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Albert E, Giménez E, Hernani R, Piñana JL, Solano C, Navarro D. Torque Teno Virus DNA Load in Blood as an Immune Status Biomarker in Adult Hematological Patients: The State of the Art and Future Prospects. Viruses 2024; 16:459. [PMID: 38543824 PMCID: PMC10974055 DOI: 10.3390/v16030459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 03/11/2024] [Accepted: 03/15/2024] [Indexed: 05/23/2024] Open
Abstract
A solid body of scientific evidence supports the assumption that Torque teno virus (TTV) DNA load in the blood compartment may behave as a biomarker of immunosuppression in solid organ transplant recipients; in this clinical setting, high or increasing TTV DNA levels precede the occurrence of infectious complications, whereas the opposite anticipates the development of acute rejection. The potential clinical value of the TTV DNA load in blood to infer the risk of opportunistic viral infection or immune-related (i.e., graft vs. host disease) clinical events in the hematological patient, if any, remains to be determined. In fact, contradictory data have been published on this matter in the allo-SCT setting. Studies addressing this topic, which we review and discuss herein, are highly heterogeneous as regards design, patient characteristics, time points selected for TTV DNA load monitoring, and PCR assays used for TTV DNA quantification. Moreover, clinical outcomes are often poorly defined. Prospective, ideally multicenter, and sufficiently powered studies with well-defined clinical outcomes are warranted to elucidate whether TTV DNA load monitoring in blood may be of any clinical value in the management of hematological patients.
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Affiliation(s)
- Eliseo Albert
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, 46010 Valencia, Spain; (E.A.); (E.G.)
| | - Estela Giménez
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, 46010 Valencia, Spain; (E.A.); (E.G.)
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, 28029 Madrid, Spain
| | - Rafael Hernani
- Hematology Service, Hospital Clínico Universitario, INCLIVA Health Research Institute, 46010 Valencia, Spain; (R.H.); (J.L.P.); (C.S.)
| | - José Luis Piñana
- Hematology Service, Hospital Clínico Universitario, INCLIVA Health Research Institute, 46010 Valencia, Spain; (R.H.); (J.L.P.); (C.S.)
| | - Carlos Solano
- Hematology Service, Hospital Clínico Universitario, INCLIVA Health Research Institute, 46010 Valencia, Spain; (R.H.); (J.L.P.); (C.S.)
- Department of Medicine, School of Medicine, University of Valencia, 46010 Valencia, Spain
| | - David Navarro
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, 46010 Valencia, Spain; (E.A.); (E.G.)
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, 28029 Madrid, Spain
- Department of Microbiology, School of Medicine, University of Valencia, 46010 Valencia, Spain
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Zhu Y, Zhao W, Yang X, Zhang Y, Lin X, Weng X, Wang Y, Cheng C, Chi Y, Wei H, Peng Z, Hu Z. Metagenomic next-generation sequencing for identification of central nervous system pathogens in HIV-infected patients. Front Microbiol 2022; 13:1055996. [PMID: 36458193 PMCID: PMC9705764 DOI: 10.3389/fmicb.2022.1055996] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 10/31/2022] [Indexed: 11/17/2023] Open
Abstract
Although considerable interest in metagenomic next-generation sequencing (mNGS) has been attracted in recent years, limited data are available regarding the performance of mNGS in HIV-associated central nervous system (CNS) infection. Here, we conducted a retrospectively analyzing of the cerebrospinal fluid (CSF) mNGS reports and other clinical data from 80 HIV-infected patients admitted to the Second Hospital of Nanjing, China from March, 2018 to March, 2022. In our study, CSF mNGS reported negative result, mono-infection, and mixed infection in 8.8, 36.2, and 55% of the patients, respectively. Epstein-Barr virus (EBV), positive in 52.5% of samples, was the most commonly reported pathogen, followed by cytomegalovirus (CMV), John Cunningham virus (JCV), torque teno virus (TTV), cryptococcus neoformans (CN), toxoplasma Gondii (TE), and mycobacterium tuberculosis (MTB). 76.2% of the EBV identification and 54.2% of the CMV identification were not considered clinically important, and relative less sequence reads were reported in the clinical unimportant identifications. The clinical importance of the presence of TTV in CSF was not clear. Detection of JCV, CN, or TE was 100% suggestive of specific CNS infection, however, 60% of the MTB reports were considered contamination. Moreover, of the 44 (55%) mixed infections reported by mNGS, only 4 (5%) were considered clinical important, and mNGS failed to identify one mixed infection. Additionally, except for MTB, CSF mNGS tended to have high sensitivity to identify the above-mentioned pathogens (almost with 100% sensitivity). Even all the diagnostic strategies were evaluated, the cause of neurological symptoms remained undetermined in 6 (7.5%) patients. Overall, our results suggest that mNGS is a very sensitive tool for detecting common opportunistic CNS pathogen in HIV-infected patients, although its performance in CNS tuberculosis is unsatisfactory. EBV and CMV are commonly detected by CSF mNGS, however, the threshold of a clinical important detection remains to be defined.
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Affiliation(s)
- Yunqi Zhu
- Department of Infectious Disease, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Wenxuan Zhao
- Department of Infectious Disease, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Xihong Yang
- Department of Infectious Disease, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yuanyuan Zhang
- Department of Infectious Disease, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Xiaoling Lin
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xing Weng
- BGI Infection Pharmaceutical Technology, BGI-Shenzhen, Shenzhen, China
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, China
| | - Yali Wang
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, China
- Clinical Infectious Disease Center of Nanjing, Nanjing, China
| | - Cong Cheng
- Department of Infectious Disease, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
- Clinical Infectious Disease Center of Nanjing, Nanjing, China
| | - Yun Chi
- Department of Infectious Disease, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
- Clinical Infectious Disease Center of Nanjing, Nanjing, China
| | - Hongxia Wei
- Department of Infectious Disease, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
- Clinical Infectious Disease Center of Nanjing, Nanjing, China
| | - Zhihang Peng
- School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zhiliang Hu
- Department of Infectious Disease, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Clinical Infectious Disease Center of Nanjing, Nanjing, China
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Emmel V, Gama B, de Paula A, Ferreira G, Binato R, Abdelhay E. Can torque teno virus be a predictor of SARS-CoV-2 disease progression in cancer patients? J Infect Chemother 2022; 28:1623-1627. [PMID: 36007694 PMCID: PMC9395288 DOI: 10.1016/j.jiac.2022.08.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/14/2022] [Accepted: 08/16/2022] [Indexed: 10/25/2022]
Abstract
INTRODUCTION Cancer patients with SARS-CoV-2 infection can experience a broad range of clinical manifestations and outcomes. Previous studies have demonstrated an association between torque teno virus (TTV) load and deficiencies of the immune system. The impact of SARS-CoV-2 and TTV viral loads in cancer patients is unknown. METHODS In this retrospective study, 157 cancer patients and 191 noncancer controls were analysed for SARS-CoV-2 RNA and TTV DNA presence. RESULTS SARS-CoV-2 RNA was detected in 66.2% of cancer patients and in 68.6% of noncancer control subjects. In SARS-CoV-2-positive patients, TTV was detectable in 79.8% of cancer patients, while in controls, TTV was detected in 71.7% of subjects. No statistically significant correlation was found between TTV and SARS-CoV-2 loads in cancer patients. However, the 100-day survival rate in cancer patients who died from COVID-19 was significantly lower in the TTV-positive group than in the TTV-negative group (P = 0.0475). In the cancer TTV-positive group, those who died also had a higher load of TTV than those who did not die (P = 0.0097). CONCLUSIONS Our findings indicated that the presence of TTV in nasopharyngeal swabs from cancer patients was related to a higher number of deaths from COVID-19 and to a higher TTV DNA load.
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Affiliation(s)
- Vanessa Emmel
- Oncovirology Laboratory, National Cancer Institute (INCA), Praça da Cruz Vermelha, 23, Rio de Janeiro, Brazil.
| | - Bianca Gama
- Oncovirology Laboratory, National Cancer Institute (INCA), Praça da Cruz Vermelha, 23, Rio de Janeiro, Brazil
| | - Alessandra de Paula
- Oncovirology Laboratory, National Cancer Institute (INCA), Praça da Cruz Vermelha, 23, Rio de Janeiro, Brazil
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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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Li X, Liu Q, Chen X, Xiao Y, Yang S, Zhang W, Chen J. The virome of bronchoalveolar lavage fluid from patients with fever of unknown origin. Future Virol 2022. [DOI: 10.2217/fvl-2020-0027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Background: Viral metagenomics, a high-throughput sequencing combined with virus sequence-independent amplification by random PCR, allows for unbiased detection of virtually any viruses present in samples. Materials & methods: In order to investigate the virome of bronchoalveolar lavage fluid from patients with fever of unknown origin, 58 samples collected from diseased patients were characterized and compared. Results: Some representatives of Anelloviridae were identified, we found the torque teno virus (TTV) accounts for the majority of virus communities and were more prevalent in the specimens of febrile patients. Phylogenetic analysis suggested that these anellovirus isolates were close to the previous TTV available in GenBank®. Conclusion: All these data indicate that the human anellovirus species TTV may associated with fever of unknown origin.
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Affiliation(s)
- Xinlin Li
- Department of Clinical Laboratory, The Affiliated People’s Hospital of Jiangsu University, No. 8 Dian Li Road, Zhenjiang, China
- School of Medicine, Jiangsu University, No. 301 Xue Fu Road, Zhenjiang, China
| | - Qi Liu
- School of Medicine, Jiangsu University, No. 301 Xue Fu Road, Zhenjiang, China
| | - Xu Chen
- School of Medicine, Jiangsu University, No. 301 Xue Fu Road, Zhenjiang, China
| | - Yuqing Xiao
- School of Medicine, Jiangsu University, No. 301 Xue Fu Road, Zhenjiang, China
| | - Shixing Yang
- School of Medicine, Jiangsu University, No. 301 Xue Fu Road, Zhenjiang, China
| | - Wen Zhang
- School of Medicine, Jiangsu University, No. 301 Xue Fu Road, Zhenjiang, China
| | - Jianguo Chen
- Department of Clinical Laboratory, The Affiliated People’s Hospital of Jiangsu University, No. 8 Dian Li Road, Zhenjiang, China
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Giacconi R, Maggi F, Macera L, Spezia PG, Pistello M, Provinciali M, Piacenza F, Basso A, Bürkle A, Moreno-Villanueva M, Dollé MET, Jansen E, Grune T, Stuetz W, Gonos ES, Schön C, Bernhardt J, Grubeck-Loebenstein B, Sikora E, Dudkowska M, Janiszewska D, Toussaint O, Debacq-Chainiaux F, Franceschi C, Capri M, Hervonen A, Hurme M, Slagboom E, Breusing N, Mocchegiani E, Malavolta M. Prevalence and Loads of Torquetenovirus in the European MARK-AGE Study Population. J Gerontol A Biol Sci Med Sci 2021; 75:1838-1845. [PMID: 31838498 DOI: 10.1093/gerona/glz293] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Indexed: 12/12/2022] Open
Abstract
Torquetenovirus (TTV) viremia has been associated with increased mortality risk in the elderly population. This work aims to investigate TTV viremia as a potential biomarker of immunosenescence. We compared levels of circulating TTV in 1813 participants of the MARK-AGE project, including human models of delayed (offspring of centenarians [GO]) and premature (Down syndrome [DS]) immunosenescence. The TTV load was positively associated with age, cytomegalovirus (CMV) antibody levels, and the Cu/Zn ratio and negatively associated with platelets, total cholesterol, and total IgM. TTV viremia was highest in DS and lowest in GO, with intermediate levels in the SGO (spouses of GO) and RASIG (Randomly Recruited Age-Stratified Individuals From The General Population) populations. In the RASIG population, TTV DNA loads showed a slight negative association with CD3+T-cells and CD4+T-cells. Finally, males with ≥4log TTV copies/mL had a higher risk of having a CD4/CD8 ratio<1 than those with lower viremia (odds ratio [OR] = 2.85, 95% confidence interval [CI]: 1.06-7.62), as well as reduced CD3+ and CD4+T-cells compared to males with lower replication rates (<4log), even after adjusting for CMV infection. In summary, differences in immune system preservation are reflected in the models of delayed and premature immunosenescence, displaying the best and worst control over TTV replication, respectively. In the general population, TTV loads were negatively associated with CD4+ cell counts, with an increased predisposition for an inverted CD4/CD8 ratio for individuals with TTV loads ≥4log copies/mL, thus promoting an immune risk phenotype.
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Affiliation(s)
- Robertina Giacconi
- Advanced Technology Center for Aging Research, IRCCS INRCA, Ancona, Italy
| | - Fabrizio Maggi
- Department of Translational Research, University of Pisa, Italy
| | - Lisa Macera
- Department of Translational Research, University of Pisa, Italy
| | | | - Mauro Pistello
- Department of Translational Research, University of Pisa, Italy
| | - Mauro Provinciali
- Advanced Technology Center for Aging Research, IRCCS INRCA, Ancona, Italy
| | - Francesco Piacenza
- Advanced Technology Center for Aging Research, IRCCS INRCA, Ancona, Italy
| | - Andrea Basso
- Advanced Technology Center for Aging Research, IRCCS INRCA, Ancona, Italy
| | - Alexander Bürkle
- Molecular Toxicology Group, Department of Biology, Box 628, University of Konstanz, Germany
| | - María Moreno-Villanueva
- Molecular Toxicology Group, Department of Biology, Box 628, University of Konstanz, Germany.,Human Performance Research Centre, Department of Sport Science, Box 30, University of Konstanz, Germany
| | - Martijn E T Dollé
- Centre for Health Protection, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Eugène Jansen
- Centre for Health Protection, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Tilman Grune
- Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), Nuthetal, Germany.,NutriAct-Competence Cluster Nutrition Research Berlin-Potsdam, Nuthetal, Germany
| | - Wolfgang Stuetz
- Institute of Biological Chemistry and Nutrition, University of Hohenheim, Stuttgart, Germany
| | - Efstathios S Gonos
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry and Biotechnology, Athens, Greece
| | | | | | | | - Ewa Sikora
- Laboratory of the Molecular Bases of Ageing, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Magdalena Dudkowska
- Laboratory of the Molecular Bases of Ageing, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Dorota Janiszewska
- Laboratory of the Molecular Bases of Ageing, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | | | | | - Claudio Franceschi
- CIG-Interdepartmental Center "L. Galvani," Alma Mater Studiorum, University of Bologna, Italy
| | - Miriam Capri
- CIG-Interdepartmental Center "L. Galvani," Alma Mater Studiorum, University of Bologna, Italy
| | | | - Mikko Hurme
- Faculty of Medicine and Biosciences, University of Tampere, Finland
| | - Eline Slagboom
- Department of Molecular Epidemiology, Leiden University Medical Centre, The Netherlands
| | - Nicolle Breusing
- Department of Applied Nutritional Science/Dietetics, Institute of Nutritional Medicine, University of Hohenheim, Stuttgart, Germany
| | | | - Marco Malavolta
- Advanced Technology Center for Aging Research, IRCCS INRCA, Ancona, Italy
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Neri L, Spezia PG, Suraci S, Macera L, Scribano S, Giusti B, Focosi D, Maggi F, Giannecchini S. Torque teno virus microRNA detection in cerebrospinal fluids of patients with neurological pathologies. J Clin Virol 2020; 133:104687. [PMID: 33176237 DOI: 10.1016/j.jcv.2020.104687] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/26/2020] [Accepted: 11/01/2020] [Indexed: 12/16/2022]
Abstract
BACKGROUND Torque teno virus (TTV) is a widespread anellovirus that establishes persistent infections in humans and represents the most abundant component of the human virome. TTV encodes microRNAs (miRNA) which are found both in viremic and not viremic subjects being potentially ideal tools for the virus to evade the immune system response and to maintain chronic infection in the host. OBJECTIVE To investigate TTV-DNA loads and TTV-miRNAs expression in cerebrospinal fluids (CSF) from subjects under analysis for the assessment of neurological diseases. STUDY DESIGN Detection of TTV-DNA and TTV-miRNAs (e. g. miRNA t1a, t3b, and tth8) were carried out from CSF samples of 93 subjects with neurological diseases by using universal real-time PCR, real-time RT-PCR, and next-generation sequencing (NGS) analyses. RESULTS TTV-DNA was detected in 11 of 93 (12 %) CSFs with a mean TTV load of 155 copies/mL. Conversely, 29 CSF samples (31 %) were positive for at least one TTV-miRNA, while 15 (16 %) CSFs contained all the TTV-miRNAs examined. Overall, TTV-miRNA tth8 was detected in 62 % of samples, followed by TTV miRNA t3b (56 %), and t1a (29 %). Interestingly, TTV-miRNAs were found in CSF samples that were negative for the presence of TTV-DNA. Next-generation sequencing analysis carried out from 4 TTV-DNA negative CSF samples detected reads mapped in TTV-miRNA sequences region. CONCLUSIONS These results shed novel light on the relationship between TTV and the central nervous system and make compelling furthered studies for investigating the potential role of TTV-miRNAs in neurological disorders.
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Affiliation(s)
- Lorenzo Neri
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | | | - Samuele Suraci
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Lisa Macera
- Department of Translational Research, University of Pisa, Italy
| | - Stefano Scribano
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Betti Giusti
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, Pisa, Italy
| | - Fabrizio Maggi
- Department of Medicine and Surgery, University of Insubria, and Laboratory of Clinical Microbiology, ASST dei Sette Laghi, Varese, Italy
| | - Simone Giannecchini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.
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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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9
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Blanco-Picazo P, Fernández-Orth D, Brown-Jaque M, Miró E, Espinal P, Rodríguez-Rubio L, Muniesa M, Navarro F. Unravelling the consequences of the bacteriophages in human samples. Sci Rep 2020; 10:6737. [PMID: 32317653 PMCID: PMC7174282 DOI: 10.1038/s41598-020-63432-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 03/31/2020] [Indexed: 12/26/2022] Open
Abstract
Bacteriophages are abundant in human biomes and therefore in human clinical samples. Although this is usually not considered, they might interfere with the recovery of bacterial pathogens at two levels: 1) by propagating in the enrichment cultures used to isolate the infectious agent, causing the lysis of the bacterial host and 2) by the detection of bacterial genes inside the phage capsids that mislead the presence of the bacterial pathogen. To unravel these interferences, human samples (n = 271) were analyzed and infectious phages were observed in 11% of blood culture, 28% of serum, 45% of ascitic fluid, 14% of cerebrospinal fluid and 23% of urine samples. The genetic content of phage particles from a pool of urine and ascitic fluid samples corresponded to bacteriophages infecting different bacterial genera. In addition, many bacterial genes packaged in the phage capsids, including antibiotic resistance genes and 16S rRNA genes, were detected in the viromes. Phage interference can be minimized applying a simple procedure that reduced the content of phages up to 3 logs while maintaining the bacterial load. This method reduced the detection of phage genes avoiding the interference with molecular detection of bacteria and reduced the phage propagation in the cultures, enhancing the recovery of bacteria up to 6 logs.
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Affiliation(s)
- Pedro Blanco-Picazo
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, Annex, Floor 0, 08028, Barcelona, Spain
| | - Dietmar Fernández-Orth
- European Genome-phenome Archive, Centre for Genomic Regulation (CRG), Doctor Aiguader 88, 08003, Barcelona, Spain
| | - Maryury Brown-Jaque
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, Annex, Floor 0, 08028, Barcelona, Spain
| | - Elisenda Miró
- Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Sant Quintí 89, 08041, Barcelona, Spain
| | - Paula Espinal
- Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Sant Quintí 89, 08041, Barcelona, Spain
| | - Lorena Rodríguez-Rubio
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, Annex, Floor 0, 08028, Barcelona, Spain
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, Annex, Floor 0, 08028, Barcelona, Spain.
| | - Ferran Navarro
- Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Sant Quintí 89, 08041, Barcelona, Spain.,Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Barcelona, Spain
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