients, suggesting the importance of studying the pulmonary microbiome in tuberculosis disease and providing new insights for future precision diagnosis and treatment.
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Affiliation(s)
- Li Ding
- Program of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Yanmin Liu
- Program of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xiaorong Wu
- Program of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Minhao Wu
- Program of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xiaoqing Luo
- Program of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Hui Ouyang
- Program of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Jinyu Xia
- Program of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Xi Liu
- Program of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Tao Ding
- Program of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
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143
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Han D, Diao Z, Lai H, Han Y, Xie J, Zhang R, Li J. Multilaboratory assessment of metagenomic next-generation sequencing for unbiased microbe detection. J Adv Res 2021; 38:213-222. [PMID: 35572414 PMCID: PMC9091723 DOI: 10.1016/j.jare.2021.09.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/24/2021] [Accepted: 09/24/2021] [Indexed: 12/12/2022] Open
Abstract
We developed a set of well-defined reference materials, which is very beneficial to monitor problems in mNGS workflows and identify optimal protocols. The high interlaboratory variability in the identification and quantitation of microbes indicates that the current mNGS protocols are in urgent need of standardization and optimization. The detection rate of mNGS for low-concentration microbes (less than 103 cell/ml) is significantly lower than that of microbes with a concentration of 104 cell/ml and higher. Only 56.7% to 83.3% of the laboratories showed a sufficient ability to obtain clear etiological diagnoses for three simulated cases combined with patient information. Addressing laboratory contamination(false positive) is an urgent task.
Introduction Metagenomic next-generation sequencing (mNGS) assay for detecting infectious agents is now in the stage of being translated into clinical practice. With no approved approaches or guidelines available, laboratories adopt customized mNGS assays to detect clinical samples. However, the accuracy, reliability, and problems of these routinely implemented assays are not clear. Objectives To evaluate the performance of 90 mNGS laboratories under routine testing conditions through analyzing identical samples. Methods Eleven microbial communities were generated using 15 quantitative microbial suspensions. They were used as reference materials to evaluate the false negatives and false positives of participating mNGS protocols, as well as the ability to distinguish genetically similar organisms and to identify true pathogens from other microbes based on fictitious case reports. Results High interlaboratory variability was found in the identification and the quantitative reads per million reads (RPM) values of each microbe in the samples, especially when testing microbes present at low concentrations (1 × 103 cell/ml or less). 42.2% (38/90) of the laboratories reported unexpected microbes (i.e. false positive problem). Only 56.7% (51/90) to 83.3% (75/90) of the laboratories showed a sufficient ability to obtain clear etiological diagnoses for three simulated cases combined with patient information. The analysis of the performance of mNGS in distinguishing genetically similar organisms in three samples revealed that only 56.6% to 63.0% of the laboratories recovered RPM ratios (RPMS. aureus/RPMS. epidermidis) within the range of a 2-fold change of the initial input ratios (indicating a relatively low level of bias). Conclusion The high interlaboratory variability found in both identifying microbes and distinguishing true pathogens emphasizes the urgent need for improving the accuracy and comparability of the results generated across different mNGS laboratories, especially in the detection of low-microbial-biomass samples.
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144
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Diao Z, Han D, Zhang R, Li J. Metagenomics next-generation sequencing tests take the stage in the diagnosis of lower respiratory tract infections. J Adv Res 2021; 38:201-212. [PMID: 35572406 PMCID: PMC9091713 DOI: 10.1016/j.jare.2021.09.012] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 09/13/2021] [Accepted: 09/25/2021] [Indexed: 02/06/2023] Open
Abstract
The applications of mNGS for LRIs span a wide range of areas including LRI diagnosis, airway microbiome analyses, human host response analyses, and prediction of drug resistance. The workflow of mNGS used in clinical practice involves the wet-lab pipeline and dry-lab pipeline, the complex workflow poses challenges for its extensive use. mNGS will become an important tool in the field of infectious disease diagnosis in the next decade.
Metagenomic next-generation sequencing (mNGS) has changed the diagnosis landscape of lower respiratory tract infections (LRIs). With the development of newer sequencing assays, it is now possible to assess all microorganisms in a sample using a single mNGS analysis. The applications of mNGS for LRIs span a wide range of areas including LRI diagnosis, airway microbiome analyses, human host response analyses, and prediction of drug resistance. mNGS is currently in an exciting transitional period; however, before implementation in a clinical setting, there are several barriers to overcome, such as the depletion of human nucleic acid, discrimination between colonization and infection, high costs, and so on. Aim of Review: In this review, we summarize the potential applications and challenges of mNGS in the diagnosis of LRIs to promote the integration of mNGS into the management of patients with respiratory tract infections in a clinical setting. Key Scientific Concepts of Review: Once its analytical validation, clinical validation and clinical utility been demonstrated, mNGS will become an important tool in the field of infectious disease diagnosis.
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145
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Huang T, Chen Y, Zhang J, He R, Qu D, Ye Q, Chen X. Rapid and accurate diagnosis of brain abscess caused by Nocardia asiatica with a combination of Ziehl-Neelsen staining and metagenomics next-generation sequencing. Eur J Neurol 2021; 28:355-357. [PMID: 32920981 DOI: 10.1111/ene.14533] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 08/31/2020] [Indexed: 11/30/2022]
Abstract
BACKGROUND AND PURPOSE Early and accurate diagnosis is vital in cerebral nocardiosis, a very rare and infectious disease associated with a high mortality rate. Herein, we report a case that a patient with brain abscess was swiftly diagnosed and successfully treated. METHODS We report a case of a 61-year-old woman with a brain abscess caused by Nocardia asiatica, diagnosed by a combination of Ziehl-Neelsen staining and metagenomics next-generation sequencing (mNGS). RESULTS A 61-year-old woman with left breast cancer resection, diabetes mellitus and a 7-month discontinuous cough and fever was admitted to our hospital. On the third day of hospitalization, she experienced a sudden loss of consciousness and was diagnosed with a brain abscess and a pathological change in cerebral mass on brain magnetic resonance imaging (MRI). Due to the failure of culturing any microorganisms from the pup, the dissected sample from the patient with Ziehl-Neelsen staining tested positive for acid-fast bacilli and was subjected to mNGS. The pathogen was identified as N. asiatica and the patient was treated accordingly with linezolid and trimethoprim-sulfamethoxazole until complete recovery was confirmed by the follow-up cerebral MRI. CONCLUSIONS This is the first case report of a brain abscess caused by N. asiatica being swiftly diagnosed by a combination of Ziehl-Neelsen staining and mNGS. This rapid diagnosis allowed us to successfully treat this rare infection.
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Affiliation(s)
- T Huang
- Department of Neurology, Fujian Medical University Union Hospital, Fuzhou, China.,Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Y Chen
- Department of Neurology, Fujian Medical University Union Hospital, Fuzhou, China.,Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - J Zhang
- Department of Neurology, Fujian Medical University Union Hospital, Fuzhou, China.,Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - R He
- Department of Neurology, Fujian Medical University Union Hospital, Fuzhou, China.,Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - D Qu
- Department of Clinical Neurosciences, Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada
| | - Q Ye
- Department of Neurology, Fujian Medical University Union Hospital, Fuzhou, China.,Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - X Chen
- Department of Neurology, Fujian Medical University Union Hospital, Fuzhou, China.,Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
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146
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van Belkum A, Almeida C, Bardiaux B, Barrass SV, Butcher SJ, Çaykara T, Chowdhury S, Datar R, Eastwood I, Goldman A, Goyal M, Happonen L, Izadi-Pruneyre N, Jacobsen T, Johnson PH, Kempf VAJ, Kiessling A, Bueno JL, Malik A, Malmström J, Meuskens I, Milner PA, Nilges M, Pamme N, Peyman SA, Rodrigues LR, Rodriguez-Mateos P, Sande MG, Silva CJ, Stasiak AC, Stehle T, Thibau A, Vaca DJ, Linke D. Host-Pathogen Adhesion as the Basis of Innovative Diagnostics for Emerging Pathogens. Diagnostics (Basel) 2021; 11:diagnostics11071259. [PMID: 34359341 PMCID: PMC8305138 DOI: 10.3390/diagnostics11071259] [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: 04/20/2021] [Revised: 06/19/2021] [Accepted: 06/21/2021] [Indexed: 12/18/2022] Open
Abstract
Infectious diseases are an existential health threat, potentiated by emerging and re-emerging viruses and increasing bacterial antibiotic resistance. Targeted treatment of infectious diseases requires precision diagnostics, especially in cases where broad-range therapeutics such as antibiotics fail. There is thus an increasing need for new approaches to develop sensitive and specific in vitro diagnostic (IVD) tests. Basic science and translational research are needed to identify key microbial molecules as diagnostic targets, to identify relevant host counterparts, and to use this knowledge in developing or improving IVD. In this regard, an overlooked feature is the capacity of pathogens to adhere specifically to host cells and tissues. The molecular entities relevant for pathogen–surface interaction are the so-called adhesins. Adhesins vary from protein compounds to (poly-)saccharides or lipid structures that interact with eukaryotic host cell matrix molecules and receptors. Such interactions co-define the specificity and sensitivity of a diagnostic test. Currently, adhesin-receptor binding is typically used in the pre-analytical phase of IVD tests, focusing on pathogen enrichment. Further exploration of adhesin–ligand interaction, supported by present high-throughput “omics” technologies, might stimulate a new generation of broadly applicable pathogen detection and characterization tools. This review describes recent results of novel structure-defining technologies allowing for detailed molecular analysis of adhesins, their receptors and complexes. Since the host ligands evolve slowly, the corresponding adhesin interaction is under selective pressure to maintain a constant receptor binding domain. IVD should exploit such conserved binding sites and, in particular, use the human ligand to enrich the pathogen. We provide an inventory of methods based on adhesion factors and pathogen attachment mechanisms, which can also be of relevance to currently emerging pathogens, including SARS-CoV-2, the causative agent of COVID-19.
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Affiliation(s)
- Alex van Belkum
- BioMérieux, Open Innovation & Partnerships, 38390 La Balme Les Grottes, France;
- Correspondence: (A.v.B.); (D.L.)
| | | | - Benjamin Bardiaux
- Institut Pasteur, Structural Biology and Chemistry, 75724 Paris, France; (B.B.); (N.I.-P.); (T.J.); (M.N.)
| | - Sarah V. Barrass
- Department of Biological Sciences, University of Helsinki, 00014 Helsinki, Finland; (S.V.B.); (S.J.B.); (A.G.)
| | - Sarah J. Butcher
- Department of Biological Sciences, University of Helsinki, 00014 Helsinki, Finland; (S.V.B.); (S.J.B.); (A.G.)
| | - Tuğçe Çaykara
- Centre for Nanotechnology and Smart Materials, 4760-034 Vila Nova de Famalicão, Portugal; (T.Ç.); (C.J.S.)
| | - Sounak Chowdhury
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, 22242 Lund, Sweden; (S.C.); (L.H.); (J.M.)
| | - Rucha Datar
- BioMérieux, Microbiology R&D, 38390 La Balme Les Grottes, France;
| | | | - Adrian Goldman
- Department of Biological Sciences, University of Helsinki, 00014 Helsinki, Finland; (S.V.B.); (S.J.B.); (A.G.)
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK; (P.H.J.); (A.K.); (J.L.B.); (A.M.); (P.A.M.); (S.A.P.)
| | - Manisha Goyal
- BioMérieux, Open Innovation & Partnerships, 38390 La Balme Les Grottes, France;
| | - Lotta Happonen
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, 22242 Lund, Sweden; (S.C.); (L.H.); (J.M.)
| | - Nadia Izadi-Pruneyre
- Institut Pasteur, Structural Biology and Chemistry, 75724 Paris, France; (B.B.); (N.I.-P.); (T.J.); (M.N.)
| | - Theis Jacobsen
- Institut Pasteur, Structural Biology and Chemistry, 75724 Paris, France; (B.B.); (N.I.-P.); (T.J.); (M.N.)
| | - Pirjo H. Johnson
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK; (P.H.J.); (A.K.); (J.L.B.); (A.M.); (P.A.M.); (S.A.P.)
| | - Volkhard A. J. Kempf
- Institute for Medical Microbiology and Infection Control, University Hospital, Goethe-University, 60596 Frankfurt am Main, Germany; (V.A.J.K.); (A.T.); (D.J.V.)
| | - Andreas Kiessling
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK; (P.H.J.); (A.K.); (J.L.B.); (A.M.); (P.A.M.); (S.A.P.)
| | - Juan Leva Bueno
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK; (P.H.J.); (A.K.); (J.L.B.); (A.M.); (P.A.M.); (S.A.P.)
| | - Anchal Malik
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK; (P.H.J.); (A.K.); (J.L.B.); (A.M.); (P.A.M.); (S.A.P.)
| | - Johan Malmström
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, 22242 Lund, Sweden; (S.C.); (L.H.); (J.M.)
| | - Ina Meuskens
- Department of Biosciences, University of Oslo, 0316 Oslo, Norway;
| | - Paul A. Milner
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK; (P.H.J.); (A.K.); (J.L.B.); (A.M.); (P.A.M.); (S.A.P.)
| | - Michael Nilges
- Institut Pasteur, Structural Biology and Chemistry, 75724 Paris, France; (B.B.); (N.I.-P.); (T.J.); (M.N.)
| | - Nicole Pamme
- School of Mathematics and Physical Sciences, University of Hull, Hull HU6 7RX, UK; (N.P.); (P.R.-M.)
| | - Sally A. Peyman
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK; (P.H.J.); (A.K.); (J.L.B.); (A.M.); (P.A.M.); (S.A.P.)
| | - Ligia R. Rodrigues
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; (L.R.R.); (M.G.S.)
| | - Pablo Rodriguez-Mateos
- School of Mathematics and Physical Sciences, University of Hull, Hull HU6 7RX, UK; (N.P.); (P.R.-M.)
| | - Maria G. Sande
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; (L.R.R.); (M.G.S.)
| | - Carla Joana Silva
- Centre for Nanotechnology and Smart Materials, 4760-034 Vila Nova de Famalicão, Portugal; (T.Ç.); (C.J.S.)
| | - Aleksandra Cecylia Stasiak
- Interfaculty Institute of Biochemistry, University of Tübingen, 72076 Tübingen, Germany; (A.C.S.); (T.S.)
| | - Thilo Stehle
- Interfaculty Institute of Biochemistry, University of Tübingen, 72076 Tübingen, Germany; (A.C.S.); (T.S.)
| | - Arno Thibau
- Institute for Medical Microbiology and Infection Control, University Hospital, Goethe-University, 60596 Frankfurt am Main, Germany; (V.A.J.K.); (A.T.); (D.J.V.)
| | - Diana J. Vaca
- Institute for Medical Microbiology and Infection Control, University Hospital, Goethe-University, 60596 Frankfurt am Main, Germany; (V.A.J.K.); (A.T.); (D.J.V.)
| | - Dirk Linke
- Department of Biosciences, University of Oslo, 0316 Oslo, Norway;
- Correspondence: (A.v.B.); (D.L.)
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147
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Wang JY, Li X, Chen JY, Tong B. Epileptic Seizure after Use of Moxifloxacin in Man with Legionella longbeachae Pneumonia. Emerg Infect Dis 2021; 26:2725-2727. [PMID: 33079050 PMCID: PMC7588506 DOI: 10.3201/eid2611.191815] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Legionellosis caused by Legionella longbeachae is diagnosed mainly by PCR. We report a case of L. longbeachae infection in mainland China, which was diagnosed by metagenomic next-generation sequencing, in a man who developed an epileptic seizure after using moxifloxacin. Metagenomic next-generation sequencing may be a useful tool to detect Legionella spp.
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148
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Malczynski M, Zhu A, Zembower T, Qi C. Diagnostic performance of Ion 16S metagenomics kit and Ion reporter metagenomics workflow for bacterial pathogen detection in culture-negative clinical specimens from sterile sources. Diagn Microbiol Infect Dis 2021; 101:115451. [PMID: 34237647 DOI: 10.1016/j.diagmicrobio.2021.115451] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/26/2021] [Accepted: 06/06/2021] [Indexed: 12/17/2022]
Abstract
PCR-based deep sequencing of 16S rRNA gene allows for detection of a wide array of bacterial pathogens in culture-negative specimens. Ion 16S metagenomics kit and Ion Reporter metagenomics workflow (Ion 16S mNGS) provides an end-to-end solution with integrated workflow. Ninety-eight clinical samples with the diagnosis generated with 16S rRNA gene PCR/chain termination (Sanger) sequencing (16S CS) was used to assess the performance of Ion 16S mNGS. Compared to species level detection of 16S CS, the Ion 16S mNGS had 88% sensitivity and 76% specificity. When accounting for genus level of detection, the Ion 16S mNGS had 100% sensitivity. Notably, Ion 16S mNGS generated diagnosis in 13% of 16S CS and culture-negative samples. In addition, Ion 16S mNGS had the advantage of detecting more than 1 pathogen in 16S CS positive samples. We showed that the workflow had high reproducibility.
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Affiliation(s)
- Michael Malczynski
- Clinical Microbiology Laboratory, Department of Pathology, Northwestern Memorial Hospital, Chicago, IL, USA
| | - Alex Zhu
- Northwestern University, Evanston, IL, USA
| | - Teresa Zembower
- Clinical Microbiology Laboratory, Department of Pathology, Northwestern Memorial Hospital, Chicago, IL, USA; Northwestern University, Evanston, IL, USA; Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, USA; Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Chao Qi
- Clinical Microbiology Laboratory, Department of Pathology, Northwestern Memorial Hospital, Chicago, IL, USA; Northwestern University, Evanston, IL, USA; Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
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149
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Thomsen K, Pedersen HP, Iversen S, Wiese L, Fuursted K, Nielsen HV, Christensen JJE, Nielsen XC. Extensive microbiological respiratory tract specimen characterization in critically ill COVID-19 patients. APMIS 2021; 129:431-437. [PMID: 33950572 PMCID: PMC8239678 DOI: 10.1111/apm.13143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 04/28/2021] [Indexed: 12/23/2022]
Abstract
Microbial co‐infections may contribute to the pulmonary deterioration in COVID‐19 patients needing intensive care treatment. The present study portrays the extent of co‐infections in COVID‐19 ICU patients. Conventional culture, molecular detections for atypical aetiologies, QiaStat‐Dx® respiratory panel V2 detecting 21 respiratory pathogens and ribosomal DNA genes 16S/18S amplicon‐based microbiome analyses were performed on respiratory samples from 34 COVID‐19 patients admitted to the ICU. Potential pathogens were detected in seven patients (21%) by culturing, in four patients (12%) by microbiome analysis and in one patient (3%) by respiratory panel. Among 20 patients receiving antibiotics prior to ICU admission, fungi (3 Candidaalbicans, 1 C. tropicalis, 1 C. dubliniensis) were cultured in 5 (15%) endotracheal aspirates. Among 14 patients who were antibiotic‐naive at ICU admission, two patients (6%) had bacterial respiratory pathogens (Staphylococcusaureus, Streptococcuspseudopneumoniae) cultured in their endotracheal aspirates. Microbiome analysis recognized four potential respiratory pathogens (3 Haemophilusinfluenza, 1 Fusobacterium necrophorum) isolated in samples from four other patients (12%). QiaStat‐Dx® respiratory panel V2 detected adenovirus in one patient (3%). The prevalence of pulmonary microbial co‐infections is modest among COVID‐19 patients upon admission to ICU. Microbiome analysis complements conventional microbial diagnostics in characterization of respiratory co‐infections.
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Affiliation(s)
- Kim Thomsen
- The Regional Department of Clinical Microbiology, Zealand University Hospital, Roskilde, Denmark
| | | | - Susanne Iversen
- Department of Anaesthesiology, Slagelse Hospital, Slagelse, Denmark
| | - Lothar Wiese
- Department of Infectious Diseases, Zealand University Hospital Roskilde, Roskilde, Denmark
| | - Kurt Fuursted
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Henrik Vedel Nielsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Jens Jørgen Elmer Christensen
- The Regional Department of Clinical Microbiology, Zealand University Hospital, Roskilde, Denmark.,Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Xiaohui Chen Nielsen
- The Regional Department of Clinical Microbiology, Zealand University Hospital, Roskilde, Denmark
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150
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Jiao M, Deng X, Yang H, Dong J, Lv J, Li F. Case Report: A Severe and Multi-Site Nocardia farcinica Infection Rapidly and Precisely Identified by Metagenomic Next-Generation Sequencing. Front Med (Lausanne) 2021; 8:669552. [PMID: 34109198 PMCID: PMC8183679 DOI: 10.3389/fmed.2021.669552] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 04/29/2021] [Indexed: 01/29/2023] Open
Abstract
Nocardia genus is an aerobic, gram-positive, and opportunistic pathogen, which mainly affects cell-mediated immunosuppressed patients. Early diagnosis and treatment greatly improve prognosis. However, the limitation of golden standard-bacterial culture exists. Here, we report a 61-year-old male with pneumonia, sepsis and intermuscular abscesses induced by Nocardia farcinica. Venous blood culture reported negative results. Former improper diagnosis and treatment did not improve his condition. With the assistant of metagenomic next-generation sequencing, the pathogen was identified as Nocardia farcinica. He was then applied with accurate treatment and had a remarkable clinical and radiological improvement.
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Affiliation(s)
- Mengfan Jiao
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Precision Medicine Center, Gene Hospital of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiang Deng
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hongfu Yang
- Department of Integrated Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Junqiang Dong
- Department of Imaging and Nuclear Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jun Lv
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Fang Li
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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