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Gholamzad A, Khakpour N, Hashemi SMA, Goudarzi Y, Ahmadi P, Gholamzad M, Mohammadi M, Hashemi M. Exploring the virome: An integral part of human health and disease. Pathol Res Pract 2024; 260:155466. [PMID: 39053136 DOI: 10.1016/j.prp.2024.155466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 07/06/2024] [Accepted: 07/12/2024] [Indexed: 07/27/2024]
Abstract
The human microbiome is a complex network of microorganisms that includes viruses, bacteria, and fungi. The gut virome is an essential component of the immune system, which is responsible for regulating the growth and responses of the host's immune system. The virome maintains a crucial role in the development of numerous diseases, including inflammatory bowel disease (IBD), Crohn's disease, and neurodegenerative disorders. The human virome has emerged as a promising biomarker and therapeutic target. This comprehensive review summarizes the present understanding of the virome and its implications in matters of health and disease, with a focus on the Human Microbiome Project.
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Affiliation(s)
- Amir Gholamzad
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Niloofar Khakpour
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyed Mohammad Ali Hashemi
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Yalda Goudarzi
- Department of Biology, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Parisa Ahmadi
- Immunology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mehrdad Gholamzad
- Department of Microbiology and Immunology, Faculty of Medicine, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| | - Mahya Mohammadi
- Student Research Committee, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mehrdad Hashemi
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Genetics, Faculty of Advanced Science and Technology ,Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
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2
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Zhu Z, Wang Y, Ning W, Liu C, Chen C. Torquetenovirus from bronchoalveolar lavage fluid as a biomarker for lung infection among immunocompromised hosts. Biomark Med 2024:1-11. [PMID: 38982729 DOI: 10.1080/17520363.2024.2366148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 05/08/2024] [Indexed: 07/11/2024] Open
Abstract
Aim: Torquetenovirus (TTV) was a promising biomarker for immunity, while lung regional TTV for evaluating the opportunistic infection among immunocompromised hosts (ICH) was unclear. Materials & methods: In the ICH and non-ICH populations, we compared the susceptibility to opportunistic infections, clinical severity and the prognosis between subgroups, respectively. Results: ICH with detectable bronchoalveolar lavage fluid (BALF)-TTV were more susceptible to lung aspergillosis and Mycobacterium infections. Furthermore, our data demonstrated that the ICH cohort with detectable BALF-TTV represented a higher clinical severity and a worse prognosis, while the above findings were not found in the non-ICH population. Conclusion: Our findings demonstrated that the BALF-TTV could act as an effective predictor for opportunistic infection for ICH that complemented the CD4+ T cell counts.
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Affiliation(s)
- Ziwen Zhu
- Department of Respiratory & Critical Medicine, The First Affiliated Hospital of Soochow University, 899 Pinghai Road, Suzhou 215006, China
| | - Yang Wang
- Department of Respiratory & Critical Medicine, The First Affiliated Hospital of Soochow University, 899 Pinghai Road, Suzhou 215006, China
| | - Weiwei Ning
- Department of Respiratory & Critical Medicine, The First Affiliated Hospital of Soochow University, 899 Pinghai Road, Suzhou 215006, China
| | - Chao Liu
- Department of Respiratory & Critical Medicine, The First Affiliated Hospital of Soochow University, 899 Pinghai Road, Suzhou 215006, China
| | - Cheng Chen
- Department of Respiratory & Critical Medicine, The First Affiliated Hospital of Soochow University, 899 Pinghai Road, Suzhou 215006, China
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3
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Diez-Martin E, Hernandez-Suarez L, Muñoz-Villafranca C, Martin-Souto L, Astigarraga E, Ramirez-Garcia A, Barreda-Gómez G. Inflammatory Bowel Disease: A Comprehensive Analysis of Molecular Bases, Predictive Biomarkers, Diagnostic Methods, and Therapeutic Options. Int J Mol Sci 2024; 25:7062. [PMID: 39000169 PMCID: PMC11241012 DOI: 10.3390/ijms25137062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 06/15/2024] [Accepted: 06/25/2024] [Indexed: 07/16/2024] Open
Abstract
In inflammatory bowel diseases (IBDs), such as Crohn's disease (CD) and ulcerative colitis (UC), the immune system relentlessly attacks intestinal cells, causing recurrent tissue damage over the lifetime of patients. The etiology of IBD is complex and multifactorial, involving environmental, microbiota, genetic, and immunological factors that alter the molecular basis of the organism. Among these, the microbiota and immune cells play pivotal roles; the microbiota generates antigens recognized by immune cells and antibodies, while autoantibodies target and attack the intestinal membrane, exacerbating inflammation and tissue damage. Given the altered molecular framework, the analysis of multiple molecular biomarkers in patients proves exceedingly valuable for diagnosing and prognosing IBD, including markers like C reactive protein and fecal calprotectin. Upon detection and classification of patients, specific treatments are administered, ranging from conventional drugs to new biological therapies, such as antibodies to neutralize inflammatory molecules like tumor necrosis factor (TNF) and integrin. This review delves into the molecular basis and targets, biomarkers, treatment options, monitoring techniques, and, ultimately, current challenges in IBD management.
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Affiliation(s)
- Eguzkiñe Diez-Martin
- Research and Development Department, IMG Pharma Biotech S.L., 48170 Zamudio, Spain
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
| | - Leidi Hernandez-Suarez
- Research and Development Department, IMG Pharma Biotech S.L., 48170 Zamudio, Spain
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
| | - Carmen Muñoz-Villafranca
- Department of Gastroenterology, University Hospital of Basurto, Avda Montevideo 18, 48013 Bilbao, Spain
| | - Leire Martin-Souto
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
| | - Egoitz Astigarraga
- Research and Development Department, IMG Pharma Biotech S.L., 48170 Zamudio, Spain
| | - Andoni Ramirez-Garcia
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
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Xepapadaki P, Megremis S, Rovina N, Wardzyńska A, Pasioti M, Kritikou M, Papadopoulos NG. Exploring the Impact of Airway Microbiome on Asthma Morbidity: A Focus on the "Constructing a 'Eubiosis Reinstatement Therapy' for Asthma-CURE" Project. Pulm Ther 2024; 10:171-182. [PMID: 38814533 PMCID: PMC11282048 DOI: 10.1007/s41030-024-00261-3] [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: 02/26/2024] [Accepted: 05/02/2024] [Indexed: 05/31/2024] Open
Abstract
The asthma pandemic imposes a huge burden on patients and health systems in both developed and developing countries. Despite available treatments, symptom control is generally suboptimal, and hospitalizations and deaths remain at unacceptably high levels. A pivotal aspect of asthma that warrants further exploration is the influence of the respiratory microbiome and virome in modulating disease activity. A plethora of studies report that the respiratory microbiome is characteristically dysbiotic in asthma. In addition, our data suggest that dysbiosis is also observed on the respiratory virome, partly characterized by the reduced abundance of bacteriophages (phages). Even though phages can naturally infect and control their bacterial prey, phage therapy has been grossly neglected in the Western world, although more recently it is more widely used as a novel tool against bacterial infections. However, it has never been used for tackling microbiome dysbiosis in human non-communicable diseases. This review provides an up-to-date understanding of the microbiome and virome's role within the airways in relation to asthma morbidity. It also advances the rationale and hypothesis for the CURE project. Specifically, the CURE project suggests that managing the respiratory microbiome through phage therapy is viable and may result in restoring eubiosis within the asthmatic airway. This entails controlling immune dysregulation and the clinical manifestation of the disease. To accomplish this goal, it is crucial to predict the effects of introducing specific phage mixtures into the intricate ecology of the airways and devise suitable interventions.
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Affiliation(s)
- Paraskevi Xepapadaki
- Allergy Department, 2nd Paediatric Clinic, National and Kapodistrian University of Athens, 41, Fidippidou, 11527, Athens, Greece.
| | - Spyridon Megremis
- Department of Genetics and Genome Biology, Centre for Phage Research, University of Leicester, Leicester, UK
| | - Nikoletta Rovina
- 1st Department of Respiratory Medicine, Sotiria Hospital, School of Medicine, National and Kapodistrian University of Athens, 11527, Athens, Greece
| | | | - Maria Pasioti
- Allergy Department, 2nd Paediatric Clinic, National and Kapodistrian University of Athens, 41, Fidippidou, 11527, Athens, Greece
| | - Maria Kritikou
- Allergy Department, 2nd Paediatric Clinic, National and Kapodistrian University of Athens, 41, Fidippidou, 11527, Athens, Greece
| | - Nikolaos G Papadopoulos
- Allergy Department, 2nd Paediatric Clinic, National and Kapodistrian University of Athens, 41, Fidippidou, 11527, Athens, Greece
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5
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Camprubí-Ferrer D, Tomazatos A, Balerdi-Sarasola L, Cobuccio LG, Van Den Broucke S, Horváth B, Van Esbroeck M, Martinez MJ, Gandasegui J, Subirà C, Saloni M, Genton B, Bottieau E, Cadar D, Muñoz J. Assessing viral metagenomics for the diagnosis of acute undifferentiated fever in returned travellers: a multicenter cohort study. J Travel Med 2024; 31:taae029. [PMID: 38381609 DOI: 10.1093/jtm/taae029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/09/2024] [Accepted: 02/17/2024] [Indexed: 02/23/2024]
Abstract
BACKGROUND Up to 45% of febrile returning travellers remain undiagnosed after a thorough diagnostic work-up, even at referral centres. Although metagenomic next-generation sequencing (mNGS) has emerged as a promising tool, evidence of its usefulness in imported fever is very limited. METHODS Travellers returning with fever were prospectively recruited in three referral clinics from November 2017 to November 2019. Unbiased mNGS optimised for virus detection was performed on serum samples of participants with acute undifferentiated febrile illness (AUFI), and results were compared to those obtained by reference diagnostic methods (RDM). RESULTS Among 507 returned febrile travellers, 433(85.4%) presented with AUFI. Dengue virus (n = 86) and Plasmodium spp. (n = 83) were the most common causes of fever. 103/433(23.8%) AUFI remained undiagnosed at the end of the follow-up.Metagenomic next-generation sequencing unveiled potentially pathogenic microorganisms in 196/433(38.7%) AUFI. mNGS identifications were more common in patients with a shorter duration of fever (42.3% in ≤5 days vs 28.7% in >5 days, P = 0.005). Potential causes of fever were revealed in 25/103(24.2%) undiagnosed AUFI and 5/23(21.7%) travellers with severe undiagnosed AUFI. Missed severe aetiologies included eight bacterial identifications and one co-infection of B19 parvovirus and Aspergillus spp.Additional identifications indicating possible co-infections occurred in 29/316(9.2%) travellers with AUFI, and in 11/128(8.6%) travellers with severe AUFI, who had received a diagnosis through RDM. The most common co-infections detected in severe AUFI were caused by Gram-negative bacteria. Serum mNGS was unable to detect >50% of infectious diagnoses achieved by RDM and also yielded 607 non-pathogenic identifications. DISCUSSION mNGS of serum can be a valuable diagnostic tool for selected travellers with undiagnosed AUFI or severe disease in addition to reference diagnostic techniques, especially during the first days of symptoms. Nevertheless, mNGS results interpretation presents a great challenge. Further studies evaluating the performance of mNGS using different sample types and protocols tailored to non-viral agents are needed.
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Affiliation(s)
- Daniel Camprubí-Ferrer
- International Health Department ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona 08036, Spain
| | - Alexandru Tomazatos
- Bernhard Nocht Institute for Tropical Medicine, National Reference Centre for Tropical Infectious Diseases, Hamburg, Germany
| | - Leire Balerdi-Sarasola
- International Health Department ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona 08036, Spain
| | - Ludovico G Cobuccio
- Center for Primary Care and Public Health, University of Lausanne, Switzerland
| | | | - Balázs Horváth
- Bernhard Nocht Institute for Tropical Medicine, National Reference Centre for Tropical Infectious Diseases, Hamburg, Germany
| | - Marjan Van Esbroeck
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Miguel J Martinez
- Microbiology Department, Hospital Clínic Barcelona, Barcelona, Spain
| | - Javier Gandasegui
- International Health Department ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona 08036, Spain
| | - Carme Subirà
- International Health Department ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona 08036, Spain
| | - Meritxell Saloni
- International Health Department ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona 08036, Spain
| | - Blaise Genton
- Center for Primary Care and Public Health, University of Lausanne, Switzerland
| | - Emmanuel Bottieau
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Dániel Cadar
- Bernhard Nocht Institute for Tropical Medicine, National Reference Centre for Tropical Infectious Diseases, Hamburg, Germany
| | - Jose Muñoz
- International Health Department ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona 08036, Spain
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Wan Y, Zhang L, Xu Z, Su Q, Leung TF, Chan D, Wong OWH, Chan S, Chan FKL, Tun HM, Ng SC. Alterations in fecal virome and bacteriome virome interplay in children with autism spectrum disorder. Cell Rep Med 2024; 5:101409. [PMID: 38307030 PMCID: PMC10897546 DOI: 10.1016/j.xcrm.2024.101409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 11/10/2023] [Accepted: 01/11/2024] [Indexed: 02/04/2024]
Abstract
Emerging evidence suggests autism spectrum disorder (ASD) is associated with altered gut bacteria. However, less is known about the gut viral community and its role in shaping microbiota in neurodevelopmental disorders. Herein, we perform a metagenomic analysis of gut-DNA viruses in 60 children with ASD and 64 age- and gender-matched typically developing children to investigate the effect of the gut virome on host bacteria in children with ASD. ASD is associated with altered gut virome composition accompanied by the enrichment of Clostridium phage, Bacillus phage, and Enterobacteria phage. These ASD-enriched phages are largely associated with disrupted viral ecology in ASD. Importantly, changes in the interplay between the gut bacteriome and virome seen in ASD may influence the encoding capacity of microbial pathways for neuroactive metabolite biosynthesis. These findings suggest an impaired bacteriome-virome ecology in ASD, which sheds light on the importance of bacteriophages in pathogenesis and the development of microbial therapeutics in ASD.
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Affiliation(s)
- Yating Wan
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China; The D.H. Chen Foundation Hub of Advanced Technology for Child Health (HATCH), The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Lin Zhang
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China; The D.H. Chen Foundation Hub of Advanced Technology for Child Health (HATCH), The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Zhilu Xu
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Qi Su
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Ting-Fan Leung
- Department of Paediatrics, The Chinese University of Hong Kong, Hong Kong SAR, China; The D.H. Chen Foundation Hub of Advanced Technology for Child Health (HATCH), The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Dorothy Chan
- Department of Paediatrics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Oscar W H Wong
- Department of Psychiatry, The Chinese University of Hong Kong, Hong Kong SAR, China; The D.H. Chen Foundation Hub of Advanced Technology for Child Health (HATCH), The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Sandra Chan
- Department of Psychiatry, The Chinese University of Hong Kong, Hong Kong SAR, China; The D.H. Chen Foundation Hub of Advanced Technology for Child Health (HATCH), The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Francis K L Chan
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong SAR, China; The D.H. Chen Foundation Hub of Advanced Technology for Child Health (HATCH), The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Hein M Tun
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China; The Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Siew C Ng
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China; The D.H. Chen Foundation Hub of Advanced Technology for Child Health (HATCH), The Chinese University of Hong Kong, Hong Kong SAR, China.
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Timmerman AL, Schönert ALM, van der Hoek L. Anelloviruses versus human immunity: how do we control these viruses? FEMS Microbiol Rev 2024; 48:fuae005. [PMID: 38337179 PMCID: PMC10883694 DOI: 10.1093/femsre/fuae005] [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: 11/09/2023] [Revised: 12/22/2023] [Accepted: 02/08/2024] [Indexed: 02/12/2024] Open
Abstract
One continuous companion and one of the major players in the human blood virome are members of the Anelloviridae family. Anelloviruses are probably found in all humans, infection occurs early in life and the composition (anellome) is thought to remain stable and personal during adulthood. The stable anellome implies a great balance between the host immune system and the virus. However, the lack of a robust culturing system hampers direct investigation of interactions between virus and host cells. Other techniques, however, including next generation sequencing, AnelloScan-antibody tests, evolution selection pressure analysis, and virus protein structures, do provide new insights into the interactions between anelloviruses and the host immune system. This review aims at providing an overview of the current knowledge on the immune mechanisms acting on anelloviruses and the countering viral mechanisms allowing immune evasion.
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Affiliation(s)
- Anne L Timmerman
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Postbus 22660, 1100 DD, Amsterdam, the Netherlands
| | - Antonia L M Schönert
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Postbus 22660, 1100 DD, Amsterdam, the Netherlands
| | - Lia van der Hoek
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Postbus 22660, 1100 DD, Amsterdam, the Netherlands
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Sarkar A, McInroy CJA, Harty S, Raulo A, Ibata NGO, Valles-Colomer M, Johnson KVA, Brito IL, Henrich J, Archie EA, Barreiro LB, Gazzaniga FS, Finlay BB, Koonin EV, Carmody RN, Moeller AH. Microbial transmission in the social microbiome and host health and disease. Cell 2024; 187:17-43. [PMID: 38181740 PMCID: PMC10958648 DOI: 10.1016/j.cell.2023.12.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 12/06/2023] [Accepted: 12/06/2023] [Indexed: 01/07/2024]
Abstract
Although social interactions are known to drive pathogen transmission, the contributions of socially transmissible host-associated mutualists and commensals to host health and disease remain poorly explored. We use the concept of the social microbiome-the microbial metacommunity of a social network of hosts-to analyze the implications of social microbial transmission for host health and disease. We investigate the contributions of socially transmissible microbes to both eco-evolutionary microbiome community processes (colonization resistance, the evolution of virulence, and reactions to ecological disturbance) and microbial transmission-based processes (transmission of microbes with metabolic and immune effects, inter-specific transmission, transmission of antibiotic-resistant microbes, and transmission of viruses). We consider the implications of social microbial transmission for communicable and non-communicable diseases and evaluate the importance of a socially transmissible component underlying canonically non-communicable diseases. The social transmission of mutualists and commensals may play a significant, under-appreciated role in the social determinants of health and may act as a hidden force in social evolution.
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Affiliation(s)
- Amar Sarkar
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.
| | - Cameron J A McInroy
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Siobhán Harty
- Independent, Tandy Court, Spitalfields, Dublin, Ireland
| | - Aura Raulo
- Department of Biology, University of Oxford, Oxford, UK; Department of Computing, University of Turku, Turku, Finland
| | - Neil G O Ibata
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Mireia Valles-Colomer
- Department of Medicine and Life Sciences, Pompeu Fabra University, Barcelona, Spain; Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Katerina V-A Johnson
- Institute of Psychology, Leiden University, Leiden, the Netherlands; Department of Psychiatry, University of Oxford, Oxford, UK
| | - Ilana L Brito
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Joseph Henrich
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Elizabeth A Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Luis B Barreiro
- Committee on Immunology, University of Chicago, Chicago, IL, USA; Department of Medicine, University of Chicago, Chicago, IL, USA; Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Francesca S Gazzaniga
- Molecular Pathology Unit, Cancer Center, Massachusetts General Hospital Research Institute, Charlestown, MA, USA; Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - B Brett Finlay
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada; Department of Biochemistry, University of British Columbia, Vancouver, BC, Canada
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA
| | - Rachel N Carmody
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Andrew H Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
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9
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Thijssen M, Devos T, Meyfroidt G, Van Ranst M, Pourkarim MR. Exploring the relationship between anellovirus load and clinical variables in hospitalized COVID-19 patients: Implications for immune activation and inflammation. IJID REGIONS 2023; 9:49-54. [PMID: 37868342 PMCID: PMC10587511 DOI: 10.1016/j.ijregi.2023.09.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/19/2023] [Accepted: 09/22/2023] [Indexed: 10/24/2023]
Abstract
Objectives Anelloviruses have been linked with host-immunocompetence and inflammation. Here, we studied the anellovirus load in hospitalized COVID-19 patients. Methods We collected samples of patients recruited in the DAWN-Plasma trial that received convalescent plasma (CP) therapy (four plasma units) combined with standard of care (SOC) or SOC of alone. Plasma samples were collected on day 0 and 6 of hospitalization and we quantified anellovirus load. With multivariate models, clinical variables were associated with changes in anellovirus load. Results Samples were collected on day 0 and 6 of 150 patients (103 CP + SOC and 47 SOC). Anellovirus load was higher on day 0 compared to day 6 and we found a significant drop in SOC patients. Patients receiving immunosuppressive drug had a lower anellovirus load (coefficient: 1.021, 95% confidence interval [CI] 0.270-1.772, P = 0.008), while patients admitted to the emergency room displayed a higher abundance on day 0 (1.308, 95% CI 0.443-2.173, P = 0.003). Unspecific markers of inflammation and organ damage, D-dimer (0.001, 95% CI <0.001-0.001, P = 0.001) and lactate dehydrogenase (0.002, 95% CI 0.001-0.004, P = 0.044), were positively associated with anellovirus load. Finally, anellovirus load on day 0 (-39.9, 95% CI -75.72 to -4.27, P = 0.029) was negatively associated with SARS-CoV-2 antibody response on day. Conclusion The results showed associations between clinical variables and anellovirus load in COVID-19 patients. Many variables share properties related to host immunocompetence or inflammation. Therefore, we expect that anellovirus abundance displays the net state of immune activation.
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Affiliation(s)
- Marijn Thijssen
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory for Clinical and Epidemiological Virology, Leuven, Belgium
| | - Timothy Devos
- University Hospitals Leuven, Department of Haematology, Department of Microbiology and Immunology, Laboratory of Molecular Immunology (Rega Institute), KU Leuven, Leuven, Belgium
| | - Geert Meyfroidt
- University Hospitals Leuven, Department of Intensive Care Medicine, Department of Cellular and Molecular Medicine, Laboratory of Intensive Care Medicine, KU Leuven, Leuven, Belgium
| | - Marc Van Ranst
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory for Clinical and Epidemiological Virology, Leuven, Belgium
| | - Mahmoud Reza Pourkarim
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory for Clinical and Epidemiological Virology, Leuven, Belgium
- Shiraz University of Medical Sciences, Health Policy Research Centre, Institute of Health, Shiraz, Iran
- Blood Transfusion Research Centre, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran
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10
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Cao L, Ma Y, Wan Z, Li B, Tian W, Zhang C, Li Y. Longitudinal anellome dynamics in the upper respiratory tract of children with acute respiratory tract infections. Virus Evol 2023; 9:vead045. [PMID: 37674817 PMCID: PMC10478798 DOI: 10.1093/ve/vead045] [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: 04/27/2023] [Revised: 07/05/2023] [Accepted: 07/11/2023] [Indexed: 09/08/2023] Open
Abstract
Anelloviruses (AVs) are ubiquitous in humans and are the most abundant components of the commensal virome. Previous studies on the diversity, transmission, and persistence of AVs mainly focused on the blood or transplanted tissues from adults; however, the profile of the anellome in the respiratory tract in children are barely known. We investigated the anellome profile and their dynamics in the upper respiratory tract from a cohort of children with acute respiratory tract infections (ARTIs). Different to that in adult, betatorquevirus is the most abundant genus, followed by alphatorquevirus. We found that the relative abundance of betatorquevirus was higher in earlier time points, and in contrast, the abundance of alphatorquevirus was higher in later time points; these results might suggest that betatorquevirus decreased with age and alphatorquevirus increased with age in childhood. No difference regarding the diversity and abundance of anellome was found between single and multiple ARTIs, consistent with the idea that AV is not associated with certain disease. Most AVs are transient, and a small proportion (8 per cent) of them were found to be possibly persistent, with persistence time ranging from 1 month to as long as 56 months. Furthermore, the individual respiratory anellome appeared to be unique and dynamic, and the replacement of existing AVs with new ones are common over different time points. These findings demonstrate that betatorquevirus may be the early colonizer in children, and the individual respiratory anellome is unique, which are featured by both chronic infections and AV community replacement.
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Affiliation(s)
- Le Cao
- Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Road, Jinshan District, Shanghai 201508, China
| | - Yingying Ma
- Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Road, Jinshan District, Shanghai 201508, China
| | - Zhenzhou Wan
- Medical Laboratory of Taizhou Fourth People’s Hospital, 99 North Gulou Road, Taizhou 225300, China
| | - Bing Li
- Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Road, Jinshan District, Shanghai 201508, China
| | - Weimin Tian
- Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Road, Jinshan District, Shanghai 201508, China
| | - Chiyu Zhang
- Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Road, Jinshan District, Shanghai 201508, China
| | - Yanpeng Li
- Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Road, Jinshan District, Shanghai 201508, China
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11
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Reyes NS, Laham G, Boccia N, García G, Jara R, Hermida E, Ricarte C, Diaz C, Soler Pujol G, Poletta FA, Echavarria M. Prospective cohort study of Torque Teno Virus (TTV) viral load kinetics and the association with graft rejection in renal transplant patients. J Clin Virol 2023; 165:105501. [PMID: 37379781 DOI: 10.1016/j.jcv.2023.105501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 04/13/2023] [Accepted: 05/30/2023] [Indexed: 06/30/2023]
Abstract
INTRODUCTION Graft survival is mainly determined by rejections and infectious complications in transplant recipients. Torque Teno Virus (TTV), a nonpathogenic and ubiquitous single-stranded DNA virus, has been proposed as a biomarker of the immune status in transplant patients. This study aimed to determine the correlation between a Home-Brew TTV PCR and R-GENE®PCR; the TTV viral load kinetics in renal transplant recipients and the association with graft rejection. MATERIALS AND METHODS Prospective cohort study on 107 adult renal transplant recipients. TTV viral load was determined in 746 plasma samples collected before and after renal transplantation by a Home-Brew PCR and a commercial PCR (R-GENE®PCR). Associations of TTV viral load with graft rejections were analyzed. RESULTS Agreement of both PCR assays was 93.2% and Pearson correlation coefficient was r: 0.902 (95%CI: 0.8881-0.9149, p < 0.0001). TTV viral load kinetics showed an initial gradual increase reaching a peak at 3 months. This highest value was followed by a slight decrease, reaching a plateau significantly higher than the initial baseline at 6 months (p < 0.0001). Between (181-270) days post-transplantation, TTV median viral load in patients with graft rejection was significantly lower, 3.59 Log10 copies/mL (by Home-Brew PCR) and 3.10 Log10 copies/mL (by R-GENE®PCR) compared to patients without graft rejection (6.14 and 5.96 Log10 copies/mL, respectively). CONCLUSIONS Significantly lower TTV viral load was observed in patients with renal rejection occurring at a median of 243 days post-transplantation. Given the dynamic behavior of TTV viral load post-transplantation, cut-off values for risk stratification to predict rejection might be determined in relation to the post-transplant period.
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Affiliation(s)
- N S Reyes
- Virology Unit (CEMIC-CONICET), Centro de Educación Médica e Investigaciones Clínicas University Hospital (CEMIC), Argentina.
| | - G Laham
- Nephrology section, CEMIC University Hospital, Argentina
| | - N Boccia
- Nephrology section, CEMIC University Hospital, Argentina
| | - G García
- Nephrology section, CEMIC University Hospital, Argentina
| | - R Jara
- Virology Unit (CEMIC-CONICET), Centro de Educación Médica e Investigaciones Clínicas University Hospital (CEMIC), Argentina
| | - E Hermida
- Virology Unit (CEMIC-CONICET), Centro de Educación Médica e Investigaciones Clínicas University Hospital (CEMIC), Argentina
| | - C Ricarte
- Virology Unit (CEMIC-CONICET), Centro de Educación Médica e Investigaciones Clínicas University Hospital (CEMIC), Argentina
| | - C Diaz
- Nephrology section, CEMIC University Hospital, Argentina
| | - G Soler Pujol
- Nephrology section, CEMIC University Hospital, Argentina
| | - F A Poletta
- Genetic Epidemiology Laboratory (CEMIC-CONICET), Argentina
| | - M Echavarria
- Virology Unit (CEMIC-CONICET), Centro de Educación Médica e Investigaciones Clínicas University Hospital (CEMIC), Argentina; Virology Laboratory, CEMIC, Argentina
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12
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Megremis S, Constantinides B, Xepapadaki P, Yap CF, Sotiropoulos AG, Bachert C, Finotto S, Jartti T, Tapinos A, Vuorinen T, Andreakos E, Robertson DL, Papadopoulos NG. Respiratory eukaryotic virome expansion and bacteriophage deficiency characterize childhood asthma. Sci Rep 2023; 13:8319. [PMID: 37221274 PMCID: PMC10205716 DOI: 10.1038/s41598-023-34730-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 05/06/2023] [Indexed: 05/25/2023] Open
Abstract
Asthma development and exacerbation is linked to respiratory virus infections. There is limited information regarding the presence of viruses during non-exacerbation/infection periods. We investigated the nasopharyngeal/nasal virome during a period of asymptomatic state, in a subset of 21 healthy and 35 asthmatic preschool children from the Predicta cohort. Using metagenomics, we described the virome ecology and the cross-species interactions within the microbiome. The virome was dominated by eukaryotic viruses, while prokaryotic viruses (bacteriophages) were independently observed with low abundance. Rhinovirus B species consistently dominated the virome in asthma. Anelloviridae were the most abundant and rich family in both health and asthma. However, their richness and alpha diversity were increased in asthma, along with the co-occurrence of different Anellovirus genera. Bacteriophages were richer and more diverse in healthy individuals. Unsupervised clustering identified three virome profiles that were correlated to asthma severity and control and were independent of treatment, suggesting a link between the respiratory virome and asthma. Finally, we observed different cross-species ecological associations in the healthy versus the asthmatic virus-bacterial interactome, and an expanded interactome of eukaryotic viruses in asthma. Upper respiratory virome "dysbiosis" appears to be a novel feature of pre-school asthma during asymptomatic/non-infectious states and merits further investigation.
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Affiliation(s)
- Spyridon Megremis
- University of Manchester, Manchester, UK.
- University of Leicester, Leicester, UK.
| | | | | | | | | | | | - Susetta Finotto
- Friedrich Alexander University Erlangen-Nurnberg, Erlangen, Germany
| | - Tuomas Jartti
- University of Turku, Turku, Finland
- University of Oulu, Oulu, Finland
| | | | | | | | | | - Nikolaos G Papadopoulos
- University of Manchester, Manchester, UK.
- National and Kapodistrian University of Athens, Athens, Greece.
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13
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Thijssen M, Tacke F, Van Espen L, Cassiman D, Naser Aldine M, Nevens F, Van Ranst M, Matthijnssens J, Pourkarim MR. Plasma virome dynamics in chronic hepatitis B virus infected patients. Front Microbiol 2023; 14:1172574. [PMID: 37228370 PMCID: PMC10203228 DOI: 10.3389/fmicb.2023.1172574] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 04/19/2023] [Indexed: 05/27/2023] Open
Abstract
The virome remains an understudied domain of the human microbiome. The role of commensal viruses on the outcome of infections with known pathogens is not well characterized. In this study we aimed to characterize the longitudinal plasma virome dynamics in chronic hepatitis B virus (HBV) infected patients. Eighty-five longitudinal plasma samples were collected from 12 chronic HBV infected individuals that were classified in the four stages of HBV infection. The virome was characterized with an optimized viral extraction protocol and deep-sequenced on a NextSeq 2500 platform. The plasma virome was primarily composed of members of the Anello- Flavi-, and Hepadnaviridae (HBV) families. The virome structure and dynamics did not correlate with the different stages of chronic HBV infection nor with the administration of antiviral therapy. We observed a higher intrapersonal similarity of viral contigs. Genomic analysis of viruses observed in multiple timepoint demonstrated the presence of a dynamic community. This study comprehensively assessed the blood virome structure in chronic HBV infected individuals and provided insights in the longitudinal development of this viral community.
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Affiliation(s)
- Marijn Thijssen
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Frank Tacke
- Department of Hepatology and Gastroenterology, Campus Virchow-Klinikum and Campus Charité Mitte, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Lore Van Espen
- Laboratory of Viral Metagenomics, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - David Cassiman
- Department of Gastroenterology and Hepatology, University Hospital Leuven, Leuven, Belgium
| | - Mahmoud Naser Aldine
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Frederik Nevens
- Department of Gastroenterology and Hepatology, University Hospital Leuven, Leuven, Belgium
| | - Marc Van Ranst
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Jelle Matthijnssens
- Laboratory of Viral Metagenomics, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Mahmoud Reza Pourkarim
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
- Health Policy Research Centre, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
- Blood Transfusion Research Centre, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran
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14
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Ryabchenko B, Šroller V, Horníková L, Lovtsov A, Forstová J, Huérfano S. The interactions between PML nuclear bodies and small and medium size DNA viruses. Virol J 2023; 20:82. [PMID: 37127643 PMCID: PMC10152602 DOI: 10.1186/s12985-023-02049-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 04/23/2023] [Indexed: 05/03/2023] Open
Abstract
Promyelocytic leukemia nuclear bodies (PM NBs), often referred to as membraneless organelles, are dynamic macromolecular protein complexes composed of a PML protein core and other transient or permanent components. PML NBs have been shown to play a role in a wide variety of cellular processes. This review describes in detail the diverse and complex interactions between small and medium size DNA viruses and PML NBs that have been described to date. The PML NB components that interact with small and medium size DNA viruses include PML protein isoforms, ATRX/Daxx, Sp100, Sp110, HP1, and p53, among others. Interaction between viruses and components of these NBs can result in different outcomes, such as influencing viral genome expression and/or replication or impacting IFN-mediated or apoptotic cell responses to viral infection. We discuss how PML NB components abrogate the ability of adenoviruses or Hepatitis B virus to transcribe and/or replicate their genomes and how papillomaviruses use PML NBs and their components to promote their propagation. Interactions between polyomaviruses and PML NBs that are poorly understood but nevertheless suggest that the NBs can serve as scaffolds for viral replication or assembly are also presented. Furthermore, complex interactions between the HBx protein of hepadnaviruses and several PML NBs-associated proteins are also described. Finally, current but scarce information regarding the interactions of VP3/apoptin of the avian anellovirus with PML NBs is provided. Despite the considerable number of studies that have investigated the functions of the PML NBs in the context of viral infection, gaps in our understanding of the fine interactions between viruses and the very dynamic PML NBs remain. The complexity of the bodies is undoubtedly a great challenge that needs to be further addressed.
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Affiliation(s)
- Boris Ryabchenko
- Department of Genetics and Microbiology, Faculty of Science, BIOCEV, Charles University, Vestec, 25250, Czech Republic
| | - Vojtěch Šroller
- Department of Genetics and Microbiology, Faculty of Science, BIOCEV, Charles University, Vestec, 25250, Czech Republic
| | - Lenka Horníková
- Department of Genetics and Microbiology, Faculty of Science, BIOCEV, Charles University, Vestec, 25250, Czech Republic
| | - Alexey Lovtsov
- Department of Genetics and Microbiology, Faculty of Science, BIOCEV, Charles University, Vestec, 25250, Czech Republic
| | - Jitka Forstová
- Department of Genetics and Microbiology, Faculty of Science, BIOCEV, Charles University, Vestec, 25250, Czech Republic
| | - Sandra Huérfano
- Department of Genetics and Microbiology, Faculty of Science, BIOCEV, Charles University, Vestec, 25250, Czech Republic.
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15
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Shah SA, Deng L, Thorsen J, Pedersen AG, Dion MB, Castro-Mejía JL, Silins R, Romme FO, Sausset R, Jessen LE, Ndela EO, Hjelmsø M, Rasmussen MA, Redgwell TA, Leal Rodríguez C, Vestergaard G, Zhang Y, Chawes B, Bønnelykke K, Sørensen SJ, Bisgaard H, Enault F, Stokholm J, Moineau S, Petit MA, Nielsen DS. Expanding known viral diversity in the healthy infant gut. Nat Microbiol 2023; 8:986-998. [PMID: 37037943 PMCID: PMC10159846 DOI: 10.1038/s41564-023-01345-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 02/17/2023] [Indexed: 04/12/2023]
Abstract
The gut microbiome is shaped through infancy and impacts the maturation of the immune system, thus protecting against chronic disease later in life. Phages, or viruses that infect bacteria, modulate bacterial growth by lysis and lysogeny, with the latter being especially prominent in the infant gut. Viral metagenomes (viromes) are difficult to analyse because they span uncharted viral diversity, lacking marker genes and standardized detection methods. Here we systematically resolved the viral diversity in faecal viromes from 647 1-year-olds belonging to Copenhagen Prospective Studies on Asthma in Childhood 2010, an unselected Danish cohort of healthy mother-child pairs. By assembly and curation we uncovered 10,000 viral species from 248 virus family-level clades (VFCs). Most (232 VFCs) were previously unknown, belonging to the Caudoviricetes viral class. Hosts were determined for 79% of phage using clustered regularly interspaced short palindromic repeat spacers within bacterial metagenomes from the same children. Typical Bacteroides-infecting crAssphages were outnumbered by undescribed phage families infecting Clostridiales and Bifidobacterium. Phage lifestyles were conserved at the viral family level, with 33 virulent and 118 temperate phage families. Virulent phages were more abundant, while temperate ones were more prevalent and diverse. Together, the viral families found in this study expand existing phage taxonomy and provide a resource aiding future infant gut virome research.
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Affiliation(s)
- Shiraz A Shah
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark.
| | - Ling Deng
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Jonathan Thorsen
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anders G Pedersen
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Moïra B Dion
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Quebec, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Quebec, Canada
| | | | - Ronalds Silins
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Fie O Romme
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Romain Sausset
- Université Paris-Saclay, INRAE, Agroparistech, Micalis institute, Jouy-en-Josas, France
| | - Leon E Jessen
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Eric Olo Ndela
- Lab de Microorganismes: Génome et Environnement, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Mathis Hjelmsø
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
| | - Morten A Rasmussen
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Tamsin A Redgwell
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
| | - Cristina Leal Rodríguez
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
| | - Gisle Vestergaard
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Yichang Zhang
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Bo Chawes
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
| | - Klaus Bønnelykke
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
| | - Søren J Sørensen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Hans Bisgaard
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
| | - Francois Enault
- Lab de Microorganismes: Génome et Environnement, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Jakob Stokholm
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Sylvain Moineau
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Quebec, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Quebec, Canada
- Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec City, Quebec, Canada
| | - Marie-Agnès Petit
- Université Paris-Saclay, INRAE, Agroparistech, Micalis institute, Jouy-en-Josas, France
| | - Dennis S Nielsen
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark.
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16
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del Rosal T, García-García ML, Casas I, Iglesias-Caballero M, Pozo F, Alcolea S, Bravo B, Rodrigo-Muñoz JM, del Pozo V, Calvo C. Torque Teno Virus in Nasopharyngeal Aspirate of Children With Viral Respiratory Infections. Pediatr Infect Dis J 2023; 42:184-188. [PMID: 36729788 PMCID: PMC9935559 DOI: 10.1097/inf.0000000000003796] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/01/2022] [Indexed: 02/03/2023]
Abstract
BACKGROUND Torque teno virus (TTV) is a ubiquitous anellovirus responsible for persistent infections and is considered a marker of immune function. The role of TTV as a facilitator of respiratory infections (RIs) is unknown. OBJECTIVES Our aim was to estimate, in a prospective study, the prevalence of TTV in the nasopharyngeal aspirate (NPA) of hospitalized children <5 years old, with RIs and correlate them with outcomes and immune response. PATIENTS AND METHODS NPA was taken for testing of 16 respiratory viruses by reverse transcription-polymerase chain reaction (PCR), TTV PCR, and immunologic study. RESULTS Sixty hospitalized children with an RI were included. A total of 51/60 patients had positive common respiratory viral (CRV) identification. A total of 23/60 (38.3%) children were TTV+ in NPA. TTV+ patients had other CRVs in 100% of cases versus 78.3% in TTV- ( P = 0.029). The TTV+ patients tended to be older, have fever, and to need pediatric intensive care unit admission more often than TTV- patients. Abnormal chest radiograph was more frequent in the TTV+ patients, odds ratios 2.6 (95% CI: 1.3-5.2). The genetic expression of filaggrin (involved in epithelial barrier integrity) was lower in TTV+ patients; however, the levels of filaggrin in the NPA were increased. CONCLUSIONS TTV infection is common in children with RI and could be associated with abnormal imaging in radiograph, greater severity and an alteration in filaggrin gene expression and protein release.
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Affiliation(s)
- Teresa del Rosal
- From the Paediatric Infectious Diseases Department, La Paz University Hospital, Madrid, Spain
- Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
- Translational Research Network in Pediatric Infectious Diseases (RITIP), Madrid, Spain
- CIBER de Enfermedades raras, CIBERER, ISCIII, Madrid, Spain
| | - Mª Luz García-García
- CIBER de Enfermedades raras, CIBERER, ISCIII, Madrid, Spain
- Pediatric Department, Severo Ochoa University Hospital, Leganés, Madrid, Spain
- CIBER de Enfermedades Infecciosas, CIBERINFEC, ISCIII, Madrid, Spain
| | - Inmaculada Casas
- Respiratory Viruses and Influenza Unit at the National Center for Microbiology (ISCIII), Madrid, Spain
| | - María Iglesias-Caballero
- Respiratory Viruses and Influenza Unit at the National Center for Microbiology (ISCIII), Madrid, Spain
| | - Francisco Pozo
- Respiratory Viruses and Influenza Unit at the National Center for Microbiology (ISCIII), Madrid, Spain
| | - Sonia Alcolea
- From the Paediatric Infectious Diseases Department, La Paz University Hospital, Madrid, Spain
- Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
- Pediatric Department, Severo Ochoa University Hospital, Leganés, Madrid, Spain
- CIBER de Enfermedades Infecciosas, CIBERINFEC, ISCIII, Madrid, Spain
| | - Blanca Bravo
- From the Paediatric Infectious Diseases Department, La Paz University Hospital, Madrid, Spain
- Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - José M. Rodrigo-Muñoz
- Department of Immunology, IIS-Fundación Jiménez Díaz, Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Victoria del Pozo
- Department of Immunology, IIS-Fundación Jiménez Díaz, Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Cristina Calvo
- From the Paediatric Infectious Diseases Department, La Paz University Hospital, Madrid, Spain
- Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
- Translational Research Network in Pediatric Infectious Diseases (RITIP), Madrid, Spain
- CIBER de Enfermedades Infecciosas, CIBERINFEC, ISCIII, Madrid, Spain
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17
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Gut Microbiota and Metabolome Changes in Three Pulmonary Hypertension Rat Models. Microorganisms 2023; 11:microorganisms11020472. [PMID: 36838437 PMCID: PMC9959815 DOI: 10.3390/microorganisms11020472] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/07/2023] [Accepted: 02/08/2023] [Indexed: 02/16/2023] Open
Abstract
Dysbiosis of the gut microbiota and metabolites is found in both pulmonary hypertension patients and pulmonary hypertension rodent models. However, the exact changes in gut microbiota during the development of pulmonary hypertension is unclear. The function of the gut microbiota is also ambiguous. Here, this study showed that the gut microbiota was disrupted in rats with hypoxia (Hyp)-, hypoxia/Sugen5416 (HySu)-, and monocrotaline (MCT)-induced pulmonary hypertension. The gut microbiota is dynamically changed during the development of Hyp-, HySu-, and MCT-induced rat pulmonary hypertension. The variation in the α diversity of the gut microbiota in Hyp-induced pulmonary hypertension rats was similar to that in rats with MCT-induced pulmonary hypertension and different from that in rats with HySu-induced pulmonary hypertension. In addition, six plasma biomarkers, His, Ala, Ser, ADMA, 2-hydroxybutyric acid, and cystathionine, were identified in Hyp-induced pulmonary hypertension rats. Furthermore, a disease-associated network connecting Streptococcus with Hyp-induced pulmonary hypertension-associated metabolites was described here, including trimethylamine N-oxide, Asp, Asn, Lys, His, Ser, Pro, and Ile.
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18
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Rovira Rubió J, Megremis S, Pasioti M, Lakoumentas J, Constantinides B, Xepapadaki P, Bachert C, Finotto S, Jartti T, Andreakos E, Stanic B, Akdis CA, Akdis M, Papadopoulos NG. Respiratory virome profiles reflect antiviral immune responses. Allergy 2023; 78:1258-1268. [PMID: 36595290 DOI: 10.1111/all.15634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 12/01/2022] [Accepted: 12/11/2022] [Indexed: 01/04/2023]
Abstract
BACKGROUND From early life, respiratory viruses are implicated in the development, exacerbation and persistence of respiratory conditions such as asthma. Complex dynamics between microbial communities and host immune responses shape immune maturation and homeostasis, influencing health outcomes. We evaluated the hypothesis that the respiratory virome is linked to systemic immune responses, using peripheral blood and nasopharyngeal swab samples from preschool-age children in the PreDicta cohort. METHODS Peripheral blood mononuclear cells from 51 children (32 asthmatics and 19 healthy controls) participating in the 2-year multinational PreDicta cohort were cultured with bacterial (Bacterial-DNA, LPS) or viral (R848, Poly:IC, RV) stimuli. Supernatants were analysed by Luminex for the presence of 22 relevant cytokines. Virome composition was obtained using untargeted high throughput sequencing of nasopharyngeal samples. The metagenomic data were used for the characterization of virome profiles and the presence of key viral families (Picornaviridae, Anelloviridae, Siphoviridae). These were correlated to cytokine secretion patterns, identified through hierarchical clustering and principal component analysis. RESULTS High spontaneous cytokine release was associated with increased presence of Prokaryotic virome profiles and reduced presence of Eukaryotic and Anellovirus profiles. Antibacterial responses did not correlate with specific viral families or virome profile; however, low antiviral responders had more Prokaryotic and less Eukaryotic virome profiles. Anelloviruses and Anellovirus-dominated profiles were equally distributed among immune response clusters. The presence of Picornaviridae and Siphoviridae was associated with low interferon-λ responses. Asthma or allergy did not modify these correlations. CONCLUSION Antiviral cytokine responses at a systemic level reflect the upper airway virome composition. Individuals with low innate interferon responses have higher abundance of Picornaviruses (mostly Rhinoviruses) and bacteriophages. Bacteriophages, particularly Siphoviridae, appear to be sensitive sensors of host antimicrobial capacity, while Anelloviruses are not correlated with TLR-induced immune responses.
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Affiliation(s)
- Judit Rovira Rubió
- Division of Infection, Immunity & Respiratory Medicine, University of Manchester, Manchester, UK
| | - Spyridon Megremis
- Division of Infection, Immunity & Respiratory Medicine, University of Manchester, Manchester, UK
| | - Maria Pasioti
- Allergy Department, 2nd Pediatric Clinic, National and Kapodistrian University of Athens, Athens, Greece
| | - John Lakoumentas
- Allergy Department, 2nd Pediatric Clinic, National and Kapodistrian University of Athens, Athens, Greece
| | - Bede Constantinides
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Paraskevi Xepapadaki
- Allergy Department, 2nd Pediatric Clinic, National and Kapodistrian University of Athens, Athens, Greece
| | - Claus Bachert
- Upper Airway Research Laboratory, Ghent University Hospital, Ghent, Belgium
| | - Susetta Finotto
- Department of Molecular Pneumology, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Tuomas Jartti
- PEDEGO Research Unit, University of Oulu, Oulu, Finland.,Department of Pediatrics and Adolescent Medicine, University of Oulu, Oulu, Finland.,Department of Pediatrics and Adolescent Medicine, Turku University Hospital and University of Turku, Turku, Finland
| | | | - Barbara Stanic
- Swiss Institute of Allergy and Asthma Research (SIAF), University Zurich, Davos, Switzerland
| | - Cezmi A Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF), University Zurich, Davos, Switzerland
| | - Mübeccel Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF), University Zurich, Davos, Switzerland
| | - Nikolaos G Papadopoulos
- Division of Infection, Immunity & Respiratory Medicine, University of Manchester, Manchester, UK.,Allergy Department, 2nd Pediatric Clinic, National and Kapodistrian University of Athens, Athens, Greece
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19
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Luciola Zanette D, Andrade Coelho KBC, de Carvalho E, Aoki MN, Nardin JM, Araújo Lalli L, dos Santos Bezerra R, Giovanetti M, Simionatto Zucherato V, Montenegro de Campos G, de Souza Todão Bernardino J, Louis Viala V, Ciccozzi M, Junior Alcantara LC, Coccuzzo Sampaio S, Elias MC, Kashima S, Tadeu Covas D, Nanev Slavov S. Metagenomic insights into the plasma virome of Brazilian patients with prostate cancer. Mol Cell Oncol 2023; 10:2188858. [PMID: 36950183 PMCID: PMC10026895 DOI: 10.1080/23723556.2023.2188858] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
Growing evidence suggests that metavirome changes could be associated increased risk for malignant cell transformation. Considering Viruses have been proposed as factors for prostate cancer induction. The objective of this study was to examine the composition of the plasma metavirome of patients with prostate cancer. Blood samples were obtained from 49 male patients with primary prostate adenocarcinoma. Thirty blood donors were included as a control group. The obtained next-generation sequencing data were analyzed using a bioinformatic pipeline for virus metagenomics. Viral reads with higher abundance were assembled in contigs and analyzed taxonomically. Viral agents of interest were also confirmed by qPCR. Anelloviruses and the Human Pegivirus-1 (HPgV-1) were the most abundant component of plasma metavirome. Clinically important viruses like hepatitis C virus (HCV), cytomegalovirus and human adenovirus type C were also identified. In comparison, the blood donor virome was exclusively composed of torque teno virus types (TTV) types. The performed HPgV-1 and HCV phylogeny revealed that these viruses belong to commonly detected in Brazil genotypes. Our study sheds light on the plasma viral abundance in patients with prostatic cancer. The obtained viral diversity allowed us to separate the patients and controls, probably suggesting that malignant processes may influence virome composition. More complex and multiple approach investigations are necessary to examine the likely causal relationship between metavirome and its nvolvement in prostate cancer.
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Affiliation(s)
- Dalila Luciola Zanette
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (FIOCRUZ), Professor Algacyr Munhoz Mader, Curitiba, Parana, Brazil
| | | | | | - Mateus Nobrega Aoki
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (FIOCRUZ), Professor Algacyr Munhoz Mader, Curitiba, Parana, Brazil
| | | | - Larissa Araújo Lalli
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (FIOCRUZ), Professor Algacyr Munhoz Mader, Curitiba, Parana, Brazil
| | - Rafael dos Santos Bezerra
- Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Marta Giovanetti
- Department of Science and Technology for Humans and the Environment, University of Campus Bio-Medico di Roma, Rome, Italy
- Laboratory of Flaviviruses, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Victória Simionatto Zucherato
- Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Gabriel Montenegro de Campos
- Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | | | | | - Massimo Ciccozzi
- Epidemiology and Statistic Unit, University of Campus Bio-Medico di Roma, Rome, Italy
| | | | | | | | - Simone Kashima
- Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Dimas Tadeu Covas
- Butantan Institute, São Paulo, São Paulo, Brazil
- Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Svetoslav Nanev Slavov
- Butantan Institute, São Paulo, São Paulo, Brazil
- Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
- CONTACT Svetoslav Nanev Slavov Laboratory of Bioinformatics, Department of Biotechnology (NuCeL), Butantan Institute in Ribeirao Preto, 2501 Tenente Catao Roxo Street, Ribeirao Preto, Sao Paulo14051-140, Brazil
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20
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Beikzadeh B. A Deeper View of Early Life Microbiota and Hygiene Hypothesis Relationship: Reducing the Risk of Allergic Diseases is Dependent on the Permanent Presence of Good Microbiota throughout Life. Int J Prev Med 2023; 14:22. [PMID: 37033283 PMCID: PMC10080566 DOI: 10.4103/ijpvm.ijpvm_170_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 09/03/2022] [Indexed: 04/11/2023] Open
Affiliation(s)
- Babak Beikzadeh
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Sciences and Technology, University of Isfahan, Isfahan, Iran
- Address for correspondence: Dr. Babak Beikzadeh, Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Sciences and Technology, University of Isfahan, P. O. Box: 8174673441, Azadi square, Isfahan, Iran. E-mail:
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21
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Lunjani N, Walsh LJ, Venter C, Power M, MacSharry J, Murphy DM, O'Mahony L. Environmental influences on childhood asthma-The effect of diet and microbiome on asthma. Pediatr Allergy Immunol 2022; 33:e13892. [PMID: 36564884 PMCID: PMC10107834 DOI: 10.1111/pai.13892] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 11/13/2022] [Indexed: 12/12/2022]
Abstract
Early life dietary patterns and timely maturation of mucosa-associated microbial communities are important factors influencing immune development and for establishing robust immune tolerance networks. Microbial fermentation of dietary components in vivo generates a vast array of molecules, some of which are integral components of the molecular circuitry that regulates immune and metabolic functions. These in turn protect against aberrant inflammatory processes and promote effector immune responses that quickly eliminate pathogens. Multiple studies suggest that changes in dietary habits, altered microbiome composition, and microbial metabolism are associated with asthma risk and disease severity. While it remains unclear whether these microbiome alterations are a cause or consequence of dysregulated immune responses, there is significant potential for using diet in targeted manipulations of the gut microbiome and its metabolic functions in promoting immune health. In this article, we will summarize our knowledge to date on the role of dietary patterns and microbiome activities on immune responses within the airways. Given the malleability of the human microbiome, its integration into the immune system, and its responsiveness to diet, this makes it a highly attractive target for therapeutic and nutritional intervention in children with asthma.
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Affiliation(s)
- Nonhlanhla Lunjani
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,Department of Dermatology, University of Cape Town, Cape Town, South Africa
| | - Laura J Walsh
- Department of Respiratory Medicine, Cork University Hospital, Cork, Ireland
| | - Carina Venter
- Section of Allergy and Immunology, University of Colorado School of Medicine, Colorado, USA.,Children's Hospital Colorado, Colorado, USA
| | - Matthew Power
- School of Microbiology, University College Cork, Cork, Ireland.,Department of Medicine, University College Cork, Cork, Ireland
| | - John MacSharry
- School of Microbiology, University College Cork, Cork, Ireland.,Department of Medicine, University College Cork, Cork, Ireland
| | - Desmond M Murphy
- Department of Respiratory Medicine, Cork University Hospital, Cork, Ireland.,Clinical Research Facility, University College Cork, Cork, Ireland
| | - Liam O'Mahony
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland.,Department of Medicine, University College Cork, Cork, Ireland
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22
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Analysis of RNA virome in rectal swabs of healthy and diarrheic pigs of different age. Comp Immunol Microbiol Infect Dis 2022; 90-91:101892. [DOI: 10.1016/j.cimid.2022.101892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 10/04/2022] [Accepted: 10/05/2022] [Indexed: 11/23/2022]
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23
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Integrated Immunologic Monitoring in Solid Organ Transplantation: The Road Toward Torque Teno Virus-guided Immunosuppression. Transplantation 2022; 106:1940-1951. [PMID: 35509090 PMCID: PMC9521587 DOI: 10.1097/tp.0000000000004153] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Potent immunosuppressive drugs have been introduced into clinical care for solid organ transplant recipients. It is now time to guide these drugs on an individual level to optimize their efficacy. An ideal tool simultaneously detects overimmunosuppression and underimmunosuppression, is highly standardized, and is straightforward to implement into routine. Randomized controlled interventional trials are crucial to demonstrate clinical value. To date, proposed assays have mainly focused on the prediction of rejection and were based on the assessment of few immune compartments. Recently, novel tools have been introduced based on a more integrated approach to characterize the immune function and cover a broader spectrum of the immune system. In this respect, the quantification of the plasma load of a highly prevalent and apathogenic virus that might reflect the immune function of its host has been proposed: the torque teno virus (TTV). Although TTV control is driven by T cells, other major immune compartments might contribute to the hosts' response. A standardized in-house polymerase chain reaction and a conformité européenne-certified commercially available polymerase chain reaction are available for TTV quantification. TTV load is associated with rejection and infection in solid organ transplant recipients, and cutoff values for risk stratification of such events have been proposed for lung and kidney transplantation. Test performance of TTV load does not allow for the diagnosis of rejection and infection but is able to define at-risk patients. Hitherto TTV load has not been used in interventional settings, but two interventional randomized controlled trials are currently testing the safety and efficacy of TTV-guided immunosuppression.
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24
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Malik J, Ahmed S, Yaseen Z, Alanazi M, Alharby TN, Alshammari HA, Anwar S. Association of SARS-CoV-2 and Polypharmacy with Gut-Lung Axis: From Pathogenesis to Treatment. ACS OMEGA 2022; 7:33651-33665. [PMID: 36164411 PMCID: PMC9491241 DOI: 10.1021/acsomega.2c02524] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 08/29/2022] [Indexed: 06/12/2023]
Abstract
SARS-CoV-2 is a novel infectious contagion leading to COVID-19 disease. The virus has affected the lives of millions of people across the globe with a high mortality rate. It predominantly affects the lung (respiratory system), but it also affects other organs, including the cardiovascular, psychological, and gastrointestinal (GIT) systems. Moreover, elderly and comorbid patients with compromised organ functioning and pre-existing polypharmacy have worsened COVID-19-associated complications. Microbiota (MB) of the lung plays an important role in developing COVID-19. The extent of damage mainly depends on the predominance of opportunistic pathogens and, inversely, with the predominance of advantageous commensals. Changes in the gut MB are associated with a bidirectional shift in the interaction among the gut with a number of vital human organs, which leads to severe disease symptoms. This review focuses on dysbiosis in the gut-lung axis, COVID-19-induced worsening of comorbidities, and the influence of polypharmacy on MB.
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Affiliation(s)
- Jonaid
Ahmad Malik
- Department
of Pharmacology and Toxicology, National
Institute of Pharmaceutical Education and Research, Guwahati, Assam 781101, India
- Department
of Biomedical Engineering, Indian Institute
of Technology Rupnagar 140001, India
| | - Sakeel Ahmed
- Department
of Pharmacology and Toxicology, National
Institute of Pharmaceutical Education and Research, Ahmedabad, Gujarat 382355, India
| | - Zahid Yaseen
- Department
of Pharmaceutical Biotechnology, Delhi Pharmaceutical
Sciences and Research University, New Delhi, Delhi 110017, India
| | - Muteb Alanazi
- Department
of Clinical Pharmacy, College of Pharmacy, University of Hail, Hail 81422, Saudi Arabia
| | - Tareq Nafea Alharby
- Department
of Clinical Pharmacy, College of Pharmacy, University of Hail, Hail 81422, Saudi Arabia
| | | | - Sirajudheen Anwar
- Department
of Pharmacology and Toxicology, College of Pharmacy, University of Hail, Hail 81422, Saudi Arabia
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25
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Genome Sequences of Anelloviruses, Genomovirus, and Papillomavirus Isolated from Nasal Pharyngeal Swabs. Microbiol Resour Announc 2022; 11:e0068122. [PMID: 35972248 PMCID: PMC9476932 DOI: 10.1128/mra.00681-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The genome sequences of three anelloviruses (genus Alphatorquevirus), a genomovirus (genus Gemykolovirus), and an unclassified papillomavirus were identified in four human nasopharyngeal swabs, and one was positive for influenza A and one for influenza B virus. The influenza B virus-positive sample had a coinfection with an anellovirus and a papillomavirus.
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26
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Cosentino MAC, D’arc M, Moreira FRR, Cavalcante LTDF, Mouta R, Coimbra A, Schiffler FB, Miranda TDS, Medeiros G, Dias CA, Souza AR, Tavares MCH, Tanuri A, Soares MA, dos Santos AFA. Discovery of two novel Torque Teno viruses in Callithrix penicillata provides insights on Anelloviridae diversification dynamics. Front Microbiol 2022; 13:1002963. [PMID: 36160188 PMCID: PMC9493276 DOI: 10.3389/fmicb.2022.1002963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 08/18/2022] [Indexed: 11/13/2022] Open
Abstract
The development of high-throughput sequencing (HTS) technologies and metagenomics protocols deeply impacted the discovery of viral diversity. Moreover, the characterization of novel viruses in the Neotropical primates (NP) is central for the comprehension of viral evolution dynamics in those hosts, due to their evolutionary proximity to Old World primates, including humans. In the present work, novel anelloviruses were detected and characterized through HTS protocols in the NP Callithrix penicillata, the common black-tufted marmoset. De novo assembly of generated sequences was carried out, and a total of 15 contigs were identified with complete Anelloviridae ORF1 gene, two of them including a flanking GC-rich region, confirming the presence of two whole novel genomes of ~3 kb. The identified viruses were monophyletic within the Epsilontorquevirus genus, a lineage harboring previously reported anelloviruses infecting hosts from the Cebidae family. The genetic divergence found in the new viruses characterized two novel species, named Epsilontorquevirus callithrichensis I and II. The phylogenetic pattern inferred for the Epsilontorquevirus genus was consistent with the topology of their host species tree, echoing a virus-host diversification model observed in other viral groups. This study expands the host span of Anelloviridae and provides insights into their diversification dynamics, highlighting the importance of sampling animal viral genomes to obtain a clearer depiction of their long-term evolutionary processes.
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Affiliation(s)
- Matheus Augusto Calvano Cosentino
- Laboratório de Diversidade e Doenças Virais, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Mirela D’arc
- Laboratório de Diversidade e Doenças Virais, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Filipe Romero Rebello Moreira
- Laboratório de Diversidade e Doenças Virais, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Department of Infectious Diseases Epidemiology, Imperial College London, London, United Kingdom
| | | | - Ricardo Mouta
- Laboratório de Diversidade e Doenças Virais, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Amanda Coimbra
- Laboratório de Diversidade e Doenças Virais, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Francine Bittencourt Schiffler
- Laboratório de Diversidade e Doenças Virais, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Thamiris dos Santos Miranda
- Laboratório de Diversidade e Doenças Virais, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gabriel Medeiros
- Laboratório de Diversidade e Doenças Virais, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Cecilia A. Dias
- Centro de Primatologia, Universidade de Brasília, Brasília, Brazil
| | | | | | - Amilcar Tanuri
- Laboratório de Virologia Molecular, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marcelo Alves Soares
- Laboratório de Diversidade e Doenças Virais, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - André Felipe Andrade dos Santos
- Laboratório de Diversidade e Doenças Virais, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- *Correspondence: André Felipe Andrade dos Santos,
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27
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Zhou JJ, Ding WC, Liu YC, Gao YL, Xu L, Geng RL, Ye Y, Chai YF. Diagnostic Value of Metagenomic Next-Generation Sequencing for Pulmonary Infection in Intensive Care Unit and Non-Intensive Care Unit Patients. Front Cell Infect Microbiol 2022; 12:929856. [PMID: 36046746 PMCID: PMC9423675 DOI: 10.3389/fcimb.2022.929856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 06/13/2022] [Indexed: 11/17/2022] Open
Abstract
Objective To evaluate the diagnostic performance of metagenomic next-generation sequencing (mNGS) and culture in pathogen detection among intensive care unit (ICU) and non-ICU patients with suspected pulmonary infection. Methods In this prospective study, sputum samples were collected from patients with suspected pulmonary infection for 2 consecutive days and then subjected to DNA or RNA sequencing by mNGS or culture; 62 ICU patients and 60 non-ICU patients were admitted. In the end, comparisons were made on the pathogen species identified by mNGS and culture, the overall performance of these two methods in pathogen detection, and the most common pathogens detected by mNGS between the ICU and non-ICU groups. Results In DNA and RNA sequencing, the positive rate of pathogen detection reached 96.69% (117/121) and 96.43% (108/112), respectively. In culture tests, the positive rate of the pathogen was 39.34% (48/122), much lower than that of DNA and RNA sequencing. In general, the positive rate of pathogen detection by sputum mNGS was significantly higher than that of sputum culture in the total and non-ICU groups (p < 0.001) but did not show a significant difference when compared to the result of sputum culture in the ICU group (p = 0.08). Haemophilus spp., Candida albicans, Enterococcus spp., and viruses from the mNGS results were excluded before comparing the overall performance of these two methods in pathogen detection. Specifically, among the 10 most common bacteria implied from the mNGS results, significant differences were observed in the number of cases of Haemophilus parainfluenzae, Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa, Stenotrophomonas maltophilia, Staphylococcus aureus, and Enterococcus faecalis between the ICU and non-ICU groups (p < 0.05). Conclusions This study demonstrated the superiority of mNGS over culture in detecting all kinds of pathogen species in sputum samples. These results indicate that mNGS may serve as a valuable tool to identify pathogens, especially for ICU patients who are more susceptible to mixed infections.
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Affiliation(s)
- Jing-Jiang Zhou
- Department of Emergency Medicine, Tianjin Medical University General Hospital, Tianjin, China
- Department of Emergency Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Wei-Chao Ding
- Department of Emergency Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Yan-Cun Liu
- Department of Emergency Medicine, Tianjin Medical University General Hospital, Tianjin, China
| | - Yu-Lei Gao
- Department of Emergency Medicine, Tianjin Medical University General Hospital, Tianjin, China
| | - Lei Xu
- Department of Emergency Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Run-Lu Geng
- Department of Emergency Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Ying Ye
- Department of Emergency Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
- *Correspondence: Ying Ye, ; Yan-Fen Chai,
| | - Yan-Fen Chai
- Department of Emergency Medicine, Tianjin Medical University General Hospital, Tianjin, China
- *Correspondence: Ying Ye, ; Yan-Fen Chai,
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28
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Selma-Royo M, Calvo-Lerma J, Bäuerl C, Esteban-Torres M, Cabrera-Rubio R, Collado MC. Human milk microbiota: what did we learn in the last 20 years? MICROBIOME RESEARCH REPORTS 2022; 1:19. [PMID: 38046359 PMCID: PMC10688795 DOI: 10.20517/mrr.2022.05] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/06/2022] [Accepted: 04/29/2022] [Indexed: 12/05/2023]
Abstract
Human milk (HM) is the gold standard for infant nutrition during the first months of life. Beyond its nutritional components, its complex bioactive composition includes microorganisms, their metabolites, and oligosaccharides, which also contribute to gut colonization and immune system maturation. There is growing evidence of the beneficial effects of bacteria present in HM. However, current research presents limited data on the presence and functions of other organisms. The potential biological impacts on maternal and infant health outcomes, the factors contributing to milk microbes' variations, and the potential functions in the infant's gut remain unclear. This review provides a global overview of milk microbiota, what the actual knowledge is, and what the gaps and challenges are for the next years.
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Affiliation(s)
| | | | | | | | | | - Maria Carmen Collado
- Department of Biotechnology, Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Valencia 46980, Spain
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29
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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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Forqué L, Albert E, Giménez E, Torres I, Carbonell N, Ferreres J, Blasco ML, Navarro D. Monitoring of Torque Teno virus DNAemia in critically ill COVID-19 patients: May it help to predict clinical outcomes? J Clin Virol 2022; 148:105082. [PMID: 35091226 PMCID: PMC8783982 DOI: 10.1016/j.jcv.2022.105082] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 02/07/2023]
Abstract
Background : Torque teno virus (TTV) DNA load in plasma directly associates with the net state of immunosuppression and inflammation in different clinical settings, including transplantation and chronic inflammatory diseases. Objectives : We investigated whether plasma TTV DNA load may predict the occurrence of certain infectious events and overall mortality in critically ill COVID-19 patients. Patients and Methods : 50 patients (median age, 65.5 years) were recruited. TTV DNA load was quantitated in serial plasma specimens by real-time PCR. Serum levels of interleukin-6, C-reactive protein, ferritin, lactate dehydrogenase, Gamma-Glutamyl Transferase (GGT), alanine transaminase (ALT) and aspartate transaminase (AST) and absolute lymphocyte counts (ALC) in paired specimens were available. Nosocomial bloodstream infections and ventilator-associated pneumonia and overall mortality were the clinical outcomes. Results : TTV DNA was detected in 38 patients (76%). A weak inverse correlation (Rho=-0.28; P = 0.004) was observed between TTV DNA loads and ALC. No direct correlation was found between TTV DNA load and serum levels of any of the above biomarkers. Patients with detectable TTV DNA had an increased risk of subsequently developing infectious events (HR 9.28; 95% CI, 1.29–69.5; P = 0.03). A trend (P = 0.05) towards higher TTV DNA area under a curve between days 7 and 17 after ICU admission (AUC7–17) was observed in patients who died, as compared to survivors. Conclusion : Our findings suggested that plasma TTV DNA load monitoring may be helpful for predicting the occurrence of severe nosocomial infections and mortality in critically ill COVID-19 patients.
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The Human Virome: Viral Metagenomics, Relations with Human Diseases, and Therapeutic Applications. Viruses 2022; 14:v14020278. [PMID: 35215871 PMCID: PMC8876576 DOI: 10.3390/v14020278] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/20/2022] [Accepted: 01/25/2022] [Indexed: 02/07/2023] Open
Abstract
The human body is colonized by a wide range of microorganisms. The field of viromics has expanded since the first reports on the detection of viruses via metagenomic sequencing in 2002. With the continued development of reference materials and databases, viral metagenomic approaches have been used to explore known components of the virome and discover new viruses from various types of samples. The virome has attracted substantial interest since the outbreak of the coronavirus disease 2019 (COVID-19) pandemic. Increasing numbers of studies and review articles have documented the diverse virome in various sites in the human body, as well as interactions between the human host and the virome with regard to health and disease. However, there have been few studies of direct causal relationships. Viral metagenomic analyses often lack standard references and are potentially subject to bias. Moreover, most virome-related review articles have focused on the gut virome and did not investigate the roles of the virome in other sites of the body in human disease. This review presents an overview of viral metagenomics, with updates regarding the relations between alterations in the human virome and the pathogenesis of human diseases, recent findings related to COVID-19, and therapeutic applications related to the human virome.
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Cardelli E, Calvigioni M, Vecchione A, Macera L, Mazzantini D, Celandroni F, Panattoni A, Pistello M, Maggi F, Ghelardi E, Mannella P. Delivery Mode Shapes the Composition of the Lower Airways Microbiota in Newborns. Front Cell Infect Microbiol 2022; 11:808390. [PMID: 35004360 PMCID: PMC8733567 DOI: 10.3389/fcimb.2021.808390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 12/10/2021] [Indexed: 12/12/2022] Open
Abstract
Radical alterations in the human microbiota composition are well-known to be associated with many pathological conditions. If these aberrations are established at the time of birth, the risk of developing correlated pathologies throughout life is significantly increased. For this reason, all newborns should begin their lives with a proper microbiota in each body district. The present study aimed at demonstrating a correlation between the mode of delivery and the development of a well-balanced microbiota in the lower airways of newborns. 44 pregnant women were enrolled in this study. Microbiological comparative analysis was carried out on tracheobronchial secretions of babies born through vaginal delivery (VD) or caesarean section (CS). All samples showed the presence of bacterial DNA, regardless of the mode of delivery. No viable cultivable bacteria were isolated from the CS samples. On the contrary, VD allowed colonization of the lower airways by alive cultivable bacteria. The identification of bacterial species revealed that Lactobacillus spp. and Bacteroides vulgatus were the most common microorganisms in the lower airways of vaginally-delivered newborns. Data obtained from quantitative PCRs showed a significantly higher total bacterial load, as well as Firmicutes and Lactobacillus spp. amount, in VD samples than CS ones, while no statistically significant difference was found in Torque Teno Virus (TTV) load between samples. Taken together, our findings confirm the hypothesis that passage through the maternal vaginal canal determines more beneficial colonization of the lower airways in newborns.
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Affiliation(s)
- Elisa Cardelli
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Marco Calvigioni
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | | | - Lisa Macera
- Microbiology Unit, Azienda Ospedaliera Universitaria Pisana, Pisa, Italy
| | - Diletta Mazzantini
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Francesco Celandroni
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Adelaide Panattoni
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Mauro Pistello
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Fabrizio Maggi
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Emilia Ghelardi
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Paolo Mannella
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
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Mallet F, Diouf L, Meunier B, Perret M, Reynier F, Leissner P, Quemeneur L, Griffiths AD, Moucadel V, Pachot A, Venet F, Monneret G, Lepape A, Rimmelé T, Tan LK, Brengel-Pesce K, Textoris J. Herpes DNAemia and TTV Viraemia in Intensive Care Unit Critically Ill Patients: A Single-Centre Prospective Longitudinal Study. Front Immunol 2021; 12:698808. [PMID: 34795661 PMCID: PMC8593420 DOI: 10.3389/fimmu.2021.698808] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 10/12/2021] [Indexed: 11/21/2022] Open
Abstract
Introduction We analysed blood DNAemia of TTV and four herpesviruses (CMV, EBV, HHV6, and HSV-1) in the REAnimation Low Immune Status Marker (REALISM) cohort of critically ill patients who had presented with either sepsis, burns, severe trauma, or major surgery. The aim was to identify common features related to virus and injury-associated pathologies and specific features linking one or several viruses to a particular pathological context. Methods Overall and individual viral DNAemia were measured over a month using quantitative PCR assays from the 377 patients in the REALISM cohort. These patients were characterised by clinical outcomes [severity scores, mortality, Intensive Care Unit (ICU)-acquired infection (IAI)] and 48 parameters defining their host response after injury (cell populations, immune functional assays, and biomarkers). Association between viraemic event and clinical outcomes or immune markers was assessed using χ2-test or exact Fisher’s test for qualitative variables and Wilcoxon test for continuous variables. Results The cumulative incidence of viral DNAemia increased from below 4% at ICU admission to 35% for each herpesvirus during the first month. EBV, HSV1, HHV6, and CMV were detected in 18%, 12%, 10%, and 9% of patients, respectively. The incidence of high TTV viraemia (>10,000 copies/ml) increased from 11% to 15% during the same period. Herpesvirus viraemia was associated with severity at admission; CMV and HHV6 viraemia correlated with mortality during the first week and over the month. The presence of individual herpesvirus during the first month was significantly associated (p < 0.001) with the occurrence of IAI, whilst herpesvirus DNAemia coupled with high TTV viraemia during the very first week was associated with IAI. Herpesvirus viraemia was associated with a lasting exacerbated host immune response, with concurrent profound immune suppression and hyper inflammation, and delayed return to immune homeostasis. The percentage of patients presenting with herpesvirus DNAemia was significantly higher in sepsis than in all other groups. Primary infection in the hospital and high IL10 levels might favour EBV and CMV reactivation. Conclusion In this cohort of ICU patients, phenotypic differences were observed between TTV and herpesviruses DNAemia. The higher prevalence of herpesvirus DNAemia in sepsis hints at further studies that may enable a better in vivo understanding of host determinants of herpesvirus viral reactivation. Furthermore, our data suggest that EBV and TTV may be useful as additional markers to predict clinical deterioration in ICU patients.
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Affiliation(s)
- François Mallet
- EA 7426 "Pathophysiology of Injury-Induced Immunosuppression" (Université Claude Bernard Lyon 1-Hospices Civils de Lyon-bioMérieux), Joint Research Unit HCL-bioMérieux, Immunology Laboratory & Anesthesia and Critical Care Medicine Department, Hospices Civils de Lyon, Edouard Herriot Hospital, Lyon, France
| | - Léa Diouf
- EA 7426 "Pathophysiology of Injury-Induced Immunosuppression" (Université Claude Bernard Lyon 1-Hospices Civils de Lyon-bioMérieux), Joint Research Unit HCL-bioMérieux, Immunology Laboratory & Anesthesia and Critical Care Medicine Department, Hospices Civils de Lyon, Edouard Herriot Hospital, Lyon, France.,IVIDATA, Levallois-Perret, France
| | - Boris Meunier
- EA 7426 "Pathophysiology of Injury-Induced Immunosuppression" (Université Claude Bernard Lyon 1-Hospices Civils de Lyon-bioMérieux), Joint Research Unit HCL-bioMérieux, Immunology Laboratory & Anesthesia and Critical Care Medicine Department, Hospices Civils de Lyon, Edouard Herriot Hospital, Lyon, France.,Soladis Inc., Cambridge, MA, United States
| | - Magali Perret
- BIOASTER Technology Research Institute, Lyon, France
| | | | | | | | - Andrew D Griffiths
- Laboratoire de Biochimie (LBC), École Supérieure de Physique et de Chimie Industrielles de la ville de Paris (ESPCI) Paris, Paris Sciences & Lettres (PSL) Université, Centre National de la Recherche Scientifique (CNRS) UMR8231, Paris, France
| | - Virginie Moucadel
- EA 7426 "Pathophysiology of Injury-Induced Immunosuppression" (Université Claude Bernard Lyon 1-Hospices Civils de Lyon-bioMérieux), Joint Research Unit HCL-bioMérieux, Immunology Laboratory & Anesthesia and Critical Care Medicine Department, Hospices Civils de Lyon, Edouard Herriot Hospital, Lyon, France
| | - Alexandre Pachot
- EA 7426 "Pathophysiology of Injury-Induced Immunosuppression" (Université Claude Bernard Lyon 1-Hospices Civils de Lyon-bioMérieux), Joint Research Unit HCL-bioMérieux, Immunology Laboratory & Anesthesia and Critical Care Medicine Department, Hospices Civils de Lyon, Edouard Herriot Hospital, Lyon, France
| | - Fabienne Venet
- EA 7426 "Pathophysiology of Injury-Induced Immunosuppression" (Université Claude Bernard Lyon 1-Hospices Civils de Lyon-bioMérieux), Joint Research Unit HCL-bioMérieux, Immunology Laboratory & Anesthesia and Critical Care Medicine Department, Hospices Civils de Lyon, Edouard Herriot Hospital, Lyon, France
| | - Guillaume Monneret
- EA 7426 "Pathophysiology of Injury-Induced Immunosuppression" (Université Claude Bernard Lyon 1-Hospices Civils de Lyon-bioMérieux), Joint Research Unit HCL-bioMérieux, Immunology Laboratory & Anesthesia and Critical Care Medicine Department, Hospices Civils de Lyon, Edouard Herriot Hospital, Lyon, France
| | - Alain Lepape
- EA 7426 "Pathophysiology of Injury-Induced Immunosuppression" (Université Claude Bernard Lyon 1-Hospices Civils de Lyon-bioMérieux), Joint Research Unit HCL-bioMérieux, Immunology Laboratory & Anesthesia and Critical Care Medicine Department, Hospices Civils de Lyon, Edouard Herriot Hospital, Lyon, France
| | - Thomas Rimmelé
- EA 7426 "Pathophysiology of Injury-Induced Immunosuppression" (Université Claude Bernard Lyon 1-Hospices Civils de Lyon-bioMérieux), Joint Research Unit HCL-bioMérieux, Immunology Laboratory & Anesthesia and Critical Care Medicine Department, Hospices Civils de Lyon, Edouard Herriot Hospital, Lyon, France
| | | | - Karen Brengel-Pesce
- EA 7426 "Pathophysiology of Injury-Induced Immunosuppression" (Université Claude Bernard Lyon 1-Hospices Civils de Lyon-bioMérieux), Joint Research Unit HCL-bioMérieux, Immunology Laboratory & Anesthesia and Critical Care Medicine Department, Hospices Civils de Lyon, Edouard Herriot Hospital, Lyon, France
| | - Julien Textoris
- EA 7426 "Pathophysiology of Injury-Induced Immunosuppression" (Université Claude Bernard Lyon 1-Hospices Civils de Lyon-bioMérieux), Joint Research Unit HCL-bioMérieux, Immunology Laboratory & Anesthesia and Critical Care Medicine Department, Hospices Civils de Lyon, Edouard Herriot Hospital, Lyon, France
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Studenic P, Bond G, Kerschbaumer A, Bécède M, Pavelka K, Karateev D, Stieger J, Puchner R, Mueller RB, Puchhammer-Stöckl E, Durechova M, Loiskandl M, Perkmann T, Olejarova M, Luchikhina E, Steiner CW, Bonelli M, Smolen JS, Aletaha D. Torque Teno Virus Quantification for Monitoring of Immunomodulation with Biological Compounds in the Treatment of Rheumatoid Arthritis. Rheumatology (Oxford) 2021; 61:2815-2825. [PMID: 34792562 DOI: 10.1093/rheumatology/keab839] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 11/02/2021] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES Rheumatoid arthritis (RA) patients who fail to respond to methotrexate (MTX) can receive biologic disease-modifying antirheumatic drugs (bDMARDs). The Torque Teno Virus (TTV) is a potential novel candidate for monitoring of immunosuppression. We explore TTV in these patients and association with clinical response to bDMARDs. METHODS The BioBio Study is a multicentre randomized open-label trial, including RA patients with insufficient response to MTX. Patients were randomized to either TNFi (infliximab, INF), anti-IL-6 (tocilizumab, TCZ), CTLA4-Ig (abatacept, ABA) or anti-CD20 (rituximab, RTX) in addition to MTX. PCR was used to quantify TTV in the peripheral blood. RESULTS TTV was measured in 95 patients (INF, n = 23; TCZ, n = 22; ABA, n = 27; RTX; n = 23). TTV increased by a median of 4.5*104 copies/ml (c/ml; inter quartile range [IQR] 0-7.5*105) after 3 months. TTV levels at month 3 were associated with SDAI (p= 0.03) and CDAI response (p= 0.026) at month 6. A TTV cut-off level of 1.2*106 c/ml at month 3 had a positive likelihood ratio of 2.7 for prediction of SDAI85% response at month 6. CONCLUSION Our data suggest that TTV levels increase upon TNF, CD20 and co-stimulation blockade and associate with clinical response to bDMARDs in RA patients. TRIAL REGISTRATION ClinicalTrials.gov; https://clinicaltrials.gov; NCT01638715.
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Affiliation(s)
- Paul Studenic
- Department of Internal Medicine 3, Division of Rheumatology, Medical University of Vienna, Austria.,Division of Rheumatology, Department of Medicine (Solna), Karolinska Institutet, Sweden
| | - Gregor Bond
- Division of Nephrology and Dialysis, Medical University of Vienna, Austria
| | - Andreas Kerschbaumer
- Department of Internal Medicine 3, Division of Rheumatology, Medical University of Vienna, Austria
| | - Manuel Bécède
- Department of Internal Medicine 3, Division of Rheumatology, Medical University of Vienna, Austria
| | - Karel Pavelka
- Institute of Rheumatology, Prague, Czech Republic.,Department of Rheumatology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Dmitry Karateev
- Department of Rheumatology, Moscow Regional Research and Clinical Institute (MONIKI), Russia
| | - Jutta Stieger
- 2nd Department of Medicine, Hietzing Hospital, Austria
| | | | - Ruediger B Mueller
- Cantonal Hospital Lucerne, Division of Rheumatology, Medical University Department, Rheumazentrum Ostschweiz St. Gallen, Switzerland
| | | | - Martina Durechova
- Department of Internal Medicine 3, Division of Rheumatology, Medical University of Vienna, Austria
| | - Michaela Loiskandl
- Department of Internal Medicine 3, Division of Rheumatology, Medical University of Vienna, Austria
| | - Thomas Perkmann
- Department of Laboratory Medicine, Medical University of Vienna, Austria
| | - Martina Olejarova
- Institute of Rheumatology, Prague, Czech Republic.,Department of Rheumatology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Elena Luchikhina
- Department of Rheumatology, Moscow Regional Research and Clinical Institute (MONIKI), Russia
| | - Carl-Walter Steiner
- Department of Internal Medicine 3, Division of Rheumatology, Medical University of Vienna, Austria
| | - Michael Bonelli
- Department of Internal Medicine 3, Division of Rheumatology, Medical University of Vienna, Austria
| | - Josef S Smolen
- Department of Internal Medicine 3, Division of Rheumatology, Medical University of Vienna, Austria
| | - Daniel Aletaha
- Department of Internal Medicine 3, Division of Rheumatology, Medical University of Vienna, Austria
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Goolam Mahomed T, Peters RPH, Allam M, Ismail A, Mtshali S, Goolam Mahomed A, Ueckermann V, Kock MM, Ehlers MM. Lung microbiome of stable and exacerbated COPD patients in Tshwane, South Africa. Sci Rep 2021; 11:19758. [PMID: 34611216 PMCID: PMC8492659 DOI: 10.1038/s41598-021-99127-w] [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: 01/27/2021] [Accepted: 09/14/2021] [Indexed: 02/08/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is characterised by the occurrence of exacerbations triggered by infections. The aim of this study was to determine the composition of the lung microbiome and lung virome in patients with COPD in an African setting and to compare their composition between the stable and exacerbated states. Twenty-four adult COPD patients were recruited from three hospitals. Sputum was collected and bacterial DNA was extracted. Targeted metagenomics was performed to determine the microbiome composition. Viral DNA and RNA were extracted from selected samples followed by cDNA conversion. Shotgun metagenomics sequencing was performed on pooled DNA and RNA. The most abundant phyla across all samples were Firmicutes and Proteobacteria. The following genera were most prevalent: Haemophilus and Streptococcus. There were no considerable differences for alpha and beta diversity measures between the disease states. However, a difference in the abundances between disease states was observed for: (i) Serratia (3% lower abundance in exacerbated state), (ii) Granulicatella (2.2% higher abundance in exacerbated state), (iii) Haemophilus (5.7% higher abundance in exacerbated state) and (iv) Veillonella (2.5% higher abundance in exacerbated state). Virome analysis showed a high abundance of the BeAn 58058 virus, a member of the Poxviridae family, in all six samples (90% to 94%). This study is among the first to report lung microbiome composition in COPD patients from Africa. In this small sample set, no differences in alpha or beta diversity between stable and exacerbated disease state was observed, but an unexpectedly high frequency of BeAn 58058 virus was observed. These observations highlight the need for further research of the lung microbiome of COPD patients in African settings.
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Affiliation(s)
- T. Goolam Mahomed
- grid.49697.350000 0001 2107 2298Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
| | - R. P. H. Peters
- grid.49697.350000 0001 2107 2298Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa ,grid.442327.40000 0004 7860 2538Foundation for Professional Development, Research Unit, East London, South Africa
| | - M. Allam
- grid.416657.70000 0004 0630 4574National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - A. Ismail
- grid.416657.70000 0004 0630 4574National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - S. Mtshali
- grid.416657.70000 0004 0630 4574National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | | | - V. Ueckermann
- grid.49697.350000 0001 2107 2298Department of Internal Medicine, University of Pretoria, Pretoria, South Africa
| | - M. M. Kock
- grid.49697.350000 0001 2107 2298Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa ,grid.416657.70000 0004 0630 4574Department of Medical Microbiology, Tshwane Academic Division, National Health Laboratory Service, Johannesburg, South Africa
| | - M. M. Ehlers
- grid.49697.350000 0001 2107 2298Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa ,grid.416657.70000 0004 0630 4574Department of Medical Microbiology, Tshwane Academic Division, National Health Laboratory Service, Johannesburg, South Africa
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Teijeiro A, Gómez RM. Wheezing-Related Relevant Factors and the Role of Viral Bronchiolitis. FRONTIERS IN ALLERGY 2021; 2:726972. [PMID: 35387057 PMCID: PMC8974738 DOI: 10.3389/falgy.2021.726972] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 09/01/2021] [Indexed: 12/17/2022] Open
Abstract
Bronchiolitis is a virus-associated infection of the lower respiratory tract exhibiting signs and symptoms of airway obstruction. Respiratory Syncytial Virus (RSV) is responsible in most cases; however, different rhinoviruses have also been implicated. Specific viruses and time until the first infection, severity of the respiratory condition, and atopic status have a determinant role in the recurrence of wheezing and asthma development. Genetics, lung function, atopic condition, the role of microbiota and environment, pollution, and obesity are considered in the present review. Emergency room visits and hospitalizations because of severe wheezing and smoking during pregnancy among others were identified as risk factors for significant morbidity in our population. Approaching determinant conditions like genetics, allergy, antiviral immunity, and environmental exposures such as farm vs. urban and viral virulence provides an opportunity to minimize morbidity of viral illness and asthma in children.
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Affiliation(s)
- Alvaro Teijeiro
- Respiratory Department, Children's Hospital, Córdoba, Argentina
| | - R. Maximiliano Gómez
- School of Health Sciences, Catholic University of Salta, Salta, Argentina
- *Correspondence: R. Maximiliano Gómez ; orcid.org/0000-0001-6898-186X
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Abstract
The healthy lung was long thought of as sterile, but recent advances using molecular sequencing approaches have detected bacteria at low levels. Healthy lung bacteria largely reflect communities present in the upper respiratory tract that enter the lung via microaspiration, which is balanced by mechanical and immune clearance and likely involves limited local replication. The nature and dynamics of the lung microbiome, therefore, differ from those of ecological niches with robust self-sustaining microbial communities. Aberrant populations (dysbiosis) have been demonstrated in many pulmonary diseases not traditionally considered microbial in origin, and potential pathways of microbe-host crosstalk are emerging. The question now is whether and how dysbiotic microbiota contribute to initiation or perpetuation of injury. The fungal microbiome and virome are less well studied. This Review highlights features of the lung microbiome, unique considerations in studying it, examples of dysbiosis in selected disease, emerging concepts in lung microbiome-host interactions, and critical areas for investigation.
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Arze CA, Springer S, Dudas G, Patel S, Bhattacharyya A, Swaminathan H, Brugnara C, Delagrave S, Ong T, Kahvejian A, Echelard Y, Weinstein EG, Hajjar RJ, Andersen KG, Yozwiak NL. Global genome analysis reveals a vast and dynamic anellovirus landscape within the human virome. Cell Host Microbe 2021; 29:1305-1315.e6. [PMID: 34320399 DOI: 10.1016/j.chom.2021.07.001] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 04/23/2021] [Accepted: 06/11/2021] [Indexed: 12/14/2022]
Abstract
Anelloviruses are a ubiquitous component of healthy human viromes and remain highly prevalent after being acquired early in life. The full extent of "anellome" diversity and its evolutionary dynamics remain unexplored. We employed in-depth sequencing of blood-transfusion donor(s)-recipient pairs coupled with public genomic resources for a large-scale assembly of anellovirus genomes and used the data to characterize global and personal anellovirus diversity through time. The breadth of the anellome is much greater than previously appreciated, and individuals harbor unique anellomes and transmit lineages that can persist for several months within a diverse milieu of endemic host lineages. Anellovirus sequence diversity is shaped by extensive recombination at all levels of divergence, hindering traditional phylogenetic analyses. Our findings illuminate the transmission dynamics and vast diversity of anelloviruses and set the foundation for future studies to characterize their biology.
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Affiliation(s)
| | | | - Gytis Dudas
- Gothenburg Global Biodiversity Centre, Gothenburg 413 19, Sweden
| | | | | | | | - Carlo Brugnara
- Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Tuyen Ong
- Ring Therapeutics, Cambridge, MA 02139, USA
| | - Avak Kahvejian
- Ring Therapeutics, Cambridge, MA 02139, USA; Flagship Pioneering, Cambridge, MA 02142, USA
| | - Yann Echelard
- Ring Therapeutics, Cambridge, MA 02139, USA; Flagship Pioneering, Cambridge, MA 02142, USA
| | - Erica G Weinstein
- Ring Therapeutics, Cambridge, MA 02139, USA; Flagship Pioneering, Cambridge, MA 02142, USA
| | - Roger J Hajjar
- Ring Therapeutics, Cambridge, MA 02139, USA; Flagship Pioneering, Cambridge, MA 02142, USA
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Dodi G, Attanasi M, Di Filippo P, Di Pillo S, Chiarelli F. Virome in the Lungs: The Role of Anelloviruses in Childhood Respiratory Diseases. Microorganisms 2021; 9:microorganisms9071357. [PMID: 34201449 PMCID: PMC8307813 DOI: 10.3390/microorganisms9071357] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/17/2021] [Accepted: 06/21/2021] [Indexed: 12/24/2022] Open
Abstract
More recently, increasing attention has been directed to exploring the function of the global virome in health and disease. Currently, by new molecular techniques, such as metagenomic DNA sequencing, the virome has been better unveiled. By investigating the human lung virome, we could provide novel insights into respiratory diseases. The virome, as a part of the microbiome, is characterized by a constant change in composition related to the type of diet, environment, and our genetic code, and other incalculable factors. The virome plays a substantial role in modulating human immune defenses and contributing to the inflammatory processes. Anelloviruses (AVs) are new components of the virome. AVs are already present during early life and reproduce without apparently causing harm to the host. The role of AVs is still unknown, but several reports have shown that AVs could activate the inflammasomes, intracellular multiprotein oligomers of the innate immune system, which show a crucial role in the host defense to several pathogens. In this narrative revision, we summarize the epidemiological data related to the possible link between microbial alterations and chronic respiratory diseases in children. Briefly, we also describe the characteristics of the most frequent viral family present in the lung virome, Anelloviridae. Furthermore, we discuss how AVs could modulate the immune system in children, affecting the development of chronic respiratory diseases, particularly asthma, the most common chronic inflammatory disease in childhood.
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Federico MJ, Denlinger LC, Corren J, Szefler SJ, Fuhlbrigge AL. Exacerbation-Prone Asthma: A Biological Phenotype or a Social Construct. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY-IN PRACTICE 2021; 9:2627-2634. [PMID: 34051392 DOI: 10.1016/j.jaip.2021.05.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 05/17/2021] [Accepted: 05/19/2021] [Indexed: 12/14/2022]
Abstract
Asthma is a complex syndrome with multiple phenotypes and endotypes. Asthma exacerbations are not only the clearest indictor of the morbidity of asthma and of the risk for mortality due to asthma, but also comprise a significant amount of the cost to care for poorly controlled asthma. There continues to be significant disparity in the prevalence, mortality, and morbidity due to asthma. Patients with asthma who suffer recurrent exacerbations are considered to have exacerbation-prone asthma (EPA). Efforts to characterize patients with frequent exacerbations show that the etiology is likely multifactorial. Research to determine the intrinsic risk factors for EPA include studies of both genetic and inflammatory biomarkers. External factors contributing to exacerbations have been extensively reviewed and include viral infection, environmental exposures, air pollution, and psychosocial and economic barriers to optimizing health. It is likely that EPA occurs when patients who have an increased underlying intrinsic/biological risk are placed in a given exposome (environments with a variety of exposures and triggers including allergens, pollution, stress, barriers, and occupational exposures). It is the social construct combined with underlying biology that frequently drives an EPA phenotype.
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Affiliation(s)
- Monica J Federico
- The Breathing Institute, Children's Hospital Colorado, and Department of Pediatrics, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colo.
| | - Loren C Denlinger
- Division of Allergy, Pulmonary, and Critical Care Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wis
| | - Jonathan Corren
- Departments of Medicine and Pediatrics, Divisions of Allergy and Clinical Immunology, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, Calif
| | - Stanley J Szefler
- The Breathing Institute, Children's Hospital Colorado, and Department of Pediatrics, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colo
| | - Anne L Fuhlbrigge
- Pulmonary Sciences and Critical Care, Department of Medicine, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colo
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Application of metagenomic next-generation sequencing in the diagnosis and treatment guidance of Pneumocystis jirovecii pneumonia in renal transplant recipients. Eur J Clin Microbiol Infect Dis 2021; 40:1933-1942. [PMID: 33880744 PMCID: PMC8057919 DOI: 10.1007/s10096-021-04254-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 04/13/2021] [Indexed: 11/19/2022]
Abstract
Pneumocystis jirovecii pneumonia (PJP) is difficult to be diagnosed, so this study explored if PJP could be diagnosed by metagenomic next-generation sequencing (mNGS) and if mNGS could guide the therapy of PJP. mNGS was successfully diagnosed 13 out of 14 PJP recipients with 11 through peripheral blood samples, verified by PCR. Ten non-PJP recipients were enrolled as the control group. Blood tests revealed a high β-D-glucan (BDG) level in all recipients with PJP during the hospitalization. Four (28.6%) of 14 PJP patients were infected with cytomegalovirus simultaneously, while 8 (57.1%) suffered from a combined infection caused by Torque teno virus. Five (35.7%) of 14 cases died of PJP or the subsequent bacteremias/bacterial pneumonia with a longer interval between the onset and diagnosis of/the available therapy against PJP than survival cases. Univariate analysis of characteristics between PJP and non-PJP recipients revealed that BDG assays was higher at the admission in PJP group (P =0.011). This present study supports the value of mNGS detection of blood sample in diagnosing PJP, which could assist clinical decision for therapy against PJ and improve outcome of PJP. The study also highlights the sensitivity of BDG assays. Cytomegalovirus and Torque teno virus infections often occur at the same time of PJP, thus can be alerts of PJP.
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Taboada B, Morán P, Serrano-Vázquez A, Iša P, Rojas-Velázquez L, Pérez-Juárez H, López S, Torres J, Ximenez C, Arias CF. The gut virome of healthy children during the first year of life is diverse and dynamic. PLoS One 2021; 16:e0240958. [PMID: 33852569 PMCID: PMC8046192 DOI: 10.1371/journal.pone.0240958] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 03/30/2021] [Indexed: 01/21/2023] Open
Abstract
In this work, we determined the diversity and dynamics of the gut virome of infants during the first year of life. Fecal samples were collected monthly, from birth to one year of age, from three healthy children living in a semi-rural village in Mexico. Most of the viral reads were classified into six families of bacteriophages including five dsDNA virus families of the order Caudovirales, with Siphoviridae and Podoviridae being the most abundant. Eukaryotic viruses were detected as early as two weeks after birth and remained present all along the first year of life. Thirty-four different eukaryotic virus families were found, where eight of these families accounted for 98% of all eukaryotic viral reads: Anelloviridae, Astroviridae, Caliciviridae, Genomoviridae, Parvoviridae, Picornaviridae, Reoviridae and the plant-infecting viruses of the Virgaviridae family. Some viruses in these families are known human pathogens, and it is surprising that they were found during the first year of life in infants without gastrointestinal symptoms. The eukaryotic virus species richness found in this work was higher than that observed in previous studies; on average between 7 and 24 virus species were identified per sample. The richness and abundance of the eukaryotic virome significantly increased during the second semester of life, probably because of an increased environmental exposure of infants with age. Our findings suggest an early and permanent contact of infants with a diverse array of bacteriophages and eukaryotic viruses, whose composition changes over time. The bacteriophages and eukaryotic viruses found in these children could represent a metastable virome, whose potential influence on the development of the infant's immune system or on the health of the infants later in life, remains to be investigated.
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Affiliation(s)
- Blanca Taboada
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Patricia Morán
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Angélica Serrano-Vázquez
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Pavel Iša
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Liliana Rojas-Velázquez
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Horacio Pérez-Juárez
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Susana López
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Javier Torres
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México
- * E-mail: (CFA); (CX); (JT)
| | - Cecilia Ximenez
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
- * E-mail: (CFA); (CX); (JT)
| | - Carlos F. Arias
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
- * E-mail: (CFA); (CX); (JT)
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Abstract
INTRODUCTION To test whether parechovirus and anellovirus, frequent enteric viruses, were associated with subsequent celiac disease (CD). We hypothesized that children who later developed CD would have increased frequency of parechovirus infections before transglutaminase 2 (TG2) antibody development. Anellovirus testing was exploratory, as a potential marker of immune status. METHODS Matched case-control design nested within a longitudinal birth cohort (the MIDIA study) of children at genetic risk of CD (carrying the human leukocyte antigen genotype DR4-DQ8/DR3-DQ2, recruited throughout Norway during 2001-2007). We retrospectively tested blood samples taken at age 3, 6, 9, and 12 months, and then annually, to determine when TG2 antibodies developed. Of 220 genetically at-risk children tested, 25 were diagnosed with CD (cases; ESPGHAN 2012 criteria) and matched for follow-up time, birthdate, and county of residence with 2 randomly selected children free from CD (controls) from the cohort. Viruses were quantified in monthly stool samples (collected from 3 through 35 months of age) using real-time polymerase chain reaction methods. RESULTS Parechovirus was detected in 222 of 2,005 stool samples (11.1%) and was more frequent in samples from cases before developing TG2 antibodies (adjusted odds ratio 1.67, 95% confidence interval 1.14-2.45, P = 0.01). The odds ratio was higher when a sample was positive for both parechovirus and enterovirus (adjusted odds ratio 4.73, 95% confidence interval 1.26-17.67, P = 0.02). Anellovirus was detected in 1,540 of 1,829 samples (84.2%), but did not differ significantly between case and control subjects. DISCUSSION Early-life parechovirus infections were associated with development of CD in genetically at-risk children.
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Uhl P, Heilos A, Bond G, Meyer E, Böhm M, Puchhammer-Stöckl E, Arbeiter K, Müller-Sacherer T, Csaicsich D, Aufricht C, Rusai K. Torque teno viral load reflects immunosuppression in paediatric kidney-transplanted patients-a pilot study. Pediatr Nephrol 2021; 36:153-162. [PMID: 32524259 PMCID: PMC7701084 DOI: 10.1007/s00467-020-04606-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/01/2020] [Accepted: 05/08/2020] [Indexed: 12/16/2022]
Abstract
BACKGROUND Chronic deterioration of kidney graft function is related to inadequate immunosuppression (IS). A novel tool to assess the individual net state of IS in transplanted patients might be the monitoring of Torque teno virus (TTV) viral load. TTV is a non-pathogen virus detectable in almost all individuals. TTV level in the peripheral blood has been linked to the immune-competence of its host and should thus reflect IS after solid organ transplantation. METHODS TTV plasma load was quantified monthly by RT-PCR for a period of 1 year in 45 kidney-transplanted children. Post-transplant time was at least 3 months. The relation of the virus DNA levels to IS and transplant-specific clinical and laboratory parameters was analysed longitudinally. RESULTS TTV DNA was detectable in 94.5% of the plasma samples. There was a significant association with the post-transplant follow-up time as well as with the type of IS regimen, with lower virus loads in patients after longer post-transplant time and mTOR inhibitor-based IS. Furthermore, a significant positive correlation with the dose of prednisolone and mycophenolate mofetil was found. CONCLUSIONS TTV levels show an association/correlation with the strength of IS. Further studies are needed in order to evaluate TTV measurement as a tool for IS monitoring for hard clinical outcomes such as presence of donor-specific antibodies, rejections or infections-common consequences of insufficient or too intense IS.
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Affiliation(s)
- Phoebe Uhl
- Department of Paediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Division of Paediatric Nephrology and Gastroenterology, Medical University of Vienna, Vienna, Austria
| | - Andreas Heilos
- Department of Paediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Division of Paediatric Nephrology and Gastroenterology, Medical University of Vienna, Vienna, Austria
| | - Gregor Bond
- Department of Medicine III, Division of Nephrology and Dialysis, Medical University of Vienna, Vienna, Austria
| | - Elias Meyer
- Center for Medical Statistics, Informatics and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | - Michael Böhm
- Department of Paediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Division of Paediatric Nephrology and Gastroenterology, Medical University of Vienna, Vienna, Austria
| | | | - Klaus Arbeiter
- Department of Paediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Division of Paediatric Nephrology and Gastroenterology, Medical University of Vienna, Vienna, Austria
| | - Thomas Müller-Sacherer
- Department of Paediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Division of Paediatric Nephrology and Gastroenterology, Medical University of Vienna, Vienna, Austria
| | - Dagmar Csaicsich
- Department of Paediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Division of Paediatric Nephrology and Gastroenterology, Medical University of Vienna, Vienna, Austria
| | - Christoph Aufricht
- Department of Paediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Division of Paediatric Nephrology and Gastroenterology, Medical University of Vienna, Vienna, Austria
| | - Krisztina Rusai
- Department of Paediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Division of Paediatric Nephrology and Gastroenterology, Medical University of Vienna, Vienna, Austria.
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Abstract
The human body hosts vast microbial communities, termed the microbiome. Less well known is the fact that the human body also hosts vast numbers of different viruses, collectively termed the 'virome'. Viruses are believed to be the most abundant and diverse biological entities on our planet, with an estimated 1031 particles on Earth. The human virome is similarly vast and complex, consisting of approximately 1013 particles per human individual, with great heterogeneity. In recent years, studies of the human virome using metagenomic sequencing and other methods have clarified aspects of human virome diversity at different body sites, the relationships to disease states and mechanisms of establishment of the human virome during early life. Despite increasing focus, it remains the case that the majority of sequence data in a typical virome study remain unidentified, highlighting the extent of unexplored viral 'dark matter'. Nevertheless, it is now clear that viral community states can be associated with adverse outcomes for the human host, whereas other states are characteristic of health. In this Review, we provide an overview of research on the human virome and highlight outstanding recent studies that explore the assembly, composition and dynamics of the human virome as well as host-virome interactions in health and disease.
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Khalifeh A, Blumstein DT, Fontenele RS, Schmidlin K, Richet C, Kraberger S, Varsani A. Diverse cressdnaviruses and an anellovirus identified in the fecal samples of yellow-bellied marmots. Virology 2020; 554:89-96. [PMID: 33388542 DOI: 10.1016/j.virol.2020.12.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 12/24/2020] [Accepted: 12/25/2020] [Indexed: 10/22/2022]
Abstract
Over that last decade, coupling multiple strand displacement approaches with high throughput sequencing have resulted in the identification of genomes of diverse groups of small circular DNA viruses. Using a similar approach but with recovery of complete genomes by PCR, we identified a diverse group of single-stranded viruses in yellow-bellied marmot (Marmota flaviventer) fecal samples. From 13 fecal samples we identified viruses in the family Genomoviridae (n = 7) and Anelloviridae (n = 1), and several others that ware part of the larger Cressdnaviricota phylum but not within established families (n = 19). There were also circular DNA molecules identified (n = 4) that appear to encode one viral-like gene and have genomes of <1545 nts. This study gives a snapshot of viruses associated with marmots based on fecal sampling.
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Affiliation(s)
- Anthony Khalifeh
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA
| | - Daniel T Blumstein
- Department of Ecology & Evolutionary Biology, Institute of the Environment & Sustainability, University of California Los Angeles, Los Angeles, CA, 90095, USA.
| | - Rafaela S Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA
| | - Kara Schmidlin
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA
| | - Cécile Richet
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA; Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, 7925, Cape Town, South Africa.
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Kulifaj D, Tilloy V, Scaon E, Guerin E, Essig M, Pichon N, Hantz S, De Bernardi A, Joannes M, Barranger C, Alain S. Viral metagenomics analysis of kidney donors and recipients: Torque teno virus genotyping and prevalence. J Med Virol 2020; 92:3301-3311. [PMID: 32658305 DOI: 10.1002/jmv.26298] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 07/07/2020] [Indexed: 12/11/2022]
Abstract
The viral load of the ubiquitous and nonpathogenic torque teno virus (TTV) is associated with the grade of immunosuppression of its host. The development of next-generation sequencing (NGS) allowed to describe the human virome of the blood compartment in transplanted patients, and showed that TTV is the most important part of the virome. This study is a descriptive retrospective pilot study of sequencing plasma samples from 15 matched donors and recipients. After sample processing, nucleic acids were amplified by rolling circle amplification and submitted to NGS by ion proton sequencing technology. Results were analyzed after mapping of reads on the 29 TTV reference genomes and de novo assembling of the reads with MIRA software. The number of TTV species present in donors and recipients was, on average, 12 in donors and 33 in recipients. TTV species predominantly present in donors were TTV-13 and TTV-18; and in recipients were TTV-P15-2, TTV-27, TTV-HD14a, and TTV-22. We highlighted a significant variability in abundance and composition in sequential samples from recipients. Temporal evolution of TTV populations was clearly observed in recipients, but no preferential transmission of a species from donor to recipient was evidenced. Diversity and population expansion were observed in kidney recipients. Further study of TTV species could help assess the potential impact of each species of this virus.
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Affiliation(s)
- Dorian Kulifaj
- INSERM UMR 1092, Université Limoges, Limoges, France
- R&D Molecular Diagnostics, bioMérieux, Verniolle, France
| | - Valentin Tilloy
- INSERM UMR 1092, Université Limoges, Limoges, France
- Herpesviruses National Reference Center, CHU Limoges, Limoges, France
- UF9481 Bioinformatics, CHU Limoges, Limoges, France
| | - Erwan Scaon
- Bioinformatics, UMS BISCEM, GEIST, Université Limoges, Limoges, France
| | - Emilie Guerin
- INSERM UMR 1092, Université Limoges, Limoges, France
- UF8843 Medical Genomics Department, CHU Limoges, Limoges, France
| | - Marie Essig
- Nephrology Department, CHU Limoges, Limoges, France
| | - Nicolas Pichon
- Intensive Care Unit Department, CHU Limoges, Limoges, France
| | - Sébastien Hantz
- INSERM UMR 1092, Université Limoges, Limoges, France
- Herpesviruses National Reference Center, CHU Limoges, Limoges, France
| | | | | | - Côme Barranger
- R&D Molecular Diagnostics, bioMérieux, Verniolle, France
| | - Sophie Alain
- INSERM UMR 1092, Université Limoges, Limoges, France
- Herpesviruses National Reference Center, CHU Limoges, Limoges, France
- UF8843 Medical Genomics Department, CHU Limoges, Limoges, France
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Thijssen M, Tacke F, Beller L, Deboutte W, Yinda KC, Nevens F, Laleman W, Van Ranst M, Pourkarim MR. Clinical relevance of plasma virome dynamics in liver transplant recipients. EBioMedicine 2020; 60:103009. [PMID: 32979836 PMCID: PMC7519289 DOI: 10.1016/j.ebiom.2020.103009] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/25/2020] [Accepted: 09/02/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The role of the microbiome in liver transplantation (LT) outcome has received a growing interest in the past decades. In contrast to bacteria, the role of endogenous viral communities, known as the virome, is poorly described. Here, we applied a viral metagenomic approach to study the dynamic evolution of circulating viruses in the plasma of LT recipients and its effect on the clinical course of patients. METHODS Patients chronically infected with hepatitis B virus (HBV) that received a LT due to endstage liver disease were included in this study. Longitudinal plasma samples were collected pre- and post-LT. Intact viral particles were isolated and sequenced on an Illumina HiSeq 2500 platform. Short read libraries were analysed with an in-house bioinformatics pipeline. Key endpoints were the dynamics of viral families and post-LT complications. FINDINGS The initiation of immunosuppression induced a bloom of the Anelloviridae that dominated the post-LT plasma virome. A variety of post-LT complication were observed. Nephrotoxicity was reported in 38% of the patients and was associated with a high abundance of anelloviruses. Besides nephrotoxicity, 16 (67%) patients experienced flares of viral or bacterial infections in post-transplant follow-up. These flares were recognized by an increased burden of anelloviruses (p < 0.05). Interestingly, no mortality was observed in patients infected with human pegivirus. INTERPRETATION These findings suggest a diagnostic potential for the Anelloviridae family in post-LT complications. Furthermore, the impact of human pegivirus infection on post-transplant survival should be further investigated. FUNDING This trial was supported by Gilead Sciences grant number BE-2017-000133.
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Affiliation(s)
- Marijn Thijssen
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, Herestraat 49, Post box 1040, BE-3000 Leuven, Belgium
| | - Frank Tacke
- Department of Hepatology and Gastroenterology, Charité - Universitätsmedizin Berlin, Campus Charité Mitte and Campus Virchow-Klinikum, Berlin, Germany
| | - Leen Beller
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, Herestraat 49, Post box 1040, BE-3000 Leuven, Belgium
| | - Ward Deboutte
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, Herestraat 49, Post box 1040, BE-3000 Leuven, Belgium
| | - Kwe Claude Yinda
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, Herestraat 49, Post box 1040, BE-3000 Leuven, Belgium
| | - Frederik Nevens
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
| | - Wim Laleman
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
| | - Marc Van Ranst
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, Herestraat 49, Post box 1040, BE-3000 Leuven, Belgium
| | - Mahmoud Reza Pourkarim
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, Herestraat 49, Post box 1040, BE-3000 Leuven, Belgium; Health Policy Research Centre, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran; Blood Transfusion Research Centre, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran.
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49
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Early life microbial exposures and allergy risks: opportunities for prevention. Nat Rev Immunol 2020; 21:177-191. [PMID: 32918062 DOI: 10.1038/s41577-020-00420-y] [Citation(s) in RCA: 133] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/31/2020] [Indexed: 02/07/2023]
Abstract
Allergies, including asthma, food allergy and atopic dermatitis, are increasing in prevalence, particularly in westernized countries. Although a detailed mechanistic explanation for this increase is lacking, recent evidence indicates that, in addition to genetic predisposition, lifestyle changes owing to modernization have an important role. Such changes include increased rates of birth by caesarean delivery, increased early use of antibiotics, a westernized diet and the associated development of obesity, and changes in indoor and outdoor lifestyle and activity patterns. Most of these factors directly and indirectly impact the formation of a diverse microbiota, which includes bacterial, viral and fungal components; the microbiota has a leading role in shaping (early) immune responses. This default programme is markedly disturbed under the influence of environmental and lifestyle risk factors. Here, we review the most important allergy risk factors associated with changes in our exposure to the microbial world and the application of this knowledge to allergy prevention strategies.
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50
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Lejeune S, Deschildre A, Le Rouzic O, Engelmann I, Dessein R, Pichavant M, Gosset P. Childhood asthma heterogeneity at the era of precision medicine: Modulating the immune response or the microbiota for the management of asthma attack. Biochem Pharmacol 2020; 179:114046. [PMID: 32446884 PMCID: PMC7242211 DOI: 10.1016/j.bcp.2020.114046] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 05/19/2020] [Indexed: 12/12/2022]
Abstract
Exacerbations are a main characteristic of asthma. In childhood, the risk is increasing with severity. Exacerbations are a strong phenotypic marker, particularly of severe and therapy-resistant asthma. These early-life events may influence the evolution and be involved in lung function decline. In children, asthma attacks are facilitated by exposure to allergens and pollutants, but are mainly triggered by microbial agents. Multiple studies have assessed immune responses to viruses, and to a lesser extend bacteria, during asthma exacerbation. Research has identified impairment of innate immune responses in children, related to altered pathogen recognition, interferon release, or anti-viral response. Influence of this host-microbiota dialog on the adaptive immune response may be crucial, leading to the development of biased T helper (Th)2 inflammation. These dynamic interactions may impact the presentations of asthma attacks, and have long-term consequences. The aim of this review is to synthesize studies exploring immune mechanisms impairment against viruses and bacteria promoting asthma attacks in children. The potential influence of the nature of infectious agents and/or preexisting microbiota on the development of exacerbation is also addressed. We then discuss our understanding of how these diverse host-microbiota interactions in children may account for the heterogeneity of endotypes and clinical presentations. Finally, improving the knowledge of the pathophysiological processes induced by infections has led to offer new opportunities for the development of preventive or curative therapeutics for acute asthma. A better definition of asthma endotypes associated with precision medicine might lead to substantial progress in the management of severe childhood asthma.
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Affiliation(s)
- Stéphanie Lejeune
- CHU Lille, Univ. Lille, Pediatric Pulmonology and Allergy Department, Hôpital Jeanne de Flandre, F-59000 Lille, France; Univ. Lille, INSERM Unit 1019, CNRS UMR 9017, CHU Lille, Institut Pasteur de Lille, Center for Infection and Immunity of Lille, F-59019 Lille Cedex, France
| | - Antoine Deschildre
- CHU Lille, Univ. Lille, Pediatric Pulmonology and Allergy Department, Hôpital Jeanne de Flandre, F-59000 Lille, France; Univ. Lille, INSERM Unit 1019, CNRS UMR 9017, CHU Lille, Institut Pasteur de Lille, Center for Infection and Immunity of Lille, F-59019 Lille Cedex, France
| | - Olivier Le Rouzic
- Univ. Lille, INSERM Unit 1019, CNRS UMR 9017, CHU Lille, Institut Pasteur de Lille, Center for Infection and Immunity of Lille, F-59019 Lille Cedex, France; CHU Lille, Univ. Lille, Department of Respiratory Diseases, F-59000 Lille Cedex, France
| | - Ilka Engelmann
- Univ. Lille, Virology Laboratory, EA3610, Institute of Microbiology, CHU Lille, F-59037 Lille Cedex, France
| | - Rodrigue Dessein
- Univ. Lille, INSERM Unit 1019, CNRS UMR 9017, CHU Lille, Institut Pasteur de Lille, Center for Infection and Immunity of Lille, F-59019 Lille Cedex, France; Univ. Lille, Bacteriology Department, Institute of Microbiology, CHU Lille, F-59037 Lille Cedex, France
| | - Muriel Pichavant
- Univ. Lille, INSERM Unit 1019, CNRS UMR 9017, CHU Lille, Institut Pasteur de Lille, Center for Infection and Immunity of Lille, F-59019 Lille Cedex, France
| | - Philippe Gosset
- Univ. Lille, INSERM Unit 1019, CNRS UMR 9017, CHU Lille, Institut Pasteur de Lille, Center for Infection and Immunity of Lille, F-59019 Lille Cedex, France.
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