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Wu J, Zhang Y, Duan J, Wei Y, Miao Y. A metagenomic next-generation sequencing (mNGS)-based analysis of bronchoalveolar lavage samples in patients with an acute exacerbation of chronic obstructive pulmonary disease. J Mol Histol 2024:10.1007/s10735-024-10225-1. [PMID: 39060894 DOI: 10.1007/s10735-024-10225-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024]
Abstract
The role of the bronchoalveolar lavage fluid (BALF) microbiome in acute exacerbations of chronic obstructive pulmonary disease (AECOPD) remains unclear. The advent of the metagenomic next-generation sequencing (mNGS) has made it possible to reveal the complex microbiome composition of the respiratory tract. This study aimed to explore whether there are differences in the BALF microbiome of AECOPD patients with different lung functions. We enrolled 55 AECOPD patients and divided them into a mild group (n = 31) and a severe group (n = 24) according to their lung function. We collected BALF and submitted it to mNGS and bioinformatics analysis. At the species level, mNGS identified 264 bacteria, 13 fungi and 12 viruses in the mild group, and 174 bacteria, 6 fungi and 6 viruses in the severe group. Mixed bacterial and viral infection occurred in both groups. At the genus level, Rothia and Veillonella were more abundant in the mild group, while Pseudomonas and Staphylococcus were more abundant in the severe group. At the species level, compared with the mild group, the relative abundance of Haemophilus influenzae and Pseudomonas aeruginosa was increased in the severe group. Besides, the BALF microbiome composition was similar between the two groups, and there was no significant difference in α and β diversity. Forced expiratory volume in 1 s/forced vital capacity (FEV1/FVC) (%) showed no significant correlation with the Shannon or Simpson index. The microbiome abundance was different between the mild and severe groups; however, microbiome diversity was similar between the two groups. Based on our findings, Haemophilus influenzae and Pseudomonas aeruginosa may be the pathogenic bacteria that cause the difference in lung function in patients with AECOPD.
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Affiliation(s)
- Junfang Wu
- Department of Respiratory Medicine, Shaanxi Provincial People's Hospital, NO.256, Friendship West Road, Beilin District, Xi'an, 710068, Shaanxi, China
| | - Yongqing Zhang
- Department of Respiratory Medicine, Shaanxi Provincial People's Hospital, NO.256, Friendship West Road, Beilin District, Xi'an, 710068, Shaanxi, China
| | - Jinjin Duan
- Department of Respiratory Medicine, Shaanxi Provincial People's Hospital, NO.256, Friendship West Road, Beilin District, Xi'an, 710068, Shaanxi, China
| | - Yiqun Wei
- Department of Respiratory Medicine, Shaanxi Provincial People's Hospital, NO.256, Friendship West Road, Beilin District, Xi'an, 710068, Shaanxi, China
| | - Yi Miao
- Department of Respiratory Medicine, Shaanxi Provincial People's Hospital, NO.256, Friendship West Road, Beilin District, Xi'an, 710068, Shaanxi, China.
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Zhang P, Liu B, Zhang S, Chang X, Zhang L, Gu D, Zheng X, Chen J, Xiao S, Wu Z, Cai X, Long M, Lu W, Zheng M, Chen R, Gao R, Zheng Y, Wu J, Feng Q, He G, Chen Y, Zheng W, Zuo W, Huang Y, Zhang X. Clinical application of targeted next-generation sequencing in severe pneumonia: a retrospective review. Crit Care 2024; 28:225. [PMID: 38978111 PMCID: PMC11232260 DOI: 10.1186/s13054-024-05009-8] [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: 02/08/2024] [Accepted: 06/27/2024] [Indexed: 07/10/2024] Open
Abstract
BACKGROUND The precise identification of the underlying causes of infectious diseases, such as severe pneumonia, is essential, and the development of next-generation sequencing (NGS) has enhanced the effectiveness of pathogen detection. However, there is limited information on the systematic assessment of the clinical use of targeted next-generation sequencing (tNGS) in cases of severe pneumonia. METHODS A retrospective analysis was conducted on 130 patients with severe pneumonia treated in the ICU from June 2022 to June 2023. The consistency of the results of tNGS, metagenomics next-generation sequencing (mNGS), and culture with the clinical diagnosis was evaluated. Additionally, the results for pathogens detected by tNGS were compared with those of culture, mNGS, and quantitative reverse transcription PCR (RT-qPCR). To evaluate the efficacy of monitoring severe pneumonia, five patients with complicated infections were selected for tNGS microbiological surveillance. The tNGS and culture drug sensitisation results were then compared. RESULTS The tNGS results for the analysis of the 130 patients showed a concordance rate of over 70% with clinical diagnostic results. The detection of pathogenic microorganisms using tNGS was in agreement with the results of culture, mNGS, and RT-qPCR. Furthermore, the tNGS results for pathogens in the five patients monitored for complicated infections of severe pneumonia were consistent with the culture and imaging test results during treatment. The tNGS drug resistance results were in line with the drug sensitivity results in approximately 65% of the cases. CONCLUSIONS The application of tNGS highlights its promise and significance in assessing the effectiveness of clinical interventions and providing guidance for anti-infection therapies for severe pneumonia.
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Affiliation(s)
- Peng Zhang
- Department of Critical Care Medicine, Jiangmen Central Hospital, Jiangmen, 529030, China
| | - Baoyi Liu
- Clinical Experimental Center, Jiangmen Engineering Technology Research Center of Clinical Biobank and Translational Research, Jiangmen Central Hospital, Jiangmen, 529030, China
| | - Shuang Zhang
- Department of Critical Care Medicine, Jiangmen Central Hospital, Jiangmen, 529030, China
| | - Xuefei Chang
- Department of Respiratory and Critical Care Medicine, Jiangmen Central Hospital, Jiangmen, 529030, China
| | - Lihe Zhang
- Department of Respiratory and Critical Care Medicine, Jiangmen Central Hospital, Jiangmen, 529030, China
| | - Dejian Gu
- Geneplus-Beijing Institute, Beijing, 102206, China
| | - Xin Zheng
- Geneplus-Beijing Institute, Beijing, 102206, China
| | - Jiaqing Chen
- Clinical Experimental Center, Jiangmen Engineering Technology Research Center of Clinical Biobank and Translational Research, Jiangmen Central Hospital, Jiangmen, 529030, China
| | - Saiyin Xiao
- Department of Critical Care Medicine, Jiangmen Central Hospital, Jiangmen, 529030, China
| | - Zhentao Wu
- Department of Critical Care Medicine, Jiangmen Central Hospital, Jiangmen, 529030, China
| | - Xuemin Cai
- Department of Critical Care Medicine, Jiangmen Central Hospital, Jiangmen, 529030, China
| | - Mingfa Long
- Department of Critical Care Medicine, Jiangmen Central Hospital, Jiangmen, 529030, China
| | - Wenjie Lu
- Clinical Experimental Center, Jiangmen Engineering Technology Research Center of Clinical Biobank and Translational Research, Jiangmen Central Hospital, Jiangmen, 529030, China
| | - Mingzhu Zheng
- Clinical Experimental Center, Jiangmen Engineering Technology Research Center of Clinical Biobank and Translational Research, Jiangmen Central Hospital, Jiangmen, 529030, China
| | | | - Rui Gao
- Geneplus-Beijing Institute, Beijing, 102206, China
| | - Yan Zheng
- Department of Research and Development, Guangdong Research Institute of Genetic Diagnostic and Engineering Technologies for Thalassemia, Hybribio Limited, Guangzhou, 510000, China
| | - Jinhua Wu
- Department of Clinical Laboratory, Jiangmen Central Hospital, Jiangmen, 529030, China
| | - Qiujuan Feng
- Department of Clinical Laboratory, Jiangmen Central Hospital, Jiangmen, 529030, China
| | - Gang He
- Department of Infectious Diseases, Jiangmen Central Hospital, Jiangmen, 529030, China
| | - Yantang Chen
- Department of Critical Care Medicine, Jiangmen Central Hospital, Jiangmen, 529030, China
| | - Weihao Zheng
- Department of Critical Care Medicine, Jiangmen Central Hospital, Jiangmen, 529030, China
| | - Wanli Zuo
- Clinical Experimental Center, Jiangmen Engineering Technology Research Center of Clinical Biobank and Translational Research, Jiangmen Central Hospital, Jiangmen, 529030, China.
- Department of Respiratory and Critical Care Medicine, Jiangmen Central Hospital, Jiangmen, 529030, China.
| | - Yanming Huang
- Clinical Experimental Center, Jiangmen Engineering Technology Research Center of Clinical Biobank and Translational Research, Jiangmen Central Hospital, Jiangmen, 529030, China.
- Department of Respiratory and Critical Care Medicine, Jiangmen Central Hospital, Jiangmen, 529030, China.
| | - Xin Zhang
- Clinical Experimental Center, Jiangmen Engineering Technology Research Center of Clinical Biobank and Translational Research, Jiangmen Central Hospital, Jiangmen, 529030, China.
- Dongguan Key Laboratory of Medical Bioactive Molecular Developmental and Translational Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, 523808, China.
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Dong T, Liang Y, Xie J, Fan W, Chen H, Han X. Integrative analyses identify opportunistic pathogens of patients with lower respiratory tract infections based on metagenomic next-generation sequencing. Heliyon 2024; 10:e30896. [PMID: 38765026 PMCID: PMC11097057 DOI: 10.1016/j.heliyon.2024.e30896] [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: 01/17/2024] [Revised: 05/06/2024] [Accepted: 05/07/2024] [Indexed: 05/21/2024] Open
Abstract
Lower respiratory tract infections (LRTIs) represent some of the most globally prevalent and detrimental diseases. Metagenomic next-generation sequencing (mNGS) technology has effectively addressed the requirement for the diagnosis of clinical infectious diseases. This study aimed at identifying and classifying opportunistic pathogens from the respiratory tract-colonizing microflora in LRTI patients using data acquired from mNGS analyses. A retrospective study was performed employing the mNGS data pertaining to the respiratory samples derived from 394 LRTIs patients. Linear discriminant analysis effect size (LEfSe) analysis was conducted to discern the discriminant bacteria. Receiver operating characteristic curves (ROC) were established to demonstrate discriminant bacterial behavior to distinguish colonization from infection. A total of 443 discriminant bacteria were identified and segregated into three cohorts contingent upon their correlation profiles, detection frequency, and relative abundance in order to distinguish pathogens from colonizing microflora. Among them, 119 emerging opportunistic pathogens (cohort 2) occupied an average area under the curve (AUC) of 0.976 for exhibiting the most prominent predictability in distinguishing colonization from infection, 39 were colonizing bacteria (cohort 1, 0.961), and 285 were rare opportunistic pathogens (cohort 3, 0.887). The LTRIs patients appeared modular in the form of cohorts depicting complex microbial co-occurrence networks, reduced diversity, and a high degree of antagonistic interactions in the respiratory tract microbiome. The study findings indicate that therapeutic interventions should target interaction networks rather than individual microbes, providing an innovative perspective for comprehending and combating respiratory infections. Conclusively, this study reports a profile of LRTIs-associated bacterial colonization and opportunistic pathogens in a relatively large-scale cohort, which might serve as a reference panel for the interpretation of mNGS results in clinical practice.
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Affiliation(s)
- Tingyan Dong
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, China
- Integrated Diagnostic Centre for Infectious Diseases, Guangzhou Huayin Medical Laboratory Center, Guangzhou, China
| | - Yueming Liang
- Department of Respiratory and Critical Care Medicine, The First People Hospital of Foshan, Foshan, China
| | - Junting Xie
- Department of Respiratory and Critical Care Medicine, The First People Hospital of Foshan, Foshan, China
| | - Wentao Fan
- Integrated Diagnostic Centre for Infectious Diseases, Guangzhou Huayin Medical Laboratory Center, Guangzhou, China
| | - Haitao Chen
- Integrated Diagnostic Centre for Infectious Diseases, Guangzhou Huayin Medical Laboratory Center, Guangzhou, China
| | - Xiaodong Han
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, China
- Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Science, Medical School, Nanjing University, Nanjing, China
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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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Li S, Han X, Ma J, Huang GH, Yang ST, Wang CM. Study on mNGS Technique in Diagnosing Pneumocystis jirovecii Pneumonia in Non-HIV-Infected Patients. Infect Drug Resist 2024; 17:1397-1405. [PMID: 38628239 PMCID: PMC11019452 DOI: 10.2147/idr.s450878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 02/07/2024] [Indexed: 04/19/2024] Open
Abstract
Objective To investigate the value of metagenomic Next-Generation Sequencing (mNGS) in diagnosing Pneumocystis jirovecii pneumonia (PJP) in non-human immunodeficiency virus (HIV)-infected patients. Methods In this retrospective study, non-HIV-infected patients with PJP and those diagnosed with non-PJP from August 2022 to December 2024 were selected as subjects. The presence of Pneumocystis jirovecii (PJ) and other co-pathogens in bronchoalveolar lavage fluid (BALF) was analyzed, and the diagnostic efficacy of NGS, polymerase chain reaction (PCR) and serum 1,3-β-D-glucan (BDG) in PJP was compared with the reference standard of clinical compound diagnosis. Results Eighty-nine non-HIV-infected patients were recruited, with dyspnea as the primary symptom (69.66%) and solid malignant tumor as the most common underlying disease (20.22%). Taking clinical compound diagnosis as the reference standard, the sensitivity, specificity, negative predictive value and positive predictive value of mNGS were higher than those detected by PCR and serum BDG. Among 42 non-HIV-infected patients with PJP who underwent mNGS and conventional pathogen detection of BALF, 6 had simple PJ infection and 36 had combined PJ infection. The detection rate of mNGS in mixed infections was significantly higher than that of conventional pathogen detection (85.71 vs 61.70%, P = 0.012). A total of 127 pathogens were detected in BALF using mNGS, among which fungi had the highest detection rate (46.46%). The fungi, viruses and bacteria detected were mainly Pneumocystis jirovecii, human gammaherpesvirus 4 and Acinetobacter baumannii. Conclusion mNGS is highly effective in diagnosing non-HIV-infected patients with PJP and exhibits ideal performance in the detection of co-pathogens. In addition, it has certain value for clinical diagnosis and guidance of targeted anti-infective drug treatment.
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Affiliation(s)
- Shuai Li
- Clinical Laboratory Center, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang, 830001, People’s Republic of China
| | - Xue Han
- Clinical Laboratory Center, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang, 830001, People’s Republic of China
| | - Jing Ma
- Clinical Laboratory Center, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang, 830001, People’s Republic of China
| | - Guo-Hong Huang
- Clinical Laboratory Center, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang, 830001, People’s Republic of China
| | - Shu-Ting Yang
- Clinical Laboratory Center, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang, 830001, People’s Republic of China
| | - Chang-Min Wang
- Clinical Laboratory Center, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang, 830001, People’s Republic of China
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Lv T, Zhao Q, Liu J, Wang S, Wu W, Miao L, Zhan P, Chen X, Huang M, Ye M, Ou Q, Zhang Y. Utilizing metagenomic next-generation sequencing for pathogen detection and diagnosis in lower respiratory tract infections in real-world clinical practice. Infection 2024; 52:625-636. [PMID: 38368306 DOI: 10.1007/s15010-024-02185-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 01/12/2024] [Indexed: 02/19/2024]
Abstract
BACKGROUND Infectious etiologies of lower respiratory tract infections (LRTIs) by the conventional microbiology tests (CMTs) can be challenging. Metagenomic next-generation sequencing (mNGS) has great potential in clinical use for its comprehensiveness in identifying pathogens, particularly those difficult-to-culture organisms. METHODS We analyzed a total of 205 clinical samples from 201 patients with suspected LRTIs using mNGS in parallel with CMTs. mNGS results were used to guide treatment adjustments for patients who had negative CMT results. The efficacy of treatment was subsequently evaluated in these patients. RESULTS mNGS-detected microorganisms in 91.7% (188/205) of the clinical samples, whereas CMTs demonstrated a lower detection rate, identifying microorganisms in only 37.6% (77/205) of samples. Compared to CMT results, mNGS exhibited a detection sensitivity of 93.5% and 95.4% in all 205 clinical samples and 180 bronchoalveolar lavage fluid (BALF) samples, respectively. A total of 114 patients (114/201; 56.7%) showed negative CMT results, among which 92 received treatment adjustments guided by their positive mNGS results. Notably, 67.4% (62/92) of patients demonstrated effective treatment, while 25% (23/92) experienced a stabilized condition. Subgroup analysis of cancer patients revealed that 41.9% (13/31) exhibited an effective response to treatment, and 35.5% (11/31) maintained a stable condition following medication adjustments guided by mNGS. CONCLUSION mNGS demonstrated great potential in identifying microorganisms of clinical significance in LRTIs. The rapid turnaround time and reduced susceptibility to the impact of antimicrobial administration make mNGS a valuable supplementary tool for diagnosis and treatment decision-making for suspected LRTIs in clinical practice.
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Affiliation(s)
- Tangfeng Lv
- Department of Respiratory and Critical Care Medicine, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210002, Jiangsu, China
| | - Qi Zhao
- Department of Pulmonary and Critical Care Medicine, Nanjing Drum Tower Hospital, Nanjing, 210008, Jiangsu, China
| | - Jia Liu
- Dinfectome Inc., Nanjing, 210000, Jiangsu, China
| | - Song Wang
- Dinfectome Inc., Nanjing, 210000, Jiangsu, China
| | - Weiwei Wu
- Dinfectome Inc., Nanjing, 210000, Jiangsu, China
| | - Liyun Miao
- Department of Respiratory and Critical Care Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, Jiangsu, China
- Yancheng Branch of Nanjing Drum Tower Hospital, Yancheng, 224002, Jiangsu, China
| | - Ping Zhan
- Department of Respiratory and Critical Care Medicine, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210002, Jiangsu, China
| | - Xiaoli Chen
- Department of Respiratory and Critical Care Medicine, Jiangsu Provincial Hospital of Integrated Chinese and Western Medicine, 100 Cross Street, Hongshan Road, Nanjing, 210028, Jiangsu, China
| | - Manman Huang
- Dinfectome Inc., Nanjing, 210000, Jiangsu, China
| | - Mingxiang Ye
- Department of Respiratory and Critical Care Medicine, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210002, Jiangsu, China
| | - Qiuxiang Ou
- Dinfectome Inc., Nanjing, 210000, Jiangsu, China
| | - Yeqing Zhang
- Department of Respiratory and Critical Care Medicine, Jiangsu Provincial Hospital of Integrated Chinese and Western Medicine, 100 Cross Street, Hongshan Road, Nanjing, 210028, Jiangsu, China.
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Yuan L, Zhu Q, Chen Q, Lai LM, Liu P, Liu Y. The microbiological diagnostic performance of metagenomic next-generation sequencing in patients with infectious diseases. Lab Med 2024; 55:132-139. [PMID: 37289931 DOI: 10.1093/labmed/lmad046] [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] [Indexed: 06/10/2023] Open
Abstract
OBJECTIVE Metagenomic next-generation sequencing (mNGS) can be used to detect pathogens in clinical infectious diseases through the sequencing analysis of microbial and host nucleic acids in clinical samples. This study aimed to assess the diagnostic performance of mNGS in patients with infections. METHODS In this study, 641 patients with infectious diseases were enrolled. These patients simultaneously underwent pathogen detection by both mNGS and microbial culture. Through statistical analysis, we judged the diagnostic performance of mNGS and microbial culture on different pathogens. RESULTS Among 641 patients, 276 cases of bacteria and 95 cases of fungi were detected by mNGS, whereas 108 cases of bacteria and 41 cases of fungi were detected by traditional cultures. Among all mixed infections, combined bacterial and viral infections were the highest (51%, 87/169), followed by combined bacterial with fungal infections (16.57%, 28/169) and mixed bacterial, fungal, and viral infections (13.61%, 23/169). Among all sample types, bronchoalveolar lavage fluid (BALF) samples had the highest positive rate (87.8%, 144/164), followed by sputum (85.4%, 76/89) and blood samples (61.2%, 158/258). For the culture method, sputum samples had the highest positive rate (47.2%, 42/89), followed by BALF (37.2%, 61/164). The positive rate of mNGS was 69.89% (448/641), which was significantly higher than that of traditional cultures (22.31% [143/641]) (P < .05). CONCLUSIONS Our results show that mNGS is an effective tool for the rapid diagnosis of infectious diseases. Compared with traditional detection methods, mNGS also showed obvious advantages in mixed infections and infections with uncommon pathogens.
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Affiliation(s)
- Lei Yuan
- Department of Clinical Laboratory, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Qing Zhu
- Department of Clinical Laboratory, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Qiang Chen
- Department of Clinical Laboratory, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Lan Min Lai
- Department of Clinical Laboratory, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Peng Liu
- Department of Clinical Laboratory, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Yang Liu
- Department of Clinical Laboratory, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
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Shen D, Lv X, Zhang H, Fei C, Feng J, Zhou J, Cao L, Ying Y, Li N, Ma X. Association between Clinical Characteristics and Microbiota in Bronchiectasis Patients Based on Metagenomic Next-Generation Sequencing Technology. Pol J Microbiol 2024; 73:59-68. [PMID: 38437464 PMCID: PMC10911701 DOI: 10.33073/pjm-2024-007] [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: 09/06/2023] [Accepted: 01/15/2024] [Indexed: 03/06/2024] Open
Abstract
This study aimed to investigate the disparities between metagenomic next-generation sequencing (mNGS) and conventional culture results in patients with bronchiectasis. Additionally, we sought to investigate the correlation between the clinical characteristics of patients and their microbiome profiles. The overarching goal was to enhance the effective management and treatment of bronchiectasis patients, providing a theoretical foundation for healthcare professionals. A retrospective survey was conducted on 67 bronchiectasis patients admitted to The First Hospital of Jiaxing from October 2019 to March 2023. Clinical baseline information, inflammatory indicators, and pathogen detection reports, including mNGS, conventional blood culture, bronchoalveolar lavage fluid (BALF) culture, and sputum culture results, were collected. By comparing the results of mNGS and conventional culture, the differences in pathogen detection rate and pathogen types were explored, and the diagnostic performance of mNGS compared to conventional culture was evaluated. Based on the various pathogens detected by mNGS, the association between clinical characteristics of bronchiectasis patients and mNGS microbiota results was analyzed. The number and types of pathogens detected by mNGS were significantly larger than those detected by conventional culture. The diagnostic efficacy of mNGS was significantly superior to conventional culture for all types of pathogens, particularly in viral detection (p < 0.01). Regarding pathogen detection rate, the bacteria with the highest detection rate were Pseudomonas aeruginosa (17/58) and Haemophilus influenzae (11/58); the fungus with the highest detection rate was Aspergillus fumigatus (10/21), and the virus with the highest detection rate was human herpes virus 4 (4/11). Differences were observed between the positive and negative groups for P. aeruginosa in terms of common scoring systems for bronchiectasis and whether the main symptom of bronchiectasis manifested as thick sputum (p < 0.05). Significant distinctions were also noted between the positive and negative groups for A. fumigatus regarding Reiff score, neutrophil percentage, bronchiectasis etiology, and alterations in treatment plans following mNGS results reporting (p < 0.05). Notably, 70% of patients with positive A. fumigatus infection opted to change their treatment plans. The correlation study between clinical characteristics of bronchiectasis patients and mNGS microbiological results revealed that bacteria, such as P. aeruginosa, and fungi, such as A. fumigatus, were associated with specific clinical features of patients. This underscored the significance of mNGS in guiding personalized treatment approaches. mNGS could identify multiple pathogens in different types of bronchiectasis samples and was a rapid and effective diagnostic tool for pathogen identification. Its use was recommended for diagnosing the causes of infections in bronchiectasis patients.
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Affiliation(s)
- Dongfeng Shen
- The Intensive Care of Unit, The First Hospital of Jiaxing (The Affiliated Hospital of Jiaxing University), Jiaxing, China
| | - Xiaodong Lv
- Department of Respiratory, The First Hospital of Jiaxing (The Affiliated Hospital of Jiaxing University), Jiaxing, China
| | - Hui Zhang
- Department of Respiratory, The First Hospital of Jiaxing (The Affiliated Hospital of Jiaxing University), Jiaxing, China
| | - Chunyuan Fei
- Department of Respiratory, The First Hospital of Jiaxing (The Affiliated Hospital of Jiaxing University), Jiaxing, China
| | - Jing Feng
- Department of Respiratory, Zhengzhou YIHE Hospital, Zhengzhou, China
| | - Jiaqi Zhou
- Department of Respiratory, The First Hospital of Jiaxing (The Affiliated Hospital of Jiaxing University), Jiaxing, China
| | - Linfeng Cao
- Department of Respiratory, The First Hospital of Jiaxing (The Affiliated Hospital of Jiaxing University), Jiaxing, China
| | - Ying Ying
- Department of Respiratory, The First Hospital of Jiaxing (The Affiliated Hospital of Jiaxing University), Jiaxing, China
| | - Na Li
- Department of Respiratory, The First Hospital of Jiaxing (The Affiliated Hospital of Jiaxing University), Jiaxing, China
| | - Xiaolong Ma
- Department of Respiratory, The First Hospital of Jiaxing (The Affiliated Hospital of Jiaxing University), Jiaxing, China
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Yao A, Wang J, Xu Q, Shah BK, Sun K, Hu F, Wang C, Xie S. Higher diagnostic value of metagenomic next-generation sequencing in acute infection than chronic infection: a multicenter retrospective study. Front Microbiol 2024; 15:1295184. [PMID: 38351916 PMCID: PMC10864100 DOI: 10.3389/fmicb.2024.1295184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 01/02/2024] [Indexed: 02/16/2024] Open
Abstract
Background The aim of this study is to compare the diagnostic value of metagenomic next-generation sequencing (mNGS) vs. conventional culture methods (CM) in chronic infection and acute infection. Methods We retrospectively analyzed the bronchoalveolar lavage fluid (BALF) of 88 patients with acute infection and 105 patients with chronic infection admitted to three hospitals from 2017 to 2022. Results The results showed that the sensitivity and specificity of mNGS were higher than those of CM. The number of patients who changed the antibiotic treatment in the mNGS positive group was larger than that of patients in the mNGS negative group in both the acute infection group (60.5 vs. 28.0%, P = 0.0022) and chronic infection group (46.2 vs. 22.6%, P = 0.01112). High levels of temperature (OR: 2.02, 95% CI: 1.18-3.70, P: 0.015), C-reactive protein (CRP) (OR: 15, 95% CI: 2.74-280.69, P: 0.011), neutrophil count (OR: 3.09, 95% CI: 1.19-8.43, P: 0.023), and low levels of lymphocyte count (OR: 3.43, 95% CI:1.26-10.21, P: 0.020) may lead to positive mNGS results in the acute infection group while no significant factor was identified to predict positive results in the chronic infection group. Conclusion mNGS could provide useful guidance on antibiotic strategies in infectious diseases and may be more valuable for the diagnosis and treatment of acute infection vs. chronic infection.
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Affiliation(s)
- Anjie Yao
- Department of Respiratory Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jiale Wang
- School of Medicine, Tongji University, Shanghai, China
| | - Qintao Xu
- Department of Respiratory Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
- School of Medicine, Tongji University, Shanghai, China
- College of Medicine, Jinggangshan University, Ji'an, China
| | | | - Kai Sun
- Department of Respiratory Medicine, ChongMing Branch of Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Feng Hu
- Department of Respiratory and Critical Care Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Changhui Wang
- Department of Respiratory Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Shuanshuan Xie
- Department of Respiratory Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
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Xiao YH, Luo ZX, Wu HW, Xu DR, Zhao R. Metagenomic next-generation sequencing for the identification of infections caused by Gram-negative pathogens and the prediction of antimicrobial resistance. Lab Med 2024; 55:71-79. [PMID: 37253164 DOI: 10.1093/labmed/lmad039] [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] [Indexed: 06/01/2023] Open
Abstract
OBJECTIVE The aim of this study was to evaluate the efficacy of metagenomic next-generation sequencing (mNGS) for the identification of Gram-negative bacteria (GNB) infections and the prediction of antimicrobial resistance. METHODS A retrospective analysis was conducted on 182 patients with diagnosis of GNB infections who underwent mNGS and conventional microbiological tests (CMTs). RESULTS The detection rate of mNGS was 96.15%, higher than CMTs (45.05%) with a significant difference (χ 2 = 114.46, P < .01). The pathogen spectrum identified by mNGS was significantly wider than CMTs. Interestingly, the detection rate of mNGS was substantially higher than that of CMTs (70.33% vs 23.08%, P < .01) in patients with but not without antibiotic exposure. There was a significant positive correlation between mapped reads and pro-inflammatory cytokines (interleukin-6 and interleukin-8). However, mNGS failed to predict antimicrobial resistance in 5 of 12 patients compared to phenotype antimicrobial susceptibility testing results. CONCLUSIONS Metagenomic next-generation sequencing has a higher detection rate, a wider pathogen spectrum, and is less affected by prior antibiotic exposure than CMTs in identifying Gram-negative pathogens. The mapped reads may reflect a pro-inflammatory state in GNB-infected patients. Inferring actual resistance phenotypes from metagenomic data remains a great challenge.
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Affiliation(s)
- Yang-Hua Xiao
- Department of Clinical Laboratory, Medical Center of Burn Plastic and Wound Repair, The First Affiliated Hospital of Nanchang University, Nanchang, China
- School of Public Health, Nanchang University, Nanchang, China
| | - Zhao-Xia Luo
- School of Public Health, Nanchang University, Nanchang, China
| | - Hong-Wen Wu
- Department of Medical Instruments, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - De-Rong Xu
- Department of Clinical Laboratory, Medical Center of Burn Plastic and Wound Repair, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Rui Zhao
- Department of Clinical Laboratory, Medical Center of Burn Plastic and Wound Repair, The First Affiliated Hospital of Nanchang University, Nanchang, China
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11
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Michel C, Martin C, Smeesters P, Goffard JC, Demuyser T, Hallin M. Next-generation sequencing: what are the needs in routine clinical microbiology? A survey among clinicians involved in infectious diseases practice. Front Med (Lausanne) 2023; 10:1225408. [PMID: 37671400 PMCID: PMC10475535 DOI: 10.3389/fmed.2023.1225408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 08/08/2023] [Indexed: 09/07/2023] Open
Abstract
Background The translation of Next-Generation Sequencing (NGS) from research to clinical microbiology is increasing rapidly, but its integration into routine clinical care struggles to catch-up. A challenge for clinical laboratories is that the substantial investments made in the required technologies and resources must meet both current and forthcoming needs. Methods To get a clinical perspective of these needs, we have sent a survey to infectious diseases clinicians of five hospitals, covering the following topics: NGS knowledge, expected syndromes and patients foreseen to benefit from NGS, and expected impact on antimicrobial prescription. Results According to clinicians, benefits of NGS are mostly expected in neurological and respiratory infections diagnostics. Conclusion A better dialog between microbiologists and clinicians about hopes and limits of NGS in microbiology may help identifying key investments needed for clinical laboratories, today and tomorrow.
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Affiliation(s)
- Charlotte Michel
- Department of Microbiology, LHUB-ULB, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Charlotte Martin
- Department of Infectious Diseases, Saint-Pierre University Hospital, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Pierre Smeesters
- Department of Pediatrics, University Hospital Brussels, Université libre de Bruxelles (ULB), Brussels, Belgium
- Department of Pediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Jean-Christophe Goffard
- Department of Internal Medicine, University Hospital Brussels, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Thomas Demuyser
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - Marie Hallin
- Centre for Environmental Health and Occupational Health, School of Public Health, University Hospital Brussels, Université libre de Bruxelles (ULB), Brussels, Belgium
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12
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Li S, Zhou P, Yang L, Tang T, Qin J, Qian J, Bo S, Yu S. Clinical Value of Sampling Time of Metagenomic Next-Generation Sequencing in Patients with Severe Pneumonia. Infect Drug Resist 2023; 16:5263-5274. [PMID: 37601559 PMCID: PMC10437727 DOI: 10.2147/idr.s424185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 08/10/2023] [Indexed: 08/22/2023] Open
Abstract
Objective Severe pneumonia is a common infectious disease with high morbidity and mortality. Early etiological diagnosis is crucial for improving the prognosis. The aim of this study is to evaluate the clinical value of sampling time of mNGS in patients with severe pneumonia. Methods This retrospective study enrolled 105 patients with severe pneumonia. mNGS was performed on bronchoalveolar lavage fluid (BALF). Patients were divided into the sampling time ≤ 72h vs sampling time >72h groups and survivors vs non-survivors groups according to their sampling time and prognosis. Clinical characteristics, the adjustment of antibiotics and clinical prognostic value were evaluated. Results Our study showed that, early sampling of mNGS can significantly shorten the mechanical ventilation time (p = 0.007) and hospitalization time (p = 0.004). In the non-survivors group, CURB-65, SOFA, and APACHE II scores were higher. Age (OR: 1.051, 95% CI: 1.004-1.100, p = 0.034), chronic respiratory diseases (OR: 4.639, 95% CI: 1.260-17.082, p = 0.021), immunosuppression (OR: 5.008, 95% CI: 1.617-15.510, p = 0.005) and SOFA score on the day of mNGS sampling (OR: 1.492, 95% CI: 1.212-1.837, p < 0.001) were independent risk factors of in-hospital mortality. The most common pathogens were Klebsiella pneumoniae and Human gammaherpesvirus 4. The proportion of appropriate and targeted antibiotics adjusted was significantly higher than that in the sampling time > 72h group, and the proportion of antifungal and antiviral agents adjusted was lower. In the early sampling group, it was significantly decreased in the CRP, PCT level and NEU% at discharge. Conclusion This study demonstrated that early sampling of mNGS could shorten the time of mechanical ventilation and hospitalization of patients with severe pneumonia. Patients with higher SOFA score on the day of sampling had a poorer prognosis. It emphasizes that early sampling of mNGS has a positive value.
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Affiliation(s)
- Shixiao Li
- Department of Clinical Microbiology Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang, People’s Republic of China
| | - Peng Zhou
- Department of Pharmacy, The Third Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, People’s Republic of China
| | - Lihong Yang
- Department of Clinical Microbiology Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang, People’s Republic of China
| | - Tianbin Tang
- Department of Clinical Microbiology Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang, People’s Republic of China
| | - Jiajia Qin
- Department of Clinical Microbiology Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang, People’s Republic of China
| | - Jiao Qian
- Department of Clinical Microbiology Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang, People’s Republic of China
| | - Shen Bo
- Department of Clinical Microbiology Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang, People’s Republic of China
| | - Sufei Yu
- Department of Clinical Microbiology Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang, People’s Republic of China
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13
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He S, Wei J, Feng J, Liu D, Wang N, Chen L, Xiong Y. The application of metagenomic next-generation sequencing in pathogen diagnosis: a bibliometric analysis based on Web of Science. Front Cell Infect Microbiol 2023; 13:1112229. [PMID: 37600953 PMCID: PMC10434771 DOI: 10.3389/fcimb.2023.1112229] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 07/18/2023] [Indexed: 08/22/2023] Open
Abstract
Background Infectious disease is a large burden on public health globally. Metagenomic next-generation sequencing (mNGS) has become popular as a new tool for pathogen diagnosis with numerous advantages compared to conventional methods. Recently, research on mNGS increases yearly. However, no bibliometric analysis has systematically presented the full spectrum of this research field. Therefore, we reviewed all the publications associated with this topic and performed this study to analyze the comprehensive status and future hotspots of mNGS for infectious disease diagnosis. Methods The literature was searched in the Web of Science Core Collection and screened without year or language restrictions, and the characteristics of the studies were also identified. The outcomes included publication years, study types, journals, countries, authorship, institutions, frontiers, and hotspots with trends. Statistical analysis and visualization were conducted using VOSviewer (version 1.6.16) and CiteSpace (version 6.1. R3). Results In total, 325 studies were included in the analysis after screening. Studies were published between 2009 and 2022 with a significantly increasing number from 1 to 118. Most of the studies were original articles and case reports. Frontiers in Cellular and Infection Microbiology and Clinical Infectious Disease were the most commonly cited and co-cited journals. Institutions and researchers from China contributed the most to this field, followed by those from the USA. The hotspots and frontiers of these studies are pneumonia, tuberculosis, and central nervous system infections. Conclusion This study determined that mNGS is a hot topic in the diagnosis of infectious diseases with development trends and provides insights into researchers, institutions, hotspots and frontiers in mNGS, which can offer references to related researchers and future research.
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Affiliation(s)
- Sike He
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Jingwen Wei
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Jiaming Feng
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Dan Liu
- Department of Periodical Press, West China Hospital, Sichuan University, Chengdu, China
| | - Neng Wang
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Liyu Chen
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Ying Xiong
- Department of Periodical Press, West China Hospital, Sichuan University, Chengdu, China
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Batool M, Galloway-Peña J. Clinical metagenomics-challenges and future prospects. Front Microbiol 2023; 14:1186424. [PMID: 37448579 PMCID: PMC10337830 DOI: 10.3389/fmicb.2023.1186424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 06/12/2023] [Indexed: 07/15/2023] Open
Abstract
Infections lacking precise diagnosis are often caused by a rare or uncharacterized pathogen, a combination of pathogens, or a known pathogen carrying undocumented or newly acquired genes. Despite medical advances in infectious disease diagnostics, many patients still experience mortality or long-term consequences due to undiagnosed or misdiagnosed infections. Thus, there is a need for an exhaustive and universal diagnostic strategy to reduce the fraction of undocumented infections. Compared to conventional diagnostics, metagenomic next-generation sequencing (mNGS) is a promising, culture-independent sequencing technology that is sensitive to detecting rare, novel, and unexpected pathogens with no preconception. Despite the fact that several studies and case reports have identified the effectiveness of mNGS in improving clinical diagnosis, there are obvious shortcomings in terms of sensitivity, specificity, costs, standardization of bioinformatic pipelines, and interpretation of findings that limit the integration of mNGS into clinical practice. Therefore, physicians must understand the potential benefits and drawbacks of mNGS when applying it to clinical practice. In this review, we will examine the current accomplishments, efficacy, and restrictions of mNGS in relation to conventional diagnostic methods. Furthermore, we will suggest potential approaches to enhance mNGS to its maximum capacity as a clinical diagnostic tool for identifying severe infections.
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Affiliation(s)
| | - Jessica Galloway-Peña
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, United States
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15
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Lu H, Yuan J, Wu Z, Wang L, Wu S, Chen Q, Zhang Z, Chen Z, Zou X, Hu Q, Feng T, Lu J, Ji L, Qiu S, Xu S, Jiang M, Li Y, Peng B, Bai Q, Cai R, Geng Y, Shi X. Distribution of drug-resistant genes in alveolar lavage fluid from patients with psittacosis and traceability analysis of causative organisms. Front Microbiol 2023; 14:1182604. [PMID: 37425996 PMCID: PMC10327639 DOI: 10.3389/fmicb.2023.1182604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 06/01/2023] [Indexed: 07/11/2023] Open
Abstract
Background Chlamydia psittaci is a small bacterium often found in birds, including poultry, and domesticated mammals, which causes psittacosis (or parrot fever) in humans. Different strains of C. psittaci respond variably to antibiotics, suggesting a possible risk of antibiotic resistance. In general, different genotypes of C. psittaci have relatively stable hosts and different pathogenicity. Methods Macrogenomic sequencing was performed using nucleic acids extracted from psittacosis patients' alveolar lavage fluid samples and analyzed for genetic variability and antibiotic resistance genes. Nucleic acid amplification sequences specific to the core coding region of the C. psittaci ompA gene were used, and a phylogenetic tree was constructed with C. psittaci genotypic sequences from other sources, including Chinese published sources. The C. psittaci found in each patient were genotyped by comparing ompA gene sequences. In addition, to better illustrate the relationship between genotype and host of C. psittaci, 60 bird fecal samples were collected from bird-selling stores for screening and C. psittaci typing. Results Macrogenomic sequence alignment revealed the presence of resistance genes in varying abundance in samples from all three patients, including C. psittaci resistance gene sequences from two patients that matched those previously published on NCBI. Based on ompA genotyping, two patients were infected with C. psittaci genotype A and one patient was infected with genotype B. All five C. psittaci-positive samples obtained from bird-selling stores were genotype A. Both genotypes are reported to be infectious to humans. The host origin of the samples and the previously reported main sources of each genotype suggested that all but one of the C. psittaci genotype A in this study were derived from parrots, while genotype B was probably derived from chickens. Conclusion The presence of bacterial resistance genes in psittacosis patients may affect the efficacy of clinical antibiotic therapy. Focusing on the developmental progression of bacterial resistance genes and differences in the therapeutic efficacy may facilitate effective treatment of clinical bacterial infections. Pathogenicity genotypes (e.g., genotype A and genotype B) are not limited to one animal host, suggesting that monitoring the development and changes of C. psittaci may help prevent transmission to humans.
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Affiliation(s)
- Huiqun Lu
- Department of Public Health Laboratory Sciences, School of Public Health, University of South China, Hengyang, China
| | - Jing Yuan
- Shenzhen Third People’s Hospital, Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, China
| | - Zeming Wu
- Shenzhen Hospital of Guangzhou University of Chinese Medicine (Futian), Shenzhen, China
| | | | - Shuang Wu
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Qiongcheng Chen
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Zhen Zhang
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Zhigao Chen
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Xuan Zou
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Qinghua Hu
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Tiejian Feng
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Jianhua Lu
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Liyin Ji
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Shuxiang Qiu
- Department of Public Health Laboratory Sciences, School of Public Health, University of South China, Hengyang, China
| | - Shiqin Xu
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Min Jiang
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Yinghui Li
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Bo Peng
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Qinqin Bai
- Department of Public Health Laboratory Sciences, School of Public Health, University of South China, Hengyang, China
| | - Rui Cai
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Yijie Geng
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Xiaolu Shi
- Department of Public Health Laboratory Sciences, School of Public Health, University of South China, Hengyang, China
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
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16
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Bao R, Mei Q, Yang T, Zhang L, Zhu C, Fan X, Wang Y, Tong F, He Y, Fang X, Geng S, Yang Y, Sheng X, Pan A. Comparison of endotracheal aspirate and bronchoalveolar lavage fluid metagenomic next-generation sequencing in severe pneumonia: a nested, matched case-control study. BMC Infect Dis 2023; 23:389. [PMID: 37303052 DOI: 10.1186/s12879-023-08376-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 06/06/2023] [Indexed: 06/13/2023] Open
Abstract
OBJECTIVES To compare clinical outcomes in patients with severe pneumonia according to the diagnostic strategy used. METHODS In this retrospective, nested, case-control study, patients with severe pneumonia who had undergone endotracheal aspirate (ETA) metagenomic next-generation sequencing of (mNGS) testing (n = 53) were matched at a ratio of 1 to 2 (n = 106) by sex, age, underlying diseases, immune status, disease severity scores, and type of pneumonia with patients who had undergone bronchoalveolar lavage fluid (BALF) mNGS. The microbiological characteristics and patient's prognosis of the two groups were compared. RESULTS An overall comparison between the two groups showed no significant differences in bacterial, fungal, viral, or mixed infections. However, subgroup analysis of 18 patients who received paired ETA and BALF mNGS showed a complete agreement rate for the two specimens of 33.3%. There were more cases for whom targeted treatment was initiated (36.79% vs. 22.64%; P = 0.043) and fewer cases who received no clinical benefit after mNGS (5.66% vs. 15.09%; P = 0.048) in the BALF group. The pneumonia improvement rate in the BALF group was significantly higher than in the ETA group (73.58% vs. 87.74%, P = 0.024). However, there were no significant differences in ICU mortality or 28-day mortality. CONCLUSIONS We do not recommend using ETA mNGS as the first-choice method for analyzing airway pathogenic specimens from severe pneumonia patients.
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Affiliation(s)
- Renren Bao
- Department of Critical Care Medicine, The Affiliated Provincial Hospital of Anhui Medical University, Hefei, 230001, Anhui, China
| | - Qing Mei
- Department of Critical Care Medicine, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, 230001, Anhui, China.
| | - Tianjun Yang
- Department of Critical Care Medicine, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, 230001, Anhui, China
| | - Lei Zhang
- Department of Critical Care Medicine, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, 230001, Anhui, China
| | - Chunyan Zhu
- Department of Critical Care Medicine, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, 230001, Anhui, China
| | - Xiaoqin Fan
- Department of Critical Care Medicine, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, 230001, Anhui, China
| | - Yinzhong Wang
- Department of Critical Care Medicine, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, 230001, Anhui, China
| | - Fei Tong
- Department of Critical Care Medicine, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, 230001, Anhui, China
| | - Yuxi He
- Department of Critical Care Medicine, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, 230001, Anhui, China
| | - Xiaowei Fang
- Department of Critical Care Medicine, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, 230001, Anhui, China
| | - Shike Geng
- Department of Critical Care Medicine, The Affiliated Provincial Hospital of Anhui Medical University, Hefei, 230001, Anhui, China
| | - Yu Yang
- Department of Critical Care Medicine, The Affiliated Provincial Hospital of Anhui Medical University, Hefei, 230001, Anhui, China
| | - Ximei Sheng
- WanNan Medical College, Wuhu, 241002, Anhui, China
| | - Aijun Pan
- Department of Critical Care Medicine, The Affiliated Provincial Hospital of Anhui Medical University, Hefei, 230001, Anhui, China.
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17
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Ogunbayo AE, Mogotsi MT, Sondlane H, Sabiu S, Nyaga MM. Metagenomics characterization of respiratory viral RNA pathogens in children under five years with severe acute respiratory infection in the Free State, South Africa. J Med Virol 2023; 95:e28753. [PMID: 37212321 PMCID: PMC10952945 DOI: 10.1002/jmv.28753] [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: 11/16/2022] [Revised: 03/14/2023] [Accepted: 04/03/2023] [Indexed: 05/23/2023]
Abstract
Prompt detection of viral respiratory pathogens is crucial in managing respiratory infection including severe acute respiratory infection (SARI). Metagenomics next-generation sequencing (mNGS) and bioinformatics analyses remain reliable strategies for diagnostic and surveillance purposes. This study evaluated the diagnostic utility of mNGS using multiple analysis tools compared with multiplex real-time PCR for the detection of viral respiratory pathogens in children under 5 years with SARI. Nasopharyngeal swabs collected in viral transport media from 84 children admitted with SARI as per the World Health Organization definition between December 2020 and August 2021 in the Free State Province, South Africa, were used in this study. The obtained specimens were subjected to mNGS using the Illumina MiSeq system, and bioinformatics analysis was performed using three web-based analysis tools; Genome Detective, One Codex and Twist Respiratory Viral Research Panel. With average reads of 211323, mNGS detected viral pathogens in 82 (97.6%) of the 84 patients. Viral aetiologies were established in nine previously undetected/missed cases with an additional bacterial aetiology (Neisseria meningitidis) detected in one patient. Furthermore, mNGS enabled the much needed viral genotypic and subtype differentiation and provided significant information on bacterial co-infection despite enrichment for RNA viruses. Sequences of nonhuman viruses, bacteriophages, and endogenous retrovirus K113 (constituting the respiratory virome) were also uncovered. Notably, mNGS had lower detectability rate for severe acute respiratory syndrome coronavirus 2 (missing 18/32 cases). This study suggests that mNGS, combined with multiple/improved bioinformatics tools, is practically feasible for increased viral and bacterial pathogen detection in SARI, especially in cases where no aetiological agent could be identified by available traditional methods.
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Affiliation(s)
- Ayodeji E. Ogunbayo
- Next Generation Sequencing Unit and Division of VirologyFaculty of Health Sciences, University of the Free StateBloemfonteinSouth Africa
| | - Milton T. Mogotsi
- Next Generation Sequencing Unit and Division of VirologyFaculty of Health Sciences, University of the Free StateBloemfonteinSouth Africa
| | - Hlengiwe Sondlane
- Next Generation Sequencing Unit and Division of VirologyFaculty of Health Sciences, University of the Free StateBloemfonteinSouth Africa
| | - Saheed Sabiu
- Department of Biotechnology and Food ScienceDurban University of TechnologyDurbanSouth Africa
| | - Martin M. Nyaga
- Next Generation Sequencing Unit and Division of VirologyFaculty of Health Sciences, University of the Free StateBloemfonteinSouth Africa
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Zhang S, Ou J, Tan Y, Yang B, Wu Y, Liu L. Metagenomic next-generation sequencing for pulmonary infections diagnosis in patients with diabetes. BMC Pulm Med 2023; 23:142. [PMID: 37106322 PMCID: PMC10141947 DOI: 10.1186/s12890-023-02441-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 04/17/2023] [Indexed: 04/29/2023] Open
Abstract
BACKGROUND Diabetes mellitus is a major cause of high mortality and poor prognosis in patients with pulmonary infections. However, limited data on the application of metagenomic next-generation sequencing (mNGS) are available for diabetic patients. This study aimed to evaluate the diagnostic performance of mNGS in diabetic patients with pulmonary infections. METHODS We retrospectively reviewed 184 hospitalized patients with pulmonary infections at Guizhou Provincial People's Hospital between January 2020 to October 2021. All patients were subjected to both mNGS analysis of bronchoalveolar lavage fluid (BALF) and conventional testing. Positive rate by mNGS and the consistency between mNGS and conventional testing results were evaluated for diabetic and non-diabetic patients. RESULTS A total of 184 patients with pulmonary infections were enrolled, including 43 diabetic patients and 141 non-diabetic patients. For diabetic patients, the microbial positive rate by mNGS was significantly higher than that detected by conventional testing methods, primarily driven by bacterial detection (microbes: 95.3% vs. 67.4%, P = 0.001; bacteria: 72.1% vs. 37.2%, P = 0.001). mNGS and traditional tests had similar positive rates with regard to fungal and viral detection in diabetic patients. Klebsiella pneumoniae was the most common pathogen identified by mNGS in patients with diabetes. Moreover, mNGS identified pathogens in 92.9% (13/14) of diabetic patients who were reported negative by conventional testing. No significant difference was found in the consistency of the two tests between diabetic and non-diabetic groups. CONCLUSIONS mNGS is superior to conventional microbiological tests for bacterial detection in diabetic patients with pulmonary infections. mNGS is a valuable tool for etiological diagnosis of pulmonary infections in diabetic patients.
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Affiliation(s)
- Siqin Zhang
- Department of Endocrinology and Metabolism, Guizhou Provincial People's Hospital, Guiyang, Guizhou, 550002, China
| | - Jing Ou
- School of Medicine, Zunyi Medical University, Zunyi, Guizhou, 563000, China
| | - Yuxue Tan
- School of Medicine, Zunyi Medical University, Zunyi, Guizhou, 563000, China
| | - Bin Yang
- Department of Central Laboratory, Guizhou Provincial People's Hospital, Guiyang, Guizhou, 550002, China
| | - Yaoyao Wu
- Department of Respiratory and Critical Medicine, Guizhou Provincial People's Hospital, No. 83, Zhongshan East Road, Guiyang, Guizhou, 550002, China
| | - Lin Liu
- Department of Respiratory and Critical Medicine, Guizhou Provincial People's Hospital, No. 83, Zhongshan East Road, Guiyang, Guizhou, 550002, China.
- NHC Key Laboratory of Pulmonary Immunological Diseases (Guizhou Provincial People's Hospital), Guiyang, Guizhou, 550002, China.
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Hong D, Wang P, Chen Y, Zhang J, Jiang W, Ye B, Li G, Zhou J, Mao W, Tong Z, Li W, Ke L. Detection of potential pathogen in pancreatic fluid aspiration with metagenomic next-generation sequencing in patients with suspected infected pancreatic necrosis. Dig Liver Dis 2023; 55:243-248. [PMID: 35948458 DOI: 10.1016/j.dld.2022.07.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 07/16/2022] [Accepted: 07/19/2022] [Indexed: 02/01/2023]
Abstract
BACKGROUND Timely and accurate microbial diagnosis is important in managing patients with infected pancreatic necrosis (IPN). AIMS To evaluate the diagnostic performance of Metagenomic next-generation sequencing (mNGS) in patients with suspected IPN. METHODS The clinical data of 40 patients with suspected IPN who underwent CT-guided pancreatic fluid aspiration were retrospectively analyzed. Microbial culture and mNGS were simultaneously applied to identify the potential pathogens. The diagnostic performance of the mNGS was assessed by sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV). RESULTS The mNGS report can be obtained significantly earlier than culture methods (42 (36-62 h) vs. 60 (42-124 h), P = 0.032). Across all the study samples, seven species of bacteria and two species of fungi were reported accordingly to the culture results, while 22 species of bacteria and two species of fungi were detected by mNGS. The sensitivity, specificity, NPV, and PPV of mNGS were 88.0%, 100%, 83.33%, and 100%, respectively. CONCLUSIONS The diagnostic accuracy of mNGS in patients with suspected IPN is satisfactory. Moreover, mNGS may broaden the range of identifiable infectious pathogens and provide a more timely diagnosis.
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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, Fuzhou, China
| | - Peng Wang
- Center of Severe Acute Pancreatitis (CSAP), Department of Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Yingjie Chen
- Department of Critical Care Medicine, Jinjiang Hospital of Traditional Chinese Medicine, Jinjiang, China
| | - Jingzhu Zhang
- Center of Severe Acute Pancreatitis (CSAP), Department of Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Wendi Jiang
- Center of Severe Acute Pancreatitis (CSAP), Department of Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Bo Ye
- Center of Severe Acute Pancreatitis (CSAP), Department of Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Gang Li
- Center of Severe Acute Pancreatitis (CSAP), Department of Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Jing Zhou
- Center of Severe Acute Pancreatitis (CSAP), Department of Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Wenjian Mao
- Center of Severe Acute Pancreatitis (CSAP), Department of Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, Nanjing, 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
- 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, Nanjing, China; National Institute of Healthcare Data Science, Nanjing University, Nanjing, 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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Xie Y, Dai B, Zhou X, Liu H, Wu W, Yu F, Zhu B. Diagnostic Value of Metagenomic Next-Generation Sequencing for Multi-Pathogenic Pneumonia in HIV-Infected Patients. Infect Drug Resist 2023; 16:607-618. [PMID: 36733920 PMCID: PMC9888013 DOI: 10.2147/idr.s394265] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 01/05/2023] [Indexed: 01/28/2023] Open
Abstract
Background To evaluate the value and challenges of real-world clinical application of metagenomic next-generation sequencing (mNGS) for bronchoalveolar lavage fluid (BALF) in HIV-infected patients with suspected multi-pathogenic pneumonia. Methods Fifty-seven HIV-infected patients with suspected mixed pneumonia who were agreed to undergo the bronchoscopy were recruited and retrospectively reviewed the results of mNGS and conventional microbiological tests (CMTs) of BALF from July 2020 to June 2022. Results 54 patients were diagnosed with pneumonia including 49 patients with definite pathogens and five patients with probable pathogens. mNGS exhibited a higher diagnostic accuracy for fungal detection than CMTs in HIV-infected patients with suspected pulmonary infection. The sensitivity of mNGS in diagnosis of pneumonia in HIV-infected patients was much higher than that of CMTs (79.6% vs 61.1%; P < 0.05). Patients with mixed infection had lower CD4 T-cell count and higher symptom duration before admitting to the hospital than those with single infection. The detection rate of mNGS for mixed infection was significantly higher than that of CMTs and more co-pathogens could be identified by mNGS. The most common pattern of mixed infection observed was fungi-virus (11/29, 37.9%), followed by fungi-virus-bacteria (6/29, 20.7%) coinfection in HIV-infected patients with multi-pathogenic pneumonia. Conclusion mNGS improved the pathogens detection rate and exhibited advantages in identifying multi-pathogenic pneumonia in HIV-infected patients. Early performance of bronchoscopy and mNGS are recommended in HIV-infected patients with low CD4 T cell counts and long duration of symptoms. The most common pattern of mixed infection observed was fungi-virus, followed by fungi-virus-bacteria coinfection in HIV infected patients with multi-pathogenic pneumonia.
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Affiliation(s)
- Yirui Xie
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The Department of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, People’s Republic of China,Correspondence: Yirui Xie; Biao Zhu, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The Department of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, 79, QingChun Road, Hangzhou, 310003, People’s Republic of China, Tel/Fax +86-571-87236416, Email ;
| | - Bohao Dai
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The Department of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, People’s Republic of China
| | - Xiaotang Zhou
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The Department of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, People’s Republic of China
| | - Huiting Liu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The Department of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, People’s Republic of China
| | - Wei Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, People’s Republic of China
| | - Fei Yu
- Key Laboratory of Clinical in vitro Diagnostic Techniques of Zhejiang Province, Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, People’s Republic of China
| | - Biao Zhu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The Department of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, People’s Republic of China
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Liu Y, Zhang R, Yao B, Yang J, Ge H, Zheng S, Guo Q, Xing J. Metagenomics next-generation sequencing provides insights into the causative pathogens from critically ill patients with pneumonia and improves treatment strategies. Front Cell Infect Microbiol 2023; 12:1094518. [PMID: 36710980 PMCID: PMC9880068 DOI: 10.3389/fcimb.2022.1094518] [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: 11/10/2022] [Accepted: 12/28/2022] [Indexed: 01/15/2023] Open
Abstract
Background The metagenomics next-generation sequencing (mNGS) is a promising technique for pathogens diagnosis. However, whether the application of mNGS in critically ill patients with pneumonia could cause anti-infection treatment adjustment and thereby affect the prognosis of these patients has not been explored. Methods We retrospectively collected the clinical data of patients diagnosed with pulmonary infection in the ICU of the Affiliated Hospital of Qingdao University from January 2018 to January 2021. These patients with pneumonia were divided into mNGS group and no-mNGS group by whether being performed NGS or not. The clinical data, including demographics, illness history, APACHE II score, length of mechanical ventilation, length of stay in the hospital, length of stay in ICU and outcome, were collected. In addition, the data of pathogens and anti-infection treatment before and after NGS were also collected. Propensity score matching was performed to evaluate the mortality and deterioration rate between NGS group and non-NGS group. Results A total of 641 patients diagnosed with pneumonia were screened, and 94 patients were excluded based on exclusion criteria. Finally, 547 patients were enrolled, including 160 patients being performed NGS. Among these 160 patients, 142 cases had NGS-positive results. In addition, new pathogens were detected in 132 specimens by NGS, which included 82 cases with virus, 18 cases with fungus, 17 cases with bacteria, 14 cases with mycoplasma, and 1 case with mycobacterium tuberculosis. Anti-infection treatments were adjusted in some patients who performed NGS, including 48 anti-bacterial treatments, 20 antifungal treatments and 20 antiviral treatments. There were no significant differences in the mortality and deterioration rate between NGS and non-NGS group, but it exhibited a trend that the mortality and deterioration rate of NGS group was lower than non-NGS group after the propensity score matching analysis (15.8% vs 24.3%, P=0.173; 25.6% vs 37.8%, P=0.093). Conclusion NGS could affect the anti-infection treatments and had a trend of reducing the mortality and deterioration rate of critically ill patients with pneumonia.
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Affiliation(s)
- Ying Liu
- Department of Critical Care Medicine, the Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Rui Zhang
- School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Bo Yao
- Department of Critical Care Medicine, the Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Jun Yang
- Department of Critical Care Medicine, the Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Huimin Ge
- Department of Critical Care Medicine, the Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Shuyun Zheng
- Department of Critical Care Medicine, the Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Qi Guo
- Department of Critical Care Medicine, the Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Jinyan Xing
- Department of Critical Care Medicine, the Affiliated Hospital of Qingdao University, Qingdao, Shandong, China,*Correspondence: Jinyan Xing,
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22
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Borroni D, Bonzano C, Sánchez-González JM, Rachwani-Anil R, Zamorano-Martín F, Pereza-Nieves J, Traverso CE, García Lorente M, Rodríguez-Calvo-de-Mora M, Esposito A, Godin F, Rocha-de-Lossada C. Shotgun metagenomic sequencing in culture negative microbial keratitis. Eur J Ophthalmol 2023:11206721221149077. [PMID: 36617769 DOI: 10.1177/11206721221149077] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
PURPOSE To evaluate the microbiota of culture negative Corneal Impression Membrane (CIM) microbial keratitis samples with the use of shotgun metagenomics analysis. METHODS DNA of microbial keratitis samples were collected with CIM and extracted using the MasterPure™ Complete DNA and RNA Purification Kit (Epicentre). DNA was fragmented by sonication into fragments of 300 to 400 base pairs (bp) using Bioruptor® (Diagenode, Belgium) and then used as a template for library preparation. DNA libraries were sequenced on Illumina® HiSeq2500. The resulting reads were quality controlled, trimmed and mapped against the human reference genome. The unmapped reads were taxonomically classified using the Kraken software. RESULTS 18 microbial keratitis samples were included in the study. Brevundimonas diminuta was found in 5 samples while 6 samples showed the presence of viral infections. Cutibacterium acnes, Staphylococcus aureus, Moraxella lacunata and Pseudomonas alcaligenes were also identified as the presumed putative cause of the infection in 7 samples. CONCLUSIONS Shotgun sequencing can be used as a diagnostic tool in microbial keratitis samples. This diagnostic method expands the available tests to diagnose eye infections and could be clinically significant in culture negative samples.
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Affiliation(s)
- Davide Borroni
- Department of Ophthalmology, Riga Stradins University, Riga, Latvia
| | - Chiara Bonzano
- DiNOGMI, University of Genoa and IRCCS San Martino Polyclinic Hospital, Genoa, Italy
| | | | | | | | | | - Carlo Enrico Traverso
- DiNOGMI, University of Genoa and IRCCS San Martino Polyclinic Hospital, Genoa, Italy
| | | | | | - Alfonso Esposito
- 18470International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Fernando Godin
- Department of Ophthalmology, Universidad El Bosque, Bogotá, Colombia
| | - Carlos Rocha-de-Lossada
- Qvision, Opththalmology Department, VITHAS Almería Hospital, Almería, Spain.,Ophthalmology Department, VITHAS Málaga, Málaga, Spain.,Hospital Regional Universitario de Málaga, Plaza del Hospital Civil, Málaga, Spain.,Departamento de Cirugía, Universidad de Sevilla, Área de Oftalmología, Doctor Fedriani, Seville, Spain
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23
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Lv M, Zhu C, Zhu C, Yao J, Xie L, Zhang C, Huang J, Du X, Feng G. Clinical values of metagenomic next-generation sequencing in patients with severe pneumonia: a systematic review and meta-analysis. Front Cell Infect Microbiol 2023; 13:1106859. [PMID: 37091676 PMCID: PMC10117876 DOI: 10.3389/fcimb.2023.1106859] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 03/22/2023] [Indexed: 04/25/2023] Open
Abstract
Background Clinical values of metagenomic next-generation sequencing (mNGS) in patients with severe pneumonia remain controversial. Therefore, we conduct this meta-analysis to evaluate the diagnostic performance of mNGS for pathogen detection and its role in the prognosis of severe pneumonia. Methods We systematically searched the literature published in PubMed, Embase, Cochrane Library, Web of Science, Clinical Trials.gov, CNKI, Wanfang Data, and CBM from the inception to the 28th September 2022. Relevant trials comparing mNGS with conventional methods applied to patients with severe pneumonia were included. The primary outcomes of this study were the pathogen-positive rate, the 28-day mortality, and the 90-day mortality; secondary outcomes included the duration of mechanical ventilation, the length of hospital stay, and the length of stay in the ICU. Results Totally, 24 publications with 3220 patients met the inclusion criteria and were enrolled in this study. Compared with conventional methods (45.78%, 705/1540), mNGS (80.48%, 1233/1532) significantly increased the positive rate of pathogen detection [OR = 6.81, 95% CI (4.59, 10.11, P < 0.001]. The pooled 28-day and 90-day mortality in mNGS group were 15.08% (38/252) and 22.36% (36/161), respectively, which were significantly lower than those in conventional methods group 33.05% (117/354) [OR = 0.35, 95% CI (0.23, 0.55), P < 0.001, I2 = 0%] and 43.43%(109/251) [OR = 0.34, 95% CI (0.21, 0.54), P < 0.001]. Meanwhile, adjusted treatment based on the results of mNGS shortened the length of hospital stay [MD = -2.76, 95% CI (- 3.56, - 1.96), P < 0.001] and the length of stay in ICU [MD = -4.11, 95% CI (- 5.35, - 2.87), P < 0.001]. Conclusion The pathogen detection positive rate of mNGS was much higher than that of conventional methods. Adjusted treatment based on mNGS results can reduce the 28-day and 90-day mortality of patients with severe pneumonia, and shorten the length of hospital and ICU stay. Therefore, mNGS advised to be applied to severe pneumonia patients as early as possible in addition to conventional methods to improve the prognosis and reduce the length of hospital stay.
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Affiliation(s)
- Minjie Lv
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Changjun Zhu
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Chenghua Zhu
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jing Yao
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Lixu Xie
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Changwen Zhang
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jianling Huang
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xingran Du
- Department of Infectious Diseases, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- Department of Respiratory and Critical Care Medicine, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- *Correspondence: Xingran Du, ; Ganzhu Feng,
| | - Ganzhu Feng
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- *Correspondence: Xingran Du, ; Ganzhu Feng,
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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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Zhao Y, Deng W, Teng J, Xu Y, Pan P, Jin D. Risk factors for 90-day all-cause mortality in post-operative central nervous system infections (PCNSIs): A retrospective study of 99 patients in China. Medicine (Baltimore) 2022; 101:e32418. [PMID: 36596030 PMCID: PMC9803491 DOI: 10.1097/md.0000000000032418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Post-operative central nervous system infections (PCNSIs) are serious complications of craniotomy. Many factors, including patient-related, surgical, and postoperative factors, affect the survival of patients with PCNSIs. Timely and effective implementation of antibiotics targeting pathogenic bacteria is crucial to reduce mortality. Metagenomic next-generation sequencing (mNGS) has been used successfully to detect pathogens associated with infectious diseases. This study was designed to evaluate the factors influencing mortality and to explore the application value of mNGS in patients with PCNSIs. We conducted a retrospective study of patients with PCNSIs in our unit from 1/12/2019 to 28/2/2021. Clinical data, cerebrospinal fluid (CSF) parameters, surgical information, and mNGS results were collected. Follow-up telephone calls were made in June 2021 for 90 days survival after discharge. 99 patients were enrolled, and the overall mortality rate was 36.4% (36/99). Kaplan-Meier survival analysis suggested that the risk factors for poor prognosis included age ≥ 53 years, Glasgow Coma scale (GCS) score ≤ 8, CSF/blood glucose ratio (C/B-Glu) ≤ 0.23, 2 or more operations, mechanical ventilation (MV), and non-mNGS test. MV and poor wound healing were independent risk factors for 90 day mortality according to the multivariate Cox proportional hazards model (OR = 6.136, P = .017, OR = 2.260, P = .035, respectively). Among the enrolled patients, causative pathogens were identified in 37. Gram-negative pathogens were found in 22 (59.5%) patients, and the remaining 15 (40.5%) were Gram-positive pathogens. Univariate analysis showed that white cell count and protein and lactate levels in the CSF of the Gram-negative group were higher than those of the Gram-positive group (P < .05). mNGS and conventional microbiological culture were tested in 34 patients, and the positive detection rate of mNGS was 52.9%, which was significantly higher than that of microbiological culture (52.9% vs 26.5%, χ2 = 4.54, P = .033). The mortality rate of PCNSIs is high, and patients with MV and poor wound healing have a higher mortality risk. Gram-negative pathogens were the predominant pathogens in the patients with PCNSIs. mNGS testing has higher sensitivity and has the potential to reduce the risk of mortality in patients with PCNSIs.
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Affiliation(s)
- Yanan Zhao
- The Neurology Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Wenjing Deng
- The Neurology Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- *Correspondence: Wenjing Deng, The Neurology Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, The Neurology Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, No.1, Jianshe Road, Zhengzhou, Henan, 450052, China (e-mail:)
| | - Junfang Teng
- The Neurology Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yafei Xu
- The Neurology Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Pengwei Pan
- The Neurology Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Di Jin
- The Neurology Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
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Deng W, Xu H, Wu Y, Li J. Diagnostic value of bronchoalveolar lavage fluid metagenomic next-generation sequencing in pediatric pneumonia. Front Cell Infect Microbiol 2022; 12:950531. [PMID: 36389175 PMCID: PMC9648200 DOI: 10.3389/fcimb.2022.950531] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 09/26/2022] [Indexed: 07/25/2023] Open
Abstract
OBJECTIVES The aim of this study was to evaluate the diagnostic value of bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) versus conventional microbiological tests (CMTs) for pediatric pneumonia. METHODS This retrospective observational study enrolled 103 children who were diagnosed with pneumonia and hospitalized at Hubei Maternity and Child Health Care Hospital between 15 October 2020 and 15 February 2022. The pneumonia diagnosis was based on clinical manifestations, lung imaging, and microbiological tests. Pathogens in the lower respiratory tract were detected using CMTs and BALF mNGS (of DNA and RNA). The diagnostic performance of BALF mNGS was compared with that of CMTs. RESULTS In 96 patients, pathogens were identified by microbiological tests. The overall pathogen detection rate of mNGS was significantly higher than that of CMTs (91.3% vs. 59.2%, p = 0.000). The diagnostic performance of mNGS varied for different pathogens; however, its sensitivity and accuracy for diagnosing bacterial and viral infections were both higher than those of CMTs (p = 0.000). For the diagnosis of fungi, the sensitivity of mNGS (87.5%) was higher than that of CMTs (25%); however, its specificity and accuracy were lower than those of CMTs (p < 0.01). For the diagnosis of Mycoplasma pneumoniae, the specificity (98.8%) and accuracy (88.3%) of mNGS were high; however, its sensitivity (42.1%) was significantly lower than that of CMTs (100%) (p = 0.001). In 96 patients with definite pathogens, 52 cases (50.5%) were infected with a single pathogen, while 44 cases (42.7%) had polymicrobial infections. Virus-bacteria and virus-virus co-infections were the most common. Staphylococcus aureus, Haemophilus influenzae, rhinovirus, cytomegalovirus, parainfluenza virus, and fungi were more likely to be associated with polymicrobial infections. CONCLUSIONS BALF mNGS improved the detection rate of pediatric pneumonia, especially in mixed infections. The diagnostic performance of BALF mNGS varies according to pathogen type. mNGS can be used to supplement CMTs. A combination of mNGS and CMTs may be the best diagnostic strategy.
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Affiliation(s)
- Wenhua Deng
- Pediatric Respiratory Department, Maternal and Child Health Hospital of Hubei Province, Wuhan, China
| | - Huan Xu
- Department of Scientific Affairs, Vision Medicals Center for Infection Diseases, Guangzhou, China
| | - Yabin Wu
- Pediatric Respiratory Department, Maternal and Child Health Hospital of Hubei Province, Wuhan, China
| | - Jie Li
- Pediatric Respiratory Department, Maternal and Child Health Hospital of Hubei Province, Wuhan, China
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Zhao YC, Ding YZ, Zhao X, Fu GW, Huang MJ, Li XX, Sun QQ, Kan YB, Li J, Wang SL, Ma WT, Xu QF, Liu QL, Li HB. Role and Clinical Application of Metagenomic Next-Generation Sequencing in Immunocompromised Patients With Acute Respiratory Failure During Veno-Venous Extracorporeal Membrane Oxygenation. Front Cell Infect Microbiol 2022; 12:877205. [PMID: 36034706 PMCID: PMC9414489 DOI: 10.3389/fcimb.2022.877205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/23/2022] [Indexed: 11/29/2022] Open
Abstract
Objectives There are few studies of metagenomic next-generation sequencing (mNGS) in immunocompromised patients assisted by veno-venous extracorporeal membrane oxygenation (vv-ECMO). The present study is aimed to investigate the pathogen-detected effect and clinical therapy value of mNGS technologies in immunocompromised patients assisted by vv-ECMO. Methods Our study retrospectively enrolled 46 immunocompromised patients supported by vv-ECMO from Jan 2017 to June 2021 at the First Affiliated Hospital of Zhengzhou University, respectively. Patients were divided into the deterioration group (Group D) (n = 31) and improvement group (Group I) (n = 15) according to their outcomes. Baseline characteristics and etiological data of patients during hospitalization of 2 groups were compared. The pathogens detected by mNGS and antibiotic regimens guided by mNGS in immunocompromised patients assisted by vv-ECMO were analyzed. Results Compared with Group I, the deterioration patients showed a higher percentage of chronic obstructive pulmonary disease (COPD) (32.3% vs. 6.7%, p < 0.01) and were significantly older (47.77 ± 16.72 years vs. 32 ± 15.05 years, p < 0.01). Within 48 h of being ECMO assisted, the consistency of the samples detected by traditional culture and mNGS at the same time was good (traditional culture vs. mNGS detection, the positive rate of bronchoalveolar lavage fluid (BALF) culture: 26.1% vs. 30.4%; the positive rate of blood sample culture: 12.2% vs. 12.2%, p > 0.05). However, mNGS detected far more pathogen species and strains than conventional culture (30 strains vs. 78 strains, p < 0.01); the most popular pathogen was Klebsiella pneumoniae. Parts of patients had their antibiotic treatment adjustments, and the improvement patients showed less usage of broad-spectrum antibiotics. Conclusions mNGS may play a relatively important role in detecting mixed pathogens and personalized antibiotic treatment in immunocompromised patients assisted by vv-ECMO.
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Affiliation(s)
- Yang-Chao Zhao
- Department of Extracorporeal Life Support Center, Department of Cardiac Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Yang-Chao Zhao,
| | - Yan-Zhong Ding
- Department of Cardiology, Cardiovascular Center, Henan Key Laboratory of Hereditary Cardiovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xi Zhao
- Department of Cardiology, Cardiovascular Center, Henan Key Laboratory of Hereditary Cardiovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Guo-Wei Fu
- Department of Extracorporeal Life Support Center, Department of Cardiac Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ming-Jun Huang
- Department of Extracorporeal Life Support Center, Department of Cardiac Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xing-Xing Li
- Department of Extracorporeal Life Support Center, Department of Cardiac Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qian-Qian Sun
- Department of Extracorporeal Life Support Center, Department of Cardiac Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ya-Bai Kan
- Department of Extracorporeal Life Support Center, Department of Cardiac Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jun Li
- Department of Extracorporeal Life Support Center, Department of Cardiac Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shi-Lei Wang
- Department of Respiration, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wen-Tao Ma
- Department of Respiration, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qin-Fu Xu
- Department of Respiration, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qi-Long Liu
- Department of Surgery ICU, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hong-Bin Li
- Department of Surgery ICU, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Hong D, Wang P, Zhang J, Li K, Ye B, Li G, Zhou J, Tong Z, Ke L, Shi S, Li W. Plasma metagenomic next-generation sequencing of microbial cell-free DNA detects pathogens in patients with suspected infected pancreatic necrosis. BMC Infect Dis 2022; 22:675. [PMID: 35931956 PMCID: PMC9356476 DOI: 10.1186/s12879-022-07662-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [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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Shi Y, Peng JM, Qin HY, Du B. Metagenomic next-generation sequencing: A promising tool for diagnosis and treatment of suspected pneumonia in rheumatic patients with acute respiratory failure: Retrospective cohort study. Front Cell Infect Microbiol 2022; 12:941930. [PMID: 35992169 PMCID: PMC9381725 DOI: 10.3389/fcimb.2022.941930] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/12/2022] [Indexed: 11/17/2022] Open
Abstract
Background The effectiveness of metagenomic next-generation sequencing (mNGS) in respiratory pathogen detection and clinical decision-making in critically rheumatic patients remains largely unexplored. Methods A single-center retrospective study of 58 rheumatic patients who were admitted to ICU due to suspected pneumonia with acute respiratory failure if they underwent both bronchoalveolar lavage fluid specimen mNGS and combined microbiological tests (CMTs) was conducted to compare their diagnostic performance, using clinical composite diagnosis as the gold standard. Treatment modifications based on mNGS results were also reviewed. Results Forty-three patients were diagnosed with microbiologically confirmed pneumonia and 15 were considered as a non-infectious disease. mNGS outperformed CMTs in the accurate diagnosis of infectious and non-infectious lung infiltration (98.1% [57/58] vs. 87.9% [51/58], P = 0.031). A total of 94 causative pathogens were defined by the gold standard and 27 patients had polymicrobial pneumonia. The sensitivity of pathogen detection and complete concordance with the gold standard by mNGS exceeded those by CMTs (92.6% [87/94] vs. 76.6% [72/94], P < 0.001 and 72.1% [31/43] vs. 51.2% [22/43], P = 0.004, respectively). Moreover, 22 pathogens were detected only by mNGS and confirmed by orthogonal test. Accordingly, the etiological diagnosis changed in 19 cases, and the empirical treatment improved in 14 cases, including 8 cases of rescue treatment and 11 of antibiotics de-escalation. At the pathogen-type level, both methods were comparable for bacteria, but mNGS was advantageous to identify viruses (accuracy: 100% vs. 81%, P = 0.004). For Pneumocystis jirovecii detection, mNGS improved the sensitivity compared with Gomori’s methenamine silver stain (91.7% vs. 4.2%, P < 0.001) and was higher than polymerase chain reaction (79.2%), but the difference was not significant (P = 0.289). In terms of Aspergillus, the better sensitivity with a combination of culture and galactomannan test than that with mNGS was found (100% vs. 66.7%, P = 0.033). Conclusions mNGS has an excellent accuracy in etiological diagnosis and pathogen detection of suspected pneumonia in critically rheumatic patients, which has potential significance for clinical decision-making. Its superiority to different types of pathogens depends on the comprehensiveness of CMTs.
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Liang M, Fan Y, Zhang D, Yang L, Wang X, Wang S, Xu J, Zhang J. Metagenomic next-generation sequencing for accurate diagnosis and management of lower respiratory tract infections. Int J Infect Dis 2022; 122:921-929. [PMID: 35908723 DOI: 10.1016/j.ijid.2022.07.060] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/07/2022] [Accepted: 07/23/2022] [Indexed: 11/24/2022] Open
Abstract
OBJECTIVES This study aimed to evaluate the clinical value of metagenomic next-generation sequencing (mNGS) in patients with suspected lower respiratory tract infections (LRTIs). METHODS This retrospective study reviewed patients with suspected LRTIs in Wuhan Union Hospital. Data including demographic, laboratory, and radiological profiles; treatment; and outcomes were recorded and analyzed. RESULTS mNGS identified pathogenic microbes in 100/140 (71.4%) patients, although 135 (96.4%) had received empiric antibiotic treatment before the mNGS tests. Single bacterial infection (35/100, 35%) was the most common type of infection in patients with positive mNGS results, followed by single fungal infection (14/100, 14%), bacterial-viral co-infection (14/100, 14%), single viral infection (12/100, 12%), bacterial-fungal co-infection (9/100, 9%), fungal-viral co-infection (9/100, 9%), and bacterial-fungal-viral co-infection (7/100, 7%). Moreover, compared with culture test, mNGS showed higher sensitivity (63/85, 74.1% vs. 22/85, 25.9% P=0.001) and lower processing time (24 h vs 48 h). Antibiotic treatment was adjusted or confirmed based on the mNGS results in 123 (87.9%) patients, including 5 (3.6%), 33 (23.6%) and 85 (60.7%) patients in whom treatment was downgraded, upgraded and unchanged, respectively, and almost all patients, regardless of escalation, de-escalation, or no change in treatment, showed significant improvement in clinical symptoms and inflammatory indicators. Additionally, 17 (12.1%) patients were referred to Wuhan Pulmonary Hospital for further treatment because of confirmed or suspected tuberculosis. CONCLUSIONS mNGS could be a promising technique for microbiological diagnosis and antibiotic management, potentially improving outcomes of patients.
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Affiliation(s)
- Mengyuan Liang
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical Collage, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei Province, 430022, China
| | - Yamin Fan
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical Collage, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei Province, 430022, China
| | - Dongmei Zhang
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical Collage, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei Province, 430022, China
| | - Lian Yang
- Department of Radiology, Union Hospital, Tongji Medical Collage, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei Province, 430022, China
| | - Xiaorong Wang
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical Collage, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei Province, 430022, China
| | - Sufei Wang
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical Collage, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei Province, 430022, China
| | - Juanjuan Xu
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical Collage, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei Province, 430022, China.
| | - Jianchu Zhang
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical Collage, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei Province, 430022, China.
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Xi Y, Zhou J, Lin Z, Liang W, Yang C, Liu D, Xu Y, Nong L, Chen S, Yu Y, He W, Zhang J, Zhang R, Liu X, Liu X, Sang L, Xu Y, Li Y. Patients with infectious diseases undergoing mechanical ventilation in the intensive care unit have better prognosis after receiving metagenomic next-generation sequencing assay. Int J Infect Dis 2022; 122:959-969. [PMID: 35908725 DOI: 10.1016/j.ijid.2022.07.062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 07/25/2022] [Accepted: 07/25/2022] [Indexed: 10/16/2022] Open
Abstract
OBJECTIVES To evaluate the relation between mNGS and the prognosis of patients with infectious diseases undergoing mechanical ventilation in the intensive care unit (ICU). DESIGN This is a single-center observational study, comparing non-randomly assigned diagnostic approaches. We analyzed the medical records of 228 patients with suspected infectious diseases undergoing mechanical ventilation in the ICU from March 2018 to May 2020. The concordance of pathogen results was also assessed for the results of mNGS, culture and PCR assays. RESULTS The 28-day mortality of the patients in the mNGS group was lower after the baseline difference correction (19.23% (20/104) vs. 29.03% (36/124) , p=0.039). Subgroup analysis showed that mNGS assay associates with improved 28-day mortality of non-immunosuppressive patients (14.06% vs. 29.82%, p=0.018) . Not performing mNGS assay, higher APACHE II score and hypertension are independent risk factors for 28-day mortality. The mNGS assay presented advantage in pathogen positivity (69.8% double positive and 25.0% mNGS positive only), and the concordance between thest two assays were 79.0%. CONCLUSIONS mNGS survey may be associated with a better prognosis as the reduction of 28-day mortality of patients with infectious diseases on mechanical ventilation in ICU. This technique presented advantage in pathogen positivity than traditional methods.
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Affiliation(s)
- Yin Xi
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Department of Pulmonary and Critical Care Medicine, 151 Yanjiang Road, Guangzhou, 510120, China
| | - Jing Zhou
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Department of Pulmonary and Critical Care Medicine, 151 Yanjiang Road, Guangzhou, 510120, China
| | - Zhimin Lin
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Department of Pulmonary and Critical Care Medicine, 151 Yanjiang Road, Guangzhou, 510120, China
| | - Weibo Liang
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Department of Pulmonary and Critical Care Medicine, 151 Yanjiang Road, Guangzhou, 510120, China
| | - Chun Yang
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Department of Pulmonary and Critical Care Medicine, 151 Yanjiang Road, Guangzhou, 510120, China
| | - Dongdong Liu
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Department of Pulmonary and Critical Care Medicine, 151 Yanjiang Road, Guangzhou, 510120, China
| | - Yonghao Xu
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Department of Pulmonary and Critical Care Medicine, 151 Yanjiang Road, Guangzhou, 510120, China
| | - Lingbo Nong
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Department of Pulmonary and Critical Care Medicine, 151 Yanjiang Road, Guangzhou, 510120, China
| | - Sibei Chen
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Department of Pulmonary and Critical Care Medicine, 151 Yanjiang Road, Guangzhou, 510120, China
| | - Yuheng Yu
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Department of Pulmonary and Critical Care Medicine, 151 Yanjiang Road, Guangzhou, 510120, China
| | - Weiqun He
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Department of Pulmonary and Critical Care Medicine, 151 Yanjiang Road, Guangzhou, 510120, China
| | - Jie Zhang
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Department of Pulmonary and Critical Care Medicine, 151 Yanjiang Road, Guangzhou, 510120, China
| | - Rong Zhang
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Department of Pulmonary and Critical Care Medicine, 151 Yanjiang Road, Guangzhou, 510120, China
| | - Xuesong Liu
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Department of Pulmonary and Critical Care Medicine, 151 Yanjiang Road, Guangzhou, 510120, China
| | - Xiaoqing Liu
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Department of Pulmonary and Critical Care Medicine, 151 Yanjiang Road, Guangzhou, 510120, China
| | - Ling Sang
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Department of Pulmonary and Critical Care Medicine, 151 Yanjiang Road, Guangzhou, 510120, China..
| | - Yuanda Xu
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Department of Pulmonary and Critical Care Medicine, 151 Yanjiang Road, Guangzhou, 510120, China..
| | - Yimin Li
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Department of Pulmonary and Critical Care Medicine, 151 Yanjiang Road, Guangzhou, 510120, China..
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Chen S, Kang Y, Li D, Li Z. Diagnostic performance of metagenomic next-generation sequencing for the detection of pathogens in bronchoalveolar lavage fluid in patients with pulmonary infections: Systematic review and meta-analysis. Int J Infect Dis 2022; 122:867-873. [PMID: 35907477 DOI: 10.1016/j.ijid.2022.07.054] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 07/04/2022] [Accepted: 07/21/2022] [Indexed: 10/16/2022] Open
Abstract
BACKGROUND The identification of pathogens in patients with pulmonary infection has always been a major challenge in medicine. Compared with sputum and throat swabs, bronchoalveolar lavage fluid (BALF) can better reflect the actual state in the lungs. However, there has not been a meta-analysis of the diagnostic efficacy of metagenomic next-generation sequencing (mNGS) in detecting pathogens in BALF from patients with pulmonary infections. METHODS Data sources were PubMed, Web of Science, Embase, and the China National Knowledge Infrastructure. The pooled sensitivity and specificity were estimated by using random-effects or fixed-effect models. Subgroup analysis was performed to reveal the effect of potential explanatory factors on the diagnostic performance measures. RESULTS The pooled sensitivity was 78% (95% confidence interval: 67-87%; I2 = 92%) and the pooled specificity was 77% (95% confidence interval: 64-94%; I2 = 74%) for mNGS. Subgroup analyses for the sensitivity of mNGS revealed that patients with pulmonary infections who were severely ill or immunocompromised significantly affected heterogeneity (P < 0.001). The positive detection rate of mNGS for pathogens in BALF of severely or immunocompromised pulmonary-infected patients was 92% (95% confidence interval: 78-100%). CONCLUSION mNGS has high diagnostic performance for BALF pathogens in patients with pulmonary infections, especially in critically ill or immunocompromised patients.
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Affiliation(s)
- Shenglin Chen
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping, Beijing 102206, China; School of Public Health, Shanxi Medical University, 56 Xinjiannanlu Street, Taiyuan 030001, Shanxi, People's Republic of China
| | - Yutong Kang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping, Beijing 102206, China
| | - Dan Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping, Beijing 102206, China
| | - Zhenjun Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping, Beijing 102206, China; School of Public Health, Shanxi Medical University, 56 Xinjiannanlu Street, Taiyuan 030001, Shanxi, People's Republic of China.
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Keskinidou C, Vassiliou AG, Dimopoulou I, Kotanidou A, Orfanos SE. Mechanistic Understanding of Lung Inflammation: Recent Advances and Emerging Techniques. J Inflamm Res 2022; 15:3501-3546. [PMID: 35734098 PMCID: PMC9207257 DOI: 10.2147/jir.s282695] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 05/04/2022] [Indexed: 12/12/2022] Open
Abstract
Acute respiratory distress syndrome (ARDS) is a life-threatening lung injury characterized by an acute inflammatory response in the lung parenchyma. Hence, it is considered as the most appropriate clinical syndrome to study pathogenic mechanisms of lung inflammation. ARDS is associated with increased morbidity and mortality in the intensive care unit (ICU), while no effective pharmacological treatment exists. It is very important therefore to fully characterize the underlying pathobiology and the related mechanisms, in order to develop novel therapeutic approaches. In vivo and in vitro models are important pre-clinical tools in biological and medical research in the mechanistic and pathological understanding of the majority of diseases. In this review, we will present data from selected experimental models of lung injury/acute lung inflammation, which have been based on clinical disorders that can lead to the development of ARDS and related inflammatory lung processes in humans, including ventilation-induced lung injury (VILI), sepsis, ischemia/reperfusion, smoke, acid aspiration, radiation, transfusion-related acute lung injury (TRALI), influenza, Streptococcus (S.) pneumoniae and coronaviruses infection. Data from the corresponding clinical conditions will also be presented. The mechanisms related to lung inflammation that will be covered are oxidative stress, neutrophil extracellular traps, mitogen-activated protein kinase (MAPK) pathways, surfactant, and water and ion channels. Finally, we will present a brief overview of emerging techniques in the field of omics research that have been applied to ARDS research, encompassing genomics, transcriptomics, proteomics, and metabolomics, which may recognize factors to help stratify ICU patients at risk, predict their prognosis, and possibly, serve as more specific therapeutic targets.
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Affiliation(s)
- Chrysi Keskinidou
- First Department of Critical Care Medicine and Pulmonary Services, School of Medicine, National and Kapodistrian University of Athens, "Evangelismos" Hospital, Athens, Greece
| | - Alice G Vassiliou
- First Department of Critical Care Medicine and Pulmonary Services, School of Medicine, National and Kapodistrian University of Athens, "Evangelismos" Hospital, Athens, Greece
| | - Ioanna Dimopoulou
- First Department of Critical Care Medicine and Pulmonary Services, School of Medicine, National and Kapodistrian University of Athens, "Evangelismos" Hospital, Athens, Greece
| | - Anastasia Kotanidou
- First Department of Critical Care Medicine and Pulmonary Services, School of Medicine, National and Kapodistrian University of Athens, "Evangelismos" Hospital, Athens, Greece
| | - Stylianos E Orfanos
- First Department of Critical Care Medicine and Pulmonary Services, School of Medicine, National and Kapodistrian University of Athens, "Evangelismos" Hospital, Athens, Greece
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Zhang P, Liu B, Zheng W, Chen Y, Wu Z, Lu Y, Ma J, Lu W, Zheng M, Wu W, Meng Z, Wu J, Zheng Y, Zhang X, Zhang S, Huang Y. Pulmonary Microbial Composition in Sepsis-Induced Acute Respiratory Distress Syndrome. Front Mol Biosci 2022; 9:862570. [PMID: 35813824 PMCID: PMC9262094 DOI: 10.3389/fmolb.2022.862570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 05/03/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Acute respiratory distress syndrome (ARDS) is an unresolved challenge in the field of respiratory and critical care, and the changes in the lung microbiome during the development of ARDS and their clinical diagnostic value remain unclear. This study aimed to explore the role of the lung microbiome in disease progression in patients with sepsis-induced ARDS and potential therapeutic targets.Methods: Patients with ARDS were divided into two groups according to the initial site of infection, intrapulmonary infection (ARDSp, 111 cases) and extrapulmonary infection (ARDSexp, 45 cases), and a total of 28 patients with mild pulmonary infections were enrolled as the control group. In this study, we sequenced the DNA in the bronchoalveolar lavage fluid collected from patients using metagenomic next-generation sequencing (mNGS) to analyze the changes in the lung microbiome in patients with different infectious site and prognosis and before and after antibiotic treatment.Results: The Shannon–Wiener index indicated a statistically significant reduction in microbial diversity in the ARDSp group compared with the ARDSexp and control groups. The ARDSp group was characterized by a reduction in microbiome diversity, mainly in the normal microbes of the lung, whereas the ARDSexp group was characterized by an increase in microbiome diversity, mainly in conditionally pathogenic bacteria and intestinal microbes. Further analysis showed that an increase in Bilophila is a potential risk factor for death in ARDSexp. An increase in Escherichia coli, Staphylococcus aureus, Candida albicans, enteric microbes, or conditional pathogens may be risk factors for death in ARDSp. In contrast, Hydrobacter may be a protective factor in ARDSp.Conclusion: Different initial sites of infection and prognoses are likely to affect the composition and diversity of the pulmonary microbiome in patients with septic ARDS. This study provides insights into disease development and exploration of potential therapeutic targets.
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Affiliation(s)
- Peng Zhang
- Department of Critical Care Medicine, Jiangmen Central Hospital, Jiangmen, China
| | - Baoyi Liu
- Clinical Experimental Center, Jiangmen Key Laboratory of Clinical Biobanks and Translational Research, Jiangmen Central Hospital, Jiangmen, China
| | - Weihao Zheng
- Department of Critical Care Medicine, Jiangmen Central Hospital, Jiangmen, China
| | - Yantang Chen
- Department of Critical Care Medicine, Jiangmen Central Hospital, Jiangmen, China
| | - Zhentao Wu
- Department of Critical Care Medicine, Jiangmen Central Hospital, Jiangmen, China
| | - Yuting Lu
- Department of Critical Care Medicine, Jiangmen Central Hospital, Jiangmen, China
| | - Jie Ma
- Department of Critical Care Medicine, Jiangmen Central Hospital, Jiangmen, China
| | - Wenjie Lu
- Clinical Experimental Center, Jiangmen Key Laboratory of Clinical Biobanks and Translational Research, Jiangmen Central Hospital, Jiangmen, China
| | - Mingzhu Zheng
- Clinical Experimental Center, Jiangmen Key Laboratory of Clinical Biobanks and Translational Research, Jiangmen Central Hospital, Jiangmen, China
| | - Wanting Wu
- Clinical Experimental Center, Jiangmen Key Laboratory of Clinical Biobanks and Translational Research, Jiangmen Central Hospital, Jiangmen, China
| | - Zijie Meng
- Clinical Experimental Center, Jiangmen Key Laboratory of Clinical Biobanks and Translational Research, Jiangmen Central Hospital, Jiangmen, China
| | - Jinhua Wu
- Department of Clinical Laboratory, Jiangmen Central Hospital, Jiangmen, China
| | - Yan Zheng
- Department of Research and Development, Guangdong Research Institute of Genetic Diagnostic and Engineering Technologies for Thalassemia, Hybribio Limited, Guangzhou, China
| | - Xin Zhang
- Clinical Experimental Center, Jiangmen Key Laboratory of Clinical Biobanks and Translational Research, Jiangmen Central Hospital, Jiangmen, China
- Dongguan Key Laboratory of Medical Bioactive Molecular Developmental and Translational Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, China
- Collaborative Innovation Center for Antitumor Active Substance Research and Development, Guangdong Medical University, Zhanjiang, China
- *Correspondence: Xin Zhang, ; Shuang Zhang, ; Yanming Huang,
| | - Shuang Zhang
- Department of Critical Care Medicine, Jiangmen Central Hospital, Jiangmen, China
- *Correspondence: Xin Zhang, ; Shuang Zhang, ; Yanming Huang,
| | - Yanming Huang
- Clinical Experimental Center, Jiangmen Key Laboratory of Clinical Biobanks and Translational Research, Jiangmen Central Hospital, Jiangmen, China
- Department of Respiratory and Critical Care Medicine, Jiangmen Central Hospital, Jiangmen, China
- *Correspondence: Xin Zhang, ; Shuang Zhang, ; Yanming Huang,
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Fu M, Feng CM, Cao LJ, Hu XW, Xu QX, Xia HL, Ji ZM, Hu NN, Xie W, Fang Y, Xia DQ, Zhang JQ. Acute Respiratory Distress Syndrome Caused by Occupational Exposure to Waterproofing Spray: A Case Report and Literature Review. Front Public Health 2022; 10:830429. [PMID: 35284363 PMCID: PMC8916539 DOI: 10.3389/fpubh.2022.830429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 01/31/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundAcute respiratory distress syndrome (ARDS) is a serious respiratory disease, caused by severe infection, trauma, shock, inhalation of harmful gases and poisons and presented with acute-onset and high mortality. Timely and accurate identification will be helpful to the treatment and prognosis of ARDS cases. Herein, we report a case of ARDS caused by occupational exposure to waterproofing spray. To our knowledge, inhalation of waterproofing spray is an uncommon cause of ARDS, and what makes our case special is that we ruled out concurrent infections with some pathogens by using metagenomic next-generation sequencing (mNGS) as an auxiliary diagnosis, which presents the most comprehensive etiological examination of similar reports.Case PresentationA previously healthy 25 years old delivery man developed hyperpyrexia, chest tightness, cough and expectoration. The symptoms occurred and gradually exacerbated after exposure to a waterproofing spray. The chest computed tomography (CT) finding showed diffuse ground glass and infiltrative shadows in both lungs. The diagnosis of ARDS related to waterproofing spray was established on the basis of comprehensive differential diagnosis and etiological examination. The patient achieved good curative effect after proper systemic glucocorticoid therapy.ConclusionsThe diagnosis and differential diagnosis of acute respiratory failure for outdoor workers, such as delivery drivers or hikers, should be considered whether toxic aerosol exposure exists from daily contacts. The case can educate the public that more attention should be paid to avoid exposure to these chemicals by aerosols/ingestion mode and some preventive strategies should be taken in occupational environment. The treatment effect of glucocorticoids is significant in ARDS patients with general chemical damage caused by inhaling toxic gases and substances.
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Affiliation(s)
- Meng Fu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of University of Science and Technology of China (Anhui Provincial Hospital), Hefei, China
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Chun-Mei Feng
- Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Le-Jie Cao
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of University of Science and Technology of China (Anhui Provincial Hospital), Hefei, China
| | - Xiao-Wen Hu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of University of Science and Technology of China (Anhui Provincial Hospital), Hefei, China
| | - Qi-xia Xu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of University of Science and Technology of China (Anhui Provincial Hospital), Hefei, China
| | - Huai-Ling Xia
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of University of Science and Technology of China (Anhui Provincial Hospital), Hefei, China
| | - Zi-Mei Ji
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of University of Science and Technology of China (Anhui Provincial Hospital), Hefei, China
| | - Na-Na Hu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of University of Science and Technology of China (Anhui Provincial Hospital), Hefei, China
| | - Wang Xie
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of University of Science and Technology of China (Anhui Provincial Hospital), Hefei, China
| | - Yuan Fang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of University of Science and Technology of China (Anhui Provincial Hospital), Hefei, China
| | - Da-Qing Xia
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of University of Science and Technology of China (Anhui Provincial Hospital), Hefei, China
- *Correspondence: Da-Qing Xia
| | - Jun-Qiang Zhang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of University of Science and Technology of China (Anhui Provincial Hospital), Hefei, China
- Jun-Qiang Zhang
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Application of mNGS in the Etiological Analysis of Lower Respiratory Tract Infections and the Prediction of Drug Resistance. Microbiol Spectr 2022; 10:e0250221. [PMID: 35171007 PMCID: PMC8849087 DOI: 10.1128/spectrum.02502-21] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Lower respiratory tract infections (LRTIs) have high morbidity and mortality rates. However, traditional etiological detection methods have not been able to meet the needs for the clinical diagnosis and prognosis of LRTIs. The rapid development of metagenomic next-generation sequencing (mNGS) provides new insights for the diagnosis and treatment of LRTIs; however, little is known about how to interpret the application of mNGS results in LRTIs. In this study, lower respiratory tract specimens from 46 patients with suspected LRTIs were tested simultaneously using conventional microbiological detection methods and mNGS. Receiver operating characteristic (ROC) curves were used to evaluate the performance of the logarithm of reads per kilobase per million mapped reads [lg(RPKM)], genomic coverage, and relative abundance of the organism in predicting the true-positive pathogenic bacteria. True-positive viruses were identified according to the lg(RPKM) threshold of bacteria. We also evaluated the ability to predict drug resistance genes using mNGS. Compared to that using conventional detection methods, the false-positive detection rate of pathogenic bacteria was significantly higher using mNGS. It was concluded from the ROC curves that the lg(RPKM) and genomic coverage contributed to the identification of pathogenic bacteria, with the performance of lg(RPKM) being the best (area under the curve [AUC] = 0.99). The corresponding lg(RPKM) threshold for identifying the pathogenic bacteria was −1.35. Thirty-five strains of true-positive virus were identified based on the lg(RPKM) threshold of bacteria, with the detection of human gammaherpesvirus 4 being the highest and prone to coinfection with Pseudomonas aeruginosa, Acinetobacter baumannii, and Stenotrophomonas maltophilia. Antimicrobial susceptibility tests (AST) revealed the resistance of bacteria containing drug resistance genes (detected by mNGS). However, the drug resistance genes of some multidrug-resistant bacteria were not detected. As an emerging technology, mNGS has shown many advantages for the unbiased etiological detection and the prediction of antibiotic resistance. However, a correct understanding of mNGS results is a prerequisite for its clinical application, especially for LRTIs. IMPORTANCE LRTIs are caused by hundreds of pathogens, and they have become a great threat to human health due to the limitations of traditional etiological detection methods. As an unbiased approach to detect pathogens, mNGS overcomes such etiological diagnostic challenges. However, there is no unified standard on how to use mNGS indicators (the sequencing reads, genomic coverage, and relative abundance of each organism) to distinguish between pathogens and colonizing microorganisms or contaminant microorganisms. Here, we selected the mNGS indicator with the best identification performance and established a cutoff value for the identification of pathogens in LRTIs using ROC curves. In addition, we also evaluated the accuracy of antibiotic resistance prediction using mNGS.
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Han SY. Clinical value of metagenomic next-generation sequencing in complicated infectious diseases. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2022; 24:210-215. [PMID: 35209988 DOI: 10.7499/j.issn.1008-8830.2110064] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Infectious diseases are commonly seen in clinical practice, and pathogen diagnosis is the key link in diagnosis and treatment; however, conventional pathogen detection methods cannot meet clinical needs due to time-consuming operation and low positive rate. As a new pathogen detection method, metagenomic next-generation sequencing (mNGS) has a wide detection range and can detect bacteria, viruses, fungi, parasites, rare pathogens, and even unknown pathogens. The technique of mNGS is unbiased and can rapidly, efficiently, and accurately obtain all nucleic acid information in test samples, analyze pathogens, and guide clinical diagnosis and treatment, thereby playing an important role in complicated infectious diseases. This article reviews the diagnostic advantages and clinical value of mNGS in bacterial, fungal, viral, and parasitic infections.
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Affiliation(s)
- Si-Yu Han
- Department of Respiratory Medicine, Hebei Children's Hospital Affiliated to Hebei Medical University, Shijiazhuang 050031, China
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Shao J, Hassouna A, Wang Y, Zhang R, Zhen L, Li R, Chen M, Liu C, Wang X, Zhang M, Wang P, Yuan S, Chen J, Lu J. Next-generation sequencing as an advanced supplementary tool for the diagnosis of pathogens in lower respiratory tract infections: An observational trial in Xi'an, China. Biomed Rep 2021; 16:14. [PMID: 35070298 PMCID: PMC8764650 DOI: 10.3892/br.2021.1497] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/07/2021] [Indexed: 11/06/2022] Open
Abstract
The application of next-generation sequencing (NGS) in routine clinical analysis is still limited. The significance of NGS in the identification of pathogens of lower respiratory tract infection should be assessed as part of routine clinical bacterial examinations and chest imaging results. In the present study, the alveolar lavage fluid samples of 30 patients (25 males and 5 females, aged 19-92 years old, with a median age of 62) were examined by routine bacterial culture and NGS, and the results of pathogen detection and identification were compared. Chest imaging showed consolidation in all 30 patients (100%), and pleural effusion in 13 of the 30 patients (43.33%). The routine bacterial culture of the lavage solution was only positive in 14 of the 30 patients (46.6%), and negative in 16 patients (53.33%). However, the positive rate of NGS test results of the lavage fluid was 100%. A total of 12 cases (40%) were completely consistent with the routine bacterial culture test, with 56 other pathogens of mixed infection detected, accounting for the short comings of the routine bacterial examination. Although NGS cannot distinguish between live and dead bacteria, it is still a useful detection technology for accurate diagnosis of clinical infectious diseases. It is worthy of adaptation in the clinic for more effective clinical management and treatment of the lower respiratory airway infection in addition to the routine bacterial culture testing.
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Affiliation(s)
- Jie Shao
- Norinco 521 Hospital, Xi'an, Shaanxi 710065, P.R. China
| | - Amira Hassouna
- School of Public Health and Interdisciplinary Studies, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland 0622, New Zealand
| | - Yaqin Wang
- Norinco 521 Hospital, Xi'an, Shaanxi 710065, P.R. China
| | - Ruirui Zhang
- Norinco 521 Hospital, Xi'an, Shaanxi 710065, P.R. China
| | - Lifang Zhen
- Norinco 521 Hospital, Xi'an, Shaanxi 710065, P.R. China
| | - Ruidan Li
- Norinco 521 Hospital, Xi'an, Shaanxi 710065, P.R. China
| | - Mingli Chen
- Norinco 521 Hospital, Xi'an, Shaanxi 710065, P.R. China
| | - Chengjie Liu
- Norinco 521 Hospital, Xi'an, Shaanxi 710065, P.R. China
| | - Xiangye Wang
- Norinco 521 Hospital, Xi'an, Shaanxi 710065, P.R. China
| | | | - Peng Wang
- Norinco 521 Hospital, Xi'an, Shaanxi 710065, P.R. China
| | - Shenghua Yuan
- Norinco 521 Hospital, Xi'an, Shaanxi 710065, P.R. China
| | - Jie Chen
- Guangzhou Sagene Biotech Co., Ltd., Guangzhou, Guangdong 510320, P.R. China
| | - Jun Lu
- School of Public Health and Interdisciplinary Studies, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland 0622, New Zealand
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Xiao Q, Shen W, Zou Y, Dong S, Tan Y, Zhang X, Yao L, Li Q, Pei W, Wang T. Sixteen cases of severe pneumonia caused by Chlamydia psittaci in South China investigated via metagenomic next-generation sequencing. J Med Microbiol 2021; 70. [PMID: 34817316 DOI: 10.1099/jmm.0.001456] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Introduction. Chlamydia psittaci is an important cause of community-acquired pneumonia (CAP). The spectrum of CAP due to Chlamydia psittaci ranges from mild, self-limited to acute respiratory failure and the early identification of this disease can be challenging. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid has the potential to improve the pathogen identification in severe CAP.Hypothesis/Gap Statement. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid has the potential to rapidly identify pathogens in severe CAP. The early identification and appropriate use of antibiotics can improve the prognosis of severe CAP caused by Chlamydia psittaci.Aim. The aim of the study is to describe the clinical spectrum of severe psittacosis pneumonia to provide a better understanding of this disease and to demonstrate that mNGS is an effective method for pathogen detection.Methodology. Retrospective case analysis from November 2019 to November 2020 was performed. Sixteen cases of severe psittacosis pneumonia were diagnosed through mNGS. Clinical features, laboratory findings, imaging features, treatment and outcome were summarized.Results. Frequent symptoms included fever (16/16, 100%), dyspnoea (16/16, 100%), cough (12/16, 75%), sputum (11/16, 69%) and headache (9/16, 56%). The median leukocytosis was within the normal range, while C-reactive proteins, CK, LDH, AST, D-Dimer were significantly elevated. The feature of computed tomography included ground-glass opacity with consolidation and multiple lobar distributions. The total number of sequences of Chlamydia psittaci identified from bronchoalveolar lavage by mNGS varied from 58 to 57115. Five patients underwent noninvasive mechanical ventilation, four patients underwent high flow humidified oxygen therapy and one patient underwent invasive mechanical ventilation. Two patients had septic shock needing vasoactive medications. All of the sixteen patients experienced full recoveries.Conclusion. The symptoms of severe CAP caused by Chlamydia psittaci were not typical while laboratory results may have some clues. The mNGS technology can early detect of psittacosis, reduce unnecessary use of antibiotics and short the course of the disease.
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Affiliation(s)
- Qiang Xiao
- Department of Respiratory Medicine, The First People's Hospital of Changde City, Hunan, PR China
| | - Wei Shen
- Department of Outpatient, The First People's Hospital of Changde City, Hunan, PR China
| | - Yeqiang Zou
- Department of Respiratory Medicine, The First People's Hospital of Changde City, Hunan, PR China
| | - Susu Dong
- Department of Respiratory Medicine, The First People's Hospital of Changde City, Hunan, PR China
| | - Yafen Tan
- Department of Respiratory Medicine, The First People's Hospital of Changde City, Hunan, PR China
| | - Xuan Zhang
- Department of Respiratory Medicine, The First People's Hospital of Changde City, Hunan, PR China
| | - Lu Yao
- Department of Respiratory Medicine, The First People's Hospital of Changde City, Hunan, PR China
| | - Qiuping Li
- Department of Respiratory Medicine, The First People's Hospital of Changde City, Hunan, PR China
| | - Wenjun Pei
- Department of Respiratory Medicine, The First People's Hospital of Changde City, Hunan, PR China
| | - Tianli Wang
- Department of Respiratory Medicine, The First People's Hospital of Changde City, Hunan, PR China
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40
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Borroni D. Clinical Metagenomic Next-Generation Sequencing has the Potential to Reduce Costs in the Management of Microbial Keratitis Patients. Cornea 2021; 40:e14. [PMID: 33782271 DOI: 10.1097/ico.0000000000002719] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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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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Sun T, Wu X, Cai Y, Zhai T, Huang L, Zhang Y, Zhan Q. Metagenomic Next-Generation Sequencing for Pathogenic Diagnosis and Antibiotic Management of Severe Community-Acquired Pneumonia in Immunocompromised Adults. Front Cell Infect Microbiol 2021; 11:661589. [PMID: 34141628 PMCID: PMC8204719 DOI: 10.3389/fcimb.2021.661589] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 05/13/2021] [Indexed: 11/13/2022] Open
Abstract
Background Metagenomic next-generation sequencing (mNGS) is a promising technique for pathogens diagnosis. However, application of mNGS in immunocompromised adults with severe community-acquired pneumonia (SCAP) is relatively limited. Methods We retrospectively reviewed 23 immunocompromised and 21 immunocompetent SCAP patients with mNGS detection from April 2019 to December 2019. The performances of pathogenic diagnosis and subsequently antibiotic adjustment in immunocompromised SCAP patients were compared to immunocompetent SCAP patients. The defined by days of therapy (DOT) method was used for estimate daily antibiotic use. Results There was a significant difference in the diagnostic positivity rate between mNGS and conventional test in both groups (P<0.001). Compared to immunocompetent patients, more mixed pathogens in immunocompromised patients were found (P=0.023). Before the availability of mNGS, the DOTs in immunocompromise patients were higher than immunocompetent patients (3.0 [3.0, 4.0] vs. 3.0 [2.0, 3.0], P=0.013). Compared to immunocompetent patients, immunocompromised patients had fewer full pathogen covered empirical antibiotic therapy (14.7% vs. 57.1%, P=0.022), more adjustments of antibiotic treatment (87.0%) vs. 57.1%, P=0.027). More than a half (13 of 23) SCAP patients in immunosuppressed group had reduced or downgraded antibiotic adjustments based on the results. Conclusions mNGS may be a useful technique for detecting mixed pathogens and personalized antibiotic treatment in immunocompromised SCAP patients.
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Affiliation(s)
- Ting Sun
- Capital Medical University China-Japan Friendship School of Clinical Medicine, Beijing, China
| | - Xiaojing Wu
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Center for Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Ying Cai
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Center for Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Tianshu Zhai
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Center for Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Linna Huang
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Center for Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Yi Zhang
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Center for Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Qingyuan Zhan
- Capital Medical University China-Japan Friendship School of Clinical Medicine, Beijing, China.,Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Center for Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
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