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Li Z, Tan L, Zhang J, Long Q, Chen Z, Xiang Z, Wu W, Guo Z, Liu H, Hu B, Yang B, Hu M. Diagnostic performance of metagenomic sequencing in patients with suspected infection: a large-scale retrospective study. Front Cell Infect Microbiol 2024; 14:1463081. [PMID: 39310785 PMCID: PMC11412945 DOI: 10.3389/fcimb.2024.1463081] [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: 07/11/2024] [Accepted: 08/12/2024] [Indexed: 09/25/2024] Open
Abstract
Background Metagenomic next-generation sequencing (mNGS) has been widely reported to identify pathogens in infectious diseases (IDs). In this work, we intended to investigate the diagnostic value and clinical acceptance of paired-samples mNGS as compared to the culture method. Methods A total of 361 patients with suspected infection were retrospectively included. With reference to the clinical diagnosis, we compared the diagnostic performance and clinical acceptance in pathogen detection between mNGS and culture tests. Moreover, the pathogen concordance of paired blood and respiratory tract (RT) samples in mNGS assay was investigated. Results Among 511 samples, 62.04% were shown to be pathogen positive by mNGS, and that for clinical diagnosis was 51.86% (265/511). When compared to culture assay (n = 428), mNGS had a significantly higher positivity rate (51.87% vs. 33.18%). With reference to the clinical diagnosis, the sensitivity of mNGS outperformed that of culture (89.08% vs. 56.72%). Importantly, mNGS exhibited a clinically accepted rate significantly superior to that of culture. In addition, the mNGS result from 53 paired blood and RT samples showed that most pairs were pathogen positive by both blood and RT, with pathogens largely being partially matched. Conclusion Through this large-scale study, we further illustrated that mNGS had a clinically accepted rate and sensitivity superior to those of the traditional culture method in diagnosing infections. Moreover, blood and paired RT samples mostly shared partial-matched positive pathogens, especially for pathogens with abundant read numbers in RT, indicating that both blood and RT mNGS can aid the identification of pathogens for respiratory system infection.
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Affiliation(s)
- Ziyang Li
- Center for Clinical Molecular Diagnostics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Li Tan
- Center for Clinical Molecular Diagnostics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jialiang Zhang
- Center for Clinical Molecular Diagnostics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qichen Long
- Center for Clinical Molecular Diagnostics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhiyang Chen
- Center for Clinical Molecular Diagnostics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhongyuan Xiang
- Center for Clinical Molecular Diagnostics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Weimin Wu
- Center for Clinical Molecular Diagnostics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhe Guo
- Center for Clinical Molecular Diagnostics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Huifang Liu
- Center for Infectious Diseases, Vision Medicals Co., Ltd, Guangzhou, Guangdong, China
| | - Bingxue Hu
- Center for Infectious Diseases, Vision Medicals Co., Ltd, Guangzhou, Guangdong, China
| | - Bin Yang
- Center for Infectious Diseases, Vision Medicals Co., Ltd, Guangzhou, Guangdong, China
| | - Min Hu
- Center for Clinical Molecular Diagnostics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
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Rimoldi SG, Tamoni A, Rizzo A, Longobardi C, Pagani C, Salari F, Matinato C, Vismara C, Gagliardi G, Cutrera M, Gismondo MR. Evaluation of 16S-Based Metagenomic NGS as Diagnostic Tool in Different Types of Culture-Negative Infections. Pathogens 2024; 13:743. [PMID: 39338934 PMCID: PMC11434932 DOI: 10.3390/pathogens13090743] [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: 08/02/2024] [Revised: 08/28/2024] [Accepted: 08/29/2024] [Indexed: 09/30/2024] Open
Abstract
Bacterial infections pose significant global health challenges, often underestimated due to difficulties in accurate diagnosis, especially when culture-based diagnostics fail. This study assesses the effectiveness of 16S-based metagenomic next generation sequencing (NGS) for identifying pathogens in culture-negative clinical samples across various medical settings. Overall, 48% of samples were collected from orthopedics, 15% from neurosurgery, and 12% in cardiac surgery, among others. The detection rate of monomicrobial infections was 68.6%, and 5.7% for polymicrobial infections. In addition, NGS detected bacteria in all samples from the lungs, head and neck, and eye specimens. Cutibacterium acnes (11%, 12/105) was the most frequent microorganism, followed by Staphylococcus epidermidis (10.4%, 11/105), and Staphylococcus aureus (9.5%, 10/105). In conclusion, 16S-targeted metagenomic sequencing enhances pathogen detection capabilities, particularly in instances where traditional cultures fail. By the combination of NGS and bacterial cultures, microbiologists might provide a more accurate diagnosis, guiding more effective treatments and potentially reducing healthcare costs associated with empirical treatments.
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Affiliation(s)
- Sara Giordana Rimoldi
- Laboratory of Clinical Microbiology, Virology and Bioemergencies, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, 20157 Milan, Italy; (S.G.R.); (A.T.); (C.L.); (C.P.); (F.S.); (G.G.); (M.C.); (M.R.G.)
| | - Alessandro Tamoni
- Laboratory of Clinical Microbiology, Virology and Bioemergencies, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, 20157 Milan, Italy; (S.G.R.); (A.T.); (C.L.); (C.P.); (F.S.); (G.G.); (M.C.); (M.R.G.)
| | - Alberto Rizzo
- Laboratory of Clinical Microbiology, Virology and Bioemergencies, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, 20157 Milan, Italy; (S.G.R.); (A.T.); (C.L.); (C.P.); (F.S.); (G.G.); (M.C.); (M.R.G.)
| | - Concetta Longobardi
- Laboratory of Clinical Microbiology, Virology and Bioemergencies, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, 20157 Milan, Italy; (S.G.R.); (A.T.); (C.L.); (C.P.); (F.S.); (G.G.); (M.C.); (M.R.G.)
| | - Cristina Pagani
- Laboratory of Clinical Microbiology, Virology and Bioemergencies, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, 20157 Milan, Italy; (S.G.R.); (A.T.); (C.L.); (C.P.); (F.S.); (G.G.); (M.C.); (M.R.G.)
| | - Federica Salari
- Laboratory of Clinical Microbiology, Virology and Bioemergencies, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, 20157 Milan, Italy; (S.G.R.); (A.T.); (C.L.); (C.P.); (F.S.); (G.G.); (M.C.); (M.R.G.)
| | - Caterina Matinato
- Microbiology and Virology Laboratory, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy;
| | - Chiara Vismara
- Clinical Microbiology Laboratory, ASST Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy;
| | - Gloria Gagliardi
- Laboratory of Clinical Microbiology, Virology and Bioemergencies, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, 20157 Milan, Italy; (S.G.R.); (A.T.); (C.L.); (C.P.); (F.S.); (G.G.); (M.C.); (M.R.G.)
| | - Miriam Cutrera
- Laboratory of Clinical Microbiology, Virology and Bioemergencies, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, 20157 Milan, Italy; (S.G.R.); (A.T.); (C.L.); (C.P.); (F.S.); (G.G.); (M.C.); (M.R.G.)
| | - Maria Rita Gismondo
- Laboratory of Clinical Microbiology, Virology and Bioemergencies, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, 20157 Milan, Italy; (S.G.R.); (A.T.); (C.L.); (C.P.); (F.S.); (G.G.); (M.C.); (M.R.G.)
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Deng QM, Zhang J, Zhang YY, Jia M, Ding DS, Fang YQ, Wang HZ, Gu HC. Diagnosis and treatment of refractory infectious diseases using nanopore sequencing technology: Three case reports. World J Clin Cases 2024; 12:5208-5216. [DOI: 10.12998/wjcc.v12.i22.5208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/29/2024] [Accepted: 06/17/2024] [Indexed: 06/30/2024] Open
Abstract
BACKGROUND Infectious diseases are still one of the greatest threats to human health, and the etiology of 20% of cases of clinical fever is unknown; therefore, rapid identification of pathogens is highly important. Traditional culture methods are only able to detect a limited number of pathogens and are time-consuming; serologic detection has window periods, false-positive and false-negative problems; and nucleic acid molecular detection methods can detect several known pathogens only once. Three-generation nanopore sequencing technology provides new options for identifying pathogens.
CASE SUMMARY Case 1: The patient was admitted to the hospital with abdominal pain for three days and cessation of defecation for five days, accompanied by cough and sputum. Nanopore sequencing of the drainage fluid revealed the presence of oral-like bacteria, leading to a clinical diagnosis of bronchopleural fistula. Cefoperazone sodium sulbactam treatment was effective. Case 2: The patient was admitted to the hospital with fever and headache, and CT revealed lung inflammation. Antibiotic treatment for Streptococcus pneumoniae, identified through nanopore sequencing of cerebrospinal fluid, was effective. Case 3: The patient was admitted to our hospital with intermittent fever and an enlarged neck mass that had persisted for more than six months. Despite antibacterial treatment, her symptoms worsened. The nanopore sequencing results indicate that voriconazole treatment is effective for Aspergillus brookii. The patient was diagnosed with mixed cell type classical Hodgkin's lymphoma with infection.
CONCLUSION Three-generation nanopore sequencing technology allows for rapid and accurate detection of pathogens in human infectious diseases.
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Affiliation(s)
- Qing-Mei Deng
- Science Island Branch, Graduate School of University of Science and Technology of China, Hefei 230031, Anhui Province, China
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Science, Hefei 230031, Anhui Province, China
- Medical Pathology Center, Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, Anhui Province, China
| | - Jian Zhang
- Medical Pathology Center, Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, Anhui Province, China
| | - Yi-Yong Zhang
- Medical Pathology Center, Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, Anhui Province, China
| | - Min Jia
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Science, Hefei 230031, Anhui Province, China
- Medical Pathology Center, Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, Anhui Province, China
| | - Du-Shan Ding
- Medical Pathology Center, Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, Anhui Province, China
| | - Yu-Qin Fang
- Medical Pathology Center, Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, Anhui Province, China
| | - Hong-Zhi Wang
- Science Island Branch, Graduate School of University of Science and Technology of China, Hefei 230031, Anhui Province, China
| | - Hong-Cang Gu
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Science, Hefei 230031, Anhui Province, China
- Medical Pathology Center, Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, Anhui Province, China
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4
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Lin Q, Yao Y, Li X, Zhang S, Guo H, Ma X, Chen W, Ru C, Wang L, Wang B, Ma Q, Zhu J, Lin X, Chen Q, Lou H, Chen Q, Chen J, Zeng Z, Zhou J, Chen Y, Yu Y, Zhou H. The application of nanopore targeted sequencing for pathogen diagnosis in bronchoalveolar lavage fluid of patients with pneumonia: a prospective multicenter study. Infect Dis (Lond) 2024; 56:128-137. [PMID: 37934028 DOI: 10.1080/23744235.2023.2276785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 10/12/2023] [Indexed: 11/08/2023] Open
Abstract
OBJECTIVE To evaluate the value of nanopore targeted sequencing in diagnosing pneumonia pathogens. METHODS This large-scale multicentre prospective study performed in 8 hospitals across China from April to October 2022. Hospitalised patients with a diagnosis of pneumonia at admission were included. Complete clinical data were collected, and bronchoalveolar lavage fluid were obtained from each patient. These samples underwent simultaneous testing using conventional microbial testing, metagenomic next-generation sequencing, and nanopore targeted sequencing. RESULTS A total of 218 patients were included. Among the 168 cases of pulmonary infection, 246 strains of pathogens were confirmed. Nanopore targeted sequencing outperformed conventional microbial testing, identifying more pathogens with a sensitivity increase of 47.9% (77.2% vs. 29.3%). Metagenomic next-generation sequencing had a sensitivity of 82.9%. Total of 70.1% patients had consistent results in both metagenomic next-generation sequencing and nanopore targeted sequencing. Nanopore targeted sequencing exhibited significantly higher sensitivity in detecting Pneumocystis jiroveci, cytomegalovirus, Mycobacterium tuberculosis, Nontuberculous mycobacteria, Streptococcus pneumoniae, and Mycoplasma pneumoniae compared to conventional microbial testing. However, metagenomic next-generation sequencing demonstrated higher sensitivity than nanopore targeted sequencing for Aspergillus (88.5% vs. 53.8%). Regarding the detection of co-infections, nanopore targeted sequencing displayed significantly higher sensitivity than conventional microbial testing (76.7% vs. 28.7%) and was on par with metagenomic next-generation sequencing (76.7% vs. 82.9%). CONCLUSION Nanopore targeted sequencing performs equally well as metagenomic next-generation sequencing in bronchoalveolar lavage fluid for pathogen diagnosis in pneumonia, both methods showing higher sensitivity than conventional microbial testing. Nanopore targeted sequencing can be considered a reliable method for diagnosing pathogens in pneumonia.
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Affiliation(s)
- Qinqing Lin
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Department of Critical Care Medicine, Affiliated Hospital of Shaoxing University, Shaoxing, China
| | - Yake Yao
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xi Li
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Shanshan Zhang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Department of Respiratory and Critical Care Medicine, Beilun People's Hospital, Ningbo, China
| | - Huimin Guo
- Zhejiang Digena Diagnosis Technology CO., Ltd., Hangzhou, Zhejiang, China
- Key Laboratory of Digital Technology in Medical Diagnostics of Zhejiang Province, Dian Diagnostics Group Co., Ltd., Hangzhou, Zhejiang, China
| | - Xiaolong Ma
- Department of Respiratory and Critical Care Medicine, The First Hospital of JiaXing, JiaXing, China
| | - Wenyu Chen
- Key Laboratory of Digital Technology in Medical Diagnostics of Zhejiang Province, Dian Diagnostics Group Co., Ltd., Hangzhou, Zhejiang, China
| | - Chuhui Ru
- Department of Respiratory and Critical Care Medicine, Red Cross Society Hospital of Hangzhou, Hangzhou, China
| | - Limin Wang
- Department of Respiratory and Critical Care Medicine, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Bin Wang
- Department of Respiratory and Critical Care Medicine, Huzhou Central Hospital, Huzhou, China
| | - Qiang Ma
- Department of Respiratory and Critical Care Medicine, The Second People's Hospital of Yuhang District, Hangzhou, China
| | - Junfei Zhu
- Department of Respiratory and Critical Care Medicine, Taizhou Central Hospital, Taizhou, China
| | - Xuemei Lin
- Department of Respiratory and Critical Care Medicine, Jiangshan People's Hospital, Quzhou, China
| | - Qi Chen
- Zhejiang Digena Diagnosis Technology CO., Ltd., Hangzhou, Zhejiang, China
- Key Laboratory of Digital Technology in Medical Diagnostics of Zhejiang Province, Dian Diagnostics Group Co., Ltd., Hangzhou, Zhejiang, China
| | - Hui Lou
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qi Chen
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Junjun Chen
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhu Zeng
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jianying Zhou
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yan Chen
- Department of Infectious Disease, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yunsong Yu
- Department of Infectious Disease, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hua Zhou
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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He S, Xiong Y, Tu T, Feng J, Fu Y, Hu X, Wang N, Li D. Diagnostic performance of metagenomic next-generation sequencing for the detection of pathogens in cerebrospinal fluid in pediatric patients with central nervous system infection: a systematic review and meta-analysis. BMC Infect Dis 2024; 24:103. [PMID: 38238719 PMCID: PMC10797782 DOI: 10.1186/s12879-024-09010-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 01/10/2024] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND Detecting pathogens in pediatric central nervous system infection (CNSI) is still a major challenge in medicine. In addition to conventional diagnostic patterns, metagenomic next-generation sequencing (mNGS) shows great potential in pathogen detection. Therefore, we systematically evaluated the diagnostic performance of mNGS in cerebrospinal fluid (CSF) in pediatric patients with CNSI. METHODS Related literature was searched in the Web of Science, PubMed, Embase, and Cochrane Library. We screened the literature and extracted the data according to the selection criteria. The quality of included studies was assessed by the Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2) tool and the certainty of the evidence was measured by the Grading of Recommendations, Assessment, Development, and Evaluations (GRADE) score system. Then, the pooled sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic odd's ratio (DOR), and area under the curve (AUC) of the summary receiver operating characteristic curve (sROC) were estimated in Stata Software and MetaDisc. Subgroup analyses were performed to investigate the potential factors that influence the diagnostic performance. RESULTS A total of 10 studies were included in the meta-analysis. The combined sensitivity was 0.68 (95% confidence interval [CI]: 0.59 to 0.76, I2 = 66.77%, p < 0.001), and the combined specificity was 0.89 (95% CI: 0.80 to 0.95, I2 = 83.37%, p < 0.001). The AUC of sROC was 0.85 (95% CI, 0.81 to 0.87). The quality level of evidence elevated by the GRADE score system was low. CONCLUSIONS Current evidence shows that mNGS presents a good diagnostic performance in pediatric CNSI. Due to the limited quality and quantity of the included studies, more high-quality studies are needed to verify the above conclusion.
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Affiliation(s)
- Sike He
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Ying Xiong
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
- Department of Periodical Press/Chinese Evidence-Based Medicine Center, West China Hospital, Sichuan University, Chengdu, China
| | - Teng Tu
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Jiaming Feng
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Yu Fu
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Xu Hu
- Department of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Neng Wang
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Dapeng Li
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug, Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, China.
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6
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Wheeler NE, Price V, Cunningham-Oakes E, Tsang KK, Nunn JG, Midega JT, Anjum MF, Wade MJ, Feasey NA, Peacock SJ, Jauneikaite E, Baker KS. Innovations in genomic antimicrobial resistance surveillance. THE LANCET. MICROBE 2023; 4:e1063-e1070. [PMID: 37977163 DOI: 10.1016/s2666-5247(23)00285-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 08/16/2023] [Accepted: 08/22/2023] [Indexed: 11/19/2023]
Abstract
Whole-genome sequencing of antimicrobial-resistant pathogens is increasingly being used for antimicrobial resistance (AMR) surveillance, particularly in high-income countries. Innovations in genome sequencing and analysis technologies promise to revolutionise AMR surveillance and epidemiology; however, routine adoption of these technologies is challenging, particularly in low-income and middle-income countries. As part of a wider series of workshops and online consultations, a group of experts in AMR pathogen genomics and computational tool development conducted a situational analysis, identifying the following under-used innovations in genomic AMR surveillance: clinical metagenomics, environmental metagenomics, gene or plasmid tracking, and machine learning. The group recommended developing cost-effective use cases for each approach and mapping data outputs to clinical outcomes of interest to justify additional investment in capacity, training, and staff required to implement these technologies. Harmonisation and standardisation of methods, and the creation of equitable data sharing and governance frameworks, will facilitate successful implementation of these innovations.
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Affiliation(s)
- Nicole E Wheeler
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, Edgbaston, UK
| | - Vivien Price
- Department of Clinical Infection, Immunology and Microbiology, Liverpool Centre for Global Health Research, University of Liverpool, Liverpool, UK
| | - Edward Cunningham-Oakes
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Kara K Tsang
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK
| | - Jamie G Nunn
- Infectious Disease Challenge Area, Wellcome Trust, London, UK
| | | | - Muna F Anjum
- Department of Bacteriology, Animal and Plant Health Agency, Surrey, UK
| | - Matthew J Wade
- Data Analytics and Surveillance Group, UK Health Security Agency, London, UK; School of Engineering, Newcastle University, Newcastle-upon-Tyne, UK
| | - Nicholas A Feasey
- Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK; Malawi Liverpool Wellcome Research Programme, Chichiri, Blantyre, Malawi
| | | | - Elita Jauneikaite
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK; NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, Hammersmith Hospital, London, UK
| | - Kate S Baker
- Centre for Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, UK; Department of Genetics, University of Cambridge, Cambridge, UK.
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Meng X, Liu Y, Li J, Wang L, Shi R, Chen Y, Zhu Y, Zhuang S. Metagenomic next-generation sequencing for diagnosis and efficacy evaluation of a critical case of SFTS complicated by invasive pulmonary aspergillosis. IDCases 2023; 33:e01884. [PMID: 37663136 PMCID: PMC10470360 DOI: 10.1016/j.idcr.2023.e01884] [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: 08/19/2023] [Accepted: 08/21/2023] [Indexed: 09/05/2023] Open
Abstract
Severe fever with thrombocytopenia syndrome (SFTS) is an emerging infectious disease caused by SFTS virus (SFTSV). SFTS patients were prone to invasive pulmonary aspergillosis (IPA), which was directly related to increased mortality. Here, we present a critical case of SFTS complicated by IPA in a previously healthy 58-year-old woman. On day 1, SFTSV and three different Aspergillus species were both detected in the patient's bronchoalveolar lavage fluid and blood through metagenomic next-generation sequencing (mNGS). After 17 days of treatment, the patient was still in poor condition and A. fumigatus was once again detected in her blood through mNGS. Then her family decided to give up treatment because of financial problems and grave prognosis. She was discharged home and died the next day. Medical personnel should be alter to the possibility of IPA in SFTS patients due to its high mortality. mNGS may be used as an auxiliary diagnostic tool and efficacy-monitoring method for suspected SFTS complicated by IPA.
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Affiliation(s)
- Xing Meng
- Department of Emergency Intensive Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yan Liu
- Genskey Medical Technology Co., Ltd, Beijing, China
| | - Jun Li
- Genskey Medical Technology Co., Ltd, Beijing, China
| | - Liang Wang
- Genskey Medical Technology Co., Ltd, Beijing, China
| | - Ruixue Shi
- Genskey Medical Technology Co., Ltd, Beijing, China
| | - Ying Chen
- Genskey Medical Technology Co., Ltd, Beijing, China
| | - Yun Zhu
- Genskey Medical Technology Co., Ltd, Beijing, China
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8
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Chapman R, Jones L, D'Angelo A, Suliman A, Anwar M, Bagby S. Nanopore-Based Metagenomic Sequencing in Respiratory Tract Infection: A Developing Diagnostic Platform. Lung 2023; 201:171-179. [PMID: 37009923 PMCID: PMC10067523 DOI: 10.1007/s00408-023-00612-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 03/14/2023] [Indexed: 04/04/2023]
Abstract
Respiratory tract infection (RTI) remains a significant cause of morbidity and mortality across the globe. The optimal management of RTI relies upon timely pathogen identification via evaluation of respiratory samples, a process which utilises traditional culture-based methods to identify offending microorganisms. This process can be slow and often prolongs the use of broad-spectrum antimicrobial therapy, whilst also delaying the introduction of targeted therapy as a result. Nanopore sequencing (NPS) of respiratory samples has recently emerged as a potential diagnostic tool in RTI. NPS can identify pathogens and antimicrobial resistance profiles with greater speed and efficiency than traditional sputum culture-based methods. Increased speed to pathogen identification can improve antimicrobial stewardship by reducing the use of broad-spectrum antibiotic therapy, as well as improving overall clinical outcomes. This new technology is becoming more affordable and accessible, with some NPS platforms requiring minimal sample preparation and laboratory infrastructure. However, questions regarding clinical utility and how best to implement NPS technology within RTI diagnostic pathways remain unanswered. In this review, we introduce NPS as a technology and as a diagnostic tool in RTI in various settings, before discussing the advantages and limitations of NPS, and finally what the future might hold for NPS platforms in RTI diagnostics.
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Affiliation(s)
- Robert Chapman
- Princess Alexandra Hospital, Hamstel Road, Harlow, CM20 1QX, UK.
| | - Luke Jones
- Department of Life Sciences, University of Bath, Bath, BA2 7AY, UK
| | - Alberto D'Angelo
- Department of Life Sciences, University of Bath, Bath, BA2 7AY, UK
| | - Ahmed Suliman
- Princess Alexandra Hospital, Hamstel Road, Harlow, CM20 1QX, UK
| | - Muhammad Anwar
- Princess Alexandra Hospital, Hamstel Road, Harlow, CM20 1QX, UK
| | - Stefan Bagby
- Department of Life Sciences, University of Bath, Bath, BA2 7AY, UK
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9
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Nakamura A, Komatsu M. Performance evaluation of whole genome metagenomics sequencing with the MinION nanopore sequencer: Microbial community analysis and antimicrobial resistance gene detection. J Microbiol Methods 2023; 206:106688. [PMID: 36764487 DOI: 10.1016/j.mimet.2023.106688] [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: 11/29/2022] [Revised: 01/31/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023]
Abstract
Recently, the human gut microbiota has been implicated in various diseases such as immunological and neuropsychiatric disorders, and comprehensive gut microbiota analysis by metagenomic analysis using next-generation sequencers has been attracting attention. In this study, we compared microbial communities of 16S rDNA metagenome sequencing (16S-meta) and whole genome metagenome sequencing (WG-meta) using the nanopore sequencer MinION and 16S-meta using the Illumina Miseq sequencer with simulated and fecal samples, and evaluated the ability of WG-meta to detect antimicrobial resistance genes. We used the commercial Microbial Community DNA Standard as the DNA standard and a simulated sample comprising 17 strains of 15 bacterial species. In the detection of antimicrobial resistance genes, we used a simulated sample and spiked fecal samples containing Escherichia coli carrying blaCTX-M-27, Klebsiella pneumoniae carrying blaOXA-48, and Staphylococcus aureus carrying mecA. WG-meta using MinION was superior to 16S-meta and could accurately analyze the microbial communities at the species level, but it underestimated or misidentified the Bacillus subtilis group, Cryptococcus neoformans, Shigella sonnei, and Campylobacter jejuni. WG-meta using MinION could analyze the microbial communities in 5 min, and antimicrobial resistance gene detection using WG-meta could be performed in >30 min in the simulated sample with fewer bacterial counts.
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Affiliation(s)
- Akihiro Nakamura
- Department of Clinical Laboratory Science, Faculty of Health Care, Tenri Health Care University, Tenri, Japan.
| | - Masaru Komatsu
- Department of Clinical Laboratory Science, Faculty of Health Care, Tenri Health Care University, Tenri, Japan
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10
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Maciel-Guerra A, Baker M, Hu Y, Wang W, Zhang X, Rong J, Zhang Y, Zhang J, Kaler J, Renney D, Loose M, Emes RD, Liu L, Chen J, Peng Z, Li F, Dottorini T. Dissecting microbial communities and resistomes for interconnected humans, soil, and livestock. THE ISME JOURNAL 2023; 17:21-35. [PMID: 36151458 PMCID: PMC9751072 DOI: 10.1038/s41396-022-01315-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 08/26/2022] [Accepted: 09/01/2022] [Indexed: 12/24/2022]
Abstract
A debate is currently ongoing as to whether intensive livestock farms may constitute reservoirs of clinically relevant antimicrobial resistance (AMR), thus posing a threat to surrounding communities. Here, combining shotgun metagenome sequencing, machine learning (ML), and culture-based methods, we focused on a poultry farm and connected slaughterhouse in China, investigating the gut microbiome of livestock, workers and their households, and microbial communities in carcasses and soil. For both the microbiome and resistomes in this study, differences are observed across environments and hosts. However, at a finer scale, several similar clinically relevant antimicrobial resistance genes (ARGs) and similar associated mobile genetic elements were found in both human and broiler chicken samples. Next, we focused on Escherichia coli, an important indicator for the surveillance of AMR on the farm. Strains of E. coli were found intermixed between humans and chickens. We observed that several ARGs present in the chicken faecal resistome showed correlation to resistance/susceptibility profiles of E. coli isolates cultured from the same samples. Finally, by using environmental sensing these ARGs were found to be correlated to variations in environmental temperature and humidity. Our results show the importance of adopting a multi-domain and multi-scale approach when studying microbial communities and AMR in complex, interconnected environments.
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Affiliation(s)
- Alexandre Maciel-Guerra
- grid.4563.40000 0004 1936 8868School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Leicestershire, LE12 5RD UK
| | - Michelle Baker
- grid.4563.40000 0004 1936 8868School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Leicestershire, LE12 5RD UK
| | - Yue Hu
- grid.4563.40000 0004 1936 8868School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Leicestershire, LE12 5RD UK
| | - Wei Wang
- grid.464207.30000 0004 4914 5614NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021 People’s Republic of China
| | - Xibin Zhang
- grid.508175.eNew Hope Liuhe Co., Ltd., Laboratory of Feed and Livestock and Poultry Products Quality & Safety Control, Ministry of Agriculture, Beijing 100102 and Weifang Heshengyuan Food Co. Ltd., Weifang, 262167 People’s Republic of China
| | - Jia Rong
- grid.508175.eNew Hope Liuhe Co., Ltd., Laboratory of Feed and Livestock and Poultry Products Quality & Safety Control, Ministry of Agriculture, Beijing 100102 and Weifang Heshengyuan Food Co. Ltd., Weifang, 262167 People’s Republic of China
| | - Yimin Zhang
- grid.440622.60000 0000 9482 4676College of Food Science and Engineering, Shandong Agricultural University, Tai’an, Shandong 271018 People’s Republic of China
| | - Jing Zhang
- grid.464207.30000 0004 4914 5614NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021 People’s Republic of China
| | - Jasmeet Kaler
- grid.4563.40000 0004 1936 8868School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Leicestershire, LE12 5RD UK
| | - David Renney
- Nimrod Veterinary Products Limited, 2, Wychwood Court, Cotswold Business Village, Moreton-in-Marsh, GL56 0JQ UK
| | - Matthew Loose
- grid.4563.40000 0004 1936 8868DeepSeq, School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, NG7 2UH UK
| | - Richard D. Emes
- grid.4563.40000 0004 1936 8868School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Leicestershire, LE12 5RD UK
| | - Longhai Liu
- grid.508175.eNew Hope Liuhe Co., Ltd., Laboratory of Feed and Livestock and Poultry Products Quality & Safety Control, Ministry of Agriculture, Beijing 100102 and Weifang Heshengyuan Food Co. Ltd., Weifang, 262167 People’s Republic of China
| | - Junshi Chen
- grid.464207.30000 0004 4914 5614NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021 People’s Republic of China
| | - Zixin Peng
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021, People's Republic of China.
| | - Fengqin Li
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021, People's Republic of China.
| | - Tania Dottorini
- School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Leicestershire, LE12 5RD, UK.
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11
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Wang C, Yan D, Huang J, Yang N, Shi J, Pan S, Lin G, Liu Y, Zhang Y, Bian X, Song Q, Qian G. The clinical application of metagenomic next-generation sequencing in infectious diseases at a tertiary hospital in China. Front Cell Infect Microbiol 2022; 12:957073. [PMID: 36601307 PMCID: PMC9806342 DOI: 10.3389/fcimb.2022.957073] [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: 05/30/2022] [Accepted: 11/25/2022] [Indexed: 12/23/2022] Open
Abstract
Background Compared with traditional diagnostic methods (TDMs), rapid diagnostic methods for infectious diseases (IDs) are urgently needed. Metagenomic next-generation sequencing (mNGS) has emerged as a promising diagnostic technology for clinical infections. Methods This retrospective observational study was performed at a tertiary hospital in China between May 2019 and August 2022. The chi-square test was used to compare the sensitivity and specificity of mNGS and TDMs. We also performed a subgroup analysis of the different pathogens and samples. Results A total of 435 patients with clinical suspicion of infection were enrolled and 372 (85.5%) patients were finally categorized as the ID group. The overall sensitivity of mNGS was significantly higher than that of the TDMs (59.7% vs. 30.1%, P < 0.05). However, there was no significant difference in the overall specificity between the two methods (83.3% vs. 89.6%, P = 0.37). In patients with identified pathogens, the positive rates of mNGS for detecting bacteria (88.7%), fungi (87.9%), viruses (96.9%), and Nontuberculous mycobacteria (NTM; 100%) were significantly higher than those of TDMs (P < 0.05). The positive rate of mNGS for detecting Mycobacterium tuberculosis was not superior to that of TDMs (77.3% vs. 54.5%, P = 0.11). The sensitivity rates of mNGS for pathogen identification in bronchoalveolar lavage fluid, blood, cerebrospinal fluid, pleural fluid, and tissue were 72.6%, 39.3%, 37.5%, 35.0% and 80.0%, respectively. Conclusion With the potential for screening multiple clinical samples, mNGS has an overall advantage over TDMs. It can effectively identify pathogens, especially those that are difficult to identify using TDMs, such as NTM, chlamydia, and parasites.
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Affiliation(s)
- Chuwen Wang
- School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Danying Yan
- Department of Infectious Diseases, Ningbo First Hospital, Ningbo University, Ningbo, Zhejiang, China
| | - Jiajia Huang
- School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Naibin Yang
- Department of Infectious Diseases, Ningbo First Hospital, Ningbo University, Ningbo, Zhejiang, China
| | - Jiejun Shi
- Department of Infectious Diseases, Ningbo First Hospital, Ningbo University, Ningbo, Zhejiang, China
| | - Shou Pan
- Hangzhou DIAN Medical Laboratory, Hangzhou, China
| | - Gaoqiang Lin
- Vision Medicals Center for Infectious Diseases, Guangzhou, Guangdong, China
| | - Ying Liu
- School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Yingying Zhang
- School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Xueyan Bian
- Department of Nephrology, Ningbo First Hospital, Ningbo University, Ningbo, Zhejiang, China,*Correspondence: Guoqing Qian, ; Qifa Song, ; Xueyan Bian,
| | - Qifa Song
- Medical Data Center, Ningbo First Hospital, Ningbo University, Ningbo, China,*Correspondence: Guoqing Qian, ; Qifa Song, ; Xueyan Bian,
| | - Guoqing Qian
- School of Medicine, Ningbo University, Ningbo, Zhejiang, China,Department of Infectious Diseases, Ningbo First Hospital, Ningbo University, Ningbo, Zhejiang, China,*Correspondence: Guoqing Qian, ; Qifa Song, ; Xueyan Bian,
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12
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Haddad SF, DeSimone DC, Chesdachai S, Gerberi DJ, Baddour LM. Utility of Metagenomic Next-Generation Sequencing in Infective Endocarditis: A Systematic Review. Antibiotics (Basel) 2022; 11:antibiotics11121798. [PMID: 36551455 PMCID: PMC9774888 DOI: 10.3390/antibiotics11121798] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/01/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
Blood cultures have been the gold standard for identifying pathogens in infective endocarditis (IE). Blood culture-negative endocarditis (BCNE), however, occurs in 40% or more of IE cases with the bulk of them due to recent antibiotic exposure prior to obtaining blood cultures. Increasingly, molecular techniques are being used for pathogen identification in cases of BCNE and more recently has included metagenomic next-generation sequencing (mNGS). We therefore performed a literature search on August 31, 2022, that assessed the mNGS in IE and 13 publications were identified and included in a systematic review. Eight (61.5%) of them focused only on IE with mNGS performed on cardiac valve tissue in four studies, plasma in three studies and cardiac implantable electronic devices (CIED) in one study. Gram-positive cocci, including Staphylococcus aureus (n = 31, 8.9%), coagulase-negative staphylococci (n = 61, 17.6%), streptococci (n = 130, 37.5%), and Enterococcus faecalis (n = 23, 6.6%) were the predominant organisms identified by mNGS. Subsequent investigations are needed to further define the utility of mNGS in BCNE and its impact on patient outcomes. Despite some pitfalls, mNGS seems to be of value in pathogen identification in IE cases, particularly in those with BCNE. This study was registered and on the Open Science Framework platform.
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Affiliation(s)
- Sara F. Haddad
- Division of Public Health, Infectious Diseases and Occupational Medicine, Department of Medicine, Mayo Clinic College of Medicine and Science, Mayo Clinic, Rochester, MN 55905, USA
- Correspondence: ; Tel.: +1-(507)-405-7588
| | - Daniel C. DeSimone
- Division of Public Health, Infectious Diseases and Occupational Medicine, Department of Medicine, Mayo Clinic College of Medicine and Science, Mayo Clinic, Rochester, MN 55905, USA
- Department of Cardiovascular Disease, Mayo Clinic College of Medicine and Science, Mayo Clinic, Rochester, MN 55905, USA
| | - Supavit Chesdachai
- Division of Public Health, Infectious Diseases and Occupational Medicine, Department of Medicine, Mayo Clinic College of Medicine and Science, Mayo Clinic, Rochester, MN 55905, USA
| | - Danielle J. Gerberi
- Mayo Clinic Library Services, Mayo Clinic College of Medicine and Science, Mayo Clinic, Rochester, MN 55905, USA
| | - Larry M. Baddour
- Division of Public Health, Infectious Diseases and Occupational Medicine, Department of Medicine, Mayo Clinic College of Medicine and Science, Mayo Clinic, Rochester, MN 55905, USA
- Department of Cardiovascular Disease, Mayo Clinic College of Medicine and Science, Mayo Clinic, Rochester, MN 55905, USA
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13
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Lin C, Bonsu AAFK, Li J, Ning C, Chen L, Zhu S, Zhong Q, Shen D, Huang G. Application of metagenomic next-generation sequencing for suspected infected pancreatic necrosis. Pancreatology 2022; 22:864-870. [PMID: 35864066 DOI: 10.1016/j.pan.2022.07.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 07/06/2022] [Accepted: 07/11/2022] [Indexed: 12/11/2022]
Abstract
BACKGROUND Metagenomic next-generation sequencing (mNGS) is increasingly used for the clinical diagnosis of infectious diseases, but there is a paucity of data regarding the application of mNGS in the early diagnosis of infected pancreatic necrosis (IPN). OBJECTIVE To investigate the clinical application value of mNGS in the pathogenic diagnosis of IPN. METHODS Forty-two patients with suspected IPN were prospectively and consecutively enrolled from August 2019 to August 2021. Blood samples were collected for mNGS and microbial culture simultaneously during fever (T ≥ 38.5 °C). For patients who had indications of surgical interventions, peri-pancreatic specimens were collected for mNGS and microbial culture simultaneously during the first surgical intervention to confirm IPN. The clinical performance of mNGS and microbial culture were compared. RESULTS A total of 21 patients (50.0%) were confirmed to have IPN during hospitalization. The sensitivity of blood mNGS was significantly higher than blood culture (95.2% vs. 23.8%, P < 0.001) in diagnosing IPN. The negative predictive value of blood mNGS was 90.0%. The turnaround time of mNGS was significantly shorter than that of microbial culture [(37.70 ± 1.44) vs. (115.23 ± 8.79) h, P < 0.01] and the average costs of mNGS accounted for 1.7% of the average total cost of hospitalization. The survival analysis demonstrates that the positive blood mNGS result was not associated with increased mortality (P = 0.119). CONCLUSIONS With more valuable diagnostic performance and shorter turnaround time, clinical mNGS represents a potential step forward in the early diagnosis of IPN.
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Affiliation(s)
- Chiayen Lin
- Department of Pancreatic Surgery, General Surgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan Province, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan Province, China
| | - Abdul Aziz F K Bonsu
- Department of Pancreatic Surgery, General Surgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan Province, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan Province, China
| | - Jiarong Li
- Department of Pancreatic Surgery, General Surgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan Province, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan Province, China
| | - Caihong Ning
- Department of Pancreatic Surgery, General Surgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan Province, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan Province, China
| | - Lu Chen
- Department of Pancreatic Surgery, General Surgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan Province, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan Province, China
| | - Shuai Zhu
- Department of Pancreatic Surgery, General Surgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan Province, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan Province, China
| | - Qiaoqing Zhong
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan Province, China; Department of Cardiovascular Medicine, Xiangya Hospital, Central South University, Changsha, 410008, Hunan Province, China
| | - Dingcheng Shen
- Department of Pancreatic Surgery, General Surgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan Province, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan Province, China.
| | - Gengwen Huang
- Department of Pancreatic Surgery, General Surgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan Province, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan Province, China.
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14
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Kouijzer JJP, Noordermeer DJ, van Leeuwen WJ, Verkaik NJ, Lattwein KR. Native valve, prosthetic valve, and cardiac device-related infective endocarditis: A review and update on current innovative diagnostic and therapeutic strategies. Front Cell Dev Biol 2022; 10:995508. [PMID: 36263017 PMCID: PMC9574252 DOI: 10.3389/fcell.2022.995508] [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: 07/16/2022] [Accepted: 09/06/2022] [Indexed: 11/13/2022] Open
Abstract
Infective endocarditis (IE) is a life-threatening microbial infection of native and prosthetic heart valves, endocardial surface, and/or indwelling cardiac device. Prevalence of IE is increasing and mortality has not significantly improved despite technological advances. This review provides an updated overview using recent literature on the clinical presentation, diagnosis, imaging, causative pathogens, treatment, and outcomes in native valve, prosthetic valve, and cardiac device-related IE. In addition, the experimental approaches used in IE research to improve the understanding of disease mechanisms and the current diagnostic pipelines are discussed, as well as potential innovative diagnostic and therapeutic strategies. This will ultimately help towards deriving better diagnostic tools and treatments to improve IE patient outcomes.
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Affiliation(s)
- Joop J. P. Kouijzer
- Thoraxcenter, Department of Biomedical Engineering, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Daniëlle J. Noordermeer
- Thoraxcenter, Department of Biomedical Engineering, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Wouter J. van Leeuwen
- Department of Cardiothoracic Surgery, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Nelianne J. Verkaik
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Kirby R. Lattwein
- Thoraxcenter, Department of Biomedical Engineering, Erasmus MC University Medical Center, Rotterdam, Netherlands
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15
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Flurin L, Wolf MJ, Fisher CR, Cano Cevallos EJ, Vaillant JJ, Pritt BS, DeSimone DC, Patel R. Pathogen Detection in Infective Endocarditis Using Targeted Metagenomics on Whole Blood and Plasma: a Prospective Pilot Study. J Clin Microbiol 2022; 60:e0062122. [PMID: 36040200 PMCID: PMC9491191 DOI: 10.1128/jcm.00621-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 08/14/2022] [Indexed: 11/20/2022] Open
Abstract
Initial microbiologic diagnosis of infective endocarditis (IE) relies on blood cultures and Bartonella and Coxiella burnetii serology. Small case series and one prospective study have preliminarily reported application of metagenomic sequencing on blood or plasma for IE diagnosis. Here, results of a prospective pilot study evaluating targeted metagenomic sequencing (tMGS) for blood-based early pathogen detection and identification in IE are reported. Subjects diagnosed with possible or definite IE at a single institution were prospectively enrolled with informed consent from October 2020 to July 2021. Blood was drawn and separated into whole blood and plasma. Both specimen types were subjected to nucleic acid extraction and PCR targeting the V1-V3 region of the 16S ribosomal RNA gene, followed by next-generation sequencing on an Illumina MiSeqTM platform. 35 subjects, 28 (80%) with definite and 7 (20%) with possible IE were enrolled, including 6 (17%) with blood culture-negative endocarditis (BCNE). Overall, 20 whole blood (59%) and 16 plasma (47%) samples tested positive (P = 0.47). When results of whole blood and plasma testing were combined, a positive tMGS result was found in 23 subjects (66%). tMGS identified a potential pathogen in 5 of 6 culture-negative IE cases. Although further study is needed, the results of this pilot study suggest that blood-based tMGS may provide pathogen identification in subjects with IE, including in culture-negative cases.
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Affiliation(s)
- Laure Flurin
- Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
- Department of Intensive Care, University Hospital of Guadeloupe, Pointe-à-Pitre, France
| | - Matthew J. Wolf
- Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
| | - Cody R. Fisher
- Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
| | - Edison J. Cano Cevallos
- Division of Public Health, Infectious Diseases and Occupational Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Memorial Healthcare System, Hollywood, Florida, USA
| | - James J. Vaillant
- Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
- Division of Public Health, Infectious Diseases and Occupational Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Bobbi S. Pritt
- Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
- Division of Public Health, Infectious Diseases and Occupational Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Daniel C. DeSimone
- Division of Public Health, Infectious Diseases and Occupational Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Department of Cardiovascular Diseases, Mayo Clinic, Rochester, Minnesota, USA
| | - Robin Patel
- Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
- Division of Public Health, Infectious Diseases and Occupational Medicine, Mayo Clinic, Rochester, Minnesota, USA
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16
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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: 25] [Impact Index Per Article: 12.5] [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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17
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Bouchiat C, Ginevra C, Benito Y, Gaillard T, Salord H, Dauwalder O, Laurent F, Vandenesch F. Improving the Diagnosis of Bacterial Infections: Evaluation of 16S rRNA Nanopore Metagenomics in Culture-Negative Samples. Front Microbiol 2022; 13:943441. [PMID: 35910644 PMCID: PMC9329087 DOI: 10.3389/fmicb.2022.943441] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 06/17/2022] [Indexed: 11/29/2022] Open
Abstract
While 16S rRNA PCR-Sanger sequencing has paved the way for the diagnosis of culture-negative bacterial infections, it does not provide the composition of polymicrobial infections. We aimed to evaluate the performance of the Nanopore-based 16S rRNA metagenomic approach, using both partial and full-length amplification of the gene, and to explore its feasibility and suitability as a routine diagnostic tool for bacterial infections in a clinical laboratory. Thirty-one culture-negative clinical samples from mono- and polymicrobial infections based on Sanger-sequencing results were sequenced on MinION using both the in-house partial amplification and the Nanopore dedicated kit for the full-length amplification of the 16S rRNA gene. Contamination, background noise definition, bacterial identification, and time-effectiveness issues were addressed. Cost optimization was also investigated with the miniaturized version of the flow cell (Flongle). The partial 16S approach had a greater sensitivity compared to the full-length kit that detected bacterial DNA in only 24/31 (77.4%) samples. Setting a threshold of 1% of total reads overcame the background noise issue and eased the interpretation of clinical samples. Results were obtained within 1 day, discriminated polymicrobial samples, and gave accurate bacterial identifications compared to Sanger-based results. We also found that multiplexing and using Flongle flow cells was a cost-effective option. The results confirm that Nanopore technology is user-friendly as well as cost- and time-effective. They also indicate that 16S rRNA targeted metagenomics is a suitable approach to be implemented for the routine diagnosis of culture-negative samples in clinical laboratories.
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Affiliation(s)
- Coralie Bouchiat
- Laboratoire de Bactériologie, Institut des Agents Infectieux, Biologie Moléculaire, Hospices Civils de Lyon, Lyon, France
- Equipe Inserm U1111, Centre International de Recherche en Infectiologie, Université de Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
- *Correspondence: Coralie Bouchiat
| | - Christophe Ginevra
- Centre National de Référence des Légionelles, Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Yvonne Benito
- Laboratoire de Bactériologie, Institut des Agents Infectieux, Biologie Moléculaire, Hospices Civils de Lyon, Lyon, France
| | - Tiphaine Gaillard
- Laboratoire de Bactériologie, Institut des Agents Infectieux, Biologie Moléculaire, Hospices Civils de Lyon, Lyon, France
- Laboratoire de biologie médicale, Hôpital d'Instruction des Armées Desgenettes, Service de Santé des Armées, Lyon, France
| | - Hélène Salord
- Laboratoire de Bactériologie, Institut des Agents Infectieux, Biologie Moléculaire, Hospices Civils de Lyon, Lyon, France
| | - Olivier Dauwalder
- Laboratoire de Bactériologie, Institut des Agents Infectieux, Biologie Moléculaire, Hospices Civils de Lyon, Lyon, France
| | - Frédéric Laurent
- Laboratoire de Bactériologie, Institut des Agents Infectieux, Biologie Moléculaire, Hospices Civils de Lyon, Lyon, France
- Equipe Inserm U1111, Centre International de Recherche en Infectiologie, Université de Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - François Vandenesch
- Laboratoire de Bactériologie, Institut des Agents Infectieux, Biologie Moléculaire, Hospices Civils de Lyon, Lyon, France
- Equipe Inserm U1111, Centre International de Recherche en Infectiologie, Université de Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
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18
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Abstract
The gold standard for confirming bacterial infections is culture-positive, which has a long sample-to-result turnaround time and poor sensitivity for unculturable and fastidious pathogens; therefore, it is hard to guide early, targeted antimicrobial therapy and reduce overuse of broad-spectrum antibiotics. Nanopore targeted sequencing (NTS) is reported to be advantageous in detection speed and range over culture in prior published reports. However, investigation of the clinical performance of NTS is deficient at present. Thus, we assessed the feasibility of NTS for the first time with cohort and systematic comparisons with traditional culture assays and PCR followed by Sanger sequencing. This retrospective study was performed on 472 samples, including 6 specimen types from 436 patients, to evaluate the clinical performance of NTS designed for identifying the microbial composition of various infections. Of these samples, 86.7% were found to be NTS positive, which was significantly higher than culture-positive (26.7%). A total of 425 significant human opportunistic bacteria and fungi detected by NTS were selected to go through validation with PCR followed by Sanger sequencing. The average accuracy rate was 85.2% (maximum 100% created by Cryptococcus neoformans, the last one 66.7% provided by both Staphylococcus haemolyticus and Moraxella osloensis, minimum 0% produced by Burkholderia cepacia). The accuracy rate also varied with sample type; the highest accuracy rate was found in pleural and ascites fluid (95.8%) followed by bronchoalveolar lavage fluid (88.7%), urine (86.8%), and wound secretions (85.0%), while the lowest was present in cerebrospinal fluid (58.8%). NTS had a diagnostic sensitivity of 94.5% and specificity of 31.8%. The positive and negative predictive values of NTS were 79.9% and 66.7%, respectively. For diagnosis of infectious diseases, the sensitivity was greatly increased by 56.7% in NTS compared with culture (94.5% vs 37.8%). Therefore, NTS can accurately detect the causative pathogens in infectious samples, particularly in pleural and ascites fluid, bronchoalveolar lavage fluid, urine, and wound secretions, with a short turnaround time of 8-14 h, and might innovatively contribute to personalizing antibiotic treatments for individuals with standardized protocols in clinical practices. IMPORTANCE Nanopore targeted sequencing (NTS) is reported to be advantageous in detection speed and range over culture in prior published reports. Investigation of the clinical performance of NTS is deficient at present. In our study, cohort and systematic comparisons among three assays (culture, NTS, and Sanger sequencing) were analyzed retrospectively for the first time. We found that NTS undoubtedly has incomparable advantages in accurately detecting the causative pathogens in infectious samples, particularly in pleural and ascites fluid, bronchoalveolar lavage fluid, urine, and wound secretions, with a short turnaround time of 8-14 h. For sterile specimens like blood and cerebrospinal fluid (CSF), the NTS outcomes should be validated using other nucleic acid based detection technology. Overall, NTS might innovatively contribute to guiding early, targeted antimicrobial therapy with lower cost and reduce overuse of broad-spectrum antibiotics.
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Li Y, Yang Q, Ding J. Metagenomic Next-generation Sequencing: Application in Infectious Diseases. EXPLORATORY RESEARCH AND HYPOTHESIS IN MEDICINE 2022; 7:19-24. [DOI: 10.14218/erhm.2021.00014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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20
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Yang Y, Che Y, Liu L, Wang C, Yin X, Deng Y, Yang C, Zhang T. Rapid absolute quantification of pathogens and ARGs by nanopore sequencing. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 809:152190. [PMID: 34890655 DOI: 10.1016/j.scitotenv.2021.152190] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/30/2021] [Accepted: 12/01/2021] [Indexed: 06/13/2023]
Abstract
Compositional nature of relative abundance data in the current standard microbiome studies limits microbial dynamics interpretations and cross-sample comparisons. Here, we demonstrate the first rapid (1-h sequencing) method coupling Nanopore metagenomic sequencing with cellular spike-in to facilitate the absolute quantification and removal assessment of pathogens and antibiotic resistance genes (ARGs) in wastewater treatment plants (WWTPs). Nanopore sequencing-based quantification results for both simple mock community and complex real environmental samples showed a high consistency with those from the widely-used Illumina and culture-based approaches. Implementing such method, we quantified 46 predominant putative pathogenic species, and 361 ARGs in three WWTP sample sets. Though high log removals of dominant pathogens (2.23 logs) and ARGs (1.98 logs) were achieved, complete removal of all pathogens and ARGs were not achieved. Noticeably, Mycobacterium spp., Clostridium_P perfringens, and Borrelia hermsii exhibited low removal, and 13 ARGs even increased in absolute abundance after the treatment. Our proposed approach manifested its profound ability in providing absolute quantitation information guiding wastewater-based epidemiological surveillance and quantitative risk assessment facilitating microbial hazards management.
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Affiliation(s)
- Yu Yang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - You Che
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Lei Liu
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Chunxiao Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Xiaole Yin
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Yu Deng
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Chao Yang
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China.
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21
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Hoang MTV, Irinyi L, Hu Y, Schwessinger B, Meyer W. Long-Reads-Based Metagenomics in Clinical Diagnosis With a Special Focus on Fungal Infections. Front Microbiol 2022; 12:708550. [PMID: 35069461 PMCID: PMC8770865 DOI: 10.3389/fmicb.2021.708550] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 12/03/2021] [Indexed: 12/12/2022] Open
Abstract
Identification of the causative infectious agent is essential in the management of infectious diseases, with the ideal diagnostic method being rapid, accurate, and informative, while remaining cost-effective. Traditional diagnostic techniques rely on culturing and cell propagation to isolate and identify the causative pathogen. These techniques are limited by the ability and the time required to grow or propagate an agent in vitro and the facts that identification based on morphological traits are non-specific, insensitive, and reliant on technical expertise. The evolution of next-generation sequencing has revolutionized genomic studies to generate more data at a cheaper cost. These are divided into short- and long-read sequencing technologies, depending on the length of reads generated during sequencing runs. Long-read sequencing also called third-generation sequencing emerged commercially through the instruments released by Pacific Biosciences and Oxford Nanopore Technologies, although relying on different sequencing chemistries, with the first one being more accurate both platforms can generate ultra-long sequence reads. Long-read sequencing is capable of entirely spanning previously established genomic identification regions or potentially small whole genomes, drastically improving the accuracy of the identification of pathogens directly from clinical samples. Long-read sequencing may also provide additional important clinical information, such as antimicrobial resistance profiles and epidemiological data from a single sequencing run. While initial applications of long-read sequencing in clinical diagnosis showed that it could be a promising diagnostic technique, it also has highlighted the need for further optimization. In this review, we show the potential long-read sequencing has in clinical diagnosis of fungal infections and discuss the pros and cons of its implementation.
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Affiliation(s)
- Minh Thuy Vi Hoang
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Westmead, NSW, Australia
| | - Laszlo Irinyi
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Westmead, NSW, Australia
- Sydney Infectious Disease Institute, The University of Sydney, Sydney, NSW, Australia
| | - Yiheng Hu
- Research School of Biology, Australia National University, Canberra, ACT, Australia
| | | | - Wieland Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Westmead, NSW, Australia
- Sydney Infectious Disease Institute, The University of Sydney, Sydney, NSW, Australia
- Westmead Hospital (Research and Education Network), Westmead, NSW, Australia
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22
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What Does 16S rRNA Gene-Targeted Next Generation Sequencing Contribute to the Study of Infective Endocarditis in Heart-Valve Tissue? Pathogens 2021; 11:pathogens11010034. [PMID: 35055982 PMCID: PMC8781873 DOI: 10.3390/pathogens11010034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 12/23/2021] [Accepted: 12/24/2021] [Indexed: 01/04/2023] Open
Abstract
Infective endocarditis (IE) is a severe and life-threatening disease. Identification of infectious etiology is essential for establishing the appropriate antimicrobial treatment and decreasing mortality. The aim of this study was to explore the potential utility of metataxonomics for improving microbiological diagnosis of IE. Here, next-generation sequencing (NGS) of the V3-V4 region of the 16S rRNA gene was performed in 27 heart valve tissues (18 natives, 5 intravascular devices, and 4 prosthetics) from 27 patients diagnosed with IE (4 of them with negative blood cultures). Metataxonomics matched with conventional diagnostic techniques in 24/27 cases (88.9%). The same bacterial family was assigned to 24 cases; the same genus, to 23 cases; and the same species, to 13 cases. In 22 of them, the etiological agent was represented by percentages > 99% of the reads and in two cases, by ~70%. Staphylococcus aureus was detected in a previously microbiological undiagnosed patient. Thus, microbiological diagnosis with 16S rRNA gene targeted-NGS was possible in one more sample than using traditional techniques. The remaining two patients showed no coincidence between traditional and 16S rRNA gene-targeted NGS microbiological diagnoses. In addition, 16S rRNA gene-targeted NGS allowed us to suggest coinfections that were supported by clinical data in one patient, and minority records also verified mixed infections in three cases. In our series, metataxonomics was valid for the identification of the causative agents, although more studies are needed before implementation of 16S rRNA gene-targeted NGS for the diagnosis of IE.
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Xia J, Xia L, Zhou H, Lin X, Xu F. Empyema caused by Streptococcus constellatus: a case report and literature review. BMC Infect Dis 2021; 21:1267. [PMID: 34930151 PMCID: PMC8686261 DOI: 10.1186/s12879-021-06955-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 12/07/2021] [Indexed: 11/29/2022] Open
Abstract
Background Streptococcus constellatus is a member of Streptococcus anginosus group (SAG) that tends to cause pyogenic infections in various sites. However, Streptococcus constellatus is easily ignored by routine clinical laboratory tests for its prolonged anaerobic culture environment. Case presentation A 71-year-old man was admitted to our hospital due to productive cough, fever, chest pain and shortness of breath for 3 weeks. Chest computed tomography showed patchy opacities and right-sided pleural effusion, so a chest tube was inserted and purulent and hemorrhagic fluid was aspirated. The routine etiological examinations of the pleural effusion were all negative, and next-generation sequencing (NGS) detected Streptococcus constellatus. Intravenous piperacillin-tazobactam 4.5 g every 8 h was used accordingly. The patient recovered and subsequent chest computed tomography confirmed the improvement. Conclusions We reported a case of empyema secondary to Streptococcus constellatus infection, which was identified by NGS, instead of bacterial culture. This case highlights the utility of NGS in detecting pathogens negative in traditional bacterial tests.
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Affiliation(s)
- Jingyan Xia
- Department of Radiation Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, China
| | - Lexin Xia
- Department of Infectious Diseases, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, China
| | - Hui Zhou
- Department of Infectious Diseases, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, China
| | - Xiuhui Lin
- Department of Infectious Diseases, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, China
| | - Feng Xu
- Department of Infectious Diseases, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, China.
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Wang Y, Zhao Y, Bollas A, Wang Y, Au KF. Nanopore sequencing technology, bioinformatics and applications. Nat Biotechnol 2021; 39:1348-1365. [PMID: 34750572 PMCID: PMC8988251 DOI: 10.1038/s41587-021-01108-x] [Citation(s) in RCA: 512] [Impact Index Per Article: 170.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 09/22/2021] [Indexed: 12/13/2022]
Abstract
Rapid advances in nanopore technologies for sequencing single long DNA and RNA molecules have led to substantial improvements in accuracy, read length and throughput. These breakthroughs have required extensive development of experimental and bioinformatics methods to fully exploit nanopore long reads for investigations of genomes, transcriptomes, epigenomes and epitranscriptomes. Nanopore sequencing is being applied in genome assembly, full-length transcript detection and base modification detection and in more specialized areas, such as rapid clinical diagnoses and outbreak surveillance. Many opportunities remain for improving data quality and analytical approaches through the development of new nanopores, base-calling methods and experimental protocols tailored to particular applications.
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Affiliation(s)
- Yunhao Wang
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Yue Zhao
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
- Biomedical Informatics Shared Resources, The Ohio State University, Columbus, OH, USA
| | - Audrey Bollas
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Yuru Wang
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Kin Fai Au
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA.
- Biomedical Informatics Shared Resources, The Ohio State University, Columbus, OH, USA.
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Anton-Vazquez V, Dworakowski R, Cannata A, Amin-Youssef G, Gunning M, Papachristidis A, MacCarthy P, Baghai M, Deshpande R, Khan H, Byrne J, Fife A. 16S rDNA PCR for the aetiological diagnosis of culture-negative infective endocarditis. Infection 2021; 50:243-249. [PMID: 34490592 DOI: 10.1007/s15010-021-01690-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 08/31/2021] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Culture-negative infective endocarditis (IE) accounts for 7-31% of all cases. Metagenomics has contributed to improving the aetiological diagnosis of IE patients undergoing valve surgery. We assessed the impact of 16S ribosomal DNA gene polymerase chain reaction (16S rDNA PCR) in the aetiological diagnosis of culture-negative IE. METHODS Between January 2016 and January 2020, clinical data from culture-negative IE patients were reviewed retrospectively. Identification of bacteria was performed using 16S rDNA PCR in heart valve specimens. RESULTS 36 out of 313 patients (12%) with culture-negative IE had their valve tissue specimens submitted for 16S rDNA PCR. 16S rDNA PCR detected and identified bacterial nucleic acid in heart valve tissue significantly more frequently compared to valve culture alone 25(70%) vs 5(12%); p < 0.05. Mean age was 57 years (SD 18) and 80% were male. Native and aortic valve were involved in 76% and 52% of cases, respectively. Streptococcus spp. (n 15) were the most commonly detected organisms, followed by bacteria of the HACEK group (Haemophilus parainfluenzae 2, Aggregatibacter actinomycetemcomitans 1), nutritionally variant streptococci (Abiotrophia defectiva 2), and one each of Staphylococcus aureus, Corynebacterium pseudodiphtheriticum, Helcococcus kunzii, Neisseria gonorrhoeae, Tropheryma whipplei. CONCLUSION 16S rDNA PCR may be a useful diagnostic tool for the identification of the causative organism in culture-negative IE. Efforts towards a shorter turnaround time for results should be consider and further studies assessing the clinical impact of this technique in culture-negative IE are needed.
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Affiliation(s)
- Vanesa Anton-Vazquez
- Department of Medical Microbiology, Kings College Hospital NHS Foundation Trust, Denmark Hill, London, SE5 9RS, UK.
| | - Rafal Dworakowski
- Department of Cardiology, Kings College Hospital NHS Foundation Trust, Denmark Hill, London, SE5 9RS, UK
| | - Antonio Cannata
- Department of Cardiology, Kings College Hospital NHS Foundation Trust, Denmark Hill, London, SE5 9RS, UK
| | - George Amin-Youssef
- Department of Cardiology, Kings College Hospital NHS Foundation Trust, Denmark Hill, London, SE5 9RS, UK
| | - Margaret Gunning
- Department of Cardiology, Kings College Hospital NHS Foundation Trust, Denmark Hill, London, SE5 9RS, UK
| | - Alexandros Papachristidis
- Department of Cardiology, Kings College Hospital NHS Foundation Trust, Denmark Hill, London, SE5 9RS, UK
| | - Phil MacCarthy
- Department of Cardiology, Kings College Hospital NHS Foundation Trust, Denmark Hill, London, SE5 9RS, UK
| | - Max Baghai
- Department of Cardiology, Kings College Hospital NHS Foundation Trust, Denmark Hill, London, SE5 9RS, UK
| | - Ranjit Deshpande
- Department of Cardiology, Kings College Hospital NHS Foundation Trust, Denmark Hill, London, SE5 9RS, UK
| | - Habib Khan
- Department of Cardiology, Kings College Hospital NHS Foundation Trust, Denmark Hill, London, SE5 9RS, UK
| | - Jonathan Byrne
- Department of Cardiology, Kings College Hospital NHS Foundation Trust, Denmark Hill, London, SE5 9RS, UK
| | - Amanda Fife
- Department of Medical Microbiology, Kings College Hospital NHS Foundation Trust, Denmark Hill, London, SE5 9RS, UK
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26
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Huang Q, Fu A, Wang Y, Zhang J, Zhao W, Cheng Y. Microbiological diagnosis of endophthalmitis using nanopore targeted sequencing. Clin Exp Ophthalmol 2021; 49:1060-1068. [PMID: 34463015 PMCID: PMC9292959 DOI: 10.1111/ceo.13992] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/25/2021] [Accepted: 08/27/2021] [Indexed: 11/28/2022]
Abstract
BACKGROUND Microorganism identification is critical for the early diagnosis and management of infectious endophthalmitis, but traditional culture can yield false-negative results. Nanopore targeted sequencing (NTS) is a third-generation sequencing technique with multiple advantages. This study aimed to test aqueous humour or vitreous fluid samples from presumed cases of infectious endophthalmitis using NTS to evaluate the feasibility of NTS in diagnosing endophthalmitis, especially for culture-negative cases. METHODS This prospective study enrolled patients who presented to the Department of Ophthalmology of Union Hospital (Wuhan, China) between June 2018 and December 2020. The samples were sent immediately for routine microbiology culture processing and NTS assay. RESULTS NTS identified microorganisms in 17 of 18 cases (94.4%) (eight culture-positive cases, nine culture-negative cases, and one case unavailable for culture). There was a high-quality match between culture and NTS for culture-positive cases. In the eight culture-negative cases and the case unavailable for culture, NTS detected either bacteria, fungi, or a mixture of bacteria and fungi in the intraocular fluids. The average waiting times for the results of bacterial and fungal cultures were 48 and 72 h, respectively. The average time for the NTS results was 12 h. CONCLUSIONS NTS appears to be a promising diagnostic platform for diagnosing infectious endophthalmitis, even for culture-negative cases.
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Affiliation(s)
- Qiong Huang
- Department of Ophthalmology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Aisi Fu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, China
| | - Yiyan Wang
- Department of Ophthalmology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jie Zhang
- Department of Ophthalmology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wanxu Zhao
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, China.,Wuhan Dgensee Clinical Laboratory Co., Ltd, Wuhan, China
| | - Yang Cheng
- Department of Ophthalmology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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27
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To RK, Ramchandar N, Gupta A, Pong A, Cannavino C, Foley J, Farnaes L, Coufal NG. Use of Plasma Metagenomic Next-generation Sequencing for Pathogen Identification in Pediatric Endocarditis. Pediatr Infect Dis J 2021; 40:486-488. [PMID: 33410648 DOI: 10.1097/inf.0000000000003038] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Pediatric infective endocarditis incurs significant morbidity and generally occurs among children with underlying heart disease. Identification of a pathogen is critical in determining appropriate therapy. However, standard diagnostic testing has limited sensitivity. We describe a case series of children with infective endocarditis in whom plasma next-generation sequencing (Karius, Redwood, CA) identified an organism in 8 of 10 cases.
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Affiliation(s)
- Rachel K To
- From the Chicago Medical School, Rosalind Franklin University of Medicine and Science, Chicago, IL
| | - Nanda Ramchandar
- Department of Pediatrics, University of California, San Diego, CA.,Rady Children's Hospital of San Diego, San Diego, CA
| | - Aamisha Gupta
- Department of Pediatrics, University of California, San Diego, CA.,Rady Children's Hospital of San Diego, San Diego, CA
| | - Alice Pong
- Department of Pediatrics, University of California, San Diego, CA.,Rady Children's Hospital of San Diego, San Diego, CA
| | - Christopher Cannavino
- Department of Pediatrics, University of California, San Diego, CA.,Rady Children's Hospital of San Diego, San Diego, CA
| | | | - Lauge Farnaes
- Rady Children's Hospital of San Diego, San Diego, CA.,Rady Children's Institute for Genomic Medicine, San Diego, CA
| | - Nicole G Coufal
- Department of Pediatrics, University of California, San Diego, CA.,Rady Children's Institute for Genomic Medicine, San Diego, CA
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28
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Zhou M, Wu Y, Kudinha T, Jia P, Wang L, Xu Y, Yang Q. Comprehensive Pathogen Identification, Antibiotic Resistance, and Virulence Genes Prediction Directly From Simulated Blood Samples and Positive Blood Cultures by Nanopore Metagenomic Sequencing. Front Genet 2021; 12:620009. [PMID: 33841495 PMCID: PMC8024499 DOI: 10.3389/fgene.2021.620009] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 02/08/2021] [Indexed: 12/11/2022] Open
Abstract
Bloodstream infection is a major cause of morbidity and mortality worldwide. We explored whether MinION nanopore sequencing could accelerate diagnosis, resistance, and virulence profiling prediction in simulated blood samples and blood cultures. One milliliter of healthy blood samples each from direct spike (sample 1), anaerobic (sample 2), and aerobic (sample 3) blood cultures with initial inoculation of ∼30 CFU/ml of a clinically isolated Klebsiella pneumoniae strain was subjected to DNA extraction and nanopore sequencing. Hybrid assembly of Illumina and nanopore reads from pure colonies of the isolate (sample 4) was used as a reference for comparison. Hybrid assembly of the reference genome identified a total of 39 antibiotic resistance genes and 77 virulence genes through alignment with the CARD and VFDB databases. Nanopore correctly detected K. pneumoniae in all three blood samples. The fastest identification was achieved within 8 h from specimen to result in sample 1 without blood culture. However, direct sequencing in sample 1 only identified seven resistance genes (20.6%) but 28 genes in samples 2–4 (82.4%) compared to the reference within 2 h of sequencing time. Similarly, 11 (14.3%) and 74 (96.1%) of the virulence genes were detected in samples 1 and 2–4 within 2 h of sequencing time, respectively. Direct nanopore sequencing from positive blood cultures allowed comprehensive pathogen identification, resistance, and virulence genes prediction within 2 h, which shows its promising use in point-of-care clinical settings.
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Affiliation(s)
- Menglan Zhou
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Yarong Wu
- Beijing Applied Biological Technologies Co., Ltd., Beijing, China
| | - Timothy Kudinha
- School of Biomedical Sciences, Charles Sturt University, Orange, NSW, Australia.,Pathology West, NSW Health Pathology, Orange, NSW, Australia
| | - Peiyao Jia
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Lei Wang
- Beijing Applied Biological Technologies Co., Ltd., Beijing, China
| | - Yingchun Xu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Qiwen Yang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
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29
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Kotova EO, Domonova EA, Kobalava ZD, Karaulova JL, Pisaryuk AS, Balatskiy AV, Akimkin VG. Modern trends in identification of causative agents in infective endocarditis. RATIONAL PHARMACOTHERAPY IN CARDIOLOGY 2021. [DOI: 10.20996/1819-6446-2021-02-14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Advances in the diagnosis and treatment of patients with infectious endocarditis are limited by the high frequency of cases with an unknown etiology and imperfection of microbiological (cultural) methods. To overcome these problems new approaches to the identification of infectious endocarditis pathogens were introduced, which allowed achieving certain positive results. However, it should be noted that despite the wide variety of diagnostic tools currently used, there is no ideal method for etiological laboratory diagnosis of infectious endocarditis. The article discusses the features and place of immunochemical, molecular biological (MALDI-TOF MS, real-time PCR, sequencing, in situ fluorescence hybridization, metagenomic methods, etc.), immunohistochemical methods, and their advantages and limitations.
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Affiliation(s)
| | | | | | | | - A. S. Pisaryuk
- Peoples’ Friendship University of Russia (RUDN);
Moscow City Hospital named after V.V. Vinogradov
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Kotova EO, Domonova EA, Kobalava ZD, Shipulina OY, Karaulova YL, Pisaryuk AS. [Infective Endocarditis with Unknown Etiology: Possibilities of Conquering and Role of Microbiologistics]. ACTA ACUST UNITED AC 2021; 61:87-97. [PMID: 33706691 DOI: 10.18087/cardio.2021.1.n1218] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/15/2020] [Accepted: 07/29/2020] [Indexed: 11/18/2022]
Abstract
Current infectious endocarditis (IE) is characterized by changes in its etiological and epidemiological profiles associated with increased incidence of IE of undetermined etiology. This requires a search for ways to enhance the effectivity of diagnosis. Microbiologistics along with high-tech methods becomes decisively important for identifying the pathogen by studying cultures of blood and tissues from the affected heart valve. This determines timely diagnosis and treatment to be introduced to medical practice as a component of personalized medicine. The article focuses on the validity and features of microbiological (cultural), immunochemical, and molecular biological [MALDI-TOF MS (matrix-activated laser desorption/ionization with time-of-flight mass spectrometry), polymerase chain reaction, sequencing] studies.
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Affiliation(s)
- E O Kotova
- Peoples' Friendship University of Russia (RUDN), Moscow
| | - E A Domonova
- Central Research Institute of Epidemiology" of The Federal Service on Customers' Rights Protection and Human Wellbeing Surveillance, Moscow
| | - Zh D Kobalava
- Peoples' Friendship University of Russia (RUDN), Moscow
| | - O Y Shipulina
- Central Research Institute of Epidemiology" of The Federal Service on Customers' Rights Protection and Human Wellbeing Surveillance, Moscow
| | - Y L Karaulova
- Peoples' Friendship University of Russia (RUDN), Moscow
| | - A S Pisaryuk
- Peoples' Friendship University of Russia (RUDN), Moscow; City Hospital named after V.V. Vinogradov, Moscow
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Sheka D, Alabi N, Gordon PMK. Oxford nanopore sequencing in clinical microbiology and infection diagnostics. Brief Bioinform 2021; 22:6109725. [PMID: 33483726 DOI: 10.1093/bib/bbaa403] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/26/2020] [Accepted: 12/09/2020] [Indexed: 12/16/2022] Open
Abstract
Extended turnaround times and large economic costs hinder the usage of currently applied screening methods for bacterial pathogen identification (ID) and antimicrobial susceptibility testing. This review provides an overview of current detection methods and their usage in a clinical setting. Issues of timeliness and cost could soon be circumvented, however, with the emergence of detection methods involving single molecule sequencing technology. In the context of bringing diagnostics closer to the point of care, we examine the current state of Oxford Nanopore Technologies (ONT) products and their interaction with third-party software/databases to assess their capabilities for ID and antimicrobial resistance (AMR) prediction. We outline and discuss a potential diagnostic workflow, enumerating (1) rapid sample prep kits, (2) ONT hardware/software and (3) third-party software and databases to improve the cost, accuracy and turnaround times for ID and AMR. Multiple studies across a range of infection types support that the speed and accuracy of ONT sequencing is now such that established ID and AMR prediction tools can be used on its outputs, and so it can be harnessed for near real time, close to the point-of-care diagnostics in common clinical circumstances.
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Affiliation(s)
- Dropen Sheka
- Department of Biochemistry & Molecular Biology, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Nikolay Alabi
- Department of Biochemistry & Molecular Biology, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Paul M K Gordon
- Cumming School of Medicine Centre for Health Genomics and Informatics, University of Calgary
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Corduneanu A, Mihalca AD, Sándor AD, Hornok S, Malmberg M, Viso NP, Bongcam-Rudloff E. The heart microbiome of insectivorous bats from Central and South Eastern Europe. Comp Immunol Microbiol Infect Dis 2021; 75:101605. [PMID: 33421678 DOI: 10.1016/j.cimid.2020.101605] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 09/22/2020] [Accepted: 12/03/2020] [Indexed: 02/03/2023]
Abstract
Host associated microbiome not only may affect the individual health-status or provide insights into the species- or group specific bacterial communities but may act as early warning signs in the assessment of zoonotic reservoirs, offering clues to predict, prevent and control possible episodes of emerging zoonoses. Bats may be carriers and reservoirs of multiple pathogens such as viruses, bacteria and parasites, showing in the same time robust immunity against many of them. The microbiota plays a fundamental role on the induction, training and function of the host immune system and the immune system has largely evolved in order to maintain the symbiotic relationship of the host with these diverse microbes. Thus, expanding our knowledge on bat-associated microbiome it can be usefully in understanding bats' outstanding immune capacities. The aim of this study was to investigate the presence of different bacterial communities in heart tissue of insectivorous bats, Nyctalus noctula, Pipistrellus pipistrellus and Rhinoplophus hipposideros, from Central and Eastern Europe using high-throughput sequencing of variable regions of the 16S rRNA. In addition, species-specific PCRs were used to validate the presence of the vector-borne pathogens Bartonella spp. and Rickettsia spp. In this study we identified a wide variety of bacterial groups, with the most abundant phyla being Proteobacteria and Firmicutes. The results showed that at individual level, the year or location had no effect on the diversity and composition of the microbiome, however host species determined both structure and abundance of the bacterial community. We report the presence of vector-borne bacteria Bartonella spp. in samples of N. noctula and indications of Rickettsia spp. in R. hipposideros. Our results provide a first insight into the bacterial community found in heart tissue of bats from Central and South Eastern Europe.
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Affiliation(s)
- Alexandra Corduneanu
- Department of Parasitology and Parasitic Diseases, University of Agricultural Sciences and Veterinary Medicine of Cluj-Napoca, Romania
| | - Andrei Daniel Mihalca
- Department of Parasitology and Parasitic Diseases, University of Agricultural Sciences and Veterinary Medicine of Cluj-Napoca, Romania
| | - Attila D Sándor
- Department of Parasitology and Parasitic Diseases, University of Agricultural Sciences and Veterinary Medicine of Cluj-Napoca, Romania; Department of Parasitology and Zoology, University of Veterinary Medicine, Budapest, Hungary.
| | - Sándor Hornok
- Department of Parasitology and Zoology, University of Veterinary Medicine, Budapest, Hungary
| | - Maja Malmberg
- Section of Virology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Box 7028, 750 07, Uppsala, Sweden; SLU Global Bioinformatics Centre, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, 750 07, Uppsala, Sweden
| | - Natalia Pin Viso
- Consejo Nacional de Investigaciones Científicas y Técnicas, Godoy Cruz 2290, 1425, Ciudad Autónoma de Buenos Aires, Argentina; Instituto de Agrobiotecnología y Biología Molecular, IABiMo, INTA-CONICET, Calle Las Cabañas y Los Reseros s/n, Casilla de Correo 25, Castelar, 1712, Buenos Aires, Argentina
| | - Erik Bongcam-Rudloff
- SLU Global Bioinformatics Centre, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, 750 07, Uppsala, Sweden
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Latorre-Pérez A, Pascual J, Porcar M, Vilanova C. A lab in the field: applications of real-time, in situ metagenomic sequencing. Biol Methods Protoc 2020; 5:bpaa016. [PMID: 33134552 PMCID: PMC7585387 DOI: 10.1093/biomethods/bpaa016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 08/07/2020] [Accepted: 08/18/2020] [Indexed: 01/18/2023] Open
Abstract
High-throughput metagenomic sequencing is considered one of the main technologies fostering the development of microbial ecology. Widely used second-generation sequencers have enabled the analysis of extremely diverse microbial communities, the discovery of novel gene functions, and the comprehension of the metabolic interconnections established among microbial consortia. However, the high cost of the sequencers and the complexity of library preparation and sequencing protocols still hamper the application of metagenomic sequencing in a vast range of real-life applications. In this context, the emergence of portable, third-generation sequencers is becoming a popular alternative for the rapid analysis of microbial communities in particular scenarios, due to their low cost, simplicity of operation, and rapid yield of results. This review discusses the main applications of real-time, in situ metagenomic sequencing developed to date, highlighting the relevance of this technology in current challenges (such as the management of global pathogen outbreaks) and in the next future of industry and clinical diagnosis.
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Affiliation(s)
| | | | - Manuel Porcar
- Darwin Bioprospecting Excellence SL, Valencia, Spain
- Institute for Integrative Systems Biology, I2SysBio, University of Valencia-CSIC, Valencia, Spain
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Blood and Bronchoalveolar Lavage Fluid Metagenomic Next-Generation Sequencing in Pneumonia. CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY 2020; 2020:6839103. [PMID: 32879643 PMCID: PMC7448216 DOI: 10.1155/2020/6839103] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 07/02/2020] [Accepted: 07/11/2020] [Indexed: 12/27/2022]
Abstract
Background Metagenomic next-generation sequencing (mNGS) has made a revolution in the mode of pathogen identification. We decided to explore the diagnostic value of blood and bronchoalveolar lavage fluid (BALF) as mNGS samples in pneumonia. Methods We retrospectively reviewed 467 mNGS results and assessed the diagnostic performance of paired blood and BALF mNGS in 39 patients with pneumonia. Results For bacteria and fungi, 16 patients had culture-confirmed pathogen diagnosis, while 13 patients were culture-negative. BALF mNGS was more sensitive than blood mNGS (81.3% vs. 25.0%, p=0.003), and the specificity in BALF and blood mNGS was not statistically significant different (76.9% vs. 84.6%, p=0.317). For 10 patients without culture test, treatments were changed in 2 patients. For viruses, Epstein-Barr virus was positive in blood mNGS in 9 patients. Human adenovirus was detected in both BALF and blood mNGS in 3 patients. Conclusion Our study suggests that BALF mNGS is more sensitive than blood mNGS in detecting bacteria and fungi, but blood also has advantages to identify the pathogens of pneumonia, especially for some viruses.
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Ma L, Ge Y, Ma H, Zhu B, Miao Q. Infective endocarditis at a tertiary-care hospital in China. J Cardiothorac Surg 2020; 15:135. [PMID: 32522279 PMCID: PMC7285574 DOI: 10.1186/s13019-020-01183-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 06/02/2020] [Indexed: 01/01/2023] Open
Abstract
Background The aim of this study was to describe the clinical features and outcome of infective endocarditis at a general hospital in China and to identify the risk factors associated with in-hospital mortality. Methods A retrospective study was conducted and all patients diagnosed with definite or possible infective endocarditis between January 2013 and June 2018 according to the modified Duke criteria were included. Results A total of 381 patients were included. The mean age was 46 years old and 66.9% patients were male patients. Community acquired IE was the most common type of infective endocarditis and Viridans Group Streptococci (37.5%) was still the most common causative pathogen. The microbial etiology of infective endocarditis varied with location of acquisition. 97 (25.5%) patients had culture-negative infective endocarditis. Vegetations were detected in 85% patients and mitral valve was the most common involved valve. Operations were performed in 72.7% patients and in-hospital mortality rate was 8.4%. The risk factors of in-hospital mortality were age old than 70 years old, heart failure, stroke and medical therapy. Conclusions Older age, heart failure, stroke and medical therapy were risk factors of in-hospital mortality. Infective endocarditis, were mainly caused by Viridans Group Streptococci, characterized by younger patients and lower mortality rate in China.
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Affiliation(s)
- Lulu Ma
- Department of Anesthesiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Ying Ge
- Department of Infectious Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Haobo Ma
- Department of Anesthesia, Critical Care and Pain Medicine, Beth Isreal Deaconess Medical Center, Boston, MA, 02215, USA
| | - Bo Zhu
- Department of Anesthesiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
| | - Qi Miao
- Department of Cardiac Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
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Yang T, Mei Q, Zhang L, Chen Z, Zhu C, Fang X, Geng S, Pan A. Hemophagocytic lymphohistiocytosis is associated with Bartonella henselae infection in a patient with multiple susceptibility genes. Ann Clin Microbiol Antimicrob 2020; 19:28. [PMID: 32517705 PMCID: PMC7281694 DOI: 10.1186/s12941-020-00370-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 05/30/2020] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Adult-onset hemophagocytic lymphohistiocytosis (HLH) is a rare and life-threatening condition, which is often triggered by certain types of infection, cancer and numerous autoimmune diseases; however, of the numerous infectious triggers associated with HLH, the consequences of Bartonella henselae infection have been rarely reported. CASE PRESENTATION A 48-year-old female presented with a 20-day history of intermittent fever accompanied by systemic rash, fatigue, anorexia and weight loss later she developed shock and unconsciousness. Blood tests showed a reduction of leukocyte, anemia and thrombocytopenia, and pathological results of a bone marrow biopsy confirmed hemophagocytic activity. Metagenomic next-generation sequencing (mNGS) analysis of the lymph node detected the presence of B. henselae. Whole exome sequencing revealed two gene variants, STXBP2 and IRF5, in this adult patient with secondary HLH. Then, she received minocycline and rifampin combination anti-infective therapy. Intravenous immunoglobulin for 5 days followed by a high dose of methylprednisolone were also administered. The patient was successfully discharged from the intensive care unit and remained in good condition after 2 months of follow-up. CONCLUSIONS mNGS served crucial roles in obtaining an etiological diagnosis, which suggested that screening for B. henselae should be considered in patients with HLH, especially those with a cat at home. In addition, the genetic defects were discovered to not only be present in primary HLH, but also in secondary HLH, even in the elderly.
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Affiliation(s)
- Tianjun Yang
- Department of Intensive Care Unit, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, 17 Lujiang Road, Hefei, Anhui, China
| | - Qing Mei
- Department of Intensive Care Unit, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, 17 Lujiang Road, Hefei, Anhui, China
| | - Lei Zhang
- Department of Intensive Care Unit, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, 17 Lujiang Road, Hefei, Anhui, China
| | - Zhendong Chen
- Department of Intensive Care Unit, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, 17 Lujiang Road, Hefei, Anhui, China
| | - Chunyan Zhu
- Department of Intensive Care Unit, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, 17 Lujiang Road, Hefei, Anhui, China
| | - Xiaowei Fang
- Department of Intensive Care Unit, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, 17 Lujiang Road, Hefei, Anhui, China
| | - Shike Geng
- Department of Intensive Care Unit, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, 17 Lujiang Road, Hefei, Anhui, China.,Department of Intensive Care Unit, Affiliated Provincial Hospital of Anhui Medical University, 17 Lujiang Road, Hefei, Anhui, China
| | - Aijun Pan
- Department of Intensive Care Unit, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, 17 Lujiang Road, Hefei, Anhui, China. .,Department of Intensive Care Unit, Affiliated Provincial Hospital of Anhui Medical University, 17 Lujiang Road, Hefei, Anhui, China.
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Preliminary assessment of nanopore-based metagenomic sequencing for the diagnosis of prosthetic joint infection. Int J Infect Dis 2020; 97:54-59. [PMID: 32439542 DOI: 10.1016/j.ijid.2020.05.044] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 05/11/2020] [Accepted: 05/12/2020] [Indexed: 01/10/2023] Open
Abstract
OBJECTIVES Pathogen identification is crucial for the diagnosis and management of periprosthetic joint infection (PJI). Although culturing methods are the foundation of pathogen detection in PJI, false-negative results often occur. Oxford nanopore sequencing (ONS) is a promising alternative for detecting pathogens and providing information on their antimicrobial resistance (AMR) profiles, without culturing. METHODS To evaluate the capability of metagenomic ONS (mONS) in detecting pathogens from PJI samples, both metagenomic next-generation sequencing (mNGS) and mONS were performed in 15 osteoarticular samples from nine consecutive PJI patients according to the modified Musculoskeletal Infection Society (MSIS) criteria. The sequencing data generated from both platforms were then analyzed for pathogen identification and AMR detection using an in-house-developed bioinformatics pipeline. RESULTS Our results showed that mONS could be applied to detect the causative pathogen and characterize its AMR features in fresh PJI samples. By real-time sequencing and analysis, pathogen identification and AMR detection from the initiation of sequencing were accelerated. CONCLUSION We showed proof of concept that mONS can function as a rapid, accurate tool in PJI diagnostic microbiology. Despite efforts to reduce host DNA, the high proportion of host DNA was still a limitation of this method that prevented full genome analysis.
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Arunasri K, Mahesh M, Sai Prashanthi G, Jayasudha R, Kalyana Chakravarthy S, Tyagi M, Pappuru RR, Shivaji S. Comparison of the Vitreous Fluid Bacterial Microbiomes between Individuals with Post Fever Retinitis and Healthy Controls. Microorganisms 2020; 8:E751. [PMID: 32429503 PMCID: PMC7285296 DOI: 10.3390/microorganisms8050751] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/23/2020] [Accepted: 05/04/2020] [Indexed: 12/21/2022] Open
Abstract
Ocular microbiome research has gained momentum in the recent past and has provided new insights into health and disease conditions. However, studies on sight threatening intraocular inflammatory diseases have remained untouched. In the present study, we attempted to identify the bacterial microbiome associated with post fever retinitis using a metagenomic sequencing approach. For this purpose, bacterial ocular microbiomes were generated from vitreous samples collected from control individuals (VC, n = 19) and individuals with post fever retinitis (PFR, n = 9), and analysed. The results revealed 18 discriminative genera in the microbiomes of the two cohorts out of which 16 genera were enriched in VC and the remaining two in PFR group. These discriminative genera were inferred to have antimicrobial, anti-inflammatory, and probiotic function. Only two pathogenic bacteria were differentially abundant in 20% of the PFR samples. PCoA and heatmap analysis showed that the vitreous microbiomes of VC and PFR formed two distinct clusters indicating dysbiosis in the vitreous bacterial microbiomes. Functional assignments and network analysis also revealed that the vitreous bacterial microbiomes in the control group exhibited more evenness in the bacterial diversity and several bacteria had antimicrobial function compared to the PFR group.
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Affiliation(s)
- Kotakonda Arunasri
- Jhaveri Microbiology Centre, Prof Brien Holden Eye Research Centre, L V Prasad Eye Institute, L V Prasad Marg, Banjara Hills, Hyderabad 500034, India; (K.A.); (M.M.); (G.S.P.); (R.J.); (S.K.C.)
| | - Malleswarapu Mahesh
- Jhaveri Microbiology Centre, Prof Brien Holden Eye Research Centre, L V Prasad Eye Institute, L V Prasad Marg, Banjara Hills, Hyderabad 500034, India; (K.A.); (M.M.); (G.S.P.); (R.J.); (S.K.C.)
| | - Gumpili Sai Prashanthi
- Jhaveri Microbiology Centre, Prof Brien Holden Eye Research Centre, L V Prasad Eye Institute, L V Prasad Marg, Banjara Hills, Hyderabad 500034, India; (K.A.); (M.M.); (G.S.P.); (R.J.); (S.K.C.)
| | - Rajagopalaboopathi Jayasudha
- Jhaveri Microbiology Centre, Prof Brien Holden Eye Research Centre, L V Prasad Eye Institute, L V Prasad Marg, Banjara Hills, Hyderabad 500034, India; (K.A.); (M.M.); (G.S.P.); (R.J.); (S.K.C.)
| | - Sama Kalyana Chakravarthy
- Jhaveri Microbiology Centre, Prof Brien Holden Eye Research Centre, L V Prasad Eye Institute, L V Prasad Marg, Banjara Hills, Hyderabad 500034, India; (K.A.); (M.M.); (G.S.P.); (R.J.); (S.K.C.)
| | - Mudit Tyagi
- Smt. Kanuri Santhamma Centre for Vitreo Retinal Diseases, L V Prasad Eye Institute, L V Prasad Marg, Banjara Hills, Hyderabad 500034, India; (M.T.); (R.R.P.)
| | - Rajeev R. Pappuru
- Smt. Kanuri Santhamma Centre for Vitreo Retinal Diseases, L V Prasad Eye Institute, L V Prasad Marg, Banjara Hills, Hyderabad 500034, India; (M.T.); (R.R.P.)
| | - Sisinthy Shivaji
- Jhaveri Microbiology Centre, Prof Brien Holden Eye Research Centre, L V Prasad Eye Institute, L V Prasad Marg, Banjara Hills, Hyderabad 500034, India; (K.A.); (M.M.); (G.S.P.); (R.J.); (S.K.C.)
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Yang M, Cousineau A, Liu X, Luo Y, Sun D, Li S, Gu T, Sun L, Dillow H, Lepine J, Xu M, Zhang B. Direct Metatranscriptome RNA-seq and Multiplex RT-PCR Amplicon Sequencing on Nanopore MinION - Promising Strategies for Multiplex Identification of Viable Pathogens in Food. Front Microbiol 2020; 11:514. [PMID: 32328039 PMCID: PMC7160302 DOI: 10.3389/fmicb.2020.00514] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 03/10/2020] [Indexed: 12/20/2022] Open
Abstract
Viable pathogenic bacteria are major biohazards that pose a significant threat to food safety. Despite the recent developments in detection platforms, multiplex identification of viable pathogens in food remains a major challenge. A novel strategy is developed through direct metatranscriptome RNA-seq and multiplex RT-PCR amplicon sequencing on Nanopore MinION to achieve real-time multiplex identification of viable pathogens in food. Specifically, this study reports an optimized universal Nanopore sample extraction and library preparation protocol applicable to both Gram-positive and Gram-negative pathogenic bacteria, demonstrated using a cocktail culture of E. coli O157:H7, Salmonella enteritidis, and Listeria monocytogenes, which were selected based on their impact on economic loss or prevalence in recent outbreaks. Further evaluation and validation confirmed the accuracy of direct metatranscriptome RNA-seq and multiplex RT-PCR amplicon sequencing using Sanger sequencing and selective media. The study also included a comparison of different bioinformatic pipelines for metatranscriptomic and amplicon genomic analysis. MEGAN without rRNA mapping showed the highest accuracy of multiplex identification using the metatranscriptomic data. EPI2ME also demonstrated high accuracy using multiplex RT-PCR amplicon sequencing. In addition, a systemic comparison was drawn between Nanopore sequencing of the direct metatranscriptome RNA-seq and RT-PCR amplicons. Both methods are comparable in accuracy and time. Nanopore sequencing of RT-PCR amplicons has higher sensitivity, but Nanopore metatranscriptome sequencing excels in read length and dealing with complex microbiome and non-bacterial transcriptome backgrounds.
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Affiliation(s)
- Manyun Yang
- Department of Biomedical and Nutritional Sciences, University of Massachusetts, Lowell, MA, United States
| | | | - Xiaobo Liu
- Department of Biomedical and Nutritional Sciences, University of Massachusetts, Lowell, MA, United States
| | - Yaguang Luo
- Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD, United States
| | - Daniel Sun
- New England Biolabs, Inc., Ipswich, MA, United States
- Department of Chemistry, Brandeis University, Waltham, MA, United States
| | - Shaohua Li
- New England Biolabs, Inc., Ipswich, MA, United States
- U.S. Food and Drug Administration, Silver Spring, MD, United States
| | - Tingting Gu
- Department of Biomedical and Nutritional Sciences, University of Massachusetts, Lowell, MA, United States
| | - Luo Sun
- New England Biolabs, Inc., Ipswich, MA, United States
| | - Hayden Dillow
- Department of Biomedical and Nutritional Sciences, University of Massachusetts, Lowell, MA, United States
| | - Jack Lepine
- Biomolecular Characterization Lab, University of Massachusetts Lowell, Lowell, MA, United States
| | - Mingqun Xu
- New England Biolabs, Inc., Ipswich, MA, United States
| | - Boce Zhang
- Department of Biomedical and Nutritional Sciences, University of Massachusetts, Lowell, MA, United States
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Wang CX, Huang Z, Fang X, Li W, Yang B, Zhang W. Comparison of broad-range polymerase chain reaction and metagenomic next-generation sequencing for the diagnosis of prosthetic joint infection. Int J Infect Dis 2020; 95:8-12. [PMID: 32251799 DOI: 10.1016/j.ijid.2020.03.055] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 03/18/2020] [Accepted: 03/24/2020] [Indexed: 12/13/2022] Open
Abstract
PURPOSE The aims of our study were to (1) evaluate the concordance of both methods for detecting prosthetic joint infection (PJI) pathogens in joint fluid and to (2) clarify whether broad-range polymerase chain reaction (BR-PCR) can be used as a verification method for metagenomic next-generation sequencing (mNGS) for PJI diagnosis. METHODS In total, 63 patients underwent total joint arthroplasty, with 45 PJI and 18 aseptic failure patients included. Joint fluids were sampled after antibiotics were withheld for more than 2 weeks, and then, culture, BR-PCR and mNGS were performed for all samples. RESULTS The joint fluid BR-PCR sensitivity was 82.2%, which was not significantly different from that of mNGS (95.6%) or culture (77.8%). The specificities of the 3 methods were all 94.4%. BR-PCR failed to identify the pathogens in 1 polymicrobial infection patient and 4 fungal infection patients. CONCLUSION mNGS was more sensitive than BR-PCR for detecting PJI pathogens in joint fluid. BR-PCR is insufficient for use as an mNGS verification method.
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Affiliation(s)
- Chao-Xin Wang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350004, China
| | - Zida Huang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350004, China
| | - Xinyu Fang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350004, China
| | - Wenbo Li
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350004, China
| | - Bin Yang
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350004, China
| | - Wenming Zhang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350004, China.
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Ramírez-Carreto S, Miranda-Zaragoza B, Rodríguez-Almazán C. Actinoporins: From the Structure and Function to the Generation of Biotechnological and Therapeutic Tools. Biomolecules 2020; 10:E539. [PMID: 32252469 PMCID: PMC7226409 DOI: 10.3390/biom10040539] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/19/2020] [Accepted: 03/21/2020] [Indexed: 12/22/2022] Open
Abstract
Actinoporins (APs) are a family of pore-forming toxins (PFTs) from sea anemones. These biomolecules exhibit the ability to exist as soluble monomers within an aqueous medium or as constitutively open oligomers in biological membranes. Through their conformational plasticity, actinoporins are considered good candidate molecules to be included for the rational design of molecular tools, such as immunotoxins directed against tumor cells and stochastic biosensors based on nanopores to analyze unique DNA or protein molecules. Additionally, the ability of these proteins to bind to sphingomyelin (SM) facilitates their use for the design of molecular probes to identify SM in the cells. The immunomodulatory activity of actinoporins in liposomal formulations for vaccine development has also been evaluated. In this review, we describe the potential of actinoporins for use in the development of molecular tools that could be used for possible medical and biotechnological applications.
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Affiliation(s)
| | | | - Claudia Rodríguez-Almazán
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca, Morelos 62210, Mexico; (S.R.-C.); (B.M.-Z.)
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42
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Petersen LM, Martin IW, Moschetti WE, Kershaw CM, Tsongalis GJ. Third-Generation Sequencing in the Clinical Laboratory: Exploring the Advantages and Challenges of Nanopore Sequencing. J Clin Microbiol 2019; 58:e01315-19. [PMID: 31619531 PMCID: PMC6935936 DOI: 10.1128/jcm.01315-19] [Citation(s) in RCA: 125] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Metagenomic sequencing for infectious disease diagnostics is an important tool that holds promise for use in the clinical laboratory. Challenges for implementation so far include high cost, the length of time to results, and the need for technical and bioinformatics expertise. However, the recent technological innovation of nanopore sequencing from Oxford Nanopore Technologies (ONT) has the potential to address these challenges. ONT sequencing is an attractive platform for clinical laboratories to adopt due to its low cost, rapid turnaround time, and user-friendly bioinformatics pipelines. However, this method still faces the problem of base-calling accuracy compared to other platforms. This review highlights the general challenges of pathogen detection in clinical specimens by metagenomic sequencing, the advantages and disadvantages of the ONT platform, and how research to date supports the potential future use of nanopore sequencing in infectious disease diagnostics.
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Affiliation(s)
- Lauren M Petersen
- Dartmouth-Hitchcock Medical Center, Department of Pathology and Laboratory Medicine, Lebanon, New Hampshire, USA
| | - Isabella W Martin
- Dartmouth-Hitchcock Medical Center, Department of Pathology and Laboratory Medicine, Lebanon, New Hampshire, USA
| | - Wayne E Moschetti
- Dartmouth-Hitchcock Medical Center, Department of Orthopaedics and Sports Medicine, Lebanon, New Hampshire, USA
| | - Colleen M Kershaw
- Dartmouth-Hitchcock Medical Center, Department of Infectious Disease and International Health, Lebanon, New Hampshire, USA
| | - Gregory J Tsongalis
- Dartmouth-Hitchcock Medical Center, Department of Pathology and Laboratory Medicine, Lebanon, New Hampshire, USA
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43
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Chan WS, Au CH, Leung HCM, Ho DN, Li D, Chan TL, Lam TW, Ma ESK, Tang BSF. Potential utility of metagenomic sequencing for improving etiologic diagnosis of infective endocarditis. Future Cardiol 2019; 15:411-424. [PMID: 31691592 DOI: 10.2217/fca-2018-0088] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Aim: To explore potential utility of metagenomic sequencing for improving etiologic diagnosis of infective endocarditis (IE) caused by fastidious bacteria. Materials & methods: Plasma and heart valves of two patients, who were diagnosed with IE caused by Bartonella quintana and Propionibacterium species, were sequenced by using Illumina MiSeq and Nanopore MinION. Results: For patient 1, B. quintana was detected in the plasma pool collected 4 days before valvular replacement surgery. For patient 2, Propionibacterium sp. oral taxon 193 was detected in the plasma sample collected on hospital day 1. Nearly complete bacterial genomes (>98%) were retrieved from resected heart valves of both patients, enabling detection of antibiotic resistance-associated features. Real-time sequencing of heart valves identified both pathogens within the first 16 min of sequencing runs. Conclusion: Metagenomic sequencing may be a helpful supplement to IE diagnostic workflow, especially when conventional tests fail to yield a diagnosis.
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Affiliation(s)
- Wai-Sing Chan
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, PR China
| | - Chun-Hang Au
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, PR China
| | - Henry Chi-Ming Leung
- Department of Computer Science, The University of Hong Kong, Hong Kong, PR China.,L3 Bioinformatics Limited, Hong Kong, PR China
| | - Dona N Ho
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, PR China
| | - Dinghua Li
- Department of Computer Science, The University of Hong Kong, Hong Kong, PR China
| | - Tsun-Leung Chan
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, PR China
| | - Tak-Wah Lam
- Department of Computer Science, The University of Hong Kong, Hong Kong, PR China.,L3 Bioinformatics Limited, Hong Kong, PR China
| | - Edmond Shiu-Kwan Ma
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, PR China
| | - Bone Siu-Fai Tang
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, PR China
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44
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Brinkmann A, Andrusch A, Belka A, Wylezich C, Höper D, Pohlmann A, Nordahl Petersen T, Lucas P, Blanchard Y, Papa A, Melidou A, Oude Munnink BB, Matthijnssens J, Deboutte W, Ellis RJ, Hansmann F, Baumgärtner W, van der Vries E, Osterhaus A, Camma C, Mangone I, Lorusso A, Marcacci M, Nunes A, Pinto M, Borges V, Kroneman A, Schmitz D, Corman VM, Drosten C, Jones TC, Hendriksen RS, Aarestrup FM, Koopmans M, Beer M, Nitsche A. Proficiency Testing of Virus Diagnostics Based on Bioinformatics Analysis of Simulated In Silico High-Throughput Sequencing Data Sets. J Clin Microbiol 2019; 57:e00466-19. [PMID: 31167846 PMCID: PMC6663916 DOI: 10.1128/jcm.00466-19] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 05/28/2019] [Indexed: 12/22/2022] Open
Abstract
Quality management and independent assessment of high-throughput sequencing-based virus diagnostics have not yet been established as a mandatory approach for ensuring comparable results. The sensitivity and specificity of viral high-throughput sequence data analysis are highly affected by bioinformatics processing using publicly available and custom tools and databases and thus differ widely between individuals and institutions. Here we present the results of the COMPARE [Collaborative Management Platform for Detection and Analyses of (Re-)emerging and Foodborne Outbreaks in Europe] in silico virus proficiency test. An artificial, simulated in silico data set of Illumina HiSeq sequences was provided to 13 different European institutes for bioinformatics analysis to identify viral pathogens in high-throughput sequence data. Comparison of the participants' analyses shows that the use of different tools, programs, and databases for bioinformatics analyses can impact the correct identification of viral sequences from a simple data set. The identification of slightly mutated and highly divergent virus genomes has been shown to be most challenging. Furthermore, the interpretation of the results, together with a fictitious case report, by the participants showed that in addition to the bioinformatics analysis, the virological evaluation of the results can be important in clinical settings. External quality assessment and proficiency testing should become an important part of validating high-throughput sequencing-based virus diagnostics and could improve the harmonization, comparability, and reproducibility of results. There is a need for the establishment of international proficiency testing, like that established for conventional laboratory tests such as PCR, for bioinformatics pipelines and the interpretation of such results.
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Affiliation(s)
- Annika Brinkmann
- Robert Koch Institute, Centre for Biological Threats and Special Pathogens 1, Berlin, Germany
| | - Andreas Andrusch
- Robert Koch Institute, Centre for Biological Threats and Special Pathogens 1, Berlin, Germany
| | - Ariane Belka
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
| | - Claudia Wylezich
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
| | - Dirk Höper
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
| | - Anne Pohlmann
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
| | - Thomas Nordahl Petersen
- Technical University of Denmark, National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Foodborne Pathogens and Genomics and European Union Reference Laboratory for Antimicrobial Resistance, Kongens Lyngby, Denmark
| | - Pierrick Lucas
- French Agency for Food, Environmental and Occupational Health and Safety, Laboratory of Ploufragan, Unit of Viral Genetics and Biosafety, Ploufragan, France
| | - Yannick Blanchard
- French Agency for Food, Environmental and Occupational Health and Safety, Laboratory of Ploufragan, Unit of Viral Genetics and Biosafety, Ploufragan, France
| | - Anna Papa
- Microbiology Department, Aristotle University of Thessaloniki, School of Medicine, Thessaloniki, Greece
| | - Angeliki Melidou
- Microbiology Department, Aristotle University of Thessaloniki, School of Medicine, Thessaloniki, Greece
| | - Bas B Oude Munnink
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, The Netherlands
| | | | | | | | - Florian Hansmann
- Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Wolfgang Baumgärtner
- Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Erhard van der Vries
- Department of Infectious Diseases and Immunology, University of Utrecht, Utrecht, The Netherlands
| | | | - Cesare Camma
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise G. Caporale, National Reference Center for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatic Analysis, Teramo, Italy
| | - Iolanda Mangone
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise G. Caporale, National Reference Center for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatic Analysis, Teramo, Italy
| | - Alessio Lorusso
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise G. Caporale, National Reference Center for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatic Analysis, Teramo, Italy
| | - Maurilia Marcacci
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise G. Caporale, National Reference Center for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatic Analysis, Teramo, Italy
| | - Alexandra Nunes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), Lisbon, Portugal
| | - Miguel Pinto
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), Lisbon, Portugal
| | - Vítor Borges
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), Lisbon, Portugal
| | - Annelies Kroneman
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Dennis Schmitz
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, The Netherlands
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Victor Max Corman
- Institute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Christian Drosten
- Institute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Terry C Jones
- Institute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Rene S Hendriksen
- Technical University of Denmark, National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Foodborne Pathogens and Genomics and European Union Reference Laboratory for Antimicrobial Resistance, Kongens Lyngby, Denmark
| | - Frank M Aarestrup
- Technical University of Denmark, National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Foodborne Pathogens and Genomics and European Union Reference Laboratory for Antimicrobial Resistance, Kongens Lyngby, Denmark
| | - Marion Koopmans
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Martin Beer
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
| | - Andreas Nitsche
- Robert Koch Institute, Centre for Biological Threats and Special Pathogens 1, Berlin, Germany
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45
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Lin JH, Wu ZY, Gong L, Wong CH, Chao WC, Yen CM, Wang CP, Wei CL, Huang YT, Liu PY. Complex Microbiome in Brain Abscess Revealed by Whole-Genome Culture-Independent and Culture-Based Sequencing. J Clin Med 2019; 8:jcm8030351. [PMID: 30871085 PMCID: PMC6462986 DOI: 10.3390/jcm8030351] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 03/04/2019] [Accepted: 03/07/2019] [Indexed: 02/07/2023] Open
Abstract
Brain abscess is a severe infectious disease with high mortality and mobility. Although culture-based techniques have been widely used for the investigation of microbial composition of brain abscess, these approaches are inherent biased. Recent studies using 16S ribosomal sequencing approaches revealed high complexity of the bacterial community involved in brain abscess but fail to detect fungal and viral composition. In the study, both culture-independent nanopore metagenomic sequencing and culture-based whole-genome sequencing using both the Illumina and the Nanopore platforms were conducted to investigate the microbial composition and genomic characterization in brain abscess. Culture-independent metagenomic sequencing revealed not only a larger taxonomic diversity of bacteria but also the presence of fungi and virus communities. The culture-based whole-genome sequencing identified a novel species in Prevotella and reconstructs a Streptococcus constellatus with a high GC-skew genome. Antibiotic-resistance genes CfxA and ErmF associated with resistance to penicillin and clindamycin were also identified in culture-based and culture-free sequencing. This study implies current understanding of brain abscess need to consider the broader diversity of microorganisms.
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Affiliation(s)
- Jyun-Hong Lin
- Department of Computer Science and Information Engineering, National Chung Cheng University, Chia-Yi 62102, Taiwan.
| | - Zong-Yen Wu
- Department of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan.
| | - Liang Gong
- Genome Technologies, The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
| | - Chee-Hong Wong
- Genome Technologies, The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
| | - Wen-Cheng Chao
- Department of Medical Research, Taichung Veterans General Hospital, Taichung 40705, Taiwan.
| | - Chun-Ming Yen
- Program in Translational Medicine, National Chung Hsing University, Taichung 40227, Taiwan.
- Department of Neurosurgery, Neurological Institute, Taichung Veterans General Hospital, Taichung 40705, Taiwan.
| | - Ching-Ping Wang
- Department of Otolaryngology-Head and Neck Surgery, Taichung Veterans General Hospital, Taichung 40705, Taiwan.
| | - Chia-Lin Wei
- Genome Technologies, The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
| | - Yao-Ting Huang
- Department of Computer Science and Information Engineering, National Chung Cheng University, Chia-Yi 62102, Taiwan.
| | - Po-Yu Liu
- Program in Translational Medicine, National Chung Hsing University, Taichung 40227, Taiwan.
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung 40705, Taiwan.
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46
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Tedersoo L, Drenkhan R, Anslan S, Morales‐Rodriguez C, Cleary M. High-throughput identification and diagnostics of pathogens and pests: Overview and practical recommendations. Mol Ecol Resour 2019; 19:47-76. [PMID: 30358140 PMCID: PMC7379260 DOI: 10.1111/1755-0998.12959] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 08/01/2018] [Accepted: 08/28/2018] [Indexed: 12/26/2022]
Abstract
High-throughput identification technologies provide efficient tools for understanding the ecology and functioning of microorganisms. Yet, these methods have been only rarely used for monitoring and testing ecological hypotheses in plant pathogens and pests in spite of their immense importance in agriculture, forestry and plant community dynamics. The main objectives of this manuscript are the following: (a) to provide a comprehensive overview about the state-of-the-art high-throughput quantification and molecular identification methods used to address population dynamics, community ecology and host associations of microorganisms, with a specific focus on antagonists such as pathogens, viruses and pests; (b) to compile available information and provide recommendations about specific protocols and workable primers for bacteria, fungi, oomycetes and insect pests; and (c) to provide examples of novel methods used in other microbiological disciplines that are of great potential use for testing specific biological hypotheses related to pathology. Finally, we evaluate the overall perspectives of the state-of-the-art and still evolving methods for diagnostics and population- and community-level ecological research of pathogens and pests.
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Affiliation(s)
- Leho Tedersoo
- Natural History Museum and Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Rein Drenkhan
- Institute of Forestry and Rural EngineeringEstonian University of Life SciencesTartuEstonia
| | - Sten Anslan
- Natural History Museum and Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | | | - Michelle Cleary
- Southern Swedish Forest Research CentreSwedish University of Agricultural SciencesAlnarpSweden
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