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Ma S, Yin Y, Guo Y, Yao C, Xu S, Luo Q, Yin G, Wang S, Wang Q, Chen H, Wang R, Jin L, Liang G, Wang H. The plasma viral communities associate with clinical profiles in a large-scale haematological patients cohort. MICROBIOME 2024; 12:137. [PMID: 39044261 PMCID: PMC11265361 DOI: 10.1186/s40168-024-01855-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 06/03/2024] [Indexed: 07/25/2024]
Abstract
BACKGROUND Haematological patients exhibit immune system abnormalities that make them susceptible to viral infections. Understanding the relationship between the virome in the blood plasma of haematological patients and their clinical characteristic is crucial for disease management. We aimed to explore the presence of viral pathogens and identify close associations between viral infections and various clinical features. RESULTS A total of 21 DNA viruses and 6 RNA viruses from 12 virus families were identified from 1383 patients. Patients with haematological diseases exhibited significantly higher diversity, prevalence, and co-detection rates of viral pathogens. During fever episodes, pathogen detection was notably higher, with Epstein-Barr virus (EBV) and Mucorales infections being the most probable culprits for fever symptoms in non-haematological patients. The detection rate of torque teno virus (TTV) significantly increases in haematological patients after transplantation and during primary lung infections. Additionally, TTV-positive patients demonstrate significantly higher absolute neutrophil counts, while C-reactive protein and procalcitonin levels are notably lower. Furthermore, TTV, cytomegalovirus, and parvovirus B19 (B19V) were found to be more prevalent in non-neutropenic patients, while non-viral pathogenic infections, such as Gram-negative bacteria and Mucorales, were more common in neutropenic patients. Pegivirus C (HPgV-C) infection often occurred post-transplantation, regardless of neutropenia. Additionally, some viruses such as TTV, B19V, EBV, and HPgV-C showed preferences for age and seasonal infections. CONCLUSIONS Analysis of the plasma virome revealed the susceptibility of haematological patients to plasma viral infections at specific disease stages, along with the occurrence of mixed infections with non-viral pathogens. Close associations were observed between the plasma virome and various clinical characteristics, as well as clinical detection parameters. Understanding plasma virome aids in auxiliary clinical diagnosis and treatment, enabling early prevention to reduce infection rates in patients and improve their quality of life. Video Abstract.
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Affiliation(s)
- Shuai Ma
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, 100044, China
- Institute of Medical Technology, Peking University Health Science Center, Beijing, China
| | - Yuyao Yin
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, 100044, China
| | - Yifan Guo
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, 100044, China
| | - Chaoqun Yao
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, 100044, China
- Institute of Medical Technology, Peking University Health Science Center, Beijing, China
| | - Siqi Xu
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Qingqing Luo
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Guankun Yin
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, 100044, China
| | - Shuyi Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, 100044, China
- Institute of Medical Technology, Peking University Health Science Center, Beijing, China
| | - Qi Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, 100044, China
| | - Hongbin Chen
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, 100044, China
| | - Ruobing Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, 100044, China
| | - Longyang Jin
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, 100044, China
| | - Guanxiang Liang
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Hui Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, 100044, China.
- Institute of Medical Technology, Peking University Health Science Center, Beijing, China.
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2
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Wang X, Stelzer-Braid S, Scotch M, Rawlinson WD. Detection of respiratory viruses directly from clinical samples using next-generation sequencing: A literature review of recent advances and potential for routine clinical use. Rev Med Virol 2022; 32:e2375. [PMID: 35775736 PMCID: PMC9539958 DOI: 10.1002/rmv.2375] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 06/01/2022] [Accepted: 06/20/2022] [Indexed: 11/15/2022]
Abstract
Acute respiratory infection is the third most frequent cause of mortality worldwide, causing over 4.25 million deaths annually. Although most diagnosed acute respiratory infections are thought to be of viral origin, the aetiology often remains unclear. The advent of next‐generation sequencing (NGS) has revolutionised the field of virus discovery and identification, particularly in the detection of unknown respiratory viruses. We systematically reviewed the application of NGS technologies for detecting respiratory viruses from clinical samples and outline potential barriers to the routine clinical introduction of NGS. The five databases searched for studies published in English from 01 January 2010 to 01 February 2021, which led to the inclusion of 52 studies. A total of 14 different models of NGS platforms were summarised from included studies. Among these models, second‐generation sequencing platforms (e.g., Illumina sequencers) were used in the majority of studies (41/52, 79%). Moreover, NGS platforms have proven successful in detecting a variety of respiratory viruses, including influenza A/B viruses (9/52, 17%), SARS‐CoV‐2 (21/52, 40%), parainfluenza virus (3/52, 6%), respiratory syncytial virus (1/52, 2%), human metapneumovirus (2/52, 4%), or a viral panel including other respiratory viruses (16/52, 31%). The review of NGS technologies used in previous studies indicates the advantages of NGS technologies in novel virus detection, virus typing, mutation identification, and infection cluster assessment. Although there remain some technical and ethical challenges associated with NGS use in clinical laboratories, NGS is a promising future tool to improve understanding of respiratory viruses and provide a more accurate diagnosis with simultaneous virus characterisation.
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Affiliation(s)
- Xinye Wang
- Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, University of New South Wales, Sydney, New South Wales, Australia.,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Sacha Stelzer-Braid
- Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, University of New South Wales, Sydney, New South Wales, Australia.,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Matthew Scotch
- Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia.,Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - William D Rawlinson
- Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, University of New South Wales, Sydney, New South Wales, Australia.,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
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3
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He Y, Fang K, Shi X, Yang D, Zhao L, Yu W, Zheng Y, Xu Y, Ma X, Chen L, Xie Y, Yu Y, Wang J, Gao Z. Enhanced DNA and RNA pathogen detection via metagenomic sequencing in patients with pneumonia. J Transl Med 2022; 20:195. [PMID: 35509078 PMCID: PMC9066823 DOI: 10.1186/s12967-022-03397-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 04/18/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Metagenomic next-generation sequencing (mNGS) is an important supplement to conventional tests for pathogen detections of pneumonia. However, mNGS pipelines were limited by irregularities, high proportion of host nucleic acids, and lack of RNA virus detection. Thus, a regulated pipeline based on mNGS for DNA and RNA pathogen detection of pneumonia is essential. METHODS We performed a retrospective study of 151 patients with pneumonia. Three conventional tests, culture, loop-mediated isothermal amplification (LAMP) and viral quantitative real-time polymerase chain reaction (qPCR) were conducted according to clinical needs, and all samples were detected using our optimized pipeline based on the mNGS (DNA and RNA) method. The performances of mNGS and three other tests were compared. Human DNA depletion was achieved respectively by MolYsis kit and pre-treatment using saponin and Turbo DNase. Three RNA library preparation methods were used to compare the detection performance of RNA viruses. RESULTS An optimized mNGS workflow was built, which had only 1-working-day turnaround time. The proportion of host DNA in the pre-treated samples decreased from 99 to 90% and microbiome reads achieved an approximately 20-fold enrichment compared with those without host removal. Meanwhile, saponin and Turbo DNase pre-treatment exhibited an advantage for DNA virus detection compared with MolYsis. Besides, our in-house RNA library preparation procedure showed a more robust RNA virus detection ability. Combining three conventional methods, 76 (76/151, 50.3%) cases had no clear causative pathogen, but 24 probable pathogens were successfully detected in 31 (31/76 = 40.8%) unclear cases using mNGS. The agreement of the mNGS with the culture, LAMP, and viral qPCR was 60%, 82%, and 80%, respectively. Compared with all conventional tests, mNGS had a sensitivity of 70.4%, a specificity of 72.7%, and an overall agreement of 71.5%. CONCLUSIONS A complete and effective mNGS workflow was built to provide timely DNA and RNA pathogen detection for pneumonia, which could effectively remove the host sequence, had a higher microbial detection rate and a broader spectrum of pathogens (especially for viruses and some pathogens that are difficult to culture). Despite the advantages, there are many challenges in the clinical application of mNGS, and the mNGS report should be interpreted with caution.
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Affiliation(s)
- Yukun He
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, 100044, China
| | - Kechi Fang
- CAS Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, 16 Lincui Road, Chaoyang District, Beijing, 100101, China.,Department of Psychology, University of Chinese Academy of Sciences, 19 A Yuquan Rd, Shijingshan District, Beijing, 100049, China
| | - Xing Shi
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, 100044, China
| | - Donghong Yang
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, 100044, China
| | - Lili Zhao
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, 100044, China
| | - Wenyi Yu
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, 100044, China
| | - Yali Zheng
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, 100044, China.,Department of Respiratory, Critical Care, and Sleep Medicine, Xiang'an Hospital of Xiamen University, Xiamen, 361101, China
| | - Yu Xu
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, 100044, China
| | - Xinqian Ma
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, 100044, China
| | - Li Chen
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, 100044, China
| | - Yu Xie
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, 100044, China
| | - Yan Yu
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, 100044, China
| | - Jing Wang
- CAS Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, 16 Lincui Road, Chaoyang District, Beijing, 100101, China. .,Department of Psychology, University of Chinese Academy of Sciences, 19 A Yuquan Rd, Shijingshan District, Beijing, 100049, China.
| | - Zhancheng Gao
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, 100044, China.
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4
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Beyond Cytomegalovirus and Epstein-Barr Virus: a Review of Viruses Composing the Blood Virome of Solid Organ Transplant and Hematopoietic Stem Cell Transplant Recipients. Clin Microbiol Rev 2020; 33:33/4/e00027-20. [PMID: 32847820 DOI: 10.1128/cmr.00027-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Viral primary infections and reactivations are common complications in patients after solid organ transplantation (SOT) and hematopoietic stem cell transplantation (HSCT) and are associated with high morbidity and mortality. Among these patients, viral infections are frequently associated with viremia. Beyond the usual well-known viruses that are part of the routine clinical management of transplant recipients, numerous other viral signatures or genomes can be identified in the blood of these patients. The identification of novel viral species and variants by metagenomic next-generation sequencing has opened up a new field of investigation and new paradigms. Thus, there is a need to thoroughly describe the state of knowledge in this field with a review of all viral infections that should be scrutinized in high-risk populations. Here, we review the eukaryotic DNA and RNA viruses identified in blood, plasma, or serum samples of pediatric and adult SOT/HSCT recipients and the prevalence of their detection, with a particular focus on recently identified viruses and those for which their potential association with disease remains to be investigated, such as members of the Polyomaviridae, Anelloviridae, Flaviviridae, and Astroviridae families. Current knowledge of the clinical significance of these viral infections with associated viremia among transplant recipients is also discussed. To ensure a comprehensive description in these two populations, individuals described as healthy (mostly blood donors) are considered for comparative purposes. The list of viruses that should be on the clinicians' radar is certainly incomplete and will expand, but the challenge is to identify those of possible clinical significance.
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5
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Wang H, Lu Z, Bao Y, Yang Y, de Groot R, Dai W, de Jonge MI, Zheng Y. Clinical diagnostic application of metagenomic next-generation sequencing in children with severe nonresponding pneumonia. PLoS One 2020; 15:e0232610. [PMID: 32497137 PMCID: PMC7272011 DOI: 10.1371/journal.pone.0232610] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 04/18/2020] [Indexed: 12/12/2022] Open
Abstract
Pneumonia is one of the most important causes of morbidity and mortality in children. Identification and characterization of pathogens that cause infections are crucial for accurate treatment and accelerated recovery. However, in most cases, the causative agent cannot be identified, which is partly due to the limited spectrum of pathogens covered by current diagnostics based on nucleic acid amplification. Therefore, in this study, we explored the application of metagenomic next-generation sequencing (mNGS) for the diagnosis of children with severe pneumonia. From April to July 2017, 32 hospitalized children with severe nonresponding pneumonia in Shenzhen Children's Hospital were included in this study. Blood tests were conducted immediately after hospitalization to assess cell counts and inflammatory markers, oropharyngeal swabs were collected to identify common pathogens by qPCR and culture. After bronchoscopy, bronchoalveolar lavage fluid (BALF) samples were collected for further pathogen identification using standardized diagnostic tests and mNGS. Blood tests were normal in 3 of the 32 children. In 9 oropharyngeal swabs, bacterial pathogens were detected, in 5 of these Mycoplasma pneumoniae was detected. Adenovirus was detected in 5 BALF samples, using the Direct Immunofluorescence Assay (DFA). In 15 cases, no common pathogens were found in BALF samples, using the current standard diagnostic tests, while in all 32 BALFs, pathogens were identified using mNGS, including adenovirus, Mycoplasma pneumoniae, Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, cytomegalovirus and bocavirus. This study shows that, with mNGS, the sensitivity of detection of the causative pathogens in children with severe nonresponding pneumonia is significantly improved. In addition, mNGS gives more strain specific information, helps to identify new pathogens and could potentially help to trace and control outbreaks. In this study, we have shown that it is possible to have the results within 24 hours, making the application of mNGS feasible for clinical diagnostics.
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MESH Headings
- Blood Cell Count
- Bronchoalveolar Lavage Fluid/microbiology
- Bronchoalveolar Lavage Fluid/virology
- Child
- Child, Preschool
- China/epidemiology
- Coinfection/microbiology
- Coinfection/virology
- DNA, Bacterial/analysis
- DNA, Viral/analysis
- Female
- Fluorescent Antibody Technique, Direct
- Humans
- Infant
- Inpatients
- Male
- Metagenome
- Metagenomics/methods
- Oropharynx/microbiology
- Oropharynx/virology
- Pneumonia, Bacterial/diagnosis
- Pneumonia, Bacterial/epidemiology
- Pneumonia, Bacterial/microbiology
- Pneumonia, Viral/diagnosis
- Pneumonia, Viral/epidemiology
- Pneumonia, Viral/virology
- Proof of Concept Study
- RNA, Viral/analysis
- Sensitivity and Specificity
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
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Affiliation(s)
- Heping Wang
- Department of Respiratory Diseases, Shenzhen Children’s Hospital, Shenzhen, China
- Section Pediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Center for Infectious Diseases, Radboud university medical center, Nijmegen, The Netherlands
| | - Zhiwei Lu
- Department of Respiratory Diseases, Shenzhen Children’s Hospital, Shenzhen, China
| | - Yaomin Bao
- Department of Respiratory Diseases, Shenzhen Children’s Hospital, Shenzhen, China
| | - Yonghong Yang
- Department of Respiratory Diseases, Shenzhen Children’s Hospital, Shenzhen, China
| | - Ronald de Groot
- Section Pediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Center for Infectious Diseases, Radboud university medical center, Nijmegen, The Netherlands
| | - Wenkui Dai
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Marien I. de Jonge
- Section Pediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Center for Infectious Diseases, Radboud university medical center, Nijmegen, The Netherlands
- * E-mail: (YZ); (MJ)
| | - Yuejie Zheng
- Department of Respiratory Diseases, Shenzhen Children’s Hospital, Shenzhen, China
- * E-mail: (YZ); (MJ)
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6
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van den Broek MFL, De Boeck I, Kiekens F, Boudewyns A, Vanderveken OM, Lebeer S. Translating Recent Microbiome Insights in Otitis Media into Probiotic Strategies. Clin Microbiol Rev 2019; 32:e00010-18. [PMID: 31270125 PMCID: PMC6750133 DOI: 10.1128/cmr.00010-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The microbiota of the upper respiratory tract (URT) protects the host from bacterial pathogenic colonization by competing for adherence to epithelial cells and by immune response regulation that includes the activation of antimicrobial and (anti-)inflammatory components. However, environmental or host factors can modify the microbiota to an unstable community that predisposes the host to infection or inflammation. One of the URT diseases most often encountered in children is otitis media (OM). The role of pathogenic bacteria like Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis in the pathogenesis of OM is well documented. Results from next-generation-sequencing (NGS) studies reveal other bacterial taxa involved in OM, such as Turicella and Alloiococcus Such studies can also identify bacterial taxa that are potentially protective against URT infections, whose beneficial action needs to be substantiated in relevant experimental models and clinical trials. Of note, lactic acid bacteria (LAB) are members of the URT microbiota and associated with a URT ecosystem that is deemed healthy, based on NGS and some experimental and clinical studies. These observations have formed the basis of this review, in which we describe the current knowledge of the molecular and clinical potential of LAB in the URT, which is currently underexplored in microbiome and probiotic research.
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Affiliation(s)
- Marianne F L van den Broek
- Environmental Ecology and Applied Microbiology Research Group, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Ilke De Boeck
- Environmental Ecology and Applied Microbiology Research Group, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Filip Kiekens
- Laboratory of Pharmaceutical Technology and Biopharmacy, Department of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Wilrijk, Belgium
| | - An Boudewyns
- Department of Otorhinolaryngology, Head and Neck Surgery, Antwerp University Hospital, Edegem, Belgium
| | - Olivier M Vanderveken
- Department of Otorhinolaryngology, Head and Neck Surgery, Antwerp University Hospital, Edegem, Belgium
- Department of Translational Neurosciences, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Sarah Lebeer
- Environmental Ecology and Applied Microbiology Research Group, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
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7
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Serge Correales YE, Hazra C, Ullah S, Lima LR, Ribeiro SJL. Precisely tailored shell thickness and Ln 3+ content to produce multicolor emission from Nd 3+-sensitized Gd 3+-based core/shell/shell UCNPs through bi-directional energy transfer. NANOSCALE ADVANCES 2019; 1:1936-1947. [PMID: 36134241 PMCID: PMC9418845 DOI: 10.1039/c9na00006b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 03/20/2019] [Indexed: 05/12/2023]
Abstract
Lanthanide (Ln3+)-doped upconversion nanoparticles (UCNPs) have been paid great attention as multiplexing agents due to their numerous uses in biological and clinical applications such as bioimaging and magnetic resonance imaging (MRI), to name a few. To achieve efficient multicolor emission from UCNPs under single 808 nm excitation and avoid detrimental cross-relaxations between the Ln3+ activator ions (positioned in either the core and/or shell in the core/shell), it is essential to design an adequate nanoparticle architecture. Herein, we demonstrate the tailoring of multicolor upconversion luminescence (UCL) from Nd3+-sensitized Gd3+-based core/shell/shell UCNPs with an architecture represented as NaGdF4:Tm3+(0.75)/Yb3+(40)/Ca2+(7)/Nd3+(1)@NaGdF4:Ca2+(7)/Nd3+(30)@NaGdF4:Yb3+(40)/Ca2+(7)/Nd3+(1)/Er3+(X = 1, 2, 3, 5, 7) [hereafter named CSS (Er3+ = 1, 2, 3, 5 and 7 mol%)]. Such UCNPs can be excited at a single wavelength (∼808 nm) without generation of any local heat. Incorporation of substantial Nd3+-sensitizers with an appropriate concentration in the middle layer allows efficient harvesting of excitation light which migrates bi-directionally across the core/shell interfaces in sync to produce blue emission from Tm3+ (activator) ions in the core as well as green and red emission from Er3+ (activator) ions in the outermost shell. Introduction of Ca2+ lowers the local crystal field symmetry around Ln3+ ions and subsequently affects their intra 4f-4f transition probability, thus enhancing the upconversion efficiency of the UCNPs. By simple and precise control of the shell thickness along with tuning the content of Ln3+ ions in each domain, multicolor UCL can be produced, ranging from blue to white. We envision that our sub-20 nm sized Nd3+-sensitized Gd3+-based UCNPs are not only potential candidates for a variety of multiplexed biological applications (without impediment of any heating effect), but also can act as MRI contrast agents in clinical diagnosis.
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Affiliation(s)
- York E Serge Correales
- Institute of Chemistry, São Paulo State University, UNESP 14800-060 Araraquara SP Brazil
| | - Chanchal Hazra
- Institute of Chemistry, São Paulo State University, UNESP 14800-060 Araraquara SP Brazil
| | - Sajjad Ullah
- Institute of Chemical Sciences, University of Peshawar 25120 Peshawar Pakistan
| | - Laís R Lima
- Institute of Chemistry, São Paulo State University, UNESP 14800-060 Araraquara SP Brazil
| | - Sidney J L Ribeiro
- Institute of Chemistry, São Paulo State University, UNESP 14800-060 Araraquara SP Brazil
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8
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Mitchell AB, Glanville AR. Introduction to Techniques and Methodologies for Characterizing the Human Respiratory Virome. Methods Mol Biol 2019; 1838:111-123. [PMID: 30128993 DOI: 10.1007/978-1-4939-8682-8_9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
There have been great advances in the methodologies available for the detection of respiratory viruses. Accompanying this, our knowledge surrounding the impact of these viruses has also made a great leap forward. We have come a long way from the once commonly accepted belief that the lower respiratory tract was sterile and that the detection of any microbial species must represent a breach in host defence and likely be associated with symptomatic infection. With the advent of molecular detection techniques and improvements in sequencing-based methodologies to make these tools more accessible and cost effective, we now know that there is an abundant and diverse ecosystem within the lower-respiratory tract. This chapter will outline the clinical impact of the human respiratory virome, techniques for sampling the lower respiratory tract, the evolution of the diagnostic tools available, and the current limitations in our instruments and knowledge in this area. The human respiratory virome is an exciting new area of research that will continue to grow with the aid of the methodologies outlined in the following chapters and the advent of even more efficient tools in the future.
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Affiliation(s)
- Alicia B Mitchell
- The Woolcock Institute of Medical Research, Sydney, NSW, Australia. .,University of Technology Sydney, Sydney, NSW, Australia. .,The Lung Transplant Unit, St. Vincent's Hospital, Sydney, NSW, Australia.
| | - Allan R Glanville
- The Lung Transplant Unit, St. Vincent's Hospital, Sydney, NSW, Australia
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9
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White SL, Rawlinson W, Boan P, Sheppeard V, Wong G, Waller K, Opdam H, Kaldor J, Fink M, Verran D, Webster A, Wyburn K, Grayson L, Glanville A, Cross N, Irish A, Coates T, Griffin A, Snell G, Alexander SI, Campbell S, Chadban S, Macdonald P, Manley P, Mehakovic E, Ramachandran V, Mitchell A, Ison M. Infectious Disease Transmission in Solid Organ Transplantation: Donor Evaluation, Recipient Risk, and Outcomes of Transmission. Transplant Direct 2019; 5:e416. [PMID: 30656214 PMCID: PMC6324914 DOI: 10.1097/txd.0000000000000852] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 08/15/2018] [Indexed: 12/11/2022] Open
Abstract
In 2016, the Transplantation Society of Australia and New Zealand, with the support of the Australian Government Organ and Tissue authority, commissioned a literature review on the topic of infectious disease transmission from deceased donors to recipients of solid organ transplants. The purpose of this review was to synthesize evidence on transmission risks, diagnostic test characteristics, and recipient management to inform best-practice clinical guidelines. The final review, presented as a special supplement in Transplantation Direct, collates case reports of transmission events and other peer-reviewed literature, and summarizes current (as of June 2017) international guidelines on donor screening and recipient management. Of particular interest at the time of writing was how to maximize utilization of donors at increased risk for transmission of human immunodeficiency virus, hepatitis C virus, and hepatitis B virus, given the recent developments, including the availability of direct-acting antivirals for hepatitis C virus and improvements in donor screening technologies. The review also covers emerging risks associated with recent epidemics (eg, Zika virus) and the risk of transmission of nonendemic pathogens related to donor travel history or country of origin. Lastly, the implications for recipient consent of expanded utilization of donors at increased risk of blood-borne viral disease transmission are considered.
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Affiliation(s)
- Sarah L White
- Central Clinical School, Sydney Medical School, The University of Sydney, Sydney, Australia
| | - William Rawlinson
- Serology and Virology Division, NSW Health Pathology Prince of Wales Hospital, Sydney, Australia
- Women's and Children's Health and Biotechnology and Biomolecular Sciences, University of New South Wales Schools of Medicine, Sydney, Australia
| | - Peter Boan
- Departments of Infectious Diseases and Microbiology, Fiona Stanley Hospital, Perth, Australia
- PathWest Laboratory Medicine, Perth, Australia
| | - Vicky Sheppeard
- Communicable Diseases Network Australia, New South Wales Health, Sydney, Australia
| | - Germaine Wong
- Centre for Transplant and Renal Research, Westmead Hospital, Sydney, Australia
- Centre for Kidney Research, The Children's Hospital at Westmead, Sydney, Australia
- Sydney School of Public Health, The University of Sydney, Sydney, Australia
| | - Karen Waller
- Central Clinical School, Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Helen Opdam
- Austin Health, Melbourne, Australia
- The Organ and Tissue Authority, Australian Government, Canberra, Australia
| | - John Kaldor
- Kirby Institute, University of New South Wales, Sydney, Australia
| | - Michael Fink
- Austin Health, Melbourne, Australia
- Department of Surgery, Melbourne Medical School, The University of Melbourne, Melbourne, Australia
| | - Deborah Verran
- Transplantation Services, Royal Prince Alfred Hospital, Sydney, Australia
| | - Angela Webster
- Centre for Transplant and Renal Research, Westmead Hospital, Sydney, Australia
- Sydney School of Public Health, The University of Sydney, Sydney, Australia
| | - Kate Wyburn
- Central Clinical School, Sydney Medical School, The University of Sydney, Sydney, Australia
- Renal Medicine, Royal Prince Alfred Hospital, Sydney, Australia
| | - Lindsay Grayson
- Austin Health, Melbourne, Australia
- Department of Surgery, Melbourne Medical School, The University of Melbourne, Melbourne, Australia
| | - Allan Glanville
- Department of Thoracic Medicine and Lung Transplantation, St Vincent's Hospital, Sydney, Australia
| | - Nick Cross
- Department of Nephrology, Canterbury District Health Board, Christchurch Hospital, Christchurch, New Zealand
| | - Ashley Irish
- Department of Nephrology, Fiona Stanley Hospital, Perth, Australia
- Faculty of Health and Medical Sciences, UWA Medical School, The University of Western Australia, Crawley, Australia
| | - Toby Coates
- Renal and Transplantation, Royal Adelaide Hospital, Adelaide, Australia
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, Australia
| | - Anthony Griffin
- Renal Transplantation, Princess Alexandra Hospital, Woolloongabba, Queensland, Australia
| | - Greg Snell
- Lung Transplant, Alfred Health, Melbourne, Victoria, Australia
| | - Stephen I Alexander
- Centre for Kidney Research, The Children's Hospital at Westmead, Sydney, Australia
| | - Scott Campbell
- Department of Renal Medicine, University of Queensland at Princess Alexandra Hospital, Woolloongabba, Queensland, Australia
| | - Steven Chadban
- Central Clinical School, Sydney Medical School, The University of Sydney, Sydney, Australia
- Renal Medicine, Royal Prince Alfred Hospital, Sydney, Australia
| | - Peter Macdonald
- Department of Cardiology, St Vincent's Hospital, Sydney, Australia
- St Vincent's Hospital Victor Chang Cardiac Research Institute, University of New South Wales, Sydney, Australia
| | - Paul Manley
- Kidney Disorders, Auckland District Health Board, Auckland City Hospital, Auckland, New Zealand
| | - Eva Mehakovic
- The Organ and Tissue Authority, Australian Government, Canberra, Australia
| | - Vidya Ramachandran
- Serology and Virology Division, NSW Health Pathology Prince of Wales Hospital, Sydney, Australia
| | - Alicia Mitchell
- Department of Thoracic Medicine and Lung Transplantation, St Vincent's Hospital, Sydney, Australia
- Woolcock Institute of Medical Research, Sydney, Australia
- School of Medical and Molecular Biosciences, University of Technology, Sydney, Australia
| | - Michael Ison
- Divisions of Infectious Diseases and Organ Transplantation, Northwestern University Feinberg School of Medicine, Chicago, IL
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10
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Detection of Viruses in Clinical Samples by Use of Metagenomic Sequencing and Targeted Sequence Capture. J Clin Microbiol 2018; 56:JCM.01123-18. [PMID: 30232133 DOI: 10.1128/jcm.01123-18] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 09/14/2018] [Indexed: 12/11/2022] Open
Abstract
Metagenomic shotgun sequencing (MSS) is a revolutionary approach to viral diagnostic testing that allows simultaneous detection of a broad range of viruses, detailed taxonomic assignment, and detection of mutations associated with antiviral drug resistance. To enhance sensitivity for virus detection, we previously developed ViroCap, a targeted sequence capture panel designed to enrich nucleic acid from a comprehensive set of eukaryotic viruses prior to sequencing. To demonstrate the utility of MSS with targeted sequence capture for detecting clinically important viruses and characterizing clinically important viral features, we used ViroCap to analyze clinical samples from a diagnostic virology laboratory containing a broad range of medically relevant viruses. From 26 samples, MSS with ViroCap detected all of the expected viruses and 30 additional viruses. Comparing sequencing after capture enrichment with standard MSS, we detected 13 viruses only with capture enrichment and observed a consistent increase in the number and percentage of viral sequence reads as well as the breadth and depth of coverage of the viral genomes. Compared with clinical testing, MSS enhanced taxonomic assignment for 15 viruses, and codons associated with antiviral drug resistance in influenza A virus, herpes simplex virus (HSV), human immunodeficiency virus (HIV), and hepatitis C virus (HCV) could be analyzed. Overall, in clinical samples, MSS with targeted sequence capture provides enhanced virus detection and information of clinical and epidemiologic relevance compared with clinical testing and MSS without targeted sequence capture.
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11
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Garcia-Nuñez M, Gallego M, Monton C, Capilla S, Millares L, Pomares X, Espasa M, Ferrari R, Moya A, Monsó E, Perez-Brocal V. The respiratory virome in chronic obstructive pulmonary disease. Future Virol 2018. [DOI: 10.2217/fvl-2018-0027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Aim: To characterize the respiratory virome in moderate/severe chronic obstructive pulmonary disease (COPD) patients using metagenomics, with healthy subjects as the reference. Patients & Methods: Sputum COPD samples were collected during stability and exacerbations with negative usual-care microbiologic analysis. Results: Eukaryotic viruses from the Anelloviridae, Herpesviridae and Retroviridae families and phages from the Shiphoviridae family were commonly found in COPD, and the respiratory virome in stability and noninfectious exacerbations showed a substantial similarity. DNA viruses with the highest relative abundance in COPD are Anelloviridae. Conclusion: These results support a colonizing role for eukaryotic viruses in COPD and highlight the importance of analyzing both DNA and RNA viruses when focusing on the respiratory virome.
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Affiliation(s)
- Marian Garcia-Nuñez
- Department of Respiratory Medicine, Parc Taulí Hospital Universitari. Institut d'Investigació i Innovació Parc Taulí I3PT, Universitat Autonoma de Barcelona, Sabadell, Spain
- Centro de Investigación en Red de Enfermedades Respiratorias, CIBERES, Bunyola, Spain
- Fundació Insitut d'Investigació GermansTrias i Pujol, Badalona, Spain
| | - Miguel Gallego
- Department of Respiratory Medicine, Parc Taulí Hospital Universitari. Institut d'Investigació i Innovació Parc Taulí I3PT, Universitat Autonoma de Barcelona, Sabadell, Spain
- Centro de Investigación en Red de Enfermedades Respiratorias, CIBERES, Bunyola, Spain
| | - Concepción Monton
- Department of Respiratory Medicine, Parc Taulí Hospital Universitari. Institut d'Investigació i Innovació Parc Taulí I3PT, Universitat Autonoma de Barcelona, Sabadell, Spain
| | - Silvia Capilla
- Department of Microbiology, Parc Taulí Hospital Universitari. Institut d'Investigació i Innovació Parc Taulí I3PT, Universitat Autonoma de Barcelona, Sabadell, Spain
| | - Laura Millares
- Department of Respiratory Medicine, Parc Taulí Hospital Universitari. Institut d'Investigació i Innovació Parc Taulí I3PT, Universitat Autonoma de Barcelona, Sabadell, Spain
- Centro de Investigación en Red de Enfermedades Respiratorias, CIBERES, Bunyola, Spain
- Fundació Insitut d'Investigació GermansTrias i Pujol, Badalona, Spain
| | - Xavier Pomares
- Department of Respiratory Medicine, Parc Taulí Hospital Universitari. Institut d'Investigació i Innovació Parc Taulí I3PT, Universitat Autonoma de Barcelona, Sabadell, Spain
- Centro de Investigación en Red de Enfermedades Respiratorias, CIBERES, Bunyola, Spain
| | - Mateu Espasa
- Department of Microbiology, Parc Taulí Hospital Universitari. Institut d'Investigació i Innovació Parc Taulí I3PT, Universitat Autonoma de Barcelona, Sabadell, Spain
| | - Rafaella Ferrari
- Genomics & Health Area, Centro Superior de Investigación en Salud Pública – Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (CSISP-FISABIO), Valencia, Spain
| | - Andres Moya
- Genomics & Health Area, Centro Superior de Investigación en Salud Pública – Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (CSISP-FISABIO), Valencia, Spain
- Department of Genetics, Institut Cavanilles de Biodiversitat i Biologia Evolutiva, (ICBiBE) Universitat de València, València, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Eduard Monsó
- Department of Respiratory Medicine, Parc Taulí Hospital Universitari. Institut d'Investigació i Innovació Parc Taulí I3PT, Universitat Autonoma de Barcelona, Sabadell, Spain
- Centro de Investigación en Red de Enfermedades Respiratorias, CIBERES, Bunyola, Spain
| | - Vicente Perez-Brocal
- Genomics & Health Area, Centro Superior de Investigación en Salud Pública – Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (CSISP-FISABIO), Valencia, Spain
- Department of Genetics, Institut Cavanilles de Biodiversitat i Biologia Evolutiva, (ICBiBE) Universitat de València, València, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
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12
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Diaz-Decaro JD, Green NM, Godwin HA. Critical evaluation of FDA-approved respiratory multiplex assays for public health surveillance. Expert Rev Mol Diagn 2018; 18:631-643. [PMID: 29886764 PMCID: PMC7103694 DOI: 10.1080/14737159.2018.1487294] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Introduction: Clinical management and identification of respiratory diseases has become more rapid and increasingly specific due to widespread use of PCR(polymerase chain reaction) multiplex technologies. Although significantly improving clinical diagnosis, multiplexed PCR assays could have a greater impact on local and global disease surveillance. The authors wish to propose methods of evaluating respiratory multiplex assays to maximize diagnostic yields specifically for surveillance efforts. Areas covered: The authors review multiplexed assays and critically assess what barriers have limited these assays for disease surveillance and how these barriers might be addressed. The manuscript focuses specifically on the case study of using multiplexed assays for surveillance of respiratory pathogens. The authors also provide a method of validation of specific surveillance measures. Expert commentary: Current commercially available respiratory multiplex PCR assays are widely used for clinical diagnosis; however, specific barriers have limited their use for surveillance. Key barriers include differences in testing phase requirements and diagnostic performance evaluation. In this work the authors clarify phase testing requirements and introduce unique diagnostic performance measures that simplify the use of these assays on a per target basis for disease surveillance.
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Affiliation(s)
- John D Diaz-Decaro
- a Los Angeles County Public Health Laboratories , Research & Training Unit , Downey , CA , USA.,b UCLA Fielding School of Public Health , Environmental Health Sciences , Los Angeles , CA , USA
| | - Nicole M Green
- a Los Angeles County Public Health Laboratories , Research & Training Unit , Downey , CA , USA
| | - Hilary A Godwin
- b UCLA Fielding School of Public Health , Environmental Health Sciences , Los Angeles , CA , USA
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13
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Unbiased Strain-Typing of Arbovirus Directly from Mosquitoes Using Nanopore Sequencing: A Field-forward Biosurveillance Protocol. Sci Rep 2018; 8:5417. [PMID: 29615665 PMCID: PMC5883038 DOI: 10.1038/s41598-018-23641-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 03/16/2018] [Indexed: 12/17/2022] Open
Abstract
The future of infectious disease surveillance and outbreak response is trending towards smaller hand-held solutions for point-of-need pathogen detection. Here, samples of Culex cedecei mosquitoes collected in Southern Florida, USA were tested for Venezuelan Equine Encephalitis Virus (VEEV), a previously-weaponized arthropod-borne RNA-virus capable of causing acute and fatal encephalitis in animal and human hosts. A single 20-mosquito pool tested positive for VEEV by quantitative reverse transcription polymerase chain reaction (RT-qPCR) on the Biomeme two3. The virus-positive sample was subjected to unbiased metatranscriptome sequencing on the Oxford Nanopore MinION and shown to contain Everglades Virus (EVEV), an alphavirus in the VEEV serocomplex. Our results demonstrate, for the first time, the use of unbiased sequence-based detection and subtyping of a high-consequence biothreat pathogen directly from an environmental sample using field-forward protocols. The development and validation of methods designed for field-based diagnostic metagenomics and pathogen discovery, such as those suitable for use in mobile “pocket laboratories”, will address a growing demand for public health teams to carry out their mission where it is most urgent: at the point-of-need.
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14
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Romero-Espinoza JA, Moreno-Valencia Y, Coronel-Tellez RH, Castillejos-Lopez M, Hernandez A, Dominguez A, Miliar-Garcia A, Barbachano-Guerrero A, Perez-Padilla R, Alejandre-Garcia A, Vazquez-Perez JA. Virome and bacteriome characterization of children with pneumonia and asthma in Mexico City during winter seasons 2014 and 2015. PLoS One 2018; 13:e0192878. [PMID: 29447223 PMCID: PMC5813968 DOI: 10.1371/journal.pone.0192878] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 01/31/2018] [Indexed: 02/07/2023] Open
Abstract
Background Acute asthma exacerbations and pneumonia are important causes of morbidity and mortality in children and may coexist in the same children, although symptom overlap may lead to difficulties in diagnosis. Microbial and viral diversity and differential abundance of either may play an important role in infection susceptibility and the development of acute and chronic respiratory diseases. Objectives To describe the virome and bacteriome present in the upper respiratory tract of hospitalized children with a clinical diagnosis of asthma and pneumonia during an acute exacerbation and an acute respiratory illness ARI episode respectively. Methods During the winter seasons of 2013–2014 and 2014–2015, 134 nasopharyngeal swabs samples of children <15 years of age with ARI hospitalized at a referral hospital for respiratory diseases were selected based on clinical diagnosis of asthma or pneumonia. The virome and bacteriome were characterized using Whole Genome Sequencing (WGS) and in-house bioinformatics analysis pipeline. Results The Asthma group was represented mainly by RV-C, BoV-1 and RSV-B and the pneumonia group by Bacteriophage EJ-1 and TTMV. TTV was found in both groups with a similar amount of reads. About bacterial composition Moraxella catarrhalis, Propionibacterium acnes and Acinetobacter were present in asthma and Veillonella parvula and Mycoplasma pneumoniae in pneumonia. Streptococcus pneumoniae and Haemophilus influenzae were mostly found with both asthma and pneumonia. Conclusions Our results show a complex viral and bacterial composition in asthma and pneumonia groups with a strong association of RV-C presence in asthmatic children. We observed Streptococcus pneumoniae and Haemophilus influenzae concurrently in both groups.
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Affiliation(s)
- Jose A. Romero-Espinoza
- Departamento de Investigación en Virología, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas, Mexico City, Mexico
| | - Yazmin Moreno-Valencia
- Departamento de Investigación en Virología, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas, Mexico City, Mexico
| | - Rodrigo H. Coronel-Tellez
- Signalisation et Réseaux de Régulations Bactériens, Institut de Biologie Intégrative de la Cellule, Paris, France
| | - Manuel Castillejos-Lopez
- Vigilancia Epidemiológica, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas, Mexico City, Mexico
| | - Andres Hernandez
- Vigilancia Epidemiológica, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas, Mexico City, Mexico
| | - Aaron Dominguez
- Sección de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Angel Miliar-Garcia
- Sección de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Arturo Barbachano-Guerrero
- Department of Microbiology and Immunology, SUNY Upstate Medical University, Syracuse, NY, United States of America
| | - Rogelio Perez-Padilla
- Departamento de Investigación en Tabaquismo y EPOC, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas, Mexico City, Mexico
| | - Alejandro Alejandre-Garcia
- Unidad de Urgencias Pediátricas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas, Mexico City, Mexico
| | - Joel A. Vazquez-Perez
- Departamento de Investigación en Virología, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas, Mexico City, Mexico
- * E-mail:
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15
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The lung microbiome. Emerg Top Life Sci 2017; 1:313-324. [PMID: 33525774 DOI: 10.1042/etls20170043] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 08/31/2017] [Accepted: 09/29/2017] [Indexed: 12/17/2022]
Abstract
Historically, our understanding of lung microbiology has relied on insight gained through culture-based diagnostic approaches that employ selective culture conditions to isolate specific pathogens. The relatively recent development of culture-independent microbiota-profiling techniques, particularly 16S rRNA (ribosomal ribonucleic acid) gene amplicon sequencing, has enabled more comprehensive characterisation of the microbial content of respiratory samples. The widespread application of such techniques has led to a fundamental shift in our view of respiratory microbiology. Rather than a sterile lung environment that can become colonised by microbes during infection, it appears that a more nuanced balance exists between what we consider respiratory health and disease, mediated by mechanisms that influence the clearance of microbes from the lungs. Where airway defences are compromised, the ongoing transient exposure of the lower airways to microbes can lead to the establishment of complex microbial communities within the lung. Importantly, the characteristics of these communities, and the manner in which they influence lung pathogenesis, can be very different from those of their constituent members when viewed in isolation. The lung microbiome, a construct that incorporates microbes, their genetic material, and the products of microbial genes, is increasingly central to our understanding of the regulation of respiratory physiology and the processes that underlie lung pathogenesis.
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16
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Carding SR, Davis N, Hoyles L. Review article: the human intestinal virome in health and disease. Aliment Pharmacol Ther 2017; 46:800-815. [PMID: 28869283 PMCID: PMC5656937 DOI: 10.1111/apt.14280] [Citation(s) in RCA: 151] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Revised: 04/07/2017] [Accepted: 08/07/2017] [Indexed: 02/06/2023]
Abstract
BACKGROUND The human virome consists of animal-cell viruses causing transient infections, bacteriophage (phage) predators of bacteria and archaea, endogenous retroviruses and viruses causing persistent and latent infections. High-throughput, inexpensive, sensitive sequencing methods and metagenomics now make it possible to study the contribution dsDNA, ssDNA and RNA virus-like particles make to the human virome, and in particular the intestinal virome. AIM To review and evaluate the pioneering studies that have attempted to characterise the human virome and generated an increased interest in understanding how the intestinal virome might contribute to maintaining health, and the pathogenesis of chronic diseases. METHODS Relevant virome-related articles were selected for review following extensive language- and date-unrestricted, electronic searches of the literature. RESULTS The human intestinal virome is personalised and stable, and dominated by phages. It develops soon after birth in parallel with prokaryotic communities of the microbiota, becoming established during the first few years of life. By infecting specific populations of bacteria, phages can alter microbiota structure by killing host cells or altering their phenotype, enabling phages to contribute to maintaining intestinal homeostasis or microbial imbalance (dysbiosis), and the development of chronic infectious and autoimmune diseases including HIV infection and Crohn's disease, respectively. CONCLUSIONS Our understanding of the intestinal virome is fragmented and requires standardised methods for virus isolation and sequencing to provide a more complete picture of the virome, which is key to explaining the basis of virome-disease associations, and how enteric viruses can contribute to disease aetiologies and be rationalised as targets for interventions.
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Affiliation(s)
- S. R. Carding
- Norwich Medical SchoolUniversity of East AngliaNorwichUK,The Gut Health and Food Safety Research ProgrammeThe Quadram InstituteNorwich Research ParkNorwichUK
| | - N. Davis
- Norwich Medical SchoolUniversity of East AngliaNorwichUK
| | - L. Hoyles
- Department of Surgery and CancerImperial College LondonLondonUK
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17
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Zou X, Tang G, Zhao X, Huang Y, Chen T, Lei M, Chen W, Yang L, Zhu W, Zhuang L, Yang J, Feng Z, Wang D, Wang D, Shu Y. Simultaneous virus identification and characterization of severe unexplained pneumonia cases using a metagenomics sequencing technique. SCIENCE CHINA. LIFE SCIENCES 2017; 60:279-286. [PMID: 27921234 PMCID: PMC7088591 DOI: 10.1007/s11427-016-0244-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Accepted: 09/21/2016] [Indexed: 02/02/2023]
Abstract
Many viruses can cause respiratory diseases in humans. Although great advances have been achieved in methods of diagnosis, it remains challenging to identify pathogens in unexplained pneumonia (UP) cases. In this study, we applied next-generation sequencing (NGS) technology and a metagenomic approach to detect and characterize respiratory viruses in UP cases from Guizhou Province, China. A total of 33 oropharyngeal swabs were obtained from hospitalized UP patients and subjected to NGS. An unbiased metagenomic analysis pipeline identified 13 virus species in 16 samples. Human rhinovirus C was the virus most frequently detected and was identified in seven samples. Human measles virus, adenovirus B 55 and coxsackievirus A10 were also identified. Metagenomic sequencing also provided virus genomic sequences, which enabled genotype characterization and phylogenetic analysis. For cases of multiple infection, metagenomic sequencing afforded information regarding the quantity of each virus in the sample, which could be used to evaluate each viruses' role in the disease. Our study highlights the potential of metagenomic sequencing for pathogen identification in UP cases.
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Affiliation(s)
- Xiaohui Zou
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, 102206, China
| | - Guangpeng Tang
- Guizhou Provincial Center for Disease Control and Prevention, Guiyang, 550004, China
| | - Xiang Zhao
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, 102206, China
| | - Yan Huang
- Guizhou Provincial Center for Disease Control and Prevention, Guiyang, 550004, China
| | - Tao Chen
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, 102206, China
| | - Mingyu Lei
- Guizhou Provincial Center for Disease Control and Prevention, Guiyang, 550004, China
| | - Wenbing Chen
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, 102206, China
| | - Lei Yang
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, 102206, China
| | - Wenfei Zhu
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, 102206, China
| | - Li Zhuang
- Guizhou Provincial Center for Disease Control and Prevention, Guiyang, 550004, China
| | - Jing Yang
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, 102206, China
| | - Zhaomin Feng
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, 102206, China
| | - Dayan Wang
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, 102206, China
| | - Dingming Wang
- Guizhou Provincial Center for Disease Control and Prevention, Guiyang, 550004, China.
| | - Yuelong Shu
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, 102206, China.
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18
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Wesolowska-Andersen A, Everman JL, Davidson R, Rios C, Herrin R, Eng C, Janssen WJ, Liu AH, Oh SS, Kumar R, Fingerlin TE, Rodriguez-Santana J, Burchard EG, Seibold MA. Dual RNA-seq reveals viral infections in asthmatic children without respiratory illness which are associated with changes in the airway transcriptome. Genome Biol 2017; 18:12. [PMID: 28103897 PMCID: PMC5244706 DOI: 10.1186/s13059-016-1140-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 12/16/2016] [Indexed: 12/01/2022] Open
Abstract
Background Respiratory illness caused by viral infection is associated with the development and exacerbation of childhood asthma. Little is known about the effects of respiratory viral infections in the absence of illness. Using quantitative PCR (qPCR) for common respiratory viruses and for two genes known to be highly upregulated in viral infections (CCL8/CXCL11), we screened 92 asthmatic and 69 healthy children without illness for respiratory virus infections. Results We found 21 viral qPCR-positive and 2 suspected virus-infected subjects with high expression of CCL8/CXCL11. We applied a dual RNA-seq workflow to these subjects, together with 25 viral qPCR-negative subjects, to compare qPCR with sequencing-based virus detection and to generate the airway transcriptome for analysis. RNA-seq virus detection achieved 86% sensitivity when compared to qPCR-based screening. We detected additional respiratory viruses in the two CCL8/CXCL11-high subjects and in two of the qPCR-negative subjects. Viral read counts varied widely and were used to stratify subjects into Virus-High and Virus-Low groups. Examination of the host airway transcriptome found that the Virus-High group was characterized by immune cell airway infiltration, downregulation of cilia genes, and dampening of type 2 inflammation. Even the Virus-Low group was differentiated from the No-Virus group by 100 genes, some involved in eIF2 signaling. Conclusions Respiratory virus infection without illness is not innocuous but may determine the airway function of these subjects by driving immune cell airway infiltration, cellular remodeling, and alteration of asthmogenic gene expression. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-1140-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Jamie L Everman
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Rebecca Davidson
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Cydney Rios
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Rachelle Herrin
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Celeste Eng
- Department of Medicine, University of California, San Francisco, CA, USA
| | | | - Andrew H Liu
- Department of Pediatrics, National Jewish Health, 1400 Jackson St, Denver, CO, 80206, USA.,Children's Hospital Colorado and University of Colorado School of Medicine, Aurora, CO, USA
| | - Sam S Oh
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Rajesh Kumar
- Department of Pediatrics, The Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Tasha E Fingerlin
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA.,Department of Biomedical Research, National Jewish Health, Denver, CO, USA
| | | | - Esteban G Burchard
- Department of Medicine, University of California, San Francisco, CA, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - Max A Seibold
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA. .,Department of Pediatrics, National Jewish Health, 1400 Jackson St, Denver, CO, 80206, USA. .,Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO, USA.
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19
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Wang CH, Nie K, Zhang Y, Wang J, Zhou SF, Li XN, Zhou HY, Qi SX, Ma XJ. An Improved Barcoded Oligonucleotide Primers-based Next-generation Sequencing Approach for Direct Identification of Viral Pathogens in Clinical Specimens. BIOMEDICAL AND ENVIRONMENTAL SCIENCES : BES 2017; 30:22-34. [PMID: 28245896 PMCID: PMC7136949 DOI: 10.3967/bes2017.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 12/20/2016] [Indexed: 06/06/2023]
Abstract
OBJECTIVE To provide a feasible and cost-effective next-generation sequencing (NGS) method for accurate identification of viral pathogens in clinical specimens, because enormous limitations impede the clinical use of common NGS, such as high cost, complicated procedures, tremendous data analysis, and high background noise in clinical samples. METHODS Viruses from cell culture materials or clinical specimens were identified following an improved NGS procedure: reduction of background noise by sample preprocessing, viral enrichment by barcoded oligonucleotide (random hexamer or non-ribosomal hexanucleotide) primer-based amplification, fragmentation-free library construction and sequencing of one-tube mixtures, as well as rapid data analysis using an in-house pipeline. RESULTS NGS data demonstrated that both barcoded primer sets were useful to simultaneously capture multiple viral pathogens in cell culture materials or clinical specimens and verified that hexanucleotide primers captured as many viral sequences as hexamers did. Moreover, direct testing of clinical specimens using this improved hexanucleotide primer-based NGS approach provided further detailed genotypes of enteroviruses causing hand, foot, and mouth disease (HFMD) and identified other potential viruses or differentiated misdiagnosis events. CONCLUSION The improved barcoded oligonucleotide primer-based NGS approach is simplified, time saving, cost effective, and appropriate for direct identification of viral pathogens in clinical practice.
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Affiliation(s)
- Chun Hua Wang
- Key Laboratory for Medical Virology, National Health and Fam-ily Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Kai Nie
- Key Laboratory for Medical Virology, National Health and Fam-ily Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Yi Zhang
- Key Laboratory for Medical Virology, National Health and Fam-ily Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Ji Wang
- Key Laboratory for Medical Virology, National Health and Fam-ily Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Shuai Feng Zhou
- Key Laboratory for Medical Virology, National Health and Fam-ily Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; Center for Disease Prevention and Control of Hunan Province, Changsha 410005, Hunan, China
| | - Xin Na Li
- Key Laboratory for Medical Virology, National Health and Fam-ily Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Hang Yu Zhou
- Key Laboratory for Medical Virology, National Health and Fam-ily Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Shun Xiang Qi
- Institute for Viral Disease Control and Prevention, Center for Disease Control and Prevention of Hebei, Shijiazhuang 050000, Hebei, China
| | - Xue Jun Ma
- Key Laboratory for Medical Virology, National Health and Fam-ily Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
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Mitchell AB, Oliver BGG, Glanville AR. Translational Aspects of the Human Respiratory Virome. Am J Respir Crit Care Med 2016; 194:1458-1464. [DOI: 10.1164/rccm.201606-1278ci] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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Abstract
New state-of-the-art techniques in sequencing offer valuable tools in both detection of mycobiota and in understanding of the molecular mechanisms of resistance against antifungal compounds and virulence. Introduction of new sequencing platform with enhanced capacity and a reduction in costs for sequence analysis provides a potential powerful tool in mycological diagnosis and research. In this review, we summarize the applications of next-generation sequencing techniques in mycology.
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Diaz MH, Winchell JM. The Evolution of Advanced Molecular Diagnostics for the Detection and Characterization of Mycoplasma pneumoniae. Front Microbiol 2016; 7:232. [PMID: 27014191 PMCID: PMC4781879 DOI: 10.3389/fmicb.2016.00232] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 02/15/2016] [Indexed: 12/12/2022] Open
Abstract
Over the past decade there have been significant advancements in the methods used for detecting and characterizing Mycoplasma pneumoniae, a common cause of respiratory illness and community-acquired pneumonia worldwide. The repertoire of available molecular diagnostics has greatly expanded from nucleic acid amplification techniques (NAATs) that encompass a variety of chemistries used for detection, to more sophisticated characterizing methods such as multi-locus variable-number tandem-repeat analysis (MLVA), Multi-locus sequence typing (MLST), matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS), single nucleotide polymorphism typing, and numerous macrolide susceptibility profiling methods, among others. These many molecular-based approaches have been developed and employed to continually increase the level of discrimination and characterization in order to better understand the epidemiology and biology of M. pneumoniae. This review will summarize recent molecular techniques and procedures and lend perspective to how each has enhanced the current understanding of this organism and will emphasize how Next Generation Sequencing may serve as a resource for researchers to gain a more comprehensive understanding of the genomic complexities of this insidious pathogen.
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Affiliation(s)
| | - Jonas M. Winchell
- Pneumonia Response and Surveillance Laboratory, Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, AtlantaGA, USA
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Wang Y, Zhu N, Li Y, Lu R, Wang H, Liu G, Zou X, Xie Z, Tan W. Metagenomic analysis of viral genetic diversity in respiratory samples from children with severe acute respiratory infection in China. Clin Microbiol Infect 2016; 22:458.e1-9. [PMID: 26802214 PMCID: PMC7172101 DOI: 10.1016/j.cmi.2016.01.006] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 12/21/2015] [Accepted: 01/11/2016] [Indexed: 12/11/2022]
Abstract
Severe acute respiratory infection (SARI) in children is thought to be mainly caused by infection with various viruses, some of which have been well characterized; however, analyses of respiratory tract viromes among children with SARI versus those without are limited. In this study, nasopharyngeal swabs from children with and without SARI (135 versus 15) were collected in China between 2008 and 2010 and subjected to multiplex metagenomic analyses using a next-generation sequencing platform. The results show that members of the Paramyxoviridae, Coronaviridae, Parvoviridae, Orthomyxoviridae, Picornaviridae, Anelloviridae and Adenoviridae families represented the most abundant species identified (>50% genome coverage) in the respiratory tracts of children with SARI. The viral population found in the respiratory tracts of children without SARI was less diverse and mainly dominated by the Anelloviridae family with only a small proportion of common epidemic respiratory viruses. Several almost complete viral genomes were assembled, and the genetic diversity was determined among several samples based on next-generation sequencing. This research provides comprehensive mapping of the viromes of children with SARI and indicates high heterogeneity of known viruses present in the childhood respiratory tract, which may benefit the detection and prevention of respiratory disease.
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Affiliation(s)
- Y Wang
- Key Laboratory of Medical Virology, Ministry of Health; National Institute for Viral Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, China
| | - N Zhu
- Key Laboratory of Medical Virology, Ministry of Health; National Institute for Viral Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, China
| | - Y Li
- Key Laboratory of Medical Virology, Ministry of Health; National Institute for Viral Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, China
| | - R Lu
- Key Laboratory of Medical Virology, Ministry of Health; National Institute for Viral Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, China
| | - H Wang
- State Key Laboratory for Infectious Disease Prevention and Control and National Institute for Communicable Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, China
| | - G Liu
- Key Laboratory of Medical Virology, Ministry of Health; National Institute for Viral Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, China
| | - X Zou
- Key Laboratory of Medical Virology, Ministry of Health; National Institute for Viral Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, China
| | - Z Xie
- Key Laboratory of Major Diseases in Children and National Key Discipline of Paediatrics Capital Medical University, Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - W Tan
- Key Laboratory of Medical Virology, Ministry of Health; National Institute for Viral Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, China.
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Bavelaar HH, Rahamat-Langendoen J, Niesters HG, Zoll J, Melchers WJ. Whole genome sequencing of fecal samples as a tool for the diagnosis and genetic characterization of norovirus. J Clin Virol 2015; 72:122-5. [DOI: 10.1016/j.jcv.2015.10.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 09/30/2015] [Accepted: 10/03/2015] [Indexed: 11/16/2022]
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