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Yao X, Zhao G, Wang L, Jia C. Study on the value of second-generation sequencing technology in the clinical diagnosis of osteoarticular brucellosis. J Orthop Res 2024; 42:2327-2335. [PMID: 38722074 DOI: 10.1002/jor.25867] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/21/2024] [Accepted: 04/23/2024] [Indexed: 10/19/2024]
Abstract
To assess the value of next-generation sequencing (NGS) technology in the diagnosis of osteoarticular brucellosis pathogenesis. Fifty eight patients admitted to the Department of Orthopaedics, Hebei Provincial Chest Hospital from January 2021 to January 2023 were retrospectively analyzed, and the patients were classified into 48 cases in the osteoarticular brucellosis group and 10 cases in the nonosteoarticular brucellosis group according to the final clinical diagnosis. All patients underwent serum agglutination test (SAT), CT-guided puncture or surgical sampling of lesions for bacteriological culture and NGS after admission. The diagnostic efficacy of these three methods for osteoarticular brucellosis was compared using the final clinical diagnosis as the reference standard. Among the 58 patients with suspected osteoarticular brucellosis, 40 cases (68.97%) were positive by NGS, 33 cases (56.89%) by SAT and 10 cases (17.24%) by culture, and the differences were statistically significant (p < 0.05). Using the final clinical diagnosis as a criterion, the sensitivity of NGS, SAT, and culture for the detection of osteoarticular brucellosis was 83.33%, 62.50%, and 20.83%, respectively, the specificity was 100.00%, 70.00%, and 100.00%, the diagnostic accuracy was 86.20%, 63.79%, and 34.49%, and the κ values were 0.799, 0.590, and 0.504, respectively. NGS has a high pathogen detection rate and sensitivity in the pathogenetic diagnosis of patients with osteoarticular brucellosis and can provide clinical guidance for the diagnosis and management of patients with osteoarticular brucellosis.
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Affiliation(s)
- Xiaowei Yao
- Department of Orthopedics, The Chest Hospital of Hebei Province, Shijiazhuang, China
| | - Guisong Zhao
- Department of Orthopedics, The Chest Hospital of Hebei Province, Shijiazhuang, China
| | - Lianbo Wang
- Department of Orthopedics, The Chest Hospital of Hebei Province, Shijiazhuang, China
| | - Chenguang Jia
- Department of Orthopedics, The Chest Hospital of Hebei Province, Shijiazhuang, China
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Chen Z, Ye T, He Y, Pan A, Mei Q. Use of pus metagenomic next-generation sequencing for efficient identification of pathogens in patients with sepsis. Folia Microbiol (Praha) 2024; 69:1003-1011. [PMID: 38341816 PMCID: PMC11379781 DOI: 10.1007/s12223-024-01134-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 01/12/2024] [Indexed: 02/13/2024]
Abstract
The positive detection rate of blood metagenomic next-generation sequencing (mNGS) was still too low to meet clinical needs, while pus from the site of primary infection may be advantageous for identification of pathogens. To assess the value of mNGS using pus in patients with sepsis, thirty-five samples were collected. Pathogen identification and mixed infection diagnosis obtained by use of mNGS or cultivation methods were compared. Fifty-three aerobic or facultative anaerobes, 59 obligate anaerobes and 7 fungi were identified by the two methods. mNGS increased the accuracy rate of diagnosing aerobic or facultative anaerobic infections from 44.4% to 94.4%; mNGS also increased the sensitivity of diagnosing obligate anaerobic infections from 52.9% to 100.0%; however, mNGS did not show any advantage in terms of fungal infections. Culture and mNGS identified 1 and 24 patients with mixed infection, respectively. For obligate anaerobes, source of microorganisms was analyzed. The odontogenic bacteria all caused empyema (n = 7) or skin and soft tissue infections (n = 5), whereas the gut-derived microbes all caused intra-abdominal infections (n = 7). We also compared the clinical characteristics of non-obligate anaerobic and obligate anaerobic infection groups. The SOFA score [9.0 (7.5, 14.3) vs. 5.0 (3.0, 8.0), P = 0.005], procalcitonin value [4.7 (1.8, 39.9) vs. 2.50 (0.7, 8.0), P = 0.035], the proportion of septic shock (66.7% vs. 35.3%, P = 0.044) and acute liver injury (66.7% vs. 23.5%, P = 0.018) in the non-obligate anaerobic infection group were significantly higher than those in the obligate anaerobic infection group. In patients with sepsis caused by purulent infection, mNGS using pus from the primary lesion may yield more valuable microbiological information.
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Affiliation(s)
- Zhendong Chen
- Department of Intensive Care Unit, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Tingting Ye
- Department of Cardiovascular Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Yuxi He
- Department of Intensive Care Unit, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Aijun Pan
- Department of Intensive Care Unit, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China.
- Department of Intensive Care Unit, The Affiliated Provincial Hospital of Anhui Medical University, Anhui, 230001, China.
- WanNan Medical College, Wuhu, 241002, Anhui, China.
| | - Qing Mei
- Department of Intensive Care Unit, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China.
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Liu H, Ran Q, Ma J, Zhang J, Tan N, Xi L, Li X, Zhang J, Lu S. Retrospective clinical and microbiologic analysis of metagenomic next-generation sequencing in the microbiological diagnosis of cutaneous infectious granulomas. Ann Clin Microbiol Antimicrob 2024; 23:84. [PMID: 39267031 PMCID: PMC11395180 DOI: 10.1186/s12941-024-00744-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 09/05/2024] [Indexed: 09/14/2024] Open
Abstract
BACKGROUND Cutaneous infectious granulomas (CIG) are localized and chronic skin infection caused by a variety of pathogens such as protozoans, bacteria, worms, viruses and fungi. The diagnosis of CIG is difficult because microbiological examination shows low sensitivity and the histomorphological findings of CIG caused by different pathogens are commonly difficult to be distinguished. OBJECTIVE The objective of this study is to explore the application of mNGS in tissue sample testing for CIG cases, and to compare mNGS with traditional microbiological methods by evaluating sensitivity and specificity. METHODS We conducted a retrospective study at the Department of Dermatology of Sun Yat-sen Memorial Hospital, Sun Yat-sen University from January 1st, 2020, to May 31st, 2024. Specimens from CIG patients with a clinical presentation of cutaneous infection that was supported by histological examination were retrospectively enrolled. Specimens were delivered to be tested for microbiological examinations and mNGS. RESULTS Our data show that mNGS detected Non-tuberculosis mycobacteria, Mycobacterium tuberculosis, fungi and bacteria in CIG. Compared to culture, mNGS showed a higher positive rate (80.77% vs. 57.7%) with high sensitivity rate (100%) and negative predictive value (100%). In addition, mNGS can detect more pathogens in one sample and can be used to detect variable samples including the samples of paraffin-embedded tissue with shorter detective time. Of the 21 patients who showed clinical improvement within a 30-day follow-up, eighteen had their treatments adjusted, including fifteen who continued treatment based on the results of mNGS. CONCLUSIONS mNGS could provide a potentially rapid and effective alternative detection method for diagnosis of cutaneous infectious granulomas and mNGS results may affect the clinical prognosis resulting from enabling the patients to initiate timely treatment.
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Affiliation(s)
- Hsingmei Liu
- Department of Dermatology and Venereology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, #107 Yanjiang West Rd., Guangzhou, 510120, Guangdong, China
| | - Qiao Ran
- Department of Dermatology and Venereology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, #107 Yanjiang West Rd., Guangzhou, 510120, Guangdong, China
- The Third People's Hospital of Zhuhai, Hezheng Road, Xiangzhou District, Zhuhai City, 519075, Guangdong, China
| | - Jianchi Ma
- Department of Dermatology and Venereology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, #107 Yanjiang West Rd., Guangzhou, 510120, Guangdong, China
| | - Jing Zhang
- Department of Dermatology and Venereology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, #107 Yanjiang West Rd., Guangzhou, 510120, Guangdong, China
| | - Ni Tan
- Department of Dermatology and Venereology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, #107 Yanjiang West Rd., Guangzhou, 510120, Guangdong, China
- Cellular and Molecular Diagnostics Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, Guangdong, China
| | - Liyan Xi
- Department of Dermatology and Venereology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, #107 Yanjiang West Rd., Guangzhou, 510120, Guangdong, China
| | - Xiqing Li
- Department of Dermatology and Venereology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, #107 Yanjiang West Rd., Guangzhou, 510120, Guangdong, China
| | - Junmin Zhang
- Department of Dermatology and Venereology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, #107 Yanjiang West Rd., Guangzhou, 510120, Guangdong, China
| | - Sha Lu
- Department of Dermatology and Venereology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, #107 Yanjiang West Rd., Guangzhou, 510120, Guangdong, China.
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Pan TJ, Luo WW, Zhang SS, Xie JY, Xu Z, Zhong YY, Zou XF, Gong HJ, Ye ML. The clinical application value of multi-site mNGS detection of patients with sepsis in intensive care units. BMC Infect Dis 2024; 24:920. [PMID: 39232674 PMCID: PMC11375821 DOI: 10.1186/s12879-024-09822-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 08/27/2024] [Indexed: 09/06/2024] Open
Abstract
BACKGROUND Sepsis remains a leading cause of mortality in intensive care units, and rapid and accurate pathogen detection is crucial for effective treatment. This study evaluated the clinical application of multi-site metagenomic next-generation sequencing (mNGS) for the diagnosis of sepsis, comparing its performance against conventional methods. METHODS A retrospective analysis was conducted on 69 patients with sepsis consecutively admitted to the Department of Intensive Care Medicine, Meizhou People's Hospital. Samples of peripheral blood and infection sites were collected for mNGS and conventional method tests to compare the positive rate of mNGS and traditional pathogen detection methods and the distribution of pathogens. The methods used in this study included a comprehensive analysis of pathogen consistency between peripheral blood and infection site samples. Additionally, the correlation between the pathogens detected and clinical outcomes was investigated. RESULTS Of the patients with sepsis, 57.97% experienced dyspnea, and 65.2% had underlying diseases, with hypertension being the most common. mNGS demonstrated a significantly higher pathogen detection rate (88%) compared to the conventional method tests (26%). The pathogen consistency rate was 60% between plasma and bronchoalveolar lavage fluid samples, and that of plasma and local body fluid samples was 63%. The most frequently detected pathogens were gram-negative bacteria, and Klebsiella pneumonia. There were no significant differences in the clinical features between the pathogens. CONCLUSION mNGS is significantly superior to conventional methods in pathogen detection. There was a notable high pathogen consistency detection between blood and local body fluid samples, supporting the clinical relevance of mNGS. This study highlights the superiority of mNGS in detecting a broad spectrum of pathogens quickly and accurately. TRIAL REGISTRATION Not applicable.
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Affiliation(s)
- Ting-Jun Pan
- The Fourth Department of Intensive Care Medicine, Meizhou People's Hospital, Meizhou, Guangdong, 514031, China.
| | - Wei-Wen Luo
- The Fourth Department of Intensive Care Medicine, Meizhou People's Hospital, Meizhou, Guangdong, 514031, China
| | - Song-Sheng Zhang
- The Fourth Department of Intensive Care Medicine, Meizhou People's Hospital, Meizhou, Guangdong, 514031, China
| | - Jie-Yao Xie
- The Fourth Department of Intensive Care Medicine, Meizhou People's Hospital, Meizhou, Guangdong, 514031, China
| | - Zhou Xu
- The Fourth Department of Intensive Care Medicine, Meizhou People's Hospital, Meizhou, Guangdong, 514031, China
| | - Ying-Yu Zhong
- The First Department of Intensive Care Medicine, Meizhou People's Hospital, Meizhou People's Hospital, Meizhou, Guangdong, 514031, China
| | - Xiao-Fen Zou
- The First Department of Intensive Care Medicine, Meizhou People's Hospital, Meizhou People's Hospital, Meizhou, Guangdong, 514031, China
| | - Hui-Juan Gong
- The Fourth Department of Intensive Care Medicine, Meizhou People's Hospital, Meizhou, Guangdong, 514031, China
| | - Mei-Ling Ye
- The First Department of Intensive Care Medicine, Meizhou People's Hospital, Meizhou People's Hospital, Meizhou, Guangdong, 514031, China
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Hu X, Jiang L, Liu X, Chang H, Dong H, Yan J, Zhou X, Kong M. The diagnostic value of bronchoalveolar lavage fluid metagenomic next-generation sequencing in critically ill patients with respiratory tract infections. Microbiol Spectr 2024; 12:e0045824. [PMID: 38916357 PMCID: PMC11302328 DOI: 10.1128/spectrum.00458-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 05/18/2024] [Indexed: 06/26/2024] Open
Abstract
Metagenomic next-generation sequencing (mNGS) is an unbiased and rapid method for detecting pathogens. This study enrolled 145 suspected severe pneumonia patients who were admitted to the Affiliated Hospital of Jining Medical University. This study primarily aimed to determine the diagnostic performance of mNGS and conventional microbiological tests (CMTs) using bronchoalveolar lavage fluid samples for detecting pathogens. Our findings indicated that mNGS performed significantly higher sensitivity (97.54% vs 28.68%, P < 0.001), coincidence (90.34% vs 35.17%, P < 0.001), and negative predictive value (80.00% vs 13.21%, P < 0.001) but performed lower specificity than CMTs (52.17% vs 87.5%, P < 0.001). Streptococcus pneumoniae as the most common bacterial pathogen had the largest proportion (22.90%, 30/131) in this study. In addition to bacteria, fungi, and virus, mNGS can detect a variety of atypical pathogens such as Mycobacterium tuberculosis and non-tuberculous. Mixed infections were common in patients with severe pneumonia, and bacterial-fungal-viral-atypical pathogens were the most complicated infection. After adjustments of antibiotics based on mNGS and CMTs, the clinical manifestation improved in 139 (95.86%, 139/145) patients. Our data demonstrated that mNGS had significant advantage in diagnosing respiratory tract infections, especially atypical pathogens and fungal infections. Pathogens were detected timely and comprehensively, contributing to the adjustments of antibiotic treatments timely and accurately, improving patient prognosis and decreasing mortality potentially.IMPORTANCEMetagenomic next-generation sequencing using bronchoalveolar lavage fluid can provide more comprehensive and accurate pathogens for respiratory tract infections, especially when considering the previous usage of empirical antibiotics before admission or complicated clinical presentation. This technology is expected to play an important role in the precise application of antimicrobial drugs in the future.
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Affiliation(s)
- Xiaohang Hu
- Medical Laboratory Science, Affiliated Hospital of Jining Medical University, Jining Medical University, Shandong Jining, China
| | - Liqing Jiang
- Medical Laboratory Science, Affiliated Hospital of Jining Medical University, Jining Medical University, Shandong Jining, China
| | - Xiaowei Liu
- Department of Intensive Care Unit, Affiliated Hospital of Jining Medical University,Jining Medical University, Shandong Jining, China
| | - Hong Chang
- Medical Laboratory Science, Affiliated Hospital of Jining Medical University, Jining Medical University, Shandong Jining, China
| | - Haixin Dong
- Medical Laboratory Science, Affiliated Hospital of Jining Medical University, Jining Medical University, Shandong Jining, China
| | - Jinyan Yan
- Medical Laboratory Science, Affiliated Hospital of Jining Medical University, Jining Medical University, Shandong Jining, China
| | - Xiaoya Zhou
- Medical Laboratory of Jining Medical University, Lin He's Academician Workstation of New Medicine and Clinical Translation in Jining Medical University, Jining Medical University, Shandong Jining, China
| | - Min Kong
- Medical Laboratory of Jining Medical University, Lin He's Academician Workstation of New Medicine and Clinical Translation in Jining Medical University, Jining Medical University, Shandong Jining, China
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Jiang L, Liang TW, Al-Odaini N, Hu Y, Huang M, Wei L, Li XY, Pan KS, Zheng DY, Jiang ZW, Wei G, Cao CW. Metagenomic Next-Generation Sequencing as an Effective Diagnostic Tool for Talaromycosis in HIV-Negative Patients. Mycopathologia 2024; 189:63. [PMID: 38985209 DOI: 10.1007/s11046-024-00866-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Accepted: 06/05/2024] [Indexed: 07/11/2024]
Abstract
The diagnosis of Talaromyces marneffei infection in HIV-negative patients remains challenging. There is an urgent need for rapid and convenient methods to diagnose this complicated disease. The aim of this study was to evaluate the diagnostic efficiency of metagenomic next-generation sequencing (mNGS) for talaromycosis in non-HIV-infected patients by comparing mNGS with traditional microbial culture. In total, 66 samples from 57 patients were analyzed via both mNGS and microbial culture. The ROC curve showed a sensitivity for mNGS of 97.22%, which was greater than that of microbial culture (61.11%). Samples from the respiratory tract, infectious skin lesions, and lymph nodes are recommended as routine samples for talaromycosis detection via mNGS. Furthermore, mNGS significantly reduced the diagnostic time compared to microbial culture. Overall, our study demonstrated that mNGS is a promising tool for rapid and accurate pathogenic detection in HIV-negative patients with talaromycosis.
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Affiliation(s)
- Li Jiang
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
- Fangchenggang Wanqing Institute of Mycosis Prevention and Control, Fangchenggang, China
| | - Tian-Wei Liang
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
- Fangchenggang Wanqing Institute of Mycosis Prevention and Control, Fangchenggang, China
| | - Najwa Al-Odaini
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
- Fangchenggang Wanqing Institute of Mycosis Prevention and Control, Fangchenggang, China
| | - Yuan Hu
- Richardson Medical Fungal Laboratory, Guangzhou Centre for Fungal Diagnostics and Research, Guangzhou, China
| | - Minli Huang
- Department of Ophthalmology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Lili Wei
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
- Fangchenggang Wanqing Institute of Mycosis Prevention and Control, Fangchenggang, China
| | - Xiu-Ying Li
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
- Fangchenggang Wanqing Institute of Mycosis Prevention and Control, Fangchenggang, China
| | - Kai-Su Pan
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
- Fangchenggang Wanqing Institute of Mycosis Prevention and Control, Fangchenggang, China
| | - Dong-Yan Zheng
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
- Fangchenggang Wanqing Institute of Mycosis Prevention and Control, Fangchenggang, China
| | - Zhi-Wen Jiang
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
- Fangchenggang Wanqing Institute of Mycosis Prevention and Control, Fangchenggang, China
| | - Gao Wei
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China.
- Fangchenggang Wanqing Institute of Mycosis Prevention and Control, Fangchenggang, China.
| | - Cun-Wei Cao
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China.
- Fangchenggang Wanqing Institute of Mycosis Prevention and Control, Fangchenggang, China.
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Hong D, Wang P, Xu Y, Xu S, Yu L, Tong Z, Li W, Qin K, Ke L. Metagenomic Next-Generation Sequencing-Based Fine-Needle Aspiration in Patients With Suspected Infected Pancreatic Necrosis. Clin Transl Gastroenterol 2024; 15:e00726. [PMID: 38870091 PMCID: PMC11272294 DOI: 10.14309/ctg.0000000000000726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Accepted: 06/06/2024] [Indexed: 06/15/2024] Open
Abstract
INTRODUCTION Fine-needle aspiration (FNA) is no longer recommended for diagnosing infected pancreatic necrosis (IPN) due to a high false-negative rate. Metagenomic next-generation sequencing (mNGS) is a valuable tool for identifying potential pathogens. We hypothesized that adding mNGS to the standard FNA procedure may increase diagnostic accuracy. METHODS This is a prospective, single-arm feasibility study enrolling patients with acute necrotizing pancreatitis complicated by suspected IPN. Computed tomography-guided FNA was performed immediately after enrollment, and the drainage samples were subjected to culture and mNGS assays simultaneously. Confirmatory IPN within the following week of the index FNA procedure was the reference standard. The diagnostic performance of FNA-mNGS and the impact of mNGS results on treatment were evaluated. Historical controls were used for comparison of clinical outcomes. RESULTS There was no significant difference between mNGS and culture in the positive rate (75% vs 70%, P = 0.723). The accuracy of FNA-mNGS was 80.0%, with a sensitivity of 82.35%, specificity of 66.67%, positive predictive value of 93.3%, and negative predictive value of 40.0%. The results of the mNGS led to treatment change in 16 of 20 patients (80%), including implementing percutaneous catheter drainage (n = 7), expanding antibiotic coverage (n = 2), percutaneous catheter drainage and expanding coverage (n = 4), narrowing antibiotic coverage (n = 1), and discontinuation of antibiotics (n = 2). The FNA-mNGS approach was not associated with improved clinical outcomes compared with the historical control group. DISCUSSION The addition of mNGS to standard FNA has comparable diagnostic accuracy with culture-based FNA and may not be associated with improved clinical outcomes.
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Affiliation(s)
- Donghuang Hong
- Department of Critical Care Medicine, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, China
- Center of Severe Acute Pancreatitis (CSAP), Department of Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Peng Wang
- Center of Severe Acute Pancreatitis (CSAP), Department of Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Yao Xu
- Center of Severe Acute Pancreatitis (CSAP), Department of Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Shan Xu
- Department of Emergency Medicine, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Lei Yu
- Department of Emergency Medicine, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zhihui Tong
- Center of Severe Acute Pancreatitis (CSAP), Department of Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Weiqin Li
- Center of Severe Acute Pancreatitis (CSAP), Department of Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
- National Institute of Healthcare Data Science, Nanjing University, Nanjing, China
| | - Kaixiu Qin
- Department of Emergency Medicine, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Lu Ke
- Center of Severe Acute Pancreatitis (CSAP), Department of Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
- National Institute of Healthcare Data Science, Nanjing University, Nanjing, China
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Wang D, Chen H, Zhao C, Song H, Zhang J, Zhao F, Liang J, Xu W, Tang Y, Xu X. The impact of neutrophil count on the results of metagenomic next-generation sequencing in immunocompromised febrile children. Heliyon 2024; 10:e32816. [PMID: 38975197 PMCID: PMC11226820 DOI: 10.1016/j.heliyon.2024.e32816] [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: 09/16/2023] [Revised: 06/09/2024] [Accepted: 06/10/2024] [Indexed: 07/09/2024] Open
Abstract
Metagenomic next-generation sequencing (mNGS) has revolutionized the detection of pathogens, particularly in immunocompromised individuals such as pediatric patients undergoing intensive chemotherapy and hematopoietic stem cell transplantation. This study aims to explore the impact of neutrophil count on the diagnostic efficacy of mNGS in diagnosing infections in pediatric patients with febrile diseases. We conducted a retrospective analysis of pediatric patients with febrile diseases in the hematology/oncology department from January 2019 to September 2022. The study included 387 patients with 516 febrile episodes. Analyzing data from 516 pediatric cases, our study found that 70.7 % had febrile neutropenia (FN) and 29.3 % had febrile without neutropenia (FWN). mNGS demonstrated a high positive detection rate of 84.9 %, compared to 29.7 % for conventional microbiological tests (CMT). While the positive detection rates of mNGS were similar in both FN and FWN groups, bacterial pathogens were more frequently detected in FN patients. Furthermore, the rate of identifying a "probable" microbial etiology was lower in the FN group (46.8 %) compared to the FWN group (65.6 %, p<0.001). When analyzing the types of organisms and specimens, the "probable" identification rates were particularly lower for viruses and fungi detected by mNGS, as well as in blood and nasopharyngeal swab samples. These findings underscore the significant influence of neutrophil counts on mNGS results in pediatric febrile patients and highlight the necessity for tailored diagnostic approaches in this population.
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Affiliation(s)
- Di Wang
- Division/Center of Pediatric Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, PR China
- The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, PR China
| | - Haipin Chen
- Division/Center of Pediatric Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, PR China
| | - Cheng Zhao
- Division/Center of Pediatric Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, PR China
| | - Hua Song
- Division/Center of Pediatric Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, PR China
- The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, PR China
| | - Jingying Zhang
- Division/Center of Pediatric Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, PR China
- The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, PR China
| | - Fenying Zhao
- Division/Center of Pediatric Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, PR China
- The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, PR China
| | - Juan Liang
- Division/Center of Pediatric Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, PR China
- The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, PR China
| | - Weiqun Xu
- Division/Center of Pediatric Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, PR China
- The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, PR China
| | - Yongmin Tang
- Division/Center of Pediatric Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, PR China
- The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, PR China
| | - Xiaojun Xu
- Division/Center of Pediatric Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, PR China
- The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, PR China
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Alicehajic A, Duivenvoorden AAM, Lenaerts K. Unveiling the molecular complexity of intestinal ischemia-reperfusion injury through omics technologies. Proteomics 2024; 24:e2300160. [PMID: 38477684 DOI: 10.1002/pmic.202300160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 02/28/2024] [Accepted: 02/29/2024] [Indexed: 03/14/2024]
Abstract
Intestinal ischemia-reperfusion injury (IR) is implicated in various clinical conditions and causes damage to the intestinal epithelium resulting in intestinal barrier loss. This presents a substantial clinical challenge, emphasizing the importance of gaining a comprehensive understanding of molecular events to aid in the identification of novel therapeutic targets. This review systematically explores the extent to which omics technologies-transcriptomics, proteomics, metabolomics, and metagenomics-have already contributed to deciphering the molecular mechanisms contributing to intestinal IR injury, in in vivo and in vitro animal and human models, and in clinical samples. Recent breakthroughs involve applying omics methodologies on exosomes, organoids, and single cells, shedding light on promising avenues and valuable targets to reduce intestinal IR injury. Future directions aimed at expediting clinical translation are discussed as well and include multi-omics data integration to facilitate the identification of key regulatory nodes driving intestinal IR injury and advancing human organoid models based on the novel insights by single-cell omics technologies, offering hope for clinical application of therapeutic strategies in the years to come.
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Affiliation(s)
- Anja Alicehajic
- Department of Surgery, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands
| | - Annet Adriana Maria Duivenvoorden
- Department of Surgery, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands
| | - Kaatje Lenaerts
- Department of Surgery, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands
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Zou YS, Cao ZL, Guo Y, Wang BB, Wang JL, Cheng R, Yang Y, Zhou XG. The application value of metagenomic next-generation sequencing technology in the diagnosis and treatment of neonatal infectious meningitis - a single center retrospective case-control study. Neurol Res 2024; 46:561-567. [PMID: 38563313 DOI: 10.1080/01616412.2024.2337523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 03/26/2024] [Indexed: 04/04/2024]
Abstract
OBJECTIVE This retrospective study was conducted to investigate the application value of metagenomics next generation sequencing (mNGS) technology in the diagnosis and treatment of neonatal infectious meningitis. METHODS From 1 January 2020 to 31 December 2022, 73 newborns suspected of infectious meningitis were hospitalized. After screening by inclusion and exclusion criteria, 69 newborns were subsequently included in the study, containing 27 cases with positive mNGS result and 42 cases with negative mNGS result. Furthermore, according to the diagnosis of meningitis, mNGS positive group and mNGS negative group were further divided into infectious meningitis with mNGS (+) group (n = 27) and infectious meningitis with mNGS (-) group (n = 26), respectively. RESULTS (1) Compared with cerebrospinal fluid (CSF) culture, mNGS has better diagnostic value [positive predictive value (PPV) = 100.00% (27/27), negative predictive value (NPV) = 38.10% (16/42), agreement rate = 62.32% (43/69), area under the curve (AUC) = 0.750, 95% confidence interval (CI): 0.636-0.864]. (2) There were significant differences in the onset age, age at first CSF test, CSF leukocyte count, CSF glucose, positive rate of CSF culture, blood leukocyte count, procalcitonin (PCT), C-reaction protein (CRP), age at first mNGS test and adjusting anti-infective medication in the comparison between infectious meningitis with mNGS (+) group and infectious meningitis with mNGS (-) group (p < 0.05). (3) mNGS could help improve the cure rate [crude odds ratio (OR) = 3.393, 95%CI: 1.072-10.737; adjusted OR = 15.580, 95%CI: 2.114-114.798]. CONCLUSION Compared with classic meningitis detection methods, mNGS has better PPV, NPV, agreement rate, and AUC. mNGS could help improve the cure rate.
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Affiliation(s)
- Yun-Su Zou
- Department of Neonates, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu, P.R. China
| | - Zhao-Lan Cao
- Department of Neonates, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu, P.R. China
| | - Yan Guo
- Department of Neonates, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu, P.R. China
| | - Bei-Bei Wang
- Department of Neonates, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu, P.R. China
| | - Jia-Li Wang
- Department of Neonates, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu, P.R. China
| | - Rui Cheng
- Department of Neonates, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu, P.R. China
| | - Yang Yang
- Department of Neonates, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu, P.R. China
| | - Xiao-Guang Zhou
- Department of Neonates, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu, P.R. China
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Liu Y, Ma Y. Clinical applications of metagenomics next-generation sequencing in infectious diseases. J Zhejiang Univ Sci B 2024; 25:471-484. [PMID: 38910493 PMCID: PMC11199093 DOI: 10.1631/jzus.b2300029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 06/06/2023] [Indexed: 05/23/2024]
Abstract
Infectious diseases are a great threat to human health. Rapid and accurate detection of pathogens is important in the diagnosis and treatment of infectious diseases. Metagenomics next-generation sequencing (mNGS) is an unbiased and comprehensive approach for detecting all RNA and DNA in a sample. With the development of sequencing and bioinformatics technologies, mNGS is moving from research to clinical application, which opens a new avenue for pathogen detection. Numerous studies have revealed good potential for the clinical application of mNGS in infectious diseases, especially in difficult-to-detect, rare, and novel pathogens. However, there are several hurdles in the clinical application of mNGS, such as: (1) lack of universal workflow validation and quality assurance; (2) insensitivity to high-host background and low-biomass samples; and (3) lack of standardized instructions for mass data analysis and report interpretation. Therefore, a complete understanding of this new technology will help promote the clinical application of mNGS to infectious diseases. This review briefly introduces the history of next-generation sequencing, mainstream sequencing platforms, and mNGS workflow, and discusses the clinical applications of mNGS to infectious diseases and its advantages and disadvantages.
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Affiliation(s)
- Ying Liu
- Department of Clinical Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua 321000, China
| | - Yongjun Ma
- Department of Clinical Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua 321000, China.
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12
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Wu Y, Wu J, Xu N, Lin M, Yue W, Chen Y, Zhang Q, Li H. Clinical application value of metagenome next-generation sequencing in pulmonary diffuse exudative lesions: a retrospective study. Front Cell Infect Microbiol 2024; 14:1367885. [PMID: 38784566 PMCID: PMC11113015 DOI: 10.3389/fcimb.2024.1367885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 04/09/2024] [Indexed: 05/25/2024] Open
Abstract
Objective This study aims to investigate the clinical application value of Metagenome Next-Generation Sequencing (mNGS) for pulmonary diffuse exudative lesions. Methods From January 1, 2014, to November 31, 2021, 136 cases with chest radiologic presentations of pulmonary diffuse exudative lesions admitted to Fujian Provincial Hospital were included in the study; of those, 77 patients underwent mNGS pathogen detection. Based on the pathogen detection outcomes and clinical diagnoses, patients were categorized into an infection group (IG) and a non-infection group (NIG). A comparison was made between the diagnostic efficacy of the mNGS technique and traditional culture methods. Meanwhile, 59 patients clinically identified as having infectious pulmonary diffuse exudative lesions but who did not receive mNGS testing were designated as the non-NGS infection group (non-IG). A retrospective cohort study was conducted on patients in both the IG and non-IG, with a 30-day all-cause mortality endpoint used for follow-up. Outcomes When compared to conventional culture methods, mNGS demonstrated an approximate 35% increase in sensitivity (80.0% vs 45.5%, P<0.001), without significant disparity in specificity (77.3% vs 95.5%, P=0.185). Under antibiotic exposure, the positivity rate detected by mNGS was notably higher than that by traditional culture methods, indicating that mNGS is less affected by exposure to antibiotics (P<0.05). Within 30 days, the all-cause mortality rate for patients in the IG versus the non-IG was 14.55% and 37.29%, respectively (P<0.05). Following a COX regression analysis to adjust for confounding factors, the analysis revealed that a CURB-65 score ≥3 points (HR=3.348, P=0.001) and existing cardiovascular disease (HR=2.473, P=0.026) were independent risk factors for these patients. Conversely, mNGS testing (HR=0.368, P=0.017) proved to be an independent protective factor. Conclusion mNGS technology makes it easier to pinpoint the cause of pulmonary diffuse infectious exudative lesions without much interference from antibiotics, helping doctors spot and diagnose these issues early on, thereby playing a key role in helping them decide the best treatment approach for patients. Such conclusions may have a bias, as the performance of traditional methods might be underestimated due to the absence of complete results from other conventional diagnostic techniques like serological testing and PCR.
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Affiliation(s)
- Yisong Wu
- Fujian Provincial Hospital, Shengli Clinical College of Fujian Medical University, Fuzhou, Fujian, China
| | - Jian Wu
- Fujian Provincial Hospital, Shengli Clinical College of Fujian Medical University, Fuzhou, Fujian, China
| | - Nengluan Xu
- Department of Infectious Diseases, Fujian Provincial Hospital, Shengli Clinical College of Fujian Medical University, Fuzhou, Fujian, China
| | - Ming Lin
- Fujian Provincial Hospital, Shengli Clinical College of Fujian Medical University, Fuzhou, Fujian, China
| | - Wenxiang Yue
- Fujian Provincial Hospital, Shengli Clinical College of Fujian Medical University, Fuzhou, Fujian, China
| | - Yusheng Chen
- Fujian Provincial Hospital, Shengli Clinical College of Fujian Medical University, Fuzhou, Fujian, China
| | - Qiongyao Zhang
- Fujian Provincial Key Laboratory of Medical Big Data Engineering, Fujian Provincial Hospital, Fuzhou, Fujian, China
| | - Hongru Li
- Department of Infectious Diseases, Fujian Provincial Hospital, Shengli Clinical College of Fujian Medical University, Fuzhou, Fujian, China
- Fujian Provincial Key Laboratory of Medical Big Data Engineering, Fujian Provincial Hospital, Fuzhou, Fujian, China
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Wang X, Zhang H, Zhang N, Zhang S, Shuai Y, Miao X, Liu Y, Qiu L, Ren S, Lai S, Han Y, Yao H, Zhang X, Fan F, Sun H, Yi H. Application value of metagenomic next-generation sequencing in hematological patients with high-risk febrile neutropenia. Front Cell Infect Microbiol 2024; 14:1366908. [PMID: 38725449 PMCID: PMC11079123 DOI: 10.3389/fcimb.2024.1366908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 04/08/2024] [Indexed: 05/12/2024] Open
Abstract
Background Metagenomic next-generation sequencing (mNGS) is a novel non-invasive and comprehensive technique for etiological diagnosis of infectious diseases. However, its practical significance has been seldom reported in the context of hematological patients with high-risk febrile neutropenia, a unique patient group characterized by neutropenia and compromised immune responses. Methods This retrospective study evaluated the results of plasma cfDNA sequencing in 164 hematological patients with high-risk febrile neutropenia. We assessed the diagnostic efficacy and clinical impact of mNGS, comparing it with conventional microbiological tests. Results mNGS identified 68 different pathogens in 111 patients, whereas conventional methods detected only 17 pathogen types in 36 patients. mNGS exhibited a significantly higher positive detection rate than conventional methods (67.7% vs. 22.0%, P < 0.001). This improvement was consistent across bacterial (30.5% vs. 9.1%), fungal (19.5% vs. 4.3%), and viral (37.2% vs. 9.1%) infections (P < 0.001 for all comparisons). The anti-infective treatment strategies were adjusted for 51.2% (84/164) of the patients based on the mNGS results. Conclusions mNGS of plasma cfDNA offers substantial promise for the early detection of pathogens and the timely optimization of anti-infective therapies in hematological patients with high-risk febrile neutropenia.
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Affiliation(s)
- Xiao Wang
- Department of Hematology, The General Hospital of Western Theater Command, Chengdu, China
| | - Huiye Zhang
- School of Pharmacy, Chengdu Medical College, Chengdu, China
- Department of Pharmacy, Chengdu Eighth People’s Hospital, Chengdu, China
| | - Nan Zhang
- Department of Hematology, The General Hospital of Western Theater Command, Chengdu, China
| | - Shan Zhang
- Department of Hematology, The General Hospital of Western Theater Command, Chengdu, China
| | - Yanrong Shuai
- Department of Hematology, The General Hospital of Western Theater Command, Chengdu, China
| | - Xiaojuan Miao
- Department of Hematology, The General Hospital of Western Theater Command, Chengdu, China
| | - Yilan Liu
- Department of Hematology, The General Hospital of Western Theater Command, Chengdu, China
| | - Ling Qiu
- Department of Hematology, The General Hospital of Western Theater Command, Chengdu, China
| | - Shihui Ren
- Department of Hematology, The General Hospital of Western Theater Command, Chengdu, China
| | - Sihan Lai
- Department of Hematology, The General Hospital of Western Theater Command, Chengdu, China
| | - Ying Han
- Department of Hematology, The General Hospital of Western Theater Command, Chengdu, China
| | - Hao Yao
- Department of Hematology, The General Hospital of Western Theater Command, Chengdu, China
| | - Xupai Zhang
- Department of Hematology, The General Hospital of Western Theater Command, Chengdu, China
| | - Fangyi Fan
- Department of Hematology, The General Hospital of Western Theater Command, Chengdu, China
| | - Haoping Sun
- Department of Hematology, The General Hospital of Western Theater Command, Chengdu, China
| | - Hai Yi
- Department of Hematology, The General Hospital of Western Theater Command, Chengdu, China
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14
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Zhang D, Li X, Wang Y, Zhao Y, Zhang H. The clinical importance of metagenomic next-generation sequencing in detecting disease-causing microorganisms in cases of sepsis acquired in the community or hospital setting. Front Microbiol 2024; 15:1384166. [PMID: 38686114 PMCID: PMC11056561 DOI: 10.3389/fmicb.2024.1384166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 03/29/2024] [Indexed: 05/02/2024] Open
Abstract
Objectives Although metagenomic next-generation sequencing (mNGS) is commonly used for diagnosing infectious diseases, clinicians face limited options due to the high costs that are not covered by basic medical insurance. The goal of this research is to challenge this bias through a thorough examination and evaluation of the clinical importance of mNGS in precisely identifying pathogenic microorganisms in cases of sepsis acquired in the community or in hospitals. Methods A retrospective observational study took place at a tertiary teaching hospital in China from January to December 2021. Data on 308 sepsis patients were collected, and the performance of etiological examination was compared between mNGS and traditional culture method. Results Two hundred twenty-nine cases were observed in the community-acquired sepsis (CAS) group and 79 cases in the hospital-acquired sepsis (HAS) group. In comparison with conventional culture, mNGS showed a significantly higher rate of positivity in both the CAS group (88.21% vs. 25.76%, adj.P < 0.001) and the HAS group (87.34% vs. 44.30%, adj.P < 0.001), particularly across various infection sites and specimens, which were not influenced by factors like antibiotic exposure or the timing and frequency of mNGS technology. Sepsis pathogens detected by mNGS were broad, especially viruses, Mycobacterium tuberculosis, and atypical pathogens, with mixed pathogens being common, particularly bacterial-viral co-detection. Based on the optimization of antimicrobial therapy using mNGS, 58 patients underwent antibiotic de-escalation, two patients were switched to antiviral therapy, and 14 patients initiated treatment for tuberculosis, resulting in a reduction in antibiotic overuse but without significant impact on sepsis prognosis. The HAS group exhibited a critical condition, poor prognosis, high medical expenses, and variations in etiology, yet the mNGS results did not result in increased medical costs for either group. Conclusions mNGS demonstrates efficacy in identifying multiple pathogens responsible for sepsis, with mixed pathogens of bacteria and viruses being prevalent. Variability in microbiological profiles among different infection setting underscores the importance of clinical vigilance. Therefore, the adoption of mNGS for microbiological diagnosis of sepsis warrants acknowledgment and promotion.
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Affiliation(s)
| | | | | | | | - Hong Zhang
- Department of Emergency Medicine, The First Affiliated Hospital of Anhui Medical University, Anhui, Hefei, China
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15
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Ma L, Zhu C, Yan T, Hu Y, Zhou J, Li Y, Du F, Zhou J. Illumina and Nanopore sequencing in culture-negative samples from suspected lower respiratory tract infection patients. Front Cell Infect Microbiol 2024; 14:1230650. [PMID: 38638824 PMCID: PMC11024257 DOI: 10.3389/fcimb.2024.1230650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 03/14/2024] [Indexed: 04/20/2024] Open
Abstract
Objective To evaluate the diagnostic value of metagenomic sequencing technology based on Illumina and Nanopore sequencing platforms for patients with suspected lower respiratory tract infection whose pathogen could not be identified by conventional microbiological tests. Methods Patients admitted to the Respiratory and Critical Care Medicine in Shanghai Ruijin Hospital were retrospectively studied from August 2021 to March 2022. Alveolar lavage or sputum was retained in patients with clinically suspected lower respiratory tract infection who were negative in conventional tests. Bronchoalveolar lavage fluid (BALF) samples were obtained using bronchoscopy. Sputum samples were collected, while BALF samples were not available due to bronchoscopy contraindications. Samples collected from enrolled patients were simultaneously sent for metagenomic sequencing on both platforms. Results Thirty-eight patients with suspected LRTI were enrolled in this study, consisting of 36 parts of alveolar lavage and 2 parts of sputum. According to the infection diagnosis, 31 patients were confirmed to be infected with pathogens, while 7 patients were diagnosed with non-infectious disease. With regard to the diagnosis of infectious diseases, the sensitivity and specificity of Illumina and Nanopore to diagnose infection in patients were 80.6% vs. 93.5% and 42.9 vs. 28.6%, respectively. In patients diagnosed with bacterial, Mycobacterium, and fungal infections, the positive rates of Illumina and Nanopore sequencer were 71.4% vs. 78.6%, 36.4% vs. 90.9%, and 50% vs. 62.5%, respectively. In terms of pathogen diagnosis, the sensitivity and specificity of pathogens detected by Illumina and Nanopore were 55.6% vs. 77.8% and 42.9% vs. 28.6%, respectively. Among the patients treated with antibiotics in the last 2 weeks, 61.1% (11/18) and 77.8% (14/18) cases of pathogens were accurately detected by Illumina and Nanopore, respectively, among which 8 cases were detected jointly. The consistency between Illumina and diagnosis was 63.9% (23/36), while the consistency between Nanopore and diagnosis was 83.3% (30/36). Between Illumina and Nanopore sequencing methods, the consistency ratio was 55% (22/42) based on pathogen diagnosis. Conclusion Both platforms play a certain value in infection diagnosis and pathogen diagnosis of CMT-negative suspected LRTI patients, providing a theoretical basis for clinical accurate diagnosis and symptomatic treatment. The Nanopore platform demonstrated potential advantages in the identification of Mycobacterium and could further provide another powerful approach for patients with suspected Mycobacterium infection.
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Affiliation(s)
- Lichao Ma
- Department of Pulmonary and Critical Care Medicine, Wuxi Branch, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Wuxi, Jiangsu, China
| | - Chi Zhu
- State Key Laboratory of Neurology and Oncology Drug Development (Jiangsu Simcere Pharmaceutical Co., Ltd, Jiangsu Simcere Diagnostics Co., Ltd.), Jiangsu, China
- Nanjing Simcere Medical Laboratory Science Co., Ltd., Jiangsu, China
| | - Tianli Yan
- Department of Respiratory and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yun Hu
- Department of Respiratory and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Juan Zhou
- Department of Pulmonary and Critical Care Medicine, Wuxi Branch, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Wuxi, Jiangsu, China
| | - Yajing Li
- Department of Pulmonary and Critical Care Medicine, Wuxi Branch, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Wuxi, Jiangsu, China
| | - Furong Du
- State Key Laboratory of Neurology and Oncology Drug Development (Jiangsu Simcere Pharmaceutical Co., Ltd, Jiangsu Simcere Diagnostics Co., Ltd.), Jiangsu, China
| | - Jianping Zhou
- Department of Respiratory and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, China
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Yuan H, Ma X, Xu J, Han P, Rao G, Chen G, Zhang K, Yang R, Han C, Jiang M. Application of metagenomic next-generation sequencing in the clinical diagnosis of infectious diseases after allo-HSCT: a single-center analysis. BMC Infect Dis 2024; 24:279. [PMID: 38438967 PMCID: PMC10910774 DOI: 10.1186/s12879-024-09153-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 02/19/2024] [Indexed: 03/06/2024] Open
Abstract
BACKGROUND We investigated the value of metagenomic next-generation sequencing (mNGS) in diagnosing infectious diseases in patients receiving allogeneic hematopoietic stem cell transplantation (allo-HSCT). METHODS Fifty-four patients who had fever following allo-HSCT from October 2019 to February 2022 were enrolled. Conventional microbiological tests (CMTs) and mNGS, along with imaging and clinical manifestations, were used to diagnose infection following allo-HSCT. The clinical diagnostic value of mNGS was evaluated. RESULTS A total of 61 mNGS tests were performed, resulting in the diagnosis of 46 cases of infectious diseases. Among these cases, there were 22 cases of viral infection, 13 cases of fungal infection, and 11 cases of bacterial infection. Moreover, 27 cases (58.7%) were classified as bloodstream infections, 15 (32.6%) as respiratory infections, 2 (4.3%) as digestive system infections, and 2 (4.3%) as central nervous system infections. Additionally, there were 8 cases with non-infectious diseases (8/54, 14.81%), including 2 cases of interstitial pneumonia, 2 cases of bronchiolitis obliterans, 2 cases of engraftment syndrome, and 2 cases of acute graft-versus-host disease. The positive detection rates of mNGS and CMT were 88.9% and 33.3%, respectively, with significant differences (P < 0.001). The sensitivity of mNGS was 97.82%, the specificity was 25%, the positive predictive value was 93.75%, and the negative predictive value was 50%. Following treatment, 51 patients showed improvement, and 3 cases succumbed to multidrug-resistant bacterial infections. CONCLUSIONS mNGS plays an important role in the early clinical diagnosis of infectious diseases after allo-HSCT, which is not affected by immunosuppression status, empiric antibiotic therapy, and multi-microbial mixed infection.
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Affiliation(s)
- Hailong Yuan
- Hematology Center, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang Institute of Hematology, No.137 Liyushan South Road, Urumqi, 830054, China
| | - Xiaolu Ma
- Department of Hematology, Guangyuan Central Hospital, Guangyuan, Sichuan Province, China
| | - Jianli Xu
- Hematology Center, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang Institute of Hematology, No.137 Liyushan South Road, Urumqi, 830054, China
| | - Peng Han
- Genskey Medical Technology Co., Ltd, Beijing, China
| | - Guanhua Rao
- Genskey Medical Technology Co., Ltd, Beijing, China
| | - Gang Chen
- Hematology Center, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang Institute of Hematology, No.137 Liyushan South Road, Urumqi, 830054, China
| | - Kaile Zhang
- Hematology Center, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang Institute of Hematology, No.137 Liyushan South Road, Urumqi, 830054, China
| | - Ruixue Yang
- Hematology Center, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang Institute of Hematology, No.137 Liyushan South Road, Urumqi, 830054, China
| | - Chuixia Han
- Hematology Center, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang Institute of Hematology, No.137 Liyushan South Road, Urumqi, 830054, China
| | - Ming Jiang
- Hematology Center, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang Institute of Hematology, No.137 Liyushan South Road, Urumqi, 830054, China.
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Zhang H, Liang R, Zhu Y, Hu L, Xia H, Li J, Ye Y. Metagenomic next-generation sequencing of plasma cell-free DNA improves the early diagnosis of suspected infections. BMC Infect Dis 2024; 24:187. [PMID: 38347444 PMCID: PMC10863141 DOI: 10.1186/s12879-024-09043-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 01/22/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND Metagenomic next-generation sequencing (mNGS) could improve the diagnosed efficiency of pathogens in bloodstream infections or sepsis. Little is known about the clinical impact of mNGS test when used for the early diagnosis of suspected infections. Herein, our main objective was to assess the clinical efficacy of utilizing blood samples to perform mNGS for early diagnosis of suspected infections, as well as to evaluate its potential in guiding antimicrobial therapy decisions. METHODS In this study, 212 adult hospitalized patients who underwent blood mNGS test in the early stage of suspected infections were enrolled. Diagnostic efficacy of mNGS test and blood culture was compared, and the clinical impact of mNGS on clinical care was analyzed. RESULTS In our study, the total detection rate of blood mNGS was significantly higher than that of culture method (74.4% vs. 12.1%, P < 0.001) in the paired mNGS test and blood culture. Blood stream infection (107, 67.3%) comprised the largest component of all the diseases in our patients, and the detection rate of single blood sample subgroup was similar with that of multiple type of samples subgroup. Among the 187 patients complained with fever, there was no difference in the diagnostic efficacy of mNGS when blood specimens or additional other specimens were used in cases presenting only with fever. While, when patients had other symptoms except fever, the performance of mNGS was superior in cases with specimens of suspected infected sites and blood collected at the same time. Guided by mNGS results, therapeutic regimens for 70.3% cases (149/212) were changed, and the average hospitalized days were significantly shortened in cases with the earlier sampling time of admission. CONCLUSION In this study, we emphasized the importance of blood mNGS in early infectious patients with mild and non-specific symptoms. Blood mNGS can be used as a supplement to conventional laboratory examination, and should be performed as soon as possible to guide clinicians to perform appropriate anti-infection treatment timely and effectively. Additionally, combining the contemporaneous samples from suspected infection sites could improve disease diagnosis and prognoses. Further research needs to be better validated in large-scale clinical trials to optimize diagnostic protocol, and the cost-utility analysis should be performed.
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Affiliation(s)
- Hui Zhang
- Department of Infectious Diseases, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Ruobing Liang
- Department of Scientific Affaires, Hugobiotech Co., Ltd, Beijing, China
| | - Yunzhu Zhu
- Department of Infectious Diseases, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Lifen Hu
- Department of Infectious Diseases, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Han Xia
- Department of Scientific Affaires, Hugobiotech Co., Ltd, Beijing, China.
| | - Jiabin Li
- Department of Infectious Diseases, The First Affiliated Hospital of Anhui Medical University, Hefei, China.
- Institute of Bacterial Resistance, Anhui Medical University, Hefei, China.
- Anhui Center for Surveillance of Bacterial Resistance, Hefei, China.
| | - Ying Ye
- Department of Infectious Diseases, The First Affiliated Hospital of Anhui Medical University, Hefei, China.
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Wang C, Yin X, Ma W, Zhao L, Wu X, Ma N, Cao Y, Zhang Q, Ma S, Xu L, Wang X. Clinical application of bronchoalveolar lavage fluid metagenomics next-generation sequencing in cancer patients with severe pneumonia. Respir Res 2024; 25:68. [PMID: 38317206 PMCID: PMC10840150 DOI: 10.1186/s12931-023-02654-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 12/25/2023] [Indexed: 02/07/2024] Open
Abstract
OBJECTIVE Metagenomic next-generation sequencing (mNGS), as an emerging technique for pathogen detection, has been widely used in clinic. However, reports on the application of mNGS in cancer patients with severe pneumonia remain limited. This study aims to evaluate the diagnostic performance of bronchoalveolar lavage fluid (BALF) mNGS in cancer patients complicated with severe pneumonia. METHODS A total of 62 cancer patients with severe pneumonia simultaneously received culture and mNGS of BALF were enrolled in this study. We systematically analyzed the diagnostic significance of BALF mNGS. Subsequently, optimization of anti-infective therapy based on the distribution of pathogens obtained from BALF mNGS was also assessed. RESULTS For bacteria and fungi, the positive detection rate of mNGS was significantly higher than culture method (91.94% versus 51.61%, P < 0.001), especially for poly-microbial infections (70.97% versus 12.90%, P < 0.001). Compared with the culture method, mNGS exhibited a diagnostic sensitivity of 100% and a specificity of 16.67%, with the positive predictive value (PPV) and negative predictive value (NPV) being 56.14% and 100%, respectively. The agreement rate between these two methods was 59.68%, whereas kappa consensus analysis indicated a poor concordance (kappa = 0.171). After receipt of BALF mNGS results, anti-infective treatment strategies in 39 out of 62 cases (62.90%) were optimized. Moreover, anti-tumor therapy was a high-risk factor for mixed infections (87.18% versus 65.22%, P = 0.04). CONCLUSIONS The present study showed that cancer patients with severe pneumonia, especially those received anti-tumor therapy, were more likely to have poly-microbial infections. BALF mNGS can provide a rapid and comprehensive pathogen distribution of pulmonary infection, making it a promising technique in clinical practice, especially for optimizing therapeutic strategies for cancer patients.
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Affiliation(s)
- Chao Wang
- Department of Critical Care Medicine, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, Jiangsu, 210009, China
- Department of Pharmacology, Nanjing Medical University, 101 Longmian Boulevard, Nanjing, Jiangsu, 210029, China
| | - Xiaojuan Yin
- Department of Pharmacology, Nanjing Medical University, 101 Longmian Boulevard, Nanjing, Jiangsu, 210029, China
| | - Wenqing Ma
- Department of Pharmacology, Nanjing Medical University, 101 Longmian Boulevard, Nanjing, Jiangsu, 210029, China
| | - Li Zhao
- Department of Pharmacology, Nanjing Medical University, 101 Longmian Boulevard, Nanjing, Jiangsu, 210029, China
| | - Xuhong Wu
- Department of Critical Care Medicine, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, Jiangsu, 210009, China
| | - Nan Ma
- Department of Critical Care Medicine, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, Jiangsu, 210009, China
| | - Yuepeng Cao
- Department of Critical Care Medicine, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, Jiangsu, 210009, China
| | - Quanli Zhang
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, 42 Baiziting Road, Xuanwu District, Nanjing, Jiangsu, 210009, China
| | - Shuliang Ma
- Department of Critical Care Medicine, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, Jiangsu, 210009, China
| | - Lin Xu
- Department of Thoracic Surgery, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, Jiangsu, 210009, China.
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, 42 Baiziting Road, Xuanwu District, Nanjing, Jiangsu, 210009, China.
| | - Xuerong Wang
- Department of Pharmacology, Nanjing Medical University, 101 Longmian Boulevard, Nanjing, Jiangsu, 210029, China.
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Wanghu H, Li Y, Huang J, Pu K, Guo F, Zhong P, Wang T, Yuan J, Yu Y, Chen J, Liu J, Chen JJ, Hu C. A novel synthetic nucleic acid mixture for quantification of microbes by mNGS. Microb Genom 2024; 10:001199. [PMID: 38358316 PMCID: PMC10926700 DOI: 10.1099/mgen.0.001199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 01/29/2024] [Indexed: 02/16/2024] Open
Abstract
Metagenomic next-generation sequencing (mNGS) provides considerable advantages in identifying emerging and re-emerging, difficult-to-detect and co-infected pathogens; however, the clinical application of mNGS remains limited primarily due to the lack of quantitative capabilities. This study introduces a novel approach, KingCreate-Quantification (KCQ) system, for quantitative analysis of microbes in clinical specimens by mNGS, which co-sequence the target DNA extracted from the specimens along with a set of synthetic dsDNA molecules used as Internal-Standard (IS). The assay facilitates the conversion of microbial reads into their copy numbers based on IS reads utilizing a mathematical model proposed in this study. The performance of KCQ was systemically evaluated using commercial mock microbes with varying IS input amounts, different proportions of human genomic DNA, and at varying amounts of sequence analysis data. Subsequently, KCQ was applied in microbial quantitation in 36 clinical specimens including blood, bronchoalveolar lavage fluid, cerebrospinal fluid and oropharyngeal swabs. A total of 477 microbe genetic fragments were screened using the bioinformatic system. Of these 83 fragments were quantitatively compared with digital droplet PCR (ddPCR), revealing a correlation coefficient of 0.97 between the quantitative results of KCQ and ddPCR. Our study demonstrated that KCQ presents a practical approach for the quantitative analysis of microbes by mNGS in clinical samples.
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Affiliation(s)
- Hailing Wanghu
- Guangzhou KingCreate Biotechnology Co., Ltd., Guangzhou, Guangdong, 510005, PR China
| | - Yingzhen Li
- Guangzhou KingCreate Biotechnology Co., Ltd., Guangzhou, Guangdong, 510005, PR China
| | - Jin Huang
- Guangzhou KingCreate Biotechnology Co., Ltd., Guangzhou, Guangdong, 510005, PR China
| | - Kangze Pu
- Guangzhou KingCreate Biotechnology Co., Ltd., Guangzhou, Guangdong, 510005, PR China
| | - Fengming Guo
- Guangzhou KingCreate Biotechnology Co., Ltd., Guangzhou, Guangdong, 510005, PR China
| | - Peiwen Zhong
- Guangzhou KingCreate Biotechnology Co., Ltd., Guangzhou, Guangdong, 510005, PR China
| | - Ting Wang
- Guangzhou KingCreate Biotechnology Co., Ltd., Guangzhou, Guangdong, 510005, PR China
| | - Jianying Yuan
- Guangzhou KingCreate Biotechnology Co., Ltd., Guangzhou, Guangdong, 510005, PR China
| | - Yan Yu
- Changsha KingMed Diagnostics Group Co., Ltd., Changsha, Huna, 410000, PR China
| | - Jiachang Chen
- Guangzhou KingCreate Biotechnology Co., Ltd., Guangzhou, Guangdong, 510005, PR China
| | - Jun Liu
- Guangzhou KingCreate Biotechnology Co., Ltd., Guangzhou, Guangdong, 510005, PR China
| | - Jason J. Chen
- Guangzhou KingCreate Biotechnology Co., Ltd., Guangzhou, Guangdong, 510005, PR China
- KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, Guangdong, 511436, PR China
| | - Chaohui Hu
- Guangzhou KingCreate Biotechnology Co., Ltd., Guangzhou, Guangdong, 510005, PR China
- KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, Guangdong, 511436, PR China
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20
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He S, Xiong Y, Tu T, Feng J, Fu Y, Hu X, Wang N, Li D. Diagnostic performance of metagenomic next-generation sequencing for the detection of pathogens in cerebrospinal fluid in pediatric patients with central nervous system infection: a systematic review and meta-analysis. BMC Infect Dis 2024; 24:103. [PMID: 38238719 PMCID: PMC10797782 DOI: 10.1186/s12879-024-09010-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 01/10/2024] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND Detecting pathogens in pediatric central nervous system infection (CNSI) is still a major challenge in medicine. In addition to conventional diagnostic patterns, metagenomic next-generation sequencing (mNGS) shows great potential in pathogen detection. Therefore, we systematically evaluated the diagnostic performance of mNGS in cerebrospinal fluid (CSF) in pediatric patients with CNSI. METHODS Related literature was searched in the Web of Science, PubMed, Embase, and Cochrane Library. We screened the literature and extracted the data according to the selection criteria. The quality of included studies was assessed by the Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2) tool and the certainty of the evidence was measured by the Grading of Recommendations, Assessment, Development, and Evaluations (GRADE) score system. Then, the pooled sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic odd's ratio (DOR), and area under the curve (AUC) of the summary receiver operating characteristic curve (sROC) were estimated in Stata Software and MetaDisc. Subgroup analyses were performed to investigate the potential factors that influence the diagnostic performance. RESULTS A total of 10 studies were included in the meta-analysis. The combined sensitivity was 0.68 (95% confidence interval [CI]: 0.59 to 0.76, I2 = 66.77%, p < 0.001), and the combined specificity was 0.89 (95% CI: 0.80 to 0.95, I2 = 83.37%, p < 0.001). The AUC of sROC was 0.85 (95% CI, 0.81 to 0.87). The quality level of evidence elevated by the GRADE score system was low. CONCLUSIONS Current evidence shows that mNGS presents a good diagnostic performance in pediatric CNSI. Due to the limited quality and quantity of the included studies, more high-quality studies are needed to verify the above conclusion.
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Affiliation(s)
- Sike He
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Ying Xiong
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
- Department of Periodical Press/Chinese Evidence-Based Medicine Center, West China Hospital, Sichuan University, Chengdu, China
| | - Teng Tu
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Jiaming Feng
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Yu Fu
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Xu Hu
- Department of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Neng Wang
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Dapeng Li
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug, Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, China.
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Yi X, Lu H, Liu X, He J, Li B, Wang Z, Zhao Y, Zhang X, Yu X. Unravelling the enigma of the human microbiome: Evolution and selection of sequencing technologies. Microb Biotechnol 2024; 17:e14364. [PMID: 37929823 PMCID: PMC10832515 DOI: 10.1111/1751-7915.14364] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 10/18/2023] [Indexed: 11/07/2023] Open
Abstract
The human microbiome plays a crucial role in maintaining health, with advances in high-throughput sequencing technology and reduced sequencing costs triggering a surge in microbiome research. Microbiome studies generally incorporate five key phases: design, sampling, sequencing, analysis, and reporting, with sequencing strategy being a crucial step offering numerous options. Present mainstream sequencing strategies include Amplicon sequencing, Metagenomic Next-Generation Sequencing (mNGS), and Targeted Next-Generation Sequencing (tNGS). Two innovative technologies recently emerged, namely MobiMicrobe high-throughput microbial single-cell genome sequencing technology and 2bRAD-M simplified metagenomic sequencing technology, compensate for the limitations of mainstream technologies, each boasting unique core strengths. This paper reviews the basic principles and processes of these three mainstream and two novel microbiological technologies, aiding readers in understanding the benefits and drawbacks of different technologies, thereby guiding the selection of the most suitable method for their research endeavours.
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Affiliation(s)
- Xin Yi
- Department of PharmacyShanxi Medical UniversityTaiyuanPeople's Republic of China
| | - Hong Lu
- Department of Clinical laboratoryThe First Hospital of Shanxi Medical UniversityTaiyuanPeople's Republic of China
| | - Xiang Liu
- NHC Key Laboratory of Pneumoconiosis, Shanxi Key Laboratory of Respiratory Diseases, Department of Pulmonary and Critical Care MedicineThe First Hospital of Shanxi Medical UniversityTaiyuanPeople's Republic of China
| | - Junyi He
- NHC Key Laboratory of Pneumoconiosis, Shanxi Key Laboratory of Respiratory Diseases, Department of Pulmonary and Critical Care MedicineThe First Hospital of Shanxi Medical UniversityTaiyuanPeople's Republic of China
| | - Bing Li
- Department of Public HealthShanxi Medical UniversityTaiyuanPeople's Republic of China
| | - Zhelong Wang
- Department of PharmacyGuangdong Pharmaceutical UniversityGuangzhouPeople's Republic of China
| | - Yujing Zhao
- NHC Key Laboratory of Pneumoconiosis, Shanxi Key Laboratory of Respiratory Diseases, Department of Pulmonary and Critical Care MedicineThe First Hospital of Shanxi Medical UniversityTaiyuanPeople's Republic of China
| | - Xinri Zhang
- NHC Key Laboratory of Pneumoconiosis, Shanxi Key Laboratory of Respiratory Diseases, Department of Pulmonary and Critical Care MedicineThe First Hospital of Shanxi Medical UniversityTaiyuanPeople's Republic of China
| | - Xiao Yu
- NHC Key Laboratory of Pneumoconiosis, Shanxi Key Laboratory of Respiratory Diseases, Department of Pulmonary and Critical Care MedicineThe First Hospital of Shanxi Medical UniversityTaiyuanPeople's Republic of China
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Bianconi I, Aschbacher R, Pagani E. Current Uses and Future Perspectives of Genomic Technologies in Clinical Microbiology. Antibiotics (Basel) 2023; 12:1580. [PMID: 37998782 PMCID: PMC10668849 DOI: 10.3390/antibiotics12111580] [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: 09/26/2023] [Revised: 10/16/2023] [Accepted: 10/25/2023] [Indexed: 11/25/2023] Open
Abstract
Recent advancements in sequencing technology and data analytics have led to a transformative era in pathogen detection and typing. These developments not only expedite the process, but also render it more cost-effective. Genomic analyses of infectious diseases are swiftly becoming the standard for pathogen analysis and control. Additionally, national surveillance systems can derive substantial benefits from genomic data, as they offer profound insights into pathogen epidemiology and the emergence of antimicrobial-resistant strains. Antimicrobial resistance (AMR) is a pressing global public health issue. While clinical laboratories have traditionally relied on culture-based antimicrobial susceptibility testing, the integration of genomic data into AMR analysis holds immense promise. Genomic-based AMR data can furnish swift, consistent, and highly accurate predictions of resistance phenotypes for specific strains or populations, all while contributing invaluable insights for surveillance. Moreover, genome sequencing assumes a pivotal role in the investigation of hospital outbreaks. It aids in the identification of infection sources, unveils genetic connections among isolates, and informs strategies for infection control. The One Health initiative, with its focus on the intricate interconnectedness of humans, animals, and the environment, seeks to develop comprehensive approaches for disease surveillance, control, and prevention. When integrated with epidemiological data from surveillance systems, genomic data can forecast the expansion of bacterial populations and species transmissions. Consequently, this provides profound insights into the evolution and genetic relationships of AMR in pathogens, hosts, and the environment.
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Affiliation(s)
- Irene Bianconi
- Laboratory of Microbiology and Virology, Provincial Hospital of Bolzano (SABES-ASDAA), Lehrkrankenhaus der Paracelsus Medizinischen Privatuniversitätvia Amba Alagi 5, 39100 Bolzano, Italy; (R.A.); (E.P.)
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23
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Jeffrey M, Denny KJ, Lipman J, Conway Morris A. Differentiating infection, colonisation, and sterile inflammation in critical illness: the emerging role of host-response profiling. Intensive Care Med 2023; 49:760-771. [PMID: 37344680 DOI: 10.1007/s00134-023-07108-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 05/22/2023] [Indexed: 06/23/2023]
Abstract
Infection results when a pathogen produces host tissue damage and elicits an immune response. Critically ill patients experience immune activation secondary to both sterile and infectious insults, with overlapping clinical phenotypes and underlying immunological mechanisms. Patients also undergo a shift in microbiota with the emergence of pathogen-dominant microbiomes. Whilst the combination of inflammation and microbial shift has long challenged intensivists in the identification of true infection, the advent of highly sensitive molecular diagnostics has further confounded the diagnostic dilemma as the number of microbial detections increases. Given the key role of the host immune response in the development and definition of infection, profiling the host response offers the potential to help unravel the conundrum of distinguishing colonisation and sterile inflammation from true infection. This narrative review provides an overview of current approaches to distinguishing colonisation from infection using routinely available techniques and proposes matrices to support decision-making in this setting. In searching for new tools to better discriminate these states, the review turns to the understanding of the underlying pathobiology of the host response to infection. It then reviews the techniques available to assess this response in a clinically applicable context. It will cover techniques including profiling of transcriptome, protein expression, and immune functional assays, detailing the current state of knowledge in diagnostics along with the challenges and opportunities. The ultimate infection diagnostic tool will likely combine an assessment of both host immune response and sensitive pathogen detection to improve patient management and facilitate antimicrobial stewardship.
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Affiliation(s)
- Mark Jeffrey
- John V Farman Intensive Care Unit, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Division of Anaesthesia, Department of Medicine, Level 4, Addenbrooke's Hospital, University of Cambridge, Hills Road, Cambridge, CB2 0QQ, UK
| | - Kerina J Denny
- Department of Intensive Care, Gold Coast University Hospital, Southport, QLD, Australia
- School of Medicine, University of Queensland, Herston, Brisbane, Australia
| | - Jeffrey Lipman
- University of Queensland Centre for Clinical Research, The University of Queensland, Brisbane, Australia
- Jamieson Trauma Institute and Intensive Care Services, Royal Brisbane and Women's Hospital, Brisbane, Australia
- Nimes University Hospital, University of Montpellier, Nimes, France
| | - Andrew Conway Morris
- John V Farman Intensive Care Unit, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
- Division of Anaesthesia, Department of Medicine, Level 4, Addenbrooke's Hospital, University of Cambridge, Hills Road, Cambridge, CB2 0QQ, UK.
- Division of Immunology, Department of Pathology, University of Cambridge, Cambridge, UK.
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Liu Q, Liu X, Hu B, Xu H, Sun R, Li P, Zhang Y, Yang H, Ma N, Sun X. Diagnostic performance and clinical impact of blood metagenomic next-generation sequencing in ICU patients suspected monomicrobial and polymicrobial bloodstream infections. Front Cell Infect Microbiol 2023; 13:1192931. [PMID: 37434786 PMCID: PMC10330723 DOI: 10.3389/fcimb.2023.1192931] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 06/09/2023] [Indexed: 07/13/2023] Open
Abstract
Introduction Early and effective application of antimicrobial medication has been evidenced to improve outcomes of patients with bloodstream infection (BSI). However, conventional microbiological tests (CMTs) have a number of limitations that hamper a rapid diagnosis. Methods We retrospectively collected 162 cases suspected BSI from intensive care unit with blood metagenomics next-generation sequencing (mNGS) results, to comparatively evaluate the diagnostic performance and the clinical impact on antibiotics usage of mNGS. Results and discussion Results showed that compared with blood culture, mNGS detected a greater number of pathogens, especially for Aspergillus spp, and yielded a significantly higher positive rate. With the final clinical diagnosis as the standard, the sensitivity of mNGS (excluding viruses) was 58.06%, significantly higher than that of blood culture (34.68%, P<0.001). Combing blood mNGS and culture results, the sensitivity improved to 72.58%. Forty-six patients had infected by mixed pathogens, among which Klebsiella pneumoniae and Acinetobacter baumannii contributed most. Compared to monomicrobial, cases with polymicrobial BSI exhibited dramatically higher level of SOFA, AST, hospitalized mortality and 90-day mortality (P<0.05). A total of 101 patients underwent antibiotics adjustment, among which 85 were adjusted according to microbiological results, including 45 cases based on the mNGS results (40 cases escalation and 5 cases de-escalation) and 32 cases on blood culture. Collectively, for patients suspected BSI in critical condition, mNGS results can provide valuable diagnostic information and contribute to the optimizing of antibiotic treatment. Combining conventional tests with mNGS may significantly improve the detection rate for pathogens and optimize antibiotic treatment in critically ill patients with BSI.
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Affiliation(s)
- Qilong Liu
- Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Xiaojing Liu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Bingxue Hu
- Department of Scientific Affairs, Vision Medicals for Infectious Diseases, Guangzhou, Guangdong Province, China
| | - Huan Xu
- Department of Scientific Affairs, Vision Medicals for Infectious Diseases, Guangzhou, Guangdong Province, China
| | - Rongqing Sun
- Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Pengfei Li
- Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Yunwei Zhang
- Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Hongfu Yang
- Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Ning Ma
- Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Xiaoge Sun
- Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
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Evaluation of extraction and enrichment methods for recovery of respiratory RNA viruses in a metagenomics approach. J Virol Methods 2023; 314:114677. [PMID: 36657602 PMCID: PMC10009504 DOI: 10.1016/j.jviromet.2023.114677] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/09/2023] [Accepted: 01/14/2023] [Indexed: 01/18/2023]
Abstract
Viral metagenomics is increasingly applied in viral detection and virome characterization. Different extraction and enrichment techniques may be adopted, however, reports on their effective influence on viral recovery is often conflicting. Using a three step enrichment steps, the effect of three extraction kits and the influence of DNase treatment with or without rRNA removal for respiratory RNA virus recovery from nasopharyngeal swab samples was evaluated. The viral cocktail containing six different RNA viruses pooled in equal volume were subjected to the different extraction and enrichment methods, sequenced using the Illumina MiSeq, and analysed using Genome Detective. The PureLink® Viral RNA/DNA Mini Kit (PureLink) was highly efficient with better recovery of all the viral agents in the cocktail. The use of rRNA treatment resulted in increased viral recovery with PureLink and QIAamp® Viral RNA Mini kit, while having comparable recovery rate as DNase only with the QIAamp® MinElute Virus Spin Kit. The observed low reads and genome coverage of some of the viruses could be attributed to their low abundance. Depending on sample matrix, extraction choice and enrichment strategy may influence recovery of respiratory RNA virus in metagenomics studies, therefore individual evaluation and adoption may be necessary for a robust result.
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Gao L, Yang T, Zhang X, Lei W, Huang JA. Rapid detection of pulmonary nocardiosis by metagenomic next generation sequencing. Diagn Microbiol Infect Dis 2023; 106:115928. [PMID: 37001227 DOI: 10.1016/j.diagmicrobio.2023.115928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 02/01/2023] [Accepted: 02/24/2023] [Indexed: 03/05/2023]
Abstract
We retrospectively analyzed 3 cases of pulmonary nocardiosis. Patients were identified by metagenomic next generation sequencing (mNGS) in the First Affiliated Hospital of Soochow University, from January 2019 to April 2022. All patients had underlying diseases, and were in immunocompromised state, with membranous nephropathy, acute lymphoblastic leukemia (ALL), and systemic lupus erythematosus (SLE), respectively. Symptoms common to all cases included fever, cough and expectoration. Chest computed tomography (CT) presented patchy shadows or nodules, with or without cavitation lesions, or pleural effusion. mNGS detected Nocardia spp. via bronchoalveolar lavage fluid (BALF) or blood samples from patients. All the patients were discharged with recovery after using the trimethoprim-sulfamethoxazole (TMP-SMX) and remained without evidence of disease during regular follow-ups. mNGS may be a tool for rapid and accurate detection and identification of pulmonary nocardiosis, but interpreting the mNGS results should be more cautious because the mNGS assay can also detect colonization.
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27
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Wei Y, Zhang T, Ma Y, Yan J, Zhan J, Zheng J, Xu Y. Clinical Evaluation of Metagenomic Next-Generation Sequencing for the detection of pathogens in BALF in severe community acquired pneumonia. Ital J Pediatr 2023; 49:25. [PMID: 36805803 PMCID: PMC9938609 DOI: 10.1186/s13052-023-01431-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 02/12/2023] [Indexed: 02/19/2023] Open
Abstract
BACKGROUND Rapid and accurate identification of pathogens is very important for the treatment of Severe community-acquired pneumonia (SCAP) in children. Metagenomic Next-generation sequencing (mNGS) has been applied in the detection of pathogenic bacteria in recent years, while the overall evaluation the application of SCAP in children is lacking. METHODS In our study, 84 cases of SCAP were enrolled. Bronchoalveolar lavage fluid (BALF) samples were analysed using mNGS; and sputum, blood, and BALF samples were analysed using conventional technology (CT). RESULTS Among the 84 children, 41 were boys, and 43 were girls, with an average age ranging from 2 months to 14 years. The pathogen detection rate of mNGS was higher than that of CT (83.3% [70/84] vs. 63.1% [53/84], P = 0.003). The mNGS was much greater than that of the CT in detecting Streptococcus pneumoniae (89.2% [25/29] vs. 44.8% [13/29], P = 0.001) and Haemophilus influenzae (91.7% [11/12] vs. 33.3% [4/12], P < 0.005). The mNGS also showed superior fungal detection performance compared with that of the CT (81.8% [9/11] vs. 18.2% [2/11], P = 0.004). The mNGS test can detect viruses, such as bocavirus, rhinovirus, and human metapneumovirus, which are not frequently recognised using CT. However, the mNGS detection rate was lower than that of the CT (52.4% [11/21] vs. 95.2% [20/21], P = 0.004) for Mycoplasma pneumoniae (MP). The detection rate of mNGS for mixed infection was greater than that of the CT, although statistical significance was not observed (26.3% [20/39] vs. 21.1% [16/39], P > 0.005). Treatment for 26 (31.0%) children was changed based on mNGS results, and their symptoms were reduced; nine patients had their antibiotic modified, five had antibiotics added, nine had their antifungal medication, and seven had their antiviral medication. CONCLUSION mNGS has unique advantages in the detection of SCAP pathogens in children, especially S. pneumoniae, H. influenzae, and fungi. However, the detection rate of MP using mNGS was lower than that of the CT. Additionally, mNGS can detect pathogens that are not generally covered by CT, which is extremely important for the modification of the treatment strategy.
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Affiliation(s)
- Yupeng Wei
- grid.265021.20000 0000 9792 1228Clinical School of Paediatrics, Tianjin Medical University, Tianjin, China ,grid.417022.20000 0004 1772 3918Department of Respiratory Medicine, Tianjin Children’s Hospital (Tianjin University Children’s Hospital), Tianjin, China ,grid.410626.70000 0004 1798 9265Department of Neonatology, Tianjin Central Hospital of Gynecology Obstetrics, Tianjin, China
| | - Tongqiang Zhang
- grid.265021.20000 0000 9792 1228Clinical School of Paediatrics, Tianjin Medical University, Tianjin, China ,grid.417022.20000 0004 1772 3918Department of Respiratory Medicine, Tianjin Children’s Hospital (Tianjin University Children’s Hospital), Tianjin, China
| | - Yuting Ma
- grid.265021.20000 0000 9792 1228Clinical School of Paediatrics, Tianjin Medical University, Tianjin, China ,grid.417022.20000 0004 1772 3918Department of Infection, Tianjin Children’s Hospital (Tianjin University Children’s Hospital), Tianjin, China
| | - Jisi Yan
- grid.265021.20000 0000 9792 1228Clinical School of Paediatrics, Tianjin Medical University, Tianjin, China ,grid.417022.20000 0004 1772 3918Department of Respiratory Medicine, Tianjin Children’s Hospital (Tianjin University Children’s Hospital), Tianjin, China ,grid.410626.70000 0004 1798 9265Department of Neonatology, Tianjin Central Hospital of Gynecology Obstetrics, Tianjin, China
| | - Jianghua Zhan
- Department of Pediatric Surgery, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China.
| | - Jun Zheng
- Department of Neonatology, Tianjin Central Hospital of Gynecology Obstetrics, Tianjin, China.
| | - Yongsheng Xu
- Department of Respiratory Medicine, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China.
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Zhang N, Ma L, Ding W. The Diagnostic Value of Blood Next-Generation Sequencing in Early Surgical Site Infection After Spine Surgery. Int J Gen Med 2023; 16:37-45. [PMID: 36636713 PMCID: PMC9830415 DOI: 10.2147/ijgm.s394255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/28/2022] [Indexed: 01/06/2023] Open
Abstract
Objective To determine the diagnostic value of blood next-generation sequencing (NGS) in early surgical site infection after spine surgery. Because the blood is sterile in healthy individuals, it is expected that blood NGS is both sensitive and specific for the detection of infection. Methods A total of 28 patients with definitive spinal surgical site infections and controls (n=30) were retrospectively included. The postoperative results of NGS and culture on different samples, such as blood and drainage fluid, were obtained and compared to evaluate the diagnostic value of blood NGS. The diagnostic value parameters (sensitivity, specificity, etc.) were calculated. Results Among the four bacteriological exam methods, blood NGS was both sensitive and specific for the determination of infection after spine surgery. The sensitivities of blood and drainage fluid NGS were similar (0.82 vs 0.89, P=0.617). However, the specificities of the two assessments differed, which were 0.97 for blood NGS and 0.40 for drainage fluid NGS (P<0.001). The sensitivities of bacterial culture were lower than those of NGS (blood: 0.82 vs 0.25, P<0.001; drainage fluid: 0.89 vs 0.61, P<0.001), regardless of the sample type. However, the specificities of bacterial culture were equal to or higher than those of NGS (blood: 0.97 vs 0.97, P=1.000; drainage fluid: 0.40 vs 0.80, P=0.002). Conclusion This article emphasizes the superiority of blood NGS in infection detection and bacterial determination in patients undergoing spine surgery. Compared with traditional drainage fluid bacterial culture and NGS, blood NGS was more sensitive and specific, and its extensive application could be expected.
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Affiliation(s)
- Nan Zhang
- Department of Spine Surgery, 3rd Hospital of Hebei Medical University, Shijiazhuang, People’s Republic of China
| | - Lei Ma
- Department of Spine Surgery, 3rd Hospital of Hebei Medical University, Shijiazhuang, People’s Republic of China
| | - Wenyuan Ding
- Department of Spine Surgery, 3rd Hospital of Hebei Medical University, Shijiazhuang, People’s Republic of China,Correspondence: Wenyuan Ding, Department of Spine Surgery, 3rd Hospital of Hebei Medical University, Shijiazhuang, Hebei Province, 050051, People’s Republic of China, Email
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Meng LN, Li G, Yuan HX, Feng XC, Liu F, Zhang SL. Utility of metagenomics next-generation sequencing in the diagnosis and treatment of severe infectious diseases in the intensive care unit. Technol Health Care 2023; 31:1887-1899. [PMID: 37302051 DOI: 10.3233/thc-220856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
BACKGROUND Metagenomic next-generation sequencing (mNGS) is a new method that combines high-throughput sequencing and bioinformatics analysis. However, it has not become as popular due to the limited testing equipment and high costs and lack of family awareness with not much relevant intensive care unit (ICU) research data. OBJECTIVE To explore the clinical use and value of metagenomics next-generation sequencing (mNGS) in patients with sepsis in the ICU. METHODS We conducted a retrospective analysis of 102 patients with sepsis admitted to the ICU of Peking University International Hospital from January 2018 to January 2022. Based on whether mNGS was performed, the identified patients were divided into the observation group (n= 51) and the control group (n= 51), respectively. Routine laboratory tests, including routine blood test, C-reactive protein, procalcitonin, and culture of suspicious lesion specimens were performed in both groups within 2 hours after admission to the ICU, while mNGS tests were performed in the observation group. Patients in both groups were routinely given initial anti-infective, anti-shock, and organ support treatment. Antibiotic regimens were optimized in a timely manner according to the etiological results. Relevant clinical data were collected. RESULTS The testing cycle of mNGS was shorter than that of the conventional culture (30.79 ± 4.01 h vs. 85.38 ± 9.94 h, P< 0.001), while the positive rate of mNGS was higher than that of the conventional culture (82.35% vs. 45.1%, P< 0.05), with obvious superiority in the detection of viruses and fungus. There were significant differences in the optimal time of antibiotics (48 h vs.100 h) and length of ICU stay (11 d vs. 16 d) between the observation group and control group (P< 0.01) respectively, with no difference in 28-day mortality (33.3% vs. 41.2%, P> 0.05). CONCLUSION mNGS is useful in the detection of sepsis-causing pathogens in the ICU with the advantages of short testing time and high positive rate. There was no difference in the 28-day outcome between the two groups, which may be related to other confounding factors such as small sample size. Additional studies with extended sample size are needed.
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Agudelo-Pérez S, Fernández-Sarmiento J, Rivera León D, Peláez RG. Metagenomics by next-generation sequencing (mNGS) in the etiological characterization of neonatal and pediatric sepsis: A systematic review. Front Pediatr 2023; 11:1011723. [PMID: 37063664 PMCID: PMC10098018 DOI: 10.3389/fped.2023.1011723] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 02/23/2023] [Indexed: 04/18/2023] Open
Abstract
Introduction Pediatric and neonatal sepsis is one of the main causes of mortality and morbidity in these age groups. Accurate and early etiological identification is essential for guiding antibiotic treatment, improving survival, and reducing complications and sequelae. Currently, the identification is based on culture-dependent methods, which has many limitations for its use in clinical practice, and obtaining its results is delayed. Next-generation sequencing enables rapid, accurate, and unbiased identification of multiple microorganisms in biological samples at the same time. The objective of this study was to characterize the etiology of neonatal and pediatric sepsis by metagenomic techniques. Methods A systematic review of the literature was carried out using the PRISMA-2020 guide. Observational, descriptive, and case report studies on pediatric patients were included, with a diagnostic evaluation by clinical criteria of sepsis based on the systemic inflammatory response, in sterile and non-sterile biofluid samples. The risk of bias assessment of the observational studies was carried out with the STROBE-metagenomics instrument and the CARE checklist for case reports. Results and Discussion Five studies with a total of 462 patients were included. Due to the data obtained from the studies, it was not possible to perform a quantitative synthesis (meta-analysis). Based on the data from the included studies, the result identified that mNGS improves the etiological identification in neonatal and pediatric sepsis, especially in the context of negative cultures and in the identification of unusual microorganisms (bacteria that are difficult to grow in culture, viruses, fungi, and parasites). The number of investigations is currently limited, and the studies are at high risk of bias. Further research using this technology would have the potential to improve the rational use of antibiotics.
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Affiliation(s)
- Sergio Agudelo-Pérez
- Department of Pediatrics, Faculty of Medicine, Universidad de La Sabana, Chia, Colombia
- Correspondence: Sergio Agudelo-Pérez
| | - Jaime Fernández-Sarmiento
- Department of Pediatrics, Faculty of Medicine, Universidad de La Sabana, Chia, Colombia
- Departament of Pediatrics and Critical Care, Fundación Cardioinfantil, Bogotá, Colombia
| | - Diana Rivera León
- Department of Pediatrics, Faculty of Medicine, Universidad de La Sabana, Chia, Colombia
| | - Ronald Guillermo Peláez
- Life Sciences and Health Research Group, Graduates School, CES University, Medellin, Colombia
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Liu G, Wang L, Li X, Zhang Y, Long H, Wang Y, Gao H, Xia H, Qian S. The value of next-generation metagenomic sequencing in pathogen detection of pleural effusions and ascites from children with sepsis. Front Cell Infect Microbiol 2023; 13:1130483. [PMID: 36891155 PMCID: PMC9986937 DOI: 10.3389/fcimb.2023.1130483] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/09/2023] [Indexed: 02/22/2023] Open
Abstract
Objective To investigate the diagnostic value of metagenomic next-generation sequencing (mNGS) using pleural effusion and ascites from children with sepsis. Methods In this study, children with sepsis or severe sepsis and appeared pleural or peritoneal effusions were enrolled, of whom the pleural effusions or ascites and blood samples were conducted pathogen detection using both conventional and mNGS methods. The samples were divided into pathogen-consistent and pathogen-inconsistent groups based on the consistency of mNGS results from different sample types, and into exudate and transudate groups based on their pleural effusion and ascites properties. The pathogen positive rates, pathogen spectrum, consistency between different sample types, and clinical diagnosis consistency were compared between mNGS and conventional pathogen tests. Results A total of 42 pleural effusions or ascites and 50 other type samples were collected from 32 children. The pathogen positive rate of the mNGS test was significantly higher than that of traditional methods (78.57% vs. 14.29%, P < 0.001) in pleural effusion and ascites samples, with a consistent rate of 66.67% between the two methods. Nearly 78.79% (26/33) of mNGS positive results of the pleural effusions and ascites samples were consistent with clinical evaluation, and 81.82% (27/33) of these positive samples reported 1-3 pathogens. The pathogen-consistent group outperformed the pathogen-inconsistent group in terms of consistency with respect to clinical evaluation (88.46% vs. 57.14%, P = 0.093), while there was no significant difference between the exudate and transudate groups (66.67% vs. 50.00%, P = 0.483). Conclusion Compared to conventional methods, mNGS has great advantages in pathogen detection of pleural effusion and ascites samples. Moreover, consistent results of mNGS tests with different sample types provide more reference values in clinical diagnosis.
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Affiliation(s)
- Gang Liu
- Department of Pediatric Intensive Care Unit, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Lijuan Wang
- Department of Pediatric Intensive Care Unit, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Xuming Li
- Department of scientific affairs, HugoBiotech Co., Ltd., Beijing, China
| | - Ye Zhang
- Department of scientific affairs, HugoBiotech Co., Ltd., Beijing, China
| | - Hu Long
- Department of scientific affairs, HugoBiotech Co., Ltd., Beijing, China
| | - Yi Wang
- Department of Pediatric Intensive Care Unit, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Hengmiao Gao
- Department of Pediatric Intensive Care Unit, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Han Xia
- Department of scientific affairs, HugoBiotech Co., Ltd., Beijing, China
- *Correspondence: Suyun Qian, ; Han Xia,
| | - Suyun Qian
- Department of Pediatric Intensive Care Unit, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
- *Correspondence: Suyun Qian, ; Han Xia,
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Qin C, Zhang S, Zhao Y, Ding X, Yang F, Zhao Y. Diagnostic value of metagenomic next-generation sequencing in sepsis and bloodstream infection. Front Cell Infect Microbiol 2023; 13:1117987. [PMID: 36844396 PMCID: PMC9950395 DOI: 10.3389/fcimb.2023.1117987] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 01/30/2023] [Indexed: 02/12/2023] Open
Abstract
Objective To evaluate the diagnostic value of metagenomic next-generation sequencing (mNGS) in sepsis and bloodstream infection (BSI). Methods A retrospective analysis of patients diagnosed with sepsis and BSI at the First Affiliated Hospital of Zhengzhou University from January 2020 to February 2022 was conducted. All the patients underwent blood culture and were divided into mNGS group and non-mNGS group according to whether mNGS was performed or not. The mNGS group was further divided into early group (< 1 day), intermediate group (1-3 days), and late group (> 3 days) according to the time of mNGS inspection. Results In 194 patients with sepsis and BSI, the positive rate of mNGS for identifying pathogens was significantly higher than that of blood culture (77.7% vs. 47.9%), and the detection period was shorter (1.41 ± 1.01 days vs. 4.82 ± 0.73 days); the difference was statistically significant (p < 0.05). The 28-day mortality rate of the mNGS group (n = 112) was significantly lower than that of the non-mNGS group (n = 82) (47.32% vs. 62.20%, p = 0.043). The total hospitalization time for the mNGS group was longer than that for the non-mNGS group (18 (9, 33) days vs. 13 (6, 23) days, p = 0.005). There was no significant difference in the ICU hospitalization time, mechanical ventilation time, vasoactive drug use time, and 90-day mortality between the two groups (p > 0.05). Sub-group analysis of patients in the mNGS group showed that the total hospitalization time and the ICU hospitalization time in the late group were longer than those in the early group (30 (18, 43) days vs. 10 (6, 26) days, 17 (6, 31) days vs. 6 (2, 10) days), and the ICU hospitalization time in the intermediate group was longer than that in the early group (6 (3, 15) days vs. 6 (2, 10) days); the differences were statistically significant (p < 0.05). The 28-day mortality rate of the early group was higher than that of the late group (70.21% vs. 30.00%), and the difference was statistically significant (p = 0.001). Conclusions mNGS has the advantages of a short detection period and a high positive rate in the diagnosis of pathogens causing BSI and, eventually, sepsis. Routine blood culture combined with mNGS can significantly reduce the mortality of septic patients with BSI. Early detection using mNGS can shorten the total hospitalization time and the ICU hospitalization time of patients with sepsis and BSI.
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Affiliation(s)
- Cuihong Qin
- General ICU, Henan Key Laboratory of Critical Care Medicine, Henan Engineering Research Center for Critical Care Medicine, Zhengzhou Key Laboratory of Sepsis, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shuguang Zhang
- General ICU, Henan Key Laboratory of Critical Care Medicine, Henan Engineering Research Center for Critical Care Medicine, Zhengzhou Key Laboratory of Sepsis, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yingying Zhao
- General ICU, Henan Key Laboratory of Critical Care Medicine, Henan Engineering Research Center for Critical Care Medicine, Zhengzhou Key Laboratory of Sepsis, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xianfei Ding
- General ICU, Henan Key Laboratory of Critical Care Medicine, Henan Engineering Research Center for Critical Care Medicine, Zhengzhou Key Laboratory of Sepsis, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Fei Yang
- General ICU, Henan Key Laboratory of Critical Care Medicine, Henan Engineering Research Center for Critical Care Medicine, Zhengzhou Key Laboratory of Sepsis, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yangchao Zhao
- Cardiopulmonary Support Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Yangchao Zhao,
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Multisite Metagenomic Next-Generation Sequencing Improved Diagnostic Performance for Sepsis-Associated Lymphopenia Patients. Microbiol Spectr 2022; 10:e0353222. [PMID: 36453923 PMCID: PMC9769823 DOI: 10.1128/spectrum.03532-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
A precise and efficient microbiological diagnosis is essential for sepsis. Metagenomic next-generation sequencing (mNGS) is a novel technique for the diagnosis of infectious diseases, but its current application in multisite sampling and interpretation remains controversial. Therefore, this study was undertaken to evaluate the reliability of multisite mNGS tests and the efficiency of plasma mNGS based on lymphocyte subset counts. A prospective observational study was performed on the intubated patients with sepsis-associated lymphopenia from January 2020 to February 2022. During the study period, data on 71 patients with sepsis-induced lymphopenia were collected. Among the 125 mNGS tests, 95 were positive for pathogens, whereas of the 166 conventional microbiological tests (CMTs), 91 were positive. The comparison showed that 38 patients (53.5%) had at least one matched pair of plasma mNGS and CMT results, while for multisite sampling, 47 patients (66.2%) had at least one. Lymphocyte subset analysis showed that T lymphocyte (577 ± 317 versus 395 ± 207, P = 0.005) and CD4+ T lymphocyte (333 ± 199 versus 230 ± 120, P = 0.009) counts were lower in the matched group. According to receiver operating characteristic (ROC) analysis, a CD4+ T lymphocyte count lower than 266 cells/mm3 was predictive of a match result. For sepsis-associated lymphopenia patients, we found that multisite mNGS tests showed a higher positivity rate. With plasma mNGS, a lower CD4+ T lymphocyte count predicted a better match result with CMT. The lymphocyte subset analysis may promote the clinical interpretation of mNGS results. IMPORTANCE This study was undertaken to evaluate the reliability of pathogenic diagnoses based on multisite mNGS detection at the clinically suspected sites and to analyze the efficiency of plasma mNGS detection based on lymphocyte subset counts in patients with sepsis-associated lymphopenia.
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He D, Liu M, Chen Q, Liu Y, Tang Y, Shen F, Wang D, Liu X. Clinical Characteristics and the Effect of Timing for Metagenomic Next-Generation Sequencing in Critically Ill Patients with Sepsis. Infect Drug Resist 2022; 15:7377-7387. [PMID: 36544992 PMCID: PMC9760579 DOI: 10.2147/idr.s390256] [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: 09/17/2022] [Accepted: 12/06/2022] [Indexed: 12/15/2022] Open
Abstract
Background Metagenomic next-generation sequencing (mNGS) has a good performance for the identification of pathogens in infectious diseases, but few studies on the clinical characteristics of mNGS and the effect of timing for mNGS in critically ill patients with sepsis. Methods We retrospectively included all patients diagnosed with sepsis after admission to the intensive care unit (ICU) of a university-affiliated hospital between Aug 1, 2019 and Apr 1, 2021. During the study period, pathogens for all enrolled subjects were obtained by mNGS. We analyzed the composition and positive rate of different samples type for mNGS. And then we used the univariable and multivariable logistic regression to explore the risk factors associated with all-cause mortality at 28 days. Results A total of 87 patients were included and 87 samples were analyzed among these patients. The most common sample for mNGS was bronchoalveolar lavage fluid (BALF), about 84% (73/87). The positive rate of pathogens identification by mNGS was higher than conventional culture (92% vs 36%, p < 0.001). In addition to the pathogens detected by conventional culture, mNGS can detect more viruses and fungi. Based on the mNGS report, clinicians made adjustments to the antibiotic regimen for 72% patients. The multivariate binary logistic regression analysis suggested that age (OR, 1.036; 95% CI, 1.005-1.067; p = 0.021) and the sequential organ failure assessment (SOFA) score on the day of mNGS sampling were independent risk factors of death at 28 days (OR, 1.204; 95% CI, 1.038-1.397; p = 0.014). Conclusion In critically ill patients with sepsis, the most common sample type for mNGS was BALF, and the positive rate of mNGS is higher than conventional cultures, especially in viruses and fungi. Meanwhile, mNGS can guide clinicians in adjusting antibiotic regimens. Age and the SOFA score on the day of mNGS sampling were independent risk factors for death.
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Affiliation(s)
- Dehua He
- Department of Critical Care Medicine, the Affiliated Hospital of Guizhou Medical University, Guiyang, People’s Republic of China
| | - Ming Liu
- Department of Critical Care Medicine, the Affiliated Hospital of Guizhou Medical University, Guiyang, People’s Republic of China
| | - Qimin Chen
- Department of Critical Care Medicine, the Affiliated Hospital of Guizhou Medical University, Guiyang, People’s Republic of China
| | - Ying Liu
- Department of Critical Care Medicine, the Affiliated Hospital of Guizhou Medical University, Guiyang, People’s Republic of China
| | - Yan Tang
- Department of Critical Care Medicine, the Affiliated Hospital of Guizhou Medical University, Guiyang, People’s Republic of China
| | - Feng Shen
- Department of Critical Care Medicine, the Affiliated Hospital of Guizhou Medical University, Guiyang, People’s Republic of China
| | - Difen Wang
- Department of Critical Care Medicine, the Affiliated Hospital of Guizhou Medical University, Guiyang, People’s Republic of China
| | - Xu Liu
- Department of Critical Care Medicine, the Affiliated Hospital of Guizhou Medical University, Guiyang, People’s Republic of China,Correspondence: Xu Liu, Department of Critical Care Medicine, the Affiliated Hospital of Guizhou Medical University, No. 28, Guiyi Street, Yunyan District, Guiyang, Guizhou, 550004, People’s Republic of China, Tel +86-851-86771459, Email
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Cao XG, Zhou SS, Wang CY, Jin K, Meng HD. The diagnostic value of next-generation sequencing technology in sepsis. Front Cell Infect Microbiol 2022; 12:899508. [PMID: 36189371 PMCID: PMC9518011 DOI: 10.3389/fcimb.2022.899508] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 08/24/2022] [Indexed: 11/13/2022] Open
Abstract
ObjectiveThis study aims to assess the clinical utility of next-generation sequencing (NGS) in sepsis diagnosis.MethodsA prospective study was conducted on patients with a high suspicion of sepsis by unknown pathogens from January 2017 to December 2021. Blood samples were taken from patients to perform NGS, blood culture (BC), leucocyte (WBC), procalcitonin (PCT), creatinine (CREA), Albumin (ALB) and C-reactive protein (CRP) tests.ResultsThe feedback time for BC was 3~5 days for bacteria and 5~7 days for fungi, while the turnover time for NGS was only 24 h. The clinical diagnosis was considered the “gold standard”. 83 patients passed our inclusion criteria and were separated into two groups by clinical diagnosis. 62 met the clinical diagnosis criteria for sepsis and 21 were non-sepsis. The data from the two groups were retrospectively compared and analyzed. Of 62 sepsis in 83 patients, 8(9.64%) were diagnosed by both BC and NGS, 51 (61.45%) by NGS only, 1(1.20%) by BC and 2 (2.41%) by conventional testing only; PCT, CREA, CRP levels and the detection rate of NGS and BC were higher in the sepsis group than in the non-sepsis group, while ALB levels were lower (p<0.05). The logistic regression results in our study revealed that NGS and ALB were independent prediction factors for sepsis (p<0.05), the area under the receiver operating characteristic curve (AUC), sensitivity and specificity of NGS for diagnosing sepsis was 0.857, 95.16% and 76.19%, while ALB was 0.728, 58.06%, 80.95%, respectively. The combination’s sensitivity, specificity and AUC of NGS and ALB were 93.55%, 85.71% and 0.935, greater than that of Albumin or NGS only (both p<0.05).ConclusionNGS can effectively and quickly identify pathogens, thereby emerges as a promising technology for sepsis diagnosis. Combination of NGS and ALB can be used for early screening and is more powerful than NGS or ALB only.
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Affiliation(s)
- Xiao-guang Cao
- Department of Emergency Medical Center, the First Affiliated Hospital of University of Science and Technology of China (Anhui Provincial Hospital), Hefei, China
| | - Shu-sheng Zhou
- Department of Emergency Medical Center, the First Affiliated Hospital of University of Science and Technology of China (Anhui Provincial Hospital), Hefei, China
| | - Chun-yan Wang
- Department of Emergency Medical Center, the First Affiliated Hospital of University of Science and Technology of China (Anhui Provincial Hospital), Hefei, China
| | - Kui Jin
- Department of Emergency Medical Center, the First Affiliated Hospital of University of Science and Technology of China (Anhui Provincial Hospital), Hefei, China
| | - Hua-dong Meng
- Department of Emergency Intensive Care Unit (EICU), the third Affiliated Hospital of Anhui Medical University, (the First People’s Hospital of Hefei), Hefei, China
- *Correspondence: Hua-dong Meng,
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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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Zhou JJ, Ding WC, Liu YC, Gao YL, Xu L, Geng RL, Ye Y, Chai YF. Diagnostic Value of Metagenomic Next-Generation Sequencing for Pulmonary Infection in Intensive Care Unit and Non-Intensive Care Unit Patients. Front Cell Infect Microbiol 2022; 12:929856. [PMID: 36046746 PMCID: PMC9423675 DOI: 10.3389/fcimb.2022.929856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 06/13/2022] [Indexed: 11/17/2022] Open
Abstract
Objective To evaluate the diagnostic performance of metagenomic next-generation sequencing (mNGS) and culture in pathogen detection among intensive care unit (ICU) and non-ICU patients with suspected pulmonary infection. Methods In this prospective study, sputum samples were collected from patients with suspected pulmonary infection for 2 consecutive days and then subjected to DNA or RNA sequencing by mNGS or culture; 62 ICU patients and 60 non-ICU patients were admitted. In the end, comparisons were made on the pathogen species identified by mNGS and culture, the overall performance of these two methods in pathogen detection, and the most common pathogens detected by mNGS between the ICU and non-ICU groups. Results In DNA and RNA sequencing, the positive rate of pathogen detection reached 96.69% (117/121) and 96.43% (108/112), respectively. In culture tests, the positive rate of the pathogen was 39.34% (48/122), much lower than that of DNA and RNA sequencing. In general, the positive rate of pathogen detection by sputum mNGS was significantly higher than that of sputum culture in the total and non-ICU groups (p < 0.001) but did not show a significant difference when compared to the result of sputum culture in the ICU group (p = 0.08). Haemophilus spp., Candida albicans, Enterococcus spp., and viruses from the mNGS results were excluded before comparing the overall performance of these two methods in pathogen detection. Specifically, among the 10 most common bacteria implied from the mNGS results, significant differences were observed in the number of cases of Haemophilus parainfluenzae, Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa, Stenotrophomonas maltophilia, Staphylococcus aureus, and Enterococcus faecalis between the ICU and non-ICU groups (p < 0.05). Conclusions This study demonstrated the superiority of mNGS over culture in detecting all kinds of pathogen species in sputum samples. These results indicate that mNGS may serve as a valuable tool to identify pathogens, especially for ICU patients who are more susceptible to mixed infections.
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Affiliation(s)
- Jing-Jiang Zhou
- Department of Emergency Medicine, Tianjin Medical University General Hospital, Tianjin, China
- Department of Emergency Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Wei-Chao Ding
- Department of Emergency Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Yan-Cun Liu
- Department of Emergency Medicine, Tianjin Medical University General Hospital, Tianjin, China
| | - Yu-Lei Gao
- Department of Emergency Medicine, Tianjin Medical University General Hospital, Tianjin, China
| | - Lei Xu
- Department of Emergency Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Run-Lu Geng
- Department of Emergency Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Ying Ye
- Department of Emergency Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
- *Correspondence: Ying Ye, ; Yan-Fen Chai,
| | - Yan-Fen Chai
- Department of Emergency Medicine, Tianjin Medical University General Hospital, Tianjin, China
- *Correspondence: Ying Ye, ; Yan-Fen Chai,
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Improving Suspected Pulmonary Infection Diagnosis by Bronchoalveolar Lavage Fluid Metagenomic Next-Generation Sequencing: a Multicenter Retrospective Study. Microbiol Spectr 2022; 10:e0247321. [PMID: 35943274 PMCID: PMC9431624 DOI: 10.1128/spectrum.02473-21] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Metagenomic next-generation sequencing (mNGS) has been gradually applied to clinical practice due to its unbiased characteristics of pathogen detection. However, its diagnostic performance and clinical value in suspected pulmonary infection need to be evaluated. We systematically reviewed the clinical data of 246 patients with suspected pulmonary infection from 4 medical institutions between January 2019 and September 2021. The diagnostic performances of mNGS and conventional testing (CT) were systematically analyzed based on bronchoalveolar lavage fluid (BALF). The impacts of mNGS and CT on diagnosis modification and treatment adjustment were also assessed. The positive rates of mNGS and CT were 47.97% and 23.17%, respectively. The sensitivity of mNGS was significantly higher than that of CT (53.49% versus 23.26%, P < 0.01), especially for infections of Mycobacterium tuberculosis (67.86% versus 17.86%, P < 0.01), atypical pathogens (100.00% versus 7.14%, P < 0.01), viruses (92.31% versus 7.69%, P < 0.01), and fungi (78.57% versus 39.29%, P < 0.01). The specificity of mNGS was superior to that of CT, with no statistical difference (90.32% versus 77.42%, P = 0.167). The positive predictive value (PPV) and negative predictive value (NPV) of mNGS were 97.46% and 21.88%, respectively. Diagnosis modification and treatment adjustment were conducted in 32 (32/246, 13.01%) and 23 (23/246, 9.35%) cases, respectively, according to mNGS results only. mNGS significantly improved the diagnosis of suspected pulmonary infection, especially infections of M.tuberculosis, atypical pathogens, viruses, and fungi, and it demonstrated the pathogen distribution of pulmonary infections. It is expected to be a promising microbiological detection and diagnostic method in clinical practice. IMPORTANCE Pulmonary infection is a heterogeneous and complex infectious disease with high morbidity and mortality worldwide. In clinical practice, a considerable proportion of the etiology of pulmonary infection is unclear, microbiological diagnosis being challenging. Metagenomic next-generation sequencing detects all nucleic acids in a sample in an unbiased manner, revealing the microbial community environment and organisms and improving the microbiological detection and diagnosis of infectious diseases in clinical settings. This study is the first multicenter, large-scale retrospective study based entirely on BALF for pathogen detection by mNGS, and it demonstrated the superior performance of mNGS for microbiological detection and diagnosis of suspected pulmonary infection, especially in infections of Mycobacterium tuberculosis, atypical pathogens, viruses, and fungi. It also demonstrated the pathogen distribution of pulmonary infections in the real world, guiding targeted treatment and improving clinical management and prognoses.
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Hong D, Wang P, Zhang J, Li K, Ye B, Li G, Zhou J, Tong Z, Ke L, Shi S, Li W. Plasma metagenomic next-generation sequencing of microbial cell-free DNA detects pathogens in patients with suspected infected pancreatic necrosis. BMC Infect Dis 2022; 22:675. [PMID: 35931956 PMCID: PMC9356476 DOI: 10.1186/s12879-022-07662-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 07/30/2022] [Indexed: 11/17/2022] Open
Abstract
Background Infected pancreatic necrosis (IPN) is a life-threatening complication of acute pancreatitis (AP). Timely diagnosis of IPN could facilitate appropriate treatment, but there is a lack of reliable non-invasive screening tests. In this study, we aimed to evaluate the diagnostic value of plasma metagenomic next-generation sequencing (mNGS) based on circulating microbial cell-free DNA in patients with suspected IPN. Methods From October 2020 to October 2021, 44 suspected IPN patients who underwent plasma mNGS were reviewed. Confirmatory diagnosis of IPN within two weeks after the index blood sampling was considered the reference standard. The confirmation of IPN relied on the microbiological results of drains obtained from the necrotic collections. The distribution of the pathogens identified by plasma mNGS was analyzed. Positive percent agreement (PPA) and negative percent agreement (NPA) were evaluated based on the conformity between the overall mNGS results and culture results of IPN drains. In addition, the clinical outcomes were compared between mNGS positive and negative patients. Results Across all the study samples, thirteen species of bacteria and five species of fungi were detected by mNGS. The positivity rate of plasma mNGS was 54.55% (24/44). Of the 24 mNGS positive cases, twenty (83.33%, 95% CI, 68.42–98.24%) were consistent with the culture results of IPN drains. The PPA and NPA of plasma mNGS for IPN were 80.0% (20/25; 95% CI, 64.32–95.68%) and 89.47% (17/19; 95% CI, 75.67–100%), respectively. Compared with the mNGS negative group, patients in the positive group had more new-onset septic shock [12 (50.0%) vs. 4 (20.0%), p = 0.039]. Conclusion IPN relevant pathogens can be identified by plasma mNGS, potentially facilitating appropriate treatment. The clinical application of mNGS in this cohort appears feasible. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-022-07662-2.
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Affiliation(s)
- Donghuang Hong
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China.,Department of Critical Care Medicine, Fujian Provincial Hospital, No.134 East Street, Fuzhou, 350001, Fujian, China
| | - Peng Wang
- Center of Severe Acute Pancreatitis (CSAP), Department of Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, No. 305 Zhongshan East Road, Nanjing, 210002, Jiangsu, China
| | - Jingzhu Zhang
- Center of Severe Acute Pancreatitis (CSAP), Department of Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, No. 305 Zhongshan East Road, Nanjing, 210002, Jiangsu, China
| | - Kaiwei Li
- Center of Severe Acute Pancreatitis (CSAP), Department of Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, No. 305 Zhongshan East Road, Nanjing, 210002, Jiangsu, China
| | - Bo Ye
- Center of Severe Acute Pancreatitis (CSAP), Department of Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, No. 305 Zhongshan East Road, Nanjing, 210002, Jiangsu, China
| | - Gang Li
- Center of Severe Acute Pancreatitis (CSAP), Department of Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, No. 305 Zhongshan East Road, Nanjing, 210002, Jiangsu, China
| | - Jing Zhou
- Center of Severe Acute Pancreatitis (CSAP), Department of Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, No. 305 Zhongshan East Road, Nanjing, 210002, Jiangsu, China
| | - Zhihui Tong
- Center of Severe Acute Pancreatitis (CSAP), Department of Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, No. 305 Zhongshan East Road, Nanjing, 210002, Jiangsu, China
| | - Lu Ke
- Center of Severe Acute Pancreatitis (CSAP), Department of Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, No. 305 Zhongshan East Road, Nanjing, 210002, Jiangsu, China.,National Institute of Healthcare Data Science, Nanjing University, Nanjing, China
| | - Songjing Shi
- Department of Critical Care Medicine, Fujian Provincial Hospital, No.134 East Street, Fuzhou, 350001, Fujian, China.
| | - Weiqin Li
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China. .,Center of Severe Acute Pancreatitis (CSAP), Department of Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, No. 305 Zhongshan East Road, Nanjing, 210002, Jiangsu, China. .,National Institute of Healthcare Data Science, Nanjing University, Nanjing, China.
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Sun L, Zhang S, Yang Z, Yang F, Wang Z, Li H, Li Y, Sun T. Clinical Application and Influencing Factor Analysis of Metagenomic Next-Generation Sequencing (mNGS) in ICU Patients With Sepsis. Front Cell Infect Microbiol 2022; 12:905132. [PMID: 35909965 PMCID: PMC9326263 DOI: 10.3389/fcimb.2022.905132] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 06/17/2022] [Indexed: 12/03/2022] Open
Abstract
Objective To analyze the clinical application and related influencing factors of metagenomic next-generation sequencing (mNGS) in patients with sepsis in intensive care unit (ICU). Methods The study included 124 patients with severe sepsis admitted to the ICU in the First Affiliated Hospital of Zhengzhou University from June 2020 to September 2021. Two experienced clinicians took blood mNGS and routine blood cultures of patients meeting the sepsis diagnostic criteria within 24 hours after sepsis was considered, and collection the general clinical data. Results mNGS positive rate was higher than traditional blood culture (67.74% vs. 19.35%). APACHE II score [odds ratio (OR)=1.096], immune-related diseases (OR=6.544), and hypertension (OR=2.819) were considered as positive independent factors for mNGS or culture-positive. The sequence number of microorganisms and pathogen detection (mNGS) type had no effect on prognosis. Age (OR=1.016), female (OR=5.963), myoglobin (OR=1.005), and positive virus result (OR=8.531) were independent risk factors of sepsis mortality. Adjusting antibiotics according to mNGS results, there was no statistical difference in the prognosis of patients with sepsis. Conclusion mNGS has the advantages of rapid and high positive rate in the detection of pathogens in patients with severe sepsis. Patients with high APACHE II score, immune-related diseases, and hypertension are more likely to obtain positive mNGS results. The effect of adjusting antibiotics according to mNGS results on the prognosis of sepsis needs to be further evaluated.
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Affiliation(s)
- Limin Sun
- General Intensive Care Unit, Zhengzhou Key Laboratory of Sepsis, Henan Key Laboratory of Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shuguang Zhang
- General Intensive Care Unit, Zhengzhou Key Laboratory of Sepsis, Henan Key Laboratory of Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ziyue Yang
- General Intensive Care Unit, Zhengzhou Key Laboratory of Sepsis, Henan Key Laboratory of Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Fei Yang
- General Intensive Care Unit, Zhengzhou Key Laboratory of Sepsis, Henan Key Laboratory of Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhenhua Wang
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hongqiang Li
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yaoguang Li
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Gene Hospital of Henan Province, Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Tongwen Sun
- General Intensive Care Unit, Zhengzhou Key Laboratory of Sepsis, Henan Key Laboratory of Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Tongwen Sun,
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Zhang L, Huang W, Zhang S, Li Q, Wang Y, Chen T, Jiang H, Kong D, Lv Q, Zheng Y, Ren Y, Liu P, Jiang Y, Chen Y. Rapid Detection of Bacterial Pathogens and Antimicrobial Resistance Genes in Clinical Urine Samples With Urinary Tract Infection by Metagenomic Nanopore Sequencing. Front Microbiol 2022; 13:858777. [PMID: 35655992 PMCID: PMC9152355 DOI: 10.3389/fmicb.2022.858777] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 04/11/2022] [Indexed: 12/24/2022] Open
Abstract
Urinary tract infections (UTIs) are among the most common acquired bacterial infections in humans. The current gold standard method for identification of uropathogens in clinical laboratories is cultivation. However, culture-based assays have substantial drawbacks, including long turnaround time and limited culturability of many potential pathogens. Nanopore sequencing technology can overcome these limitations and detect pathogens while also providing reliable predictions of drug susceptibility in clinical samples. Here, we optimized a metagenomic nanopore sequencing (mNPS) test for pathogen detection and identification in urine samples of 76 patients with acute uncomplicated UTIs. We first used twenty of these samples to show that library preparation by the PCR Barcoding Kit (PBK) led to the highest agreement of positive results with gold standard clinical culture tests, and enabled antibiotic resistance detection in downstream analyses. We then compared the detection results of mNPS with those of culture-based diagnostics and found that mNPS sensitivity and specificity of detection were 86.7% [95% confidence interval (CI), 73.5-94.1%] and 96.8% (95% CI, 82.4-99.9%), respectively, indicating that the mNPS method is a valid approach for rapid and specific detection of UTI pathogens. The mNPS results also performed well at predicting antibiotic susceptibility phenotypes. These results demonstrate that our workflow can accurately diagnose UTI-causative pathogens and enable successful prediction of drug-resistant phenotypes within 6 h of sample receipt. Rapid mNPS testing is thus a promising clinical diagnostic tool for infectious diseases, based on clinical urine samples from UTI patients, and shows considerable potential for application in other clinical infections.
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Affiliation(s)
- Lei Zhang
- College of Life Science, Yantai University, Yantai, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Wenhua Huang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Shengwei Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China.,Department of Clinical Laboratory, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Qian Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Ye Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Ting Chen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Hua Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Decong Kong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Qingyu Lv
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Yuling Zheng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Yuhao Ren
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Peng Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Yongqiang Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Ying Chen
- College of Life Science, Yantai University, Yantai, China
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Wang D, Lai M, Song H, Zhang JY, Zhao FY, Liang J, Xu WQ, Tang YM, Xu XJ. Integration of Interleukin-6 Improves the Diagnostic Precision of Metagenomic Next-Generation Sequencing for Infection in Immunocompromised Children. Front Microbiol 2022; 13:819467. [PMID: 35391735 PMCID: PMC8982073 DOI: 10.3389/fmicb.2022.819467] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 01/24/2022] [Indexed: 11/13/2022] Open
Abstract
The performance of metagenomic next-generation sequencing (mNGS) in identifying pathogens in immunocompromised children was not very clear. The purpose of this study is to assess the performance of mNGS in this population and to investigate whether the integration of serum cytokines and mNGS assay could improve diagnostic accuracy. We retrospectively collected the clinical data of pediatric patients who suffered febrile diseases and underwent mNGS determination simultaneously in the department of hematology/oncology between January 2019 and March 2021. Specimens were sent for conventional microbiological test (CMT), mNGS, and serum cytokine measurement in parallel. A total of 258 episodes of febrile diseases were enrolled, mNGS was positive in 224 cases, while CMT was positive in 78 cases. mNGS and CMT were both positive in 70 (27.1%) cases and were both negative in 26 (10.1%) cases. There were 154 (59.7%) cases positive by mNGS only while 8 (3.1%) were positive by CMT only. It was common that two or more pathogens were simultaneously detected by mNGS in a single specimen, with only 61 tests identified a single organism. Whether the organisms reported by mNGS were the microbiological etiology of infection was evaluated. Of the 224 cases with positive mNGS results, 135 (58.4%), 30 (13.0%), and 59 (28.6%) were considered as "probable," "possible," and "unlikely," respectively. Patients with high IL-6 (≥ 390 pg/ml) were likely to be bacterial infection. Although mNGS reported mixed pathogens, 84.6% (33/39) and 83.3% (10/12) of patients presenting high IL-6 were confirmed as bacterial infection in the training and validation cohort, respectively. In conclusion, mNGS analysis demonstrates promising diagnostic potential in rapidly identifying clinically relevant pathogens. Given the detection of many clinically irrelevant organisms, the integration of IL-6 improves the precision of mNGS results interpretation.
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Affiliation(s)
- Di Wang
- Division/Center of Hematology-Oncology, The Children's Hospital of Zhejiang University School of Medicine, Hangzhou, China.,The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, Hangzhou, China
| | - Min Lai
- Division/Center of Hematology-Oncology, The Children's Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Hua Song
- Division/Center of Hematology-Oncology, The Children's Hospital of Zhejiang University School of Medicine, Hangzhou, China.,The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, Hangzhou, China
| | - Jing-Ying Zhang
- Division/Center of Hematology-Oncology, The Children's Hospital of Zhejiang University School of Medicine, Hangzhou, China.,The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, Hangzhou, China
| | - Fen-Ying Zhao
- Division/Center of Hematology-Oncology, The Children's Hospital of Zhejiang University School of Medicine, Hangzhou, China.,The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, Hangzhou, China
| | - Juan Liang
- Division/Center of Hematology-Oncology, The Children's Hospital of Zhejiang University School of Medicine, Hangzhou, China.,The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, Hangzhou, China
| | - Wei-Qun Xu
- Division/Center of Hematology-Oncology, The Children's Hospital of Zhejiang University School of Medicine, Hangzhou, China.,The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, Hangzhou, China
| | - Yong-Min Tang
- Division/Center of Hematology-Oncology, The Children's Hospital of Zhejiang University School of Medicine, Hangzhou, China.,The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, Hangzhou, China
| | - Xiao-Jun Xu
- Division/Center of Hematology-Oncology, The Children's Hospital of Zhejiang University School of Medicine, Hangzhou, China.,The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, Hangzhou, China
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Zhao E, Wang D, Li N, Huang S, Zhao Z, Hu S, He X, Wen G. Clinical study on the diagnosis of porcine streptococcal meningitis with negative blood and cerebrospinal fluid culture by next-generation sequencing. Eur J Med Res 2021; 26:85. [PMID: 34344456 PMCID: PMC8330088 DOI: 10.1186/s40001-021-00554-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 07/15/2021] [Indexed: 11/21/2022] Open
Abstract
Background Streptococcus suis (Ss) is a Gram-positive and anaerobic zoonotic pathogen that is susceptible to all populations and can cause meningitis, septicemia, endocarditis and arthritis in humans. Methods In this study, patients with meningitis who were admitted to our hospital with negative blood and cerebrospinal fluid culture were divided into a next-generation sequencing group and a control group. In the next-generation sequencing group, we used the next-generation sequencing method to detect pathogenic bacteria in the patients’ cerebrospinal fluid. In the control group, we used blood and cerebrospinal fluid bacterial culture method to detect pathogenic bacteria in the patients' cerebrospinal fluid. The detection rates of pathogenic bacteria in the cerebrospinal fluid of the two groups were compared and analyzed. Results A total of 18 patients were included in this study, including 8 patients in the next-generation sequencing group and 10 patients in the control group. The mean age (P = 0.613) and mean disease duration (P = 0.294) were similar in both groups. Patients in the next-generation sequencing group had a leukocyte count of 13.13 ± 4.79 × 109, a neutrophil percentage of 83.39 ± 10.36%, and a C-reactive protein level of 134.95 ± 107.69 mg/L. Patients in the control group had a temperature of 38.32 ± 1.07, a leukocyte count of 8.00 ± 2.99 × 109, and a neutrophil percentage of 74.61 ± 8.89%, and C-reactive protein level was 4.75 ± 6.8 mg/L. The statistical results showed that the leukocytes (P = 0.013) and C-reactive protein levels (P = 0.001) were significantly higher in the patients of the next-generation sequencing group than in the control group. No statistically significant differences were seen in body temperature and neutrophil percentage between the two groups (P > 0.05). The incidence of intracranial pressure and meningeal irritation signs were similar in the two groups (P > 0.05). The detection rate of Streptococcus suis in the cerebrospinal fluid of patients in the next-generation sequencing group was 100%, and the detection rate of Streptococcus suis in the cerebrospinal fluid of the control group was 0%. Conclusion The detection rate of Streptococcus suis infection in cerebrospinal fluid by next-generation sequencing was significantly higher than that by blood and cerebrospinal fluid bacterial culture. Therefore, the diagnosis of porcine streptococcal meningitis by next-generation sequencing method is worthy of clinical promotion and application.
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Affiliation(s)
- Eryi Zhao
- Department of Neurology, Hainan General Hospital, Hainan Affilicated Hospital of Hainan Medical University, Haikou, 570311, Hainan, China
| | - Daimei Wang
- Department of Pharmacy, Hainan General Hospital, Hainan Affilicated Hospital of Hainan Medical University, Haikou, 570311, Hainan, China
| | - Na Li
- Department of Pharmacy, Qianjiang Central Hospital of Chongqing, No. 63 of Road 9, Chengxi Street, Qianjiang District, Chongqing, 409099, China.
| | - Shixiong Huang
- Department of Neurology, Hainan General Hospital, Hainan Affilicated Hospital of Hainan Medical University, Haikou, 570311, Hainan, China
| | - Zhongyan Zhao
- Department of Neurology, Hainan General Hospital, Hainan Affilicated Hospital of Hainan Medical University, Haikou, 570311, Hainan, China
| | - Shijun Hu
- Department of Neurology, Hainan General Hospital, Hainan Affilicated Hospital of Hainan Medical University, Haikou, 570311, Hainan, China
| | - Xiangying He
- Department of Neurology, Hainan General Hospital, Hainan Affilicated Hospital of Hainan Medical University, Haikou, 570311, Hainan, China
| | - Guoqiang Wen
- Department of Neurology, Hainan General Hospital, Hainan Affilicated Hospital of Hainan Medical University, Haikou, 570311, Hainan, China
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Xie G, Zhao B, Wang X, Bao L, Xu Y, Ren X, Ji J, He T, Zhao H. Exploring the Clinical Utility of Metagenomic Next-Generation Sequencing in the Diagnosis of Pulmonary Infection. Infect Dis Ther 2021; 10:1419-1435. [PMID: 34117999 PMCID: PMC8322361 DOI: 10.1007/s40121-021-00476-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 05/28/2021] [Indexed: 11/29/2022] Open
Abstract
INTRODUCTION We aimed to explore the real-world clinical application value and challenges of metagenomic next-generation sequencing (mNGS) for pulmonary infection diagnosis. METHODS We retrospectively reviewed the results of mNGS and conventional tests from 140 hospitalized patients with suspected pulmonary infections from January 2019 to December 2020. The sample types included bronchoalveolar lavage fluid, lung tissue by transbronchial lung biopsy, pleural effusion, blood, and bronchial sputum. Apart from the mNGS reports that our patients received, an extra comprehensive and thorough literature search was conducted. RESULTS Significant differences were noticed in the positive detection rates of pathogens between mNGS and conventional diagnostic testing (115/140, 82.14% vs 50/140, 35.71%, P < 0.05). The percentage of mNGS-positive patients was significantly higher than that of conventional testing-positive patients with regard to bacterial detection (P < 0.01), but no significant differences were found with regard to fungal detection (P = 0.67). Significant statistical differences were found between mixed infection cases (15, 22.70%) and single infection cases (4, 7.84%) in terms of diabetes (P = 0.03). The most frequent pattern of mixed infection was bacteria and fungi mixed infection (40, 40/89 = 44.94%), followed by bacteria mixed infection (29, 29/89 = 32.58%). The sensitivity of mNGS in pulmonary infection diagnosis was much higher than that of conventional test (89.17% vs 50.00%; P < 0.01), but the specificity was the opposite (75.00% vs 81.82%; P > 0.05). CONCLUSION mNGS is a valuable tool for the detection of pulmonary infections, especially mixed pulmonary infections. The most common combinations we found were bacterial-fungal coinfection and bacterial-bacterial coinfection. Still, there are many challenges in the clinical application of mNGS in the diagnosis of pulmonary infections. There is still a lot of work to be done in interpreting the mNGS reports, because both clinical judgment and literature analysis strategy need to be refined.
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Affiliation(s)
- Guijuan Xie
- Department of Respiratory, The Affiliated Wuxi Second People's Hospital of Nanjing Medical University, Wuxi, China.,Affiliated Wuxi Clinical College of Nantong University, Wuxi, China
| | - Bo Zhao
- Affiliated Wuxi Clinical College of Nantong University, Wuxi, China.,Department of Gastroenterology, The Affiliated Wuxi Second People's Hospital of Nanjing Medical University, Wuxi, China
| | - Xun Wang
- Department of Respiratory, The Affiliated Wuxi Second People's Hospital of Nanjing Medical University, Wuxi, China.,Affiliated Wuxi Clinical College of Nantong University, Wuxi, China
| | - Liang Bao
- Department of Respiratory, The Affiliated Wuxi Second People's Hospital of Nanjing Medical University, Wuxi, China.,Affiliated Wuxi Clinical College of Nantong University, Wuxi, China
| | - Yiming Xu
- Department of Respiratory, The Affiliated Wuxi Second People's Hospital of Nanjing Medical University, Wuxi, China.,Affiliated Wuxi Clinical College of Nantong University, Wuxi, China
| | - Xian Ren
- Department of Respiratory, The Affiliated Wuxi Second People's Hospital of Nanjing Medical University, Wuxi, China.,Affiliated Wuxi Clinical College of Nantong University, Wuxi, China
| | - Jiali Ji
- Department of Respiratory, The Affiliated Wuxi Second People's Hospital of Nanjing Medical University, Wuxi, China.,Affiliated Wuxi Clinical College of Nantong University, Wuxi, China
| | - Ting He
- Department of Respiratory, The Affiliated Wuxi Second People's Hospital of Nanjing Medical University, Wuxi, China.,Affiliated Wuxi Clinical College of Nantong University, Wuxi, China
| | - Hongqing Zhao
- Department of Respiratory, The Affiliated Wuxi Second People's Hospital of Nanjing Medical University, Wuxi, China. .,Affiliated Wuxi Clinical College of Nantong University, Wuxi, China.
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Impaired cardiac function is associated with mortality in patients with acute COVID-19 infection. Clin Res Cardiol 2020; 109:1491-1499. [PMID: 32537662 PMCID: PMC7293880 DOI: 10.1007/s00392-020-01683-0] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 05/28/2020] [Indexed: 01/08/2023]
Abstract
Background COVID-19 infection may cause severe respiratory distress and is associated with increased morbidity and mortality. Impaired cardiac function and/or pre-existing cardiovascular disease may be associated with poor prognosis. In the present study, we report a comprehensive cardiovascular characterization in the first consecutive collective of patients that was admitted and treated at the University Hospital of Tübingen, Germany. Methods 123 consecutive patients with COVID-19 were included. Routine blood sampling, transthoracic echocardiography and electrocardiography were performed at hospital admission. Results We found that impaired left-ventricular and right-ventricular function as well as tricuspid regurgitation > grade 1 were significantly associated with higher mortality. Furthermore, elevated levels of myocardial distress markers (troponin-I and NT pro-BNP) were associated with poor prognosis in this patient collective. Conclusion Impaired cardiac function is associated with poor prognosis in COVID-19 positive patients. Consequently, treatment of these patients should include careful guideline-conform cardiovascular evaluation and treatment. Thus, formation of a competent Cardio-COVID-19 team may represent a major clinical measure to optimize therapy of cardiovascular patients during this pandemic.
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