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Xing Z, Jiang H, Liu X, Chai Q, Xin Z, Zhu C, Bao Y, Chen H, Gao H, Ma D. Integrating DNA/RNA microbe detection and host response for accurate diagnosis, treatment and prognosis of childhood infectious meningitis and encephalitis. J Transl Med 2024; 22:583. [PMID: 38902725 PMCID: PMC11191231 DOI: 10.1186/s12967-024-05370-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 06/02/2024] [Indexed: 06/22/2024] Open
Abstract
BACKGROUND Infectious meningitis/encephalitis (IM) is a severe neurological disease that can be caused by bacterial, viral, and fungal pathogens. IM suffers high morbidity, mortality, and sequelae in childhood. Metagenomic next-generation sequencing (mNGS) can potentially improve IM outcomes by sequencing both pathogen and host responses and increasing the diagnosis accuracy. METHODS Here we developed an optimized mNGS pipeline named comprehensive mNGS (c-mNGS) to monitor DNA/RNA pathogens and host responses simultaneously and applied it to 142 cerebrospinal fluid samples. According to retrospective diagnosis, these samples were classified into three categories: confirmed infectious meningitis/encephalitis (CIM), suspected infectious meningitis/encephalitis (SIM), and noninfectious controls (CTRL). RESULTS Our pipeline outperformed conventional methods and identified RNA viruses such as Echovirus E30 and etiologic pathogens such as HHV-7, which would not be clinically identified via conventional methods. Based on the results of the c-mNGS pipeline, we successfully detected antibiotic resistance genes related to common antibiotics for treating Escherichia coli, Acinetobacter baumannii, and Group B Streptococcus. Further, we identified differentially expressed genes in hosts of bacterial meningitis (BM) and viral meningitis/encephalitis (VM). We used these genes to build a machine-learning model to pinpoint sample contaminations. Similarly, we also built a model to predict poor prognosis in BM. CONCLUSIONS This study developed an mNGS-based pipeline for IM which measures both DNA/RNA pathogens and host gene expression in a single assay. The pipeline allows detecting more viruses, predicting antibiotic resistance, pinpointing contaminations, and evaluating prognosis. Given the comparable cost to conventional mNGS, our pipeline can become a routine test for IM.
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Affiliation(s)
- Zhihao Xing
- Biobank & Clinical laboratory & Department of Respiratory Medicine, Shenzhen Children's Hospital of Shantou University Medical College, Shenzhen, Guangdong, China
- Institute of Pediatrics, Shenzhen Children's Hospital, Shenzhen, Guangdong, China
| | - Hanfang Jiang
- Clinical laboratory, Shenzhen Children's Hospital, Shenzhen, Guangdong, China
| | - Xiaorong Liu
- Biobank & Clinical laboratory & Department of Respiratory Medicine, Shenzhen Children's Hospital of Shantou University Medical College, Shenzhen, Guangdong, China
- Institute of Pediatrics, Shenzhen Children's Hospital, Shenzhen, Guangdong, China
| | - Qiang Chai
- Institute of Pediatrics, Shenzhen Children's Hospital, Shenzhen, Guangdong, China
| | - Zefeng Xin
- Institute of Pediatrics, Shenzhen Children's Hospital, Shenzhen, Guangdong, China
| | - Chunqing Zhu
- Institute of Pediatrics, Shenzhen Children's Hospital, Shenzhen, Guangdong, China
- Clinical laboratory, Shenzhen Children's Hospital, Shenzhen, Guangdong, China
| | - Yanmin Bao
- Department of Respiratory Medicine, Shenzhen Children's Hospital, Shenzhen, Guangdong, China
| | - Hongyu Chen
- Clinical laboratory, Shenzhen Children's Hospital, Shenzhen, Guangdong, China
| | - Hongdan Gao
- Medical Testing, Bengbu Medical College, Bengbu, Anhui, China
| | - Dongli Ma
- Institute of Pediatrics, Shenzhen Children's Hospital, Shenzhen, Guangdong, China.
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Conradie T, Caparros-Martin JA, Egan S, Kicic A, Koks S, Stick SM, Agudelo-Romero P. Exploring the Complexity of the Human Respiratory Virome through an In Silico Analysis of Shotgun Metagenomic Data Retrieved from Public Repositories. Viruses 2024; 16:953. [PMID: 38932245 PMCID: PMC11209621 DOI: 10.3390/v16060953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 05/31/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND Respiratory viruses significantly impact global morbidity and mortality, causing more disease in humans than any other infectious agent. Beyond pathogens, various viruses and bacteria colonize the respiratory tract without causing disease, potentially influencing respiratory diseases' pathogenesis. Nevertheless, our understanding of respiratory microbiota is limited by technical constraints, predominantly focusing on bacteria and neglecting crucial populations like viruses. Despite recent efforts to improve our understanding of viral diversity in the human body, our knowledge of viral diversity associated with the human respiratory tract remains limited. METHODS Following a comprehensive search in bibliographic and sequencing data repositories using keyword terms, we retrieved shotgun metagenomic data from public repositories (n = 85). After manual curation, sequencing data files from 43 studies were analyzed using EVEREST (pipEline for Viral assEmbly and chaRactEriSaTion). Complete and high-quality contigs were further assessed for genomic and taxonomic characterization. RESULTS Viral contigs were obtained from 194 out of the 868 FASTQ files processed through EVEREST. Of the 1842 contigs that were quality assessed, 8% (n = 146) were classified as complete/high-quality genomes. Most of the identified viral contigs were taxonomically classified as bacteriophages, with taxonomic resolution ranging from the superkingdom level down to the species level. Captured contigs were spread across 25 putative families and varied between RNA and DNA viruses, including previously uncharacterized viral genomes. Of note, airway samples also contained virus(es) characteristic of the human gastrointestinal tract, which have not been previously described as part of the lung virome. Additionally, by performing a meta-analysis of the integrated datasets, ecological trends within viral populations linked to human disease states and their biogeographical distribution along the respiratory tract were observed. CONCLUSION By leveraging publicly available repositories of shotgun metagenomic data, the present study provides new insights into viral genomes associated with specimens from the human respiratory tract across different disease spectra. Further studies are required to validate our findings and evaluate the potential impact of these viral communities on respiratory tract physiology.
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Affiliation(s)
- Talya Conradie
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, Perth, WA 6009, Australia
- Medical, Molecular and Forensic Sciences, Murdoch University, Perth, WA 6150, Australia
| | | | - Siobhon Egan
- Medical, Molecular and Forensic Sciences, Murdoch University, Perth, WA 6150, Australia
- Centre for Computational and Systems Medicine, Health Future Institute, Murdoch University, Perth, WA 6150, Australia
| | - Anthony Kicic
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, Perth, WA 6009, Australia
- Department of Respiratory and Sleep Medicine, Perth Children’s Hospital for Children, Perth, WA 6009, Australia
- Centre for Cell Therapy and Regenerative Medicine, School of Medicine and Pharmacology, Perth, WA 6009, Australia
- School of Population Health, Curtin University, Perth, WA 6102, Australia
| | - Sulev Koks
- Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA 6150, Australia
| | - Stephen M. Stick
- Department of Respiratory and Sleep Medicine, Perth Children’s Hospital for Children, Perth, WA 6009, Australia
- Centre for Cell Therapy and Regenerative Medicine, School of Medicine and Pharmacology, Perth, WA 6009, Australia
| | - Patricia Agudelo-Romero
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, Perth, WA 6009, Australia
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
- European Virus Bioinformatics Centre, Friedrich-Schiller-Universitat Jena, 07737 Jena, Germany
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3
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Azoulay E, Maertens J, Lemiale V. How I manage acute respiratory failure in patients with hematological malignancies. Blood 2024; 143:971-982. [PMID: 38232056 DOI: 10.1182/blood.2023021414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/29/2023] [Accepted: 12/04/2023] [Indexed: 01/19/2024] Open
Abstract
ABSTRACT Acute respiratory failure (ARF) is common in patients with hematological malignancies notably those with acute leukemia, myelodysplastic syndrome, or allogeneic stem cell transplantation. ARF is the leading reason for intensive care unit (ICU) admission, with a 35% case fatality rate. Failure to identify the ARF cause is associated with mortality. A prompt, well-designed diagnostic workup is crucial. The investigations are chosen according to pretest diagnostic probabilities, estimated by the DIRECT approach: D stands for delay, or time since diagnosis; I for pattern of immune deficiency; R and T for radiological evaluation; E refers to clinical experience, and C to the clinical picture. Thorough familiarity with rapid diagnostic tests helps to decrease the use of bronchoscopy with bronchoalveolar lavage, which can cause respiratory status deterioration in those patients with hypoxemia. A prompt etiological diagnosis shortens the time on unnecessary empirical treatments, decreasing iatrogenic harm and costs. High-quality collaboration between intensivists and hematologists and all crossdisciplinary health care workers is paramount. All oxygen delivery systems should be considered to minimize invasive mechanical ventilation. Treatment of the malignancy is started or continued in the ICU under the guidance of the hematologists. The goal is to use the ICU as a bridge to recovery, with the patient returning to the hematology ward in sufficiently good clinical condition to receive optimal anticancer treatment.
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Affiliation(s)
- Elie Azoulay
- Intensive Care Department, Saint-Louis University Hospital, Paris-Cité University, Paris, France
| | - Johan Maertens
- Department of Microbiology, Immunology, and Transplantation, KU Leuven, Leuven, Belgium
- Department of Hematology, University Hospitals Leuven, Leuven, Belgium
| | - Virginie Lemiale
- Intensive Care Department, Saint-Louis University Hospital, Paris-Cité University, Paris, France
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Goraichuk IV, Harden M, Spackman E, Suarez DL. The 28S rRNA RT-qPCR assay for host depletion evaluation to enhance avian virus detection in Illumina and Nanopore sequencing. Front Microbiol 2024; 15:1328987. [PMID: 38351914 PMCID: PMC10864109 DOI: 10.3389/fmicb.2024.1328987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/09/2024] [Indexed: 02/16/2024] Open
Abstract
Abundant host and bacterial sequences can obscure the detection of less prevalent viruses in untargeted next-generation sequencing (NGS). Efficient removal of these non-targeted sequences is vital for accurate viral detection. This study presents a novel 28S ribosomal RNA (rRNA) RT-qPCR assay designed to assess the efficiency of avian rRNA depletion before conducting costly NGS for the detection of avian RNA viruses. The comprehensive evaluation of this 28S-test focuses on substituting DNase I with alternative DNases in our established depletion protocols and finetuning essential parameters for reliable host rRNA depletion. To validate the effectiveness of the 28S-test, we compared its performance with NGS results obtained from both Illumina and Nanopore sequencing platforms. This evaluation utilized swab samples from chickens infected with highly pathogenic avian influenza virus, subjected to established and modified depletion protocols. Both methods significantly reduced host rRNA levels, but using the alternative DNase had superior performance. Additionally, utilizing the 28S-test, we explored cost- and time-effective strategies, such as reduced probe concentrations and other alternative DNase usage, assessed the impact of filtration pre-treatment, and evaluated various experimental parameters to further optimize the depletion protocol. Our findings underscore the value of the 28S-test in optimizing depletion methods for advancing improvements in avian disease research through NGS.
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Affiliation(s)
- Iryna V. Goraichuk
- Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agriculture Research Service, U.S. Department of Agriculture, Athens, GA, United States
| | - Mark Harden
- College of Veterinary Medicine, Tuskegee University, Tuskegee, AL, United States
| | - Erica Spackman
- Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agriculture Research Service, U.S. Department of Agriculture, Athens, GA, United States
| | - David L. Suarez
- Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agriculture Research Service, U.S. Department of Agriculture, Athens, GA, United States
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Wang ZY, Li LL, Cao XL, Li P, Du J, Zou MJ, Wang LL. Clinical application of amplification-based versus amplification-free metagenomic next-generation sequencing test in infectious diseases. Front Cell Infect Microbiol 2023; 13:1138174. [PMID: 38094744 PMCID: PMC10716234 DOI: 10.3389/fcimb.2023.1138174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 11/07/2023] [Indexed: 12/18/2023] Open
Abstract
Background Recently, metagenomic next-generation sequencing (mNGS) has been used in the diagnosis of infectious diseases (IDs) as an emerging and powerful tool. However, whether the complicated methodological variation in mNGS detections makes a difference in their clinical performance is still unknown. Here we conducted a method study on the clinical application of mNGS tests in the DNA detection of IDs. Methods We analyzed the effect of several potential factors in the whole process of mNGS for DNA detection on microorganism identification in 98 samples of suspected ID patients by amplification-based mNGS. The amplification-based and amplification-free mNGS tests were successfully performed in 41 samples. Then we compared the clinical application of the two mNGS methods in the DNA detection of IDs. Results We found that a higher concentration of extracted nucleic acid was more conducive to detecting microorganisms. Other potential factors, such as read depth and proportion of human reads, might not be attributed to microorganism identification. The concordance rate of amplification-based and amplification-free mNGS results was 80.5% (33/41) in the patients with suspected IDs. Amplification-based mNGS showed approximately 16.7% higher sensitivity than amplification-free mNGS. However, 4 cases with causative pathogens only detected by amplification-based mNGS were finally proved false-positive. In addition, empirical antibiotic treatments were adjusted in 18 patients following mNGS testing with unexpected pathogens. Conclusions Amplification-based and amplification-free mNGS tests showed their specific advantages and disadvantages in the diagnosis of IDs. The clinical application of mNGS still needs more exploration from a methodological perspective. With advanced technology and standardized procedure, mNGS will play a promising role in the diagnosis of IDs and help guide the use of antibiotics.
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Affiliation(s)
- Zhe-Ying Wang
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, Shandong, China
- Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, Jinan, Shandong, China
| | - Lu-Lu Li
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Xue-Lei Cao
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, Shandong, China
- Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, Jinan, Shandong, China
| | - Ping Li
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, Shandong, China
- Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, Jinan, Shandong, China
| | - Jian Du
- Department of Urology, The First Affiliated Hospital of Shandong First Medical University, Jinan, Shandong, China
| | - Ming-Jin Zou
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Li-Li Wang
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, Shandong, China
- Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, Jinan, Shandong, China
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Rollin J, Rong W, Massart S. Cont-ID: detection of sample cross-contamination in viral metagenomic data. BMC Biol 2023; 21:217. [PMID: 37833740 PMCID: PMC10576407 DOI: 10.1186/s12915-023-01708-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 09/20/2023] [Indexed: 10/15/2023] Open
Abstract
BACKGROUND High-throughput sequencing (HTS) technologies completed by the bioinformatic analysis of the generated data are becoming an important detection technique for virus diagnostics. They have the potential to replace or complement the current PCR-based methods thanks to their improved inclusivity and analytical sensitivity, as well as their overall good repeatability and reproducibility. Cross-contamination is a well-known phenomenon in molecular diagnostics and corresponds to the exchange of genetic material between samples. Cross-contamination management was a key drawback during the development of PCR-based detection and is now adequately monitored in routine diagnostics. HTS technologies are facing similar difficulties due to their very high analytical sensitivity. As a single viral read could be detected in millions of sequencing reads, it is mandatory to fix a detection threshold that will be informed by estimated cross-contamination. Cross-contamination monitoring should therefore be a priority when detecting viruses by HTS technologies. RESULTS We present Cont-ID, a bioinformatic tool designed to check for cross-contamination by analysing the relative abundance of virus sequencing reads identified in sequence metagenomic datasets and their duplication between samples. It can be applied when the samples in a sequencing batch have been processed in parallel in the laboratory and with at least one specific external control called Alien control. Using 273 real datasets, including 68 virus species from different hosts (fruit tree, plant, human) and several library preparation protocols (Ribodepleted total RNA, small RNA and double-stranded RNA), we demonstrated that Cont-ID classifies with high accuracy (91%) viral species detection into (true) infection or (cross) contamination. This classification raises confidence in the detection and facilitates the downstream interpretation and confirmation of the results by prioritising the virus detections that should be confirmed. CONCLUSIONS Cross-contamination between samples when detecting viruses using HTS (Illumina technology) can be monitored and highlighted by Cont-ID (provided an alien control is present). Cont-ID is based on a flexible methodology relying on the output of bioinformatics analyses of the sequencing reads and considering the contamination pattern specific to each batch of samples. The Cont-ID method is adaptable so that each laboratory can optimise it before its validation and routine use.
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Affiliation(s)
- Johan Rollin
- Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, 5030, Gembloux, Belgium
- DNAVision, 6041, Gosselies, Belgium
| | - Wei Rong
- Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, 5030, Gembloux, Belgium
| | - Sébastien Massart
- Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, 5030, Gembloux, Belgium.
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Tulloch RL, Kim K, Sikazwe C, Michie A, Burrell R, Holmes EC, Dwyer DE, Britton PN, Kok J, Eden JS. RAPID prep: A Simple, Fast Protocol for RNA Metagenomic Sequencing of Clinical Samples. Viruses 2023; 15:v15041006. [PMID: 37112986 PMCID: PMC10146689 DOI: 10.3390/v15041006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 04/12/2023] [Accepted: 04/17/2023] [Indexed: 04/29/2023] Open
Abstract
Emerging infectious disease threats require rapid response tools to inform diagnostics, treatment, and outbreak control. RNA-based metagenomics offers this; however, most approaches are time-consuming and laborious. Here, we present a simple and fast protocol, the RAPIDprep assay, with the aim of providing a cause-agnostic laboratory diagnosis of infection within 24 h of sample collection by sequencing ribosomal RNA-depleted total RNA. The method is based on the synthesis and amplification of double-stranded cDNA followed by short-read sequencing, with minimal handling and clean-up steps to improve processing time. The approach was optimized and applied to a range of clinical respiratory samples to demonstrate diagnostic and quantitative performance. Our results showed robust depletion of both human and microbial rRNA, and library amplification across different sample types, qualities, and extraction kits using a single workflow without input nucleic-acid quantification or quality assessment. Furthermore, we demonstrated the genomic yield of both known and undiagnosed pathogens with complete genomes recovered in most cases to inform molecular epidemiological investigations and vaccine design. The RAPIDprep assay is a simple and effective tool, and representative of an important shift toward the integration of modern genomic techniques with infectious disease investigations.
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Affiliation(s)
- Rachel L Tulloch
- Centre for Virus Research, Westmead Institute for Medical Research, Westmead, NSW 2145, Australia
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Karan Kim
- Centre for Virus Research, Westmead Institute for Medical Research, Westmead, NSW 2145, Australia
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Chisha Sikazwe
- PathWest Laboratory Medicine WA, Department of Microbiology, Nedlands, WA 6009, Australia
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Alice Michie
- PathWest Laboratory Medicine WA, Department of Microbiology, Nedlands, WA 6009, Australia
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Rebecca Burrell
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Departments of Infectious Diseases and Microbiology, The Children's Hospital at Westmead, Westmead, NSW 2145, Australia
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Dominic E Dwyer
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- NSW Health Pathology Institute for Clinical Pathology and Medical Research, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Philip N Britton
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Departments of Infectious Diseases and Microbiology, The Children's Hospital at Westmead, Westmead, NSW 2145, Australia
| | - Jen Kok
- NSW Health Pathology Institute for Clinical Pathology and Medical Research, Westmead Hospital, Westmead, NSW 2145, Australia
| | - John-Sebastian Eden
- Centre for Virus Research, Westmead Institute for Medical Research, Westmead, NSW 2145, Australia
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
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Wang D, Zhang L, Cai Z, Liu Y. Diagnosis of Acute Q Fever in a Patient by Using Metagenomic Next-Generation Sequencing: A Case Report. Infect Drug Resist 2023; 16:1923-1930. [PMID: 37025192 PMCID: PMC10072143 DOI: 10.2147/idr.s405697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 03/23/2023] [Indexed: 04/03/2023] Open
Abstract
Background Q fever is a zoonotic disease caused by Coxiella burnetii infection, with domestic ruminants as the main source of infection and tick bites as one of the transmission vectors. The clinical manifestations of Q fever are varied and atypical. For the reason that C. burnetii is a strictly intracellular pathogen, it is difficult to be diagnosed by traditional culture methods. Additionally, serological and molecular diagnostic methods to assist in the diagnosis of Q fever are not routinely performed in most clinical laboratories. Therefore, early and rapid diagnosis of Q fever is a challenge. Case Presentation In the present study, a 34-year-old male patient presented with an acute onset and symptoms such as high fever, lethargy, pulmonary infection, and liver damage. In addition, he had a history of tick bites. Despite conducting relevant laboratory and radiological examinations, the etiology remained unknown. Subsequently, we detected the sequence reads of C. burnetii in a venous blood sample using metagenomic next-generation sequencing (mNGS), and the symptoms of patients were significantly improved after timely treatment with the special drug tetracycline. To our knowledge, this is the first report of Q fever associated with C. burnetii detected directly from venous blood sample in Wuhan, China. Conclusion Metagenomic next-generation sequencing is a new diagnostic technology that provides rapid and accurate detection of unexplained infections, including Q fever. Its application plays a crucial role in clinical diagnosis for identifying elusive pathogens.
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Affiliation(s)
- Dong Wang
- Department of Clinical Laboratory, Wuhan Asia General Hospital, Wuhan Asia General Hospital Affiliated to Wuhan University of Science and Technology, Wuhan, Hubei Province, 430056, People’s Republic of China
| | - Litao Zhang
- Department of Clinical Laboratory, Wuhan Asia General Hospital, Wuhan Asia General Hospital Affiliated to Wuhan University of Science and Technology, Wuhan, Hubei Province, 430056, People’s Republic of China
| | - Zhifang Cai
- Pulmonary and Critical Care Medicine, Hankou Hospital of Wuhan, Hankou Hospital Affiliated to Wuhan University of Science and Technology, Wuhan, Hubei Province, 430012, People’s Republic of China
| | - Yumei Liu
- Pulmonary and Critical Care Medicine, Hankou Hospital of Wuhan, Hankou Hospital Affiliated to Wuhan University of Science and Technology, Wuhan, Hubei Province, 430012, People’s Republic of China
- Correspondence: Yumei Liu, Email
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Vereecke N, Woźniak A, Pauwels M, Coppens S, Nauwynck H, Cybulski P, Theuns S, Stadejek T. Successful Whole Genome Nanopore Sequencing of Swine Influenza A Virus (swIAV) Directly from Oral Fluids Collected in Polish Pig Herds. Viruses 2023; 15:v15020435. [PMID: 36851649 PMCID: PMC9962634 DOI: 10.3390/v15020435] [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: 12/28/2022] [Revised: 01/20/2023] [Accepted: 01/31/2023] [Indexed: 02/09/2023] Open
Abstract
Influenza A virus (IAV) is a single-stranded, negative-sense RNA virus and a common cause of seasonal flu in humans. Its genome comprises eight RNA segments that facilitate reassortment, resulting in a great variety of IAV strains. To study these processes, the genetic code of each segment should be unraveled. Fortunately, new third-generation sequencing approaches allow for cost-efficient sequencing of IAV segments. Sequencing success depends on various factors, including proper sample storage and processing. Hence, this work focused on the effect of storage of oral fluids and swIAV sequencing. Oral fluids (n = 13) from 2017 were stored at -22 °C and later transferred to -80 °C. Other samples (n = 21) were immediately stored at -80 °C. A reverse transcription quantitative PCR (RT-qPCR) pre- and post-storage was conducted to assess IAV viral loads. Next, samples were subjected to two IAV long-read nanopore sequencing methods to evaluate success in this complex matrix. A significant storage-associated loss of swIAV loads was observed. Still, a total of 17 complete and 6 near-complete Polish swIAV genomes were obtained. Genotype T, (H1avN2, seven herds), P (H1N1pdm09, two herds), U (H1avN1, three herds), and A (H1avN1, 1 herd) were circulated on Polish farms. In conclusion, oral fluids can be used for long-read swIAV sequencing when considering appropriate storage and segment amplification protocols, which allows us to monitor swIAV in an animal-friendly and cost-efficient manner.
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Affiliation(s)
- Nick Vereecke
- Laboratory of Virology, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium
- PathoSense BV, 2500 Lier, Belgium
- Correspondence: (N.V.); (A.W.); (T.S.)
| | - Aleksandra Woźniak
- Department of Pathology and Veterinary Diagnostic, Institute of Veterinary Medicine, Warsaw University of Life Sciences-SGGW, 02-776 Warsaw, Poland
- Correspondence: (N.V.); (A.W.); (T.S.)
| | | | | | - Hans Nauwynck
- Laboratory of Virology, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium
- PathoSense BV, 2500 Lier, Belgium
| | - Piotr Cybulski
- Goodvalley Agro S.A., Dworcowa 25, 77-320 Przechlewo, Poland
| | - Sebastiaan Theuns
- Laboratory of Virology, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium
- PathoSense BV, 2500 Lier, Belgium
| | - Tomasz Stadejek
- Department of Pathology and Veterinary Diagnostic, Institute of Veterinary Medicine, Warsaw University of Life Sciences-SGGW, 02-776 Warsaw, Poland
- Correspondence: (N.V.); (A.W.); (T.S.)
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10
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Sandybayev N, Beloussov V, Strochkov V, Solomadin M, Granica J, Yegorov S. Next Generation Sequencing Approaches to Characterize the Respiratory Tract Virome. Microorganisms 2022; 10:microorganisms10122327. [PMID: 36557580 PMCID: PMC9785614 DOI: 10.3390/microorganisms10122327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/17/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022] Open
Abstract
The COVID-19 pandemic and heightened perception of the risk of emerging viral infections have boosted the efforts to better understand the virome or complete repertoire of viruses in health and disease, with a focus on infectious respiratory diseases. Next-generation sequencing (NGS) is widely used to study microorganisms, allowing the elucidation of bacteria and viruses inhabiting different body systems and identifying new pathogens. However, NGS studies suffer from a lack of standardization, in particular, due to various methodological approaches and no single format for processing the results. Here, we review the main methodological approaches and key stages for studies of the human virome, with an emphasis on virome changes during acute respiratory viral infection, with applications for clinical diagnostics and epidemiologic analyses.
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Affiliation(s)
- Nurlan Sandybayev
- Kazakhstan-Japan Innovation Center, Kazakh National Agrarian Research University, Almaty 050010, Kazakhstan
- Correspondence: ; Tel.: +7-778312-2058
| | - Vyacheslav Beloussov
- Kazakhstan-Japan Innovation Center, Kazakh National Agrarian Research University, Almaty 050010, Kazakhstan
- Molecular Genetics Laboratory TreeGene, Almaty 050009, Kazakhstan
| | - Vitaliy Strochkov
- Kazakhstan-Japan Innovation Center, Kazakh National Agrarian Research University, Almaty 050010, Kazakhstan
| | - Maxim Solomadin
- School of Pharmacy, Karaganda Medical University, Karaganda 100000, Kazakhstan
| | - Joanna Granica
- Molecular Genetics Laboratory TreeGene, Almaty 050009, Kazakhstan
| | - Sergey Yegorov
- Michael G. DeGroote Institute for Infectious Disease Research, Faculty of Health Sciences, McMaster University, Hamilton, ON L8S 4LB, Canada
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11
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Bal A, Destras G, Sabatier M, Pichon M, Regue H, Oriol G, Gillet Y, Lina B, Brengel-Pesce K, Josset L, Morfin F. Metagenomic Analysis Reveals High Abundance of Torque Teno Mini Virus in the Respiratory Tract of Children with Acute Respiratory Illness. Viruses 2022; 14:v14050955. [PMID: 35632697 PMCID: PMC9143613 DOI: 10.3390/v14050955] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 01/30/2023] Open
Abstract
Human Anelloviridae is a highly prevalent viral family, including three main genera—Alphatorquevirus (Torque teno virus, TTV), Betatorquevirus (Torque teno mini virus, TTMV), and Gammatorquevirus (Torque teno midi virus, TTMDV). To date, the characterization of Anelloviridae in the respiratory tract of children with acute respiratory infection (ARI) has been poorly reported and mainly focused on TTV. We performed a metagenomic analysis of eight respiratory samples collected from children with an ARI of unknown etiology (eight samples tested negative with a multiplex PCR assay, out of the 39 samples initially selected based on negative routine diagnostic testing). A total of 19 pediatric respiratory samples that tested positive for respiratory syncytial virus (RSV, n = 13) or influenza virus (n = 6) were also sequenced. Anelloviridae reads were detected in 16/27 samples, including 6/8 negative samples, 7/13 RSV samples and 3/6 influenza samples. For samples with a detection of at least one Anelloviridae genus, TTMV represented 87.1 (66.1−99.2)% of Anelloviridae reads, while TTV and TTMDV represented 0.8 (0.0−9.6)% and 0.7 (0.0−7.1)%, respectively (p < 0.001). Our findings highlight a high prevalence of TTMV in respiratory samples of children with an ARI of unknown etiology, as well as in samples with an RSV or influenza infection. Larger studies are needed to explore the role of TTMV in childhood respiratory diseases.
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Affiliation(s)
- Antonin Bal
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire Associé au Centre National de Référence des Virus des Infections Respiratoires, Hospices Civils de Lyon, 69004 Lyon, France; (A.B.); (G.D.); (M.S.); (B.L.)
- Univ Lyon, Université Lyon 1, CIRI, Inserm U1111 CNRS UMR5308, Virpath, 69007 Lyon, France
- GenEPII Platform, Institut des Agents Infectieux, Hospices Civils de Lyon, 69004 Lyon, France;
| | - Gregory Destras
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire Associé au Centre National de Référence des Virus des Infections Respiratoires, Hospices Civils de Lyon, 69004 Lyon, France; (A.B.); (G.D.); (M.S.); (B.L.)
- Univ Lyon, Université Lyon 1, CIRI, Inserm U1111 CNRS UMR5308, Virpath, 69007 Lyon, France
- GenEPII Platform, Institut des Agents Infectieux, Hospices Civils de Lyon, 69004 Lyon, France;
| | - Marina Sabatier
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire Associé au Centre National de Référence des Virus des Infections Respiratoires, Hospices Civils de Lyon, 69004 Lyon, France; (A.B.); (G.D.); (M.S.); (B.L.)
- Univ Lyon, Université Lyon 1, CIRI, Inserm U1111 CNRS UMR5308, Virpath, 69007 Lyon, France
| | - Maxime Pichon
- Bacteriology Laboratory, Infectious Agents Department, Centre Hospitalier Universitaire de Poitiers, 86021 Poitiers, France;
- Inserm U1070 Pharmacology of Antimicrobial Agents and Resistance, University of Poitiers, 86073 Poitiers, France
| | - Hadrien Regue
- GenEPII Platform, Institut des Agents Infectieux, Hospices Civils de Lyon, 69004 Lyon, France;
| | - Guy Oriol
- Laboratoire Commun de Recherche HCL-bioMerieux, Centre Hospitalier Lyon Sud, 69495 Pierre-Bénite, France; (G.O.); (K.B.-P.)
| | - Yves Gillet
- Hospices Civils de Lyon, Urgences Pédiatriques, Hôpital Femme Mère Enfant, 69500 Bron, France;
| | - Bruno Lina
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire Associé au Centre National de Référence des Virus des Infections Respiratoires, Hospices Civils de Lyon, 69004 Lyon, France; (A.B.); (G.D.); (M.S.); (B.L.)
- Univ Lyon, Université Lyon 1, CIRI, Inserm U1111 CNRS UMR5308, Virpath, 69007 Lyon, France
- GenEPII Platform, Institut des Agents Infectieux, Hospices Civils de Lyon, 69004 Lyon, France;
| | - Karen Brengel-Pesce
- Laboratoire Commun de Recherche HCL-bioMerieux, Centre Hospitalier Lyon Sud, 69495 Pierre-Bénite, France; (G.O.); (K.B.-P.)
| | - Laurence Josset
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire Associé au Centre National de Référence des Virus des Infections Respiratoires, Hospices Civils de Lyon, 69004 Lyon, France; (A.B.); (G.D.); (M.S.); (B.L.)
- Univ Lyon, Université Lyon 1, CIRI, Inserm U1111 CNRS UMR5308, Virpath, 69007 Lyon, France
- GenEPII Platform, Institut des Agents Infectieux, Hospices Civils de Lyon, 69004 Lyon, France;
- Correspondence: (L.J.); (F.M.)
| | - Florence Morfin
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire Associé au Centre National de Référence des Virus des Infections Respiratoires, Hospices Civils de Lyon, 69004 Lyon, France; (A.B.); (G.D.); (M.S.); (B.L.)
- Univ Lyon, Université Lyon 1, CIRI, Inserm U1111 CNRS UMR5308, Virpath, 69007 Lyon, France
- GenEPII Platform, Institut des Agents Infectieux, Hospices Civils de Lyon, 69004 Lyon, France;
- Correspondence: (L.J.); (F.M.)
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12
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Shi Y, Wang G, Lau HCH, Yu J. Metagenomic Sequencing for Microbial DNA in Human Samples: Emerging Technological Advances. Int J Mol Sci 2022; 23:ijms23042181. [PMID: 35216302 PMCID: PMC8877284 DOI: 10.3390/ijms23042181] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/06/2022] [Accepted: 02/11/2022] [Indexed: 02/04/2023] Open
Abstract
Whole genome metagenomic sequencing is a powerful platform enabling the simultaneous identification of all genes from entirely different kingdoms of organisms in a complex sample. This technology has revolutionised multiple areas from microbiome research to clinical diagnoses. However, one of the major challenges of a metagenomic study is the overwhelming non-microbial DNA present in most of the host-derived specimens, which can inundate the microbial signals and reduce the sensitivity of microorganism detection. Various host DNA depletion methods to facilitate metagenomic sequencing have been developed and have received considerable attention in this context. In this review, we present an overview of current host DNA depletion approaches along with explanations of their underlying principles, advantages and disadvantages. We also discuss their applications in laboratory microbiome research and clinical diagnoses and, finally, we envisage the direction of the further perfection of metagenomic sequencing in samples with overabundant host DNA.
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Affiliation(s)
| | | | | | - Jun Yu
- Correspondence: ; Tel.: +852-37636099; Fax:+852-21445330
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13
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Li X, Liu Q, Chen X, Xiao Y, Yang S, Zhang W, Chen J. The virome of bronchoalveolar lavage fluid from patients with fever of unknown origin. Future Virol 2022. [DOI: 10.2217/fvl-2020-0027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Background: Viral metagenomics, a high-throughput sequencing combined with virus sequence-independent amplification by random PCR, allows for unbiased detection of virtually any viruses present in samples. Materials & methods: In order to investigate the virome of bronchoalveolar lavage fluid from patients with fever of unknown origin, 58 samples collected from diseased patients were characterized and compared. Results: Some representatives of Anelloviridae were identified, we found the torque teno virus (TTV) accounts for the majority of virus communities and were more prevalent in the specimens of febrile patients. Phylogenetic analysis suggested that these anellovirus isolates were close to the previous TTV available in GenBank®. Conclusion: All these data indicate that the human anellovirus species TTV may associated with fever of unknown origin.
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Affiliation(s)
- Xinlin Li
- Department of Clinical Laboratory, The Affiliated People’s Hospital of Jiangsu University, No. 8 Dian Li Road, Zhenjiang, China
- School of Medicine, Jiangsu University, No. 301 Xue Fu Road, Zhenjiang, China
| | - Qi Liu
- School of Medicine, Jiangsu University, No. 301 Xue Fu Road, Zhenjiang, China
| | - Xu Chen
- School of Medicine, Jiangsu University, No. 301 Xue Fu Road, Zhenjiang, China
| | - Yuqing Xiao
- School of Medicine, Jiangsu University, No. 301 Xue Fu Road, Zhenjiang, China
| | - Shixing Yang
- School of Medicine, Jiangsu University, No. 301 Xue Fu Road, Zhenjiang, China
| | - Wen Zhang
- School of Medicine, Jiangsu University, No. 301 Xue Fu Road, Zhenjiang, China
| | - Jianguo Chen
- Department of Clinical Laboratory, The Affiliated People’s Hospital of Jiangsu University, No. 8 Dian Li Road, Zhenjiang, China
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14
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Importance of Adequate qPCR Controls in Infection Control. Diagnostics (Basel) 2021; 11:diagnostics11122373. [PMID: 34943608 PMCID: PMC8700483 DOI: 10.3390/diagnostics11122373] [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: 11/22/2021] [Revised: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 11/22/2022] Open
Abstract
Respiratory screening assays lacking Sample Adequacy Controls (SAC) may result in inadequate sample quality and thus false negative results. The non-adequate samples might represent a significant proportion of the total performed tests, thus resulting in sub-optimal infection control measures with implications that may be critical during pandemic times. The quantitative sample adequacy threshold can be established empirically, measuring the change in the frequency of positive results, as a function of the numerical value of “sample adequacy”. Establishing a quantitative threshold for SAC requires a big number/volume of tests to be analyzed in order to have a statistically valid result. Herein, we are offering for the first time clear clinical evidence that a subset of results, which did not pass minimal sample adequacy criteria, have a significantly lower frequency of positivity compared with the “adequate” samples. Flagging these results and/or re-sampling them is a mitigation strategy, which can dramatically improve infection control measures.
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Schuele L, Cassidy H, Peker N, Rossen JWA, Couto N. Future potential of metagenomics in clinical laboratories. Expert Rev Mol Diagn 2021; 21:1273-1285. [PMID: 34755585 DOI: 10.1080/14737159.2021.2001329] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Rapid and sensitive diagnostic strategies are necessary for patient care and public health. Most of the current conventional microbiological assays detect only a restricted panel of pathogens at a time or require a microbe to be successfully cultured from a sample. Clinical metagenomics next-generation sequencing (mNGS) has the potential to unbiasedly detect all pathogens in a sample, increasing the sensitivity for detection and enabling the discovery of unknown infectious agents. AREAS COVERED High expectations have been built around mNGS; however, this technique is far from widely available. This review highlights the advances and currently available options in terms of costs, turnaround time, sensitivity, specificity, validation, and reproducibility of mNGS as a diagnostic tool in clinical microbiology laboratories. EXPERT OPINION The need for a novel diagnostic tool to increase the sensitivity of microbial diagnostics is clear. mNGS has the potential to revolutionise clinical microbiology. However, its role as a diagnostic tool has yet to be widely established, which is crucial for successfully implementing the technique. A clear definition of diagnostic algorithms that include mNGS is vital to show clinical utility. Similarly to real-time PCR, mNGS will one day become a vital tool in any testing algorithm.
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Affiliation(s)
- Leonard Schuele
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands
| | - Hayley Cassidy
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands
| | - Nilay Peker
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands
| | - John W A Rossen
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands.,Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Natacha Couto
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands.,The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
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16
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Diao Z, Han D, Zhang R, Li J. Metagenomics next-generation sequencing tests take the stage in the diagnosis of lower respiratory tract infections. J Adv Res 2021; 38:201-212. [PMID: 35572406 PMCID: PMC9091713 DOI: 10.1016/j.jare.2021.09.012] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 09/13/2021] [Accepted: 09/25/2021] [Indexed: 02/06/2023] Open
Abstract
The applications of mNGS for LRIs span a wide range of areas including LRI diagnosis, airway microbiome analyses, human host response analyses, and prediction of drug resistance. The workflow of mNGS used in clinical practice involves the wet-lab pipeline and dry-lab pipeline, the complex workflow poses challenges for its extensive use. mNGS will become an important tool in the field of infectious disease diagnosis in the next decade.
Metagenomic next-generation sequencing (mNGS) has changed the diagnosis landscape of lower respiratory tract infections (LRIs). With the development of newer sequencing assays, it is now possible to assess all microorganisms in a sample using a single mNGS analysis. The applications of mNGS for LRIs span a wide range of areas including LRI diagnosis, airway microbiome analyses, human host response analyses, and prediction of drug resistance. mNGS is currently in an exciting transitional period; however, before implementation in a clinical setting, there are several barriers to overcome, such as the depletion of human nucleic acid, discrimination between colonization and infection, high costs, and so on. Aim of Review: In this review, we summarize the potential applications and challenges of mNGS in the diagnosis of LRIs to promote the integration of mNGS into the management of patients with respiratory tract infections in a clinical setting. Key Scientific Concepts of Review: Once its analytical validation, clinical validation and clinical utility been demonstrated, mNGS will become an important tool in the field of infectious disease diagnosis.
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17
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HTS-Based Diagnostics of Sugarcane Viruses: Seasonal Variation and Its Implications for Accurate Detection. Viruses 2021; 13:v13081627. [PMID: 34452491 PMCID: PMC8402784 DOI: 10.3390/v13081627] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/09/2021] [Accepted: 08/13/2021] [Indexed: 01/26/2023] Open
Abstract
Rapid global germplasm trade has increased concern about the spread of plant pathogens and pests across borders that could become established, affecting agriculture and environment systems. Viral pathogens are of particular concern due to their difficulty to control once established. A comprehensive diagnostic platform that accurately detects both known and unknown virus species, as well as unreported variants, is playing a pivotal role across plant germplasm quarantine programs. Here we propose the addition of high-throughput sequencing (HTS) from total RNA to the routine quarantine diagnostic workflow of sugarcane viruses. We evaluated the impact of sequencing depth needed for the HTS-based identification of seven regulated sugarcane RNA/DNA viruses across two different growing seasons (spring and fall). Our HTS analysis revealed that viral normalized read counts (RPKM) was up to 23-times higher in spring than in the fall season for six out of the seven viruses. Random read subsampling analyses suggested that the minimum number of reads required for reliable detection of RNA viruses was 0.5 million, with a viral genome coverage of at least 92%. Using an HTS-based total RNA metagenomics approach, we identified all targeted viruses independent of the time of the year, highlighting that higher sequencing depth is needed for the identification of DNA viruses.
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18
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Pelegrin AC, Palmieri M, Mirande C, Oliver A, Moons P, Goossens H, van Belkum A. Pseudomonas aeruginosa: a clinical and genomics update. FEMS Microbiol Rev 2021; 45:6273131. [PMID: 33970247 DOI: 10.1093/femsre/fuab026] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 05/07/2021] [Indexed: 12/13/2022] Open
Abstract
Antimicrobial resistance (AMR) has become a global medical priority that needs urgent resolution. Pseudomonas aeruginosa is a versatile, adaptable bacterial species with widespread environmental occurrence, strong medical relevance, a diverse set of virulence genes and a multitude of intrinsic and possibly acquired antibiotic resistance traits. P. aeruginosa causes a wide variety of infections and has an epidemic-clonal population structure. Several of its dominant global clones have collected a wide variety of resistance genes rendering them multi-drug resistant (MDR) and particularly threatening groups of vulnerable individuals including surgical patients, immunocompromised patients, Caucasians suffering from cystic fibrosis (CF) and more. AMR and MDR especially are particularly problematic in P. aeruginosa significantly complicating successful antibiotic treatment. In addition, antimicrobial susceptibility testing (AST) of P. aeruginosa can be cumbersome due to its slow growth or the massive production of exopolysaccharides and other extracellular compounds. For that reason, phenotypic AST is progressively challenged by genotypic methods using whole genome sequences (WGS) and large-scale phenotype databases as a framework of reference. We here summarize the state of affairs and the quality level of WGS-based AST for P. aeruginosa mostly from clinical origin.
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Affiliation(s)
- Andreu Coello Pelegrin
- bioMérieux, Data Analytics Unit, 3 Route du Port Michaud, 38390 La Balme les Grottes, France
| | - Mattia Palmieri
- bioMérieux, Data Analytics Unit, 3 Route du Port Michaud, 38390 La Balme les Grottes, France
| | - Caroline Mirande
- bioMérieux, R&D Microbiology, Route du Port Michaud, 38390 La Balme-les-Grottes, France
| | - Antonio Oliver
- Servicio de Microbiología, Módulo J, segundo piso, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), Ctra. Valldemossa, 79, 07120 Palma de Mallorca, Spain
| | - Pieter Moons
- Laboratory of Medical Microbiology, University of Antwerp, Universiteitsplein 1, building S, 2610 Wilrijk, Antwerp, Belgium
| | - Herman Goossens
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Alex van Belkum
- bioMérieux, Open Innovation and Partnerships, 3 Route du Port Michaud, 38390 La Balme Les Grottes, France
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19
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Fitzpatrick AH, Rupnik A, O'Shea H, Crispie F, Keaveney S, Cotter P. High Throughput Sequencing for the Detection and Characterization of RNA Viruses. Front Microbiol 2021; 12:621719. [PMID: 33692767 PMCID: PMC7938315 DOI: 10.3389/fmicb.2021.621719] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 01/20/2021] [Indexed: 12/12/2022] Open
Abstract
This review aims to assess and recommend approaches for targeted and agnostic High Throughput Sequencing of RNA viruses in a variety of sample matrices. HTS also referred to as deep sequencing, next generation sequencing and third generation sequencing; has much to offer to the field of environmental virology as its increased sequencing depth circumvents issues with cloning environmental isolates for Sanger sequencing. That said however, it is important to consider the challenges and biases that method choice can impart to sequencing results. Here, methodology choices from RNA extraction, reverse transcription to library preparation are compared based on their impact on the detection or characterization of RNA viruses.
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Affiliation(s)
- Amy H. Fitzpatrick
- Food Biosciences, Teagasc Food Research Centre, Fermoy, Ireland
- Shellfish Microbiology, Marine Institute, Oranmore, Ireland
- Biological Sciences, Munster Technological University, Cork, Ireland
| | | | - Helen O'Shea
- Biological Sciences, Munster Technological University, Cork, Ireland
| | - Fiona Crispie
- Food Biosciences, Teagasc Food Research Centre, Fermoy, Ireland
| | | | - Paul Cotter
- Food Biosciences, Teagasc Food Research Centre, Fermoy, Ireland
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20
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Regnault B, Bigot T, Ma L, Pérot P, Temmam S, Eloit M. Deep Impact of Random Amplification and Library Construction Methods on Viral Metagenomics Results. Viruses 2021; 13:v13020253. [PMID: 33562285 PMCID: PMC7915491 DOI: 10.3390/v13020253] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/27/2021] [Accepted: 02/03/2021] [Indexed: 12/16/2022] Open
Abstract
Clinical metagenomics is a broad-range agnostic detection method of pathogens, including novel microorganisms. A major limit is the low pathogen load compared to the high background of host nucleic acids. To overcome this issue, several solutions exist, such as applying a very high depth of sequencing, or performing a relative enrichment of viral genomes associated with capsids. At the end, the quantity of total nucleic acids is often below the concentrations recommended by the manufacturers of library kits, which necessitates to random amplify nucleic acids. Using a pool of 26 viruses representative of viral diversity, we observed a deep impact of the nature of sample (total nucleic acids versus RNA only), the reverse transcription, the random amplification and library construction method on virus recovery. We further optimized the two most promising methods and assessed their performance with fully characterized reference virus stocks. Good genome coverage and limit of detection lower than 100 or 1000 genome copies per mL of plasma, depending on the genome viral type, were obtained from a three million reads dataset. Our study reveals that optimized random amplification is a technique of choice when insufficient amounts of nucleic acid are available for direct libraries constructions.
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Affiliation(s)
- Béatrice Regnault
- Pathogen Discovery Laboratory, Institut Pasteur, 75015 Paris, France; (B.R.); (P.P.); (S.T.)
| | - Thomas Bigot
- Bioinformatics and Biostatistics Hub, Computational Biology Department, Institut Pasteur, 75015 Paris, France;
| | - Laurence Ma
- Biomics Platform, C2RT, Institut Pasteur, 75015 Paris, France;
| | - Philippe Pérot
- Pathogen Discovery Laboratory, Institut Pasteur, 75015 Paris, France; (B.R.); (P.P.); (S.T.)
| | - Sarah Temmam
- Pathogen Discovery Laboratory, Institut Pasteur, 75015 Paris, France; (B.R.); (P.P.); (S.T.)
| | - Marc Eloit
- Pathogen Discovery Laboratory, Institut Pasteur, 75015 Paris, France; (B.R.); (P.P.); (S.T.)
- Ecole Nationale Vétérinaire d’Alfort, 94700 Maisons-Alfort, France
- Correspondence: ; Tel.: +33-1-44-38-92-16
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21
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Barragan M, Guillén JJ, Martin-Palomino N, Rodriguez A, Vassena R. Undetectable viral RNA in oocytes from SARS-CoV-2 positive women. Hum Reprod 2021; 36:390-394. [PMID: 32998162 PMCID: PMC7543480 DOI: 10.1093/humrep/deaa284] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 09/22/2020] [Indexed: 01/05/2023] Open
Abstract
A central concern for the safe provision of ART during the current coronavirus disease 2019 (CODIV-19) pandemic is the possibility of vertical transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection through gametes and preimplantation embryos. Unfortunately, data on SARS-CoV-2 viral presence in oocytes of infected individuals are not available to date. We describe the case of two women who underwent controlled ovarian stimulation and tested positive to SARS-CoV-2 infection by PCR on the day of oocyte collection. The viral RNA for gene N was undetectable in all the oocytes analyzed from the two women.
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Affiliation(s)
- M Barragan
- Clinica EUGIN, Carrer de Balmes 236, Barcelona 08006, Spain
| | - J J Guillén
- Clinica EUGIN, Carrer de Balmes 236, Barcelona 08006, Spain
| | | | - A Rodriguez
- Clinica EUGIN, Carrer de Balmes 236, Barcelona 08006, Spain
| | - R Vassena
- Clinica EUGIN, Carrer de Balmes 236, Barcelona 08006, Spain
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22
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Li N, Cai Q, Miao Q, Song Z, Fang Y, Hu B. High-Throughput Metagenomics for Identification of Pathogens in the Clinical Settings. SMALL METHODS 2021; 5:2000792. [PMID: 33614906 PMCID: PMC7883231 DOI: 10.1002/smtd.202000792] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/24/2020] [Indexed: 05/25/2023]
Abstract
The application of sequencing technology is shifting from research to clinical laboratories owing to rapid technological developments and substantially reduced costs. However, although thousands of microorganisms are known to infect humans, identification of the etiological agents for many diseases remains challenging as only a small proportion of pathogens are identifiable by the current diagnostic methods. These challenges are compounded by the emergence of new pathogens. Hence, metagenomic next-generation sequencing (mNGS), an agnostic, unbiased, and comprehensive method for detection, and taxonomic characterization of microorganisms, has become an attractive strategy. Although many studies, and cases reports, have confirmed the success of mNGS in improving the diagnosis, treatment, and tracking of infectious diseases, several hurdles must still be overcome. It is, therefore, imperative that practitioners and clinicians understand both the benefits and limitations of mNGS when applying it to clinical practice. Interestingly, the emerging third-generation sequencing technologies may partially offset the disadvantages of mNGS. In this review, mainly: a) the history of sequencing technology; b) various NGS technologies, common platforms, and workflows for clinical applications; c) the application of NGS in pathogen identification; d) the global expert consensus on NGS-related methods in clinical applications; and e) challenges associated with diagnostic metagenomics are described.
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Affiliation(s)
- Na Li
- Department of Infectious DiseasesZhongshan HospitalFudan UniversityShanghai200032China
| | - Qingqing Cai
- Genoxor Medical Science and Technology Inc.Zhejiang317317China
| | - Qing Miao
- Department of Infectious DiseasesZhongshan HospitalFudan UniversityShanghai200032China
| | - Zeshi Song
- Genoxor Medical Science and Technology Inc.Zhejiang317317China
| | - Yuan Fang
- Genoxor Medical Science and Technology Inc.Zhejiang317317China
| | - Bijie Hu
- Department of Infectious DiseasesZhongshan HospitalFudan UniversityShanghai200032China
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Ebinger A, Fischer S, Höper D. A theoretical and generalized approach for the assessment of the sample-specific limit of detection for clinical metagenomics. Comput Struct Biotechnol J 2020; 19:732-742. [PMID: 33552445 PMCID: PMC7822954 DOI: 10.1016/j.csbj.2020.12.040] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 12/16/2020] [Accepted: 12/24/2020] [Indexed: 12/18/2022] Open
Abstract
Metagenomics is a powerful tool to identify novel or unexpected pathogens, since it is generic and relatively unbiased. The limit of detection (LOD) is a critical parameter for the routine application of methods in the clinical diagnostic context. Although attempts for the determination of LODs for metagenomics next-generation sequencing (mNGS) have been made previously, these were only applicable for specific target species in defined samples matrices. Therefore, we developed and validated a generalized probability-based model to assess the sample-specific LOD of mNGS experiments (LODmNGS). Initial rarefaction analyses with datasets of Borna disease virus 1 human encephalitis cases revealed a stochastic behavior of virus read detection. Based on this, we transformed the Bernoulli formula to predict the minimal necessary dataset size to detect one virus read with a probability of 99%. We validated the formula with 30 datasets from diseased individuals, resulting in an accuracy of 99.1% and an average of 4.5 ± 0.4 viral reads found in the calculated minimal dataset size. We demonstrated by modeling the virus genome size, virus-, and total RNA-concentration that the main determinant of mNGS sensitivity is the virus-sample background ratio. The predicted LODmNGS for the respective pathogenic virus in the datasets were congruent with the virus-concentration determined by RT-qPCR. Theoretical assumptions were further confirmed by correlation analysis of mNGS and RT-qPCR data from the samples of the analyzed datasets. This approach should guide standardization of mNGS application, due to the generalized concept of LODmNGS.
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Affiliation(s)
- Arnt Ebinger
- Institute for Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems, Mecklenburg-Western Pomerania, Germany
| | - Susanne Fischer
- Institute of Infectology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems, Mecklenburg-Western Pomerania, Germany
| | - Dirk Höper
- Institute for Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems, Mecklenburg-Western Pomerania, Germany
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24
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Santiago-Rodriguez TM, Garoutte A, Adams E, Nasser W, Ross MC, La Reau A, Henseler Z, Ward T, Knights D, Petrosino JF, Hollister EB. Metagenomic Information Recovery from Human Stool Samples Is Influenced by Sequencing Depth and Profiling Method. Genes (Basel) 2020; 11:E1380. [PMID: 33233349 PMCID: PMC7700633 DOI: 10.3390/genes11111380] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 12/20/2022] Open
Abstract
Sequencing of the 16S rRNA gene (16S) has long been a go-to method for microbiome characterization due to its accessibility and lower cost compared to shotgun metagenomic sequencing (SMS). However, 16S sequencing rarely provides species-level resolution and cannot provide direct assessment of other taxa (e.g., viruses and fungi) or functional gene content. Shallow shotgun metagenomic sequencing (SSMS) has emerged as an approach to bridge the gap between 16S sequencing and deep metagenomic sequencing. SSMS is cost-competitive with 16S sequencing, while also providing species-level resolution and functional gene content insights. In the present study, we evaluated the effects of sequencing depth on marker gene-mapping- and alignment-based annotation of bacteria in healthy human stool samples. The number of identified taxa decreased with lower sequencing depths, particularly with the marker gene-mapping-based approach. Other annotations, including viruses and pathways, also showed a depth-dependent effect on feature recovery. These results refine the understanding of the suitability and shortcomings of SSMS, as well as annotation tools for metagenomic analyses in human stool samples. Results may also translate to other sample types and may open the opportunity to explore the effect of sequencing depth and annotation method.
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Affiliation(s)
| | - Aaron Garoutte
- Diversigen Inc., Houston, TX 77021, USA; (A.G.); (E.A.); (W.N.); (J.F.P.); (E.B.H.)
| | - Emmase Adams
- Diversigen Inc., Houston, TX 77021, USA; (A.G.); (E.A.); (W.N.); (J.F.P.); (E.B.H.)
| | - Waleed Nasser
- Diversigen Inc., Houston, TX 77021, USA; (A.G.); (E.A.); (W.N.); (J.F.P.); (E.B.H.)
| | - Matthew C. Ross
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX 77030, USA;
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alex La Reau
- Diversigen Inc., Saint Paul, MN 55112, USA; (A.L.R.); (Z.H.); (T.W.); (D.K.)
| | - Zachariah Henseler
- Diversigen Inc., Saint Paul, MN 55112, USA; (A.L.R.); (Z.H.); (T.W.); (D.K.)
| | - Tonya Ward
- Diversigen Inc., Saint Paul, MN 55112, USA; (A.L.R.); (Z.H.); (T.W.); (D.K.)
| | - Dan Knights
- Diversigen Inc., Saint Paul, MN 55112, USA; (A.L.R.); (Z.H.); (T.W.); (D.K.)
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Biotechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN 55455, USA
| | - Joseph F. Petrosino
- Diversigen Inc., Houston, TX 77021, USA; (A.G.); (E.A.); (W.N.); (J.F.P.); (E.B.H.)
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX 77030, USA;
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Emily B. Hollister
- Diversigen Inc., Houston, TX 77021, USA; (A.G.); (E.A.); (W.N.); (J.F.P.); (E.B.H.)
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25
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Sabatier M, Bal A, Destras G, Regue H, Quéromès G, Cheynet V, Lina B, Bardel C, Brengel-Pesce K, Navratil V, Josset L. Comparison of Nucleic Acid Extraction Methods for a Viral Metagenomics Analysis of Respiratory Viruses. Microorganisms 2020; 8:E1539. [PMID: 33036303 PMCID: PMC7601816 DOI: 10.3390/microorganisms8101539] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/03/2020] [Accepted: 10/05/2020] [Indexed: 12/25/2022] Open
Abstract
Viral metagenomics next-generation sequencing (mNGS) is increasingly being used to characterize the human virome. The impact of viral nucleic extraction on virome profiling has been poorly studied. Here, we aimed to compare the sensitivity and sample and reagent contamination of three extraction methods used for viral mNGS: two automated platforms (eMAG; MagNA Pure 24, MP24) and the manual QIAamp Viral RNA Mini Kit (QIAamp). Clinical respiratory samples (positive for Respiratory Syncytial Virus or Herpes Simplex Virus), one mock sample (including five viruses isolated from respiratory samples), and a no-template control (NTC) were extracted and processed through an mNGS workflow. QIAamp yielded a lower proportion of viral reads for both clinical and mock samples. The sample cross-contamination was higher when using MP24, with up to 36.09% of the viral reads mapping to mock viruses in the NTC (vs. 1.53% and 1.45% for eMAG and QIAamp, respectively). The highest number of viral reads mapping to bacteriophages in the NTC was found with QIAamp, suggesting reagent contamination. Our results highlight the importance of the extraction method choice for accurate virome characterization.
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Affiliation(s)
- Marina Sabatier
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France; (M.S.); (A.B.); (G.D.); (H.R.); (B.L.)
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France;
- Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France
| | - Antonin Bal
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France; (M.S.); (A.B.); (G.D.); (H.R.); (B.L.)
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France;
- Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France
| | - Grégory Destras
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France; (M.S.); (A.B.); (G.D.); (H.R.); (B.L.)
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France;
- Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France
| | - Hadrien Regue
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France; (M.S.); (A.B.); (G.D.); (H.R.); (B.L.)
| | - Grégory Quéromès
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France;
| | - Valérie Cheynet
- Laboratoire Commun de Recherche Hospices Civils de Lyon—bioMérieux, Centre Hospitalier Lyon Sud, F-69310 Pierre-Bénite, France; (V.C.); (K.B.-P.)
| | - Bruno Lina
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France; (M.S.); (A.B.); (G.D.); (H.R.); (B.L.)
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France;
- Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France
| | - Claire Bardel
- Université Lyon 1, Laboratoire de Biométrie et Biologie Evolutive, CNRS UMR5558, F-69100 Villeurbanne, France;
| | - Karen Brengel-Pesce
- Laboratoire Commun de Recherche Hospices Civils de Lyon—bioMérieux, Centre Hospitalier Lyon Sud, F-69310 Pierre-Bénite, France; (V.C.); (K.B.-P.)
| | - Vincent Navratil
- PRABI, Rhône Alpes Bioinformatics Center, UCBL, Université Claude Bernard Lyon 1, F-69000 Lyon, France;
- European Virus Bioinformatics Center, Leutragraben 1, D-07743 Jena, Germany
| | - Laurence Josset
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France; (M.S.); (A.B.); (G.D.); (H.R.); (B.L.)
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France;
- Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France
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26
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Charre C, Ginevra C, Sabatier M, Regue H, Destras G, Brun S, Burfin G, Scholtes C, Morfin F, Valette M, Lina B, Bal A, Josset L. Evaluation of NGS-based approaches for SARS-CoV-2 whole genome characterisation. Virus Evol 2020; 6:veaa075. [PMID: 33318859 PMCID: PMC7665770 DOI: 10.1093/ve/veaa075] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Since the beginning of the COVID-19 outbreak, SARS-CoV-2 whole-genome sequencing (WGS) has been performed at unprecedented rate worldwide with the use of very diverse Next-Generation Sequencing (NGS) methods. Herein, we compare the performance of four NGS-based approaches for SARS-CoV-2 WGS. Twenty-four clinical respiratory samples with a large scale of Ct values (from 10.7 to 33.9) were sequenced with four methods. Three used Illumina sequencing: an in-house metagenomic NGS (mNGS) protocol and two newly commercialised kits including a hybridisation capture method developed by Illumina (DNA Prep with Enrichment kit and Respiratory Virus Oligo Panel, RVOP), and an amplicon sequencing method developed by Paragon Genomics (CleanPlex SARS-CoV-2 kit). We also evaluated the widely used amplicon sequencing protocol developed by ARTIC Network and combined with Oxford Nanopore Technologies (ONT) sequencing. All four methods yielded near-complete genomes (>99%) for high viral loads samples (n = 8), with mNGS and RVOP producing the most complete genomes. For mid viral loads (Ct 20–25), amplicon-based enrichment methods led to genome coverage >99 per cent for all samples while 1/8 sample sequenced with RVOP and 2/8 samples sequenced with mNGS had a genome coverage below 99 per cent. For low viral loads (Ct ≥25), amplicon-based enrichment methods were the most sensitive techniques. All methods were highly concordant in terms of identity in complete consensus sequence. Just one mismatch in three samples was observed in CleanPlex vs the other methods, due to the dedicated bioinformatics pipeline setting a high threshold to call SNP compared to reference sequence. Importantly, all methods correctly identified a newly observed 34nt-deletion in ORF6 but required specific bioinformatic validation for RVOP. Finally, as a major warning for targeted techniques, a loss of coverage in any given region of the genome should alert to a potential rearrangement or a SNP in primer-annealing or probe-hybridizing regions and would require further validation using unbiased metagenomic sequencing.
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Affiliation(s)
- Caroline Charre
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France.,Université de Lyon, Université Claude Bernard Lyon 1 (UCBL1), Lyon, France.,Centre de recherche en cancérologie (CRCL), INSERM U1052- 69008, Lyon, France
| | - Christophe Ginevra
- CIRI, Centre International de Recherche en Infectiologie, (Team pathogenesis of Legionella), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon 69007, France.,Hospices Civils de Lyon, Centre National de Référence des Légionelles, Lyon, France
| | - Marina Sabatier
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France.,Université de Lyon, Université Claude Bernard Lyon 1 (UCBL1), Lyon, France.,Université de Lyon, Virpath, CIRI, INSERM U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Hadrien Regue
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France.,Université de Lyon, Université Claude Bernard Lyon 1 (UCBL1), Lyon, France
| | - Grégory Destras
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France.,Université de Lyon, Université Claude Bernard Lyon 1 (UCBL1), Lyon, France.,Université de Lyon, Virpath, CIRI, INSERM U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France.,Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France
| | - Solenne Brun
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France.,Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France
| | - Gwendolyne Burfin
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France.,Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France
| | - Caroline Scholtes
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France.,Université de Lyon, Université Claude Bernard Lyon 1 (UCBL1), Lyon, France.,Centre de recherche en cancérologie (CRCL), INSERM U1052- 69008, Lyon, France
| | - Florence Morfin
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France.,Université de Lyon, Université Claude Bernard Lyon 1 (UCBL1), Lyon, France.,Université de Lyon, Virpath, CIRI, INSERM U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France.,Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France
| | - Martine Valette
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France.,Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France
| | - Bruno Lina
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France.,Université de Lyon, Université Claude Bernard Lyon 1 (UCBL1), Lyon, France.,Université de Lyon, Virpath, CIRI, INSERM U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France.,Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France
| | - Antonin Bal
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France.,Université de Lyon, Université Claude Bernard Lyon 1 (UCBL1), Lyon, France.,Université de Lyon, Virpath, CIRI, INSERM U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France.,Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France
| | - Laurence Josset
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France.,Université de Lyon, Université Claude Bernard Lyon 1 (UCBL1), Lyon, France.,Université de Lyon, Virpath, CIRI, INSERM U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France.,Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France
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Abstract
BACKGROUND During the past decade, breakthroughs in sequencing technology and computational biology have provided the basis for studies of the myriad ways in which microbial communities ("microbiota") in and on the human body influence human health and disease. In almost every medical specialty, there is now a growing interest in accurate and replicable profiling of the microbiota for use in diagnostic and therapeutic application. CONTENT This review provides an overview of approaches, challenges, and considerations for diagnostic applications borrowing from other areas of molecular diagnostics, including clinical metagenomics. Methodological considerations and evolving approaches for microbiota profiling from mitochondrially encoded 16S rRNA-based amplicon sequencing to metagenomics and metatranscriptomics are discussed. To improve replicability, at least the most vulnerable steps in testing workflows will need to be standardized and continuous efforts needed to define QC standards. Challenges such as purity of reagents and consumables, improvement of reference databases, and availability of diagnostic-grade data analysis solutions will require joint efforts across disciplines and with manufacturers. SUMMARY The body of literature supporting important links between the microbiota at different anatomic sites with human health and disease is expanding rapidly and therapeutic manipulation of the intestinal microbiota is becoming routine. The next decade will likely see implementation of microbiome diagnostics in diagnostic laboratories to fully capitalize on technological and scientific advances and apply them in routine medical practice.
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Affiliation(s)
- Robert Schlaberg
- Department of Pathology, University of Utah, Salt Lake City, UT.,ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT.,IDbyDNA Inc., San Francisco, CA
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28
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Janes VA, van der Laan JS, Matamoros S, Mende DR, de Jong MD, Schultsz C. Thermus thermophilus DNA can be used as internal control for process monitoring of clinical metagenomic next-generation sequencing of urine samples. J Microbiol Methods 2020; 176:106005. [PMID: 32687865 DOI: 10.1016/j.mimet.2020.106005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 07/14/2020] [Accepted: 07/14/2020] [Indexed: 12/20/2022]
Abstract
INTRODUCTION Metagenomics is increasingly considered for clinical diagnostics. In order for this technology to become integrated in the clinical microbiology laboratory, process controls are required. Molecular diagnostic tests typically integrate an internal control (IC) to detect potential sources of variation and technical failure. However, few studies report on the integration of an IC in metagenomics. AIM We aimed to develop an easy-to-use IC method for the process control of library preparation and sequencing applied to metagenomics in clinical microbiology diagnostics using Thermus thermophilus DNA. METHODOLOGY DNA was extracted from urine samples and sequenced on the Ion Torrent Proton in the absence and presence of incremental concentrations (0.5-2-5%) of IC. Between aliquots of each sample, we compared the IC relative abundance (RA), and after in silico subtraction of IC reads, analysed microbial composition and the RA of pathogens. The optimal IC concentration was defined as the lowest concentration still detectable in all samples with the smallest impact on the microbial composition. RESULTS The RA of IC correlated linearly with the spiked IC concentration (r2 = 0.99). IC added in a concentration of 0.5% of the total DNA concentration was detectable in all sample aliquots, regardless of human-bacterial DNA proportion, and after in silico removal gave the smallest difference in RA of pathogens compared to the sample aliquot sequenced in the absence of IC. The microbial composition in the presence and absence of IC was highly similar after in silico removal of IC reads (median BC-dissimilarity per sample: 0.059), provided samples had a mean of >10,000 bacterial reads. CONCLUSION T. thermophilus DNA at a percentage of 0.5% of the total DNA concentration was successfully applied for the process control of metagenomics of urine samples. We demonstrated negligible alterations in sample microbial composition after in silico subtraction of IC reads. This approach contributes toward implementation of metagenomics in the clinical microbiology laboratory.
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Affiliation(s)
- Victoria A Janes
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology, Amsterdam, the Netherlands.
| | - Jennifer S van der Laan
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology, Amsterdam, the Netherlands
| | - Sébastien Matamoros
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology, Amsterdam, the Netherlands
| | - Daniel R Mende
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology, Amsterdam, the Netherlands
| | - Menno D de Jong
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology, Amsterdam, the Netherlands
| | - Constance Schultsz
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology, Amsterdam, the Netherlands; Amsterdam UMC, University of Amsterdam, Department of Global Health, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam, the Netherlands
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29
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Bal A, Sabatier M, Wirth T, Coste-Burel M, Lazrek M, Stefic K, Brengel-Pesce K, Morfin F, Lina B, Schuffenecker I, Josset L. Emergence of enterovirus D68 clade D1, France, August to November 2018. ACTA ACUST UNITED AC 2020; 24. [PMID: 30670143 PMCID: PMC6344839 DOI: 10.2807/1560-7917.es.2019.24.3.1800699] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We report a seasonal increase of enterovirus D68 (EV-D68) cases in France, with 54 cases detected between 19 August and 14 November 2018. Molecular typing revealed that 20 of 32 of the isolates belonged to clade D1, only sporadically detected before in France. Median age of D1-cases was 42 years, 10 developed severe respiratory signs and one had neurological complications. The 2018-D1 viruses showed a genetic divergence of 3.34 % with D1 viruses identified previously.
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Affiliation(s)
- Antonin Bal
- Laboratoire Commun de Recherche Hospices Civils de Lyon-bioMerieux, Centre Hospitalier Lyon Sud, Pierre-Bénite, France.,Université Lyon 1, Faculté de Médecine Lyon Est, CIRI, Inserm U1111, CNRS UMR5308, Virpath, Lyon, France.,Laboratoire de Virologie, Institut des Agents Infectieux, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France.,Centre National de Référence des Enterovirus et Parechovirus, Hospices Civils de Lyon, Lyon, France
| | - Marina Sabatier
- Université Lyon 1, Faculté de Médecine Lyon Est, CIRI, Inserm U1111, CNRS UMR5308, Virpath, Lyon, France.,Laboratoire de Virologie, Institut des Agents Infectieux, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France.,Centre National de Référence des Enterovirus et Parechovirus, Hospices Civils de Lyon, Lyon, France
| | - Thierry Wirth
- Institut Systématique, Evolution, Biodiversité (ISYEB), EPHE, MNHN, CNRS, Sorbonne Université, Paris, France.,Laboratoire Biologie Intégrative des Populations, Evolution Moléculaire, EPHE, PSL Université, Paris, France
| | - Marianne Coste-Burel
- Laboratoire de Virologie, UIC9 CIC infectieux, Centre Hospitalier Universitaire de Nantes, Nantes, France
| | - Mouna Lazrek
- Laboratoire de Virologie, EA3610, Centre Hospitalier Universitaire de Lille, Université de Lille, Lille, France
| | - Karl Stefic
- Laboratoire de Virologie and CNR VIH-Laboratoire Associé, Centre Hospitalier Régional Universitaire de Tours, Tours, France.,INSERM U1259, Université de Tours, Tours, France
| | - Karen Brengel-Pesce
- Laboratoire Commun de Recherche Hospices Civils de Lyon-bioMerieux, Centre Hospitalier Lyon Sud, Pierre-Bénite, France
| | - Florence Morfin
- Université Lyon 1, Faculté de Médecine Lyon Est, CIRI, Inserm U1111, CNRS UMR5308, Virpath, Lyon, France.,Laboratoire de Virologie, Institut des Agents Infectieux, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France
| | - Bruno Lina
- Université Lyon 1, Faculté de Médecine Lyon Est, CIRI, Inserm U1111, CNRS UMR5308, Virpath, Lyon, France.,Laboratoire de Virologie, Institut des Agents Infectieux, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France.,Centre National de Référence des Enterovirus et Parechovirus, Hospices Civils de Lyon, Lyon, France
| | - Isabelle Schuffenecker
- Laboratoire de Virologie, Institut des Agents Infectieux, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France.,Centre National de Référence des Enterovirus et Parechovirus, Hospices Civils de Lyon, Lyon, France
| | - Laurence Josset
- Université Lyon 1, Faculté de Médecine Lyon Est, CIRI, Inserm U1111, CNRS UMR5308, Virpath, Lyon, France.,Laboratoire de Virologie, Institut des Agents Infectieux, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France.,Centre National de Référence des Enterovirus et Parechovirus, Hospices Civils de Lyon, Lyon, France
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30
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Desdouits M, de Graaf M, Strubbia S, Oude Munnink BB, Kroneman A, Le Guyader FS, Koopmans MPG. Novel opportunities for NGS-based one health surveillance of foodborne viruses. ONE HEALTH OUTLOOK 2020; 2:14. [PMID: 33829135 PMCID: PMC7993515 DOI: 10.1186/s42522-020-00015-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 05/01/2020] [Indexed: 05/15/2023]
Abstract
Foodborne viral infections rank among the top 5 causes of disease, with noroviruses and hepatitis A causing the greatest burden globally. Contamination of foods by infected food handlers or through environmental pollution are the main sources of foodborne illness, with a lesser role for consumption of products from infected animals. Viral partial genomic sequencing has been used for more than two decades to track foodborne outbreaks and whole genome or metagenomics next-generation-sequencing (NGS) are new additions to the toolbox of food microbiology laboratories. We discuss developments in the field of targeted and metagenomic NGS, with an emphasis on application in food virology, the challenges and possible solutions towards future routine application.
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Affiliation(s)
- Marion Desdouits
- IFREMER, Laboratoire de Microbiologie, LSEM/SG2M, Nantes, France
| | - Miranda de Graaf
- Viroscience Department, Erasmus Medical Centre, Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| | - Sofia Strubbia
- IFREMER, Laboratoire de Microbiologie, LSEM/SG2M, Nantes, France
| | - Bas B. Oude Munnink
- Viroscience Department, Erasmus Medical Centre, Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| | - Annelies Kroneman
- Centre for Infectious Disease Control, National Institute of Public Health and the Environment, Bilthoven, The Netherlands
| | | | - Marion P. G. Koopmans
- Viroscience Department, Erasmus Medical Centre, Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
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31
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Van Borm S, Fu Q, Winand R, Vanneste K, Hakhverdyan M, Höper D, Vandenbussche F. Evaluation of a commercial exogenous internal process control for diagnostic RNA virus metagenomics from different animal clinical samples. J Virol Methods 2020; 283:113916. [PMID: 32574649 DOI: 10.1016/j.jviromet.2020.113916] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/09/2020] [Accepted: 06/09/2020] [Indexed: 12/20/2022]
Abstract
Metagenomic next generation sequencing (mNGS) is increasingly recognized as an important complementary tool to targeted human and animal infectious disease diagnostics. It is, however, sensitive to biases and errors that are currently not systematically evaluated by the implementation of quality controls (QC) for the diagnostic use of mNGS. We evaluated a commercial reagent (Mengovirus extraction control kit, CeraamTools, bioMérieux) as an exogenous internal control for mNGS. It validates the integrity of reagents and workflow, the efficient isolation of viral nucleic acids and the absence of inhibitors in individual samples (verified using a specific qRT-PCR). Moreover, it validates the efficient generation of viral sequence data in individual samples (verified by normalized mengoviral read counts in the metagenomic analysis). We show that when using a completely random metagenomics workflow: (1) Mengovirus RNA can be reproducibly detected in different animal sample types (swine feces and sera, wild bird cloacal swabs), except for tissue samples (swine lung); (2) the Mengovirus control kit does not contain other contaminating viruses that may affect metagenomic experiments (using a cutoff of minimum 1 Kraken classified read per million (RPM)); (3) the addition of 2.17 × 106Mengovirus copies/mL of sample does not affect the virome composition of pig fecal samples or wild bird cloacal swab samples; (4) Mengovirus Cq values (using as cutoff the upper limit of the 99 % confidence interval of Cq values for a given sample matrix) allow the identification of samples with poor viral RNA extraction or high inhibitor load; (5) Mengovirus normalized read counts (cutoff RPM > 1) allow the identification of samples where the viral sequences are outcompeted by host or bacterial target sequences in the random metagenomic workflow. The implementation of two QC testing points, a first one after RNA extraction (Mengoviral qRT-PCR) and a second one after metagenomic data analysis provide valuable information for the validation of individual samples and results. Their implementation in addition to external controls validating runs or experiments should be carefully considered for a given sample type and workflow.
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Affiliation(s)
- Steven Van Borm
- Department of Animal Infectious Diseases, Sciensano, Groeselenbergstraat 99, 1180, Brussels, Belgium.
| | - Qiang Fu
- Transversal Activities in Applied Genomics, Sciensano, Rue Juliette Wytsmanstraat 14, 1050, Brussels, Belgium
| | - Raf Winand
- Transversal Activities in Applied Genomics, Sciensano, Rue Juliette Wytsmanstraat 14, 1050, Brussels, Belgium
| | - Kevin Vanneste
- Transversal Activities in Applied Genomics, Sciensano, Rue Juliette Wytsmanstraat 14, 1050, Brussels, Belgium
| | | | - Dirk Höper
- FLI, Friedrich Löffler Institut, Südufer 10, 17493 Greifswald, Germany
| | - Frank Vandenbussche
- Department of Animal Infectious Diseases, Sciensano, Groeselenbergstraat 99, 1180, Brussels, Belgium
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32
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Bolatti EM, Zorec TM, Montani ME, Hošnjak L, Chouhy D, Viarengo G, Casal PE, Barquez RM, Poljak M, Giri AA. A Preliminary Study of the Virome of the South American Free-Tailed Bats ( Tadarida brasiliensis) and Identification of Two Novel Mammalian Viruses. Viruses 2020; 12:v12040422. [PMID: 32283670 PMCID: PMC7232368 DOI: 10.3390/v12040422] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/01/2020] [Accepted: 04/03/2020] [Indexed: 12/12/2022] Open
Abstract
Bats provide important ecosystem services as pollinators, seed dispersers, and/or insect controllers, but they have also been found harboring different viruses with zoonotic potential. Virome studies in bats distributed in Asia, Africa, Europe, and North America have increased dramatically over the past decade, whereas information on viruses infecting South American species is scarce. We explored the virome of Tadarida brasiliensis, an insectivorous New World bat species inhabiting a maternity colony in Rosario (Argentina), by a metagenomic approach. The analysis of five pooled oral/anal swab samples indicated the presence of 43 different taxonomic viral families infecting a wide range of hosts. By conventional nucleic acid detection techniques and/or bioinformatics approaches, the genomes of two novel viruses were completely covered clustering into the Papillomaviridae (Tadarida brasiliensis papillomavirus type 1, TbraPV1) and Genomoviridae (Tadarida brasiliensis gemykibivirus 1, TbGkyV1) families. TbraPV1 is the first papillomavirus type identified in this host and the prototype of a novel genus. TbGkyV1 is the first genomovirus reported in New World bats and constitutes a new species within the genus Gemykibivirus. Our findings extend the knowledge about oral/anal viromes of a South American bat species and contribute to understand the evolution and genetic diversity of the novel characterized viruses.
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Affiliation(s)
- Elisa M. Bolatti
- Grupo Virología Humana, Instituto de Biología Molecular y Celular de Rosario (CONICET), Suipacha 590, Rosario 2000, Argentina; (E.M.B.); (D.C.); (G.V.)
- Área Virología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina;
| | - Tomaž M. Zorec
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, SI-1000 Ljubljana, Slovenia; (T.M.Z.); (L.H.)
| | - María E. Montani
- Museo Provincial de Ciencias Naturales “Dr. Ángel Gallardo”, San Lorenzo 1949, Rosario 2000, Argentina;
- Programa de Conservación de los Murciélagos de Argentina, Miguel Lillo 251, San Miguel de Tucumán 4000, Argentina;
- Programa de Investigaciones de Biodiversidad Argentina, Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, Miguel Lillo 205, San Miguel de Tucumán 4000, Argentina
| | - Lea Hošnjak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, SI-1000 Ljubljana, Slovenia; (T.M.Z.); (L.H.)
| | - Diego Chouhy
- Grupo Virología Humana, Instituto de Biología Molecular y Celular de Rosario (CONICET), Suipacha 590, Rosario 2000, Argentina; (E.M.B.); (D.C.); (G.V.)
- Área Virología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina;
| | - Gastón Viarengo
- Grupo Virología Humana, Instituto de Biología Molecular y Celular de Rosario (CONICET), Suipacha 590, Rosario 2000, Argentina; (E.M.B.); (D.C.); (G.V.)
| | - Pablo E. Casal
- Área Virología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina;
| | - Rubén M. Barquez
- Programa de Conservación de los Murciélagos de Argentina, Miguel Lillo 251, San Miguel de Tucumán 4000, Argentina;
- Programa de Investigaciones de Biodiversidad Argentina, Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, Miguel Lillo 205, San Miguel de Tucumán 4000, Argentina
| | - Mario Poljak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, SI-1000 Ljubljana, Slovenia; (T.M.Z.); (L.H.)
- Correspondence: (M.P.); (A.A.G.); Tel.: +386-1-543-7454 (M.P.); +54-341-435-0661 (ext. 116) (A.A.G.); Fax: +54-341-439-0465 (A.A.G.)
| | - Adriana A. Giri
- Grupo Virología Humana, Instituto de Biología Molecular y Celular de Rosario (CONICET), Suipacha 590, Rosario 2000, Argentina; (E.M.B.); (D.C.); (G.V.)
- Área Virología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina;
- Correspondence: (M.P.); (A.A.G.); Tel.: +386-1-543-7454 (M.P.); +54-341-435-0661 (ext. 116) (A.A.G.); Fax: +54-341-439-0465 (A.A.G.)
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33
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Bal A, Destras G, Gaymard A, Bouscambert-Duchamp M, Valette M, Escuret V, Frobert E, Billaud G, Trouillet-Assant S, Cheynet V, Brengel-Pesce K, Morfin F, Lina B, Josset L. Molecular characterization of SARS-CoV-2 in the first COVID-19 cluster in France reveals an amino acid deletion in nsp2 (Asp268del). Clin Microbiol Infect 2020; 26:960-962. [PMID: 32234449 PMCID: PMC7142683 DOI: 10.1016/j.cmi.2020.03.020] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 03/21/2020] [Indexed: 11/30/2022]
Affiliation(s)
- A Bal
- Centre National de Référence des Virus Respiratoires, Hospices Civils de Lyon, Lyon, France; Laboratoire de Virologie, Institut des Agents Infectieux, Hôpital de La Croix-Rousse, Hospices Civils de Lyon, Lyon, France; Université Lyon 1, Faculté de Médecine Lyon Est, CIRI, Inserm U1111 CNRS UMR5308, Virpath, Lyon, France; Laboratoire Commun de Recherche Hospices Civils de Lyon-bioMérieux, Centre Hospitalier Lyon Sud, Pierre-Bénite, France
| | - G Destras
- Centre National de Référence des Virus Respiratoires, Hospices Civils de Lyon, Lyon, France; Laboratoire de Virologie, Institut des Agents Infectieux, Hôpital de La Croix-Rousse, Hospices Civils de Lyon, Lyon, France; Université Lyon 1, Faculté de Médecine Lyon Est, CIRI, Inserm U1111 CNRS UMR5308, Virpath, Lyon, France
| | - A Gaymard
- Centre National de Référence des Virus Respiratoires, Hospices Civils de Lyon, Lyon, France; Laboratoire de Virologie, Institut des Agents Infectieux, Hôpital de La Croix-Rousse, Hospices Civils de Lyon, Lyon, France; Université Lyon 1, Faculté de Médecine Lyon Est, CIRI, Inserm U1111 CNRS UMR5308, Virpath, Lyon, France
| | - M Bouscambert-Duchamp
- Centre National de Référence des Virus Respiratoires, Hospices Civils de Lyon, Lyon, France; Laboratoire de Virologie, Institut des Agents Infectieux, Hôpital de La Croix-Rousse, Hospices Civils de Lyon, Lyon, France
| | - M Valette
- Centre National de Référence des Virus Respiratoires, Hospices Civils de Lyon, Lyon, France; Laboratoire de Virologie, Institut des Agents Infectieux, Hôpital de La Croix-Rousse, Hospices Civils de Lyon, Lyon, France
| | - V Escuret
- Centre National de Référence des Virus Respiratoires, Hospices Civils de Lyon, Lyon, France; Laboratoire de Virologie, Institut des Agents Infectieux, Hôpital de La Croix-Rousse, Hospices Civils de Lyon, Lyon, France; Université Lyon 1, Faculté de Médecine Lyon Est, CIRI, Inserm U1111 CNRS UMR5308, Virpath, Lyon, France
| | - E Frobert
- Centre National de Référence des Virus Respiratoires, Hospices Civils de Lyon, Lyon, France; Laboratoire de Virologie, Institut des Agents Infectieux, Hôpital de La Croix-Rousse, Hospices Civils de Lyon, Lyon, France; Université Lyon 1, Faculté de Médecine Lyon Est, CIRI, Inserm U1111 CNRS UMR5308, Virpath, Lyon, France
| | - G Billaud
- Centre National de Référence des Virus Respiratoires, Hospices Civils de Lyon, Lyon, France; Laboratoire de Virologie, Institut des Agents Infectieux, Hôpital de La Croix-Rousse, Hospices Civils de Lyon, Lyon, France
| | - S Trouillet-Assant
- Université Lyon 1, Faculté de Médecine Lyon Est, CIRI, Inserm U1111 CNRS UMR5308, Virpath, Lyon, France; Laboratoire Commun de Recherche Hospices Civils de Lyon-bioMérieux, Centre Hospitalier Lyon Sud, Pierre-Bénite, France
| | - V Cheynet
- Laboratoire Commun de Recherche Hospices Civils de Lyon-bioMérieux, Centre Hospitalier Lyon Sud, Pierre-Bénite, France
| | - K Brengel-Pesce
- Laboratoire Commun de Recherche Hospices Civils de Lyon-bioMérieux, Centre Hospitalier Lyon Sud, Pierre-Bénite, France
| | - F Morfin
- Centre National de Référence des Virus Respiratoires, Hospices Civils de Lyon, Lyon, France; Laboratoire de Virologie, Institut des Agents Infectieux, Hôpital de La Croix-Rousse, Hospices Civils de Lyon, Lyon, France; Université Lyon 1, Faculté de Médecine Lyon Est, CIRI, Inserm U1111 CNRS UMR5308, Virpath, Lyon, France
| | - B Lina
- Centre National de Référence des Virus Respiratoires, Hospices Civils de Lyon, Lyon, France; Laboratoire de Virologie, Institut des Agents Infectieux, Hôpital de La Croix-Rousse, Hospices Civils de Lyon, Lyon, France; Université Lyon 1, Faculté de Médecine Lyon Est, CIRI, Inserm U1111 CNRS UMR5308, Virpath, Lyon, France
| | - L Josset
- Centre National de Référence des Virus Respiratoires, Hospices Civils de Lyon, Lyon, France; Laboratoire de Virologie, Institut des Agents Infectieux, Hôpital de La Croix-Rousse, Hospices Civils de Lyon, Lyon, France; Université Lyon 1, Faculté de Médecine Lyon Est, CIRI, Inserm U1111 CNRS UMR5308, Virpath, Lyon, France.
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34
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van Boheemen S, van Rijn AL, Pappas N, Carbo EC, Vorderman RHP, Sidorov I, van T Hof PJ, Mei H, Claas ECJ, Kroes ACM, de Vries JJC. Retrospective Validation of a Metagenomic Sequencing Protocol for Combined Detection of RNA and DNA Viruses Using Respiratory Samples from Pediatric Patients. J Mol Diagn 2020; 22:196-207. [PMID: 31837435 PMCID: PMC7106021 DOI: 10.1016/j.jmoldx.2019.10.007] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 09/16/2019] [Accepted: 10/07/2019] [Indexed: 02/07/2023] Open
Abstract
Viruses are the main cause of respiratory tract infections. Metagenomic next-generation sequencing (mNGS) enables unbiased detection of all potential pathogens. To apply mNGS in viral diagnostics, sensitive and simultaneous detection of RNA and DNA viruses is needed. Herein, were studied the performance of an in-house mNGS protocol for routine diagnostics of viral respiratory infections with potential for automated pan-pathogen detection. The sequencing protocol and bioinformatics analysis were designed and optimized, including exogenous internal controls. Subsequently, the protocol was retrospectively validated using 25 clinical respiratory samples. The developed protocol using Illumina NextSeq 500 sequencing showed high repeatability. Use of the National Center for Biotechnology Information's RefSeq database as opposed to the National Center for Biotechnology Information's nucleotide database led to enhanced specificity of classification of viral pathogens. A correlation was established between read counts and PCR cycle threshold value. Sensitivity of mNGS, compared with PCR, varied up to 83%, with specificity of 94%, dependent on the cutoff for defining positive mNGS results. Viral pathogens only detected by mNGS, not present in the routine diagnostic workflow, were influenza C, KI polyomavirus, cytomegalovirus, and enterovirus. Sensitivity and analytical specificity of this mNGS protocol were comparable to PCR and higher when considering off-PCR target viral pathogens. One single test detected all potential viral pathogens and simultaneously obtained detailed information on detected viruses.
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Affiliation(s)
- Sander van Boheemen
- Department of Medical Microbiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Anneloes L van Rijn
- Department of Medical Microbiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands.
| | - Nikos Pappas
- Sequencing Analysis Support Core, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Ellen C Carbo
- Department of Medical Microbiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Ruben H P Vorderman
- Sequencing Analysis Support Core, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Igor Sidorov
- Department of Medical Microbiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Peter J van T Hof
- Sequencing Analysis Support Core, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Hailiang Mei
- Sequencing Analysis Support Core, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Eric C J Claas
- Department of Medical Microbiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Aloys C M Kroes
- Department of Medical Microbiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Jutte J C de Vries
- Department of Medical Microbiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
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35
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Ung L, Bispo PJM, Doan T, Van Gelder RN, Gilmore MS, Lietman T, Margolis TP, Zegans ME, Lee CS, Chodosh J. Clinical metagenomics for infectious corneal ulcers: Rags to riches? Ocul Surf 2020; 18:1-12. [PMID: 31669750 PMCID: PMC9837861 DOI: 10.1016/j.jtos.2019.10.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 10/21/2019] [Indexed: 01/17/2023]
Abstract
The emergence of clinical metagenomics as an unbiased, hypothesis-free approach to diagnostic testing is set to fundamentally alter the way infectious diseases are detected. Long envisioned as the solution to the limitations of culture-based conventional microbiology, next generation sequencing methods will soon mature, and our attention will inevitably turn to how they can be applied to areas of medicine which need it most urgently. In ophthalmology, the demand for this technology is particularly pressing for the care of infectious corneal ulcers, where current diagnostic tests may fail to identify a causative organism in over half of cases. However, the optimism found in the budding discourse surrounding clinical metagenomics belies the reality that clinicians and scientists will soon be inundated by oppressive volumes of sequencing data, much of which will be foreign and unfamiliar. Therefore, our success in translating clinical metagenomics is likely to hinge on how we make sense of these data, and understanding its implications for the interpretation and implementation of sequencing into routine clinical care. In this consortium-led review, we provide an outline of these data-related issues and how they may be used to inform technical workflows, with the hope that we may edge closer to realizing the potential of clinical metagenomics for this important unmet need.
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Affiliation(s)
- Lawson Ung
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA; Infectious Disease Institute and Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Paulo J M Bispo
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA; Infectious Disease Institute and Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Thuy Doan
- Francis I. Proctor Foundation, Department of Ophthalmology, University of California, San Francisco, CA, USA
| | | | - Michael S Gilmore
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA; Infectious Disease Institute and Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Thomas Lietman
- Francis I. Proctor Foundation, Department of Ophthalmology, University of California, San Francisco, CA, USA
| | - Todd P Margolis
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine in Saint Louis, Saint Louis, USA
| | - Michael E Zegans
- Department of Surgery (Ophthalmology), and Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, USA
| | - Cecilia S Lee
- Department of Ophthalmology, University of Washington, Seattle, WA, USA.
| | - James Chodosh
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA; Infectious Disease Institute and Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA.
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36
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Han D, Li Z, Li R, Tan P, Zhang R, Li J. mNGS in clinical microbiology laboratories: on the road to maturity. Crit Rev Microbiol 2019; 45:668-685. [PMID: 31691607 DOI: 10.1080/1040841x.2019.1681933] [Citation(s) in RCA: 160] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metagenomic next-generation sequencing (mNGS) is increasingly being applied in clinical laboratories for unbiased culture-independent diagnosis. Whether it can be a next routine pathogen identification tool has become a topic of concern. We review the current implementation of this new technology for infectious disease diagnostics and discuss the feasibility of transforming mNGS into a routine diagnostic test. Since 2008, numerous studies from over 20 countries have revealed the practicality of mNGS in the work-up of undiagnosed infectious diseases. mNGS performs well in identifying rare, novel, difficult-to-detect and coinfected pathogens directly from clinical samples and presents great potential in resistance prediction by sequencing the antibiotic resistance genes, providing new diagnostic evidence that can be used to guide treatment options and improve antibiotic stewardship. Many physicians recognized mNGS as a last resort method to address clinical infection problems. Although several hurdles, such as workflow validation, quality control, method standardisation, and data interpretation, remain before mNGS can be implemented routinely in clinical laboratories, they are temporary and can be overcome by rapidly evolving technologies. With more validated workflows, lower cost and turnaround time, and simplified interpretation criteria, mNGS will be widely accepted in clinical practice. Overall, mNGS is transforming the landscape of clinical microbiology laboratories, and to ensure that it is properly utilised in clinical diagnosis, both physicians and microbiologists should have a thorough understanding of the power and limitations of this method.
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Affiliation(s)
- Dongsheng Han
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Ziyang Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Rui Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Ping Tan
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Rui Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
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37
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Bal A, Oriol G, Josset L, Generenaz L, Sarkozy C, Sesques P, Salles G, Morfin F, Lina B, Becker J, Reynier F, Mallet F, Pachot A, Cheynet V, Brengel-Pesce K, Trouillet-Assant S. Metagenomic Investigation of Torque Teno Mini Virus-SH in Hematological Patients. Front Microbiol 2019; 10:1898. [PMID: 31620095 PMCID: PMC6759482 DOI: 10.3389/fmicb.2019.01898] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 07/31/2019] [Indexed: 11/28/2022] Open
Abstract
A new member of Anelloviridae, named torque teno mini virus (TTMV)-SH, was recently identified in the serum of three Hodgkin’s lymphoma patients suggesting that TTMV-SH may be associated with this type of hematological malignancy. We investigated by metagenomic analysis the presence of TTMV-SH-related viruses in plasma samples (n = 323) collected from patients with various hematological malignancies (multiple myeloma (MM, n = 256), non-Hodgkin’s lymphoma (NHL, n = 20), acute myeloid leukemia (n = 10)) and from healthy donors (n = 37). TTMV-SH-related strains were identified in 24 samples corresponding to four MM and one NHL patients. Phylogenic analysis revealed that the 24 isolates were close to the TTMV-SH strains previously identified, sharing 79.6–86.7% ORF1 nucleotide sequence identity. These results suggest that TTMV-SH-related viruses might be found in hematological diseases other than Hodgkin’s lymphoma. Due to the high genetic variability within Anelloviridae species, the association between a particular medical condition and a new genotype should be interpreted with caution.
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Affiliation(s)
- Antonin Bal
- Laboratoire Commun de Recherche Hospices Civils de Lyon - bioMérieux, Centre Hospitalier Lyon Sud, Pierre-Bénite, France.,Laboratoire de Virologie, Institut des Agents Infectieux, Groupement Hospitalier Nord, Hospices Civils de Lyon, Lyon, France.,CIRI, Inserm U1111 CNRS UMR5308, Virpath, Univ Lyon, Université Lyon 1, Lyon, France
| | - Guy Oriol
- Laboratoire Commun de Recherche Hospices Civils de Lyon - bioMérieux, Centre Hospitalier Lyon Sud, Pierre-Bénite, France
| | - Laurence Josset
- Laboratoire de Virologie, Institut des Agents Infectieux, Groupement Hospitalier Nord, Hospices Civils de Lyon, Lyon, France.,CIRI, Inserm U1111 CNRS UMR5308, Virpath, Univ Lyon, Université Lyon 1, Lyon, France
| | - Laurence Generenaz
- Laboratoire Commun de Recherche Hospices Civils de Lyon - bioMérieux, Centre Hospitalier Lyon Sud, Pierre-Bénite, France
| | - Clémentine Sarkozy
- Service d'hématologie clinique, Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, Pierre-Bénite, France
| | - Pierre Sesques
- Service d'hématologie clinique, Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, Pierre-Bénite, France
| | - Gilles Salles
- Service d'hématologie clinique, Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, Pierre-Bénite, France
| | - Florence Morfin
- Laboratoire de Virologie, Institut des Agents Infectieux, Groupement Hospitalier Nord, Hospices Civils de Lyon, Lyon, France.,CIRI, Inserm U1111 CNRS UMR5308, Virpath, Univ Lyon, Université Lyon 1, Lyon, France
| | - Bruno Lina
- Laboratoire de Virologie, Institut des Agents Infectieux, Groupement Hospitalier Nord, Hospices Civils de Lyon, Lyon, France.,CIRI, Inserm U1111 CNRS UMR5308, Virpath, Univ Lyon, Université Lyon 1, Lyon, France
| | - Jérémie Becker
- BIOASTER, Genomics and Transcriptomics Technological Unit, Lyon, France
| | - Frédéric Reynier
- BIOASTER, Genomics and Transcriptomics Technological Unit, Lyon, France
| | - François Mallet
- Laboratoire Commun de Recherche Hospices Civils de Lyon - bioMérieux, Centre Hospitalier Lyon Sud, Pierre-Bénite, France
| | - Alexandre Pachot
- Laboratoire Commun de Recherche Hospices Civils de Lyon - bioMérieux, Centre Hospitalier Lyon Sud, Pierre-Bénite, France
| | - Valérie Cheynet
- Laboratoire Commun de Recherche Hospices Civils de Lyon - bioMérieux, Centre Hospitalier Lyon Sud, Pierre-Bénite, France
| | - Karen Brengel-Pesce
- Laboratoire Commun de Recherche Hospices Civils de Lyon - bioMérieux, Centre Hospitalier Lyon Sud, Pierre-Bénite, France
| | - Sophie Trouillet-Assant
- Laboratoire Commun de Recherche Hospices Civils de Lyon - bioMérieux, Centre Hospitalier Lyon Sud, Pierre-Bénite, France.,CIRI, Inserm U1111 CNRS UMR5308, Virpath, Univ Lyon, Université Lyon 1, Lyon, France
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Altan E, Dib JC, Gulloso AR, Escribano Juandigua D, Deng X, Bruhn R, Hildebrand K, Freiden P, Yamamoto J, Schultz-Cherry S, Delwart E. Effect of Geographic Isolation on the Nasal Virome of Indigenous Children. J Virol 2019; 93:e00681-19. [PMID: 31189707 PMCID: PMC6694818 DOI: 10.1128/jvi.00681-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 05/29/2019] [Indexed: 11/20/2022] Open
Abstract
The influence of living in small remote villages on the diversity of viruses in the nasal mucosa was investigated in three Colombian villages with very different levels of geographic isolation. Metagenomic analysis was used to characterize viral nucleic acids in nasal swabs from 63 apparently healthy young children. Sequences from human virus members of the families Anelloviridae, Papillomaviridae, Picornaviridae, Herpesviridae, Polyomaviridae, Adenoviridae, and Paramyxoviridae were detected in decreasing proportions of children. The number of papillomavirus infections detected was greater among Hispanic children most exposed to outside contacts, while anellovirus infections were more common in the isolated indigenous villages. The diversity of the other human viruses detected did not differ among the villages. Closely related variants of rhinovirus A or B were identified in 2 to 4 children from each village, reflecting ongoing transmission clusters. Genomes of viruses not currently known to infect humans, including members of the families Parvoviridae, Partitiviridae, Dicistroviridae, and Iflaviridae and circular Rep-encoding single-stranded DNA (CRESS-DNA) virus, were also detected in nasal swabs, possibly reflecting environmental contamination from insect, fungal, or unknown sources. Despite the high levels of geographic and cultural isolation, the overall diversity of human viruses in the nasal passages of children was not reduced in highly isolated indigenous villages, indicating ongoing exposure to globally circulating viruses.IMPORTANCE Extreme geographic and cultural isolation can still be found in some indigenous South American villages. Such isolation may be expected to limit the introduction of otherwise common and widely distributed viruses. Very small population sizes may also result in rapid local viral extinction due to a lack of seronegative subjects to maintain transmission chains for rapidly cleared viruses. We compared the viruses in the nasal passages of young children in three villages with increasing levels of geographic isolation. We found that isolation did not reduce the overall diversity of viral infections. Multiple infections with nearly identical rhinoviruses could be detected within each village, likely reflecting recent viral introductions and transmission clusters among epidemiologically linked members of these very small communities. We conclude that, despite their geographic isolation, remote indigenous villages show evidence of ongoing exposure to globally circulating viruses.
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Affiliation(s)
- Eda Altan
- Vitalant Research Institute, San Francisco, California, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Juan Carlos Dib
- Universidad del Norte, Barranquilla, Atlantico, Colombia
- Fundación Salud Para el Trópico-Tropical Health Foundation, Santa Marta, Magdalena, Colombia
| | - Andres Rojas Gulloso
- Fundación Salud Para el Trópico-Tropical Health Foundation, Santa Marta, Magdalena, Colombia
| | | | - Xutao Deng
- Vitalant Research Institute, San Francisco, California, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Roberta Bruhn
- Vitalant Research Institute, San Francisco, California, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Kristen Hildebrand
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Pamela Freiden
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Janie Yamamoto
- Vitalant Research Institute, San Francisco, California, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Stacey Schultz-Cherry
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Eric Delwart
- Vitalant Research Institute, San Francisco, California, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA
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Metagenomic Next-Generation Sequencing Reveals Individual Composition and Dynamics of Anelloviruses during Autologous Stem Cell Transplant Recipient Management. Viruses 2018; 10:v10110633. [PMID: 30441786 PMCID: PMC6266913 DOI: 10.3390/v10110633] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 11/06/2018] [Accepted: 11/09/2018] [Indexed: 12/13/2022] Open
Abstract
Over recent years, there has been increasing interest in the use of the anelloviruses, the major component of the human virome, for the prediction of post-transplant complications such as severe infections. Due to an important diversity, the comprehensive characterization of this viral family over time has been poorly studied. To overcome this challenge, we used a metagenomic next-generation sequencing (mNGS) approach with the aim of determining the individual anellovirus profile of autologous stem cell transplant (ASCT) patients. We conducted a prospective pilot study on a homogeneous patient cohort regarding the chemotherapy regimens that included 10 ASCT recipients. A validated viral mNGS workflow was used on 108 plasma samples collected at 11 time points from diagnosis to 90 days post-transplantation. A complex interindividual variability in terms of abundance and composition was noticed. In particular, a strong sex effect was found and confirmed using quantitative PCR targeting torque teno virus, the most abundant anellovirus. Interestingly, an important turnover in the anellovirus composition was observed during the course of the disease revealing a strong intra-individual variability. Although more studies are needed to better understand anellovirus dynamics, these findings are of prime importance for their future use as biomarkers of immune competence.
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