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Pradier A, Masouridi-Levrat S, Bosshard C, Dantin C, Vu DL, Zanella MC, Boely E, Tapparel C, Kaiser L, Chalandon Y, Simonetta F, Roosnek E. Torque Teno Virus as a Potential Biomarker for Complications and Survival After Allogeneic Hematopoietic Stem Cell Transplantation. Front Immunol 2020; 11:998. [PMID: 32536920 PMCID: PMC7267041 DOI: 10.3389/fimmu.2020.00998] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 04/27/2020] [Indexed: 12/20/2022] Open
Abstract
Impaired immune reconstitution after allogeneic hematopoietic stem cell transplantation (HSCT) contributes to increased risk of cancer relapse and infection resulting in significant morbidity and mortality. Unfortunately, effective strategies to functionally assess the quality of immune reconstitution are still missing. Quantification of in vivo replication of the ubiquitous, non-pathogenic virus Torque Teno Virus (TTV) has been reported in small series as a test to functionally evaluate the quality of post-transplant immune reconstitution. In the present study, we analyzed by quantitative PCR TTV titers in plasma samples from a large cohort of 168 allogeneic HSCT recipients. Our analysis confirms that TTV titers peaked at 100 days post-transplant, followed by progressive normalization thereafter. Negative correlation of TTV titers with T cell absolute numbers during the first year post-transplant points to the restoration of an active anti-TTV immunity. Univariable and multivariable linear regression analysis demonstrated that donor CMV positive serostatus, donor type and immune suppression resulting from GVHD treatment affected the restoration of anti-TTV immunity. Importantly, higher TTV titers at 100 days after transplantation were associated with worse overall survival and higher risk of acute GVHD and infections. Our results provide new insights into the factors affecting the dynamics of TTV replication and indicate that TTV is a potentially useful biomarker to assess immune reconstitution and to predict complications and outcomes of allogeneic HSCT.
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Affiliation(s)
- Amandine Pradier
- Division of Hematology, Department of Oncology, Faculty of Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Stavroula Masouridi-Levrat
- Division of Hematology, Department of Oncology, Faculty of Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Carine Bosshard
- Division of Hematology, Department of Oncology, Faculty of Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Carole Dantin
- Division of Hematology, Department of Oncology, Faculty of Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Diem-Lan Vu
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Marie-Céline Zanella
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Elsa Boely
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Caroline Tapparel
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Laurent Kaiser
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Yves Chalandon
- Division of Hematology, Department of Oncology, Faculty of Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Federico Simonetta
- Division of Hematology, Department of Oncology, Faculty of Medicine, Geneva University Hospitals, Geneva, Switzerland.,Translational Research Center for Oncohematology, Department of Internal Medicine Specialties, University of Geneva, Geneva, Switzerland
| | - Eddy Roosnek
- Division of Hematology, Department of Oncology, Faculty of Medicine, Geneva University Hospitals, Geneva, Switzerland
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152
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Sloan P, Rodriguez C, Bedell BA, Murray J, Dagle J, Ryckman K, Holtz L. Alphatorquevirus is the most prevalent virus identified in blood from a matched maternal-infant preterm cohort. J Matern Fetal Neonatal Med 2020; 35:1636-1642. [PMID: 32401076 PMCID: PMC8529647 DOI: 10.1080/14767058.2020.1763298] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Objective: To determine the prevalence of virus in a previously uncharacterized matched maternal-infant preterm cohort and test if viral presence or viral load correlate with histologic chorioamnionitis, spontaneous preterm labor or pre-eclampsia.Study Design: Using qRT-PCR/qPCR we tested plasma or whole blood samples from 56 matched maternal and premature infant dyads for: adenovirus, anellovirus (alphatorquevirus and betatorquevirus), cytomegalovirus (CMV), Epstein-Barr virus (EBV), enterovirus, human herpesvirus 6 (HHV6), parechovirus, and parvovirus B19.Result: Viral detection was more common in maternal samples 29/56 (52%) than in cord blood from their infants (4/56 (7%)) (p ≤ .0001). No significant difference in viral load or viral prevalence was identified between pregnancies with and without histologic chorioamnionitis, spontaneous preterm labor or pre-eclampsia.Conclusion: Despite frequent detection of virus in maternal samples, virus was less frequently detected in the infants. Additionally, there was no association of presence or quantity of virus in maternal blood with histologic chorioamnionitis, spontaneous preterm labor or pre-eclampsia in this small, but well-defined cohort. Future studies are necessary to further characterize the role of virus in placental inflammatory states and pregnancy outcomes.
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Affiliation(s)
- Patrick Sloan
- Department of Pediatrics Division of Newborn Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Cynthia Rodriguez
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Bruce A Bedell
- Department of Pediatrics, University of Iowa, Iowa City, IA, USA
| | - Jeffrey Murray
- Department of Pediatrics, University of Iowa, Iowa City, IA, USA
| | - John Dagle
- Department of Pediatrics, University of Iowa, Iowa City, IA, USA
| | - Kelli Ryckman
- Department of Epidemiology, College of Public Health and Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Lori Holtz
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
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153
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Webb B, Rakibuzzaman A, Ramamoorthy S. Torque teno viruses in health and disease. Virus Res 2020; 285:198013. [PMID: 32404273 DOI: 10.1016/j.virusres.2020.198013] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/02/2020] [Accepted: 05/04/2020] [Indexed: 12/19/2022]
Abstract
Torque teno viruses (TTVs) are small, ubiquitous, viruses with a highly diverse, single-stranded, negative sense DNA genome and wide host range. They are detected at high rates in both healthy and diseased individuals and are considered a significant part of the mammalian virome. Similar to human TTVs, swine TTVs (TTSuVs) are epidemiologically linked to several coinfections including porcine circovirus types 2 and 3 and the porcine reproductive and respiratory disease syndrome virus. Experimental infection of gnotobiotic pigs with TTSuVs resulted in lesions in multiple organs and exacerbation of coinfections, making TTSuVs the only members of the Anelloviridae family with experimental evidence for pathogenicity. However, due to the lack of reliable cell culture and animal models, mechanistic studies on viral immunity and pathogenesis are limited. The objective of this review is to summarize the current status of knowledge regarding the biology, detection, pathogenesis and public health significance of TTSuVs, while identifying gaps in knowledge which limit the field.
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Affiliation(s)
- Brett Webb
- Veterinary Diagnostic Laboratory, North Dakota State University, Fargo, ND, United States
| | - Agm Rakibuzzaman
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, United States
| | - Sheela Ramamoorthy
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, United States.
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154
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Abstract
OBJECTIVES Improving immune status of people living with HIV through antiretroviral therapy (ART) may also reduce shedding of other viruses in semen. We characterized the seminal fluid virome of men with HIV and tested potential associations between viruses present and CD4 T-cell count, HIV viremia, and antiretroviral therapy (ART) status. DESIGN AND METHODS Metagenomics was used to enrich and sequence viral nucleic acids from the seminal fluid of 55 semen samples from 42 men living with HIV from San Francisco with a median age of 33 (IQR, 28.7-45) and median CD4 T-cell counts of 837 cells/μl (IQR, 258-1571 cells/μl). All samples were collected between 2005 and 2015, and ART status was ascertained from medical records. RESULTS Anelloviruses, cytomegalovirus (CMV), and multiple genotypes of human papillomaviruses were detected. Participants shed from 0 to 4 distinct human viruses. Longitudinally collected seminal fluid samples showed changes in the viruses shed. Viruses were more frequently shed by individuals with detectable HIV viremia (43.7 vs. 15.4%, P = 0.042). A trend was seen for increased shedding by individuals who were not on ART (42.8 vs. 17.8%, P = 0.082) or with CD4 T-cell count less than 350 cells/μl (35.3 vs. 20%, P = 0.27). CONCLUSION Seminal fluid from men with HIV from San Francisco contains nucleic acids from three different DNA viral families. A greater number of viruses, particularly CMV, were shed by participants with detectable HIV viremia (18.9 vs. 0%, P = 0.022). Control of viremia through ART may lower shedding of other viruses in semen in addition to HIV.
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155
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Klouda T, Chiel L, Davis J, Boyer D. Pediatric Lung Transplant: Influences of Viral and Fungal Infections on Outcomes and Viral Markers as a Predictor of Outcome. Am J Respir Crit Care Med 2020; 201:1146-1148. [PMID: 32223550 DOI: 10.1164/rccm.201910-2037rr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Timothy Klouda
- Division of Pulmonary Medicine, Boston Children's Hospital, Boston, Massachusetts
| | - Laura Chiel
- Division of Pulmonary Medicine, Boston Children's Hospital, Boston, Massachusetts
| | - Jaclyn Davis
- Division of Pulmonary Medicine, Boston Children's Hospital, Boston, Massachusetts
| | - Debra Boyer
- Division of Pulmonary Medicine, Boston Children's Hospital, Boston, Massachusetts
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156
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Reshetnyak VI, Maev IV, Burmistrov AI, Chekmazov IA, Karlovich TI. Torque teno virus in liver diseases: On the way towards unity of view. World J Gastroenterol 2020; 26:1691-1707. [PMID: 32351287 PMCID: PMC7183866 DOI: 10.3748/wjg.v26.i15.1691] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 03/23/2020] [Accepted: 03/26/2020] [Indexed: 02/06/2023] Open
Abstract
The review presents the data accumulated for more than 20 years of research of torque teno virus (TTV). Its molecular genetic structure, immunobiology, epidemiology, diagnostic methods, possible replication sites, and pathogenicity factors are described. TTV is a virus that is frequently detectable in patients with different viral hepatitides, in cases of hepatitis without an obvious viral agent, as well as in a healthy population. There is evidence suggesting that biochemical and histological changes occur in liver tissue and bile duct epithelium in TTV monoinfection. There are sufficient histological signs of liver damage, which confirm that the virus can undergo a replicative cycle in hepatocytes. Along with this, cytological hybridization in TTV-infected cells has shown no substantial cytopathic (cell-damaging) effects that are characteristic of pathogenic hepatotropic viruses. Studying TTV has led to the evolution of views on its role in the development of human pathology. The first ideas about the hepatotropism of the virus were gradually reformed as new data became available on the prevalence of the virus and its co-infection with other viruses, including the viruses of the known types of hepatitides. The high prevalence of TTV in the human population indicates its persistence in the body as a virome and a non-pathogenic virus. It has recently been proposed that the level of TTV DNA in the blood of patients undergoing organ transplantation should be used as an endogenous marker of the body’s immune status. The available data show the polytropism of the virus and deny the fact that TTV can be assigned exclusively to hepatitis viruses. Fortunately, the rare detection of the damaging effect of TTV on hepatic and bile duct epithelial cells may be indirect evidence of its conditionally pathogenic properties. The ubiquity of the virus and the variability of its existence in humans cannot put an end to its study.
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Affiliation(s)
- Vasiliy I Reshetnyak
- Department of Propaedeutic of Internal Diseases and Gastroenterology, A.I. Yevdokimov Moscow State University of Medicine and Dentistry, Moscow 127473, Russia
| | - Igor V Maev
- Department of Propaedeutic of Internal Diseases and Gastroenterology, A.I. Yevdokimov Moscow State University of Medicine and Dentistry, Moscow 127473, Russia
| | - Alexandr I Burmistrov
- Department of Propaedeutic of Internal Diseases and Gastroenterology, A.I. Yevdokimov Moscow State University of Medicine and Dentistry, Moscow 127473, Russia
| | - Igor A Chekmazov
- Central Clinical Hospital with Polyclinic, Presidential Administration of the Russian Federation, Moscow 121359, Russia
| | - Tatiana I Karlovich
- Central Clinical Hospital with Polyclinic, Presidential Administration of the Russian Federation, Moscow 121359, Russia
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157
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Guo G, Ye L, Shi X, Yan K, Huang J, Lin K, Xing D, Ye S, Wu Y, Li B, Chen C, Xue X, Zhang H. Dysbiosis in Peripheral Blood Mononuclear Cell Virome Associated With Systemic Lupus Erythematosus. Front Cell Infect Microbiol 2020; 10:131. [PMID: 32328467 PMCID: PMC7153479 DOI: 10.3389/fcimb.2020.00131] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 03/11/2020] [Indexed: 12/23/2022] Open
Abstract
Objective: Pathogen infection plays a role in the development and progression of systemic lupus erythematosus (SLE). Previous studies showed that peripheral blood mononuclear cells (PBMCs) harbor many viral communities. However, little is known about the viral components and the expression profiles of SLE-associated virome. We aimed to identify viral taxonomic markers of SLE that might be used in the detection of disease or in predicting its outcome. Methods: Non-human sequence data from high-throughput transcriptome sequencing of PBMC samples from 10 SLE patients and 10 healthy individuals were used for taxonomic alignment against an integrated virome reference genome database. Based on abundance profiles of SLE-associated virome species, genera, or host, Random Forests model was used to identify the viruses associated with SLE diagnostic markers. Spearman's correlation and functional clustering was used to analyze the interaction of candidate virome dysbiosis and SLE-associated differentially expressed genes. Results: A total of 419 viruses (38 human associated viruses, 350 phage, and 31 other viruses) was detected and the diversity of the PBMC virome was significantly increased in patients with SLE compared to the healthy controls (HCs). Viral taxa discriminated the cases from the controls, with an area under the receiver operating characteristic curve of 0.883, 0.695, and 0.540 for species, genus, and host, respectively. Clinical subgroup analysis showed that candidate PBMC viral markers were associated with stable- and active-stage SLE. Functional analyses showed that virome dysbiosis was mainly relevant to cellular and metabolic processes. Conclusion: We identified virome signatures associated with SLE, which might help develop tools to identify SLE patients or predict the disease stage.
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Affiliation(s)
- Gangqiang Guo
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Lele Ye
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China.,Department of Gynecologic Oncology, Wenzhou Central Hospital, Wenzhou, China
| | - Xinyu Shi
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Kejing Yan
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Jingjing Huang
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Kangming Lin
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Dong Xing
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Sisi Ye
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Yuqing Wu
- Second Clinical College, Wenzhou Medical University, Wenzhou, China
| | - Baoqing Li
- Department of Laboratory Medicine, Second Affiliated Hospital & Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China
| | - Chaosheng Chen
- Department of Nephrology, First Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Xiangyang Xue
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Huidi Zhang
- Department of Nephrology, First Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
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158
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Kim KW, Allen DW, Briese T, Couper JJ, Barry SC, Colman PG, Cotterill AM, Davis EA, Giles LC, Harrison LC, Harris M, Haynes A, Horton JL, Isaacs SR, Jain K, Lipkin WI, McGorm K, Morahan G, Morbey C, Pang ICN, Papenfuss AT, Penno MAS, Sinnott RO, Soldatos G, Thomson RL, Vuillermin P, Wentworth JM, Wilkins MR, Rawlinson WD, Craig ME. Higher frequency of vertebrate-infecting viruses in the gut of infants born to mothers with type 1 diabetes. Pediatr Diabetes 2020; 21:271-279. [PMID: 31800147 DOI: 10.1111/pedi.12952] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 11/07/2019] [Accepted: 11/10/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Microbial exposures in utero and early life shape the infant microbiome, which can profoundly impact on health. Compared to the bacterial microbiome, very little is known about the virome. We set out to characterize longitudinal changes in the gut virome of healthy infants born to mothers with or without type 1 diabetes using comprehensive virome capture sequencing. METHODS Healthy infants were selected from Environmental Determinants of Islet Autoimmunity (ENDIA), a prospective cohort of Australian children with a first-degree relative with type 1 diabetes, followed from pregnancy. Fecal specimens were collected three-monthly in the first year of life. RESULTS Among 25 infants (44% born to mothers with type 1 diabetes) at least one virus was detected in 65% (65/100) of samples and 96% (24/25) of infants during the first year of life. In total, 26 genera of viruses were identified and >150 viruses were differentially abundant between the gut of infants with a mother with type 1 diabetes vs without. Positivity for any virus was associated with maternal type 1 diabetes and older infant age. Enterovirus was associated with older infant age and maternal smoking. CONCLUSIONS We demonstrate a distinct gut virome profile in infants of mothers with type 1 diabetes, which may influence health outcomes later in life. Higher prevalence and greater number of viruses observed compared to previous studies suggests significant underrepresentation in existing virome datasets, arising most likely from less sensitive techniques used in data acquisition.
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Affiliation(s)
- Ki Wook Kim
- School of Women's and Children's Health, University of New South Wales, Sydney, New South Wales, Australia
| | - Digby W Allen
- School of Women's and Children's Health, University of New South Wales, Sydney, New South Wales, Australia
| | - Thomas Briese
- Center for Infection and Immunity and Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York
| | - Jennifer J Couper
- Robinson Research Institute and Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - Simon C Barry
- Robinson Research Institute and Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - Peter G Colman
- Department of Diabetes and Endocrinology, The Royal Melbourne Hospital Victoria, Melbourne, Victoria, Australia
| | - Andrew M Cotterill
- Department of Endocrinology, Queensland Children's Hospital, South Brisbane, Queensland, Australia
| | - Elizabeth A Davis
- Telethon Kids Institute, The University of Western Australia, Perth, Western Australia, Australia
| | - Lynne C Giles
- School of Public Health, University of Adelaide, Adelaide, South Australia, Australia
| | - Leonard C Harrison
- Walter and Eliza Hall Institute and Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Mark Harris
- Department of Endocrinology, Queensland Children's Hospital, South Brisbane, Queensland, Australia
| | - Aveni Haynes
- Telethon Kids Institute, The University of Western Australia, Perth, Western Australia, Australia
| | - Jessica L Horton
- School of Women's and Children's Health, University of New South Wales, Sydney, New South Wales, Australia
| | - Sonia R Isaacs
- School of Women's and Children's Health, University of New South Wales, Sydney, New South Wales, Australia
| | - Komal Jain
- Center for Infection and Immunity and Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York
| | - Walter I Lipkin
- Center for Infection and Immunity and Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York
| | - Kelly McGorm
- Robinson Research Institute and Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - Grant Morahan
- Centre for Diabetes Research, Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia
| | - Claire Morbey
- Hunter Diabetes Centre, Newcastle, New South Wales, Australia
| | - Ignatius C N Pang
- School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, New South Wales, Australia
| | - Anthony T Papenfuss
- Walter and Eliza Hall Institute and Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Megan A S Penno
- Robinson Research Institute and Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - Richard O Sinnott
- Department of Computing and Information Systems, University of Melbourne, Melbourne, Victoria, Australia
| | - Georgia Soldatos
- Monash Centre for Health Research and Implementation, School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | - Rebecca L Thomson
- Robinson Research Institute and Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - Peter Vuillermin
- School of Medicine, Deakin University, Geelong, Victoria, Australia
| | - John M Wentworth
- Walter and Eliza Hall Institute and Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Marc R Wilkins
- School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, New South Wales, Australia
| | - William D Rawlinson
- School of Women's and Children's Health, University of New South Wales, Sydney, New South Wales, Australia.,Serology and Virology Division, SEALS Microbiology, Prince of Wales Hospital, Sydney, New South Wales, Australia
| | - Maria E Craig
- School of Women's and Children's Health, University of New South Wales, Sydney, New South Wales, Australia.,Institute of Endocrinology and Diabetes, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
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159
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Poore GD, Kopylova E, Zhu Q, Carpenter C, Fraraccio S, Wandro S, Kosciolek T, Janssen S, Metcalf J, Song SJ, Kanbar J, Miller-Montgomery S, Heaton R, Mckay R, Patel SP, Swafford AD, Knight R. Microbiome analyses of blood and tissues suggest cancer diagnostic approach. Nature 2020; 579:567-574. [PMID: 32214244 PMCID: PMC7500457 DOI: 10.1038/s41586-020-2095-1] [Citation(s) in RCA: 628] [Impact Index Per Article: 157.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 02/06/2020] [Indexed: 01/05/2023]
Abstract
Systematic characterization of the cancer microbiome provides the opportunity to develop techniques that exploit non-human, microorganism-derived molecules in the diagnosis of a major human disease. Following recent demonstrations that some types of cancer show substantial microbial contributions1-10, we re-examined whole-genome and whole-transcriptome sequencing studies in The Cancer Genome Atlas11 (TCGA) of 33 types of cancer from treatment-naive patients (a total of 18,116 samples) for microbial reads, and found unique microbial signatures in tissue and blood within and between most major types of cancer. These TCGA blood signatures remained predictive when applied to patients with stage Ia-IIc cancer and cancers lacking any genomic alterations currently measured on two commercial-grade cell-free tumour DNA platforms, despite the use of very stringent decontamination analyses that discarded up to 92.3% of total sequence data. In addition, we could discriminate among samples from healthy, cancer-free individuals (n = 69) and those from patients with multiple types of cancer (prostate, lung, and melanoma; 100 samples in total) solely using plasma-derived, cell-free microbial nucleic acids. This potential microbiome-based oncology diagnostic tool warrants further exploration.
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Affiliation(s)
- Gregory D Poore
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Evguenia Kopylova
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Clarity Genomics, Beerse, Belgium
| | - Qiyun Zhu
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Carolina Carpenter
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Serena Fraraccio
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Stephen Wandro
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Tomasz Kosciolek
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Malopolska Centre of Biotechnology, Jagiellonian University in Krakow, Krakow, Poland
| | - Stefan Janssen
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Algorithmic Bioinformatics, Department of Biology and Chemistry, Justus Liebig University Gießen, Gießen, Germany
| | - Jessica Metcalf
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA
| | - Se Jin Song
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Jad Kanbar
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sandrine Miller-Montgomery
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Robert Heaton
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Rana Mckay
- Moores Cancer Center, University of California San Diego Health, La Jolla, CA, USA
| | - Sandip Pravin Patel
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego Health, La Jolla, CA, USA
| | - Austin D Swafford
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Rob Knight
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
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160
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Epitope-Containing Short Peptides Capture Distinct IgG Serodynamics That Enable Differentiating Infected from Vaccinated Animals for Live-Attenuated Vaccines. J Virol 2020; 94:JVI.01573-19. [PMID: 31896600 PMCID: PMC7158722 DOI: 10.1128/jvi.01573-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 12/16/2019] [Indexed: 12/25/2022] Open
Abstract
Differentiating infected from vaccinated animals (DIVA) strategies have been central enabling techniques in several successful viral disease elimination programs. However, owing to their long and uncertain development process, no DIVA-compatible vaccines are available for many important diseases. We report herein a new DIVA strategy based on hybrid protein-peptide microarrays which can theoretically work with any vaccine. Leading from our findings from peste des petits ruminants (PPR) virus, we found 4 epitope-containing short peptides (ECSPs) which have distinct IgG serodynamics: anti-ECSP IgGs only exist for 10 to 60 days postvaccination (dpv), while anti-protein IgGs remained at high levels for >1,000 dpv. These data enabled the design of a DIVA diagnostic microarray containing 4 ECSPs and 3 proteins, which, unlike competitive enzyme-linked immunosorbent assay (cELISA) and virus neutralization tests (VNTs), enables ongoing monitoring of serological differences between vaccinated individuals and individuals exposed to the pathogen. For 25 goats after 60 dpv, 13 were detected with positive anti-ECSP IgGs, indicating recent infections in vaccinated goat herds. These DIVA diagnostic microarrays will almost certainly facilitate eradication programs for (re)emerging pathogens and zoonoses.IMPORTANCE Outbreaks of infectious diseases caused by viruses, such as pseudorabies (PR), foot-and-mouth disease (FMD), and PPR viruses, led to economic losses reaching billions of dollars. Both PR and FMD were eliminated in several countries via large-scale vaccination programs using DIVA-compatible vaccines, which lack the gE protein and nonstructural proteins, respectively. However, there are still extensive challenges facing the development and deployment of DIVA-compatible vaccines because they are time-consuming and full of uncertainty. Further, the negative marker strategy used for DIVA-compatible vaccines is no longer functional for live-attenuated vaccines. To avoid these disadvantageous scenarios, a new strategy is desired. Here, we made the exciting discovery that different IgG serodynamics can be monitored when using protein-based assays versus arrays comprising ECSPs. This DIVA microarray strategy should, in theory, work for any vaccine.
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161
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Burnham P, Gomez-Lopez N, Heyang M, Cheng AP, Lenz JS, Dadhania DM, Lee JR, Suthanthiran M, Romero R, De Vlaminck I. Separating the signal from the noise in metagenomic cell-free DNA sequencing. MICROBIOME 2020; 8:18. [PMID: 32046792 PMCID: PMC7014780 DOI: 10.1186/s40168-020-0793-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 01/20/2020] [Indexed: 05/09/2023]
Abstract
BACKGROUND Cell-free DNA (cfDNA) in blood, urine, and other biofluids provides a unique window into human health. A proportion of cfDNA is derived from bacteria and viruses, creating opportunities for the diagnosis of infection via metagenomic sequencing. The total biomass of microbial-derived cfDNA in clinical isolates is low, which makes metagenomic cfDNA sequencing susceptible to contamination and alignment noise. RESULTS Here, we report low biomass background correction (LBBC), a bioinformatics noise filtering tool informed by the uniformity of the coverage of microbial genomes and the batch variation in the absolute abundance of microbial cfDNA. We demonstrate that LBBC leads to a dramatic reduction in false positive rate while minimally affecting the true positive rate for a cfDNA test to screen for urinary tract infection. We next performed high-throughput sequencing of cfDNA in amniotic fluid collected from term uncomplicated pregnancies or those complicated with clinical chorioamnionitis with and without intra-amniotic infection. CONCLUSIONS The data provide unique insight into the properties of fetal and maternal cfDNA in amniotic fluid, demonstrate the utility of cfDNA to screen for intra-amniotic infection, support the view that the amniotic fluid is sterile during normal pregnancy, and reveal cases of intra-amniotic inflammation without infection at term. Video abstract.
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Affiliation(s)
- Philip Burnham
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Nardhy Gomez-Lopez
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS), Bethesda, MD, USA
- Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, Detroit, MI, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Michael Heyang
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | | | - Joan Sesing Lenz
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Darshana M Dadhania
- Department of Transplantation Medicine, New York Presbyterian Hospital-Weill Cornell Medical Center, New York, NY, USA
| | - John Richard Lee
- Department of Transplantation Medicine, New York Presbyterian Hospital-Weill Cornell Medical Center, New York, NY, USA
| | - Manikkam Suthanthiran
- Department of Transplantation Medicine, New York Presbyterian Hospital-Weill Cornell Medical Center, New York, NY, USA
| | - Roberto Romero
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS), Bethesda, MD, USA
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
- Department of Epidemiology and Biostatistics, College of Human Medicine, East Lansing, MI, USA
- Department of Obstetrics and Gynecology, University of Michigan Health System, Ann Arbor, MI, USA
- Detroit Medical Center, Detroit, MI, USA
- Department of Obstetrics and Gynecology, Florida International University, Miami, Florida, USA
| | - Iwijn De Vlaminck
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA.
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162
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Anellovirus Dynamics Are Associated With Primary Graft Dysfunction in Lung Transplantation. Transplant Direct 2020; 6:e521. [PMID: 32095507 PMCID: PMC7004632 DOI: 10.1097/txd.0000000000000969] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 11/21/2019] [Accepted: 11/23/2019] [Indexed: 11/25/2022] Open
Abstract
Primary graft dysfunction (PGD) is the leading cause of early death in lung transplant. Anelloviruses are small circular DNA viruses that have been noted to be present at elevated levels in immunosuppressed patients. They have been associated with both short- and long-term outcomes in lung transplant, and we hypothesized that anellovirus dynamics might be associated with the development of PGD.
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163
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Shah AA, Wang D, Hirsch E. Nucleic Acid-Based Screening of Maternal Serum to Detect Viruses in Women with Labor or PROM. Reprod Sci 2020; 27:537-544. [PMID: 31925769 DOI: 10.1007/s43032-019-00051-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 06/12/2019] [Indexed: 01/12/2023]
Abstract
The purpose of this study was to determine whether timing of the initiating event of spontaneous labor (either uterine contractions with intact fetal membranes or rupture of membranes prior to labor (PROM)) is associated with maternal viral infection. It was a prospective case control study of women with either spontaneous labor or PROM occurring < 37 weeks' gestation ("cases") or at term ("controls"). An initial unbiased screen for viruses was performed with next-generation sequencing (NGS) in serum pooled from eight cases delivered by C/S and represents a range of gestational ages, membrane rupture status, and presence or absence of chorioamnionitis. Custom PCR was used to query individual patient samples from the original cohort. The NGS screen generated 15 million reads. Seven unique viral sequences were detected in two cases, all identified as torque teno virus (TTV), an ubiquitous DNA anellovirus of no known pathogenicity. Using nested and semi-nested PCR, sera from 72 patients (47 cases and 25 matched controls, stratified by ROM status) were screened for the 3 subtypes of anelloviruses (TTV, TTMDV, or TTMV). These were found in 43/47 cases (91%) and 16/25 controls (64%) (p = 0.012, OR = 5.9 (95% CI = 1.4-29.9)). In logistic regression, pregnant women with at least one type of anellovirus were more likely to experience preterm labor than those with no anellovirus (p = 0.03, aOR = 4.6, CI = 1.2-18.7). Among women experiencing a spontaneous initiating event of labor, TTV virus was more likely to be present in the serum of preterm than term patients. TTV may have a role in determining the timing of parturition.
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Affiliation(s)
- Ankit A Shah
- Department of Obstetrics and Gynecology, NorthShore University Health System, 2650 Ridge Ave, Evanston, IL, USA.,Department of Obstetrics and Gynecology, Pritzker School of Medicine, University of Chicago, 5801 S Ellis Ave, Chicago, IL, 60637, USA
| | - David Wang
- Departments of Molecular Microbiology and Pathology & Immunology, Washington University School of Medicine, 660 S Euclid Ave, St. Louis, MO, 63110, USA
| | - Emmet Hirsch
- Department of Obstetrics and Gynecology, NorthShore University Health System, 2650 Ridge Ave, Evanston, IL, USA. .,Department of Obstetrics and Gynecology, Pritzker School of Medicine, University of Chicago, 5801 S Ellis Ave, Chicago, IL, 60637, USA.
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164
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Detection of Torque Teno Virus (TTV) and TTV-Like Minivirus in patients with presumed infectious endophthalmitis in India. PLoS One 2020; 15:e0227121. [PMID: 31910220 PMCID: PMC6946165 DOI: 10.1371/journal.pone.0227121] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 12/11/2019] [Indexed: 12/04/2022] Open
Abstract
Human anelloviruses (Torque Teno Virus (TTV) and TTV Like Mini Virus (TLMV)) are now being reported at a high prevalence across the world, with a controversial disease-inducing potential. The aim of this study was to investigate the role of these anellovirus in vitreous of patients with presumed infectious endophthalmitis. After informed consent, vitreous fluid from patients with endophthalmitis (n = 103) and non-infectious pathologies (n = 102) were analyzed for the presence of TTV and TLMV DNA by qPCR with the limit of quantification defined as 100 copies per reaction. Among the patients clinically diagnosed with endophthalmitis, 29 of the 40 culture proven samples (72.5%) and 42 out of 63 (66.6%) of culture-negative samples were positive for presence of TTV/TLMV. Interestingly, 51 of the 102 (50%) samples in the control group were also positive for TTV/TLMV. Comparing the clinical outcome among patients diagnosed with endophthalmitis, we observed no significant association in the final visual acuity of patients who were positive for presence of TTV/TLMV, however, these patients had significantly higher repeat antibiotic injections (p = 0.03). Further evidence is however needed to correlate TTV / TLMV with a particular pathology or group of pathologies in the eye.
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165
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Hirsch HH. Spatiotemporal Virus Surveillance for Severe Acute Respiratory Infections in Resource-limited Settings: How Deep Need We Go? Clin Infect Dis 2020; 68:1126-1128. [PMID: 30099498 PMCID: PMC7108180 DOI: 10.1093/cid/ciy663] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 08/06/2018] [Indexed: 12/22/2022] Open
Affiliation(s)
- Hans H Hirsch
- Division of Infection Diagnostics, Department of Biomedicine, University of Basel, Switzerland.,Transplantation and Clinical Virology, Department of Biomedicine, University of Basel, Switzerland.,Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Switzerland
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166
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Troll CJ, Kapp J, Rao V, Harkins KM, Cole C, Naughton C, Morgan JM, Shapiro B, Green RE. A ligation-based single-stranded library preparation method to analyze cell-free DNA and synthetic oligos. BMC Genomics 2019; 20:1023. [PMID: 31881841 PMCID: PMC6935139 DOI: 10.1186/s12864-019-6355-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 11/29/2019] [Indexed: 12/16/2022] Open
Abstract
Background Cell-free DNA (cfDNA), present in circulating blood plasma, contains information about prenatal health, organ transplant reception, and cancer presence and progression. Originally developed for the genomic analysis of highly degraded ancient DNA, single-stranded DNA (ssDNA) library preparation methods are gaining popularity in the field of cfDNA analysis due to their efficiency and ability to convert short, fragmented DNA into sequencing libraries without altering DNA ends. However, current ssDNA methods are costly and time-consuming. Results Here we present an efficient ligation-based single-stranded library preparation method that is engineered to produce complex libraries in under 2.5 h from as little as 1 nanogram of input DNA without alteration to the native ends of template molecules. Our method, called Single Reaction Single-stranded LibrarY or SRSLY, ligates uniquely designed Next-Generation Sequencing (NGS) adapters in a one-step combined phosphorylation/ligation reaction that foregoes end-polishing. Using synthetic DNA oligos and cfDNA, we demonstrate the efficiency and utility of this approach and compare with existing double-stranded and single-stranded approaches for library generation. Finally, we demonstrate that cfDNA NGS data generated from SRSLY can be used to analyze DNA fragmentation patterns to deduce nucleosome positioning and transcription factor binding. Conclusions SRSLY is a versatile tool for converting short and fragmented DNA molecules, like cfDNA fragments, into sequencing libraries while retaining native lengths and ends.
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Affiliation(s)
| | - Joshua Kapp
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, 95064, USA
| | - Varsha Rao
- Claret Bioscience LLC, Santa Cruz, CA, 95060, USA
| | | | - Charles Cole
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | | | | | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, 95064, USA.,Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Richard E Green
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
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167
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Schmitz J, Kobbe G, Kondakci M, Schuler E, Magorsch M, Adams O. The Value of Torque Teno Virus (TTV) as a Marker for the Degree of Immunosuppression in Adult Patients after Hematopoietic Stem Cell Transplantation (HSCT). Biol Blood Marrow Transplant 2019; 26:643-650. [PMID: 31712192 DOI: 10.1016/j.bbmt.2019.11.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 10/25/2019] [Accepted: 11/04/2019] [Indexed: 12/28/2022]
Abstract
Torque teno virus (TTV) is a nonenveloped, single-stranded, circular DNA virus of the family of Anelloviridae. The first contact with TTV usually occurs in early childhood, followed by persistent infection in bone marrow and lymphocytes. Increased levels of TTV-DNA are found in the serum in various states of immune deficiency. The objective of this study was to assess if monitoring of TTV viremia after allogeneic hematopoietic stem cell transplantation (allo-HSCT) is a predictive marker for immune-related clinical complications. In a retrospective study, 2054 whole-blood samples from 123 patients were tested for viral loads of TTV-DNA by real-time PCR within 345 days after allo-HSCT. We enrolled all patients who underwent allo-HSCT between September 2015 and April 2018. Clinical and laboratory data were collected and statistically analyzed. Patients with an underlying lymphatic malignancy had significantly higher torque teno (TT) viral loads compared with patients with an underlying malignant myeloid disease (P < .05). Complete remission before allo-HSCT correlated significantly with higher TT viral loads after allo-HSCT (P < .05). Myeloablative conditioning regimens led to significantly higher TT viral loads than reduced-intensity conditioning regimens (P < .05). A higher anti-thymocyte globulin (ATG) dose was associated with a significantly higher TT viral load. We did not observe any significant differences of TT viral load correlating with accompanying clinically relevant events such as virus reactivations (cytomegalovirus, Epstein-Barr virus, Adenovirus), acute graft-versus-host disease (aGVHD), relapse, or death. TT viral load after allo-HSCT did weakly correlate with T cell, T suppressor cell, T helper cell, and natural killer and B cell count. Although statistically significant differences between study groups were observed, virus reactivations, aGVHD, and clinical outcomes could not be predicted by monitoring TTV viremia. Therefore, TTV seems not to be suitable as a marker for the degree of immunosuppression or as a prognostic marker for clinically critical events in patients after allo-HSCT.
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Affiliation(s)
- Julia Schmitz
- Institute for Virology, Medical Faculty, University of Duesseldorf, Duesseldorf, Germany
| | - Guido Kobbe
- Department of Haematology, Oncology and Clinical Immunology, University Hospital of Duesseldorf, Duesseldorf, Germany
| | - Mustafa Kondakci
- Department of Haematology, Oncology and Clinical Immunology, University Hospital of Duesseldorf, Duesseldorf, Germany
| | - Esther Schuler
- Department of Haematology, Oncology and Clinical Immunology, University Hospital of Duesseldorf, Duesseldorf, Germany
| | - Max Magorsch
- Technical University of Dortmund, Dortmund, Germany
| | - Ortwin Adams
- Institute for Virology, Medical Faculty, University of Duesseldorf, Duesseldorf, Germany.
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168
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Sawaswong V, Fahsbender E, Altan E, Kemthong T, Deng X, Malaivijitnond S, Payungporn S, Delwart E. High Diversity and Novel Enteric Viruses in Fecal Viromes of Healthy Wild and Captive Thai Cynomolgus Macaques ( Macaca fascicularis). Viruses 2019; 11:E971. [PMID: 31652508 PMCID: PMC6832579 DOI: 10.3390/v11100971] [Citation(s) in RCA: 14] [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: 09/09/2019] [Revised: 10/06/2019] [Accepted: 10/07/2019] [Indexed: 02/06/2023] Open
Abstract
Cynomolgus macaques are common across South East Asian countries including Thailand. The National Primate Research Center of Thailand, Chulalongkorn University (NPRCT-CU) captures wild-borne cynomolgus macaque for research use. Limited information is available on the enteric viruses and possible zoonotic infections into or from cynomolgus macaques. We characterized and compare the fecal virome of two populations; healthy wild-originated captive cynomolgus macaques (n = 43) reared in NPRCT-CU and healthy wild cynomolgus macaques (n = 35). Over 90% of recognized viral sequence reads amplified from feces were from bacterial viruses. Viruses from seven families of mammalian viruses were also detected (Parvoviridae, Anelloviridae, Picornaviridae, Adenoviridae, Papillomaviridae, Herpesviridae, and Caliciviridae). The genomes of a member of a new picornavirus genus we named Mafapivirus, a primate chapparvovirus, and a circular Rep-encoding single-strand (CRESS) DNA virus were also characterized. Higher abundance of CRESS DNA viruses of unknown tropism and invertebrate-tropic ambidensovirus were detected in wild versus captive macaques likely reflecting dietary differences. Short term rearing in captivity did not have a pronounced effect on the diversity of mammalian viruses of wild cynomolgus macaques. This study is the first report of the fecal virome of cynomolgus macaques, non-human primates frequently used in biomedical research and vaccination studies.
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Affiliation(s)
- Vorthon Sawaswong
- Vitalant Research Institute, San Francisco, CA 94118, USA.
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand.
| | - Elizabeth Fahsbender
- Vitalant Research Institute, San Francisco, CA 94118, USA.
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 9413, USA.
| | - Eda Altan
- Vitalant Research Institute, San Francisco, CA 94118, USA.
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 9413, USA.
| | - Taratorn Kemthong
- National Primate Research Center-Chulalongkorn University, Saraburi 18110, Thailand.
| | - Xutao Deng
- Vitalant Research Institute, San Francisco, CA 94118, USA.
| | | | - Sunchai Payungporn
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand.
- Center of Excellence in Systems Biology, Chulalongkorn University (CUSB), Bangkok 10330, Thailand.
| | - Eric Delwart
- Vitalant Research Institute, San Francisco, CA 94118, USA.
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 9413, USA.
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169
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van der Pol Y, Mouliere F. Toward the Early Detection of Cancer by Decoding the Epigenetic and Environmental Fingerprints of Cell-Free DNA. Cancer Cell 2019; 36:350-368. [PMID: 31614115 DOI: 10.1016/j.ccell.2019.09.003] [Citation(s) in RCA: 166] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 07/18/2019] [Accepted: 09/06/2019] [Indexed: 12/15/2022]
Abstract
Widespread adaptation of liquid biopsy for the early detection of cancer has yet to reach clinical utility. Circulating tumor DNA is commonly detected though the presence of genetic alterations, but only a minor fraction of tumor-derived cell-free DNA (cfDNA) fragments exhibit mutations. The cellular processes occurring in cancer development mark the chromatin. These epigenetic marks are reflected by modifications in the cfDNA methylation, fragment size, and structure. In this review, we describe how going beyond DNA sequence information alone, by analyzing cfDNA epigenetic and immune signatures, boosts the potential of liquid biopsy for the early detection of cancer.
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Affiliation(s)
- Ymke van der Pol
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Florent Mouliere
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands.
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170
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Ison MG, Hirsch HH. Community-Acquired Respiratory Viruses in Transplant Patients: Diversity, Impact, Unmet Clinical Needs. Clin Microbiol Rev 2019; 32:e00042-19. [PMID: 31511250 PMCID: PMC7399564 DOI: 10.1128/cmr.00042-19] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Patients undergoing solid-organ transplantation (SOT) or allogeneic hematopoietic cell transplantation (HCT) are at increased risk for infectious complications. Community-acquired respiratory viruses (CARVs) pose a particular challenge due to the frequent exposure pre-, peri-, and posttransplantation. Although influenza A and B viruses have a top priority regarding prevention and treatment, recent molecular diagnostic tests detecting an array of other CARVs in real time have dramatically expanded our knowledge about the epidemiology, diversity, and impact of CARV infections in the general population and in allogeneic HCT and SOT patients. These data have demonstrated that non-influenza CARVs independently contribute to morbidity and mortality of transplant patients. However, effective vaccination and antiviral treatment is only emerging for non-influenza CARVs, placing emphasis on infection control and supportive measures. Here, we review the current knowledge about CARVs in SOT and allogeneic HCT patients to better define the magnitude of this unmet clinical need and to discuss some of the lessons learned from human influenza virus, respiratory syncytial virus, parainfluenzavirus, rhinovirus, coronavirus, adenovirus, and bocavirus regarding diagnosis, prevention, and treatment.
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Affiliation(s)
- Michael G Ison
- Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Hans H Hirsch
- Transplantation & Clinical Virology, Department of Biomedicine, University of Basel, Basel, Switzerland
- Clinical Virology, Laboratory Medicine, University Hospital Basel, Basel, Switzerland
- Infectious Diseases & Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
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171
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Jaksch P, Kundi M, Görzer I, Muraközy G, Lambers C, Benazzo A, Hoetzenecker K, Klepetko W, Puchhammer-Stöckl E. Torque Teno Virus as a Novel Biomarker Targeting the Efficacy of Immunosuppression After Lung Transplantation. J Infect Dis 2019; 218:1922-1928. [PMID: 30053048 DOI: 10.1093/infdis/jiy452] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 07/17/2018] [Indexed: 12/17/2022] Open
Abstract
Torque teno viruses (TTV) are small DNA-viruses, of the genus Alphatorquevirus, whose replication is linked to immune status. TTV load may be an indicator for efficacy of IS in lung transplant recipients (LTRs). In a prospective single-center-study 143 LTRs were followed up and tested by quantitative TTV-DNA PCR. Using multivariate Cox-regression contribution of TTV-load to the occurrence of severe infections, chronic lung allograft dysfunction (CLAD), acute cellular rejection (ACR), and death was assessed. During follow-up 28 (20%) patients developed infections with a rate of 7.7 per 100 patient-years (PY). The hazard-ratio (HR) associated with a one-log10 increase of TTV-load before the event was 5.05. CLAD occurred with a rate of 6.0%-PY. HR for a 1 log10 increase of the lowest TTV level before the event was 0.71 (CI: 0.54-0.93). TTV-load predicts clinical events and may be useful to optimize IS during the first years of follow-up of LTRs.
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Affiliation(s)
- Peter Jaksch
- Division of Thoracic Surgery, Department of Surgery
| | | | - Irene Görzer
- Department of Virology, Medical University of Vienna, Austria
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172
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Strassl R, Schiemann M, Doberer K, Görzer I, Puchhammer-Stöckl E, Eskandary F, Kikic Ž, Gualdoni GA, Vossen MG, Rasoul-Rockenschaub S, Herkner H, Böhmig GA, Bond G. Quantification of Torque Teno Virus Viremia as a Prospective Biomarker for Infectious Disease in Kidney Allograft Recipients. J Infect Dis 2019; 218:1191-1199. [PMID: 30007341 PMCID: PMC6490304 DOI: 10.1093/infdis/jiy306] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 05/17/2018] [Indexed: 12/14/2022] Open
Abstract
Background Drug-induced immunosuppression following kidney transplantation is crucial to prevent allograft rejection, but increases risk for infectious disease. Tailoring of drug dosing to prevent both rejection and infection is greatly desirable. The apathogenic and ubiquitous torque teno virus (TTV) reflects immunocompetence of the host and might be a potential candidate for immunologic monitoring. Methods To assess TTV as an infection biomarker, virus load was prospectively quantified in peripheral blood of 169 consecutive renal allograft recipients at the Medical University Vienna. Results Patients with infection showed higher TTV levels compared to patients without infection (4.2 × 108 copies/mL [interquartile range, IQR, 2.7 × 107–1.9 × 109] vs 2.9 × 107 [IQR 1.0 × 106–7.2 × 108]; P = .006). Differences in TTV load became evident almost 3 months before infection (median 77 days, IQR 19–98). Each log level of TTV copies/mL increased the odds ratio for infection by 23% (95% confidence interval 1.04–1.45; P = .014). TTV >3.1 × 109 copies/mL corresponded to 90% sensitivity to predict infections. Logistic regression demonstrated independent association between TTV levels and infection. Conclusions TTV quantification predicts infection after kidney transplantation and might be a potential tool to tailor immunosuppressive drug therapy.
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Affiliation(s)
- Robert Strassl
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Austria
| | - Martin Schiemann
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Austria
| | - Konstantin Doberer
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Austria
| | - Irene Görzer
- Department of Virology, Medical University of Vienna, Austria
| | | | - Farsad Eskandary
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Austria
| | - Željko Kikic
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Austria
| | - Guido A Gualdoni
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Austria
| | - Mathias G Vossen
- Division of Infectious Diseases, Department of Medicine I, Medical University of Vienna, Austria
| | | | - Harald Herkner
- Department of Emergency Medicine, Medical University of Vienna, Austria
| | - Georg A Böhmig
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Austria
| | - Gregor Bond
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Austria
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173
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Ghose C, Ly M, Schwanemann LK, Shin JH, Atab K, Barr JJ, Little M, Schooley RT, Chopyk J, Pride DT. The Virome of Cerebrospinal Fluid: Viruses Where We Once Thought There Were None. Front Microbiol 2019; 10:2061. [PMID: 31555247 PMCID: PMC6742758 DOI: 10.3389/fmicb.2019.02061] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 08/21/2019] [Indexed: 01/21/2023] Open
Abstract
Traditionally, medicine has held that some human body sites are sterile and that the introduction of microbes to these sites results in infections. This paradigm shifted significantly with the discovery of the human microbiome and acceptance of these commensal microbes living across the body. However, the central nervous system (CNS) is still believed by many to be sterile in healthy people. Using culture-independent methods, we examined the virome of cerebrospinal fluid (CSF) from a cohort of mostly healthy human subjects. We identified a community of DNA viruses, most of which were identified as bacteriophages. Compared to other human specimen types, CSF viromes were not ecologically distinct. There was a high alpha diversity cluster that included feces, saliva, and urine, and a low alpha diversity cluster that included CSF, body fluids, plasma, and breast milk. The high diversity cluster included specimens known to have many bacteria, while other specimens traditionally assumed to be sterile formed the low diversity cluster. There was an abundance of viruses shared among CSF, breast milk, plasma, and body fluids, while each generally shared less with urine, feces, and saliva. These shared viruses ranged across different virus families, indicating that similarities between these viromes represent more than just a single shared virus family. By identifying a virome in the CSF of mostly healthy individuals, it is now less likely that any human body site is devoid of microbes, which further highlights the need to decipher the role that viral communities may play in human health.
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Affiliation(s)
| | - Melissa Ly
- Department of Pathology, University of California, San Diego, San Diego, CA, United States
| | - Leila K Schwanemann
- Department of Pathology, University of California, San Diego, San Diego, CA, United States
| | - Ji Hyun Shin
- Department of Pathology, University of California, San Diego, San Diego, CA, United States
| | - Katayoon Atab
- Department of Pathology, University of California, San Diego, San Diego, CA, United States
| | - Jeremy J Barr
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia
| | - Mark Little
- Department of Biology, San Diego State University, San Diego, CA, United States
| | - Robert T Schooley
- Department of Medicine, University of California, San Diego, San Diego, CA, United States
| | - Jessica Chopyk
- Department of Pathology, University of California, San Diego, San Diego, CA, United States
| | - David T Pride
- Department of Pathology, University of California, San Diego, San Diego, CA, United States.,Department of Medicine, University of California, San Diego, San Diego, CA, United States
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174
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Altan E, Dib JC, Gulloso AR, Escribano Juandigua D, Deng X, Bruhn R, Hildebrand K, Freiden P, Yamamoto J, Schultz-Cherry S, Delwart E. Effect of Geographic Isolation on the Nasal Virome of Indigenous Children. J Virol 2019; 93:e00681-19. [PMID: 31189707 PMCID: PMC6694818 DOI: 10.1128/jvi.00681-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 05/29/2019] [Indexed: 11/20/2022] Open
Abstract
The influence of living in small remote villages on the diversity of viruses in the nasal mucosa was investigated in three Colombian villages with very different levels of geographic isolation. Metagenomic analysis was used to characterize viral nucleic acids in nasal swabs from 63 apparently healthy young children. Sequences from human virus members of the families Anelloviridae, Papillomaviridae, Picornaviridae, Herpesviridae, Polyomaviridae, Adenoviridae, and Paramyxoviridae were detected in decreasing proportions of children. The number of papillomavirus infections detected was greater among Hispanic children most exposed to outside contacts, while anellovirus infections were more common in the isolated indigenous villages. The diversity of the other human viruses detected did not differ among the villages. Closely related variants of rhinovirus A or B were identified in 2 to 4 children from each village, reflecting ongoing transmission clusters. Genomes of viruses not currently known to infect humans, including members of the families Parvoviridae, Partitiviridae, Dicistroviridae, and Iflaviridae and circular Rep-encoding single-stranded DNA (CRESS-DNA) virus, were also detected in nasal swabs, possibly reflecting environmental contamination from insect, fungal, or unknown sources. Despite the high levels of geographic and cultural isolation, the overall diversity of human viruses in the nasal passages of children was not reduced in highly isolated indigenous villages, indicating ongoing exposure to globally circulating viruses.IMPORTANCE Extreme geographic and cultural isolation can still be found in some indigenous South American villages. Such isolation may be expected to limit the introduction of otherwise common and widely distributed viruses. Very small population sizes may also result in rapid local viral extinction due to a lack of seronegative subjects to maintain transmission chains for rapidly cleared viruses. We compared the viruses in the nasal passages of young children in three villages with increasing levels of geographic isolation. We found that isolation did not reduce the overall diversity of viral infections. Multiple infections with nearly identical rhinoviruses could be detected within each village, likely reflecting recent viral introductions and transmission clusters among epidemiologically linked members of these very small communities. We conclude that, despite their geographic isolation, remote indigenous villages show evidence of ongoing exposure to globally circulating viruses.
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Affiliation(s)
- Eda Altan
- Vitalant Research Institute, San Francisco, California, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Juan Carlos Dib
- Universidad del Norte, Barranquilla, Atlantico, Colombia
- Fundación Salud Para el Trópico-Tropical Health Foundation, Santa Marta, Magdalena, Colombia
| | - Andres Rojas Gulloso
- Fundación Salud Para el Trópico-Tropical Health Foundation, Santa Marta, Magdalena, Colombia
| | | | - Xutao Deng
- Vitalant Research Institute, San Francisco, California, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Roberta Bruhn
- Vitalant Research Institute, San Francisco, California, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Kristen Hildebrand
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Pamela Freiden
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Janie Yamamoto
- Vitalant Research Institute, San Francisco, California, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Stacey Schultz-Cherry
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Eric Delwart
- Vitalant Research Institute, San Francisco, California, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA
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175
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Kinetics of Torque Teno Virus-DNA Plasma Load Predict Rejection in Lung Transplant Recipients. Transplantation 2019; 103:815-822. [PMID: 30234787 DOI: 10.1097/tp.0000000000002436] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND Lung transplantation is the only therapeutic option in end-stage lung diseases; however, survival after transplantation is limited by acute and chronic rejection or infectious events being results of inappropriate immunosuppression. Torque Teno Viruses (TTVs) are ubiquitous DNA viruses in humans but not found to be causative for any disease. However, some reports suggest that TTV-DNA levels reflect the grade of immunosuppression with higher levels being found in more immunosuppressed individuals. METHODS We investigated the TTV-DNA levels in 34 lung transplant recipients within their first year after transplantation by quantitative real-time polymerase chain reaction. Clinical data were extracted from charts. RESULTS In accordance with previous results TTV-DNA levels increase after lung transplantation reaching a steady state after 3 months. The TTV-DNA levels were not correlated with immunosuppressive trough levels and a selective increase was not observed with other DNA viruses. In steady state TTV-DNA levels were significantly higher in patients with infectious complications compared to the group of patients without. Additionally, TTV-DNA levels decreased significantly before biopsy-proven rejection. Sensitivity of a 10-fold decrease in TTV-DNA levels for a subsequent rejection episode was 0.74 with a specificity of 0.99. CONCLUSIONS In summary, TTV-DNA might be used as an additional tool to monitor immunosuppression in lung transplant recipients. Higher TTV-DNA levels reflect more intense immunosuppression, whereas the TTV-DNA kinetic (ie, decrease of TTV-DNA levels) indicate rejection.
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176
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A cell-free DNA metagenomic sequencing assay that integrates the host injury response to infection. Proc Natl Acad Sci U S A 2019; 116:18738-18744. [PMID: 31451660 DOI: 10.1073/pnas.1906320116] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
High-throughput metagenomic sequencing offers an unbiased approach to identify pathogens in clinical samples. Conventional metagenomic sequencing, however, does not integrate information about the host, which is often critical to distinguish infection from infectious disease, and to assess the severity of disease. Here, we explore the utility of high-throughput sequencing of cell-free DNA (cfDNA) after bisulfite conversion to map the tissue and cell types of origin of host-derived cfDNA, and to profile the bacterial and viral metagenome. We applied this assay to 51 urinary cfDNA isolates collected from a cohort of kidney transplant recipients with and without bacterial and viral infection of the urinary tract. We find that the cell and tissue types of origin of urinary cfDNA can be derived from its genome-wide profile of methylation marks, and strongly depend on infection status. We find evidence of kidney and bladder tissue damage due to viral and bacterial infection, respectively, and of the recruitment of neutrophils to the urinary tract during infection. Through direct comparison to conventional metagenomic sequencing as well as clinical tests of infection, we find this assay accurately captures the bacterial and viral composition of the sample. The assay presented here is straightforward to implement, offers a systems view into bacterial and viral infections of the urinary tract, and can find future use as a tool for the differential diagnosis of infection.
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177
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178
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Armstrong AE, Rossoff J, Hollemon D, Hong DK, Muller WJ, Chaudhury S. Cell-free DNA next-generation sequencing successfully detects infectious pathogens in pediatric oncology and hematopoietic stem cell transplant patients at risk for invasive fungal disease. Pediatr Blood Cancer 2019; 66:e27734. [PMID: 30941906 DOI: 10.1002/pbc.27734] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 03/04/2019] [Accepted: 03/11/2019] [Indexed: 02/03/2023]
Abstract
BACKGROUND We sought to determine if next-generation sequencing (NGS) of microbial cell-free DNA (cfDNA) in plasma would detect pathogens in pediatric patients at risk for invasive fungal disease (IFD). PROCEDURES Pediatric hematology, oncology, and stem cell transplant patients deemed at risk for new IFD had blood samples drawn at three time-points separated by 1-month intervals. The primary outcome measure was detection of fungal pathogens compared to standard clinical testing. Secondary outcomes included identification of other infectious pathogens, relationship to European Organization for Research and Treatment of Cancer's Invasive Fungal Infections Cooperative Group and the National Institute of Allergy and Infectious Diseases' Mycoses Study Group (EORTC/MSG) guidelines, and assessment of antifungal therapy. RESULTS NGS identified fungal pathogens in seven of 40 at-risk patients for IFD and results were identical in four of six proven cases, including Aspergillus fumigatus by lung biopsy, Candida albicans by blood or pancreatic pseudocyst cultures, and Rhizopus delemar by skin biopsy. Rhizopus oryzae identified on skin biopsy and A. fumigatus isolated on day 27 of 28 of culture from lung biopsy were not detected by cfDNA NGS, possibly due to lack of bloodstream penetration and questionable pathogenicity, respectively. Numerous DNA viruses were detected in patients with prolonged febrile neutropenia or abnormal imaging. Extended antifungal therapy was used in 73% of patients. Follow-up cfDNA sequencing in patients who were positive at enrollment was negative at 1 and 2 months. CONCLUSIONS cfDNA NGS detected fungal pathogens from blood confirming its potential to guide treatment decisions in pediatric patients at risk for IFD and limit excessive empiric antifungal use. Future studies are needed to better understand the sensitivity and specificity of this approach.
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Affiliation(s)
- Amy E Armstrong
- Division of Hematology, Oncology and Transplantation, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois
| | - Jenna Rossoff
- Division of Hematology, Oncology and Transplantation, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois
| | | | | | - William J Muller
- Division of Infectious Diseases, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois.,Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Sonali Chaudhury
- Division of Hematology, Oncology and Transplantation, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois.,Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
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179
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Martín-López M, Albert E, Fernández-Ruiz M, González-Álvaro I, Rodríguez E, Aguado JM, Navarro D, Pablos JL. Torque teno virus viremia in patients with chronic arthritis: Influence of biologic therapies. Semin Arthritis Rheum 2019; 50:166-171. [PMID: 31324467 DOI: 10.1016/j.semarthrit.2019.06.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 06/07/2019] [Accepted: 06/25/2019] [Indexed: 02/08/2023]
Abstract
OBJECTIVE Torque teno virus (TTV) is a highly prevalent non-pathogenic anellovirus whose plasma levels may be a biomarker of immunosuppression. The aim of this study was to assess whether specific immune-targeting with different biologic drugs may differentially modulate TTV viremia in arthritis patients. METHODS TTV DNA load was quantified by PCR in a cross-sectional sample of 79 patients with chronic arthritis on biologic therapy (abatacept, infliximab, rituximab or tocilizumab), 31 patients treated with conventional DMARDs (methotrexate and/or leflunomide), and 54 healthy individuals. Longitudinal changes in TTV load were analysed in a second group of 59 patients at baseline and 4-months after biologic therapy. Correlations between clinical or biological characteristics of recruited patients and TTV viremia were also analysed. RESULTS In the cross-sectional study, TTV load was significantly higher in patients who received abatacept, infliximab or tocilizumab compared to healthy individuals. Patients treated with rituximab or conventional DMARDs showed TTV loads similar to healthy controls. In the longitudinal study, an increase in the TTV load was observed after anti-TNF, tocilizumab, abatacept and rituximab, but not after secukinumab therapy. Correlations between TTV load and clinical variables such as disease duration, concomitant glucocorticoid or DMARDs therapy, lymphocytes or previous infections were not found. A non-significant trend towards higher TTV load was observed in therapy responders. CONCLUSION Patients with chronic arthritis on biologic but not on conventional DMARD or anti-IL17 therapy have increased TTV viremia. This observation provides a basis to prospectively explore the potential value of TTV load as a potential pharmacodynamic biomarker.
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Affiliation(s)
- María Martín-López
- Department of Rheumatology, Hospital Universitario 12 de Octubre, Instituto de Investigación Hospital 12 de Octubre (imas12), Madrid, Spain.
| | - Eliseo Albert
- Department of Microbiology, Instituto de Investigación INCLIVA, Hospital Clínico, Valencia, Spain
| | - Mario Fernández-Ruiz
- Unit of Infectious Diseases, Hospital Universitario 12 de Octubre, Instituto de Investigación Hospital 12 de Octubre (imas12), Madrid, Spain
| | | | - Esther Rodríguez
- Department of Rheumatology, Hospital Universitario 12 de Octubre, Instituto de Investigación Hospital 12 de Octubre (imas12), Madrid, Spain
| | - José M Aguado
- Unit of Infectious Diseases, Hospital Universitario 12 de Octubre, Instituto de Investigación Hospital 12 de Octubre (imas12), Madrid, Spain; Universidad Complutense de Madrid, Madrid, Spain
| | - David Navarro
- Department of Microbiology, Instituto de Investigación INCLIVA, Hospital Clínico, Valencia, Spain
| | - José L Pablos
- Department of Rheumatology, Hospital Universitario 12 de Octubre, Instituto de Investigación Hospital 12 de Octubre (imas12), Madrid, Spain; Universidad Complutense de Madrid, Madrid, Spain
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180
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Freer G, Maggi F, Pistello M. Virome and Inflammasomes, a Finely Tuned Balance with Important Consequences for the Host Health. Curr Med Chem 2019; 26:1027-1044. [PMID: 28982318 DOI: 10.2174/0929867324666171005112921] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Revised: 07/06/2017] [Accepted: 07/27/2017] [Indexed: 12/21/2022]
Abstract
BACKGROUND The virome is a network of viruses normally inhabiting humans. It forms a conspicuous portion of the so-called microbiome, once generically referred to as resident flora. Indeed, viruses infecting humans without leading to clinical disease are increasingly recognized as part of the microbiome and have an impact on the development of our immune system. In addition, they activate inflammasomes, multiprotein complexes that assemble in cells and that are responsible for the downstream effects of sensing pathogens. OBJECTIVE This review aims at summarizing the evidence on the role of the virome in modulating inflammation and emphasizes evidence for Anelloviruses as useful molecular markers to monitor inflammatory processes and immune system competence. METHOD We carried out a review of the literature published in the last 5 years and summarized older literature to take into account ground-breaking discoveries concerning inflammasome assembly and virome. RESULTS A massive amount of data recently emerging demonstrate that the microbiome closely reflects what we eat, and many other unexpected variables. Composition, location, and amount of the microbiome have an impact on innate and adaptive immune defences. Viruses making up the virome contribute to shaping the immune system. Anelloviruses, the best known of such viruses, are present in most human beings, persistently without causing apparent disease. Depending on their interplay with such viruses, inflammasomes instruct host defences to tolerate or forfeit a specific microorganism. CONCLUSION The virome plays an important role in shaping human immune defences and contributes to inflammatory processes by quenching or increasing them.
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Affiliation(s)
- Giulia Freer
- Retrovirus Center and Virology Section, Department of Translational Research, University of Pisa, Pisa, Italy
| | | | - Mauro Pistello
- Retrovirus Center and Virology Section, Department of Translational Research, University of Pisa, Pisa, Italy.,Virology Unit, Pisa University Hospital, Pisa, Italy
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181
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Ramesh A, Nakielny S, Hsu J, Kyohere M, Byaruhanga O, de Bourcy C, Egger R, Dimitrov B, Juan YF, Sheu J, Wang J, Kalantar K, Langelier C, Ruel T, Mpimbaza A, Wilson MR, Rosenthal PJ, DeRisi JL. Metagenomic next-generation sequencing of samples from pediatric febrile illness in Tororo, Uganda. PLoS One 2019; 14:e0218318. [PMID: 31220115 PMCID: PMC6586300 DOI: 10.1371/journal.pone.0218318] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 05/31/2019] [Indexed: 12/15/2022] Open
Abstract
Febrile illness is a major burden in African children, and non-malarial causes of fever are uncertain. In this retrospective exploratory study, we used metagenomic next-generation sequencing (mNGS) to evaluate serum, nasopharyngeal, and stool specimens from 94 children (aged 2–54 months) with febrile illness admitted to Tororo District Hospital, Uganda. The most common microbes identified were Plasmodium falciparum (51.1% of samples) and parvovirus B19 (4.4%) from serum; human rhinoviruses A and C (40%), respiratory syncytial virus (10%), and human herpesvirus 5 (10%) from nasopharyngeal swabs; and rotavirus A (50% of those with diarrhea) from stool. We also report the near complete genome of a highly divergent orthobunyavirus, tentatively named Nyangole virus, identified from the serum of a child diagnosed with malaria and pneumonia, a Bwamba orthobunyavirus in the nasopharynx of a child with rash and sepsis, and the genomes of two novel human rhinovirus C species. In this retrospective exploratory study, mNGS identified multiple potential pathogens, including 3 new viral species, associated with fever in Ugandan children.
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Affiliation(s)
- Akshaya Ramesh
- Weill Institute for Neurosciences, University of California, San Francisco, California, United States of America
- Department of Neurology, University of California, San Francisco, California, United States of America
- * E-mail: (AR); (JLD)
| | - Sara Nakielny
- Department of Biochemistry and Biophysics, University of California, San Francisco, California, United States of America
| | - Jennifer Hsu
- Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, California, United States of America
| | - Mary Kyohere
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | | | - Charles de Bourcy
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Rebecca Egger
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Boris Dimitrov
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Yun-Fang Juan
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Jonathan Sheu
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - James Wang
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Katrina Kalantar
- Department of Biochemistry and Biophysics, University of California, San Francisco, California, United States of America
| | - Charles Langelier
- Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, California, United States of America
| | - Theodore Ruel
- Division of Pediatric Infectious Diseases and Global Health, Department of Pediatrics, University of California, San Francisco, California, United States of America
| | - Arthur Mpimbaza
- Child Health and Development Centre, Makerere University, Kampala, Uganda
| | - Michael R. Wilson
- Weill Institute for Neurosciences, University of California, San Francisco, California, United States of America
- Department of Neurology, University of California, San Francisco, California, United States of America
| | - Philip J. Rosenthal
- Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, California, United States of America
| | - Joseph L. DeRisi
- Department of Biochemistry and Biophysics, University of California, San Francisco, California, United States of America
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
- * E-mail: (AR); (JLD)
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182
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Roquilly A, Torres A, Villadangos JA, Netea MG, Dickson R, Becher B, Asehnoune K. Pathophysiological role of respiratory dysbiosis in hospital-acquired pneumonia. THE LANCET RESPIRATORY MEDICINE 2019; 7:710-720. [PMID: 31182406 DOI: 10.1016/s2213-2600(19)30140-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 03/06/2019] [Accepted: 03/08/2019] [Indexed: 12/19/2022]
Abstract
Hospital-acquired pneumonia is a major cause of morbidity and mortality. The incidence of hospital-acquired pneumonia remains high globally and treatment can often be ineffective. Here, we review the available data and unanswered questions surrounding hospital-acquired pneumonia, discuss alterations of the respiratory microbiome and of the mucosal immunity in patients admitted to hospital, and explore potential approaches to stratify patients for tailored treatments. The lungs have been considered a sterile organ for decades because microbiological culture techniques had shown negative results. Culture-independent techniques have shown that healthy lungs harbour a diverse and dynamic ecosystem of bacteria, changing our comprehension of respiratory physiopathology. Understanding dysbiosis of the respiratory microbiome and altered mucosal immunity in patients with critical illness holds great promise to develop targeted host-directed immunotherapy to reduce ineffective treatment, to improve patient outcomes, and to tackle the global threat of resistant bacteria that cause these infections.
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Affiliation(s)
- A Roquilly
- Department of Anesthesiology and Critical Care, CHU Nantes, Nantes, France; Department of Microbiology and Immunology, Faculty of Medicine, University of Nantes, Nantes, France
| | - A Torres
- Servei de Pneumologia, Hospital Clinic, Universitat de Barcelona Institut d'investigació Biomédica August Pi i Sunyer, Centro de Investigación Biomédica en Red.Enfermedades Respiratorias, Barcelona, Spain
| | - J A Villadangos
- Department of Microbiology and Immunology, Doherty Institute of Infection and Immunity and Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia
| | - M G Netea
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - R Dickson
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA; Michigan Center for Integrative Research in Critical Care; Ann Arbor, MI, USA
| | - B Becher
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - K Asehnoune
- Department of Anesthesiology and Critical Care, CHU Nantes, Nantes, France; Department of Microbiology and Immunology, Faculty of Medicine, University of Nantes, Nantes, France.
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184
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Mallet F, Perret M, Tran T, Meunier B, Guichard A, Tabone O, Mommert M, Brengel-Pesce K, Venet F, Pachot A, Monneret G, Reynier F, Védrine C, Leissner P, Moucadel V, Lepape A, Textoris J. Early herpes and TTV DNAemia in septic shock patients: a pilot study. Intensive Care Med Exp 2019; 7:28. [PMID: 31104220 PMCID: PMC6525672 DOI: 10.1186/s40635-019-0256-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 05/03/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Septic shock patients exhibit an increased incidence of viral reactivation. Precise timing of such reactivation-as an early marker of immune suppression, or as a consequence of the later-is not known precisely. Here, using a fully designed nucleic acid extraction automated procedure together with tailored commercial PCR kits, we focused on the description of early reactivation within the first week of ICU admission of several herpes viruses and Torque Teno virus (TTV) in 98 septic shock patients. RESULTS Most of septic shock patients had at least one viremia event during the first week (88%). TTV and herpesviruses were detected in 56% and 53% of septic shock patient, respectively. The two most frequent herpesviruses detected within the first week were EBV (35%) and HSV1 (26%). Different kinetic were observed among herpesviruses, faster for EBV and HSV1 than for CMV and HHV6. Although no association was found between herpes viremia and secondary infections, patients with herpesviridae-related viremia were more severe, e.g., higher SOFA scores and plasma lactate levels. While reactivating only 1 virus was not associated with mortality, patients with multiple viremia events had higher ICU mortality. Surprisingly, EBV + TTV early reactivation seemed associated with a lower D28 mortality. No clear association was observed between viremia and immune biomarkers. CONCLUSION Applying a semi-automated process of viral DNAemia determination to this cohort of 98 patients with septic shock, we observed that the number of patients with positive viremia increased during the first week in the ICU. Of note, there was no improvement in predicting the outcome when using viremia status. Nevertheless, this pilot study, introducing standardized procedures from extraction to detection, provides the basis for future standardized diagnostic criteria. A prospective longitudinal clinical study using these procedures will enable determination of whether such viremia is due to a lack of a latent virus control by the immune system or a true clinical viral infection.
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Affiliation(s)
- François Mallet
- EA 7426 Pathophysiology of Injury-induced Immunosuppression, University of Lyon1-Hospices Civils de Lyon-bioMérieux, Hôpital Edouard Herriot, 5 Place d'Arsonval, 69437, Lyon Cedex 3, France. .,Joint research unit, Hospice Civils de Lyon, bioMérieux, Centre Hospitalier Lyon Sud, 165 Chemin du Grand Revoyet, 69310, Pierre-Benite, France.
| | - Magali Perret
- BIOASTER Technology Research Institute, Lyon, France
| | - Trang Tran
- BIOASTER Technology Research Institute, Lyon, France
| | - Boris Meunier
- EA 7426 Pathophysiology of Injury-induced Immunosuppression, University of Lyon1-Hospices Civils de Lyon-bioMérieux, Hôpital Edouard Herriot, 5 Place d'Arsonval, 69437, Lyon Cedex 3, France.,Soladis, Lyon, France
| | - Audrey Guichard
- Joint research unit, Hospice Civils de Lyon, bioMérieux, Centre Hospitalier Lyon Sud, 165 Chemin du Grand Revoyet, 69310, Pierre-Benite, France
| | - Olivier Tabone
- EA 7426 Pathophysiology of Injury-induced Immunosuppression, University of Lyon1-Hospices Civils de Lyon-bioMérieux, Hôpital Edouard Herriot, 5 Place d'Arsonval, 69437, Lyon Cedex 3, France
| | - Marine Mommert
- Joint research unit, Hospice Civils de Lyon, bioMérieux, Centre Hospitalier Lyon Sud, 165 Chemin du Grand Revoyet, 69310, Pierre-Benite, France
| | - Karen Brengel-Pesce
- Joint research unit, Hospice Civils de Lyon, bioMérieux, Centre Hospitalier Lyon Sud, 165 Chemin du Grand Revoyet, 69310, Pierre-Benite, France
| | - Fabienne Venet
- EA 7426 Pathophysiology of Injury-induced Immunosuppression, University of Lyon1-Hospices Civils de Lyon-bioMérieux, Hôpital Edouard Herriot, 5 Place d'Arsonval, 69437, Lyon Cedex 3, France.,Hospices Civils de Lyon, Immunology Laboratory, Groupement Hospitalier Edouard Herriot, Lyon, France
| | - Alexandre Pachot
- EA 7426 Pathophysiology of Injury-induced Immunosuppression, University of Lyon1-Hospices Civils de Lyon-bioMérieux, Hôpital Edouard Herriot, 5 Place d'Arsonval, 69437, Lyon Cedex 3, France
| | - Guillaume Monneret
- EA 7426 Pathophysiology of Injury-induced Immunosuppression, University of Lyon1-Hospices Civils de Lyon-bioMérieux, Hôpital Edouard Herriot, 5 Place d'Arsonval, 69437, Lyon Cedex 3, France.,Hospices Civils de Lyon, Immunology Laboratory, Groupement Hospitalier Edouard Herriot, Lyon, France
| | | | | | | | - Virginie Moucadel
- EA 7426 Pathophysiology of Injury-induced Immunosuppression, University of Lyon1-Hospices Civils de Lyon-bioMérieux, Hôpital Edouard Herriot, 5 Place d'Arsonval, 69437, Lyon Cedex 3, France
| | - Alain Lepape
- Intensive Care Unit, Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, Pierre Bénite, France.,Emerging Pathogens Laboratory, Epidemiology and International Health, International Center for Infectiology Research (CIRI), Lyon, France.,Hospices Civils de Lyon, bioMérieux Joint Research Unit, Groupement Hospitalier Edouard Herriot, Lyon, France
| | - Julien Textoris
- EA 7426 Pathophysiology of Injury-induced Immunosuppression, University of Lyon1-Hospices Civils de Lyon-bioMérieux, Hôpital Edouard Herriot, 5 Place d'Arsonval, 69437, Lyon Cedex 3, France. .,Hospices Civils de Lyon, Department of Anaesthesiology and Critical Care Medicine, Groupement Hospitalier Edouard Herriot, Université Claude Bernard Lyon 1, Lyon, France.
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185
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Solis M, Velay A, Gantner P, Bausson J, Filipputtu A, Freitag R, Moulin B, Caillard S, Fafi-Kremer S. Torquetenovirus viremia for early prediction of graft rejection after kidney transplantation. J Infect 2019; 79:56-60. [PMID: 31100359 DOI: 10.1016/j.jinf.2019.05.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 01/02/2019] [Accepted: 05/10/2019] [Indexed: 12/15/2022]
Abstract
OBJECTIVES New biomarkers reflecting the degree of immunosuppression in transplant recipients are needed to provide an optimal personalized balance between rejection and infection risks. METHODS For this purpose, we investigated TTV viremia dynamics in 66 kidney transplant recipients followed up for two years after transplantation, in relation to BK virus infection and graft rejection. RESULTS After transplantation, TTV viremia rose by ≥2 log10 copies/mL from baseline to month 3, then declined by ≥1 log10 copies/mL thereafter. Higher TTV viremia was associated with recipients of a deceased donor, a lower count of CD8+ T cells and a higher BKV viremia. Importantly, TTV loads were significantly lower in KTR who would later display graft rejection; indeed, patients with TTV viremia lower than 3.4 log10 copies/mL at transplantation or lower than 4.2 log10 copies/mL at month 1 had a higher risk of developing graft rejection in the two following years (hazard ratio (HR) at D0 = 7.30, p = 0.0007 and HR at M1 = 6.16, p = 0.001). CONCLUSIONS TTV viremia measurement at early times post transplantation predicts graft rejection and would represent a useful tool to improve kidney transplant monitoring.
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Affiliation(s)
- M Solis
- Laboratoire de Virologie, Hôpitaux Universitaires de Strasbourg, 3 rue Koeberlé, F-67000 Strasbourg, France; INSERM UMR S1109, LabEx Transplantex, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
| | - A Velay
- Laboratoire de Virologie, Hôpitaux Universitaires de Strasbourg, 3 rue Koeberlé, F-67000 Strasbourg, France; INSERM UMR S1109, LabEx Transplantex, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
| | - P Gantner
- Laboratoire de Virologie, Hôpitaux Universitaires de Strasbourg, 3 rue Koeberlé, F-67000 Strasbourg, France; INSERM UMR S1109, LabEx Transplantex, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
| | - J Bausson
- Laboratoire de Virologie, Hôpitaux Universitaires de Strasbourg, 3 rue Koeberlé, F-67000 Strasbourg, France
| | - A Filipputtu
- Laboratoire de Virologie, Hôpitaux Universitaires de Strasbourg, 3 rue Koeberlé, F-67000 Strasbourg, France
| | - R Freitag
- Laboratoire de Virologie, Hôpitaux Universitaires de Strasbourg, 3 rue Koeberlé, F-67000 Strasbourg, France
| | - B Moulin
- INSERM UMR S1109, LabEx Transplantex, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France; Département de Néphrologie et Transplantation, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - S Caillard
- INSERM UMR S1109, LabEx Transplantex, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France; Département de Néphrologie et Transplantation, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - S Fafi-Kremer
- Laboratoire de Virologie, Hôpitaux Universitaires de Strasbourg, 3 rue Koeberlé, F-67000 Strasbourg, France; INSERM UMR S1109, LabEx Transplantex, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France.
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186
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Temporal virus serological profiling of kidney graft recipients using VirScan. Proc Natl Acad Sci U S A 2019; 116:10899-10904. [PMID: 31085644 DOI: 10.1073/pnas.1821166116] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
At this time, pretransplant viral screening of donors and recipients is based on serological status and limited to certain viruses. After transplantation, patient follow-up is based on a monitoring strategy using ELISA or PCR. Such approaches exclude other emerging viruses that can affect the transplant outcome. Recently, a multiplex unbiased array, VirScan, was developed. This tool allows the detection of antibodies against viruses, using a synthetic human virome, with minimal serum and cost. We decided to test the value of VirScan in the follow-up of a cohort of transplant recipients. We enrolled 45 kidney transplant recipients and performed virus serological profiling at day 0 and day +365, using VirScan. We compared the results obtained with ELISA/PCR assays. We detected antibody responses to 39 of the 206 species of virus present in the VirScan library, with an average of 12 species of virus per sample. VirScan gave similar results to PCR/ELISA screening tests. Using VirScan, we found that anti-viral antibody responses were largely conserved in patients during the first year after transplantation, regardless of immunosuppressive treatment. Our study suggests VirScan offers an unprecedented opportunity to screen and monitor posttransplant virus infection in a cost-effective, easy, and unbiased manner.
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187
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Focosi D, Maggi F. Torque teno virus monitoring in transplantation: The quest for standardization. Am J Transplant 2019; 19:1599-1601. [PMID: 30468687 DOI: 10.1111/ajt.15194] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, Pisa, Italy
| | - Fabrizio Maggi
- Department of Translational Research, University of Pisa, Pisa, Italy
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188
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Morsiani C, Bacalini MG, Santoro A, Garagnani P, Collura S, D'Errico A, de Eguileor M, Grazi GL, Cescon M, Franceschi C, Capri M. The peculiar aging of human liver: A geroscience perspective within transplant context. Ageing Res Rev 2019; 51:24-34. [PMID: 30772626 DOI: 10.1016/j.arr.2019.02.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 02/13/2019] [Accepted: 02/13/2019] [Indexed: 02/06/2023]
Abstract
An appraisal of recent data highlighting aspects inspired by the new Geroscience perspective are here discussed. The main findings are summarized as follows: i) liver has to be considered an immunological organ, and new studies suggest a role for the recently described cells named telocytes; ii) the liver-gut axis represents a crucial connection with environment and life style habits and may influence liver diseases onset; iii) the physiological aging of liver shows relatively modest alterations. Nevertheless, several molecular changes appear to be relevant: a) an increase of microRNA-31-5p; -141-3p; -200c-3p expressions after 60 years of age; b) a remodeling of genome-wide DNA methylation profile evident until 60 years of age and then plateauing; c) changes in transcriptome including the metabolic zones of hepatocyte lobules; d) liver undergoes an accelerated aging in presence of chronic inflammation/liver diseases in a sort of continuum, largely as a consequence of unhealthy life styles and exposure to environmental noxious agents. We argue that chronic liver inflammation has all the major characteristics of "inflammaging" and likely sustains the onset and progression of liver diseases. Finally, we propose to use a combination of parameters, mostly obtained by omics such as transcriptomics and epigenomics, to evaluate in deep both the biological age of liver (in comparison with the chronological age) and the effects of donor-recipient age-mismatches in the context of liver transplant.
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Affiliation(s)
- Cristina Morsiani
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy.
| | | | - Aurelia Santoro
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy; CIG-Interdepartmental Center "Galvani", University of Bologna, Bologna, Italy
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy; CIG-Interdepartmental Center "Galvani", University of Bologna, Bologna, Italy; Clinical Chemistry Department of Laboratory Medicine, Karolinska Institutet at Huddinge University Hospital, Stockholm, Sweden; Laboratory of Cell Biology, Rizzoli Orthopaedic Institute, Bologna, Italy; CNR Institute of Molecular Genetics, Unit of Bologna, Bologna, Italy; Center for Applied Biomedical Research (CRBA), St. Orsola-Malpighi University Hospital, Bologna, Italy
| | - Salvatore Collura
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Antonia D'Errico
- Pathology Unit, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), S. Orsola-Malpighi Hospital, University of Bologna, Bologna 40138, Italy
| | - Magda de Eguileor
- DBSV-Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, Varese, Italy
| | | | - Matteo Cescon
- DIMEC-Department of Medical and Surgical Sciences, S. Orsola-Malpighi Hospital, Bologna, Italy
| | - Claudio Franceschi
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy; Department of Applied Mathematics of the Institute of ITMM, National Research Lobachevsky State University of Nizhny Novgorod, Russian Federation
| | - Miriam Capri
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy; CIG-Interdepartmental Center "Galvani", University of Bologna, Bologna, Italy; CSR-Centro di Studio per la Ricerca dell'Invecchiamento, University of Bologna, Bologna, Italy
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189
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Macera L, Spezia PG, Medici C, Rofi E, Del Re M, Focosi D, Mazzetti P, Navarro D, Antonelli G, Danesi R, Pistello M, Maggi F. Comparative evaluation of molecular methods for the quantitative measure of torquetenovirus viremia, the new surrogate marker of immune competence. J Med Virol 2019; 94:491-498. [PMID: 31002743 DOI: 10.1002/jmv.25488] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 03/31/2019] [Accepted: 04/14/2019] [Indexed: 12/27/2022]
Abstract
BACKGROUND Torquetenovirus (TTV) viremia is emerging as a promising tool to assess functional immune competence, to predict posttransplant immune-related complications, and eventually to customize immunosuppression. METHODS In this study, 327 blood samples were tested using two real-time PCR (rtPCR) assays both targeted to the untranslated region of the TTV genome. The first assay was an in-house rtPCR developed by our group, the second one was the recently marketed TTV R-GENE assay. RESULTS In the validation study, the TTV R-GENE showed good performances in precision and reproducibility, and sensitivity as low as 12 TTV DNA copies/mL, like previously reported for the in-house rtPCR. The Bland-Altman analysis showed that the mean difference between the two methods was -0.3 log copies/mL. In the comparison study, 69% and 72% of samples were detected positive by rtPCR and TTV R-GENE, respectively (94% concordance, κ = 0.88). Performances did not differ between the two rtPCRs by type of TTV group examined. When a newly-developed in-house digital droplet PCR was applied for TTV quantification and used as an alternative method of comparison on 94 samples, the results strongly correlated with those obtained by the two rtPCR methods (99% concordance). CONCLUSION In summary, all the molecular methods assayed are highly sensitive and accurate in quantitation of TTV DNA in blood samples.
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Affiliation(s)
- Lisa Macera
- Department of Translational Research, University of Pisa, Pisa, Italy.,Virology Division, Pisa University Hospital, Pisa, Italy
| | | | - Chiara Medici
- Virology Division, Pisa University Hospital, Pisa, Italy
| | - Eleonora Rofi
- Clinical Pharmacology and Pharmacogenetics Unit, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Marzia Del Re
- Clinical Pharmacology and Pharmacogenetics Unit, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Daniele Focosi
- North-Western Tuscany Blood Bank Division, Pisa University Hospital, Pisa, Italy
| | - Paola Mazzetti
- Department of Translational Research, University of Pisa, Pisa, Italy.,Virology Division, Pisa University Hospital, Pisa, Italy
| | - David Navarro
- Department of Microbiology, School of Medicine, University of Valencia, Valencia, Spain
| | - Guido Antonelli
- Department of Molecular Medicine, Laboratory of Virology and Pasteur Institute-Cenci Bolognetti Foundation, Sapienza University of Rome, Rome, Italy
| | - Romano Danesi
- Clinical Pharmacology and Pharmacogenetics Unit, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Mauro Pistello
- Department of Translational Research, University of Pisa, Pisa, Italy.,Virology Division, Pisa University Hospital, Pisa, Italy
| | - Fabrizio Maggi
- Department of Translational Research, University of Pisa, Pisa, Italy.,Virology Division, Pisa University Hospital, Pisa, Italy
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190
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Rezahosseini O, Drabe CH, Sørensen SS, Rasmussen A, Perch M, Ostrowski SR, Nielsen SD. Torque-Teno virus viral load as a potential endogenous marker of immune function in solid organ transplantation. Transplant Rev (Orlando) 2019; 33:137-144. [PMID: 30981537 DOI: 10.1016/j.trre.2019.03.004] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/29/2019] [Accepted: 03/31/2019] [Indexed: 12/27/2022]
Abstract
Solid organ transplantation (SOT) recipients receive immunosuppressive therapy to avoid rejection of the transplanted organ. Immunosuppressive therapy increases the risk of infections. However, no existing marker reliably reveals the status of the immune function in SOT recipients. Torque-Teno virus or Transfusion-transmitted virus (TTV) has gained attention as a possible endogenous marker of the immune function. TTV is a non-enveloped, circular single strand DNA virus, and it may be considered a part of the human virome. In a bidirectional relationship, the immune system detects TTV and TTV may also modulate the activity of immune system. These characteristics have made the virus a possible candidate indicator of immune function. In this systematic review, we describe the role and potential function of TTV viral load as an endogenous marker of the immune function and consequently the level of immune suppression in SOT recipients.
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Affiliation(s)
- Omid Rezahosseini
- Viro-immunology Research Unit, Department of Infectious Diseases 8632, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Camilla Heldbjerg Drabe
- Viro-immunology Research Unit, Department of Infectious Diseases 8632, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | | | - Allan Rasmussen
- Department of Surgical Gastroenterology and Transplantation, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Michael Perch
- Department of Cardiology, Section for Lung Transplantation, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Sisse Rye Ostrowski
- Department of Clinical Immunology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Susanne Dam Nielsen
- Viro-immunology Research Unit, Department of Infectious Diseases 8632, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark.
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191
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Fernández-Ruiz M, Albert E, Giménez E, Ruiz-Merlo T, Parra P, López-Medrano F, San Juan R, Polanco N, Andrés A, Navarro D, Aguado JM. Monitoring of alphatorquevirus DNA levels for the prediction of immunosuppression-related complications after kidney transplantation. Am J Transplant 2019; 19:1139-1149. [PMID: 30346659 DOI: 10.1111/ajt.15145] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 09/10/2018] [Accepted: 09/29/2018] [Indexed: 01/25/2023]
Abstract
The replication kinetics of nonpathogenic anelloviruses belonging to the Alphatorquevirus genus (such as torque teno virus) might reflect the overall state of posttransplant immunosuppression. We analyzed 221 kidney transplant (KT) recipients in whom plasma alphatorquevirus DNA load was quantified by real-time polymerase chain reaction at baseline and regularly through the first 12 posttransplant months. Study outcomes included posttransplant infection and a composite of opportunistic infection and/or de novo malignancy (immunosuppression-related adverse event [iRAE]). Alphatorquevirus DNA loads at month 1 were higher among patients who subsequently developed posttransplant infection (P = .023) or iRAE (P = .009). Likewise, those with iRAE beyond months 3 and 6 also exhibited higher peak viral loads over the preceding periods. Areas under the curve for log10 alphatorquevirus DNAemia estimated by months 1 or 6 were significantly higher in patients experiencing study outcomes. Alphatorquevirus DNA loads above 3.15 and 4.56 log10 copies/mL at month 1 predicted the occurrence of posttransplant infection (adjusted hazard ratio [aHR]: 2.88; 95% confidence interval [CI]: 1.13-7.36; P = .027) and iRAE (aHR: 5.17; 95% CI: 2.01-13.33; P = .001). In conclusion, posttransplant monitoring of plasma alphatorquevirus DNA kinetics may be useful to identify KT recipients at increased risk of immunosuppression-related complications.
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Affiliation(s)
- Mario Fernández-Ruiz
- Unit of Infectious Diseases, Hospital Universitario "12 de Octubre," Instituto de Investigación Sanitaria Hospital "12 de Octubre" (imas12), School of Medicine, Universidad Complutense, Madrid, Spain.,Spanish Network for Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain
| | - Eliseo Albert
- Microbiology Service, Hospital Clínico Universitario, Instituto de Investigación Sanitaria INCLIVA, Valencia, Spain
| | - Estela Giménez
- Microbiology Service, Hospital Clínico Universitario, Instituto de Investigación Sanitaria INCLIVA, Valencia, Spain
| | - Tamara Ruiz-Merlo
- Unit of Infectious Diseases, Hospital Universitario "12 de Octubre," Instituto de Investigación Sanitaria Hospital "12 de Octubre" (imas12), School of Medicine, Universidad Complutense, Madrid, Spain.,Spanish Network for Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain
| | - Patricia Parra
- Unit of Infectious Diseases, Hospital Universitario "12 de Octubre," Instituto de Investigación Sanitaria Hospital "12 de Octubre" (imas12), School of Medicine, Universidad Complutense, Madrid, Spain.,Spanish Network for Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain
| | - Francisco López-Medrano
- Unit of Infectious Diseases, Hospital Universitario "12 de Octubre," Instituto de Investigación Sanitaria Hospital "12 de Octubre" (imas12), School of Medicine, Universidad Complutense, Madrid, Spain.,Spanish Network for Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain
| | - Rafael San Juan
- Unit of Infectious Diseases, Hospital Universitario "12 de Octubre," Instituto de Investigación Sanitaria Hospital "12 de Octubre" (imas12), School of Medicine, Universidad Complutense, Madrid, Spain.,Spanish Network for Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain
| | - Natalia Polanco
- Department of Nephrology, Hospital Universitario "12 de Octubre", Instituto de Investigación Sanitaria Hospital "12 de Octubre" (imas12), School of Medicine, Universidad Complutense, Madrid, Spain
| | - Amado Andrés
- Department of Nephrology, Hospital Universitario "12 de Octubre", Instituto de Investigación Sanitaria Hospital "12 de Octubre" (imas12), School of Medicine, Universidad Complutense, Madrid, Spain
| | - David Navarro
- Microbiology Service, Hospital Clínico Universitario, Instituto de Investigación Sanitaria INCLIVA, Valencia, Spain.,Department of Microbiology, School of Medicine, University of Valencia, Valencia, Spain
| | - José María Aguado
- Unit of Infectious Diseases, Hospital Universitario "12 de Octubre," Instituto de Investigación Sanitaria Hospital "12 de Octubre" (imas12), School of Medicine, Universidad Complutense, Madrid, Spain.,Spanish Network for Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain
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192
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Abbas AA, Young JC, Clarke EL, Diamond JM, Imai I, Haas AR, Cantu E, Lederer DJ, Meyer K, Milewski RK, Olthoff KM, Shaked A, Christie JD, Bushman FD, Collman RG. Bidirectional transfer of Anelloviridae lineages between graft and host during lung transplantation. Am J Transplant 2019; 19:1086-1097. [PMID: 30203917 PMCID: PMC6411461 DOI: 10.1111/ajt.15116] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 09/05/2018] [Accepted: 09/05/2018] [Indexed: 01/25/2023]
Abstract
Solid organ transplantation disrupts virus-host relationships, potentially resulting in viral transfer from donor to recipient, reactivation of latent viruses, and new viral infections. Viral transfer, colonization, and reactivation are typically monitored using assays for specific viruses, leaving the behavior of full viral populations (the "virome") understudied. Here we sought to investigate the temporal behavior of viruses from donor lungs and transplant recipients comprehensively. We interrogated the bronchoalveolar lavage and blood viromes during the peritransplant period and 6-16 months posttransplant in 13 donor-recipient pairs using shotgun metagenomic sequencing. Anelloviridae, ubiquitous human commensal viruses, were the most abundant human viruses identified. Herpesviruses, parvoviruses, polyomaviruses, and bacteriophages were also detected. Anelloviridae populations were complex, with some donor organs and hosts harboring multiple contemporaneous lineages. We identified transfer of Anelloviridae lineages from donor organ to recipient serum in 4 of 7 cases that could be queried, and immigration of lineages from recipient serum into the allograft in 6 of 10 such cases. Thus, metagenomic analyses revealed that viral populations move between graft and host in both directions, showing that organ transplantation involves implantation of both the allograft and commensal viral communities.
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Affiliation(s)
- A. A. Abbas
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - J. C. Young
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - E. L. Clarke
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - J. M. Diamond
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA,Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - I Imai
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - A. R. Haas
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - E. Cantu
- Department of Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - D. J. Lederer
- Departments of Medicine and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, NY
| | - K. Meyer
- School of Medicine and Public Health, University of Wisconsin, Madison, WI
| | - R. K. Milewski
- Department of Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - K. M. Olthoff
- Department of Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - A. Shaked
- Department of Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - J. D. Christie
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA,Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - F. D. Bushman
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - R. G. Collman
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA,Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
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193
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Albert E, Solano C, Giménez E, Focosi D, Pérez A, Macera L, Piñana JL, Mateo EM, Boluda JCH, Maggi F, Navarro D. Kinetics of Alphatorquevirus plasma DNAemia at late times after allogeneic hematopoietic stem cell transplantation. Med Microbiol Immunol 2019; 208:253-258. [PMID: 30852649 DOI: 10.1007/s00430-019-00586-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 02/21/2019] [Indexed: 12/11/2022]
Abstract
Torque teno virus (TTV) plasma DNA load has been consistently shown to be a surrogate biomarker of immunosuppression in solid organ transplant recipients. It is uncertain whether it may behave similarly in allogeneic hematopoietic stem cell transplant recipients (allo-HSCT). Here, we characterized the dynamics of TTV DNAemia in patients undergoing T-cell replete allo-SCT at late times after transplantation (> day + 100). This retrospective single-center observational study included 33 allo-HSCT patients. Plasma TTV DNA loads were quantified by real-time PCR before initiating the conditioning regimen and at different time points after transplant. Absolute lymphocyte counts (ALC) were measured by flow cytometry. Overall, TTV DNA load increased steadily after engraftment, reaching a peak by day + 90; afterwards, it remained relatively constant until day + 210. TTV DNA loads measured within days + 120 and + 210 correlated inversely with paired ALC, while both parameters did correlate directly within days + 20 and + 60. The median TTV DNA area under a curve between days + 90 and + 210 [(AUC)90-210] was significantly higher in patients who received corticosteroids within this time frame for treatment of graft versus host disease (either acute, chronic or both) than in controls (P = 0.025). In summary, TTV DNA load may mirror the degree of immunosuppression at late times after allo-HSCT.
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Affiliation(s)
- Eliseo Albert
- Microbiology Service, Hospital Clínico Universitario, Institute for Research INCLIVA, Valencia, Spain
| | - Carlos Solano
- Hematology Service, Hospital Clínico Universitario, Institute for Research INCLIVA, Valencia, Spain.,Department of Medicine, School of Medicine, University of Valencia, Valencia, Spain
| | - Estela Giménez
- Microbiology Service, Hospital Clínico Universitario, Institute for Research INCLIVA, Valencia, Spain
| | - Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, Pisa, Italy
| | - Ariadna Pérez
- Hematology Service, Hospital Clínico Universitario, Institute for Research INCLIVA, Valencia, Spain
| | - Lisa Macera
- Virology Unit, Pisa University Hospital, Pisa, Italy
| | - José Luis Piñana
- Hematology Service, Hospital Clínico Universitario, Institute for Research INCLIVA, Valencia, Spain
| | - Eva María Mateo
- Microbiology Service, Hospital Clínico Universitario, Institute for Research INCLIVA, Valencia, Spain
| | | | - Fabrizio Maggi
- Virology Unit, Pisa University Hospital, Pisa, Italy.,Department of Translational Research, University of Pisa, Pisa, Italy
| | - David Navarro
- Microbiology Service, Hospital Clínico Universitario, Institute for Research INCLIVA, Valencia, Spain. .,Department of Microbiology, School of Medicine, University of Valencia, Av. Blasco Ibáñez 17, 46010, Valencia, Spain.
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194
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Dharnidharka VR, Ruzinova MB, Chen C, Parameswaran P, O'Gorman H, Goss CW, Gu H, Storch GA, Wylie K. Metagenomic analysis of DNA viruses from posttransplant lymphoproliferative disorders. Cancer Med 2019; 8:1013-1023. [PMID: 30697958 PMCID: PMC6434222 DOI: 10.1002/cam4.1985] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 12/15/2018] [Accepted: 12/27/2018] [Indexed: 12/16/2022] Open
Abstract
Posttransplant lymphoproliferative disorders (PTLDs), 50%-80% of which are strongly associated with Epstein-Barr virus (EBV), carry a high morbidity and mortality. Most clinical/epidemiological/tumor characteristics do not consistently associate with worse patient survival, so our aim was to identify if other viral genomic characteristics associated better with survival. We extracted DNA from stored paraffin-embedded PTLD tissues at our center, identified viral sequences by metagenomic shotgun sequencing (MSS), and analyzed the data in relation to clinical outcomes. Our study population comprised 69 PTLD tissue samples collected between 1991 and 2015 from 60 subjects. Nucleotide sequences from at least one virus were detected by MSS in 86% (59/69) of the tissues (EBV in 61%, anelloviruses 52%, gammapapillomaviruses 14%, CMV 7%, and HSV in 3%). No viruses were present in higher proportion in EBV-negative PTLD (compared to EBV-positive PTLD). In univariable analysis, death within 5 years of PTLD diagnosis was associated with anellovirus (P = 0.037) and gammapapillomavirus (P = 0.036) detection by MSS, higher tissue qPCR levels of the predominant human anellovirus species torque teno virus (TTV; P = 0.016), T cell type PTLD, liver, brain or bone marrow location. In multivariable analyses, T cell PTLD (P = 0.006) and TTV PCR level (P = 0.012) remained significant. In EBV-positive PTLD, EBNA-LP, EBNA1 and EBNA3C had significantly higher levels of nonsynonymous gene variants compared to the other EBV genes. Multiple viruses are detectable in PTLD tissues by MSS. Anellovirus positivity, not EBV positivity,was associated with worse patient survival in our series. Confirmation and extension of this work in larger multicenter studies is desirable.
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Affiliation(s)
- Vikas R. Dharnidharka
- Division of Pediatric NephrologyWashington University School of MedicineSt LouisMOUSA
| | - Marianna B. Ruzinova
- Department of Pathology and ImmunologyWashington University School of MedicineSt LouisMOUSA
| | - Chun‐Cheng Chen
- Department of SurgeryWashington University School of MedicineSt LouisMOUSA
| | - Priyanka Parameswaran
- Division of Pediatric NephrologyWashington University School of MedicineSt LouisMOUSA
| | - Harry O'Gorman
- Division of Pediatric NephrologyWashington University School of MedicineSt LouisMOUSA
| | - Charles W. Goss
- Department of BiostatisticsWashington University School of MedicineSt LouisMOUSA
| | - Hongjie Gu
- Department of BiostatisticsWashington University School of MedicineSt LouisMOUSA
| | - Gregory A. Storch
- Division of Pediatric Infectious DiseasesWashington University School of MedicineSt LouisMOUSA
| | - Kristine Wylie
- Division of Pediatric Infectious DiseasesWashington University School of MedicineSt LouisMOUSA
- McDonnell Genome InstituteWashington University School of MedicineSt LouisMOUSA
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195
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Eibach D, Hogan B, Sarpong N, Winter D, Struck NS, Adu-Sarkodie Y, Owusu-Dabo E, Schmidt-Chanasit J, May J, Cadar D. Viral metagenomics revealed novel betatorquevirus species in pediatric inpatients with encephalitis/meningoencephalitis from Ghana. Sci Rep 2019; 9:2360. [PMID: 30787417 PMCID: PMC6382885 DOI: 10.1038/s41598-019-38975-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 11/28/2018] [Indexed: 02/07/2023] Open
Abstract
The cause of acute encephalitis/meningoencephalitis in pediatric patients remains often unexplained despite extensive investigations for large panel of pathogens. To explore a possible viral implication, we investigated the virome of cerebrospinal fluid specimens of 70 febrile pediatric inpatients with clinical compatible encephalitis/meningoencephalitis. Using viral metagenomics, we detected and genetically characterized three novel human Torque teno mini virus (TTMV) species (TTMV-G1-3). Phylogenetically, TTMV-G1-3 clustered in three novel monophyletic lineages within genus Betatorquevirus of the Anelloviridae family. TTMV-G1-3 were highly prevalent in diseased children, but absent in the healthy cohort which may indicate an association of TTMV species with febrile illness. With 2/3 detected malaria co-infection, it remains unclear if these novel anellovirus species are causative agents or increase disease severity by interaction with malaria parasites. The presence of the viruses 28 days after initiating antimalarial and/or antibiotic treatment suggests a still active viral infection likely as effect of parasitic and/or bacterial co-infection that may have initiated a modulated immune system environment for viral replication or a defective virus clearance. This study increases the current knowledge on the genetic diversity of TTMV and strengthens that human anelloviruses can be considered as biomarkers for strong perturbations of the immune system in certain pathological conditions.
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Affiliation(s)
- Daniel Eibach
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, 20359, Germany.,German Center for Infection Research, Hamburg-Borstel-Lübeck-Riems, Borstel, 20359, Germany
| | - Benedikt Hogan
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, 20359, Germany.,German Center for Infection Research, Hamburg-Borstel-Lübeck-Riems, Borstel, 20359, Germany
| | - Nimako Sarpong
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, 40080, Ghana
| | - Doris Winter
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, 20359, Germany
| | - Nicole S Struck
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, 20359, Germany
| | - Yaw Adu-Sarkodie
- Department of Clinical Microbiology, Kwame Nkrumah University of Science and Technology, Kumasi, 40080, Ghana
| | - Ellis Owusu-Dabo
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, 40080, Ghana
| | - Jonas Schmidt-Chanasit
- German Center for Infection Research, Hamburg-Borstel-Lübeck-Riems, Borstel, 20359, Germany.,Department of Arbovirology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, 20359, Germany
| | - Jürgen May
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, 20359, Germany.,German Center for Infection Research, Hamburg-Borstel-Lübeck-Riems, Borstel, 20359, Germany
| | - Daniel Cadar
- German Center for Infection Research, Hamburg-Borstel-Lübeck-Riems, Borstel, 20359, Germany. .,Department of Arbovirology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, 20359, Germany.
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196
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The detection of donor-derived cell-free DNA may serve as a biomarker for the early detection of chronic lung allograft dysfunction. EBioMedicine 2019; 40:13-14. [PMID: 30737085 PMCID: PMC6413678 DOI: 10.1016/j.ebiom.2019.01.044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 01/22/2019] [Indexed: 01/08/2023] Open
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197
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Yinda CK, Vanhulle E, Conceição-Neto N, Beller L, Deboutte W, Shi C, Ghogomu SM, Maes P, Van Ranst M, Matthijnssens J. Gut Virome Analysis of Cameroonians Reveals High Diversity of Enteric Viruses, Including Potential Interspecies Transmitted Viruses. mSphere 2019; 4:e00585-18. [PMID: 30674646 PMCID: PMC6344602 DOI: 10.1128/msphere.00585-18] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 12/17/2018] [Indexed: 12/11/2022] Open
Abstract
Diarrhea remains one of the most common causes of deaths in children. A limited number of studies have investigated the prevalence of enteric pathogens in Cameroon, and as in many other African countries, the cause of many diarrheal episodes remains unexplained. A proportion of these unknown cases of diarrhea are likely caused by yet-unidentified viral agents, some of which could be the result of (recent) interspecies transmission from animal reservoirs, like bats. Using viral metagenomics, we screened fecal samples of 221 humans (almost all with gastroenteritis symptoms) between 0 and 89 years of age with different degrees of bat contact. We identified viruses belonging to families that are known to cause gastroenteritis such as Adenoviridae, Astroviridae, Caliciviridae, Picornaviridae, and Reoviridae Interestingly, a mammalian orthoreovirus, picobirnaviruses, a smacovirus, and a pecovirus were also found. Although there was no evidence of interspecies transmission of the most common human gastroenteritis-related viruses (Astroviridae, Caliciviridae, and Reoviridae), the phylogenies of the identified orthoreovirus, picobirnavirus, and smacovirus indicate a genetic relatedness of these viruses identified in stools of humans and those of bats and/or other animals. These findings points out the possibility of interspecies transmission or simply a shared host of these viruses (bacterial, fungal, parasitic, …) present in both animals (bats) and humans. Further screening of bat viruses in humans or vice versa will elucidate the epidemiological potential threats of animal viruses to human health. Furthermore, this study showed a huge diversity of highly divergent novel phages, thereby expanding the existing phageome considerably.IMPORTANCE Despite the availability of diagnostic tools for different enteric viral pathogens, a large fraction of human cases of gastroenteritis remains unexplained. This could be due to pathogens not tested for or novel divergent viruses of potential animal origin. Fecal virome analyses of Cameroonians showed a very diverse group of viruses, some of which are genetically related to those identified in animals. This is the first attempt to describe the gut virome of humans from Cameroon. Therefore, the data represent a baseline for future studies on enteric viral pathogens in this area and contribute to our knowledge of the world's virome. The studies also highlight the fact that more viruses may be associated with diarrhea than the typical known ones. Hence, it provides meaningful epidemiological information on diarrhea-related viruses in this area.
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Affiliation(s)
- Claude Kwe Yinda
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, KU Leuven-University of Leuven, Leuven, Belgium
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory for Clinical and Epidemiological Virology, KU Leuven-University of Leuven, Leuven, Belgium
| | - Emiel Vanhulle
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, KU Leuven-University of Leuven, Leuven, Belgium
| | - Nádia Conceição-Neto
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, KU Leuven-University of Leuven, Leuven, Belgium
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory for Clinical and Epidemiological Virology, KU Leuven-University of Leuven, Leuven, Belgium
| | - Leen Beller
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, KU Leuven-University of Leuven, Leuven, Belgium
| | - Ward Deboutte
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, KU Leuven-University of Leuven, Leuven, Belgium
| | - Chenyan Shi
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, KU Leuven-University of Leuven, Leuven, Belgium
| | - Stephen Mbigha Ghogomu
- Department of Biochemistry and Molecular Biology, Biotechnology Unit, Molecular and Cell Biology Laboratory, University of Buea, Buea, Cameroon
| | - Piet Maes
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory for Clinical and Epidemiological Virology, KU Leuven-University of Leuven, Leuven, Belgium
| | - Marc Van Ranst
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory for Clinical and Epidemiological Virology, KU Leuven-University of Leuven, Leuven, Belgium
| | - Jelle Matthijnssens
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, KU Leuven-University of Leuven, Leuven, Belgium
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198
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Eskandary F, Dürr M, Budde K, Doberer K, Reindl-Schwaighofer R, Waiser J, Wahrmann M, Regele H, Spittler A, Lachmann N, Firbas C, Mühlbacher J, Bond G, Halloran PF, Chong E, Jilma B, Böhmig GA. Clazakizumab in late antibody-mediated rejection: study protocol of a randomized controlled pilot trial. Trials 2019; 20:37. [PMID: 30635033 PMCID: PMC6329051 DOI: 10.1186/s13063-018-3158-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Accepted: 12/22/2018] [Indexed: 01/23/2023] Open
Abstract
Background Late antibody-mediated rejection (ABMR) triggered by donor-specific antibodies (DSA) is a cardinal cause of kidney allograft dysfunction and loss. Diagnostic criteria for this rejection type are well established, but effective treatment remains a major challenge. Recent randomized controlled trials (RCT) have failed to demonstrate the efficacy of widely used therapies, such as rituximab plus intravenous immunoglobulin or proteasome inhibition (bortezomib), reinforcing a great need for new therapeutic concepts. One promising target in this context may be interleukin-6 (IL-6), a pleiotropic cytokine known to play an important role in inflammation and adaptive immunity. Methods This investigator-driven RCT was designed to assess the safety and efficacy of clazakizumab, a genetically engineered humanized monoclonal antibody directed against IL-6. The study will include 20 DSA-positive kidney allograft recipients diagnosed with ABMR ≥ 365 days after transplantation. Participants will be recruited at two study sites in Austria and Germany (Medical University of Vienna; Charité University Medicine Berlin). First, patients will enter a three-month double-blind RCT (1,1 randomization, stratification according to ABMR phenotype and study site) and will receive either clazakizumab (subcutaneous administration of 25 mg in monthly intervals) or placebo. In a second open-label part of the trial (months 4–12), all patients will receive clazakizumab at 25 mg every month. The primary endpoint is safety and tolerability. Secondary endpoints are the pharmacokinetics and pharmacodynamics of clazakizumab, its effect on drug metabolism in the liver, DSA characteristics, morphological ABMR lesions and molecular gene expression patterns in three- and 12-month protocol biopsies, serum/urinary biomarkers of inflammation and endothelial activation/injury, Torque Teno viral load as a measure of overall immunosuppression, kidney function, urinary protein excretion, as well as transplant and patient survival. Discussion Currently, there is no treatment proven to be effective in halting the progression of late ABMR. Based on the hypothesis that antagonizing the effects of IL-6 improves the outcome of DSA-positive late ABMR by counteracting DSA-triggered inflammation and B cell/plasma cell-driven alloimmunity, we suggest that our trial has the potential to provide proof of concept of a novel treatment of this type of rejection. Trial registration ClinicalTrials.gov, NCT03444103. Registered on 23 February 2018 (retrospective registration). Electronic supplementary material The online version of this article (10.1186/s13063-018-3158-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Farsad Eskandary
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Währinger Gürtel 18-20, A-1090, Vienna, Austria
| | - Michael Dürr
- Department of Nephrology, Charité University Medicine Berlin, Berlin, Germany
| | - Klemens Budde
- Department of Nephrology, Charité University Medicine Berlin, Berlin, Germany
| | - Konstantin Doberer
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Währinger Gürtel 18-20, A-1090, Vienna, Austria
| | - Roman Reindl-Schwaighofer
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Währinger Gürtel 18-20, A-1090, Vienna, Austria
| | - Johannes Waiser
- Department of Nephrology, Charité University Medicine Berlin, Berlin, Germany
| | - Markus Wahrmann
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Währinger Gürtel 18-20, A-1090, Vienna, Austria
| | - Heinz Regele
- Department of Clinical Pathology, Medical University of Vienna, Vienna, Austria
| | - Andreas Spittler
- Core Facility Flow Cytometry, Medical University of Vienna, Vienna, Austria
| | - Nils Lachmann
- Centre for Tumor Medicine, H&I Laboratory, Charité University Medicine Berlin, Berlin, Germany
| | - Christa Firbas
- Department of Clinical Pharmacology, Medical University of Vienna, Währinger Gürtel 18-20, A-1090, Vienna, Austria
| | - Jakob Mühlbacher
- Department of Surgery, Medical University of Vienna, Vienna, Austria
| | - Gregor Bond
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Währinger Gürtel 18-20, A-1090, Vienna, Austria
| | - Philipp F Halloran
- Alberta Transplant Applied Genomics Centre, Faculty of Medicine & Dentistry, #250 Heritage Medical Research Centre, University of Alberta, Edmonton, AB, Canada
| | | | - Bernd Jilma
- Department of Clinical Pharmacology, Medical University of Vienna, Währinger Gürtel 18-20, A-1090, Vienna, Austria.
| | - Georg A Böhmig
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Währinger Gürtel 18-20, A-1090, Vienna, Austria.
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199
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Stefanaki C. The Gut Microbiome Beyond the Bacteriome—The Neglected Role of Virome and Mycobiome in Health and Disease. MICROBIOME AND METABOLOME IN DIAGNOSIS, THERAPY, AND OTHER STRATEGIC APPLICATIONS 2019. [DOI: 10.1016/b978-0-12-815249-2.00003-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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200
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Lin Y, Wang BX, Zhang NN, Zhang L, Gao ZB, Tian J, Jiang X. Metagenomic Analysis Identified Stenotrophomonas maltophilia Pneumonia in an Infant Suffering From Unexplained Very Severe Pneumonia. Front Pediatr 2019; 7:380. [PMID: 31608265 PMCID: PMC6761247 DOI: 10.3389/fped.2019.00380] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 09/03/2019] [Indexed: 11/26/2022] Open
Abstract
Pneumonia poses a significant global morbidity and mortality burden on children. Etiological diagnosis and matched anti-microbial therapy are particularly important for very severe pneumonia. Although great advances have been achieved in diagnostic approaches, it remains challenging to identify pathogens in unexplained pneumonia (UP) cases. In this study, we applied next-generation sequencing (NGS) technology and a metagenomic approach to detect and characterize respiratory bactiera in an UP case in infant. Stenotrophomonas maltophilia was the only bacterial pathogen detected in blood. Metagenomic sequencing also provided bacteria genomic sequences, which could be used to evaluate the role of this pathogen in the disease. This NGS method has the potential to improve the identification of causative organisms in patients with pneumonia and the delivery of appropriate, pathogen-directed antibiotic therapy.
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Affiliation(s)
- Yan Lin
- Department of Pediatrics, Tangdu Hospital, Air Force Medical University, Xi'an, China
| | - Bao-Xi Wang
- Department of Pediatrics, Tangdu Hospital, Air Force Medical University, Xi'an, China
| | - Ni-Ni Zhang
- Department of Pediatrics, Tangdu Hospital, Air Force Medical University, Xi'an, China
| | - Lei Zhang
- Department of Pediatrics, Tangdu Hospital, Air Force Medical University, Xi'an, China
| | - Zhi-Bo Gao
- Department of Pediatrics, Tangdu Hospital, Air Force Medical University, Xi'an, China
| | - Jiao Tian
- Department of Pediatrics, Tangdu Hospital, Air Force Medical University, Xi'an, China
| | - Xun Jiang
- Department of Pediatrics, Tangdu Hospital, Air Force Medical University, Xi'an, China
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