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Luo J, Xie R, Bao C, Lin J, Xu Y, Yan X, Yang Z, Feng L, Wu J, Chen D, He Z, Kong J. Analysis of pulmonary microecology and clinical characteristics of patients carrying human herpesvirus. Future Microbiol 2024; 19:1071-1080. [PMID: 38899531 PMCID: PMC11323855 DOI: 10.1080/17460913.2024.2357994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Accepted: 05/17/2024] [Indexed: 06/21/2024] Open
Abstract
Aim: To investigate the impact of human herpes virus (HHV) carriage on lung microbiota, and its correlation with clinical features and laboratory indicators in patients.Methods: Retrospective analysis was conducted on 30 outpatient lung infection cases, which were divided into HHV (n = 15) and non-HHV (n = 15) groups. mNGS detected microbial composition. Microbial diversity and abundance were tested using Shannon and Chao1 indices. Their relationship with laboratory indicators were explored.Results: Significant differences in microbial abundance and distribution were found between two groups (p < 0.05). Moreover, HHV group showed negative correlations (p < 0.05) between Prevotella, Porphyromonas, Streptococcus and basophil/eosinophil percentages.Conclusion: HHV carriage impacts lung microbiota, emphasizing the need for clinicians to pay attention to HHV reactivation in outpatient lung infection patients.
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Affiliation(s)
- Jing Luo
- Department of Respiratory & Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Province, 530021, China
| | - Rui Xie
- Department of Respiratory & Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Province, 530021, China
| | - Chongxi Bao
- Department of Respiratory & Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Province, 530021, China
| | - Jinyan Lin
- Department of Respiratory & Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Province, 530021, China
| | - Yang Xu
- Department of Respiratory & Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Province, 530021, China
| | - Xuexin Yan
- Department of Respiratory & Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Province, 530021, China
| | - Zhen Yang
- Department of Respiratory & Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Province, 530021, China
| | - Li Feng
- Department of Respiratory & Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Province, 530021, China
| | - Jianing Wu
- Department of Respiratory & Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Province, 530021, China
| | - Dan Chen
- Department of Respiratory & Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Province, 530021, China
| | - Zaiqing He
- Department of Respiratory & Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Province, 530021, China
| | - Jinliang Kong
- Department of Respiratory & Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Province, 530021, 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 X, Xie L, Shi Z, Zhou M. Application of mNGS in the study of pulmonary microbiome in pneumoconiosis complicated with pulmonary infection patients and exploration of potential biomarkers. Front Cell Infect Microbiol 2023; 13:1200157. [PMID: 37545858 PMCID: PMC10403237 DOI: 10.3389/fcimb.2023.1200157] [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: 04/04/2023] [Accepted: 06/26/2023] [Indexed: 08/08/2023] Open
Abstract
Background Pneumoconiosis patients have a high prevalence of pulmonary infections, which can complicate diagnosis and treatment. And there is no comprehensive study of the microbiome of patients with pneumoconiosis. The application of metagenomic next-generation sequencing (mNGS) fills the gap to some extent by analyzing the lung microbiota of pneumoconiosis population while achieving accurate diagnosis. Methods We retrospectively analyzed 44 patients with suspected pneumoconiosis complicated with pulmonary infection between Jan 2020 and Nov 2022. Bronchoalveolar lavage fluid (BALF) specimens from 44 patients were collected and tested using the mNGS technology. Results Among the lung microbiome of pneumoconiosis patients with complicated pulmonary infection (P group), the most frequently detected bacteria and fungi at the genus level were Streptococcus and Aspergillus, at the species level were Streptococcus pneumoniae and Aspergillus flavus, respectively, and the most frequently detected DNA virus was Human gammaherpesvirus 4. There was no significant difference in α diversity between the P group and the non-pneumoconiosis patients complicated with pulmonary infection group (Non-P group) in pulmonary flora, while P< 0.01 for β diversity analysis, and the differential species between the two groups were Mycobacterium colombiense and Fusobacterium nucleatum. In addition, we monitored a high distribution of Malassezia and Pneumocystis in the P group, while herpes virus was detected in the majority of samples. Conclusions Overall, we not only revealed a comprehensive lung microbiome profile of pneumoconiosis patients, but also compared the differences between their microbiome and that of non-pneumoconiosis complicated with pulmonary infection patients. This provides a good basis for a better understanding of the relationship between pneumoconiosis and microorganisms, and for the search of potential biomarkers.
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Affiliation(s)
- Xingya Yuan
- Department of Respiratory Medicine, West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Linshen Xie
- Department of Respiratory Medicine, West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | | | - Min Zhou
- Department of Respiratory Medicine, West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
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Evaluation of extraction and enrichment methods for recovery of respiratory RNA viruses in a metagenomics approach. J Virol Methods 2023; 314:114677. [PMID: 36657602 PMCID: PMC10009504 DOI: 10.1016/j.jviromet.2023.114677] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/09/2023] [Accepted: 01/14/2023] [Indexed: 01/18/2023]
Abstract
Viral metagenomics is increasingly applied in viral detection and virome characterization. Different extraction and enrichment techniques may be adopted, however, reports on their effective influence on viral recovery is often conflicting. Using a three step enrichment steps, the effect of three extraction kits and the influence of DNase treatment with or without rRNA removal for respiratory RNA virus recovery from nasopharyngeal swab samples was evaluated. The viral cocktail containing six different RNA viruses pooled in equal volume were subjected to the different extraction and enrichment methods, sequenced using the Illumina MiSeq, and analysed using Genome Detective. The PureLink® Viral RNA/DNA Mini Kit (PureLink) was highly efficient with better recovery of all the viral agents in the cocktail. The use of rRNA treatment resulted in increased viral recovery with PureLink and QIAamp® Viral RNA Mini kit, while having comparable recovery rate as DNase only with the QIAamp® MinElute Virus Spin Kit. The observed low reads and genome coverage of some of the viruses could be attributed to their low abundance. Depending on sample matrix, extraction choice and enrichment strategy may influence recovery of respiratory RNA virus in metagenomics studies, therefore individual evaluation and adoption may be necessary for a robust result.
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Xu J, Zhou P, Liu J, Zhao L, Fu H, Han Q, Wang L, Wu W, Ou Q, Ma Y, He J. Utilizing Metagenomic Next-Generation Sequencing (mNGS) for Rapid Pathogen Identification and to Inform Clinical Decision-Making: Results from a Large Real-World Cohort. Infect Dis Ther 2023; 12:1175-1187. [PMID: 36988865 PMCID: PMC10147866 DOI: 10.1007/s40121-023-00790-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/07/2023] [Indexed: 03/30/2023] Open
Abstract
INTRODUCTION Clinical metagenomic next-generation sequencing (mNGS) has proven to be a powerful diagnostic tool in pathogen detection. However, its clinical utility has not been thoroughly evaluated. METHODS In this single-center prospective study at the First Affiliated Hospital of Soochow University, a total of 228 samples from 215 patients suspected of having acute or chronic infections between June 2018 and December 2018 were studied. Samples that met the mNGS quality control (QC) criteria (N = 201) were simultaneously analyzed using conventional tests (CTs), including multiple clinical microbiological tests and real-time PCR (if applicable). RESULTS Pathogen detection results of mNGS in the 201 QC-passed samples were compared to CTs and exhibited a sensitivity of 98.8%, specificity of 38.5%, and accuracy of 87.1%. Specifically, 109 out of 160 (68.1%) CT+/mNGS+ samples exhibited concordant results at the species/genus level, 25 samples (15.6%) showed overlapping results, while the remaining 26 samples (16.3%) had discordant results between the CT and mNGS assays. In addition, mNGS could identify pathogens at the species level, whereas only the genera of some pathogens could be identified by CT. In this cohort, mNGS results were used to guide treatment plans in 24 out of 41 cases that had available follow-up information, and the symptoms were improved in over 70% (17/24) of them. CONCLUSION Our data demonstrated the analytic performance of our mNGS pipeline for pathogen detection using a large clinical cohort and strongly supports the notion that in clinical practice, mNGS represents a valuable supplementary tool to CTs to rapidly determine etiological factors of various types of infection and to guide treatment decision-making.
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Affiliation(s)
- Jie Xu
- Clinical Laboratory Center, The First Affiliated Hospital of Soochow University, Suzhou, 215031, China
| | - Peng Zhou
- Center of Translational Medicine and Clinical Laboratory, Dushu Lake Hospital Affiliated to Soochow University, Suzhou, 215028, China
| | - Jia Liu
- Dinfectome Inc., NanjingJiangsu, 210000, China
| | - Lina Zhao
- Department of Laboratory Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Hailong Fu
- Clinical Laboratory Center, The First Affiliated Hospital of Soochow University, Suzhou, 215031, China
| | - Qingzhen Han
- Center of Translational Medicine and Clinical Laboratory, Dushu Lake Hospital Affiliated to Soochow University, Suzhou, 215028, China
| | - Lin Wang
- Center of Translational Medicine and Clinical Laboratory, Dushu Lake Hospital Affiliated to Soochow University, Suzhou, 215028, China
| | - Weiwei Wu
- Dinfectome Inc., NanjingJiangsu, 210000, China
| | - Qiuxiang Ou
- Dinfectome Inc., NanjingJiangsu, 210000, China
| | - Yutong Ma
- Dinfectome Inc., NanjingJiangsu, 210000, China
| | - Jun He
- Clinical Laboratory Center, The First Affiliated Hospital of Soochow University, Suzhou, 215031, China.
- HLA Laboratory of Jiangsu Institute of Hematology, Collaborative Innovation Center of Hematology, The First Affiliated Hospital of Soochow University, 13/F (West), Hospital Comprehensive Building, No.899 Ping Hai Road, Suzhou, 215031, Jiangsu, China.
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Wang J, Ye J, Yang L, Chen X, Fang H, Liu Z, Xia G, Zhang Y, Zhang Z. Inconsistency analysis between metagenomic next-generation sequencing results of cerebrospinal fluid and clinical diagnosis with suspected central nervous system infection. BMC Infect Dis 2022; 22:764. [PMID: 36180859 PMCID: PMC9523998 DOI: 10.1186/s12879-022-07729-0] [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: 04/11/2022] [Accepted: 09/09/2022] [Indexed: 12/02/2022] Open
Abstract
Background Recently, with the rapid progress of metagenomic next-generation sequencing (mNGS), inconsistency between mNGS results and clinical diagnoses has become more common. There is currently no reasonable explanation for this, and the interpretation of mNGS reports still needs to be standardised. Methods A retrospective analysis was conducted on 47 inpatients with suspected central nervous system (CNS) infections, and clinical data were recorded. The final diagnosis was determined by an expert group based on the patient’s clinical manifestation, laboratory examination, and response to treatment. mNGS results were compared with the final diagnosis, and any inconsistencies that occurred were investigated. Finally, the credibility of mNGS results was evaluated using the integral approach, which consists of three parts: typical clinical features, positive results with the traditional method, and cerebrospinal fluid cells ≥ 100 (× 106/L) or protein ≥ 500 mg/L, with one point for each item. Results Forty-one patients with suspected CNS infection were assigned to infected (ID, 31/41, 75.61%) and non-infected groups (NID, 10/41, 24.39%) after assessment by a panel of experts according to the composite diagnostic criteria. For mNGS-positive results, 20 of the 24 pathogens were regarded as contaminants when the final score was ≤ 1. The remaining 11 pathogens detected by mNGS were all true positives, which was consistent with the clinical diagnosis when the score was ≥ 2. For mNGS negative results, when the score was ≥ 2, the likelihood of infection may be greater than when the score is ≤ 1. Conclusion The integral method is effective for evaluating mNGS results. Regardless of whether the mNGS result was positive or negative, the possibility of infection was greater when the score was ≥ 2. A negative mNGS result does not necessarily indicate that the patient was not clinically infected, and, therefore, clinical features are more important. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-022-07729-0.
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Affiliation(s)
- Jin Wang
- Department of Infectious Diseases, The Second Hospital of Anhui Medical University, Hefei, 230601, China
| | - Jun Ye
- Department of Infectious Diseases, The Second Hospital of Anhui Medical University, Hefei, 230601, China
| | - Liqi Yang
- Department of Infection Management, The Second Hospital of Anhui Medical University, Hefei, China
| | - Xiangfeng Chen
- Department of Infection Management, The Second Hospital of Anhui Medical University, Hefei, China
| | - Haoshu Fang
- Department of Pathophysiology, Anhui Medical University, Hefei, China
| | - Zhou Liu
- Department of Clinical Laboratory, The Second Hospital of Anhui Medical University, Hefei, China
| | - Guomei Xia
- Department of Infectious Diseases, The Second Hospital of Anhui Medical University, Hefei, 230601, China
| | - Yafei Zhang
- Department of Infectious Diseases, The Second Hospital of Anhui Medical University, Hefei, 230601, China
| | - Zhenhua Zhang
- Department of Infectious Diseases, The Second Hospital of Anhui Medical University, Hefei, 230601, China.
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Qu C, Chen Y, Ouyang Y, Huang W, Liu F, Yan L, Lu R, Zeng Y, Liu Z. Metagenomics next-generation sequencing for the diagnosis of central nervous system infection: A systematic review and meta-analysis. Front Neurol 2022; 13:989280. [PMID: 36203993 PMCID: PMC9530978 DOI: 10.3389/fneur.2022.989280] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 08/29/2022] [Indexed: 11/13/2022] Open
Abstract
Objective It is widely acknowledged that central nervous system (CNS) infection is a serious infectious disease accompanied by various complications. However, the accuracy of current detection methods is limited, leading to delayed diagnosis and treatment. In recent years, metagenomic next-generation sequencing (mNGS) has been increasingly adopted to improve the diagnostic yield. The present study sought to evaluate the value of mNGS in CNS infection diagnosis. Methods Following the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) 2022 guidelines, we searched relevant articles published in seven databases, including PubMed, Web of Science, and Cochrane Library, published from January 2014 to January 2022. High-quality articles related to mNGS applications in the CNS infection diagnosis were included. The comparison between mNGS and the gold standard of CNS infection, such as culture, PCR or serology, and microscopy, was conducted to obtain true positive (TP), true negative (TN), false positive (FP), and false negative (FN) values, which were extracted for sensitivity and specificity calculation. Results A total of 272 related studies were retrieved and strictly selected according to the inclusion and exclusion criteria. Finally, 12 studies were included for meta-analysis and the pooled sensitivity was 77% (95% CI: 70–82%, I2 = 39.69%) and specificity was 96% (95% CI: 93–98%, I2 = 72.07%). Although no significant heterogeneity in sensitivity was observed, a sub-group analysis was conducted based on the pathogen, region, age, and sample pretreatment method to ascertain potential confounders. The area under the curve (AUC) of the summary receiver operating characteristic curve (SROC) of mNGS for CNS infection was 0.91 (95% CI: 0.88–0.93). Besides, Deek's Funnel Plot Asymmetry Test indicated no publication bias in the included studies (Figure 3, p > 0.05). Conclusion Overall, mNGS exhibits good sensitivity and specificity for diagnosing CNS infection and diagnostic performance during clinical application by assisting in identifying the pathogen. However, the efficacy remains inconsistent, warranting subsequent studies for further performance improvement during its clinical application. Study registration number INPLASY202120002
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Affiliation(s)
- Chunrun Qu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- Xiangya School of Medicine, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Yu Chen
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Yuzhen Ouyang
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Weicheng Huang
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Fangkun Liu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Luzhe Yan
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Ruoyu Lu
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Yu Zeng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Yu Zeng
| | - Zhixiong Liu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Zhixiong Liu
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Zoghi S, Masoudi MS, Taheri R. The Evolving Role of Next Generation Sequencing in Pediatric Neurosurgery: a Call for Action for Research, Clinical Practice, and Optimization of Care. World Neurosurg 2022; 168:232-242. [PMID: 36122859 DOI: 10.1016/j.wneu.2022.09.056] [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: 07/10/2022] [Revised: 09/12/2022] [Accepted: 09/13/2022] [Indexed: 11/29/2022]
Abstract
NGS (Next-Generation Sequencing) is one of the most promising technologies that have truly revolutionized many aspects of clinical practice in recent years. It has been and is increasingly applied in many disciplines of medicine; however, it appears that pediatric neurosurgery despite its great potential has not truly embraced this new technology and is hesitant to employ it in its routine practice and guidelines. In this review, we briefly summarized the developments that lead to the establishment of NGS technology, reviewed the current applications and potentials of NGS in the disorders treated by pediatric neurosurgeons, and lastly discuss the steps we need to take to better harness NGS in pediatric neurosurgery.
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Affiliation(s)
- Sina Zoghi
- Department of Neurosurgery, Shiraz University of Medical Sciences, Shiraz, Iran; Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Reza Taheri
- Department of Neurosurgery, Shiraz University of Medical Sciences, Shiraz, Iran.
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Zheng YR, Lin SH, Chen YK, Cao H, Chen Q. Application of metagenomic next-generation sequencing in the detection of pathogens in bronchoalveolar lavage fluid of infants with severe pneumonia after congenital heart surgery. Front Microbiol 2022; 13:954538. [PMID: 35992666 PMCID: PMC9391048 DOI: 10.3389/fmicb.2022.954538] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 07/08/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundMetagenomic next-generation sequencing (mNGS) has become a valuable diagnostic tool in clinical etiology detection due to its rapidity, accuracy, and high throughput. However, the role of this technology in the diagnosis and treatment of infants with severe pneumonia after congenital heart surgery is still unclear.MethodsWe conducted a retrospective cohort study of infants with severe pneumonia after congenital heart surgery. Samples were collected from infants in the hospital’s cardiac intensive care unit between January 2010 and January 2022. The conventional microbiological test (CMT) group consisted of patients who underwent routine microbiological examination, and the infants’ bronchoalveolar lavage fluid was examined. The mNGS group consisted of patients who underwent mNGS and routine microbiological examinations.ResultsThe overall positive rate of mNGS was significantly higher than that of CMT (88.4 vs. 62.5%, P = 0.009). After receipt of the microbiological results, 30/43 (70%) patients in the mNGS group had a change in antibiotic use compared with 14/40 (35%) in the CMT group (P = 0.002). Subsequently, after adjusting the treatment plan according to the microbiological test results, the number of people with improved pulmonary infection in the mNGS group was significantly higher than that in the CMT group (63 vs. 28%, P < 0.05). In addition, the duration of invasive ventilation, length of CICU stay and total hospital length of stay in the mNGS group were significantly lower than those in the CMT group (P < 0.05).ConclusionmNGS is a valuable tool to determine the etiology of infants with severe pneumonia after congenital heart disease surgery. It can significantly improve the sensitivity of pathogen detection, which can help determine appropriate antimicrobial drugs, improve the diagnostic accuracy of the disease, and improve outcomes.
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Affiliation(s)
- Yi-Rong Zheng
- Department of Cardiac Surgery, Fujian Branch of Shanghai Children’s Medical Center, Fuzhou, China
- Fujian Children’s Hospital, Fuzhou, China
- Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Women and Children’s Critical Diseases Research, Fujian Maternity and Child Health Hospital, Fuzhou, China
| | - Shi-Hao Lin
- Department of Cardiac Surgery, Fujian Branch of Shanghai Children’s Medical Center, Fuzhou, China
- Fujian Children’s Hospital, Fuzhou, China
- Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Women and Children’s Critical Diseases Research, Fujian Maternity and Child Health Hospital, Fuzhou, China
| | - Yu-Kun Chen
- Department of Cardiac Surgery, Fujian Branch of Shanghai Children’s Medical Center, Fuzhou, China
- Fujian Children’s Hospital, Fuzhou, China
- Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Women and Children’s Critical Diseases Research, Fujian Maternity and Child Health Hospital, Fuzhou, China
| | - Hua Cao
- Department of Cardiac Surgery, Fujian Branch of Shanghai Children’s Medical Center, Fuzhou, China
- Fujian Children’s Hospital, Fuzhou, China
- Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Women and Children’s Critical Diseases Research, Fujian Maternity and Child Health Hospital, Fuzhou, China
| | - Qiang Chen
- Department of Cardiac Surgery, Fujian Branch of Shanghai Children’s Medical Center, Fuzhou, China
- Fujian Children’s Hospital, Fuzhou, China
- Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Women and Children’s Critical Diseases Research, Fujian Maternity and Child Health Hospital, Fuzhou, China
- *Correspondence: Qiang Chen,
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Diagnostic accuracy of the metagenomic next-generation sequencing (mNGS) for detection of bacterial meningoencephalitis: a systematic review and meta-analysis. Eur J Clin Microbiol Infect Dis 2022; 41:881-891. [PMID: 35474146 DOI: 10.1007/s10096-022-04445-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 04/12/2022] [Indexed: 11/03/2022]
Abstract
The early diagnosis of bacterial meningoencephalitis (BM/E) is difficult, and delay in diagnosis can cause complications leading to neurological impairment/death. In cases of unexplained BM/E, the metagenomic NGS (mNGS) offers an advantage over conventional methods, especially when a rare pathogen is implicated or the patient is on antibiotics. This study aims to evaluate and compare the diagnostic efficacy of mNGS for the diagnosis of BM/E using cerebrospinal fluid (CSF) specimens versus a composite reference standard (CRS). The electronic databases (Embase, PubMed, and Web of Science) were searched up to 15 June 2021. Studies such as cohort, case-control, prospective, or retrospective studies that assessed the diagnostic efficacy of mNGS in suspected bacterial meningitis/encephalitis cases were included. Ten studies met the inclusion criteria, including three retrospective and seven prospective studies. The sensitivity of mNGS for diagnosis of BM/E from CSF samples ranged from 33 (95% CI: 13-62) to 98% (95% CI: 76-99). The specificity of mNGS ranged from 67 (95% CI: 55-78) to 98% (95% CI: 95-99). The estimated AUC (area under curve) by hierarchical summary receiver operating characteristic (HSROC) of the studies being analyzed was 0.912. The meta-regression analysis demonstrated that the different types of studies (single-center vs. multi-center) had an effect on the specificity of mNGS for BM/E compared with CRS (90% vs. 96%, meta-regression P < 0.05). The current analysis revealed moderate diagnostic accuracy of mNGS. This approach can be helpful, especially in cases of undiagnosed BM/E by identification of organism and subsequently accelerating the patient management.
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Karvouniaris M, Brotis A, Tsiakos K, Palli E, Koulenti D. Current Perspectives on the Diagnosis and Management of Healthcare-Associated Ventriculitis and Meningitis. Infect Drug Resist 2022; 15:697-721. [PMID: 35250284 PMCID: PMC8896765 DOI: 10.2147/idr.s326456] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 02/05/2022] [Indexed: 12/31/2022] Open
Abstract
Ventriculitis or post-neurosurgical meningitis or healthcare-associated ventriculitis and meningitis (VM) is a severe infection that complicates central nervous system operations or is related to the use of neurosurgical devices or drainage catheters. It can further deteriorate patients who have already presented significant neurologic injury and is associated with high morbidity, mortality, and poor functional outcome. VM can be difficult to distinguish from aseptic meningitis, inflammation that follows hemorrhagic strokes and neurosurgical operations. The associated microorganisms can be either skin flora or nosocomial pathogens, most commonly, Gram-negative bacteria. Classical microbiology can fail to isolate the culprit pathogen. Novel cerebrospinal fluid (CSF) biomarkers and molecular microbiology can fill the diagnostic gap and expedite pathogen identification and treatment. The pathogens may demonstrate significant resistant patterns and their antibiotic treatment can be difficult, as many important drug classes, including the beta-lactams and the glycopeptides, hardly penetrate to the CSF, and do not achieve therapeutic levels at the site of the infection. Treatment modifications, such as higher daily dose and prolonged or continuous administration, might increase antibiotic levels in the site of infection and facilitate pathogens clearance. However, in the case of therapeutic failure or infection due to difficult-to-treat bacteria, the direct antibiotic instillation into the CSF, in addition to the intravenous antibiotic delivery, may help in the resolution of infection. However, intraventricular antibiotic therapy may result in aseptic meningitis and seizures, concerning the administration of aminoglycosides, polymyxins, and vancomycin. Meanwhile, bacteria form biofilms on the catheter or the device that should routinely be removed. Novel neurosurgical treatment modalities comprise endoscopic evacuation of debris and irrigation of the ventricles. VM prevention includes perioperative antibiotics, antimicrobial impregnated catheters, and the implementation of standardized protocols, regarding catheter insertion and manipulation.
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Affiliation(s)
- Marios Karvouniaris
- Intensive Care Unit, AHEPA University Hospital, Thessaloniki, Greece
- Correspondence: Marios Karvouniaris, ACHEPA University Hospital, S.Kiriakidi 1, Thessaloniki, 54636, Greece, Tel +302313303645, Fax +302313303096, Email
| | - Alexandros Brotis
- Neurosurgery Department, University Hospital of Larissa, Larissa, Greece
| | | | - Eleni Palli
- Intensive Care Unit, University Hospital of Larissa, Larissa, Greece
| | - Despoina Koulenti
- Second Critical Care Department, Attikon University Hospital, Athens, Greece
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
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Cai S, Yang Y, Pan J, Miao Q, Jin W, Ma Y, Zhou C, Gao X, Wang C, Hu B. The clinical value of valve metagenomic next-generation sequencing when applied to the etiological diagnosis of infective endocarditis. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1490. [PMID: 34805352 PMCID: PMC8573444 DOI: 10.21037/atm-21-2488] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/04/2021] [Indexed: 12/22/2022]
Abstract
Background Metagenomic next-generation sequencing (mNGS) is widely applied in the etiological diagnosis of infectious diseases. However, the clinical practice of mNGS in infective endocarditis (IE) is relatively less studied. This research aimed to assess the etiological diagnostic value of valve mNGS in IE. Methods We retrospectively analyzed 49 IE patients who underwent cardiac valve surgery in Zhongshan Hospital, Fudan University, Shanghai from 1 June 2018 to 30 November 2020. Among these IE patients, 28 were culture positive and 21 were culture negative. The culture results of the culture-positive IE patients were set as gold standard to assess the sensitivity and specificity of valve mNGS in the etiological diagnosis of IE. We studied the positive detection rate of pathogens by valve mNGS among the culture-negative IE patients. During the same period, we also collected the resected valves of 8 patients with non-infective valvular diseases for mNGS as negative controls. Results The valve mNGS results of the culture-positive IE patients were the exact same as their culture results. Both the sensitivity and specificity of valve mNGS were 100%. The positive detection rate of pathogens by valve mNGS was 100% among the culture-negative IE patients. The stringent mapped reads number of genera (SMRNG), relative abundance of genera, stringent mapped reads number of species (SMRN), relative abundance of species, and coverage rate of valve mNGS results were significantly higher in culture-positive IE participants than in culture-negative IE participants. The valve mNGS results of the 8 participants with non-infective valvular diseases were all negative. Conclusions Valve mNGS is a promising technology for the etiological diagnosis of IE, especially culture-negative IE, and it may be used to guide precise antibiotic treatment after surgery.
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Affiliation(s)
- Sishi Cai
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Ye Yang
- Department of Cardiac Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jue Pan
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Qing Miao
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Wenting Jin
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yuyan Ma
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chunmei Zhou
- Department of Microbiology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xiaodong Gao
- Department of Hospital Infection Management, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chunsheng Wang
- Department of Cardiac Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Bijie Hu
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China.,Department of Hospital Infection Management, Zhongshan Hospital, Fudan University, Shanghai, China
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