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Balks J, Grumaz S, Mazzitelli S, Neder U, Lemloh L, Melaku T, Glaser K, Mueller A, Kipfmueller F. Microbial cell-free DNA-sequencing as an addition to conventional diagnostics in neonatal sepsis. Pediatr Res 2024:10.1038/s41390-024-03448-1. [PMID: 39143203 DOI: 10.1038/s41390-024-03448-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 06/04/2024] [Accepted: 07/24/2024] [Indexed: 08/16/2024]
Abstract
BACKGROUND Bloodstream infections remain a challenge for neonatologists, as traditional culture-based methods are time-consuming and rely on adequate blood volume. Next-generation sequencing (NGS) offers an alternative, as it can identify microbial cell-free DNA (mcfDNA) in a small blood sample, providing rapid pathogen detection. This study aimed to assess the diagnostic performance of DISQVER®-NGS compared to blood cultures in neonatal patients with suspected sepsis. METHODS In neonates with suspected sepsis, blood cultures and samples for NGS were prospectively collected. Patients were divided into four categories: 1) sepsis, blood culture positive, 2) clinical sepsis, culture negative, 3) suspected sepsis, 4) validation cohort. RESULTS NGS detected bacterial, viral or fungal mcfDNA in 24 of 82 samples. Blood cultures were collected in 46 of 84 patients (15/46 positive). DISQVER® correctly identified pathogens in 9/15 patients with a positive blood culture, two with intrinsic resistance to their antibiotic regimen. In seven samples NGS reported the mcfDNA of bacteria that could have theoretically grown in culture but did not. CONCLUSIONS NGS may enhance sensitivity in sepsis diagnostics by detecting mcfDNA in neonates with suspected sepsis. Interpreting NGS results requires correlation with clinical data, laboratory values, and routine microbiological tests for a comprehensive understanding of the patient's condition. IMPACT Conventional blood culture methods have limitations in accuracy and turnaround time. The study aimed to investigate the diagnostic performance of the Next-Generation Sequencing method DISQVER® compared to traditional blood cultures in neonatal patients with suspected sepsis. Our findings suggest that NGS has the potential to augment the precision of conventional diagnostic techniques, can lead to improved detection of pathogens and targeted treatment approaches in neonatal sepsis. It is emphasized that further validation and integration with clinical and microbiological data are required to ensure optimal clinical utility.
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Affiliation(s)
- Julian Balks
- Division of Neonatology and Pediatric Intensive Care, Children's Hospital, University of Bonn, Bonn, Germany
- Institute of Medical Microbiology, Immunology and Parasitology (IMMIP), University Hospital Bonn, Bonn, Germany
| | | | | | | | - Lotte Lemloh
- Division of Neonatology and Pediatric Intensive Care, Children's Hospital, University of Bonn, Bonn, Germany
| | - Tamene Melaku
- Division of Neonatology and Pediatric Intensive Care, Children's Hospital, University of Bonn, Bonn, Germany
| | - Kirsten Glaser
- Division of Neonatology, Department of Women's and Children's Health, University Medical Center Leipzig, Leipzig, Germany
| | - Andreas Mueller
- Division of Neonatology and Pediatric Intensive Care, Children's Hospital, University of Bonn, Bonn, Germany
| | - Florian Kipfmueller
- Division of Neonatology and Pediatric Intensive Care, Children's Hospital, University of Bonn, Bonn, Germany.
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Liu Y, Wu W, Xiao Y, Zou H, Hao S, Jiang Y. Application of metagenomic next-generation sequencing and targeted metagenomic next-generation sequencing in diagnosing pulmonary infections in immunocompetent and immunocompromised patients. Front Cell Infect Microbiol 2024; 14:1439472. [PMID: 39165919 PMCID: PMC11333343 DOI: 10.3389/fcimb.2024.1439472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Accepted: 07/09/2024] [Indexed: 08/22/2024] Open
Abstract
Background Metagenomic next-generation sequencing (mNGS) technology has been widely used to diagnose various infections. Based on the most common pathogen profiles, targeted mNGS (tNGS) using multiplex PCR has been developed to detect pathogens with predesigned primers in the panel, significantly improving sensitivity and reducing economic burden on patients. However, there are few studies on summarizing pathogen profiles of pulmonary infections in immunocompetent and immunocompromised patients in Jilin Province of China on large scale. Methods From January 2021 to December 2023, bronchoalveolar lavage fluid (BALF) or sputum samples from 546 immunocompetent and immunocompromised patients with suspected community-acquired pneumonia were collected. Pathogen profiles in those patients on whom mNGS was performed were summarized. Additionally, we also evaluated the performance of tNGS in diagnosing pulmonary infections. Results Combined with results of mNGS and culture, we found that the most common bacterial pathogens were Pseudomonas aeruginosa, Klebsiella pneumoniae, and Acinetobacter baumannii in both immunocompromised and immunocompetent patients with high detection rates of Staphylococcus aureus and Enterococcus faecium, respectively. For fungal pathogens, Pneumocystis jirovecii was commonly detected in patients, while fungal infections in immunocompetent patients were mainly caused by Candida albicans. Most of viral infections in patients were caused by Human betaherpesvirus 5 and Human gammaherpesvirus 4. It is worth noting that, compared with immunocompetent patients (34.9%, 76/218), more mixed infections were found in immunocompromised patients (37.8%, 14/37). Additionally, taking final comprehensive clinical diagnoses as reference standard, total coincidence rate of BALF tNGS (81.4%, 48/59) was much higher than that of BALF mNGS (40.0%, 112/280). Conclusions Our findings supplemented and classified the pathogen profiles of pulmonary infections in immunocompetent and immunocompromised patients in Jilin Province of China. Most importantly, our findings can accelerate the development and design of tNGS specifically used for regional pulmonary infections.
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Affiliation(s)
- Yong Liu
- Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, China
| | - Wencai Wu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - Yunping Xiao
- Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, China
| | - Hongyan Zou
- Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, China
| | - Sijia Hao
- Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, China
| | - Yanfang Jiang
- Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, China
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Cai X, Sun C, Zhong H, Cai Y, Cao M, Wang L, Sun W, Tao Y, Ma G, Huang B, Yan S, Zhong J, Wang J, Lu Y, Guan Y, Song M, Wang Y, Li Y, Su X. The value of metagenomic next-generation sequencing with different nucleic acid extracting methods of cell-free DNA or whole-cell DNA in the diagnosis of non-neutropenic pulmonary aspergillosis. Front Cell Infect Microbiol 2024; 14:1398190. [PMID: 39135636 PMCID: PMC11317373 DOI: 10.3389/fcimb.2024.1398190] [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: 03/09/2024] [Accepted: 07/09/2024] [Indexed: 08/15/2024] Open
Abstract
Purpose Metagenomic next-generation sequencing(mNGS) is a novel molecular diagnostic technique. For nucleic acid extraction methods, both whole-cell DNA (wcDNA) and cell-free DNA (cfDNA) are widely applied with the sample of bronchoalveolar lavage fluid (BALF). We aim to evaluate the clinical value of mNGS with cfDNA and mNGS with wcDNA for the detection of BALF pathogens in non-neutropenic pulmonary aspergillosis. Methods mNGS with BALF-cfDNA, BALF-wcDNA and conventional microbiological tests (CMTs) were performed in suspected non-neutropenic pulmonary aspergillosis. The diagnostic value of different assays for pulmonary aspergillosis was compared. Results BALF-mNGS (cfDNA, wcDNA) outperformed CMTs in terms of microorganisms detection. Receiver operating characteristic (ROC) analysis indicated BALF-mNGS (cfDNA, wcDNA) was superior to culture and BALF-GM. Combination diagnosis of either positive for BALF-mNGS (cfDNA, wcDNA) or CMTs is more sensitive than CMTs alone in the diagnosis of pulmonary aspergillosis (BALF-cfDNA+CMTs/BALF-wcDNA+CMTs vs. CMTs: ROC analysis: 0.813 vs.0.66, P=0.0142/0.796 vs.0.66, P=0.0244; Sensitivity: 89.47% vs. 47.37%, P=0.008/84.21% vs. 47.37%, P=0.016). BALF-cfDNA showed a significantly greater reads per million (RPM) than BALF-wcDNA. The area under the ROC curve (AUC) for RPM of Aspergillus detected by BALF-cfDNA, used to predict "True positive" pulmonary aspergillosis patients, was 0.779, with a cut-off value greater than 4.5. Conclusion We propose that the incorporation of BALF-mNGS (cfDNA, wcDNA) with CMTs improves diagnostic precision in the identification of non-neutropenic pulmonary aspergillosis when compared to CMTs alone. BALF-cfDNA outperforms BALF-wcDNA in clinical value.
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Affiliation(s)
- Xiaomin Cai
- Department of Respiratory and Critical Care Medicine, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
- Department of Respiratory and Critical Medicine, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Chao Sun
- Department of Respiratory and Critical Medicine, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Huanhuan Zhong
- Department of Respiratory and Critical Medicine, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Suzhou University, Suzhou, China
| | - Yuchen Cai
- Department of Respiratory and Critical Medicine, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Min Cao
- Department of Respiratory and Critical Care Medicine, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Li Wang
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Wenkui Sun
- Department of Respiratory and Critical Care Medicine, Jiangsu Province Hospital, The First Affiliated of Nanjing Medical University, Nanjing, China
| | - Yujian Tao
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Yangzhou University, Yangzhou, China
| | - Guoer Ma
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Baoju Huang
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Shengmei Yan
- Department of Respiratory and Critical Medicine, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Jinjin Zhong
- Department of Respiratory and Critical Medicine, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Jiamei Wang
- Department of Respiratory and Critical Care Medicine, Jinling Hospital, Nanjing Medical University, Nanjing, China
| | - Yajie Lu
- Department of Respiratory and Critical Medicine, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Yuanlin Guan
- Department of Research and Development, Hugobiotech Co., Ltd., Beijing, China
| | - Mengyue Song
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Suzhou University, Suzhou, China
| | - Yujie Wang
- Department of Respiratory and Critical Medicine, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Yuanyuan Li
- Department of Respiratory and Critical Medicine, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Xin Su
- Department of Respiratory and Critical Care Medicine, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
- Department of Respiratory and Critical Medicine, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
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Song J, Liu S, Xie Y, Zhang C, Xu C. Diagnostic value of DNA or RNA-based metagenomic next-generation sequencing in lower respiratory tract infections. Heliyon 2024; 10:e30712. [PMID: 38765131 PMCID: PMC11098835 DOI: 10.1016/j.heliyon.2024.e30712] [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: 01/17/2024] [Revised: 05/02/2024] [Accepted: 05/02/2024] [Indexed: 05/21/2024] Open
Abstract
Objectives We aimed to evaluate and compare the diagnostic performance of RNA-mNGS and DNA-mNGS workflow in bacterial pneumonia, fungal pneumonia and tuberculosis. Methods A total of 134 cases suspected pneumonia undergoing both DNA and RNA based mNGS of bronchoalveolar lavage fluid (BALF) and also traditional etiological examination were evaluated retrospectively.Sensitivity, specificity, PPV, NPV and accuracy rate of DNA and RNA based mNGS were estimated. Results In the diagnosis performance of bacterial pathogens in LRTIs,the specificity of RNA-mNGS was higher than that of DNA-mNGS(82.3 % vs. 61.9 %, P < 0.01). There was no significant difference of sensitivity between the two process(71.4 % vs. 85.7 %, P = 0.375).In the diagnosis performance of fungal pathogens in LRTIs,the specificity of RNA-mNGS was higher than that of DNA-mNGS (72.3 % vs. 27.3 %,p < 0.001). There was no significant difference of sensitivity between the two process(96.5 % vs. 98.8 %,p = 0.125).In the diagnosis performance of tuberculosis in LRTIs,the sensitivity of DNA-mNGS was higher than that of RNA-mNGS (91.7 % vs. 33.3 %,p = 0.016),the specificity was similar in the two process (100 %). Conclusions RNA-mNGS may reduced the misdiagnosis rate of bacterial and fungal pathogens in LRTIs.Compared to RNA-mNGS, DNA-mNGS may could improve the diagnostic rate of tuberculosis.
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Affiliation(s)
- Jiafu Song
- Department of Respiratory and Critical Care Medicine, The Affiliated Lianyungang Hospital of Xuzhou Medical University, Lianyungang, Jiangsu, China
| | - Suxia Liu
- Department of Critical Care Medicine, The Affiliated Lianyungang Hospital of Xuzhou Medical University, Lianyungang, Jiangsu, China
| | - Yongpeng Xie
- Department of Critical Care Medicine, The Affiliated Lianyungang Hospital of Xuzhou Medical University, Lianyungang, Jiangsu, China
| | - Chen Zhang
- Department of Medicine, Dinfectome Inc., Nanjing, Jiangsu, China
| | - Caiyun Xu
- Department of Critical Care Medicine, The Affiliated Lianyungang Hospital of Xuzhou Medical University, Lianyungang, Jiangsu, China
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Chai S, Wang C, Liu Y, Xia J, Wang X, Shi J. Distribution Patterns of Pathogens Causing Lower Respiratory Tract Infection Based on Metagenomic Next-Generation Sequencing. Infect Drug Resist 2023; 16:6635-6645. [PMID: 37840830 PMCID: PMC10576460 DOI: 10.2147/idr.s421383] [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: 05/30/2023] [Accepted: 09/14/2023] [Indexed: 10/17/2023] Open
Abstract
Purpose Lower Respiratory Tract Infection (LRTI) is a leading cause of morbidity and mortality worldwide. In this study, the distribution patterns of causative pathogens in LRTI were evaluated within a city-level hospital by combining conventional microbiological tests (CMT) with metagenomic next-generation sequencing (mNGS). Patients and Methods This retrospective cohort study involved 160 patients suspected of having LRTI in a single center. Specimens, including bronchoalveolar lavage fluid (BALF), blood, tissue, sputum, and pus were utilized to identify pathogens. The seasonal prevalence of pathogens and co-pathogens involved in multiple infections was analyzed. Results A total of 137 patients with 156 samples were included in this study. Pseudomonas aeruginosa, Corynebacterium striatum, Klebsiella pneumoniae, Candida, and human herpesvirus were the top prevalent pathogens. We observed seasonal dynamic variation in the top prevalent bacteria (Pseudomonas aeruginosa and Klebsiella pneumoniae) and herpesvirus (Epstein-Barr virus and Human herpesvirus-7). The majority of patients had single bacterial infections, followed by instances of bacterial-viral co-infections, as well as mixed infections involving bacteria, fungi, and viruses. Notably, the spectrum of co-infecting pathogens was broader among the elderly population, and positive Spearman correlations were observed among these co-infecting pathogens. Conclusion Co-infections were prevalent among patients with LRTI, and the pathogens displayed distinct seasonal distribution patterns. The findings underscored the significance of comprehending pathogen distribution and epidemic patterns, which can serve as a basis for early etiological identification.
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Affiliation(s)
- Shukun Chai
- Department of Respiratory Medicine, Shijiazhuang People’s Hospital, Shijiazhuang, Hebei, 050051, People’s Republic of China
| | - Chuan Wang
- Department of Respiratory Medicine, Shijiazhuang People’s Hospital, Shijiazhuang, Hebei, 050051, People’s Republic of China
| | - Yi Liu
- Department of Respiratory Medicine, Shijiazhuang People’s Hospital, Shijiazhuang, Hebei, 050051, People’s Republic of China
| | - Jingrong Xia
- Department of Respiratory Medicine, Shijiazhuang People’s Hospital, Shijiazhuang, Hebei, 050051, People’s Republic of China
| | - Xiaolin Wang
- Department of Respiratory Medicine, Shijiazhuang People’s Hospital, Shijiazhuang, Hebei, 050051, People’s Republic of China
| | - Jinying Shi
- Department of Respiratory Medicine, Shijiazhuang People’s Hospital, Shijiazhuang, Hebei, 050051, People’s Republic of China
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Abstract
PURPOSE OF REVIEW The coronavirus disease 2019 pandemic demonstrated broad utility of pathogen sequencing with rapid methodological progress alongside global distribution of sequencing infrastructure. This review considers implications for now moving clinical metagenomics into routine service, with respiratory metagenomics as the exemplar use-case. RECENT FINDINGS Respiratory metagenomic workflows have completed proof-of-concept, providing organism identification and many genotypic antimicrobial resistance determinants from clinical samples in <6 h. This enables rapid escalation or de-escalation of empiric therapy for patient benefit and reducing selection of antimicrobial resistance, with genomic-typing available in the same time-frame. Attention is now focussed on demonstrating clinical, health-economic, accreditation, and regulatory requirements. More fundamentally, pathogen sequencing challenges the traditional culture-orientated time frame of microbiology laboratories, which through automation and centralisation risks becoming increasingly separated from the clinical setting. It presents an alternative future where infection experts are brought together around a single genetic output in an acute timeframe, aligning the microbiology target operating model with the wider human genomic and digital strategy. SUMMARY Pathogen sequencing is a transformational proposition for microbiology laboratories and their infectious diseases, infection control, and public health partners. Healthcare systems that link output from routine clinical metagenomic sequencing, with pandemic and antimicrobial resistance surveillance, will create valuable tools for protecting their population against future infectious diseases threats.
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Affiliation(s)
- Jonathan D Edgeworth
- Department of Infectious Diseases, Guy's & St Thomas' NHS Foundation Trust & Department of Infectious Diseases, Kings College London, UK
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Wu X, Liang R, Xiao Y, Liu H, Zhang Y, Jiang Y, Liu M, Tang J, Wang W, Li W, Hu L, Wang A, Yu F, Xia H. Application of targeted next generation sequencing technology in the diagnosis of Mycobacterium Tuberculosis and first line drugs resistance directly from cell-free DNA of bronchoalveolar lavage fluid. J Infect 2023; 86:399-401. [PMID: 36706961 DOI: 10.1016/j.jinf.2023.01.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/26/2023]
Affiliation(s)
- Xiaocui Wu
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Ruobing Liang
- Department of Scientific Affaires, Hugobiotech Co., Ltd., Beijing, China
| | - Yanqun Xiao
- Department of Molecular Biology, Shanghai Centre for Clinical Laboratory, Shanghai, China
| | - Huan Liu
- Department of Scientific Affaires, Hugobiotech Co., Ltd., Beijing, China
| | - Ye Zhang
- Department of Scientific Affaires, Hugobiotech Co., Ltd., Beijing, China
| | - Yue Jiang
- Department of Scientific Affaires, Hugobiotech Co., Ltd., Beijing, China
| | - Mengdi Liu
- Department of Scientific Affaires, Hugobiotech Co., Ltd., Beijing, China
| | - Jianzhong Tang
- Department of Scientific Affaires, Hugobiotech Co., Ltd., Beijing, China
| | - Wei Wang
- Department of Scientific Affaires, Hugobiotech Co., Ltd., Beijing, China
| | - Wei Li
- Department of Scientific Affaires, Hugobiotech Co., Ltd., Beijing, China
| | - Long Hu
- Department of Scientific Affaires, Hugobiotech Co., Ltd., Beijing, China
| | - Aihua Wang
- Department of Laboratory Medicine, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Fangyou Yu
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China.
| | - Han Xia
- Department of Scientific Affaires, Hugobiotech Co., Ltd., Beijing, China.
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