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Maqsood R, Wu LI, Brennan DC, Lim ES. Longitudinal alterations in the urinary virome of kidney transplant recipients are influenced by BK viremia and patient sex. Microbiol Spectr 2024; 12:e0405523. [PMID: 38916313 PMCID: PMC11302341 DOI: 10.1128/spectrum.04055-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 05/30/2024] [Indexed: 06/26/2024] Open
Abstract
Little is known about the urinary virome and how it interacts with the host, particularly in renal transplant diseases. Using metagenomic sequencing, we characterized the urinary virome of 23 kidney transplant recipients longitudinally (11 BKV+ patients and 12 BKV- patients). We applied linear mixed effects models, PERMANOVA, k-means clustering, and MaAsLin2 algorithms to determine virome signatures associated with post-transplant time, BK viremia status, and patient sex. We found that the richness and alpha diversity of urinary virome were significantly different in renal transplant recipients with BKV+ over time in comparison to BKV- (richness P = 0.012, alpha P < 0.0001). Female BKV- patients had significantly higher virome richness than males (P = 0.0063). Virome beta diversity was significantly different between patients by BKV status (P < 0.001). Additionally, we identified underlying interactions between patient sex and BKV status, in terms of virome beta diversity (P = 0.008). BK polyomavirus infections were primarily of subtypes IA, IB1, and IB2. The non-BK dominant samples clustered into six urinary virome community states. BKV- samples had more anelloviruses than BKV+ samples though this difference was not statistically significant. Lastly, we identified specific viruses, associated with BKV+ and time in our samples. Our results indicate that dynamic alterations in the urinary virome over the post-transplant period in kidney transplant recipients can be shaped by BK viremia and patient sex. These findings advance our fundamental understanding of the urinary virome and support a new line of investigation in renal disease and transplantation. IMPORTANCE The urinary microbiome is increasingly implicated in renal health and disease. While most research focuses on bacteria communities of the microbiome, factors that influence the urinary virome are not understood. Here, we investigated the urinary virome of 23 adult kidney transplant recipients longitudinally over 14 weeks post-transplant. We show that alterations in the urinary virome are associated with kidney transplant recipients with BK polyomavirus viremia that can lead to BK nephropathy and allograft rejection. By modeling the temporal dynamics post-transplant, we delineated specific profiles of the urinary virome associated with patient sex and urinary community states. These findings reveal fundamental aspects of the urinary virome that can be leveraged to better manage kidney diseases.
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Affiliation(s)
- Rabia Maqsood
- Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Lily I. Wu
- Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Daniel C. Brennan
- Department of Medicine, Division of Nephrology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Efrem S. Lim
- Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
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2
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Grygorcewicz B, Gliźniewicz M, Jabłońska J, Augustyniak A, Olszewska P, Wojciuk B, Miłek D, Serwin N, Czajkowski A, Cecerska-Heryć E, Rakoczy R, Cymbaluk-Płoska A. Bacteriophage-based approach for treatment of urinary tract infections: a quick outlook. APMIS 2024; 132:81-93. [PMID: 38031200 DOI: 10.1111/apm.13362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 11/08/2023] [Indexed: 12/01/2023]
Abstract
Urinary tract infections (UTIs) are among the most common bacterial infections affecting millions worldwide. The increasing emergence of antibiotic-resistant bacteria has become a serious concern in managing UTIs. Therefore, there is a growing interest in using bacteriophages as an alternative or adjunct therapy for UTIs. Bacteriophages are viruses that infect and kill bacteria, making them a promising tool for treating UTIs caused by antibiotic-resistant bacteria. This article provides a quick outlook on using bacteriophages to treat UTIs. We summarize the current understanding of the biology of bacteriophages, the challenges associated with developing phage-based therapies, and the promising results of several case reports and clinical trials. We also highlight the potential of phage therapy as a valuable tool in the fight against antibiotic-resistant UTIs. This quick outlook on a bacteriophage-based approach for treating UTIs offers a timely and informative summary of the current research in this field.
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Affiliation(s)
- Bartłomiej Grygorcewicz
- Faculty of Pharmacy, Medical Biotechnology and Laboratory Medicine, Pomeranian Medical University in Szczecin, Szczecin, Poland
- Department of Chemical and Process Engineering, Faculty of Chemical Technology and Engineering, West Pomeranian University of Technology, Szczecin, Szczecin, Poland
| | - Marta Gliźniewicz
- Faculty of Pharmacy, Medical Biotechnology and Laboratory Medicine, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Joanna Jabłońska
- Department of Chemical and Process Engineering, Faculty of Chemical Technology and Engineering, West Pomeranian University of Technology, Szczecin, Szczecin, Poland
| | - Adrian Augustyniak
- Department of Chemical and Process Engineering, Faculty of Chemical Technology and Engineering, West Pomeranian University of Technology, Szczecin, Szczecin, Poland
- Chair of Building Materials and Construction Chemistry, Technische Universität Berlin, Germany, Berlin, Germany
- Institute of Biology, University of Szczecin, Szczecin, Poland
| | - Patrycja Olszewska
- Faculty of Pharmacy, Medical Biotechnology and Laboratory Medicine, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Bartosz Wojciuk
- Department of Immunology Diagnostics, Chair of Microbiology, Immunology and Laboratory Medicine, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Dominika Miłek
- Faculty of Pharmacy, Medical Biotechnology and Laboratory Medicine, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Natalia Serwin
- Faculty of Pharmacy, Medical Biotechnology and Laboratory Medicine, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Artur Czajkowski
- Faculty of Pharmacy, Medical Biotechnology and Laboratory Medicine, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Elżbieta Cecerska-Heryć
- Faculty of Pharmacy, Medical Biotechnology and Laboratory Medicine, Pomeranian Medical University in Szczecin, Szczecin, Poland
- Department of Chemical and Process Engineering, Faculty of Chemical Technology and Engineering, West Pomeranian University of Technology, Szczecin, Szczecin, Poland
| | - Rafał Rakoczy
- Department of Chemical and Process Engineering, Faculty of Chemical Technology and Engineering, West Pomeranian University of Technology, Szczecin, Szczecin, Poland
| | - Aneta Cymbaluk-Płoska
- Department of Reconstructive Surgery and Gynecological Oncology, Pomeranian Medical University in Szczecin, Szczecin, Poland
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3
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Elsayed NS, Wolfe AJ, Burk RD. Urine microbiome in individuals with an impaired immune system. Front Cell Infect Microbiol 2024; 13:1308665. [PMID: 38274734 PMCID: PMC10808152 DOI: 10.3389/fcimb.2023.1308665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 12/21/2023] [Indexed: 01/27/2024] Open
Abstract
With the advent of next generation sequencing, it is now appreciated that human urine is not sterile. Recent investigations of the urinary microbiome (urobiome) have provided insights into several urological diseases. Urobiome dysbiosis, defined as non-optimal urine microbiome composition, has been observed in many disorders; however, it is not clear whether this dysbiosis is the cause of urinary tract disorders or a consequence. In addition, immunologically altered disorders are associated with higher rates of urinary tract infections. These disorders include immunoproliferative and immunodeficiency diseases, cancer, and immunosuppressant therapy in transplant recipients. In this review, we examine the current state of knowledge of the urobiome in immunologically altered diseases, its composition and metabolomic consequences. We conclude that more data are required to describe the urobiome in immune altered states, knowledge that could facilitate understanding the role of the urobiome and its pathophysiological effects on urinary tract infections and other disorders of the urinary tract.
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Affiliation(s)
- Noha S. Elsayed
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Alan J. Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States
| | - Robert D. Burk
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, United States
- Departments of Microbiology and Immunology, Epidemiology and Population Health, and Obstetrics & Gynecology and Women’s Health, Albert Einstein College of Medicine, Bronx, NY, United States
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4
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Wang H, Xu S, Li S, Su B, Sherrill-Mix S, Liang G. Virome in immunodeficiency: what we know currently. Chin Med J (Engl) 2023; 136:2647-2657. [PMID: 37914672 PMCID: PMC10684123 DOI: 10.1097/cm9.0000000000002899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Indexed: 11/03/2023] Open
Abstract
ABSTRACT Over the past few years, the human virome and its complex interactions with microbial communities and the immune system have gained recognition as a crucial factor in human health. Individuals with compromised immune function encounter distinctive challenges due to their heightened vulnerability to a diverse range of infectious diseases. This review aims to comprehensively explore and analyze the growing evidence regarding the role of the virome in immunocompromised disease status. By surveying the latest literature, we present a detailed overview of virome alterations observed in various immunodeficiency conditions. We then delve into the influence and mechanisms of these virome changes on the pathogenesis of specific diseases in immunocompromised individuals. Furthermore, this review explores the clinical relevance of virome studies in the context of immunodeficiency, highlighting the potential diagnostic and therapeutic gains from a better understanding of virome contributions to disease manifestations.
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Affiliation(s)
- Hu Wang
- Beijing Key Laboratory for HIV/AIDS Research, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Siqi Xu
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Shuang Li
- Beijing Key Laboratory for HIV/AIDS Research, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Bin Su
- Beijing Key Laboratory for HIV/AIDS Research, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Scott Sherrill-Mix
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Guanxiang Liang
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
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Eldem V, Kuralay SC, Özdoğan G, Özçelik GH, Aydın D, Çakmak G, Gürler MÖ, Çay SB, Çınar YU, Dikmen F, Yusuf I, Obut O, Kayalar Ö, Zararsız GE, Edizadeh M, Zararsız G, Akdeniz E, Özgür H, Tekin IM. Comprehensive analysis of circulating viral DNA in maternal plasma at population-scale using low-pass whole-genome sequencing. Genomics 2023; 115:110556. [PMID: 36599399 DOI: 10.1016/j.ygeno.2022.110556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 11/04/2022] [Accepted: 12/30/2022] [Indexed: 01/02/2023]
Abstract
As the most readily adopted molecular screening test, low-pass WGS of maternal plasma cell-free DNA for aneuploidy detection generates a vast amount of genomic data. This large-scale method also allows for high-throughput virome screening. NIPT sequencing data, yielding 6.57 terabases of data from 187.8 billion reads, from 12,951 pregnant Turkish women was used to investigate the prevalence and abundance of viral DNA in plasma. Among the 22 virus sequences identified in 12% of participants were human papillomavirus, herpesvirus, betaherpesvirus and anellovirus. We observed a unique pattern of circulating viral DNA with a high prevalence of papillomaviruses. The prevalence of herpesviruses/anellovirus was similar among Turkish, European and Dutch populations. Hepatitis B prevalence was remarkably low in Dutch, European and Turkish populations, but higher in China. WGS data revealed that herpesvirus/anelloviruses are naturally found in European populations. This represents the first comprehensive research on the plasma virome of pregnant Turkish women.
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Affiliation(s)
- Vahap Eldem
- Department of Biology, Faculty of Science, Istanbul University, Istanbul 34134, Turkey.
| | - Selim Can Kuralay
- Department of Biology, Faculty of Science, Istanbul University, Istanbul 34134, Turkey
| | - Gülperi Özdoğan
- GENOKS Genetic Disease Diagnostic Center, Ankara 06560, Turkey
| | | | - Dilşah Aydın
- GENOKS Genetic Disease Diagnostic Center, Ankara 06560, Turkey
| | - Gökçe Çakmak
- GENOKS Genetic Disease Diagnostic Center, Ankara 06560, Turkey
| | | | - Selahattin Barış Çay
- Department of Biology, Faculty of Science, Istanbul University, Istanbul 34134, Turkey
| | - Yusuf Ulaş Çınar
- Department of Biology, Faculty of Science, Istanbul University, Istanbul 34134, Turkey
| | - Fatih Dikmen
- Department of Biology, Faculty of Science, Istanbul University, Istanbul 34134, Turkey
| | - Ishak Yusuf
- GENOKS Genetic Disease Diagnostic Center, Ankara 06560, Turkey
| | - Onur Obut
- Department of Biology, Faculty of Science, Istanbul University, Istanbul 34134, Turkey
| | - Özgecan Kayalar
- Koc University Research Center for Translational Medicine (KUTTAM), Koc University School of Medicine, Istanbul 34010, Turkey
| | - Gözde Ertürk Zararsız
- Department of Biostatistics, Erciyes University Medical Faculty, Kayseri 38280, Turkey; Erciyes University, Drug Application and Research Center (ERFARMA), Kayseri 38280, Turkey
| | - Masoud Edizadeh
- GENOKS Genetic Disease Diagnostic Center, Ankara 06560, Turkey
| | - Gökmen Zararsız
- Department of Biostatistics, Erciyes University Medical Faculty, Kayseri 38280, Turkey; Erciyes University, Drug Application and Research Center (ERFARMA), Kayseri 38280, Turkey
| | - Eren Akdeniz
- GENOKS Genetic Disease Diagnostic Center, Ankara 06560, Turkey
| | - Hilal Özgür
- GENOKS Genetic Disease Diagnostic Center, Ankara 06560, Turkey
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Dynamics of Human Anelloviruses in Plasma and Clinical Outcomes Following Kidney Transplantation. Transplantation 2023; 107:511-520. [PMID: 36042550 DOI: 10.1097/tp.0000000000004292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
BACKGROUND Torque teno virus, the major member of the genus Alphatorquevirus , is an emerging biomarker of the net state of immunosuppression after kidney transplantation. Genetic diversity constitutes a main feature of the Anelloviridae family, although its posttransplant dynamics and clinical correlates are largely unknown. METHODS The relative abundance of Alphatorquevirus , Betatorquevirus , and Gammatorquevirus genera was investigated by high-throughput sequencing in plasma specimens obtained at various points during the first posttransplant year (n = 91 recipients). Total loads of all members of the Anelloviridae family were also quantified by an "in-house" polymerase chain reaction assay targeting conserved DNA sequences (n = 195 recipients). In addition to viral kinetics, clinical study outcomes included serious infection, immunosuppression-related adverse event (opportunistic infection and cancer)' and acute rejection. RESULTS Alphatorquevirus DNA was detected in all patients at every point, with an increase from pretransplantation to month 1. A variable proportion of recipients had detectable Betatorquevirus and Gammatorquevirus at lower frequencies. At least 1 change in the predominant genus (mainly as early transition to Alphatorquevirus predominance) was shown in 35.6% of evaluable patients. Total anelloviruses DNA levels increased from baseline to month 1, to peak by month 3 and decrease thereafter, and were higher in patients treated with T-cell depleting agents. There was a significant albeit weak-to-moderate correlation between total anelloviruses and TTV DNA levels. No associations were found between the predominant Anelloviridae genus or total anelloviruses DNA levels and clinical outcomes. CONCLUSIONS Our study provides novel insight into the evolution of the anellome after kidney transplantation.
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7
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Hejtmánková A, Caisová H, Tomanová T, Španielová H. The role of the DE and EF loop of BKPyV VP1 in the serological cross-reactivity between subtypes. Virus Res 2023; 324:199031. [PMID: 36587871 DOI: 10.1016/j.virusres.2022.199031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 12/12/2022] [Accepted: 12/21/2022] [Indexed: 12/31/2022]
Abstract
BK virus (BKPyV) is a causative agent of BKPyV-associated nephropathy and graft rejections in kidney transplant patients. It establishes persistent infection in the kidneys, which can lead to reactivation in an immunosuppressed state or transmission to kidney recipients. Complications in the case of donor-derived infections can be caused by differences between the four known BKPyV subtypes, as prior infection with one subtype does not guarantee protection against de novo infection with other subtypes. The recipient and donor pretransplant serotyping is not routinely performed since simple ELISA tests employing antigens derived from the major viral capsid protein 1 (VP1) are hindered by the high cross-reactivity of anti-VP1 antibodies against all subtypes. Identifying subtype-specific epitopes in VP1 could lead to the design of specific antigens and the improvement of serodiagnostics for kidney transplantation. We aimed to study the surface residues responsible for the interactions with the subtype-specific antibodies by focusing on the DE and EF loops of VP1, which have only a small number of distinct amino acid differences between the most common subtypes, BKPyV-I and BKPyV-IV. We designed two mutant virus-like particles (VLPs): we introduced BKPyV-I characteristic amino acid residues (either H139N in the DE loop or D175E and I178V changes in the EF loop) into the base sequence of a BKPyV-IV VP1. This way, we created BKPyV-IV mutant VLPs with the sequence of either the BKPyV-I DE loop or the BKPyV-I EF loop. These mutants were then used as competing antigens in an antigen competition assay with a panel of patient sera, and changes in antibody reactivity were assessed by ELISA. We found that the changes introduced into the BKPyV-IV VP1 EF loop restrict antibody recognition in most samples and that converting the BKPyV-IV DE loop into its BKPyV-I equivalent attracts anti-VP1 BKPyV-I antibodies. Although our results did not lead to the discovery of a subtype-specific epitope on the VP1, they suggested that the arrangement of the EF loop in VP1 might dictate the mode of interaction between virus and anti-VP1 antibodies in general and that the interactions between the antibodies and the viral capsid might be very complex. Consequently, an antigen competition assay as an assay to distinguish between BKPyV serotypes might prove difficult to interpret.
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Affiliation(s)
- Alžběta Hejtmánková
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague 2, Czech Republic
| | - Helena Caisová
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague 2, Czech Republic
| | - Tereza Tomanová
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague 2, Czech Republic
| | - Hana Španielová
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague 2, Czech Republic; Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 542/2, 166 10, Praha 5, Czech Republic.
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8
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Sen T, Thummer RP. The Impact of Human Microbiotas in Hematopoietic Stem Cell and Organ Transplantation. Front Immunol 2022; 13:932228. [PMID: 35874759 PMCID: PMC9300833 DOI: 10.3389/fimmu.2022.932228] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/06/2022] [Indexed: 11/18/2022] Open
Abstract
The human microbiota heavily influences most vital aspects of human physiology including organ transplantation outcomes and transplant rejection risk. A variety of organ transplantation scenarios such as lung and heart transplantation as well as hematopoietic stem cell transplantation is heavily influenced by the human microbiotas. The human microbiota refers to a rich, diverse, and complex ecosystem of bacteria, fungi, archaea, helminths, protozoans, parasites, and viruses. Research accumulating over the past decade has established the existence of complex cross-species, cross-kingdom interactions between the residents of the various human microbiotas and the human body. Since the gut microbiota is the densest, most popular, and most studied human microbiota, the impact of other human microbiotas such as the oral, lung, urinary, and genital microbiotas is often overshadowed. However, these microbiotas also provide critical and unique insights pertaining to transplantation success, rejection risk, and overall host health, across multiple different transplantation scenarios. Organ transplantation as well as the pre-, peri-, and post-transplant pharmacological regimens patients undergo is known to adversely impact the microbiotas, thereby increasing the risk of adverse patient outcomes. Over the past decade, holistic approaches to post-transplant patient care such as the administration of clinical and dietary interventions aiming at restoring deranged microbiota community structures have been gaining momentum. Examples of these include prebiotic and probiotic administration, fecal microbial transplantation, and bacteriophage-mediated multidrug-resistant bacterial decolonization. This review will discuss these perspectives and explore the role of different human microbiotas in the context of various transplantation scenarios.
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Affiliation(s)
| | - Rajkumar P. Thummer
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India
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Kenneally C, Murphy CP, Sleator RD, Culligan EP. The Urinary Microbiome and Biological Therapeutics: Novel Therapies For Urinary Tract Infections. Microbiol Res 2022; 259:127010. [DOI: 10.1016/j.micres.2022.127010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 12/12/2022]
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Abstract
PURPOSE OF REVIEW Research in the past decade has revealed important implications for the microbiome in human health. Studies have defined a distinct gut microbiota in kidney transplant recipients and have recently linked the microbiota to infectious complications, similar to the allogeneic stem cell transplant population. RECENT FINDINGS In this review, we focus on the metabolism of immunosuppressive medications by the gut microbiota and on the urinary microbiome in the setting of infectious and immunological complications. We highlight seminal studies showing the role of specific gut microbiota in the direct metabolism of tacrolimus into a lesser effective immunosuppressant as well as the role of the gut microbiota in the metabolism of mycophenolic acid (MPA) glucuronide. We describe distinct urinary microbiota patterns in kidney transplant recipients with interstitial fibrosis tubular atrophy, chronic allograft nephropathy, tolerance, and bacterial and viral complications. SUMMARY The microbiota has important implications for immunosuppressive medications and immunological outcomes in kidney transplant recipients. Further research is needed to better delineate the impact of the metabolism of tacrolimus and MPA by gut bacteria and the role of the urine microbiota in the development of immunological and infectious complications.
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Affiliation(s)
| | | | - Tarek Barbar
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine
| | - John R Lee
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine
- Department of Transplantation Medicine, New York Presbyterian Hospital-Weill Cornell Medical Center, New York, New York, USA
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11
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Salabura A, Łuniewski A, Kucharska M, Myszak D, Dołęgowska B, Ciechanowski K, Kędzierska-Kapuza K, Wojciuk B. Urinary Tract Virome as an Urgent Target for Metagenomics. Life (Basel) 2021; 11:life11111264. [PMID: 34833140 PMCID: PMC8618529 DOI: 10.3390/life11111264] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/13/2021] [Accepted: 11/15/2021] [Indexed: 12/19/2022] Open
Abstract
Virome—a part of a microbiome—is a term used to describe all viruses found in the specific organism or system. Recently, as new technologies emerged, it has been confirmed that kidneys and the lower urinary tract are colonized not only by the previously described viruses, but also completely novel species. Viruses can be both pathogenic and protective, as they often carry important virulence factors, while at the same time represent anti-inflammatory functions. This paper aims to show and compare the viral species detected in various, specific clinical conditions. Because of the unique characteristics of viruses, new sequencing techniques and databases had to be developed to conduct research on the urinary virome. The dynamic development of research on the human microbiome suggests that the detailed studies on the urinary system virome will provide answers to many questions about the risk factors for civilization, cancer, and autoimmune diseases.
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Affiliation(s)
- Agata Salabura
- Clinic of Nephrology, Internal Medicine and Transplantation, Pomeranian Medical University in Szczecin, 70-123 Szczecin, Poland;
- Correspondence: ; Tel.: +48-664-477-450
| | - Aleksander Łuniewski
- Department of Immunological Diagnostics, Pomeranian Medical University in Szczecin, 70-123 Szczecin, Poland; (A.Ł.); (M.K.); (D.M.); (B.D.); (B.W.)
| | - Maria Kucharska
- Department of Immunological Diagnostics, Pomeranian Medical University in Szczecin, 70-123 Szczecin, Poland; (A.Ł.); (M.K.); (D.M.); (B.D.); (B.W.)
| | - Denis Myszak
- Department of Immunological Diagnostics, Pomeranian Medical University in Szczecin, 70-123 Szczecin, Poland; (A.Ł.); (M.K.); (D.M.); (B.D.); (B.W.)
| | - Barbara Dołęgowska
- Department of Immunological Diagnostics, Pomeranian Medical University in Szczecin, 70-123 Szczecin, Poland; (A.Ł.); (M.K.); (D.M.); (B.D.); (B.W.)
| | - Kazimierz Ciechanowski
- Clinic of Nephrology, Internal Medicine and Transplantation, Pomeranian Medical University in Szczecin, 70-123 Szczecin, Poland;
| | - Karolina Kędzierska-Kapuza
- Center of Postgraduate Medical Education in Warsaw, Department of Gastroenterological Surgery and Transplantology, 137 Wołoska St., 02-507 Warsaw, Poland;
| | - Bartosz Wojciuk
- Department of Immunological Diagnostics, Pomeranian Medical University in Szczecin, 70-123 Szczecin, Poland; (A.Ł.); (M.K.); (D.M.); (B.D.); (B.W.)
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12
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Arze CA, Springer S, Dudas G, Patel S, Bhattacharyya A, Swaminathan H, Brugnara C, Delagrave S, Ong T, Kahvejian A, Echelard Y, Weinstein EG, Hajjar RJ, Andersen KG, Yozwiak NL. Global genome analysis reveals a vast and dynamic anellovirus landscape within the human virome. Cell Host Microbe 2021; 29:1305-1315.e6. [PMID: 34320399 DOI: 10.1016/j.chom.2021.07.001] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 04/23/2021] [Accepted: 06/11/2021] [Indexed: 12/14/2022]
Abstract
Anelloviruses are a ubiquitous component of healthy human viromes and remain highly prevalent after being acquired early in life. The full extent of "anellome" diversity and its evolutionary dynamics remain unexplored. We employed in-depth sequencing of blood-transfusion donor(s)-recipient pairs coupled with public genomic resources for a large-scale assembly of anellovirus genomes and used the data to characterize global and personal anellovirus diversity through time. The breadth of the anellome is much greater than previously appreciated, and individuals harbor unique anellomes and transmit lineages that can persist for several months within a diverse milieu of endemic host lineages. Anellovirus sequence diversity is shaped by extensive recombination at all levels of divergence, hindering traditional phylogenetic analyses. Our findings illuminate the transmission dynamics and vast diversity of anelloviruses and set the foundation for future studies to characterize their biology.
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Affiliation(s)
| | | | - Gytis Dudas
- Gothenburg Global Biodiversity Centre, Gothenburg 413 19, Sweden
| | | | | | | | - Carlo Brugnara
- Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Tuyen Ong
- Ring Therapeutics, Cambridge, MA 02139, USA
| | - Avak Kahvejian
- Ring Therapeutics, Cambridge, MA 02139, USA; Flagship Pioneering, Cambridge, MA 02142, USA
| | - Yann Echelard
- Ring Therapeutics, Cambridge, MA 02139, USA; Flagship Pioneering, Cambridge, MA 02142, USA
| | - Erica G Weinstein
- Ring Therapeutics, Cambridge, MA 02139, USA; Flagship Pioneering, Cambridge, MA 02142, USA
| | - Roger J Hajjar
- Ring Therapeutics, Cambridge, MA 02139, USA; Flagship Pioneering, Cambridge, MA 02142, USA
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13
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Mormando R, Wolfe AJ, Putonti C. Discriminating between JCPyV and BKPyV in Urinary Virome Data Sets. Viruses 2021; 13:v13061041. [PMID: 34072839 PMCID: PMC8230216 DOI: 10.3390/v13061041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 05/15/2021] [Accepted: 05/27/2021] [Indexed: 11/21/2022] Open
Abstract
Polyomaviruses are abundant in the human body. The polyomaviruses JC virus (JCPyV) and BK virus (BKPyV) are common viruses in the human urinary tract. Prior studies have estimated that JCPyV infects between 20 and 80% of adults and that BKPyV infects between 65 and 90% of individuals by age 10. However, these two viruses encode for the same six genes and share 75% nucleotide sequence identity across their genomes. While prior urinary virome studies have repeatedly reported the presence of JCPyV, we were interested in seeing how JCPyV prevalence compares to BKPyV. We retrieved all publicly available shotgun metagenomic sequencing reads from urinary microbiome and virome studies (n = 165). While one third of the data sets produced hits to JCPyV, upon further investigation were we able to determine that the majority of these were in fact BKPyV. This distinction was made by specifically mining for JCPyV and BKPyV and considering uniform coverage across the genome. This approach provides confidence in taxon calls, even between closely related viruses with significant sequence similarity.
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Affiliation(s)
- Rita Mormando
- Bioinformatics Program, Loyola University Chicago, Chicago, IL 60660, USA;
| | - Alan J. Wolfe
- Department of Microbiology and Immunology, Stitch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA;
| | - Catherine Putonti
- Bioinformatics Program, Loyola University Chicago, Chicago, IL 60660, USA;
- Department of Microbiology and Immunology, Stitch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA;
- Department of Biology, Loyola University Chicago, Chicago, IL 60660, USA
- Correspondence:
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14
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Prezioso C, Van Ghelue M, Pietropaolo V, Moens U. Detection of Quebec Polyomavirus DNA in Samples from Different Patient Groups. Microorganisms 2021; 9:microorganisms9051082. [PMID: 34070030 PMCID: PMC8158138 DOI: 10.3390/microorganisms9051082] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/14/2021] [Accepted: 05/17/2021] [Indexed: 12/16/2022] Open
Abstract
Polyomaviruses infect many species, including humans. So far, 15 polyomaviruses have been described in humans, but it remains to be established whether all of these are genuine human polyomaviruses. The most recent polyomavirus to be detected in a person is Quebec polyomavirus (QPyV), which was identified in a metagenomic analysis of a stool sample from an 85-year-old hospitalized man. We used PCR to investigate the presence of QPyV DNA in urine samples from systemic lupus erythematosus (SLE) patients (67 patients; 135 samples), multiple sclerosis patients (n = 35), HIV-positive patients (n = 66) and pregnant women (n = 65). Moreover, cerebrospinal fluid from patients with suspected neurological diseases (n = 63), nasopharyngeal aspirates from patients (n = 80) with respiratory symptoms and plasma samples from HIV-positive patients (n = 65) were examined. QPyV DNA was found in urine from 11 (16.4%), 10 (15.4%) and 5 (14.3%) SLE patients, pregnant women, and multiple sclerosis patients, respectively. No QPyV DNA could be detected in the other samples. Alignment with the only available QPyV sequence in the GenBank revealed amino acid substitutions in the HI-loop of capsid protein VP1 in 6/28 of the isolates. Our results show that QPyV viruria can occur, but whether it may cause clinical symptoms in the patients remains to be determined.
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Affiliation(s)
- Carla Prezioso
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, 00185 Rome, Italy;
- IRCSS San Raffaele Pisana, Microbiology of Chronic Neuro-degenerative Pathologies, 00163 Rome, Italy
| | - Marijke Van Ghelue
- Department of Medical Genetics, Division of Child and Adolescent Health, University Hospital of North Norway, 9038 Tromsø, Norway;
- Department of Clinical Medicine, Faculty of Health Sciences, University of Tromsø—The Arctic University of Norway, 9037 Tromsø, Norway
| | - Valeria Pietropaolo
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, 00185 Rome, Italy;
- Correspondence: (V.P.); (U.M.)
| | - Ugo Moens
- Department of Medical Biology, Faculty of Health Sciences, University of Tromsø—The Arctic University of Norway, 9037 Tromsø, Norway
- Correspondence: (V.P.); (U.M.)
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15
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Schreiber PW, Kufner V, Hübel K, Schmutz S, Zagordi O, Kaur A, Bayard C, Greiner M, Zbinden A, Capaul R, Böni J, Hirsch HH, Mueller TF, Mueller NJ, Trkola A, Huber M. Metagenomic Virome Sequencing in Living Donor and Recipient Kidney Transplant Pairs Revealed JC Polyomavirus Transmission. Clin Infect Dis 2020; 69:987-994. [PMID: 30508036 PMCID: PMC7108204 DOI: 10.1093/cid/ciy1018] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 11/29/2018] [Indexed: 12/29/2022] Open
Abstract
Background Before kidney transplantation, donors and recipients are routinely screened for viral pathogens using specific tests. Little is known about unrecognized viruses of the urinary tract that potentially result in transmission. Using an open metagenomic approach, we aimed to comprehensively assess virus transmission in living-donor kidney transplantation. Methods Living kidney donors and their corresponding recipients were enrolled at the time of transplantation. Follow-up study visits for recipients were scheduled 4–6 weeks and 1 year thereafter. At each visit, plasma and urine samples were collected and transplant recipients were evaluated for signs of infection or other transplant-related complications. For metagenomic analysis, samples were enriched for viruses, amplified by anchored random polymerase chain reaction (PCR), and sequenced using high-throughput metagenomic sequencing. Viruses detected by sequencing were confirmed using real-time PCR. Results We analyzed a total of 30 living kidney donor and recipient pairs, with a follow-up of at least 1 year. In addition to viruses commonly detected during routine post-transplant virus monitoring, metagenomic sequencing detected JC polyomavirus (JCPyV) in the urine of 7 donors and their corresponding recipients. Phylogenetic analysis confirmed infection with the donor strain in 6 cases, suggesting transmission from the transplant donor to the recipient, despite recipient seropositivity for JCPyV at the time of transplantation. Conclusions Metagenomic sequencing identified frequent transmission of JCPyV from kidney transplant donors to recipients. Considering the high incidence rate, future studies within larger cohorts are needed to define the relevance of JCPyV infection and the donor’s virome for transplant outcomes.
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Affiliation(s)
- Peter W Schreiber
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich
| | - Verena Kufner
- Institute of Medical Virology, University Hospital Zurich, and University of Zurich
| | - Kerstin Hübel
- Department of Nephrology, University Hospital Zurich, and University of Zurich
| | - Stefan Schmutz
- Institute of Medical Virology, University Hospital Zurich, and University of Zurich
| | - Osvaldo Zagordi
- Institute of Medical Virology, University Hospital Zurich, and University of Zurich
| | - Amandeep Kaur
- Department of Biomedicine, University of Basel, Switzerland
| | - Cornelia Bayard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich
| | - Michael Greiner
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich
| | - Andrea Zbinden
- Institute of Medical Virology, University Hospital Zurich, and University of Zurich
| | - Riccarda Capaul
- Institute of Medical Virology, University Hospital Zurich, and University of Zurich
| | - Jürg Böni
- Institute of Medical Virology, University Hospital Zurich, and University of Zurich
| | - Hans H Hirsch
- Department of Biomedicine, University of Basel, Switzerland
| | - Thomas F Mueller
- Department of Nephrology, University Hospital Zurich, and University of Zurich
| | - Nicolas J Mueller
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich
| | - Alexandra Trkola
- Institute of Medical Virology, University Hospital Zurich, and University of Zurich
| | - Michael Huber
- Institute of Medical Virology, University Hospital Zurich, and University of Zurich
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16
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Beyond Cytomegalovirus and Epstein-Barr Virus: a Review of Viruses Composing the Blood Virome of Solid Organ Transplant and Hematopoietic Stem Cell Transplant Recipients. Clin Microbiol Rev 2020; 33:33/4/e00027-20. [PMID: 32847820 DOI: 10.1128/cmr.00027-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Viral primary infections and reactivations are common complications in patients after solid organ transplantation (SOT) and hematopoietic stem cell transplantation (HSCT) and are associated with high morbidity and mortality. Among these patients, viral infections are frequently associated with viremia. Beyond the usual well-known viruses that are part of the routine clinical management of transplant recipients, numerous other viral signatures or genomes can be identified in the blood of these patients. The identification of novel viral species and variants by metagenomic next-generation sequencing has opened up a new field of investigation and new paradigms. Thus, there is a need to thoroughly describe the state of knowledge in this field with a review of all viral infections that should be scrutinized in high-risk populations. Here, we review the eukaryotic DNA and RNA viruses identified in blood, plasma, or serum samples of pediatric and adult SOT/HSCT recipients and the prevalence of their detection, with a particular focus on recently identified viruses and those for which their potential association with disease remains to be investigated, such as members of the Polyomaviridae, Anelloviridae, Flaviviridae, and Astroviridae families. Current knowledge of the clinical significance of these viral infections with associated viremia among transplant recipients is also discussed. To ensure a comprehensive description in these two populations, individuals described as healthy (mostly blood donors) are considered for comparative purposes. The list of viruses that should be on the clinicians' radar is certainly incomplete and will expand, but the challenge is to identify those of possible clinical significance.
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17
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Legoff J, Michonneau D, Socie G. The virome in hematology-Stem cell transplantation and beyond. Semin Hematol 2020; 57:19-25. [PMID: 32690140 DOI: 10.1053/j.seminhematol.2020.05.001] [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: 06/07/2019] [Accepted: 05/06/2020] [Indexed: 12/23/2022]
Abstract
The virome has been recently studied in hematology and mostly in the setting of allogeneic hematopoietic stem cell transplantation. However, in hematology (as in the setting of nonhematological disorders) the study of the microbiome (that indeed includes the virome) is a growing field. The overall field is moving beyond species catalogue to the understanding of the complex ecological relationship that microbes have with each other and with their host. Here we review the existing literature on the virome in transplant recipients and in other settings, and discuss potential applications of the virome study in hematology.
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Affiliation(s)
- Jérôme Legoff
- Université de Paris, INSERM U976, Paris, France; Microbiology department, Virology laboratory, Saint Louis Hospital, Paris, France
| | - David Michonneau
- Université de Paris, INSERM U976, Paris, France; Hematology-Transplantation, Saint Louis Hospital, Paris, France
| | - Gérard Socie
- Université de Paris, INSERM U976, Paris, France; Hematology-Transplantation, Saint Louis Hospital, Paris, France.
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18
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Mollerup S, Asplund M, Friis-Nielsen J, Kjartansdóttir KR, Fridholm H, Hansen TA, Herrera JAR, Barnes CJ, Jensen RH, Richter SR, Nielsen IB, Pietroni C, Alquezar-Planas DE, Rey-Iglesia A, Olsen PVS, Rajpert-De Meyts E, Groth-Pedersen L, von Buchwald C, Jensen DH, Gniadecki R, Høgdall E, Langhoff JL, Pete I, Vereczkey I, Baranyai Z, Dybkaer K, Johnsen HE, Steiniche T, Hokland P, Rosenberg J, Baandrup U, Sicheritz-Pontén T, Willerslev E, Brunak S, Lund O, Mourier T, Vinner L, Izarzugaza JMG, Nielsen LP, Hansen AJ. High-Throughput Sequencing-Based Investigation of Viruses in Human Cancers by Multienrichment Approach. J Infect Dis 2020; 220:1312-1324. [PMID: 31253993 PMCID: PMC6743825 DOI: 10.1093/infdis/jiz318] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 06/27/2019] [Indexed: 01/10/2023] Open
Abstract
Background Viruses and other infectious agents cause more than 15% of human cancer cases. High-throughput sequencing-based studies of virus-cancer associations have mainly focused on cancer transcriptome data. Methods In this study, we applied a diverse selection of presequencing enrichment methods targeting all major viral groups, to characterize the viruses present in 197 samples from 18 sample types of cancerous origin. Using high-throughput sequencing, we generated 710 datasets constituting 57 billion sequencing reads. Results Detailed in silico investigation of the viral content, including exclusion of viral artefacts, from de novo assembled contigs and individual sequencing reads yielded a map of the viruses detected. Our data reveal a virome dominated by papillomaviruses, anelloviruses, herpesviruses, and parvoviruses. More than half of the included samples contained 1 or more viruses; however, no link between specific viruses and cancer types were found. Conclusions Our study sheds light on viral presence in cancers and provides highly relevant virome data for future reference.
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Affiliation(s)
- Sarah Mollerup
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Maria Asplund
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Jens Friis-Nielsen
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | | | - Helena Fridholm
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Thomas Arn Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - José Alejandro Romero Herrera
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark.,Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | | | - Randi Holm Jensen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Stine Raith Richter
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Ida Broman Nielsen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Carlotta Pietroni
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - David E Alquezar-Planas
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Alba Rey-Iglesia
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Pernille V S Olsen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Ewa Rajpert-De Meyts
- Department of Growth and Reproduction, Copenhagen University Hospital (Rigshospitalet), Denmark
| | - Line Groth-Pedersen
- Department of Pediatrics and Adolescent Medicine, University Hospital Rigshospitalet, Denmark
| | - Christian von Buchwald
- Department of Otorhinolaryngology, Head and Neck Surgery and Audiology, Rigshospitalet, Copenhagen University Hospital
| | - David H Jensen
- Department of Otorhinolaryngology, Head and Neck Surgery and Audiology, Rigshospitalet, Copenhagen University Hospital
| | - Robert Gniadecki
- Department of Dermato-Venerology, Faculty of Health Sciences, Copenhagen University Hospital, Bispebjerg Hospital, Denmark
| | - Estrid Høgdall
- Department of Pathology, Herlev and Gentofte Hospital, University of Copenhagen, Denmark
| | - Jill Levin Langhoff
- Department of Pathology, Herlev and Gentofte Hospital, University of Copenhagen, Denmark
| | - Imre Pete
- National Institute of Oncology, Department of Gynecology, Budapest, Hungary
| | - Ildikó Vereczkey
- National Institute of Oncology, Department of Gynecology, Budapest, Hungary
| | - Zsolt Baranyai
- 1st Department of Surgery, Semmelweis University, Budapest, Hungary
| | - Karen Dybkaer
- Department of Clinical Medicine, Aalborg University, Denmark
| | | | | | - Peter Hokland
- Department of Clinical Medicine, Department of Haematology, Aarhus University Hospital, Denmark
| | - Jacob Rosenberg
- Department of Surgery, Herlev and Gentofte Hospital, University of Copenhagen, Denmark
| | - Ulrik Baandrup
- Center for Clinical Research, North Denmark Regional Hospital and Department of Clinical Medicine, Aalborg University, Hjørring, Denmark
| | - Thomas Sicheritz-Pontén
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark.,Centre of Excellence for Omics-Driven Computational Biodiscovery, AIMST University, Kedah, Malaysia
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Søren Brunak
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark.,Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Ole Lund
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | - Tobias Mourier
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Lasse Vinner
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Jose M G Izarzugaza
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | - Lars Peter Nielsen
- Department of Autoimmunology and Biomarkers, Statens Serum Institut, Copenhagen S, Denmark
| | - Anders Johannes Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
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19
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Sepulveda M, Pirozzolo I, Alegre ML. Impact of the microbiota on solid organ transplant rejection. Curr Opin Organ Transplant 2020; 24:679-686. [PMID: 31577594 DOI: 10.1097/mot.0000000000000702] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
PURPOSE OF REVIEW The microbiota in mammalian hosts can affect maturation and function of the immune system and has been associated with health and disease. We will review new findings on how this dynamic environmental factor impacts alloimmunity and therapy in transplant hosts. RECENT FINDINGS The microbiota changes after transplantation and immunosuppressive therapy. New data indicate that different microbial community structures have distinct impact on graft outcome, from promoting, to inhibiting or being neutral to transplant survival. In addition, we will address reciprocal interactions between the microbiota and immunosuppressive drugs, as well as the suitability of the microbiota as a predictive biomarker and its utility as adjunct therapy in transplantation. SUMMARY Advances in microbiome sequencing and wider availability of gnotobiotic facilities are enabling mechanistic investigations into the commensal communities and pathways that modulate allograft outcome, responsiveness to immunosuppression and side effects of drugs. A better understanding of the functions of the microbiota may help mitigate drug toxicity, predict drug dosage and dampen alloimmunity in transplant patients.
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20
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Abstract
The discovery of bacteria in the female urinary bladder has fundamentally changed current dogma regarding the urinary tract and related urinary disorders. Previous research characterized many of the bacterial components of the female urinary tract, but the viral fraction of this community is largely unknown. Viruses within the human microbiota far outnumber bacterial cells, with the most abundant viruses being those that infect bacteria (bacteriophages). Similar to observations within the microbiota of the gut and oral cavity, preliminary surveys of the urinary tract and bladder microbiota indicate a rich diversity of uncharacterized bacteriophage (phage) species. Phages are vital members of the microbiota, having critical roles in shaping bacterial metabolism and community structure. Although phages have been discovered in the urinary tract, such as phages that infect Escherichia coli, sampling them is challenging owing to low biomass, possible contamination when using non-invasive methods and the invasiveness of methods that reduce the potential for contamination. Phages could influence bladder health, but an understanding of the association between phage communities, bacterial populations and bladder health is in its infancy. However, evidence suggests that phages can defend the host against pathogenic bacteria and, therefore, modulation of the microbiome using phages has therapeutic potential for lower urinary tract symptoms. Furthermore, as natural predators of bacteria, phages have garnered renewed interest for their use as antimicrobial agents, for instance, in the treatment of urinary tract infections.
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21
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Lee Q, Padula MP, Pinello N, Williams SH, O'Rourke MB, Fumagalli MJ, Orkin JD, Song R, Shaban B, Brenner O, Pimanda JE, Weninger W, de Souza WM, Melin AD, Wong JJL, Crim MJ, Monette S, Roediger B, Jolly CJ. Murine and related chapparvoviruses are nephro-tropic and produce novel accessory proteins in infected kidneys. PLoS Pathog 2020; 16:e1008262. [PMID: 31971979 PMCID: PMC6999912 DOI: 10.1371/journal.ppat.1008262] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 02/04/2020] [Accepted: 12/08/2019] [Indexed: 12/21/2022] Open
Abstract
Mouse kidney parvovirus (MKPV) is a member of the provisional genus Chapparvovirus that causes renal disease in immune-compromised mice, with a disease course reminiscent of polyomavirus-associated nephropathy in immune-suppressed kidney transplant patients. Here we map four major MKPV transcripts, created by alternative splicing, to a common initiator region, and use mass spectrometry to identify “p10” and “p15” as novel chapparvovirus accessory proteins produced in MKPV-infected kidneys. p15 and the splicing-dependent putative accessory protein NS2 are conserved in all near-complete amniote chapparvovirus genomes currently available (from mammals, birds and a reptile). In contrast, p10 may be encoded only by viruses with >60% amino acid identity to MKPV. We show that MKPV is kidney-tropic and that the bat chapparvovirus DrPV-1 and a non-human primate chapparvovirus, CKPV, are also found in the kidneys of their hosts. We propose, therefore, that many mammal chapparvoviruses are likely to be nephrotropic. Parvoviruses are small, genetically simple single-strand DNA viruses that remain viable outside their hosts for very long periods of time. They cause disease in several domesticated species and in humans. Mouse kidney parvovirus (MKPV) is a causative agent of kidney failure in immune-compromised mice and is the only member of the provisional Chapparvovirus genus for which the complete genome including telomeres is known. Here, we show that MKPV propagates almost exclusively in the kidneys of mice infected naturally, wherein it produces novel accessory proteins whose coding regions are conserved in amniote-associated chapparvovirus sequences. We assemble a closely related complete viral genome present in DNA extracted from the kidney of a wild Cebus imitator monkey, and show that another related chapparvovirus is preferentially found in kidneys of the vampire bat Desmodus rotundus. We conclude that many mammal-hosted chapparvovirus are adapted to the kidney niche and may therefore cause disease following kidney stress in multiple species.
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Affiliation(s)
- Quintin Lee
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Matthew P. Padula
- Proteomics Core Facility, University of Technology Sydney, Sydney, NSW, Australia
| | - Natalia Pinello
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Simon H. Williams
- Center for Infection & Immunity, Mailman School of Public Health, Columbia University, New York, NY, United States of America
| | - Matthew B. O'Rourke
- Kolling Institute of Medical Research, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Marcilio Jorge Fumagalli
- Virology Research Center, School of Medicine of Ribeirão Preto of the University of São Paulo, Ribeirão Preto, Brazil
| | - Joseph D. Orkin
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
- Department of Anthropology and Archaeology, University of Calgary, Alberta, Canada
| | - Renhua Song
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Babak Shaban
- Melbourne Integrative Genomics, University of Melbourne, Melbourne, Victoria, Australia
| | - Ori Brenner
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - John E. Pimanda
- Lowy Cancer Research Centre, University of New South Wales Sydney, Sydney, NSW, Australia
| | - Wolfgang Weninger
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - William Marciel de Souza
- Virology Research Center, School of Medicine of Ribeirão Preto of the University of São Paulo, Ribeirão Preto, Brazil
| | - Amanda D. Melin
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
- Department of Medical Genetics and Alberta Children’s Hospital Research Institute, Cumming School of Medicine, University of Calgary, Alberta, Canada
| | - Justin J.-L. Wong
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Marcus J. Crim
- Microbiology and Aquatic Diagnostics, IDEXX BioAnalytics, Discovery Drive, Columbia, MO, United States of America
| | - Sébastien Monette
- Laboratory of Comparative Pathology, Center of Comparative Medicine and Pathology, Memorial Sloan Kettering Cancer Center, The Rockefeller University, Weill Cornell Medicine, New York, NY, United States of America
| | - Ben Roediger
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Autoimmunity, Transplantation, Inflammation (ATI) Disease Area, Novartis Institutes for Biomedical Research, Basel, Switzerland
- * E-mail: (BR); (CJJ)
| | - Christopher J. Jolly
- Lowy Cancer Research Centre, University of New South Wales Sydney, Sydney, NSW, Australia
- * E-mail: (BR); (CJJ)
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22
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Ackerman AL, Chai TC. The Bladder is Not Sterile: an Update on the Urinary Microbiome. CURRENT BLADDER DYSFUNCTION REPORTS 2019; 14:331-341. [PMID: 32612735 DOI: 10.1007/s11884-019-00543-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Purpose of Review The article discusses (1) techniques used to study bacterial urinary microbiota; (2) existence of non-bacterial urinary microbiota; (3) associations between changes in urinary microbiota and various benign lower urinary tract disorders. Recent Findings Urine harbors a diverse microbial community that resides within it. A multitude of studies have identified differences in these communities associated with urologic conditions, suggesting that microbial communities may maintain normal bladder homeostasis. Technological advances in analytic approaches have improved our understanding of the urinary microbiome. The choice of urine sampling method (voided, catheterized, or aspirated) will significantly influence microbiome findings. Sex and age highly influence urinary microbiota; in addition to rigorous inclusion criteria, microbial studies must be sufficiently powered to overcome the substantial interindividual variability of urinary microbiota. Regardless of these complicating factors, studies have identified microbial patterns correlating with both urologic diagnoses and treatment responses. Summary Without a clear understanding of the variability of and exogenous influences on the urinary microbiota in the absence of disease, it has been challenging to reveal the microbial patterns responsible for disease pathophysiology. Host mechanisms in response to the urinary microbiome are also poorly understood. Additional research can address whether the manipulation of urinary microbiota will benefit lower urinary tract health.
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Affiliation(s)
- A Lenore Ackerman
- Cedars-Sinai Medical Center, 99 N. La Cienega Blvd. Suite M102, Beverly Hills, CA 90211, USA
| | - Toby C Chai
- Boston Medical Center, Boston University School of Medicine, 725 Albany St., Suite 3B, Shapiro Building, Boston, MA 02118, USA
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Wojciuk B, Salabura A, Grygorcewicz B, Kędzierska K, Ciechanowski K, Dołęgowska B. Urobiome: In Sickness and in Health. Microorganisms 2019; 7:microorganisms7110548. [PMID: 31717688 PMCID: PMC6921077 DOI: 10.3390/microorganisms7110548] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/16/2019] [Accepted: 10/31/2019] [Indexed: 12/16/2022] Open
Abstract
The human microbiome has been proven to contribute to the human condition, both in health and in disease. The metagenomic approach based on next-generation sequencing has challenged the dogma of urine sterility. The human urobiome consists of bacteria and eukaryotic viruses as well as bacteriophages, which potentially represent the key factor. There have been several significant findings with respect to the urobiome in the context of urological disorders. Still, the research on the urobiome in chronic kidney disease and kidney transplantation remains underrepresented, as does research on the role of the virome in the urinary microbiota. In this review, we present recent findings on the urobiome with a particular emphasis on chronic kidney disease and post-kidney transplantation status. Challenges and opportunities arising from the research on the human urobiome will also be discussed.
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Affiliation(s)
- Bartosz Wojciuk
- Department of Immunological Diagnostics, Pomeranian Medical University in Szczecin, 70-123 Szczecin, Poland
- Correspondence: ; Tel.: +48-914-661-654
| | - Agata Salabura
- Clinic of Nephrology, Internal Medicine and Transplantation, Pomeranian Medical University in Szczecin, 70-123 Szczecin, Poland; (A.S.); (K.K.); (K.C.)
| | - Bartłomiej Grygorcewicz
- Department of Laboratory Medicine, Pomeranian Medical University in Szczecin, 70-123 Szczecin, Poland; (B.G.); (B.D.)
| | - Karolina Kędzierska
- Clinic of Nephrology, Internal Medicine and Transplantation, Pomeranian Medical University in Szczecin, 70-123 Szczecin, Poland; (A.S.); (K.K.); (K.C.)
| | - Kazimierz Ciechanowski
- Clinic of Nephrology, Internal Medicine and Transplantation, Pomeranian Medical University in Szczecin, 70-123 Szczecin, Poland; (A.S.); (K.K.); (K.C.)
| | - Barbara Dołęgowska
- Department of Laboratory Medicine, Pomeranian Medical University in Szczecin, 70-123 Szczecin, Poland; (B.G.); (B.D.)
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24
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Thongprayoon C, Khoury NJ, Bathini T, Aeddula NR, Boonpheng B, Leeaphorn N, Ungprasert P, Bruminhent J, Lertjitbanjong P, Watthanasuntorn K, Chesdachai S, Mao MA, Cheungpasitporn W. BK polyomavirus genotypes in renal transplant recipients in the United States: A meta-analysis. J Evid Based Med 2019; 12:291-299. [PMID: 31769221 DOI: 10.1111/jebm.12366] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 09/13/2019] [Accepted: 11/03/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND In the United States, increasing ethnic diversity has been apparent. However, the epidemiology and trends of BKV genotypes remain unclear. This meta-analysis was conducted with the aim to assess the prevalence of BKV genotypes among kidney transplant (KTx) recipients in the United States. METHODS A comprehensive literature review was conducted through October 2018 utilizing MEDLINE, Embase, and Cochrane Database to identify studies that reported the prevalence of BKV subtypes and/or subgroups in KTx recipients in the United States. Pooled prevalence rates were combined using random effects, generic inverse variance method. The protocol for this study is registered with PROSPERO (no. CRD42019134582). RESULTS A total of eight observational studies with a total of 193 samples (urine, blood, and kidney tissues) from 188 BKV-infected KTX recipients were enrolled. Overall, the pooled estimated prevalence rates of BKV subtypes were 72.2% (95% confidence of interval [CI]: 62.7-80.0%) for subtype I, 6.8% (95% CI: 2.5-16.9%) for subtype II, 8.3% (95% CI: 4.4-15.1%) for subtype III, and 16.1% (95% CI: 10.4-24.2%) for subtype IV, respectively. While metaregression analysis demonstrated a significant positive correlation between year of study and the prevalence of BKV subtype I (slopes = +0.1023, P = .01), there were no significant correlations between year of study and percentages of BKV subtype II-IV (P > .05). Among KTx recipients with BKV subtype I, the pooled estimated percentages of BKV subgroups were 22.4% (95% CI: 13.7-34.5%) for subgroup Ia, 30.6% (95% CI: 17.7-47.5%) for subgroup Ib1, 47.7% (95% CI: 35.8-59.9%) for subgroup Ib2, and 4.1% (95% CI:1.2-13.3%) for subgroup Ic, respectively. CONCLUSION BKV subtype I is the most prevalent subtype among KTx recipients in the United States and its prevalence seems to increasing overtime. Subgroup Ib2 is the most common subgroup among BKV subtype I.
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Affiliation(s)
| | - Nadeen J Khoury
- Division of Nephrology and Hypertension, Henry Ford Health System, Detroit, Michigan
| | - Tarun Bathini
- Department of Internal Medicine, University of Arizona, Tucson, Arizona
| | - Narothama Reddy Aeddula
- Department of Medicine, Indiana University School of Medicine and, Deaconess Health System, Evansville, Indiana
| | - Boonphiphop Boonpheng
- Department of Internal Medicine, East Tennessee State University, Johnson City, Tennessee
| | - Napat Leeaphorn
- Renal Transplant Program, University of Missouri-Kansas City School of Medicine/Saint Luke's Health System, Kansas City, Missouri
| | - Patompong Ungprasert
- Clinical Epidemiology Unit, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Jackrapong Bruminhent
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | | | | | | | - Michael A Mao
- Division of Nephrology and Hypertension, Mayo Clinic, Jacksonville, Florida
| | - Wisit Cheungpasitporn
- Division of Nephrology, Department of Medicine, University of Mississippi Medical Center, Mississippi
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25
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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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26
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Garretto A, Hatzopoulos T, Putonti C. virMine: automated detection of viral sequences from complex metagenomic samples. PeerJ 2019; 7:e6695. [PMID: 30993039 PMCID: PMC6462185 DOI: 10.7717/peerj.6695] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 02/26/2019] [Indexed: 12/29/2022] Open
Abstract
Metagenomics has enabled sequencing of viral communities from a myriad of different environments. Viral metagenomic studies routinely uncover sequences with no recognizable homology to known coding regions or genomes. Nevertheless, complete viral genomes have been constructed directly from complex community metagenomes, often through tedious manual curation. To address this, we developed the software tool virMine to identify viral genomes from raw reads representative of viral or mixed (viral and bacterial) communities. virMine automates sequence read quality control, assembly, and annotation. Researchers can easily refine their search for a specific study system and/or feature(s) of interest. In contrast to other viral genome detection tools that often rely on the recognition of viral signature sequences, virMine is not restricted by the insufficient representation of viral diversity in public data repositories. Rather, viral genomes are identified through an iterative approach, first omitting non-viral sequences. Thus, both relatives of previously characterized viruses and novel species can be detected, including both eukaryotic viruses and bacteriophages. Here we present virMine and its analysis of synthetic communities as well as metagenomic data sets from three distinctly different environments: the gut microbiota, the urinary microbiota, and freshwater viromes. Several new viral genomes were identified and annotated, thus contributing to our understanding of viral genetic diversity in these three environments.
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Affiliation(s)
- Andrea Garretto
- Bioinformatics Program, Loyola University of Chicago, Chicago, IL, United States of America
| | - Thomas Hatzopoulos
- Department of Computer Science, Loyola University of Chicago, Chicago, IL, United States of America
| | - Catherine Putonti
- Bioinformatics Program, Loyola University of Chicago, Chicago, IL, United States of America.,Department of Computer Science, Loyola University of Chicago, Chicago, IL, United States of America.,Department of Biology, Loyola University of Chicago, Chicago, IL, United States of America.,Department of Microbiology and Immunology, Loyola University of Chicago, Maywood, IL, United States of America
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27
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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: 69] [Impact Index Per Article: 13.8] [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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28
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Handala L, Descamps V, Morel V, Castelain S, François C, Duverlie G, Helle F, Brochot E. No correlation between Torque Teno virus viral load and BK virus replication after kidney transplantation. J Clin Virol 2019; 116:4-6. [PMID: 30986626 DOI: 10.1016/j.jcv.2019.03.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 03/20/2019] [Accepted: 03/30/2019] [Indexed: 12/30/2022]
Abstract
BACKGROUND Assessment of the intensity of immunosuppression in transplant recipients to estimate the risk of rejection and infection is not entirely satisfactory at the present time. Determination of Torque teno virus (TTV) viral load appears to be a promising tool in this setting. OBJECTIVES We evaluated the level of replication and kinetics of TTV during the first three months after kidney transplantation compared to BK virus replication. RESULTS In a retrospective cohort of 116 renal transplant recipients, TTV viral load gradually increased during the first three months post-transplantation with no significant difference or discriminatory threshold between patients with and without BK virus replication. However, the level of TTV replication appeared to be indirectly related to the risk of BK virus replication, particularly according to the induction treatment used (antithymocyte globulin: ATG or basiliximab). Among patients receiving ATG, those receiving cyclosporine had significantly lower TTV viral loads (p < 0.01) with threefold lower reactivation of BKPyV (13 vs 37%) 3 months post-transplantation. Similarly, among the women in our cohort, TTV viral load was significantly higher in women receiving ATG (6.58 ± 1.57 versus 4.62 ± 2.0 log10 copies/mL for basiliximab: p < 0.01), also with threefold higher BKPyV reactivation frequencies (40 vs 13,3%). CONCLUSION The multiparametric variation of TTV viral load does not appear to be individually appropriate for the early detection or monitoring of possible post-transplant BKPyV virus reactivation in renal transplant recipients.
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Affiliation(s)
- Lynda Handala
- Department of Virology, Amiens University Medical Center, Amiens, France; AGIR Research Unit, EA4294, Jules Verne University of Picardie, Amiens, France
| | - Véronique Descamps
- Department of Virology, Amiens University Medical Center, Amiens, France; AGIR Research Unit, EA4294, Jules Verne University of Picardie, Amiens, France
| | - Virginie Morel
- Department of Virology, Amiens University Medical Center, Amiens, France; AGIR Research Unit, EA4294, Jules Verne University of Picardie, Amiens, France
| | - Sandrine Castelain
- Department of Virology, Amiens University Medical Center, Amiens, France; AGIR Research Unit, EA4294, Jules Verne University of Picardie, Amiens, France
| | - Catherine François
- Department of Virology, Amiens University Medical Center, Amiens, France; AGIR Research Unit, EA4294, Jules Verne University of Picardie, Amiens, France
| | - Gilles Duverlie
- Department of Virology, Amiens University Medical Center, Amiens, France; AGIR Research Unit, EA4294, Jules Verne University of Picardie, Amiens, France
| | - François Helle
- Department of Virology, Amiens University Medical Center, Amiens, France; AGIR Research Unit, EA4294, Jules Verne University of Picardie, Amiens, France
| | - Etienne Brochot
- Department of Virology, Amiens University Medical Center, Amiens, France; AGIR Research Unit, EA4294, Jules Verne University of Picardie, Amiens, France.
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29
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Hejtmánková A, Roubalová K, Forejtová A, Žáčková Suchanová J, Forstová J, Viklický O, Španielová H. Prevalence of antibodies against BKPyV subtype I and IV in kidney transplant recipients and in the general Czech population. J Med Virol 2019; 91:856-864. [PMID: 30609063 DOI: 10.1002/jmv.25388] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 12/24/2018] [Indexed: 01/04/2023]
Abstract
Active infection with BK polyomavirus (BKPyV) may cause serious complications in transplantation settings. Recently, the level of BKPyV IgG seroreactivity in graft donors has been shown to predict viremia and BKPyV-associated nephropathy in kidney transplant (KTx) recipients. Pretransplantation testing of the donor and recipient BKPyV serostatus could, therefore, identify patients at high risk. For the development of serological immunoassays, antibody response to the predominant BKPyV subtypes (BKPyV-I and BKPyV-IV) was studied using virus-like particle (VLP)-based enzyme-linked immunosorbent assay (ELISA). VLPs made from the capsid protein, VP1, derived from BKPyV-I and BKPyV-IV subtypes were produced using a baculovirus expression system and used as antigens. The tests were used for IgG antibody determination in 50 KTx recipients and 111 healthy blood donors. While 87% of samples reacted with mixed BKPyV-I and BKPyV-IV antigens, only 49% of samples were reactive in both ELISA tests when using BKPyV-I or BKPyV-IV antigens separately. Twenty-seven percent of healthy blood donors and 26% of KTx recipients were reactive only with BKPyV-I, while 9% and 20% were reactive only with BKPyV-IV, respectively. To determine the specificities of the antigens, selected seropositive samples were retested after preadsorption with soluble BKPyV-I, BKPyV-IV, or JC polyomavirus antigens. The experiments confirmed that recombinant VP1 VLP-based ELISAs predominantly detected BKPyV type-specific antibodies. The results imply that anti-BKPyV antibody ELISA tests should contain a mixture of subtype-specific VLP-based antigens instead of antigen derived from the most prevalent BKPyV-I subtype. The tests can be used for serological surveys of BKPyV infection and improved KTx patient management.
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Affiliation(s)
- Alžběta Hejtmánková
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czech Republic
| | | | | | - Jiřina Žáčková Suchanová
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jitka Forstová
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Ondřej Viklický
- Department of Nephrology, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Hana Španielová
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czech Republic
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30
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Ranjan R, Rani A, Finn PW, Perkins DL. Multiomic Strategies Reveal Diversity and Important Functional Aspects of Human Gut Microbiome. BIOMED RESEARCH INTERNATIONAL 2018; 2018:6074918. [PMID: 30584534 PMCID: PMC6280293 DOI: 10.1155/2018/6074918] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Accepted: 09/26/2018] [Indexed: 11/28/2022]
Abstract
It is well accepted that dysbiosis of microbiota is associated with disease; however, the biological mechanisms that promote susceptibility or resilience to disease remain elusive. One of the major limitations of previous microbiome studies has been the lack of complementary metatranscriptomic (functional) data to complement the interpretation of metagenomics (bacterial abundance). The purpose of this study was twofold, first to evaluate the bacterial diversity and differential gene expression of gut microbiota using complementary shotgun metagenomics (MG) and metatranscriptomics (MT) from same fecal sample. Second, to compare sequence data using different Illumina platforms and with different sequencing parameters as new sequencers are introduced, and to determine if the data are comparable on different platforms. In this study, we perform ultradeep metatranscriptomic shotgun sequencing for a sample that we previously analyzed with metagenomics shotgun sequencing. We performed sequencing analysis using different Illumina platforms, with different sequencing and analysis parameters. Our results suggest that use of different Illumina platform did not lead to detectable bias in the sequencing data. The analysis of the sample using MG and MT approach shows that some species genes are highly represented in the MT than in the MG, indicating that some species are highly metabolically active. Our analysis also shows that ~52% of the genes in the metagenome are in the metatranscriptome and therefore are robustly expressed. The functions of the low and rare abundance bacterial species remain poorly understood. Our observations indicate that among the low abundant species analyzed in this study some were found to be more metabolically active compared to others, and can contribute distinct profiles of biological functions that may modulate the host-microbiota and bacteria-bacteria interactions.
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Affiliation(s)
- Ravi Ranjan
- Department of Medicine, University of Illinois, Chicago, IL 60612, USA
| | - Asha Rani
- Department of Medicine, University of Illinois, Chicago, IL 60612, USA
| | - Patricia W. Finn
- Department of Medicine, University of Illinois, Chicago, IL 60612, USA
| | - David L. Perkins
- Department of Medicine, University of Illinois, Chicago, IL 60612, USA
- Department of Bioengineering, University of Illinois, Chicago, IL 60612, USA
- Department of Surgery, University of Illinois, Chicago, IL 60612, USA
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31
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Herrmann A, Sandmann L, Adams O, Herrmann D, Dirks M, Widera M, Westhaus S, Kaiser R, di Cristanziano V, Manns MP, Korth J, Richter N, Anastasiou O, Timm J, von Hahn T, Ciesek S. Role of BK polyomavirus (BKV) and Torque teno virus (TTV) in liver transplant recipients with renal impairment. J Med Microbiol 2018; 67:1496-1508. [PMID: 30136921 DOI: 10.1099/jmm.0.000823] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
PURPOSE Renal impairment is a common complication after liver transplantation (LT). While BK polyomavirus (BKV) has been linked to renal failure in kidney transplant recipients, Torque teno virus (TTV) is a surrogate marker for immunosuppression that does not have a clear association with any human disease. The impact of BKV and TTV on renal impairment after LT is unknown. METHODOLOGY In this retrospective study, urine and serum samples from 136 liver transplant recipients were screened for BKV and TTV by quantitative PCR. In addition, serum was screened for BKV-specific antibodies and the VP1 typing region was sequenced for BKV genotyping. All parameters were correlated with clinical data.Results/Key findings. BK viruria was detected up to 21 years after transplantation in 16.9 % of cases. BK viraemia was detected in 8.7 % of patients with BK viruria up to 4 years after LT. BKV-specific antibodies were detected in 93.6 % of all LT recipients and correlated with BKV viral load in urine. There was no correlation between renal impairment and the detection of BK DNA in urine (OR 0.983). TTV DNA was detected in 84.6 % of serum samples and in 66.6 % of urine samples. The TTV viral load in serum correlated with the BKV viral load but had no impact on renal impairment. CONCLUSION Our data indicate that the detection of BKV and TTV is not a risk factor for renal impairment after LT. A correlation of TTV and BKV viral load seems to be an indicator for the immune status of the host.
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Affiliation(s)
- Anke Herrmann
- 1Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Hannover, Germany
| | - Lisa Sandmann
- 2Department of Gastroenterology, Hepatology and Endocrinology, Hanover Medical School, Hannover, Germany
| | - Ortwin Adams
- 3Institute for Virology, University Hospital Düsseldorf, Faculty of Medicine, University Düsseldorf, Düsseldorf, Germany
| | - Dominik Herrmann
- 4Thoraxzentrum Ruhrgebiet, Department of Thoracic Surgery, Evangelisches Krankenhaus, Herne, Germany
| | - Miriam Dirks
- 1Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Hannover, Germany
| | - Marek Widera
- 1Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Hannover, Germany
| | - Sandra Westhaus
- 1Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Hannover, Germany
| | - Rolf Kaiser
- 5German Center for Infection Research, DZIF, Germany.,6Institute for Virology, University of Cologne, Cologne, Germany
| | | | - Michael P Manns
- 2Department of Gastroenterology, Hepatology and Endocrinology, Hanover Medical School, Hannover, Germany.,5German Center for Infection Research, DZIF, Germany
| | - Johannes Korth
- 1Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Hannover, Germany
| | - Nico Richter
- 7Department of General, Visceral and Transplant Surgery, Hannover Medical School, Hannover, Germany
| | - Olympia Anastasiou
- 1Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Hannover, Germany
| | - Jörg Timm
- 3Institute for Virology, University Hospital Düsseldorf, Faculty of Medicine, University Düsseldorf, Düsseldorf, Germany
| | - Thomas von Hahn
- 2Department of Gastroenterology, Hepatology and Endocrinology, Hanover Medical School, Hannover, Germany.,5German Center for Infection Research, DZIF, Germany
| | - Sandra Ciesek
- 5German Center for Infection Research, DZIF, Germany.,1Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Hannover, Germany
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32
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Garretto A, Thomas-White K, Wolfe AJ, Putonti C. Detecting viral genomes in the female urinary microbiome. J Gen Virol 2018; 99:1141-1146. [PMID: 29889019 PMCID: PMC6171713 DOI: 10.1099/jgv.0.001097] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 05/26/2018] [Indexed: 12/17/2022] Open
Abstract
Viruses are the most abundant component of the human microbiota. Recent evidence has uncovered a rich diversity of viruses within the female bladder, including both bacteriophages and eukaryotic viruses. We conducted whole-genome sequencing of the bladder microbiome of 30 women: 10 asymptomatic 'healthy' women and 20 women with an overactive bladder. These metagenomes include sequences representative of human, bacterial and viral DNA. This analysis, however, focused specifically on viral sequences. Using the bioinformatic tool virMine, we discovered sequence fragments, as well as complete genomes, of bacteriophages and the eukaryotic virus JC polyomavirus. The method employed here is a critical proof of concept: the genomes of viral populations within the low-biomass bladder microbiota can be reconstructed through whole-genome sequencing of the entire microbial community.
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Affiliation(s)
- Andrea Garretto
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, USA
| | - Krystal Thomas-White
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, USA
- Present address: 325 Sharon Park Dr, Suite 522, Menlo Park, CA, USA
| | - Alan J. Wolfe
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, USA
| | - Catherine Putonti
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, USA
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, USA
- Department of Biology, Loyola University Chicago, Chicago, IL, USA
- Department of Computer Science, Loyola University Chicago, Chicago, IL, USA
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Kotton CN. Torque Teno Virus: Predictor of Infection After Solid Organ Transplant? J Infect Dis 2018; 218:1185-1187. [DOI: 10.1093/infdis/jiy384] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 06/23/2018] [Indexed: 12/25/2022] Open
Affiliation(s)
- Camille Nelson Kotton
- Transplant Infectious Disease and Compromised Host Program, Infectious Diseases Division, Massachusetts General Hospital
- Harvard Medical School, Boston
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Sigdel TK, Mercer N, Nandoe S, Nicora CD, Burnum-Johnson K, Qian WJ, Sarwal MM. Urinary Virome Perturbations in Kidney Transplantation. Front Med (Lausanne) 2018; 5:72. [PMID: 29725592 PMCID: PMC5916966 DOI: 10.3389/fmed.2018.00072] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 03/02/2018] [Indexed: 12/22/2022] Open
Abstract
The human microbiome is important for health and plays a role in essential metabolic functions and protection from certain pathogens. Conversely, dysbiosis of the microbiome is seen in the context of various diseases. Recent studies have highlighted that a complex microbial community containing hundreds of bacteria colonizes the healthy urinary tract, but little is known about the human urinary viruses in health and disease. To evaluate the human urinary virome in the context of kidney transplantation (tx), variations in the composition of the urinary virome were evaluated in urine samples from normal healthy volunteers as well as patients with kidney disease after they had undergone kidney tx. Liquid chromatography-mass spectrometry/mass spectrometry analysis was undertaken on a selected cohort of 142 kidney tx patients and normal healthy controls, from a larger biobank of 770 kidney biopsy matched urine samples. In addition to analysis of normal healthy control urine, the cohort of kidney tx patients had biopsy confirmed phenotype classification, coincident with the urine sample analyzed, of stable grafts (STA), acute rejection, BK virus nephritis, and chronic allograft nephropathy. We identified 37 unique viruses, 29 of which are being identified for the first time in human urine samples. The composition of the human urinary virome differs in health and kidney injury, and the distribution of viral proteins in the urinary tract may be further impacted by IS exposure, diet and environmental, dietary, or cutaneous exposure to various insecticides and pesticides.
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Affiliation(s)
- Tara K. Sigdel
- Department of Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Neil Mercer
- Department of Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Sharvin Nandoe
- Department of Surgery, University of California, San Francisco, San Francisco, CA, United States
- Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Carrie D. Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Kristin Burnum-Johnson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Minnie M. Sarwal
- Department of Surgery, University of California, San Francisco, San Francisco, CA, United States
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35
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Bacteriophages of the Urinary Microbiome. J Bacteriol 2018; 200:JB.00738-17. [PMID: 29378882 DOI: 10.1128/jb.00738-17] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 01/11/2018] [Indexed: 01/01/2023] Open
Abstract
Bacterial viruses (bacteriophages) play a significant role in microbial community dynamics. Within the human gastrointestinal tract, for instance, associations among bacteriophages (phages), microbiota stability, and human health have been discovered. In contrast to the gastrointestinal tract, the phages associated with the urinary microbiota are largely unknown. Preliminary metagenomic surveys of the urinary virome indicate a rich diversity of novel lytic phage sequences at an abundance far outnumbering that of eukaryotic viruses. These surveys, however, exclude the lysogenic phages residing within the bacteria of the bladder. To characterize this phage population, we examined 181 genomes representative of the phylogenetic diversity of bacterial species within the female urinary microbiota and found 457 phage sequences, 226 of which were predicted with high confidence. Phages were prevalent within the bladder bacteria: 86% of the genomes examined contained at least one phage sequence. Most of these phages are novel, exhibiting no discernible sequence homology to sequences in public data repositories. The presence of phages with substantial sequence similarity within the microbiota of different women supports the existence of a core community of phages within the bladder. Furthermore, the observed variation between the phage populations of women with and without overactive bladder symptoms suggests that phages may contribute to urinary health. To complement our bioinformatic analyses, viable phages were cultivated from the bacterial isolates for characterization; a novel coliphage was isolated, which is obligately lytic in the laboratory strain Escherichia coli C. Sequencing of bacterial genomes facilitates a comprehensive cataloguing of the urinary virome and reveals phage-host interactions.IMPORTANCE Bacteriophages are abundant within the human body. However, while some niches have been well surveyed, the phage population within the urinary microbiome is largely unknown. Our study is the first survey of the lysogenic phage population within the urinary microbiota. Most notably, the abundance of prophage exceeds that of the bacteria. Furthermore, many of the prophage sequences identified exhibited no recognizable sequence homology to sequences in data repositories. This suggests a rich diversity of uncharacterized phage species present in the bladder. Additionally, we observed a variation in the abundances of phages between bacteria isolated from asymptomatic "healthy" individuals and those with urinary symptoms, thus suggesting that, like phages within the gut, phages within the bladder may contribute to urinary health.
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Abstract
Urine culture and microscopy techniques are used to profile the bacterial species present in urinary tract infections. To gain insight into the urinary flora, we analyzed clinical laboratory features and the microbial metagenome of 121 clean-catch urine samples. 16S rDNA gene signatures were successfully obtained for 116 participants, while metagenome sequencing data was successfully generated for samples from 49 participants. Although 16S rDNA sequencing was more sensitive, metagenome sequencing allowed for a more comprehensive and unbiased representation of the microbial flora, including eukarya and viral pathogens, and of bacterial virulence factors. Urine samples positive by metagenome sequencing contained a plethora of bacterial (median 41 genera/sample), eukarya (median 2 species/sample) and viral sequences (median 3 viruses/sample). Genomic analyses suggested cases of infection with potential pathogens that are often missed during routine urine culture due to species specific growth requirements. While conventional microbiological methods are inadequate to identify a large diversity of microbial species that are present in urine, genomic approaches appear to more comprehensively and quantitatively describe the urinary microbiome.
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B Kopp J. Banff Classification of Polyomavirus Nephropathy: A New Tool for Research and Clinical Practice. J Am Soc Nephrol 2018; 29:354-355. [PMID: 29371421 PMCID: PMC5791080 DOI: 10.1681/asn.2017121328] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Affiliation(s)
- Jeffrey B Kopp
- Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
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Santiago-Rodriguez TM. Identification and Quantification of DNA Viral Populations in Human Urine Using Next-Generation Sequencing Approaches. Methods Mol Biol 2018; 1838:191-200. [PMID: 30128998 DOI: 10.1007/978-1-4939-8682-8_14] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The human urinary virome is comprised by diverse communities of both eukaryotic viruses and bacteriophages. Identification and quantification of human urinary viruses was limited to PCR-based and culture methods. Detection of viruses in human urine has long been associated with disease, but advances in next-generation sequencing have shown that it harbors robust viral communities. Human urinary viral communities are mainly comprised by bacteriophages and Human Papillomaviruses (HPVs) that remain to be characterized in association with health and diverse urinary disease states. In the present chapter, the methods to identify and quantify DNA viral populations in human urine using next-generation sequencing are described.
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Affiliation(s)
- Tasha M Santiago-Rodriguez
- ATCC-Center for Translational Microbiology, Institute for Life Science Entrepreneurship, Union, NJ, USA.
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The Human Virome: Implications for Clinical Practice in Transplantation Medicine. J Clin Microbiol 2017; 55:2884-2893. [PMID: 28724557 DOI: 10.1128/jcm.00489-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Advances in DNA sequencing technology have provided an unprecedented opportunity to study the human virome. Transplant recipients and other immunocompromised hosts are at particular risk for developing virus-related pathology; thus, the impact of the virome on health and disease may be even more relevant in this population. Here, we discuss technical considerations in studying the human virome, the current literature on the virome in transplant recipients, and near-future applications of sequence-based findings that can further our understanding of viruses in transplantation medicine.
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Zaza G, Dalla Gassa A, Felis G, Granata S, Torriani S, Lupo A. Impact of maintenance immunosuppressive therapy on the fecal microbiome of renal transplant recipients: Comparison between an everolimus- and a standard tacrolimus-based regimen. PLoS One 2017; 12:e0178228. [PMID: 28542523 PMCID: PMC5443527 DOI: 10.1371/journal.pone.0178228] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 05/10/2017] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The gut microbiome is the full set of microbes living in the gastrointestinal tract and is emerging as an important dynamic/fluid system that, if altered by environmental, dietetic or pharmacological factors, could considerably influence drug response. However, the immunosuppressive drug-induced modifications of this system are still poorly defined. METHODS We employed an innovative bioinformatics approach to assess differences in the whole-gut microbial metagenomic profile of 20 renal transplant recipients undergoing maintenance treatment with two different immunosuppressive protocols. Nine patients were treated with everolimus plus mycophenolate mofetil (EVE+MMF group), and 11 patients were treated with a standard therapy with tacrolimus plus mycophenolate mofetil (TAC+MMF group). RESULTS A statistical analysis of comparative high-throughput data demonstrated that although similar according to the degree of Shannon diversity (alpha diversity) at the taxonomic level, three functional genes clearly discriminated EVE+MMF versus TAC+MMF (cutoff: log2 fold change≥1, FDR≤0.05). Flagellar motor switch protein (fliNY) and type IV pilus assembly protein pilM (pilM) were significantly enriched in TAC+MMF-treated patients, while macrolide transport system mrsA (msrA) was more abundant in patients treated with EVE+MMF. Finally, PERMANOVA revealed that among the variables analyzed and included in our model, only the consumption of sugar significantly influenced beta diversity. CONCLUSIONS Our study, although performed on a relatively small number of patients, showed, for the first time, specific immunosuppressive-related effects on fecal microbiome of renal transplant recipients and it suggested that the analysis of the gut microbes community could represent a new tool to better understand the effects of drugs currently employed in organ transplantations. However, multicenter studies including healthy controls should be undertaken to better address this objective.
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Affiliation(s)
- Gianluigi Zaza
- Renal Unit, Department of Medicine, University Hospital of Verona, Verona, Italy
- * E-mail:
| | | | - Giovanna Felis
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Simona Granata
- Renal Unit, Department of Medicine, University Hospital of Verona, Verona, Italy
| | - Sandra Torriani
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Antonio Lupo
- Renal Unit, Department of Medicine, University Hospital of Verona, Verona, Italy
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