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Pawłowski T, Radkowski M, Perlejewski K, Laskus T, Małyszczak K. The Severity of Depressive Symptoms as an Independent Predictor of Sustained Virological Response During Treatment of Hepatitis C With Pegylated Interferon-α2a and Oral Ribavirin. Psychosom Med 2024; 86:124-128. [PMID: 38193776 DOI: 10.1097/psy.0000000000001274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
BACKGROUND Sustained virological response (SVR) is the best indicator of successful therapy for hepatitis C virus (HCV) infection. Patients with chronic HCV infection treated with pegylated interferon-α and ribavirin (PEG-IFN-α/RBV) can achieve SVR 56% of the time. OBJECTIVES This study aimed to evaluate baseline predictors of SVR in patients treated with PEG-IFN-α/RBV for HCV chronic infection. METHODS A total of 101 patients receiving PEG-IFN-α/RBV for chronic HCV infection participated in the prospective cohort study. Symptoms of depression were assessed with the Montgomery-Åsberg Depression Rating Scale (MADRS) before the treatment. The multivariate regression analysis was applied to determine predictors of SVR. RESULTS Of a total of 101 patients included, 99 patients reached the primary end point-24 weeks after completing treatment. After the initial analysis of probable predictive variables, the logistic analysis included age, sex, HCV genetic type, and MADRS score. The HCV genotype (odds ratio = 0.22 [confidence interval = 0.073-0.68, p = .008) and MADRS score (OR = 0.88 [confidence interval = 0.80-0.98), p = .013]) predicted an SVR outcome. CONCLUSIONS The severity of depressive symptoms before treatment and HCV genotype are independent predictors of SVR.
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Affiliation(s)
- Tomasz Pawłowski
- From the Division of Psychotherapy and Psychosomatic Medicine, Department of Psychiatry (Pawłowski, Małyszczak), Wrocław Medical University, Wrocław; Departments of Immunopathology of Infectious and Parasitic Diseases (Radkowski, Perlejewski) and Adults Infectious Diseases (Laskus), Medical University of Warsaw, Warsaw, Poland
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Radkowski M, Grabarczyk P, Kryczka T, Caraballo Cortès K, Kubicka-Russel D, Janiak M, Osuch S, Perlejewski K, Laskus T. Cytokine profile and viral diversity in the early seronegative stage of community-acquired hepatitis C virus (HCV) infection. Sci Rep 2023; 13:20045. [PMID: 37973814 PMCID: PMC10654698 DOI: 10.1038/s41598-023-47335-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 11/12/2023] [Indexed: 11/19/2023] Open
Abstract
Most Hepatitis C virus (HCV)-infected subjects develop chronic infection, whereas a minority clear the virus in the early phase of infection. We analyzed factors associated with outcome (chronicity vs clearance) during the preclinical seronegative phase of community-acquired HCV infection. Among 17.5 million blood donations in the years 2000-2016, 124 blood donors were found to be HCV RNA-positive/anti-HCV-negative. All were contacted after 0.5-12.7 years and 40 responded and provided blood sample. Hypervariable region 1 was analyzed by ultradeep pyrosequencing and cytokines in serum were quantified by Luminex (R&D Systems) multiplex immunoassay. Twenty-one (52.5%) donors were found to be HCV-RNA-positive, while 19 (47.5%) were HCV RNA negative (none received antiviral treatment). All but one seroconverted to anti-HCV. Donors with resolving hepatitis did not differ significantly from donors with chronic infection with respect to age, genotypes, IL28B polymorphisms, number of viral variants, nucleotide diversity per site or the overall number of nucleotide substitutions. However, the former group had significantly higher levels of IL-1beta, IL-1RA, IL-6, IFN-gamma and FGF-2 in serum. In our study of community-acquired acute hepatitis C approximately half of all subjects eliminated the virus spontaneously, and this clearance was associated with marked cytokine response in the early seronegative stage of infection.
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Affiliation(s)
- Marek Radkowski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Piotr Grabarczyk
- Department of Virology, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Tomasz Kryczka
- Department of Development of Nursing and Social and Medical Sciences, Medical University of Warsaw, Warsaw, Poland
| | - Kamila Caraballo Cortès
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Dorota Kubicka-Russel
- Department of Virology, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Maciej Janiak
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Sylwia Osuch
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Karol Perlejewski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Tomasz Laskus
- Department of Adult Infectious Diseases, Medical University of Warsaw, 37 Wolska St., 01-201, Warsaw, Poland.
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Caraballo Cortés K, Osuch S, Perlejewski K, Radkowski M, Janiak M, Berak H, Rauch A, Fehr JS, Hoffmann M, Günthard HF, Metzner KJ. T-Cell Exhaustion in HIV-1/Hepatitis C Virus Coinfection Is Reduced After Successful Treatment of Chronic Hepatitis C. Open Forum Infect Dis 2023; 10:ofad514. [PMID: 37953817 PMCID: PMC10633785 DOI: 10.1093/ofid/ofad514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 10/19/2023] [Indexed: 11/14/2023] Open
Abstract
Background T-cell responses during chronic viral infections become exhausted, which is reflected by upregulation of inhibitory receptors (iRs) and increased interleukin 10 (IL-10). We assessed 2 iRs-PD-1 (programmed cell death protein 1) and Tim-3 (T-cell immunoglobulin and mucin domain-containing protein 3)-and IL-10 mRNAs in peripheral blood mononuclear cells (PBMCs) and their soluble analogs (sPD-1, sTim-3, and IL-10) in plasma in chronic HIV-1/hepatitis C virus (HCV) coinfection and explored the effect of HCV treatment on these markers. We also aimed to establish whether iR expression may be determined by the HCV CD8+ T-cell immunodominant epitope sequence. Methods Plasma and PBMCs from 31 persons with chronic HIV-1/HCV coinfection from the Swiss HIV Cohort Study were collected before and after HCV treatment. As controls, 45 persons who were HIV-1 negative with chronic HCV infection were recruited. Exhaustion markers were assessed by enzyme-linked immunosorbent assay in plasma and by quantitative reverse transcription polymerase chain reaction in PBMCs. Analysis of an HCV epitope sequence was conducted by next-generation sequencing: HLA-A*02-restricted NS31073-1081 and NS31406-1415 and HLA-A*01-restricted NS31436-1444. Results The study revealed higher plasma sPD-1 (P = .0235) and IL-10 (P = .002) levels and higher IL-10 mRNA in PBMCs (P = .0149) in HIV-1/HCV coinfection. A decrease in plasma sPD-1 (P = .0006), sTim-3 (P = .0136), and IL-10 (P = .0003) and Tim-3 mRNA in PBMCs (P = .0210) was observed following successful HCV treatment. Infection with the HLA-A*01-restricted NS31436-1444 ATDALMTGY prototype variant was related to higher sTim-3 levels than infection with the ATDALMTGF escape variant (P = .0326). Conclusions The results underscore the synergistic effect of coinfection on expression of exhaustion markers, their reduction following successful HCV treatment and imply that iR levels may operate on an epitope-specific manner.
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Affiliation(s)
- Kamila Caraballo Cortés
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Sylwia Osuch
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Karol Perlejewski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Marek Radkowski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Maciej Janiak
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Hanna Berak
- Outpatient Clinic, Warsaw Hospital for Infectious Diseases, Warsaw, Poland
| | - Andri Rauch
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Jan S Fehr
- Department of Public and Global Health, Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich, Switzerland
| | - Matthias Hoffmann
- Division of Infectious Diseases, Cantonal Hospital Olten, Olten, Switzerland
| | - Huldrych F Günthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Karin J Metzner
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
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Perlejewski K, Radkowski M, Pawełczyk A, Rydzanicz M, Dzieciątkowski T, Makowiecki M, Paciorek M, Welc-Falęciak R, Horban A, Laskus T. Enteroviral central nervous system infections in patients with Lyme neuroborreliosis. Ticks Tick Borne Dis 2023; 14:102253. [PMID: 37729847 DOI: 10.1016/j.ttbdis.2023.102253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 08/21/2023] [Accepted: 09/10/2023] [Indexed: 09/22/2023]
Abstract
Patients with Lyme neuroborreliosis (LNB) are rarely tested for the presence of neurovirulent viruses other than tick-borne encephalitis virus (TBEV); however, such coinfections could be of clinical importance. The aim of the study was to search for the presence of neurotropic viruses in a LNB patients. Fourteen patients admitted with signs and symptoms of neuroinfection who were eventually diagnosed to have LNB (according to the guidelines of the European Federation of Neurological Societies) were subjects of the study. Sera and cerebrospinal fluid (CSF) collected at the time of initial presentation were tested for viral pathogens most common in our geographical area: human enteroviruses (EV), herpes simplex virus type 1 and 2, varicella-zoster virus, Epstein-Barr virus, cytomegalovirus, human herpesvirus type 6, human adenoviruses, and TBEV using PCR/RT-PCR and serological assays. RNA and DNA-based metagenomic next-generation sequencing (mNGS) was used to detect other viral pathogens. EV was detected in CSF from two (14 %) LNB patients and viral loads were similar (220 and 270 copies/ml). The mMGS analysis were performed on CSFs from 10 patients and generated a total 213,750,885 NGS reads, 0.05 % of which were viral. However, none of potential pathogens fulfilled the criteria for positive viral detection by mNGS. Using a number of PCR/RT-PCR assays and mNGS we identified EV infection in two out of 14 LNB patients. The possible co-occurrence of enterovirus and Lyme neuroborreliosis infections may warrant further research.
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Affiliation(s)
- Karol Perlejewski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Pawińskiego 3c, Warsaw 02-106, Poland.
| | - Marek Radkowski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Pawińskiego 3c, Warsaw 02-106, Poland
| | - Agnieszka Pawełczyk
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Pawińskiego 3c, Warsaw 02-106, Poland
| | - Małgorzata Rydzanicz
- Department of the Medical Genetics, Medical University of Warsaw, Pawińskiego 3c, Warsaw 02-106, Poland
| | - Tomasz Dzieciątkowski
- Department of Microbiology, Medical University of Warsaw, Chalubińskiego 5, Warsaw 02-004, Poland
| | - Michał Makowiecki
- Department of Adults Infectious Diseases, Medical University of Warsaw, Wolska 37, Warsaw 01-201, Poland
| | - Marcin Paciorek
- Department of Adults Infectious Diseases, Medical University of Warsaw, Wolska 37, Warsaw 01-201, Poland
| | - Renata Welc-Falęciak
- Department of Parasitology, Faculty of Biology, University of Warsaw, Miecznikowa 1, Warsaw 02-096, Poland
| | - Andrzej Horban
- Department of Adults Infectious Diseases, Medical University of Warsaw, Wolska 37, Warsaw 01-201, Poland
| | - Tomasz Laskus
- Department of Adults Infectious Diseases, Medical University of Warsaw, Wolska 37, Warsaw 01-201, Poland
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Radkowski M, Kryczka T, Szymańska-Kotwica B, Berak H, Horban A, Pawłowski T, Perlejewski K, Laskus T. Depression and Cognitive Dysfunction in Patients with Chronic Hepatitis C: Correlation with Viral Replication in the Peripheral Blood Mononuclear Cells and Cytokines in Serum. Int J Mol Sci 2023; 24:15351. [PMID: 37895030 PMCID: PMC10607636 DOI: 10.3390/ijms242015351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
Chronic hepatitis C virus (HCV) infection is commonly associated with depression and cognitive dysfunction, the cause of which could be related to the HCV neuroinvasion and/or state of chronic inflammation. Viral sequences and proteins were previously detected in the brain and since blood leukocytes can cross the blood-brain barrier, they could provide viral access to the CNS. Eighty chronic hepatitis C patients were tested for viral replication in PBMCs (detection of the HCV RNA-negative strand) and serum cytokines. Depression was assessed by the Beck Depression Inventory (BDI), neuroticism by the Eysenck Personality Inventory (N/EPO-R), and anxiety by the State-Trait Anxiety Inventory (STAI) while neurocognitive testing included the Wisconsin Card Sorting Test (WCST), Ruff Figural Fluency Test (RFFT), California Verbal Learning Test (CVLT), and Grooved Pegboard Test (GPT). The HCV RNA-negative strand was detected in PBMCs from 24 (30%) patients and these patients had significantly higher BDI scores (median 12.5 [IQR] 6.3-20.5 vs. median 8.00 [IQR] 3-12; p = 0.013). Both depression and anxiety correlated positively with IL-8 while cognitive flexibility, executive function, problem-solving skills, memory, and motor functioning correlated negatively with some proinflammatory cytokines. Our findings suggest that due to chronic HCV infection, the brain function is negatively affected by both viral replication in PBMCs and by the immune activation state.
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Affiliation(s)
- Marek Radkowski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, 02-106 Warsaw, Poland; (M.R.); (K.P.)
| | - Tomasz Kryczka
- Department of Development of Nursing and Social and Medical Sciences, Medical University of Warsaw, 01-445 Warsaw, Poland;
| | - Bogna Szymańska-Kotwica
- Outpatient Clinic, Warsaw Hospital for Infectious Diseases, 01-201 Warsaw, Poland; (B.S.-K.); (H.B.)
| | - Hanna Berak
- Outpatient Clinic, Warsaw Hospital for Infectious Diseases, 01-201 Warsaw, Poland; (B.S.-K.); (H.B.)
| | - Andrzej Horban
- Department of Adult Infectious Diseases, Medical University of Warsaw, 01-201 Warsaw, Poland
| | - Tomasz Pawłowski
- Department of Psychiatry, Wroclaw Medical University, 50-367 Wroclaw, Poland;
| | - Karol Perlejewski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, 02-106 Warsaw, Poland; (M.R.); (K.P.)
| | - Tomasz Laskus
- Department of Adult Infectious Diseases, Medical University of Warsaw, 01-201 Warsaw, Poland
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Perlejewski K, Radkowski M, Rydzanicz M, Dzieciątkowski T, Silling S, Wieczorek M, Makowiecki M, Horban A, Laskus T. Metagenomic search of viral coinfections in herpes simplex encephalitis patients. J Neurovirol 2023; 29:588-597. [PMID: 37490185 PMCID: PMC10645616 DOI: 10.1007/s13365-023-01157-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/16/2023] [Accepted: 06/26/2023] [Indexed: 07/26/2023]
Abstract
Little is known about concomitant central nervous system (CNS) infections by more than one virus. Current diagnostics are based on molecular tests for particular pathogens making it difficult to identify multi-viral infections. In the present study, we applied DNA- and RNA-based next-generation sequencing metagenomics (mNGS) to detect viruses in cerebrospinal fluids from 20 patients with herpes simplex encephalitis. Coinfection was detected in one patient: sequences in cerebrospinal fluids matched enterovirus A (2.660 reads; 4% of recovered genome) and enterovirus B (1.571 reads; 13% of recovered genome). Subsequent PCR combined with serotyping allowed to identify human echovirus 6, a representative of enterovirus B. Several other mNGS hits (human pegivirus, Merkel cell polyomavirus, human papillomavirus type 5) were not considered to represent a genuine signal as they could not be confirmed by specific RT-PCR/PCR. HSV DNA, while being detectable by PCR in every patient, was detected by mNGS in only one. In conclusion, contaminations and false signals may complicate mNGS interpretation; however, the method can be useful in diagnostics of viral coinfections in CNS, particularly in the case of rare pathogens.
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Affiliation(s)
- Karol Perlejewski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Pawinskiego 3c, 02-106, Warsaw, Poland.
| | - Marek Radkowski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Pawinskiego 3c, 02-106, Warsaw, Poland
| | - Małgorzata Rydzanicz
- Department of Medical Genetics, Medical University of Warsaw, Pawinskiego 3c, 02-106, Warsaw, Poland
| | - Tomasz Dzieciątkowski
- Department of Microbiology, Medical University of Warsaw, Chalubińskiego 5, 02-004, Warsaw, Poland
| | - Steffi Silling
- Institute of Virology, National Reference Center for Papilloma- and Polyomaviruses, University of Cologne, Faculty of Medicine, University Hospital Cologne, Fürst-Pückler-Straße 56, 50935, Cologne, Germany
| | - Magdalena Wieczorek
- Department of Virology, National Institute of Public Health-National Institute of Hygiene, Chocimska 24, 00-791, Warsaw, Poland
| | - Michał Makowiecki
- Department of Adults Infectious Diseases, Medical University of Warsaw, Wolska 37, 01-201, Warsaw, Poland
| | - Andrzej Horban
- Department of Adults Infectious Diseases, Medical University of Warsaw, Wolska 37, 01-201, Warsaw, Poland
| | - Tomasz Laskus
- Department of Adults Infectious Diseases, Medical University of Warsaw, Wolska 37, 01-201, Warsaw, Poland
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Osuch S, Laskus T, Perlejewski K, Berak H, Bukowska-Ośko I, Pollak A, Zielenkiewicz M, Radkowski M, Caraballo Cortés K. CD8 + T-Cell Exhaustion Phenotype in Chronic Hepatitis C Virus Infection Is Associated With Epitope Sequence Variation. Front Immunol 2022; 13:832206. [PMID: 35386708 PMCID: PMC8977521 DOI: 10.3389/fimmu.2022.832206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/16/2022] [Indexed: 12/20/2022] Open
Abstract
Background and Aims During chronic hepatitis C virus (HCV) infection, CD8+ T-cells become functionally exhausted, undergoing progressive phenotypic changes, i.e., overexpression of “inhibitory” molecules such as PD-1 (programmed cell death protein 1) and/or Tim-3 (T-cell immunoglobulin and mucin domain-containing molecule-3). The extreme intrahost genetic diversity of HCV is a major mechanism of immune system evasion, facilitating epitope escape. The aim of the present study was to determine whether T-cell exhaustion phenotype in chronic HCV infection is related to the sequence repertoire of NS3 viral immunodominant epitopes. Methods The study population was ninety prospective patients with chronic HCV genotype 1b infection. Populations of peripheral blood CD8+ T-cells expressing PD-1/Tim-3 were assessed by multiparametric flow cytometry, including HCV-specific T-cells after magnetic-based enrichment using MHC-pentamer. Autologous epitope sequences were inferred from next-generation sequencing. The correction of sequencing errors and genetic variants reconstruction was performed using Quasirecomb. Results There was an interplay between the analyzed epitopes sequences and exhaustion phenotype of CD8+ T-cells. A predominance of NS31406 epitope sequence, representing neither prototype KLSGLGLNAV nor cross-reactive variants (KLSSLGLNAV, KLSGLGINAV or KLSALGLNAV), was associated with higher percentage of HCV-specific CD8+PD-1+Tim-3+ T-cells, P=0.0102. Variability (at least two variants) of NS31406 epitope sequence was associated with increased frequencies of global CD8+PD-1+Tim-3+ T-cells (P=0.0197) and lower frequencies of CD8+PD-1−Tim-3− T-cells (P=0.0079). In contrast, infection with NS31073 dominant variant epitope (other than prototype CVNGVCWTV) was associated with lower frequency of global CD8+PD-1+Tim-3+ T-cells (P=0.0054). Conclusions Our results indicate that PD-1/Tim-3 receptor expression is largely determined by viral epitope sequence and is evident for both HCV-specific and global CD8+ T-cells, pointing to the importance of evaluating autologous viral epitope sequences in the investigation of CD8+ T-cell exhaustion in HCV infection.
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Affiliation(s)
- Sylwia Osuch
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Tomasz Laskus
- Department of Adult Infectious Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Karol Perlejewski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Hanna Berak
- Outpatient Clinic, Warsaw Hospital for Infectious Diseases, Warsaw, Poland
| | - Iwona Bukowska-Ośko
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Agnieszka Pollak
- Department of Human Genetics, Medical University of Warsaw, Warsaw, Poland
| | | | - Marek Radkowski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Kamila Caraballo Cortés
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
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Grochowska M, Perlejewski K, Laskus T, Radkowski M. The Role of Gut Microbiota in Gastrointestinal Tract Cancers. Arch Immunol Ther Exp (Warsz) 2022; 70:7. [PMID: 35112169 PMCID: PMC8810472 DOI: 10.1007/s00005-021-00641-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 11/16/2021] [Indexed: 02/07/2023]
Abstract
Disturbances in gastrointestinal (GI) microbiota could play a significant role in the development of GI cancers, but the underlying mechanisms remain largely unclear. While some bacteria seem to facilitate carcinogenesis, others appear to be protective. So far only one bacterium (Helicobacter pylori) has been classified by the International Agency for Cancer Research as carcinogenic in humans but many other are the subject of intense research. Most studies on the role of microbiota in GI tract oncogenesis focus on pancreatic and colorectal cancers with the following three species: Helicobacter pylori, Escherichia coli, and Porphyromonas gingivalis as likely causative factors. This review summarizes the role of bacteria in GI tract oncogenesis.
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Affiliation(s)
- Marta Grochowska
- Department of Immunopathology, Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland.
| | - Karol Perlejewski
- Department of Immunopathology, Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Tomasz Laskus
- Department of Adult Infectious Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Marek Radkowski
- Department of Immunopathology, Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
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Jurasz H, Pawłowski T, Perlejewski K. Contamination Issue in Viral Metagenomics: Problems, Solutions, and Clinical Perspectives. Front Microbiol 2021; 12:745076. [PMID: 34745046 PMCID: PMC8564396 DOI: 10.3389/fmicb.2021.745076] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/17/2021] [Indexed: 12/16/2022] Open
Abstract
We describe the most common internal and external sources and types of contamination encountered in viral metagenomic studies and discuss their negative impact on sequencing results, particularly for low-biomass samples and clinical applications. We also propose some basic recommendations for reducing the background noise in viral shotgun metagenomic (SM) studies, which would limit the bias introduced by various classes of contaminants. Regardless of the specific viral SM protocol, contamination cannot be totally avoided; in particular, the issue of reagent contamination should always be addressed with high priority. There is an urgent need for the development and validation of standards for viral metagenomic studies especially if viral SM protocols will be more widely applied in diagnostics.
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Affiliation(s)
- Henryk Jurasz
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Tomasz Pawłowski
- Division of Psychotherapy and Psychosomatic Medicine, Department of Psychiatry, Wrocław Medical University, Wrocław, Poland
| | - Karol Perlejewski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
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Paciorek M, Bieńkowski C, Krogulec D, Bednarska A, Kowalczyk M, Makowiecki M, Bursa D, Skrzat-Klapaczyńska A, Perlejewski K, Radkowski M, Laskus T, Horban A. Differences and similarities in clinical manifestations of Listeria monocytogenes and Mycobacterium tuberculous meningitis. Przegl Epidemiol 2021; 74:326-335. [PMID: 33115221 DOI: 10.32394/pe.74.25] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
INTRODUCTION Tuberculous meningitis (TbM) and meningitis caused by Listeria monocytogenes (LM) require different treatment regimens and have grave prognosis if therapy is delayed. THE AIM OF THE STUDY Comparison of clinical manifestations, laboratory features and outcome of TbM and LM. MATERIAL AND METHODS We retrospectively analyzed records of 402 patients with community acquired bacterial meningitis (BM) who were hospitalized between January 2010 and September 2019. RESULTS LM and TbM were diagnosed in 28 (7.0%) and 23 (5.7%) patients, respectively. Patients with TbM were more likely to present with hydrocephalus (p<0.001), scored lower on the Thwaites Index (TI) (p<0.001) and had longer duration of symptoms prior to hospitalization (p=0.001). Furthermore, TbM patients had lower concentration of c-reactive protein (CRP) (p<0.001) and lower white blood cells count (WBC) (p=0.035). When compared to BM patients with etiology other than LM and TbM (nLnTbM), TbM patients presented with lower concentration of CRP (p<0.001), and procalcitonin (PCT) (p<0.001), lower WBC (p<0.001), and lower granulocyte percentage of CSF cytosis (p<0.001), but were more likely to present with hydrocephalus (p<0.001), aphasia (p=0.003) and hemiparesis (p=0.008). In comparison with the nLnTbM group, LM patients had lower concentration of CRP (p=0.01), lower WBC (p<0.001), and lower granulocyte percentage of CSF cytosis (p<0.016). LM patients were also more likely to have concomitant cancer (p=0.008), receive immunosuppressive treatment (p<0.001) or be immunocompromised (p=0.015). CONCLUSIONS TbM patients had less pronounced inflammation but more severe central nervous system complications compared to patients with LM and other etiologies. Furthermore, LM patients, but not TbM patients, were often immunocompromised.
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Affiliation(s)
- Marcin Paciorek
- Department of Adult's Infectious Diseases, Medical University of Warsaw, Poland
| | - Carlo Bieńkowski
- Department of Adult's Infectious Diseases, Medical University of Warsaw, Poland.,Doctoral School, Medical University of Warsaw, Poland
| | - Dominika Krogulec
- Department of Adult's Infectious Diseases, Medical University of Warsaw, Poland
| | - Agnieszka Bednarska
- Department of Adult's Infectious Diseases, Medical University of Warsaw, Poland
| | - Monika Kowalczyk
- Department of Adult's Infectious Diseases, Medical University of Warsaw, Poland
| | - Michał Makowiecki
- Department of Adult's Infectious Diseases, Medical University of Warsaw, Poland
| | - Dominik Bursa
- Department of Adult's Infectious Diseases, Medical University of Warsaw, Poland
| | | | - Karol Perlejewski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Poland
| | - Marek Radkowski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Poland
| | - Tomasz Laskus
- Department of Adult's Infectious Diseases, Medical University of Warsaw, Poland
| | - Andrzej Horban
- Department of Adult's Infectious Diseases, Medical University of Warsaw, Poland
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Jaworska K, Konop M, Hutsch T, Perlejewski K, Radkowski M, Grochowska M, Bielak-Zmijewska A, Mosieniak G, Sikora E, Ufnal M. Trimethylamine But Not Trimethylamine Oxide Increases With Age in Rat Plasma and Affects Smooth Muscle Cells Viability. J Gerontol A Biol Sci Med Sci 2021; 75:1276-1283. [PMID: 31411319 DOI: 10.1093/gerona/glz181] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Indexed: 01/01/2023] Open
Abstract
It has been suggested that trimethylamine oxide (TMAO), a liver oxygenation product of gut bacteria-produced trimethylamine (TMA), is a marker of cardiovascular risk. However, mechanisms of the increase and biological effects of TMAO are obscure. Furthermore, the potential role of TMAO precursor, that is TMA, has not been investigated. We evaluated the effect of age, a cardiovascular risk factor, on plasma levels of TMA and TMAO, gut bacteria composition, gut-to-blood penetration of TMA, histological and hemodynamic parameters in 3-month-old and 18-month-old, male, Sprague-Dawley and Wistar-Kyoto rats. Cytotoxicity of TMA and TMAO was studied in human vascular smooth muscle cells. Older rats showed significantly different gut bacteria composition, a significantly higher gut-to-blood TMA penetration, and morphological and hemodynamic alterations in intestines. In vitro, TMA at concentration of 500 µmol/L (2-fold higher than in portal blood) decreased human vascular smooth muscle cells viability. In contrast, TMAO at 1,000-fold higher concentration than physiological one had no effect on human vascular smooth muscle cells viability. In conclusion, older rats show higher plasma level of TMA due to a "leaky gut". TMA but not TMAO affects human vascular smooth muscle cells viability. We propose that TMA but not TMAO may be a marker and mediator of cardiovascular risk.
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Affiliation(s)
- Kinga Jaworska
- Department of Experimental Physiology and Pathophysiology, Laboratory of Centre for Preclinical Research, Medical University of Warsaw, Warsaw, Poland
| | - Marek Konop
- Department of Experimental Physiology and Pathophysiology, Laboratory of Centre for Preclinical Research, Medical University of Warsaw, Warsaw, Poland
| | - Tomasz Hutsch
- Department of Experimental Physiology and Pathophysiology, Laboratory of Centre for Preclinical Research, Medical University of Warsaw, Warsaw, Poland
| | - Karol Perlejewski
- Department of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University, Warsaw, Poland
| | - Marek Radkowski
- Department of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University, Warsaw, Poland
| | - Marta Grochowska
- Department of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University, Warsaw, Poland
| | - Anna Bielak-Zmijewska
- Laboratory of Molecular Bases of Aging, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Grażyna Mosieniak
- Laboratory of Molecular Bases of Aging, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Ewa Sikora
- Laboratory of Molecular Bases of Aging, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Marcin Ufnal
- Department of Experimental Physiology and Pathophysiology, Laboratory of Centre for Preclinical Research, Medical University of Warsaw, Warsaw, Poland
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12
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Perlejewski K, Bukowska-Ośko I, Rydzanicz M, Dzieciątkowski T, Zakrzewska-Pniewska B, Podlecka-Piętowska A, Filipiak A, Barć K, Caraballo Cortés K, Pawełczyk A, Radkowski M, Laskus T. Search for viral agents in cerebrospinal fluid in patients with multiple sclerosis using real-time PCR and metagenomics. PLoS One 2020; 15:e0240601. [PMID: 33112911 PMCID: PMC7592794 DOI: 10.1371/journal.pone.0240601] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 09/29/2020] [Indexed: 12/21/2022] Open
Abstract
Multiple sclerosis (MS) is a chronic, immune-mediated demyelinating disease of the central nervous system of unclear etiology, but there is some evidence that viral infections could be responsible for triggering autoimmune mechanisms against myelin. We searched for viral RNA and DNA in cerebrospinal fluid (CSF) of 34 MS patients and 13 controls using RT-PCR/PCR against common neurotropic viruses. In addition, shotgun DNA- and RNA-based metagenomics were done in 13 MS patients and 4 controls. Specific quantitative real-time RT-PCR/PCR testing revealed the presence of viral nucleic acid in seven (20.59%) MS patients and in one (7.69%) control patient. In MS patients the most frequently detected was human herpesvirus type 6 (HHV-6; 3 cases; 8.82%); followed by Epstein-Barr virus (EBV; 2 cases; 5.88%), varicella zoster virus (VZV; 1 case; 2.94%) and Enterovirus (EV; 1 case; 2.94%). The single identified virus among controls was EBV (7.69%). DNA and RNA metagenomic assays did not identify any known eukaryotic viruses even though three of the analyzed samples were low-level positive by specific quantitative real-time PCR. In conclusion, we detected the presence of Herpesviridae and occasionally Enteroviridae in CSF from patients with MS but their prevalence was not significantly higher than among controls. Metagenomic analysis seems to be less sensitive than real-time RT-PCR/PCR and it did not detect any potential viral pathogens.
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Affiliation(s)
- Karol Perlejewski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
- * E-mail:
| | - Iwona Bukowska-Ośko
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Małgorzata Rydzanicz
- Department of the Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | | | | | | | - Agata Filipiak
- University Clinical Center of Medical University of Warsaw, Medical University of Warsaw, Warsaw, Poland
| | - Krzysztof Barć
- University Clinical Center of Medical University of Warsaw, Medical University of Warsaw, Warsaw, Poland
| | - Kamila Caraballo Cortés
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Agnieszka Pawełczyk
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Marek Radkowski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Tomasz Laskus
- Department of Adult Infectious Diseases, Medical University of Warsaw, Warsaw, Poland
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Perlejewski K, Pawełczyk A, Bukowska-Ośko I, Rydzanicz M, Dzieciątkowski T, Paciorek M, Makowiecki M, Caraballo Cortés K, Grochowska M, Radkowski M, Laskus T. Search for Viral Infections in Cerebrospinal Fluid From Patients With Autoimmune Encephalitis. Open Forum Infect Dis 2020; 7:ofaa468. [PMID: 33209955 PMCID: PMC7643957 DOI: 10.1093/ofid/ofaa468] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 09/30/2020] [Indexed: 12/19/2022] Open
Abstract
Background It has been reported that virus-mediated brain tissue damage can lead to autoimmune encephalitis (AE) characterized by the presence of antibodies against neuronal surface antigens. In the study, we investigate the presence of viruses in cerebrospinal fluid (CSF) from patients with AE using reverse transcription polymerase chain reaction (RT-PCR)/PCR and shotgun metagenomics. Methods CSF samples collected from 200 patients with encephalitis were tested for the presence of antibodies against antiglutamate receptor (NMDAR), contactin-associated protein 2 (CASPR2), glutamate receptors (type AMPA1/2), leucine-rich glioma-inactivated protein 1 (LGI1), dipeptidyl aminopeptidase-like protein 6 (DPPX), and GABA B receptor, and those found positive were further analyzed with real-time RT-PCR/PCR for common viral neuroinfections and shotgun DNA- and RNA-based metagenomics. Results Autoantibodies against neuronal cells were detected in CSF from 8 individuals (4% of all encephalitis patients): 7 (3.5%) had anti-NMDAR and 1 (0.5%) had anti-GABA B. RT-PCR/PCR identified human herpes virus type 1 (HSV-1; 300 copies/mL) and the representative of Enterovirus genus (550 copies/mL) in 1 patient each. Torque teno virus (TTV) was found in another patient using metagenomic analysis, and its presence was confirmed by specific PCR. Conclusions We detected the presence of HSV, TTV, and Enterovirus genus in CSF samples from 3 out of 8 AE patients. These findings support the concept of viral involvement in the pathogenesis of this disease.
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Affiliation(s)
- Karol Perlejewski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Agnieszka Pawełczyk
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Iwona Bukowska-Ośko
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | | | | | - Marcin Paciorek
- Department of Adult Infectious Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Michał Makowiecki
- Department of Adult Infectious Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Kamila Caraballo Cortés
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Marta Grochowska
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Marek Radkowski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Tomasz Laskus
- Department of Adult Infectious Diseases, Medical University of Warsaw, Warsaw, Poland
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14
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Perlejewski K, Bukowska-Ośko I, Rydzanicz M, Pawełczyk A, Caraballo Cortѐs K, Osuch S, Paciorek M, Dzieciątkowski T, Radkowski M, Laskus T. Next-generation sequencing in the diagnosis of viral encephalitis: sensitivity and clinical limitations. Sci Rep 2020; 10:16173. [PMID: 32999423 PMCID: PMC7528011 DOI: 10.1038/s41598-020-73156-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 09/07/2020] [Indexed: 12/12/2022] Open
Abstract
Identification of pathogens causing viral encephalitis remains challenging, and in over 50% of cases the etiologic factor remains undetermined. Next-generation sequencing (NGS) based metagenomics has been successfully used to detect novel and rare infections, but its value for routine diagnosis of encephalitis remains unclear. The aim of the present study was to determine the sensitivity of shotgun metagenomic sequencing protocols, which include preamplification, and testing it against cerebrospinal fluid (CSF) samples from encephalitis patients. For sensitivity testing HIV and HBV positive sera were serially diluted in CSF from an uninfected patient. NGS repeatedly detected HIV and HBV sequences present at concentrations from 105 to 102 and from 105 to 10 viral copies/reaction, respectively. However, when the same protocols were applied to RT-PCR/PCR positive CSF samples from 6 patients with enteroviral encephalitis (median viral load 47 copies/ml) and 15 patients with HSV, CMV or VZV encephalitis (median viral load 148 copies/ml), only 7 (28.6%) were identified as positive. In conclusions, while NGS has the advantage of being able to identify a wide range of potential pathogens it seems to be less sensitive compared to the standard amplification-based assays in the diagnosis of encephalitis, where low viral loads are common.
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Affiliation(s)
- Karol Perlejewski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland.
| | - Iwona Bukowska-Ośko
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Małgorzata Rydzanicz
- Department of the Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Agnieszka Pawełczyk
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Kamila Caraballo Cortѐs
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Sylwia Osuch
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Marcin Paciorek
- Department of Adult Infectious Diseases, Medical University of Warsaw, Warsaw, Poland
| | | | - Marek Radkowski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Tomasz Laskus
- Department of Adult Infectious Diseases, Medical University of Warsaw, Warsaw, Poland
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15
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Osuch S, Laskus T, Berak H, Perlejewski K, Metzner KJ, Paciorek M, Radkowski M, Caraballo Cortés K. Decrease of T-cells exhaustion markers programmed cell death-1 and T-cell immunoglobulin and mucin domain-containing protein 3 and plasma IL-10 levels after successful treatment of chronic hepatitis C. Sci Rep 2020; 10:16060. [PMID: 32994477 PMCID: PMC7524731 DOI: 10.1038/s41598-020-73137-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 08/31/2020] [Indexed: 02/07/2023] Open
Abstract
During chronic hepatitis C virus (HCV) infection, both CD4+ and CD8+ T-cells become functionally exhausted, which is reflected by increased expression of programmed cell death-1 (PD-1) and T-cell immunoglobulin and mucin domain-containing protein 3 (Tim-3), and elevated anti-inflammatory interleukin 10 (IL-10) plasma levels. We studied 76 DAA-treated HCV-positive patients and 18 non-infected controls. Flow cytometry measured pretreatment frequencies of CD4+PD-1+, CD4+PD-1+Tim-3+ and CD8+PD-1+Tim-3+ T-cells and IL-10 levels measured by ELISA were significantly higher and CD4+PD-1−Tim-3− and CD8+PD-1−Tim-3− T-cells were significantly lower in patients than in controls. Treatment resulted in significant decrease of CD4+Tim-3+, CD8+Tim-3+, CD4+PD-1+Tim-3+ and CD8+PD-1+Tim-3+ T-cell frequencies as well as IL-10 levels and increase in CD4+PD-1−Tim-3− and CD8+PD-1−Tim-3− T-cells. There were no significant changes in the frequencies of CD4+PD-1+ T-cells, while CD8+PD-1+ T-cells increased. Patients with advanced liver fibrosis had higher PD-1 and lower Tim-3 expression on CD4+T-cells and treatment had little or no effect on the exhaustion markers. HCV-specific CD8+T-cells frequency has declined significantly after treatment, but their PD-1 and Tim-3 expression did not change. Successful treatment of chronic hepatitis C with DAA is associated with reversal of immune exhaustion phenotype, but this effect is absent in patients with advanced liver fibrosis.
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Affiliation(s)
- Sylwia Osuch
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, 3c Pawińskiego Street, 02-106, Warsaw, Poland
| | - Tomasz Laskus
- Department of Adult Infectious Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Hanna Berak
- Outpatient Clinic, Warsaw Hospital for Infectious Diseases, Warsaw, Poland
| | - Karol Perlejewski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, 3c Pawińskiego Street, 02-106, Warsaw, Poland
| | - Karin J Metzner
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Marcin Paciorek
- Department of Adult Infectious Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Marek Radkowski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, 3c Pawińskiego Street, 02-106, Warsaw, Poland
| | - Kamila Caraballo Cortés
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, 3c Pawińskiego Street, 02-106, Warsaw, Poland.
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Caraballo Cortés K, Osuch S, Perlejewski K, Pawełczyk A, Kaźmierczak J, Janiak M, Jabłońska J, Nazzal K, Stelmaszczyk‐Emmel A, Berak H, Bukowska‐Ośko I, Paciorek M, Laskus T, Radkowski M. Expression of programmed cell death protein 1 and T-cell immunoglobulin- and mucin-domain-containing molecule-3 on peripheral blood CD4+CD8+ double positive T cells in patients with chronic hepatitis C virus infection and in subjects who spontaneously cleared the virus. J Viral Hepat 2019; 26:942-950. [PMID: 30972915 PMCID: PMC6850126 DOI: 10.1111/jvh.13108] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 01/21/2019] [Accepted: 03/18/2019] [Indexed: 12/12/2022]
Abstract
Chronic hepatitis C virus (HCV) infection is characterized by increased proportion of CD4+CD8+ double positive (DP) T cells, but their role in this infection is unclear. In chronic hepatitis C, immune responses to HCV become functionally exhausted, which manifests itself by increased expression of programmed cell death protein 1 (PD-1) and T-cell immunoglobulin- and mucin-domain-containing molecule-3 (Tim-3) on T cells. The aim of our study was to determine PD-1 and Tim-3 phenotype of DP T cells in subjects with naturally resolved and chronic HCV infection. Peripheral blood mononuclear cells from 16 patients with chronic infection and 14 subjects who cleared HCV in the past were stained with anti-CD3, anti-CD4, anti-CD8, anti-PD-1 and anti-Tim-3 antibodies and, in 12 HLA-A*02-positive subjects, MHC class I pentamer with HCV NS31406 epitope. In chronic and past HCV infection, proportions of total DP T cells and PD-1+ DP T cells were similar but significantly higher than in healthy controls. DP T cells were more likely to be PD-1+ than either CD4+ or CD8+ single positive (SP) T cells. HCV-specific cells were present in higher proportions among DP T cells than among CD8+ SP T cells in both patient groups. Furthermore, while the majority of HCV-specific DP T cells were PD-1+, the proportion of HCV-specific CD8+ T cells which were PD-1+ was 4.9 and 1.9 times lower (chronic and past infection, respectively). PD-1 and Tim-3 were predominantly expressed on CD4high CD8low and CD4low CD8high cells, respectively, and co-expression of both markers was uncommon.
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Affiliation(s)
- Kamila Caraballo Cortés
- Department of Immunopathology of Infectious and Parasitic DiseasesMedical University of WarsawWarsawPoland
| | - Sylwia Osuch
- Department of Immunopathology of Infectious and Parasitic DiseasesMedical University of WarsawWarsawPoland
| | - Karol Perlejewski
- Department of Immunopathology of Infectious and Parasitic DiseasesMedical University of WarsawWarsawPoland
| | - Agnieszka Pawełczyk
- Department of Immunopathology of Infectious and Parasitic DiseasesMedical University of WarsawWarsawPoland
| | - Justyna Kaźmierczak
- Department of Immunopathology of Infectious and Parasitic DiseasesMedical University of WarsawWarsawPoland
| | - Maciej Janiak
- Department of Immunopathology of Infectious and Parasitic DiseasesMedical University of WarsawWarsawPoland
| | - Joanna Jabłońska
- Clinic for Infectious, Tropical Diseases and HepatologyMedical University of WarsawWarsawPoland
| | - Khalil Nazzal
- Clinic for Infectious, Tropical Diseases and HepatologyMedical University of WarsawWarsawPoland
| | - Anna Stelmaszczyk‐Emmel
- Department of Laboratory Diagnostics and Clinical Immunology of Developmental AgeMedical University of WarsawWarsawPoland
| | - Hanna Berak
- Outpatient ClinicWarsaw Hospital for Infectious DiseasesWarsawPoland
| | - Iwona Bukowska‐Ośko
- Department of Immunopathology of Infectious and Parasitic DiseasesMedical University of WarsawWarsawPoland
| | - Marcin Paciorek
- Department of Infectious DiseasesMedical University of WarsawWarsawPoland
| | - Tomasz Laskus
- Department of Immunopathology of Infectious and Parasitic DiseasesMedical University of WarsawWarsawPoland
| | - Marek Radkowski
- Department of Immunopathology of Infectious and Parasitic DiseasesMedical University of WarsawWarsawPoland
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Bukowska-Ośko I, Perlejewski K, Pawełczyk A, Rydzanicz M, Pollak A, Popiel M, Cortés KC, Paciorek M, Horban A, Dzieciątkowski T, Radkowski M, Laskus T. Human Pegivirus in Patients with Encephalitis of Unclear Etiology, Poland. Emerg Infect Dis 2019; 24:1785-1794. [PMID: 30226156 PMCID: PMC6154136 DOI: 10.3201/eid2410.180161] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Sequence analysis of human pegivirus from 3 patients indicates that the central nervous system constitutes a separate viral compartment from serum. Human pegivirus (HPgV), previously called hepatitis G virus or GB virus C, is a lymphotropic virus with undefined pathology. Because many viruses from the family Flaviviridae, to which HPgV belongs, are neurotropic, we studied whether HPgV could infect the central nervous system. We tested serum and cerebrospinal fluid samples from 96 patients with a diagnosis of encephalitis for a variety of pathogens by molecular methods and serology; we also tested for autoantibodies against neuronal antigens. We found HPgV in serum and cerebrospinal fluid from 3 patients who had encephalitis of unclear origin; that is, all the markers that had been tested were negative. Single-strand confirmation polymorphism and next-generation sequencing analysis revealed differences between the serum and cerebrospinal fluid–derived viral sequences, which is compatible with the presence of a separate HPgV compartment in the central nervous system. It is unclear whether HPgV was directly responsible for encephalitis in these patients.
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Bukowska-Ośko I, Perlejewski K, Caraballo Cortés K, Pollak A, Berak H, Pawełczyk A, Horban A, Kosińska J, Płoski R, Laskus T, Radkowski M. Corrigendum: Next-generation Sequencing Analysis of New Genotypes Appearing During Antiviral Treatment of Chronic Hepatitis C Reveals that These Are Selected from Pre-existing Minor Strains. J Gen Virol 2019; 100:543. [PMID: 30632957 DOI: 10.1099/jgv.0.001225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Iwona Bukowska-Ośko
- 1Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, 3C Pawinskiego Street, 02-106 Warsaw, Poland
| | - Karol Perlejewski
- 1Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, 3C Pawinskiego Street, 02-106 Warsaw, Poland
| | - Kamila Caraballo Cortés
- 1Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, 3C Pawinskiego Street, 02-106 Warsaw, Poland
| | - Agnieszka Pollak
- 2Institute of Physiology and Pathology of Hearing, 17 Mokra Street, Kajetany 05-830 Nadarzyn, Poland
| | - Hanna Berak
- 3Hospital for Infectious Diseases, 37 Wolska Street, 01-201 Warsaw, Poland
| | - Agnieszka Pawełczyk
- 1Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, 3C Pawinskiego Street, 02-106 Warsaw, Poland
| | - Andrzej Horban
- 3Hospital for Infectious Diseases, 37 Wolska Street, 01-201 Warsaw, Poland.,4Department of Infectious Diseases, Warsaw Medical University, Warsaw, Poland
| | - Joanna Kosińska
- 5Department of Medical Genetics, Medical University of Warsaw, 3C Pawinskiego Street, 02-106 Warsaw, Poland
| | - Rafał Płoski
- 5Department of Medical Genetics, Medical University of Warsaw, 3C Pawinskiego Street, 02-106 Warsaw, Poland
| | - Tomasz Laskus
- 1Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, 3C Pawinskiego Street, 02-106 Warsaw, Poland
| | - Marek Radkowski
- 1Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, 3C Pawinskiego Street, 02-106 Warsaw, Poland
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Ufnal M, Bielinska K, Konop M, Radkowski M, Grochowska M, Perlejewski K, Huc T, Motooka D, Nakamura S. The Effect of Salt And Enalapril on Gut Bacteria Composition And Blood Level of Gut Bacteria‐derived Cardiovascular Markers. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.582.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | | | | | | | | | - Tomasz Huc
- Medical University of WarsawWarsawPoland
| | - Daisuke Motooka
- Department of Infection MetagenomicsGenome Information Research CenterResearch Institute for Microbial DiseasesOsaka UniversityOsakaJapan
| | - Shota Nakamura
- Department of Infection MetagenomicsGenome Information Research CenterResearch Institute for Microbial DiseasesOsaka UniversityOsakaJapan
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20
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Bielinska K, Radkowski M, Grochowska M, Perlejewski K, Huc T, Jaworska K, Motooka D, Nakamura S, Ufnal M. High salt intake increases plasma trimethylamine N-oxide (TMAO) concentration and produces gut dysbiosis in rats. Nutrition 2018; 54:33-39. [PMID: 29705499 DOI: 10.1016/j.nut.2018.03.004] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 03/01/2018] [Indexed: 11/30/2022]
Abstract
OBJECTIVE A high-salt diet is considered a cardiovascular risk factor; however, the mechanisms are not clear. Research suggests that gut bacteria-derived metabolites such as trimethylamine N-oxide (TMAO) are markers of cardiovascular diseases. We evaluated the effect of high salt intake on gut bacteria and their metabolites plasma level. METHODS Sprague Dawley rats ages 12-14 wk were maintained on either water (controls) or 0.9% or 2% sodium chloride (NaCl) water solution (isotonic and hypertonic groups, respectively) for 2 wk. Blood plasma, urine, and stool samples were analyzed for concentrations of trimethylamine (TMA; a TMAO precursor), TMAO, and indoxyl sulfate (indole metabolite). The gut-blood barrier permeability to TMA and TMA liver clearance were assessed at baseline and after TMA intracolonic challenge test. Gut bacterial flora was analyzed with a 16S ribosomal ribonucleic acid (rRNA) gene sequence analysis. RESULTS The isotonic and hypertonic groups showed a significantly higher plasma TMAO and significantly lower 24-hr TMAO urine excretion than the controls. However, the TMA stool level was similar between the groups. There was no significant difference between the groups in gut-blood barrier permeability and TMA liver clearance. Plasma indoxyl concentration and 24-hr urine indoxyl excretion were similar between the groups. There was a significant difference between the groups in gut bacteria composition. CONCLUSIONS High salt intake increases plasma TMAO concentration, which is associated with decreased TMAO urine excretion. Furthermore, high salt intake alters gut bacteria composition. These findings suggest that salt intake affects an interplay between gut bacteria and their host homeostasis.
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Affiliation(s)
- Klaudia Bielinska
- Department of Experimental Physiology and Pathophysiology, Laboratory of Centre for Preclinical Research, Medical University of Warsaw, Warsaw, Poland
| | - Marek Radkowski
- Department of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University, Warsaw, Poland
| | - Marta Grochowska
- Department of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University, Warsaw, Poland
| | - Karol Perlejewski
- Department of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University, Warsaw, Poland
| | - Tomasz Huc
- Department of Experimental Physiology and Pathophysiology, Laboratory of Centre for Preclinical Research, Medical University of Warsaw, Warsaw, Poland
| | - Kinga Jaworska
- Department of Experimental Physiology and Pathophysiology, Laboratory of Centre for Preclinical Research, Medical University of Warsaw, Warsaw, Poland
| | - Daisuke Motooka
- Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Shota Nakamura
- Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Marcin Ufnal
- Department of Experimental Physiology and Pathophysiology, Laboratory of Centre for Preclinical Research, Medical University of Warsaw, Warsaw, Poland.
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Konop M, Radkowski M, Grochowska M, Perlejewski K, Samborowska E, Ufnal M. Enalapril decreases rat plasma concentration of TMAO, a gut bacteria-derived cardiovascular marker. Biomarkers 2018; 23:380-385. [PMID: 29363331 DOI: 10.1080/1354750x.2018.1432689] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
INTRODUCTION Increased plasma level of trimethylamine N-oxide (TMAO), a bacterial metabolite of choline, is associated with an increased cardiovascular risk. Indoxyl sulfate, a bacterial metabolite of tryptophan, is thought to be associated with higher mortality in cardiorenal syndrome. We hypothesized that enalapril, a well-established drug reducing cardiovascular mortality, may affect the plasma level of gut bacteria-derived metabolites and gut bacteria composition. MATERIALS AND METHODS 14-16-week-old Wistar rats were maintained either on water (controls) or water solution of enalapril for two weeks (5.3 or 12.6 mg/kg b.w.). Blood plasma and urine were analyzed for the concentration of TMAO and indoxyl sulfate using liquid chromatography coupled with triple-quadrupole mass spectrometry. Gut bacteria composition was analyzed with 16S rRNA gene sequence analysis. RESULTS Rats treated with enalapril showed a significantly lower plasma TMAO level and a trend towards higher 24 h urine excretion of TMA and TMAO. Plasma indoxyl level was similar between the groups. There was no significant difference between the groups in gut bacteria composition. CONCLUSIONS Enalapril decreases rat plasma TMAO, but does not affect the plasma level of indoxyl sulfate and gut bacteria composition. The enalapril-induced decrease in plasma TMAO level may be of therapeutic and diagnostic importance.
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Affiliation(s)
- Marek Konop
- a Department of Experimental Physiology and Pathophysiology, Laboratory of Centre for Preclinical Research , Medical University of Warsaw , Warsaw , Poland
| | - Marek Radkowski
- b Department of Immunopathology of Infectious and Parasitic Diseases , Warsaw Medical University , Warsaw , Poland
| | - Marta Grochowska
- b Department of Immunopathology of Infectious and Parasitic Diseases , Warsaw Medical University , Warsaw , Poland
| | - Karol Perlejewski
- b Department of Immunopathology of Infectious and Parasitic Diseases , Warsaw Medical University , Warsaw , Poland
| | - Emilia Samborowska
- c Mass Spectrometry Laboratory , Institute of Biochemistry and Biophysics, Polish Academy of Sciences , Warsaw , Poland
| | - Marcin Ufnal
- a Department of Experimental Physiology and Pathophysiology, Laboratory of Centre for Preclinical Research , Medical University of Warsaw , Warsaw , Poland
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22
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Janiak M, Caraballo Cortés K, Perlejewski K, Kubicka-Russel D, Grabarczyk P, Demkow U, Radkowski M. Next-Generation Sequencing of Hepatitis C Virus (HCV) Mixed-Genotype Infections in Anti-HCV-Negative Blood Donors. Adv Exp Med Biol 2018; 1096:65-71. [PMID: 29594753 DOI: 10.1007/5584_2018_190] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The infection with more than one hepatitis C virus (HCV) genotype especially in subjects with a high risk of multiple HCV exposures has been demonstrated. The role of HCV mixed-genotype infection in viral persistence and treatment effect is not fully understood. The prevalence of such infection varies greatly depending on the technique used for genotype determination and studied population. Next-generation sequencing (NGS) which is suitable for extensive analysis of complex viral populations is a method of choice for studying mixed infections. The aim of the present study was to determine the prevalence of mixed-genotype HCV infections in the Polish seronegative, HCV-RNA-positive blood donors (n = 76). Two-step PCR was used for amplification of 5'-UTR of HCV. Using pyrosequencing altogether, 381,063 reads were obtained. The raw reads were trimmed and subjected to similarity analysis against the entire unfiltered NCBI nt database. Results obtained from NGS were compared with the standard genotyping. One (1.3%) mixed-genotype [3a, 2989 reads (94.8%); 1b, 164 reads (5.2%)] infection was found in a sample diagnosed as genotype 3a only by routine testing. Two samples were identified with different genotypes, compared to routine testing. In conclusion, NGS is a sensitive method for HCV genotyping. The prevalence of mixed-genotype HCV infections in blood donors is low.
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Affiliation(s)
- Maciej Janiak
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Kamila Caraballo Cortés
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland.
| | - Karol Perlejewski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Dorota Kubicka-Russel
- Department of Virology, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Piotr Grabarczyk
- Department of Virology, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Urszula Demkow
- Department of Laboratory Medicine and Clinical Immunology of Developmental Age, Medical University of Warsaw, Warsaw, Poland
| | - Marek Radkowski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
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Radkowski M, Opoka-Kegler J, Cortes KC, Bukowska-Ośko I, Perlejewski K, Pawełczyk A, Laskus T. Corrigendum: Evidence for immune activation in patients with residual hepatitis C virus RNA long after successful treatment with IFN and ribavirin. J Gen Virol 2017; 98:3122. [PMID: 29214971 DOI: 10.1099/jgv.0.000970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Marek Radkowski
- Department of Immunopathology, Warsaw Medical University, Warsaw, Poland
| | | | | | | | - Karol Perlejewski
- Department of Immunopathology, Warsaw Medical University, Warsaw, Poland
| | | | - Tomasz Laskus
- Department of Immunopathology, Warsaw Medical University, Warsaw, Poland
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24
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Lipowski D, Popiel M, Perlejewski K, Nakamura S, Bukowska-Osko I, Rzadkiewicz E, Dzieciatkowski T, Milecka A, Wenski W, Ciszek M, Debska-Slizien A, Ignacak E, Cortes KC, Pawelczyk A, Horban A, Radkowski M, Laskus T. A Cluster of Fatal Tick-borne Encephalitis Virus Infection in Organ Transplant Setting. J Infect Dis 2017; 215:896-901. [PMID: 28453842 DOI: 10.1093/infdis/jix040] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 01/17/2017] [Indexed: 12/15/2022] Open
Abstract
Background Tick-borne encephalitis virus (TBEV) infection has become a major health problem in Europe and is currently a common cause of viral brain infection in many countries. Encephalitis in transplant recipients, althrough rare, is becoming a recognized complication. Our study provides the first description of transmission of TBEV through transplantation of solid organs. Methods Three patients who received solid organ transplants from a single donor (2 received kidney, and 1 received liver) developed encephalitis 17-49 days after transplantation and subsequently died. Blood and autopsy tissue samples were tested by next-generation sequencing (NGS) and reverse transcription polymerase chain reaction (RT-PCR). Results All 3 recipients were first analyzed in autopsy brain tissue samples and/or cerebrospinal fluid by NGS, which yielded 24-52 million sequences per sample and 9-988 matched TBEV sequences in each patient. The presence of TBEV was confirmed by RT-PCR in all recipients and in the donor, and direct sequencing of amplification products corroborated the presence of the same viral strain. Conclusions We demonstrated transmission of TBEV by transplantation of solid organs. In such a setting, TBEV infection may be fatal, probably due to pharmacological immunosuppression. Organ donors should be screened for TBEV when coming from or visiting endemic areas.
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Affiliation(s)
- Dariusz Lipowski
- Department of Infectious Diseases, Warsaw Medical University, Warsaw, Poland
| | - Marta Popiel
- Department of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University, Warsaw, Poland
| | - Karol Perlejewski
- Department of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University, Warsaw, Poland
| | - Shota Nakamura
- Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Iwona Bukowska-Osko
- Department of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University, Warsaw, Poland
| | - Ewa Rzadkiewicz
- Department of Infectious Diseases, Warsaw Medical University, Warsaw, Poland
| | | | - Anna Milecka
- Department of General and Endocrine Surgery and Transplantation Medical University of Gdansk, Gdansk, Poland
| | | | - Michal Ciszek
- Department of Immunology, Warsaw Medical University, Warsaw, Poland
| | - Alicja Debska-Slizien
- Department of Nephrology, Transplantation and Internal Diseases, Gdansk Medical University, Gdansk, Poland
| | - Ewa Ignacak
- Department of Nephrology, Kraków Medical University Hospital, Poland
| | - Kamila Caraballo Cortes
- Department of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University, Warsaw, Poland
| | - Agnieszka Pawelczyk
- Department of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University, Warsaw, Poland
| | - Andrzej Horban
- Department of Infectious Diseases, Warsaw Medical University, Warsaw, Poland
| | - Marek Radkowski
- Department of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University, Warsaw, Poland
| | - Tomasz Laskus
- Department of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University, Warsaw, Poland
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25
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Popiel M, Perlejewski K, Bednarska A, Dzieciątkowski T, Paciorek M, Lipowski D, Jabłonowska M, Czeszko-Paprocka H, Bukowska-Ośko I, Caraballo Cortes K, Pawełczyk A, Fic M, Horban A, Radkowski M, Laskus T. Viral etiologies in adult patients with encephalitis in Poland: A prospective single center study. PLoS One 2017; 12:e0178481. [PMID: 28570620 PMCID: PMC5453691 DOI: 10.1371/journal.pone.0178481] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 05/12/2017] [Indexed: 12/30/2022] Open
Abstract
Encephalitis is a severe neurological syndrome associated with high morbidity and mortality as well as long-term neurological sequelae. Despite being an important public health problem, very few extensive population-based studies were conducted so far in the world and none in Central Europe. Altogether 114 consecutive patients meeting the initial criteria for encephalitis were enrolled at the Warsaw Hospital for Infectious Diseases between June 2012 and July 2015. Eighteen patients were secondarily excluded from the analysis due to incomplete data or noinfectious cause. Potential pathogen sequences were searched for by molecular methods in the cerebrospinal fluid (CSF) and specific antibodies were detected in CSF and sera. An infectious agent was identified in 41 patients (42.7%). The most frequently diagnosed infections were Human herpesvirus 1 (HHV-1) (22 cases, 24%) followed by Enterovirus (6 cases, 6.3%), Varicella zoster virus (VZV) (5 cases, 5.2%), Tick-borne encephalitis virus (TBEV) (6 cases, 6.3%) and Cytomegalovirus (CMV) (2 cases, 2.1%). There were no cases of human adenovirus, Human herpesvirus 6 (HHV-6) or West Nile virus (WNV) infection identified. In 55 cases (57.3%) the cause of encephalitis remained unknown. Compared to patients in whom the diagnosis was determined the latter group contained more women, was less likely to manifest fever and had lower CSF pleocytosis (p < 0.05) In summary, we identified HHV-1 followed by Enterovirus, VZV and TBEV as the most common causes of encephalitis among adult patients in Poland. In a large proportion of patients the cause of encephalitis remained unknown.
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Affiliation(s)
- Marta Popiel
- Department of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University, Warsaw, Poland
| | - Karol Perlejewski
- Department of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University, Warsaw, Poland
| | - Agnieszka Bednarska
- Department of Infectious Diseases, Warsaw Medical University, Warsaw, Poland
- Hospital for Infectious Diseases, Warsaw, Poland
| | | | | | - Dariusz Lipowski
- Department of Infectious Diseases, Warsaw Medical University, Warsaw, Poland
| | | | | | - Iwona Bukowska-Ośko
- Department of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University, Warsaw, Poland
| | - Kamila Caraballo Cortes
- Department of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University, Warsaw, Poland
| | - Agnieszka Pawełczyk
- Department of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University, Warsaw, Poland
| | - Maria Fic
- Department of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University, Warsaw, Poland
| | - Andrzej Horban
- Department of Infectious Diseases, Warsaw Medical University, Warsaw, Poland
| | - Marek Radkowski
- Department of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University, Warsaw, Poland
| | - Tomasz Laskus
- Department of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University, Warsaw, Poland
- * E-mail:
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Bukowska-Ośko I, Perlejewski K, Nakamura S, Motooka D, Stokowy T, Kosińska J, Popiel M, Płoski R, Horban A, Lipowski D, Caraballo Cortés K, Pawełczyk A, Demkow U, Stępień A, Radkowski M, Laskus T. Sensitivity of Next-Generation Sequencing Metagenomic Analysis for Detection of RNA and DNA Viruses in Cerebrospinal Fluid: The Confounding Effect of Background Contamination. Adv Exp Med Biol 2016:53-62. [PMID: 27405447 DOI: 10.1007/5584_2016_42] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Next-generation sequencing (NGS) followed by metagenomic enables the detection and identification of known as well as novel pathogens. It could be potentially useful in the diagnosis of encephalitis, caused by a variety of microorganisms. The aim of the present study was to evaluate the sensitivity of isothermal RNA amplification (Ribo-SPIA) followed by NGS metagenomic analysis in the detection of human immunodeficiency virus (HIV) and herpes simplex virus (HSV) in cerebrospinal fluid (CSF). Moreover, we analyzed the contamination background. We detected 102 HIV copies and 103 HSV copies. The analysis of control samples (two water samples and one CSF sample from an uninfected patient) revealed the presence of human DNA in the CSF sample (91 % of all reads), while the dominating sequences in water were qualified as 'other', related to plants, plant viruses, and synthetic constructs, and constituted 31 % and 60 % of all reads. Bacterial sequences represented 5.9 % and 21.4 % of all reads in water samples and 2.3 % in the control CSF sample. The bacterial sequences corresponded mainly to Psychrobacter, Acinetobacter, and Corynebacterium genera. In conclusion, Ribo-SPIA amplification followed by NGS metagenomic analysis is sensitive for detection of RNA and DNA viruses. Contamination seems common and thus the results should be confirmed by other independent methods such as RT-PCR and PCR. Despite these reservations, NGS seems to be a promising method for the diagnosis of viral infections.
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Affiliation(s)
- Iwona Bukowska-Ośko
- Department of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University, 3C Pawińskiego St, 02-106, Warsaw, Poland
| | - Karol Perlejewski
- Department of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University, 3C Pawińskiego St, 02-106, Warsaw, Poland.
| | - Shota Nakamura
- Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, Japan
| | - Daisuke Motooka
- Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, Japan
| | - Tomasz Stokowy
- Department of Clinical Science, Bergen University, 5021, Bergen, Norway
| | - Joanna Kosińska
- Department of the Medical Genetics, Warsaw Medical University, 3C Pawińskiego St, 02-106, Warsaw, Poland
| | - Marta Popiel
- Department of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University, 3C Pawińskiego St, 02-106, Warsaw, Poland
| | - Rafał Płoski
- Department of the Medical Genetics, Warsaw Medical University, 3C Pawińskiego St, 02-106, Warsaw, Poland
| | - Andrzej Horban
- Municipal Hospital for Infectious Diseases, 37 Wolska St, 01-201, Warsaw, Poland
| | - Dariusz Lipowski
- Municipal Hospital for Infectious Diseases, 37 Wolska St, 01-201, Warsaw, Poland
| | - Kamila Caraballo Cortés
- Department of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University, 3C Pawińskiego St, 02-106, Warsaw, Poland
| | - Agnieszka Pawełczyk
- Department of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University, 3C Pawińskiego St, 02-106, Warsaw, Poland
| | - Urszula Demkow
- Department of Laboratory Medicine and Clinical Immunology of Developmental Age, Warsaw Medical University, 24 Marszałkowska St, 00-576, Warsaw, Poland
| | - Adam Stępień
- Department of Neurology, Military Institute of Medicine, 128 Szaserów St, 04-141, Warsaw, Poland
| | - Marek Radkowski
- Department of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University, 3C Pawińskiego St, 02-106, Warsaw, Poland
| | - Tomasz Laskus
- Department of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University, 3C Pawińskiego St, 02-106, Warsaw, Poland
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Jabłońska J, Pawłowski T, Laskus T, Zalewska M, Inglot M, Osowska S, Perlejewski K, Bukowska-Ośko I, Cortes KC, Pawełczyk A, Ząbek P, Radkowski M. Erratum to: 'The correlation between pretreatment cytokine expression patterns in peripheral blood mononuclear cells with chronic hepatitis c outcome'. BMC Infect Dis 2016; 16:104. [PMID: 26936257 PMCID: PMC4774028 DOI: 10.1186/s12879-016-1423-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Affiliation(s)
- Joanna Jabłońska
- Department of Hepatology and Acquired Immunodeficiences, Medical University of Warsaw, Warsaw, Poland
| | - Tomasz Pawłowski
- Division of Psychotherapy and Psychosomatic Medicine, Wrocław Medical University, Wrocław, Poland
| | - Tomasz Laskus
- Department of Immunopathology of Infectious Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Małgorzata Zalewska
- Department of Infectious Diseases, Hepatology and Acquired Immune Deficiences, Wrocław Medical University, Wrocław, Poland
| | - Małgorzata Inglot
- Department of Infectious Diseases, Hepatology and Acquired Immune Deficiences, Wrocław Medical University, Wrocław, Poland
| | - Sylwia Osowska
- Department of General Surgery and Clinical Nutrition, Medical University of Warsaw, Warsaw, Poland
| | - Karol Perlejewski
- Department of Immunopathology of Infectious Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Iwona Bukowska-Ośko
- Department of Immunopathology of Infectious Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Kamila Caraballo Cortes
- Department of Immunopathology of Infectious Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Agnieszka Pawełczyk
- Department of Immunopathology of Infectious Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Piotr Ząbek
- Municipal Hospital of Infectious Diseases, Warsaw, Poland
| | - Marek Radkowski
- Department of Immunopathology of Infectious Diseases, Medical University of Warsaw, Warsaw, Poland.
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28
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Caraballo Cortes K, Zagordi O, Jabłońska J, Pawełczyk A, Kubisa N, Perlejewski K, Bukowska-Ośko I, Płoski R, Radkowski M, Laskus T. Spouse-to-Spouse Transmission and Evolution of Hypervariable Region 1 and 5' Untranslated Region of Hepatitis C Virus Analyzed by Next-Generation Sequencing. PLoS One 2016; 11:e0150311. [PMID: 26918636 PMCID: PMC4769329 DOI: 10.1371/journal.pone.0150311] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 02/11/2016] [Indexed: 12/16/2022] Open
Abstract
Hepatitis C virus (HCV) transmission between spouses remains poorly characterized, largely due to the limited availability of samples from the early stage of infection, as well as methodological constraints. A fifty-eight year-old male developed acute hepatitis C infection and his 53-year old spouse has been HCV-positive for over 10 years. Serum samples were collected from both at the time of acute hepatitis C diagnosis in male (baseline) and then at 9 and 13 months. Hypervariable region 1 (HVR1) and 5’ untranslated region (5’UTR) sequences were amplified and subjected to next generation sequencing (NGS) using a pyrosequencing platform. Genetic variants were inferred by Shorah reconstruction method and compared by phylogenetic and sequence diversity analysis. As the sequencing error of the procedure was previously determined to be ≤ 1.5%, the analysis was conducted with and without the 1.5% cut-off with regard to the frequency of variants. No identical HVR1 variants were identified in spouses at baseline and follow-up samples regardless whether the cut-off was applied or not. However, there was high similarity (98.3%) between a minor baseline donor variant (1.7% frequency) and the most abundant baseline recipient variant (62.5% frequency). Furthermore, donor and recipient strains clustered together when compared to 10 control subjects from the same area and infected with the same HCV subtype. There was an increase in HVR1 complexity (number of genetic variants) over time in both spouses. In contrast, the 5'UTR region was stable and of low complexity throughout the study. In conclusion, intrafamilial HCV transmission may be established by a very minor variant and investigation of this phenomenon requires high-sensitivity assays, such as NGS.
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Affiliation(s)
- Kamila Caraballo Cortes
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
- * E-mail:
| | - Osvaldo Zagordi
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Joanna Jabłońska
- Clinics of Infectious, Tropical Diseases and Hepatology, Medical University of Warsaw, Warsaw, Poland
| | - Agnieszka Pawełczyk
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Natalia Kubisa
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Karol Perlejewski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Iwona Bukowska-Ośko
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Marek Radkowski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Tomasz Laskus
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
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Perlejewski K, Bukowska-Ośko I, Nakamura S, Motooka D, Stokowy T, Płoski R, Rydzanicz M, Zakrzewska-Pniewska B, Podlecka-Piętowska A, Nojszewska M, Gogol A, Caraballo Cortés K, Demkow U, Stępień A, Laskus T, Radkowski M. Metagenomic Analysis of Cerebrospinal Fluid from Patients with Multiple Sclerosis. Adv Exp Med Biol 2016; 935:89-98. [PMID: 27311319 DOI: 10.1007/5584_2016_25] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Multiple sclerosis (MS) is a chronic inflammatory demyelinating disease of central nervous system of unknown etiology. However, some infectious agents have been suggested to play a significant role in its pathogenesis. Next-generation sequencing (NGS) and metagenomics can be employed to characterize microbiome of MS patients and to identify potential causative pathogens. In this study, 12 patients with idiopathic inflammatory demyelinating disorders (IIDD) of the central nervous system were studied: one patient had clinically isolated syndrome, one patient had recurrent optic neuritis, and ten patients had multiple sclerosis (MS). In addition, there was one patient with other non-inflammatory neurological disease. Cerebrospinal fluid (CSF) was sampled from all patients. RNA was extracted from CSF and subjected to a single-primer isothermal amplification followed by NGS and comprehensive data analysis. Altogether 441,608,474 reads were obtained and mapped using blastn. In a CSF sample from the patient with clinically isolated syndrome, 11 varicella-zoster virus reads were found. Other than that similar bacterial, fungal, parasitic, and protozoan reads were identified in all samples, indicating a common presence of contamination in metagenomics. In conclusion, we identified varicella zoster virus sequences in one out of the 12 patients with IIDD, which suggests that this virus could be occasionally related to the MS pathogenesis. A widespread bacterial contamination seems inherent to NGS and complicates the interpretation of results.
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Affiliation(s)
- Karol Perlejewski
- Department of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University, 3C Pawińskiego Street, Warsaw, 02-106, Poland
| | - Iwona Bukowska-Ośko
- Department of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University, 3C Pawińskiego Street, Warsaw, 02-106, Poland.
| | - Shota Nakamura
- Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Osaka, Japan
| | - Daisuke Motooka
- Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Osaka, Japan
| | - Tomasz Stokowy
- Department of Clinical Science, University of Bergen, Bergen, 5021, Norway
| | - Rafał Płoski
- Department of the Medical Genetics, Warsaw Medical University, 3C Pawińskiego Street, Warsaw, 02-106, Poland
| | - Małgorzata Rydzanicz
- Department of the Medical Genetics, Warsaw Medical University, 3C Pawińskiego Street, Warsaw, 02-106, Poland
| | | | | | - Monika Nojszewska
- Department of Neurology, Warsaw Medical University, 1A Banacha, Warsaw, 02-097, Poland
| | - Anna Gogol
- Department of Neurology, Warsaw Medical University, 1A Banacha, Warsaw, 02-097, Poland
| | - Kamila Caraballo Cortés
- Department of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University, 3C Pawińskiego Street, Warsaw, 02-106, Poland
| | - Urszula Demkow
- Department of Laboratory Medicine and Clinical Immunology of Developmental Age, Medical University of Warsaw, 24 Marszałkowska Street, Warsaw, 00-576, Poland
| | - Adam Stępień
- Department of Neurology, Military Institute of Medicine, 128 Szaserów Street, Warsaw, 04-141, Poland
| | - Tomasz Laskus
- Department of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University, 3C Pawińskiego Street, Warsaw, 02-106, Poland
| | - Marek Radkowski
- Department of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University, 3C Pawińskiego Street, Warsaw, 02-106, Poland
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Jabłońska J, Pawłowski T, Laskus T, Zalewska M, Inglot M, Osowska S, Perlejewski K, Bukowska-Ośko I, Cortes KC, Pawełczyk A, Ząbek P, Radkowski M. The correlation between pretreatment cytokine expression patterns in peripheral blood mononuclear cells with chronic hepatitis C outcome. BMC Infect Dis 2015; 15:556. [PMID: 26637466 PMCID: PMC4670510 DOI: 10.1186/s12879-015-1305-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 12/01/2015] [Indexed: 12/24/2022] Open
Abstract
Backgroud Cytokine response against hepatitis C virus (HCV) is likely to determine the natural course of infection as well as the outcome of antiviral treatment. However, the role of particular cytokines remains unclear. The current study analyzed activation of cytokine response in chronic hepatitis C patients undergoing standard antiviral treatment. Methods Twenty-two patients were treated with pegylated interferon and ribavirin. Twenty-six different cytokine transcripts were measured quantitatively in peripheral blood mononuclear cells (PBMC) before and after therapy and correlated with therapy outcome as well as with clinical and liver histological data. Results We found that patients who achieved sustained virological response (SVR) showed higher pretreatment cytokine response when compared to subjects in whom therapy was unsuccessful. The differentially expressed factors included IL-8, IL-16, TNF-α, GM-CSF, MCP-2, TGF-β, and IP-10. Serum ALT activity and/or histological grading also positively correlated with the expression of IL-1α, IL-4, IL-6, IL-10, IL-12, IL-15, GM-CSF, M-CSF, MCP-2 and TGF-β. Conclusion Pretreatment activation of the immune system, as reflected by cytokines transcripts upregulation, positively correlates with treatment outcome and closely reflects liver inflammatory activity.
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Affiliation(s)
- Joanna Jabłońska
- Department of Hepatology and Acquired Immunodeficiences, Medical University of Warsaw, Warsaw, Poland.
| | - Tomasz Pawłowski
- Division of Psychotherapy and Psychosomatic Medicine, Wrocław Medical University, Wrocław, Poland.
| | - Tomasz Laskus
- Department of Immunopathology of Infectious Diseases, Medical University of Warsaw, Warsaw, Poland.
| | - Małgorzata Zalewska
- Department of Infectious Diseases, Hepatology and Acquired Immune Deficiences, Wrocław Medical University, Wrocław, Poland.
| | - Małgorzata Inglot
- Department of Infectious Diseases, Hepatology and Acquired Immune Deficiences, Wrocław Medical University, Wrocław, Poland.
| | - Sylwia Osowska
- Department of General Surgery and Clinical Nutrition, Medical University of Warsaw, Warsaw, Poland.
| | - Karol Perlejewski
- Department of Immunopathology of Infectious Diseases, Medical University of Warsaw, Warsaw, Poland.
| | - Iwona Bukowska-Ośko
- Department of Immunopathology of Infectious Diseases, Medical University of Warsaw, Warsaw, Poland.
| | - Kamila Caraballo Cortes
- Department of Immunopathology of Infectious Diseases, Medical University of Warsaw, Warsaw, Poland.
| | - Agnieszka Pawełczyk
- Department of Immunopathology of Infectious Diseases, Medical University of Warsaw, Warsaw, Poland.
| | - Piotr Ząbek
- Municipal Hospital of Infectious Diseases, Warsaw, Poland.
| | - Marek Radkowski
- Department of Immunopathology of Infectious Diseases, Medical University of Warsaw, Warsaw, Poland.
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Perlejewski K, Popiel M, Laskus T, Nakamura S, Motooka D, Stokowy T, Lipowski D, Pollak A, Lechowicz U, Caraballo Cortés K, Stępień A, Radkowski M, Bukowska-Ośko I. Next-generation sequencing (NGS) in the identification of encephalitis-causing viruses: Unexpected detection of human herpesvirus 1 while searching for RNA pathogens. J Virol Methods 2015; 226:1-6. [PMID: 26424618 DOI: 10.1016/j.jviromet.2015.09.010] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 09/24/2015] [Accepted: 09/24/2015] [Indexed: 11/18/2022]
Abstract
BACKGROUND Encephalitis is a severe neurological syndrome usually caused by viruses. Despite significant progress in diagnostic techniques, the causative agent remains unidentified in the majority of cases. The aim of the present study was to test an alternative approach for the detection of putative pathogens in encephalitis using next-generation sequencing (NGS). METHODS RNA was extracted from cerebrospinal fluid (CSF) from a 60-year-old male patient with encephalitis and subjected to isothermal linear nucleic acid amplification (Ribo-SPIA, NuGen) followed by next-generation sequencing using MiSeq (Illumina) system and metagenomics data analysis. RESULTS The sequencing run yielded 1,578,856 reads overall and 2579 reads matched human herpesvirus I (HHV-1) genome; the presence of this pathogen in CSF was confirmed by specific PCR. In subsequent experiments we found that the DNAse I treatment, while lowering the background of host-derived sequences, lowered the number of detectable HHV-1 sequences by a factor of 4. Furthermore, we found that the routine extraction of total RNA by the Chomczynski method could be used for identification of both DNA and RNA pathogens in typical clinical settings, as it results in retention of a significant amount of DNA. CONCLUSION In summary, it seems that NGS preceded by nucleic acid amplification could supplement currently used diagnostic methods in encephalitis.
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Affiliation(s)
- Karol Perlejewski
- Department of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University, 3C Pawinskiego Street, 02-106 Warsaw, Poland.
| | - Marta Popiel
- Department of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University, 3C Pawinskiego Street, 02-106 Warsaw, Poland; Postgraduate School of Molecular Medicine, 61 Żwirki i Wigury Street, 02-091 Warsaw, Poland.
| | - Tomasz Laskus
- Department of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University, 3C Pawinskiego Street, 02-106 Warsaw, Poland.
| | - Shota Nakamura
- Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University 3-1 Yamadaoka, Suita-City, Osaka, Japan.
| | - Daisuke Motooka
- Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University 3-1 Yamadaoka, Suita-City, Osaka, Japan.
| | - Tomasz Stokowy
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway.
| | - Dariusz Lipowski
- Municipal Hospital for Infectious Diseases, 37 Wolska Street, 01-201 Warsaw, Poland.
| | - Agnieszka Pollak
- Department of Genetics, Institute of Physiology and Pathology of Hearing, Mochnackiego 10, 02-042 Warsaw, Poland.
| | - Urszula Lechowicz
- Department of Genetics, Institute of Physiology and Pathology of Hearing, Mochnackiego 10, 02-042 Warsaw, Poland.
| | - Kamila Caraballo Cortés
- Department of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University, 3C Pawinskiego Street, 02-106 Warsaw, Poland.
| | - Adam Stępień
- Department of Neurology, Military Institute of Medicine, 128 Szaserów Street, 04-141 Warsaw, Poland.
| | - Marek Radkowski
- Department of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University, 3C Pawinskiego Street, 02-106 Warsaw, Poland.
| | - Iwona Bukowska-Ośko
- Department of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University, 3C Pawinskiego Street, 02-106 Warsaw, Poland.
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Cortés KC, Zagordi O, Perlejewski K, Laskus T, Maroszek K, Bukowska-Ośko I, Pawełczyk A, Płoski R, Berak H, Horban A, Radkowski M. Deep sequencing of hepatitis C virus hypervariable region 1 reveals no correlation between genetic heterogeneity and antiviral treatment outcome. BMC Infect Dis 2014; 14:389. [PMID: 25016390 PMCID: PMC4226954 DOI: 10.1186/1471-2334-14-389] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 07/07/2014] [Indexed: 01/26/2023] Open
Abstract
Background Hypervariable region 1 (HVR1) contained within envelope protein 2 (E2) gene is the most variable part of HCV genome and its translation product is a major target for the host immune response. Variability within HVR1 may facilitate evasion of the immune response and could affect treatment outcome. The aim of the study was to analyze the impact of HVR1 heterogeneity employing sensitive ultra-deep sequencing, on the outcome of PEG-IFN-α (pegylated interferon α) and ribavirin treatment. Methods HVR1 sequences were amplified from pretreatment serum samples of 25 patients infected with genotype 1b HCV (12 responders and 13 non-responders) and were subjected to pyrosequencing (GS Junior, 454/Roche). Reads were corrected for sequencing error using ShoRAH software, while population reconstruction was done using three different minimal variant frequency cut-offs of 1%, 2% and 5%. Statistical analysis was done using Mann–Whitney and Fisher’s exact tests. Results Complexity, Shannon entropy, nucleotide diversity per site, genetic distance and the number of genetic substitutions were not significantly different between responders and non-responders, when analyzing viral populations at any of the three frequencies (≥1%, ≥2% and ≥5%). When clonal sample was used to determine pyrosequencing error, 4% of reads were found to be incorrect and the most abundant variant was present at a frequency of 1.48%. Use of ShoRAH reduced the sequencing error to 1%, with the most abundant erroneous variant present at frequency of 0.5%. Conclusions While deep sequencing revealed complex genetic heterogeneity of HVR1 in chronic hepatitis C patients, there was no correlation between treatment outcome and any of the analyzed quasispecies parameters.
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Affiliation(s)
- Kamila Caraballo Cortés
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, 3c Pawińskiego Street, 02-106 Warsaw, Poland.
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