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Hauner A, Rogé S, Vanlerberghe V, Lepore L, Ndayisenga F, Shyaka A, Van Esbroeck M, Situma S, Nasimiyu C, Ahuka-Mundeke S, Njenga MK, Breiman RF, Masumu J, Mukadi-Bamuleka D, Ariën KK. Technical validation of a multiplex real-time PCR for combined detection of Rift Valley fever, chikungunya, Zika and dengue viruses. J Virol Methods 2025; 337:115174. [PMID: 40345597 DOI: 10.1016/j.jviromet.2025.115174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2025] [Revised: 05/02/2025] [Accepted: 05/06/2025] [Indexed: 05/11/2025]
Abstract
Several arthropod-borne (arbo)-viruses have overlapping symptoms, insect vectors and geographical occurrence. With little known about the importance of arboviruses as cause of acute undifferentiated fever (AUF) in East and Central Africa (ECA), there is a clear need for a multiplex-PCR allowing for multi-pathogen surveillance. A multiplex real-time RT-PCR (RDCZ-multiplex) was developed and validated for the simultaneous detection of Rift Valley fever virus (RVFV), dengue virus 1-4 (DENV), chikungunya virus (CHIKV) and Zika virus (ZIKV). Phocine distemper virus (PDV) was added to the PCR as sample extraction control. Validation was conducted following the MIQE-guidelines using a panel of retrospective clinical samples and Quality Control for Molecular Diagnostics (QCMD, https://www.qcmd.org/en/) samples with the simplex-PCR as reference. These included samples from RVFV in animals (n = 19), DENV (n = 15), CHIKV (n = 11), ZIKV (n = 2) and YFV (n = 1, QCMD), and 14 negative endemic controls. Extractions and PCRs were done with commercially available kits. Some loss of sensitivity was observed at low target concentrations for RVFV, DENV1 and DENV4, when comparing the standard curves of simplex-PCRs with the multiplex-PCR. The limit of detection of the multiplex-PCR was 2064 copies/ml for CHIKV, 3587 copies/ml for DENV1, 30,249 copies/ml for ZIKV and 73 PFU/ml for RVFV. Specificity of the multiplex-PCRs was 100 %. For 12 out of 48 positive samples with high Cq values, RVFV (n = 7), CHIKV (n = 2), DENV1 (n = 2), YFV (n = 1), the multiplex-PCRs were negative. Although PCR sensitivity of the RDCZ-multiplex is slightly lower with low target concentrations, it offers a useful tool for molecular surveillance and clinical diagnosis for arboviruses for the ECA-region.
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Affiliation(s)
- Anne Hauner
- Department of Biomedical Sciences, Unit of Virology, Institute of Tropical Medicine, Antwerp, Belgium.
| | - Stijn Rogé
- DRC office, Institute of Tropical Medicine, Antwerp, Belgium
| | - Veerle Vanlerberghe
- Department of Public Health, Unit of Emerging Infectious Diseases, Institute of Tropical Medicine, Antwerp, Belgium
| | - Luciana Lepore
- Department of Public Health, Unit of Emerging Infectious Diseases, Institute of Tropical Medicine, Antwerp, Belgium
| | - Fabrice Ndayisenga
- Rwanda Agriculture and Animal Resources Development Board, Kigali, Rwanda
| | - Anselme Shyaka
- Center for One Health, University of Global Health Equity, Butaro, Rwanda
| | - Marjan Van Esbroeck
- Department of Clinical Science, Institute of Tropical Medicine, Antwerp, Belgium
| | - Silvia Situma
- Washington State University Global Health-Kenya, Nairobi, Kenya
| | | | | | | | | | - Justin Masumu
- National Institute for Biomedical Research INRB, Kinshasa, Congo
| | - Daniel Mukadi-Bamuleka
- Rodolphe Mérieux INRB-Goma Laboratory, Goma, North Kivu, Congo; Service of Microbiology, Department of Medical Biology, Faculty of Medicine, University of Kinshasa, Kinshasa, Congo; Department of Virology, Institut National de Recherche Biomédicale, INRB, Kinshasa, Congo
| | - Kevin K Ariën
- Department of Biomedical Sciences, Unit of Virology, Institute of Tropical Medicine, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
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Camp JV, Nowotny N, Aberle SW, Redlberger-Fritz M. Retrospective Screening for Zoonotic Viruses in Encephalitis Cases in Austria, 2019-2023, Reveals Infection with Lymphocytic Choriomeningitis Virus but Not with Rustrela Virus or Tahyna Virus. Viruses 2025; 17:300. [PMID: 40143231 PMCID: PMC11945919 DOI: 10.3390/v17030300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2025] [Revised: 02/14/2025] [Accepted: 02/20/2025] [Indexed: 03/28/2025] Open
Abstract
Zoonotic viruses may be neglected as etiologies of meningoencephalitis in humans. We performed retrospective testing of cerebrospinal fluid from encephalitis cases in biobank material for three zoonotic or potentially zoonotic viruses: rustrela virus (Rubivirus strelense, Matonaviridae); Tahyna virus (Orthobunyavirus tahynaense, Peribunyaviridae); and lymphocytic choriomeningitis virus ("LCMV", Mammarenavirus choriomeningitidis, Arenaviridae). The cohort consisted of 443 samples, received for routine diagnostic testing year-round between January 2019 and February 2023, and were negative for herpes simplex viruses, varicella zoster virus, and enteroviruses. Using published RT-qPCR protocols, we did not detect rustrela virus or Tahyna virus in any sample. Using a herein described RT-qPCR protocol, we detected LCMV in one sample. Partial genetic sequencing of the virus suggested that the virus was locally acquired. Our study provides information about the incidence of these viruses in humans in Austria when encephalitis is suspected.
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Affiliation(s)
- Jeremy V. Camp
- Center for Virology, Medical University of Vienna, 1095 Vienna, Austria; (S.W.A.); (M.R.-F.)
| | - Norbert Nowotny
- Department of Biological Sciences and Pathobiology, Center of Pathobiology, University of Veterinary Medicine Vienna, 1210 Vienna, Austria;
- Department of Basic Medical Sciences, College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Health, Dubai P.O. Box 505055, United Arab Emirates
| | - Stephan W. Aberle
- Center for Virology, Medical University of Vienna, 1095 Vienna, Austria; (S.W.A.); (M.R.-F.)
| | - Monika Redlberger-Fritz
- Center for Virology, Medical University of Vienna, 1095 Vienna, Austria; (S.W.A.); (M.R.-F.)
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3
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Van Goethem S, Van Lint P, Willems P, Van Herendael B, Hoet K. Value of pneumococcal PCR in respiratory samples for exclusion of pneumococcal pneumonia. JAC Antimicrob Resist 2023; 5:dlad115. [PMID: 37941720 PMCID: PMC10629468 DOI: 10.1093/jacamr/dlad115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 10/16/2023] [Indexed: 11/10/2023] Open
Abstract
Background Streptococcus pneumoniae is the main aetiological agent in bacterial pneumonia. Therefore pneumococcal PCR is often included in respiratory multiplex PCR panels, both commercial and in-house. But respiratory PCR results for S. pneumoniae are difficult to interpret due to frequent non-pathogenic colonization on the mucosal surface of the upper airways with pneumococci or to cross-reaction of the PCR target in non-pneumococcal streptococci. In this study we investigated the value of lytA gene pneumococcal PCR in patients presenting with pneumonia. Objectives To assess the utility of lytA gene detection for S. pneumoniae in a respiratory multiplex quantitative PCR (qPCR) panel for patients presenting with pneumonia. Methods A retrospective study was conducted for lytA gene results as target for S. pneumoniae in hospitalized patients who were diagnosed with pneumonia and for which a respiratory multiplex PCR panel was performed. Patients were classified as 'probable', 'possible' or 'unlikely' of having a pneumococcal pneumonia. Results A sensitivity of 71.4% and specificity of 89.6% were found, corresponding to a negative predictive value and positive predictive value of 97.6% and 34.2%, respectively, when considering 'probable' versus 'possible/unlikely'. In the PCR-positive cases we found a statistically significant difference in semi-quantitative Ct values between the 'probable' and the 'possible/unlikely' groups. Conclusions We conclude that a negative qPCR for the lytA gene in a respiratory sample is highly predictive of a negative S. pneumoniae culture and is possibly sufficient to exclude S. pneumoniae as a causative agent. Respiratory pneumococcal PCR has a high negative predictive value for pneumococcal disease but the positive predictive value is low.
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Affiliation(s)
- Sam Van Goethem
- Laboratory of Medical Microbiology, Vaccine and Infectious Diseases Institute, University of Antwerp, Antwerp, Belgium
- Hospital Outbreak Support Team, ZAS Hospital Network, Antwerp, Belgium
| | - Philippe Van Lint
- Medical Microbiology Laboratory, GZA Hospitals Antwerp, Antwerp, Belgium
| | - Philippe Willems
- Medical Microbiology Laboratory, GZA Hospitals Antwerp, Antwerp, Belgium
| | | | - Katrien Hoet
- Medical Microbiology Laboratory, GZA Hospitals Antwerp, Antwerp, Belgium
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4
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Goyal PA, Bankar NJ, Mishra VH, Borkar SK, Makade JG. Revolutionizing Medical Microbiology: How Molecular and Genomic Approaches Are Changing Diagnostic Techniques. Cureus 2023; 15:e47106. [PMID: 38022057 PMCID: PMC10646819 DOI: 10.7759/cureus.47106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
Molecular and genomic approaches have revolutionized medical microbiology by offering faster and more accurate diagnostic techniques for infectious diseases. Traditional methods, which include culturing microbes and biochemical testing, are time-consuming and may not detect antibiotic-resistant strains. In contrast, molecular and genomic methods, including polymerase chain reaction (PCR)-based techniques and whole-genome sequencing, provide rapid and precise detection of pathogens, early-stage diseases, and antibiotic-resistant strains. These approaches have advantages such as high sensitivity and specificity, the potential for targeted therapies, and personalized medicine. However, implementing molecular and genomic techniques faces challenges related to cost, equipment, expertise, and data analysis. Ethical and legal considerations regarding patient privacy and genetic data usage also arise. Nonetheless, the future of medical microbiology lies in the widespread adoption of molecular and genomic approaches, which can lead to improved patient outcomes and the identification of antibiotic-resistant strains. Continued advancements, education, and exploration of ethical implications are necessary to fully harness the potential of molecular and genomic techniques in medical microbiology.
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Affiliation(s)
- Poyasha A Goyal
- Microbiology, Datta Meghe Medical College, Datta Meghe Institute of Higher Education and Research (DU), Wardha, IND
| | - Nandkishor J Bankar
- Microbiology, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research (DU), Wardha, IND
| | - Vaishnavi H Mishra
- Microbiology, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research (DU), Wardha, IND
| | - Sonali K Borkar
- Community Medicine, Datta Meghe Medical College, Datta Meghe Institute of Higher Education and Research (DU), Wardha, IND
| | - Jagadish G Makade
- Community Medicine, Datta Meghe Medical College, Datta Meghe Institute of Medical Sciences(DU), Wardha, IND
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Raymenants J, Geenen C, Budts L, Thibaut J, Thijssen M, De Mulder H, Gorissen S, Craessaerts B, Laenen L, Beuselinck K, Ombelet S, Keyaerts E, André E. Indoor air surveillance and factors associated with respiratory pathogen detection in community settings in Belgium. Nat Commun 2023; 14:1332. [PMID: 36898982 PMCID: PMC10005919 DOI: 10.1038/s41467-023-36986-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 02/27/2023] [Indexed: 03/12/2023] Open
Abstract
Currently, the real-life impact of indoor climate, human behaviour, ventilation and air filtration on respiratory pathogen detection and concentration are poorly understood. This hinders the interpretability of bioaerosol quantification in indoor air to surveil respiratory pathogens and transmission risk. We tested 341 indoor air samples from 21 community settings in Belgium for 29 respiratory pathogens using qPCR. On average, 3.9 pathogens were positive per sample and 85.3% of samples tested positive for at least one. Pathogen detection and concentration varied significantly by pathogen, month, and age group in generalised linear (mixed) models and generalised estimating equations. High CO2 and low natural ventilation were independent risk factors for detection. The odds ratio for detection was 1.09 (95% CI 1.03-1.15) per 100 parts per million (ppm) increase in CO2, and 0.88 (95% CI 0.80-0.97) per stepwise increase in natural ventilation (on a Likert scale). CO2 concentration and portable air filtration were independently associated with pathogen concentration. Each 100ppm increase in CO2 was associated with a qPCR Ct value decrease of 0.08 (95% CI -0.12 to -0.04), and portable air filtration with a 0.58 (95% CI 0.25-0.91) increase. The effects of occupancy, sampling duration, mask wearing, vocalisation, temperature, humidity and mechanical ventilation were not significant. Our results support the importance of ventilation and air filtration to reduce transmission.
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Affiliation(s)
- Joren Raymenants
- Laboratory of Clinical Microbiology, KU Leuven, Herestraat 49, 3000, Leuven, Belgium.
- Department of General Internal Medicine, University Hospitals Leuven, Herestraat 49, 3000, Leuven, Belgium.
| | - Caspar Geenen
- Laboratory of Clinical Microbiology, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Lore Budts
- Department of Laboratory Medicine, National Reference Center of Respiratory Pathogens, University Hospitals Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Jonathan Thibaut
- Laboratory of Clinical Microbiology, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Marijn Thijssen
- Laboratory of Clinical and Epidemiological Virology (Rega Institute), KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Hannelore De Mulder
- Laboratory of Clinical Microbiology, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Sarah Gorissen
- Laboratory of Clinical Microbiology, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Bastiaan Craessaerts
- Department of Laboratory Medicine, National Reference Center of Respiratory Pathogens, University Hospitals Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Lies Laenen
- Laboratory of Clinical Microbiology, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
- Department of Laboratory Medicine, National Reference Center of Respiratory Pathogens, University Hospitals Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Kurt Beuselinck
- Department of Laboratory Medicine, National Reference Center of Respiratory Pathogens, University Hospitals Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Sien Ombelet
- Department of Laboratory Medicine, National Reference Center of Respiratory Pathogens, University Hospitals Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Els Keyaerts
- Department of Laboratory Medicine, National Reference Center of Respiratory Pathogens, University Hospitals Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Emmanuel André
- Laboratory of Clinical Microbiology, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
- Department of Laboratory Medicine, National Reference Center of Respiratory Pathogens, University Hospitals Leuven, Herestraat 49, 3000, Leuven, Belgium
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6
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Rinaldi L, Krücken J, Martinez-Valladares M, Pepe P, Maurelli MP, de Queiroz C, Castilla Gómez de Agüero V, Wang T, Cringoli G, Charlier J, Gilleard JS, von Samson-Himmelstjerna G. Advances in diagnosis of gastrointestinal nematodes in livestock and companion animals. ADVANCES IN PARASITOLOGY 2022; 118:85-176. [PMID: 36088084 DOI: 10.1016/bs.apar.2022.07.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Diagnosis of gastrointestinal nematodes in livestock and companion animals has been neglected for years and there has been an historical underinvestment in the development and improvement of diagnostic tools, undermining the undoubted utility of surveillance and control programmes. However, a new impetus by the scientific community and the quickening pace of technological innovations, are promoting a renaissance of interest in developing diagnostic capacity for nematode infections in veterinary parasitology. A cross-cutting priority for diagnostic tools is the development of pen-side tests and associated decision support tools that rapidly inform on the levels of infection and morbidity. This includes development of scalable, parasite detection using artificial intelligence for automated counting of parasitic elements and research towards establishing biomarkers using innovative molecular and proteomic methods. The aim of this review is to assess the state-of-the-art in the diagnosis of helminth infections in livestock and companion animals and presents the current advances of diagnostic methods for intestinal parasites harnessing (i) automated methods for copromicroscopy based on artificial intelligence, (ii) immunodiagnosis, and (iii) molecular- and proteome-based approaches. Regardless of the method used, multiple factors need to be considered before diagnostics test results can be interpreted in terms of control decisions. Guidelines on how to apply diagnostics and how to interpret test results in different animal species are increasingly requested and some were recently made available in veterinary parasitology for the different domestic species.
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Affiliation(s)
- Laura Rinaldi
- Department of Veterinary Medicine and Animal Production, University of Naples "Federico II", Naples, Italy.
| | - J Krücken
- Institute for Parasitology and Tropical Veterinary Medicine, Veterinary Centre for Resistance Research, Freie Universität Berlin, Berlin, Germany
| | - M Martinez-Valladares
- Instituto de Ganadería de Montaña (CSIC-Universidad de León), Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de León, León, Spain
| | - P Pepe
- Department of Veterinary Medicine and Animal Production, University of Naples "Federico II", Naples, Italy
| | - M P Maurelli
- Department of Veterinary Medicine and Animal Production, University of Naples "Federico II", Naples, Italy
| | - C de Queiroz
- Faculty of Veterinary Medicine, 3331 Hospital Drive, Host-Parasite Interactions (HPI) Program University of Calgary, Calgary, Alberta, Canada; Faculty of Veterinary Medicine, St Georges University, Grenada
| | - V Castilla Gómez de Agüero
- Instituto de Ganadería de Montaña (CSIC-Universidad de León), Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de León, León, Spain
| | - T Wang
- Kreavet, Kruibeke, Belgium
| | - Giuseppe Cringoli
- Department of Veterinary Medicine and Animal Production, University of Naples "Federico II", Naples, Italy
| | | | - J S Gilleard
- Faculty of Veterinary Medicine, 3331 Hospital Drive, Host-Parasite Interactions (HPI) Program University of Calgary, Calgary, Alberta, Canada
| | - G von Samson-Himmelstjerna
- Institute for Parasitology and Tropical Veterinary Medicine, Veterinary Centre for Resistance Research, Freie Universität Berlin, Berlin, Germany
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Bergallo M, Montanari P, Loiacono E, Galliano I. A novel TaqMAMA assay for allelic discrimination of immunoproteasome subunit PSMB8 in pediatric patients. Minerva Pediatr (Torino) 2022; 74:301-307. [DOI: 10.23736/s2724-5276.16.04675-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Abstract
The diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has ramifications on both an individual level and a public health level. The use of appropriate testing mechanisms is paramount to preventing transmission, along with offering treatment to those who are infected and show appropriate symptomatology. The choice of employing a specific test often relies on laboratory capabilities, including the abilities of the medical technologists, the cost of testing platforms, and the individual quirks of each test. This chapter intends to discuss the relevant issues relating to diagnostic testing for SARS-CoV-2, including specimen types and collection methods, viral detection methods, and serological testing.
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9
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Impact of Collection Volume and DNA Extraction Method on the Detection of Biomarkers and HPV DNA in First-Void Urine. Molecules 2021; 26:molecules26071989. [PMID: 33915837 PMCID: PMC8036936 DOI: 10.3390/molecules26071989] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/22/2021] [Accepted: 03/27/2021] [Indexed: 12/22/2022] Open
Abstract
The potential of first-void (FV) urine as a non-invasive liquid biopsy for detection of human papillomavirus (HPV) DNA and other biomarkers has been increasingly recognized over the past decade. In this study, we investigated whether the volume of this initial urine stream has an impact on the analytical performance of biomarkers. In parallel, we evaluated different DNA extraction protocols and introduced an internal control in the urine preservative. Twenty-five women, diagnosed with high-risk HPV, provided three home-collected FV urine samples using three FV urine collection devices (Colli-Pee) with collector tubes that differ in volume (4, 10, 20 mL). Each collector tube was prefilled with Urine Conservation Medium spiked with phocine herpesvirus 1 (PhHV-1) DNA as internal control. Five different DNA extraction protocols were compared, followed by PCR for GAPDH and PhHV-1 (qPCR), HPV DNA, and HBB (HPV-Risk Assay), and ACTB (methylation-specific qPCR). Results showed limited effects of collection volume on human and HPV DNA endpoints. In contrast, significant variations in yield for human endpoints were observed for different DNA extraction methods (p < 0.05). Additionally, the potential of PhHV-1 as internal control to monitor FV urine collection, storage, and processing was demonstrated.
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10
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Ögren J, Dienus O, Matussek A. Optimization of routine microscopic and molecular detection of parasitic protozoa in SAF-fixed faecal samples in Sweden. Infect Dis (Lond) 2019; 52:87-96. [DOI: 10.1080/23744235.2019.1682188] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Affiliation(s)
- Jessica Ögren
- Clinical Microbiology, Region Jönköping County, Jönköping, Sweden
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Olaf Dienus
- Clinical Microbiology, Region Jönköping County, Jönköping, Sweden
| | - Andreas Matussek
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Laboratory Medicine, Region Jönköping County, Jönköping, Sweden
- Karolinska University Laboratory, Stockholm, Sweden
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11
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Berglund B, Dienus O, Sokolova E, Berglind E, Matussek A, Pettersson T, Lindgren PE. Occurrence and removal efficiency of parasitic protozoa in Swedish wastewater treatment plants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 598:821-827. [PMID: 28458199 DOI: 10.1016/j.scitotenv.2017.04.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 04/03/2017] [Accepted: 04/03/2017] [Indexed: 06/07/2023]
Abstract
Giardia intestinalis, Cryptosporidium spp., Entamoeba histolytica and Dientamoeba fragilis are parasitic protozoa and causative agents of gastroenteritis in humans. G. intestinalis and Cryptosporidium spp. in particular are the most common protozoa associated with waterborne outbreaks in high-income countries. Surveillance of protozoan prevalence in wastewater and evaluation of wastewater treatment removal efficiencies of protozoan pathogens is therefore imperative for assessment of human health risk. In this study, influent and effluent wastewater samples from three wastewater treatment plants in Sweden were collected over nearly one year and assessed for prevalence of parasitic protozoa. Quantitative real-time PCR using primers specific for the selected protozoa Cryptosporidium spp., G. intestinalis, E. histolytica, Entamoeba dispar and D. fragilis was used for protozoan DNA detection and assessment of wastewater treatment removal efficiencies. Occurrence of G. intestinalis, E. dispar and D. fragilis DNA was assessed in both influent (44, 30 and 39 out of 51 samples respectively) and effluent wastewater (14, 9 and 33 out of 51 samples respectively) in all three wastewater treatment plants. Mean removal efficiencies of G. intestinalis, E. dispar and D. fragilis DNA quantities, based on all three wastewater treatment plants studied varied between 67 and 87%, 37-75% and 20-34% respectively. Neither E. histolytica nor Cryptosporidium spp. were detected in any samples. Overall, higher quantities of protozoan DNA were observed from February to June 2012. The high prevalence of protozoa in influent wastewater indicates the need for continued monitoring of these pathogens in wastewater-associated aquatic environments to minimise the potential risk for human infection.
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Affiliation(s)
- Björn Berglund
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden.
| | - Olaf Dienus
- County Hospital Ryhov, Division of Medical Services, Clinical Microbiology Laboratory, Jönköping, Sweden
| | - Ekaterina Sokolova
- Department of Civil and Environmental Engineering, Water Environment Technology, Chalmers University of Technology, Gothenburg, Sweden
| | - Emma Berglind
- County Hospital Ryhov, Division of Medical Services, Clinical Microbiology Laboratory, Jönköping, Sweden
| | - Andreas Matussek
- County Hospital Ryhov, Division of Medical Services, Clinical Microbiology Laboratory, Jönköping, Sweden; Karolinska University Laboratory, Stockholm, Sweden
| | - Thomas Pettersson
- Department of Civil and Environmental Engineering, Water Environment Technology, Chalmers University of Technology, Gothenburg, Sweden
| | - Per-Eric Lindgren
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden; County Hospital Ryhov, Division of Medical Services, Clinical Microbiology Laboratory, Jönköping, Sweden
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12
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Bergallo M, Galliano I, Montanari P, Brusin MR, Finotti S, Paderi G, Gabiano C. Development of a quantitative real-time PCR assay for sapovirus in children under 5-years-old in Regina Margherita Hospital of Turin, Italy. Can J Microbiol 2017; 63:296-302. [DOI: 10.1139/cjm-2016-0482] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Gastroenteritis is a common disease in children. It is characterized by diarrhea, vomiting, abdominal pain, and fever. Sapovirus (SaV) is a causative agent of acute gastroenteritis, but it causes milder illness than do rotavirus and norovirus. There is high variability in the analytical performance of quantitative PCR-based assays among clinical laboratories. This study developed a reverse transcription real-time PCR method to detect SaV in fecal specimens collected from children under 5-years-old with acute gastroenteritis. Of 137 episodes of acute gastroenteritis, 15 (10.9%) were associated with SaV genomic detection, with a median viral load of 6.6(log10) ± 7.1(log10) genomes/mg fecal specimens. There was a significant difference in detection rate between males and females (9.48% (13/15) vs. 1.46% (2/15), p = 0.0232). Among the 15 SaV-positive cases, 6 were also positive for rotavirus. Viral RNA recovery rate ranged from 46% to 77% in the manual RNAzol protocol and from 31% to 90% in the automated Maxwell protocol. We also studied whether human genomic DNA influences the sensitivity of the assay: its presence caused a decrease in PCR sensitivity. The development of a laboratory-designed real-time PCR TaqMan assay for quantitative detection of SaV and the optimization and standardization of this assay, using stools of children with acute gastroenteritis, are described.
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Affiliation(s)
- Massimiliano Bergallo
- Department of Public Health and Pediatric Sciences, University of Turin, Medical School, 10136 Turin, Italy
| | - Ilaria Galliano
- Department of Public Health and Pediatric Sciences, University of Turin, Medical School, 10136 Turin, Italy
| | - Paola Montanari
- Department of Public Health and Pediatric Sciences, University of Turin, Medical School, 10136 Turin, Italy
| | - Martina Rosa Brusin
- Struttura Complessa, Pediatric University Regina Margherita Hospital, Piazza Polonia 94, 1016 Turin, Italy
| | - Serena Finotti
- Department of Public Health and Pediatric Sciences, University of Turin, Medical School, 10136 Turin, Italy
| | - Giulia Paderi
- Department of Public Health and Pediatric Sciences, University of Turin, Medical School, 10136 Turin, Italy
| | - Clara Gabiano
- Struttura Complessa, Pediatric University Regina Margherita Hospital, Piazza Polonia 94, 1016 Turin, Italy
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Wang X, Liu F, Jiang L, Bao Y, Xiao Y, Wang H. Use of chimeric influenza viruses as a novel internal control for diagnostic rRT-PCR assays. Appl Microbiol Biotechnol 2016; 100:1667-1676. [PMID: 26474983 PMCID: PMC7080162 DOI: 10.1007/s00253-015-7042-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 09/15/2015] [Accepted: 09/24/2015] [Indexed: 02/01/2023]
Abstract
Real-time quantitative reverse transcriptase polymerase chain reaction (rRT-PCR) is now widely used to detect viral pathogens in various human specimens. The application of internal controls to validate the entire process of these assays is necessary to prevent false-negative results caused by unexpected inhibition or inefficient extraction. In the present study, we describe a strategy to produce a stable internal control for rRT-PCR by packaging foreign RNA into influenza virions using plasmid-based reverse genetics technology. The envelope structure of influenza virus can effectively protect RNA segments from RNase digestion, which provides an advantage for its routine use as an internal control. Utilizing this approach, we successfully generated a recombinant influenza virus (rPR8-HCV) containing the 5′ untranslated region (5′ UTR) of the hepatitis C virus (HCV) RNA genome. After inactivation and purification, the rPR8-HCV particles were demonstrated to be RNase resistant and stable at 4 °C for at least 252 days in human plasma, with no degradation even after being frozen and thawed multiple times. These results were reproducible in the COBAS TaqMan HCV test for 164 days. Moreover, the chimeric influenza virus particles could be easily produced in embryonated eggs and were noninfectious after inactivation treatment. Additionally, this strategy could also be adapted for real-time clinical applications of other RNA targets, providing a universal approach with broad clinical applications in rRT-PCR assays.
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Affiliation(s)
- Xueliang Wang
- Shanghai Centre for Clinical Laboratory, 528 Hongshan Road, Shanghai, 200126, China
| | - Fen Liu
- Shanghai Institute of Biological Products, 1262 West Yanan Road, Shanghai, 200052, China
| | - Lingli Jiang
- Shanghai Centre for Clinical Laboratory, 528 Hongshan Road, Shanghai, 200126, China
| | - Yun Bao
- Shanghai Centre for Clinical Laboratory, 528 Hongshan Road, Shanghai, 200126, China
| | - Yanqun Xiao
- Shanghai Centre for Clinical Laboratory, 528 Hongshan Road, Shanghai, 200126, China
| | - Hualiang Wang
- Shanghai Centre for Clinical Laboratory, 528 Hongshan Road, Shanghai, 200126, China.
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Huff JL, Lynch MP, Nettikadan S, Johnson JC, Vengasandra S, Henderson E. Label-Free Protein and Pathogen Detection Using the Atomic Force Microscope. ACTA ACUST UNITED AC 2016; 9:491-7. [PMID: 15452335 DOI: 10.1177/1087057104268803] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The atomic force microscope (AFM) uses a sharp micron-scale tip to scan and amplify surface features, providing exceptionally detailed topographical information with magnification on the order of ×106. This instrument is used extensively for quality control in the computer and semiconductor industries and is becoming a progressively more important tool in the biological sciences. Advantages of the AFM for biological application include the ability to obtain information in a direct, label-free manner and the ability to image in solution, providing real-time data acquisition under physiologically relevant conditions. A novel application of the AFM currently under development combines its surface profiling capabilities with fixed immuno-capture using antibodies immobilized in a nanoarray format. This provides a distinctive platform for direct, label-free detection and characterization of viral particles and other pathogens.
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15
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Bergallo M, Loiacono E, Rizzo G, Caiazzo M, Palladino G, Amore A. Development of a degenerated TaqMan real-time Q-PCR for detection of bacteria-free DNA in dialysis fluid. Biotechnol Appl Biochem 2016; 64:443-448. [PMID: 27067406 PMCID: PMC7161787 DOI: 10.1002/bab.1498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 03/30/2016] [Indexed: 11/05/2022]
Abstract
Bacterial-derived DNA fragments (BDNAs) have been shown to be present in a dialysis fluid, to pass through dialyzer membranes, and to induce interleukin 6 (IL-6) in mononuclear cells. DNA fragments are thought to be derived from microorganisms inhabiting hemodialysis water and fluid. The primary aim of the present study was to develop two degenerated TaqMan real-time quantitative-PCR (Q-PCR) for detection of a broad range of bacterial DNA that specifically detect 16S ribosomal DNA (rDNA) (862 and 241 bp) and evaluate the efficiency of the Bellco Selecta resin to capture the BDNAs in the dialysis fluid. For this purpose, we decided to compare measurements of unfragmented samples (9.8 × 105 Escherichia coli genome) with artificially fragmented DNA samples. We assessed two broad-range real-time PCR targeting bacterial 16S rRNA genes for detection of fragmented and unfragmented bacterial DNA in the dialytic fluid and demonstrated that Bellco Selecta resin is capable of retaining these types of bacterial DNA.
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Affiliation(s)
- Massimiliano Bergallo
- Dipartimento di Scienze della Sanità Pubblica e Pediatriche, Scuola di Medicina, Università di Torino, Torino, Italy.,Laboratorio di Citoimmunodiagnostica, Azienda Ospedaliero-Universitaria Città della Salute e della Scienza di Torino, Torino, Italy
| | - Elisa Loiacono
- SC Nefrologia-Dialisi e Trapianto Pediatrico, Azienda Ospedaliero-Universitaria Città della Salute e della Scienza di Torino, Torino, Italy
| | - Giovanna Rizzo
- Dipartimento di Scienze della Sanità Pubblica e Pediatriche, Scuola di Medicina, Università di Torino, Torino, Italy
| | | | | | - Alessandro Amore
- SC Nefrologia-Dialisi e Trapianto Pediatrico, Azienda Ospedaliero-Universitaria Città della Salute e della Scienza di Torino, Torino, Italy
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16
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Intracranial hemorrhage and other symptoms in infants associated with human parechovirus in Vienna, Austria. Eur J Pediatr 2015; 174:1639-47. [PMID: 26109012 DOI: 10.1007/s00431-015-2583-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 05/21/2015] [Accepted: 06/15/2015] [Indexed: 10/23/2022]
Abstract
UNLABELLED The human parechovirus (HPeV), mainly genotype 3, may cause severe illness in young infants and neonates, including sepsis-like illness and central nervous system (CNS) infection. We lack data concerning the impact and symptoms of HPeV infection in infants in Austria. The aim of the study is to evaluate the spectrum of symptoms and findings in infants with the parechovirus in Vienna and its environs. Patients younger than 3 months of age, with clinically suspected sepsis-like illness or CNS infection and a positive polymerase chain reaction (PCR) for HPeV, were included in the study. Medical records were analyzed retrospectively. Twenty patients were included in the study from 2009 to 2013. The most frequent manifestations were fever and neurological symptoms (89 and 80 %, respectively). Fifty percent of the infants had white blood cell counts out of range. The most notable aspect was cerebral hemorrhage in three neonates, which has not been reported earlier in association with HPeV infection. CONCLUSION In Austria, HPeV is a relevant pathogen in sepsis-like disease in infants. The clinical presentation is similar to that described in other studies; cerebral hemorrhage is a new aspect. WHAT IS KNOWN • Parechovirus infection can cause severe illness in infants. • Symptoms have been described to involve all organs; sepsis-like signs, fever, and irritability are most frequent. WHAT IS NEW • Also in Austria, HPeV plays an important role in severe illnesses in infants. • Severe intracranial hemorrhage is described as a new finding.
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17
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GRAY J, COUPLAND LJ. The increasing application of multiplex nucleic acid detection tests to the diagnosis of syndromic infections. Epidemiol Infect 2014; 142:1-11. [PMID: 24093495 PMCID: PMC9152551 DOI: 10.1017/s0950268813002367] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 08/30/2013] [Accepted: 08/30/2013] [Indexed: 02/04/2023] Open
Abstract
On 14 January 2013, the US Food and Drug Administration (FDA) announced permission for a multiplex nucleic acid test, the xTAG® Gastrointestinal Pathogen Panel (GPP) (Luminex Corporation, USA), which simultaneously detects 11 common viral, bacterial and parasitic causes of infectious gastroenteritis, to be marketed in the USA. This announcement reflects the current move towards the development and commercialization of detection technologies based on nucleic acid amplification techniques for diagnosis of syndromic infections. We discuss the limitations and advantages of nucleic acid amplification techniques and the recent advances in Conformité Européene - in-vitro diagnostic (CE-IVD)-approved multiplex real-time PCR kits for the simultaneous detection of multiple targets within the clinical diagnostics market.
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Affiliation(s)
- J. GRAY
- Norwich Medical School, University of East Anglia, NRP Innovation Centre, Norwich Research Park, Norwich, Norfolk, UK
- Specialist Virology Centre, Department of Microbiology, Norfolk and Norwich University Hospitals NHS Foundation Trust, NRP Innovation Centre, Norwich Research Park, Norwich, Norfolk, UK
| | - L. J. COUPLAND
- Specialist Virology Centre, Department of Microbiology, Norfolk and Norwich University Hospitals NHS Foundation Trust, NRP Innovation Centre, Norwich Research Park, Norwich, Norfolk, UK
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18
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Hatt JK, Ritalahti KM, Ogles DM, Lebrón CA, Löffler FE. Design and application of an internal amplification control to improve Dehalococcoides mccartyi 16S rRNA gene enumeration by qPCR. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2013; 47:11131-8. [PMID: 24053159 DOI: 10.1021/es4019817] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Dehalococcoides mccartyi (Dhc) strains are keystone bacteria for reductive dechlorination of chlorinated ethenes to nontoxic ethene in contaminated aquifers. Enumeration of Dhc biomarker genes using quantitative real-time PCR (qPCR) in groundwater is a key component of site assessment and bioremediation monitoring. Unfortunately, standardized qPCR procedures that recognize impaired measurements due to PCR inhibition, low template DNA concentrations, or analytical error are not available, thus limiting confidence in qPCR data. To improve contemporary approaches for enumerating Dhc in environmental samples, multiplex qPCR assays were designed to quantify the Dhc 16S rRNA gene and one of two different internal amplification controls (IACs): a modified Dhc 16S rRNA gene fragment (Dhc*) and the firefly luciferase gene luc. The Dhc* IAC exhibited competitive inhibition in qPCR with the Dhc 16S rRNA gene template when the ratio of either target was 100-fold greater than the other target. A multiplex qPCR assay with the luc IAC avoided competitive inhibition and accurately quantified Dhc abundances ranging from ∼10 to 10(7) 16S rRNA gene copies per reaction. The addition of ∼10(6) E. coli luc IAC to simulated groundwater amended with the Dhc-containing consortium KB-1 yielded reproducible luc counts after DNA extraction and multiplex qPCR enumeration. The application of the luc IAC assay improved Dhc biomarker gene quantification from simulated groundwater samples and is a valuable approach for "ground truthing" qPCR data obtained in different laboratories, thus reducing ambiguity associated with qPCR enumeration and reproducibility.
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Affiliation(s)
- Janet K Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology , 311 Ferst Drive, Atlanta, Georgia 30332, United States
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19
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Abstract
Nucleic acids are the ultimate biomarker and real-time PCR (qPCR) is firmly established as the method of choice for nucleic acid detection. Together, they allow the accurate, sensitive and specific identification of pathogens, and the use of qPCR has become routine in diagnostic laboratories. The reliability of qPCR-based assays relies on a combination of optimal sample selection, assay design and validation as well as appropriate data analysis and the "Minimal Information for the Publication of real-time PCR" (MIQE) guidelines aim to improve both the reliability of assay design as well as the transparency of reporting, essential conditions if qPCR is to remain the benchmark technology for molecular diagnosis.
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Affiliation(s)
- Gemma Johnson
- Blizard Institute of Cell and Molecular Science, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
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20
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Vagnozzi A, Riblet SM, Zavala G, García M. Optimization of a duplex real-time PCR method for relative quantitation of infectious laryngotracheitis virus. Avian Dis 2012; 56:406-10. [PMID: 22856202 DOI: 10.1637/9883-081111-resnote.1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Infectious laryngotracheitis is a highly contagious respiratory disease of chickens controlled by biosecurity and vaccination with live attenuated or recombinant vaccines. Infectious laryngotracheitis virus (ILTV) infections are characterized by a peak of viral replication in the trachea followed by a steady decrease in replication that results in the establishment of latency. Estimation of viral load is an important tool to determine the stage of ILTV infection. Here, a multiplex real-time PCR was optimized for the quantification of ILTV genomes. Quantification of viral genomes was based on the amplification of the ILTV UL44 gene, and sample variability was normalized using the chicken (Gallusgallus domesticus) alpha2-collagen gene as an endogenous control in a duplex reaction.
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Affiliation(s)
- Ariel Vagnozzi
- Poultry Diagnostic and Research Center, Department of Health Population, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
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21
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Crook T, Benavides J, Russell G, Gilray J, Maley M, Willoughby K. Bovine herpesvirus 1 abortion: current prevalence in the United Kingdom and evidence of hematogenous spread within the fetus in natural cases. J Vet Diagn Invest 2012; 24:662-70. [PMID: 22649159 DOI: 10.1177/1040638712448187] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
While Bovine herpesvirus 1 (BoHV-1) has been known as a cause of bovine abortion for nearly 50 years, information is limited on the current prevalence of BoHV-1 abortion in the United Kingdom, or about the mode of virus dissemination to cause infection of the fetus. The present study aimed to investigate these issues by surveying the prevalence of BoHV-1 in abortion cases in the United Kingdom, and comparing diagnostic methods to determine which are most efficient in BoHV-1-induced abortion. Where BoHV-1 DNA was detected, viral load was compared in fetal tissues, using real-time polymerase chain reaction (PCR), supported by histopathology and immunohistochemistry (IHC) to investigate virus dissemination in bovine abortions. A total of 400 U.K. bovine abortion cases were studied; PCR detected BoHV-1 nucleic acids in 10 cases, suggestive histopathological lesions were observed in 8, and positive IHC staining was observed in 9. In routine diagnosis, BoHV-1 was identified in 2 of these cases, highlighting the utility of using molecular diagnostic tests such as real-time PCR to achieve high sensitivity in potentially autolyzed tissues. The study of different fetal samples showed the highest viral load in the liver, along with severe multifocal necrotic hepatitis, suggesting either a clear tropism of the virus for this organ or that it is the first location to be reached in the fetus. Presence of viral antigen in endothelial cells of the placenta, brain, or heart suggest a hematogenous spread of virus from placenta to the liver, through the umbilical vein, and then to the rest of the organs via fetal blood vessels.
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Affiliation(s)
- Tara Crook
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, EH26 0PZ, Scotland
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22
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Traitement des infections sévères à staphylocoques dorés résistants à la méticilline : vancomycine ou nouvelles molécules ? Données récentes. MEDECINE INTENSIVE REANIMATION 2012. [DOI: 10.1007/s13546-012-0471-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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23
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Development of a real time PCR assay for rapid detection of Vibrio parahaemolyticus from seafood. Protein Cell 2012; 3:204-12. [PMID: 22477699 DOI: 10.1007/s13238-012-2017-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2011] [Accepted: 01/09/2012] [Indexed: 10/28/2022] Open
Abstract
A real time PCR assay for the detection of Vibrio parahaemolyticus in seafood samples was developed using a novel specific target and a competitive internal amplification control (IAC). The specificity of this assay was evaluated using 390 bacterial strains including V. parahaemolyticus, and other strains belonging to Vibrio and non-Vibrio species. The real time PCR assay unambiguously distinguished V. parahaemolyticus with a detection sensitivity of 4.8 fg per PCR with purified genomic DNA or 1 CFU per reaction by counting V. parahaemolyticus colonies. The assays of avoiding interference demonstrated that, even in the presence of 2.1 μg genomic DNA or 10(7) CFU background bacteria, V. parahaemolyticus could still be accurately detected. In addition, the IAC was used to indicate false-negative results, and lower than 94 copies of IAC per reaction had no influence on the detection limit. Ninety-six seafood samples were tested, of which 58 (60.4%) were positive, including 3 false negative results. Consequently, the real time PCR assay is effective for the rapid detection of V. parahaemotyticus contaminants in seafood.
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24
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Laboratory Diagnosis of Infection Due to Viruses, Chlamydia, Chlamydophila, and Mycoplasma. PRINCIPLES AND PRACTICE OF PEDIATRIC INFECTIOUS DISEASES 2012. [PMCID: PMC7152074 DOI: 10.1016/b978-1-4377-2702-9.00289-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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25
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Strenger V, Pfurtscheller K, Wendelin G, Aberle SW, Nacheva EP, Zöhrer B, Zenz W, Nagel B, Zobel G, Popow-Kraupp T. Differentiating inherited human herpesvirus type 6 genome from primary human herpesvirus type 6 infection by means of dried blood spot from the newborn screening card. J Pediatr 2011; 159:859-61. [PMID: 21840541 DOI: 10.1016/j.jpeds.2011.06.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Revised: 05/16/2011] [Accepted: 06/24/2011] [Indexed: 11/26/2022]
Abstract
To differentiate active human herpesvirus type 6 (HHV-6) infection from inherited HHV-6 (iHHV-6), we analyzed dried blood spots from archived newborn screening cards in 3 patients with high HHV-6 DNA copy numbers. Two patients were positive for HHV-6 DNA as neonates suggesting iHHV-6. In 1 patient, the absence of HHV-6 DNA excluded iHHV-6.
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Affiliation(s)
- Volker Strenger
- Department of Paediatrics and Adolescent Medicine, Medical University of Graz, Graz, Austria.
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26
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Update on the Detection and Characterization of Bacterial Pathogens by Nucleic Acid Amplification. Mol Microbiol 2011. [DOI: 10.1128/9781555816834.ch23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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27
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Polley SD, Boadi S, Watson J, Curry A, Chiodini PL. Detection and species identification of microsporidial infections using SYBR Green real-time PCR. J Med Microbiol 2010; 60:459-466. [PMID: 21183599 DOI: 10.1099/jmm.0.026781-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Diagnosis of microsporidial infections is routinely performed by light microscopy, with unequivocal non-molecular species identification achievable only through electron microscopy. This study describes a single SYBR Green real-time PCR assay for the simultaneous detection and species identification of such infections. This assay was highly sensitive, routinely detecting infections containing 400 parasites (g stool sample)(-1), whilst species identification was achieved by differential melt curves on a Corbett Life Science Rotor-Gene 3000. A modification of the QIAamp DNA tissue extraction protocol allowed the semi-automated extraction of DNA from stools for the routine diagnosis of microsporidial infection by real-time PCR. Of 168 stool samples routinely analysed for microsporidian spores, only five were positive by microscopy. By comparison, 17 were positive for microsporidial DNA by real-time analysis, comprising 14 Enterocytozoon bieneusi, one Encephalitozoon cuniculi and two separate Pleistophora species infections.
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Affiliation(s)
- Spencer D Polley
- Department of Clinical Parasitology, Hospital for Tropical Diseases, University College London Hospitals NHS Foundation Trust, Mortimer Market, Capper Street, London WC1E 6JB, UK
| | - Samuel Boadi
- Department of Clinical Parasitology, Hospital for Tropical Diseases, University College London Hospitals NHS Foundation Trust, Mortimer Market, Capper Street, London WC1E 6JB, UK
| | - Julie Watson
- Department of Clinical Parasitology, Hospital for Tropical Diseases, University College London Hospitals NHS Foundation Trust, Mortimer Market, Capper Street, London WC1E 6JB, UK
| | - Alan Curry
- Health Protection Agency, Regional Microbiology Network, North West Regional Laboratory, PO Box 209, Clinical Sciences Building, Manchester Royal Infirmary, Oxford Road, Manchester M13 9WZ, UK
| | - Peter L Chiodini
- London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
- Department of Clinical Parasitology, Hospital for Tropical Diseases, University College London Hospitals NHS Foundation Trust, Mortimer Market, Capper Street, London WC1E 6JB, UK
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28
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Danial J, Noel M, Templeton KE, Cameron F, Mathewson F, Smith M, Cepeda JA. Real-time evaluation of an optimized real-time PCR assay versus Brilliance chromogenic MRSA agar for the detection of meticillin-resistant Staphylococcus aureus from clinical specimens. J Med Microbiol 2010; 60:323-328. [PMID: 21109629 DOI: 10.1099/jmm.0.025288-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A total of 1204 meticillin-resistant Staphylococcus aureus (MRSA) screens (3340 individual swabs) were tested to evaluate a staphylococcal cassette chromosome mec (SCCmec) real-time PCR. In total, 148 (12.3 %) of the screens were MRSA-positive, where 146 (12.1 %) were MRSA-positive by the SCCmec real-time PCR assay. In contrast, 128 (10.6 %) screens were MRSA-positive by culture. One hundred and twenty-six (10.5 %) of the screens were positive by both culture and PCR. Twenty of the 1204 screens (1.66 %) were negative by culture but positive by PCR; these samples were sequenced. In 14 of the cases, a homology search confirmed the sequence as SCCmec, indicating that these samples could be considered true positives. Two of the 1204 (0.2 %) screens were positive by culture and negative by PCR. The mean turnaround time (TAT) for PCR-negative swabs was 6 h 12 min and for PCR-positive swabs was 6 h 48 min. In comparison, for culture-negative swabs the mean TAT was 29 h 30 min and for culture-positive swabs was 69 h. The cost per swab for routine culture was £0.41 (€0.48) and that of the real-time PCR assay was £2.35 (€2.75). This optimized, in-house, inexpensive, real-time PCR test maintained a very high sensitivity and specificity when evaluated under real-time laboratory conditions. The TAT of this real-time PCR assay was substantially lower than that of chromogenic culture. It was also maintained throughout the entire process, which can be taken as an indirect measure of test performance. This study showed that implementation of a molecular test can be achieved with limited resources in a standard microbiology laboratory.
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Affiliation(s)
- J Danial
- Department of Microbiology, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - M Noel
- Department of Microbiology, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - K E Templeton
- Department of Microbiology, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - F Cameron
- Department of Microbiology, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - F Mathewson
- Department of Microbiology, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - M Smith
- Department of Microbiology, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - J A Cepeda
- Department of Microbiology, Basingstoke and North Hampshire Hospital, Basingstoke, UK.,Department of Microbiology, Royal Infirmary of Edinburgh, Edinburgh, UK
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29
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Improvement of HRV Quantification Using cRNA-Based Standards for Real Time RT-PCR. Mol Biotechnol 2010; 48:15-8. [DOI: 10.1007/s12033-010-9343-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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30
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Mahmoud KA, Luong JHT. A Sensitive Electrochemical Assay for Early Detection of HIV-1 Protease Using Ferrocene-Peptide Conjugate/Au Nanoparticle/Single Walled Carbon Nanotube Modified Electrode. ANAL LETT 2010. [DOI: 10.1080/00032711003653924] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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31
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Using Epstein-Barr viral load assays to diagnose, monitor, and prevent posttransplant lymphoproliferative disorder. Clin Microbiol Rev 2010; 23:350-66. [PMID: 20375356 DOI: 10.1128/cmr.00006-09] [Citation(s) in RCA: 164] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Epstein-Barr virus (EBV) DNA measurement is being incorporated into routine medical practice to help diagnose, monitor, and predict posttransplant lymphoproliferative disorder (PTLD) in immunocompromised graft recipients. PTLD is an aggressive neoplasm that almost always harbors EBV DNA within the neoplastic lymphocytes, and it is often fatal if not recognized and treated promptly. Validated protocols, commercial reagents, and automated instruments facilitate implementation of EBV load assays by real-time PCR. When applied to either whole blood or plasma, EBV DNA levels reflect clinical status with respect to EBV-related neoplasia. While many healthy transplant recipients have low viral loads, high EBV loads are strongly associated with current or impending PTLD. Complementary laboratory assays as well as histopathologic examination of lesional tissue help in interpreting modest elevations in viral load. Circulating EBV levels in serial samples reflect changes in tumor burden and represent an effective, noninvasive tool for monitoring the efficacy of therapy. In high-risk patients, serial testing permits early clinical intervention to prevent progression toward frank PTLD. Restoring T cell immunity against EBV is a major strategy for overcoming PTLD, and novel EBV-directed therapies are being explored to thwart virus-driven neoplasia.
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32
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Whiley DM, Sloots TP. Molecular Amplification Methods in Diagnostic Virology. INFECTIOUS DISEASE AND THERAPY 2010. [DOI: 10.3109/9781420084962.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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Molecular Diagnostics and Comparative Genomics in Clinical Microbiology. MOLECULAR DIAGNOSTICS 2010. [PMCID: PMC7150202 DOI: 10.1016/b978-0-12-374537-8.00030-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Initially, the availability of molecular diagnostics was considered a panacea, but replacement of conventional tests for detection and identification of microorganisms by molecular procedures eventually gathered momentum. This chapter describes current state-of-the-art molecular diagnostics and comparative genomics in medical microbiology to provide an understanding of infectious disease over the coming years. Nucleic acid-based tests are being introduced with increasing speed into routine clinical microbiology laboratories. Some of the problems remaining to be solved prior to general acceptance of nucleic acid-mediated detection and identification of microbial pathogens are reviewed. Historic objections are slowly being taken apart, and an accelerated introduction of molecular diagnostics is being pursued in many cases. Clear improvement in clinical testing is achieved by introducing molecular tests. Therefore, swift introduction of such tests into clinical practice is important to be pursued. Several PCR tests show increased sensitivity, excellent specificity, and cost effectiveness highlighting the success of the novel applications in the field of bacterial infections. Finally, some of the problems remaining to be solved prior to general acceptation of nucleic acid-mediated detection and identification of microbial pathogens are also reviewed.
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Drago F, Broccolo F, Rebora A. Pityriasis rosea: an update with a critical appraisal of its possible herpesviral etiology. J Am Acad Dermatol 2009; 61:303-18. [PMID: 19615540 DOI: 10.1016/j.jaad.2008.07.045] [Citation(s) in RCA: 134] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2008] [Revised: 07/21/2008] [Accepted: 07/21/2008] [Indexed: 01/26/2023]
Abstract
Pityriasis rosea is an acute, self-healing exanthem characterized by oval erythematous-squamous lesions of the trunk and limbs, that usually spares face, scalp, palms, and soles. Constitutional symptoms, which have the character of true prodromes; clinical features, which resemble those of the known exanthems; and many epidemiologic data all suggest an infectious origin. A host of infectious agents have been incriminated, but, recently, human herpesvirus 6 and 7 have been extensively studied. The goal of this review is to outline the epidemiologic, clinical, histologic, and ultrastructural features of pityriasis rosea, but mainly to stress its possible human herpesvirus nature. In addition, clues have been added to help the reader to go through the complex subtleties of the virologic investigation.
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Affiliation(s)
- Francesco Drago
- Department of Endocrinological and Metabolic Sciences, Section of Dermatology, University of Genoa, Genoa, Italy
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Hoffmann B, Beer M, Reid SM, Mertens P, Oura CAL, van Rijn PA, Slomka MJ, Banks J, Brown IH, Alexander DJ, King DP. A review of RT-PCR technologies used in veterinary virology and disease control: sensitive and specific diagnosis of five livestock diseases notifiable to the World Organisation for Animal Health. Vet Microbiol 2009; 139:1-23. [PMID: 19497689 DOI: 10.1016/j.vetmic.2009.04.034] [Citation(s) in RCA: 124] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2008] [Revised: 04/15/2009] [Accepted: 04/28/2009] [Indexed: 12/31/2022]
Abstract
Real-time, reverse transcription polymerase chain reaction (rRT-PCR) has become one of the most widely used methods in the field of molecular diagnostics and research. The potential of this format to provide sensitive, specific and swift detection and quantification of viral RNAs has made it an indispensable tool for state-of-the-art diagnostics of important human and animal viral pathogens. Integration of these assays into automated liquid handling platforms for nucleic acid extraction increases the rate and standardisation of sample throughput and decreases the potential for cross-contamination. The reliability of these assays can be further enhanced by using internal controls to validate test results. Based on these advantageous characteristics, numerous robust rRT-PCRs systems have been developed and validated for important epizootic diseases of livestock. Here, we review the rRT-PCR assays that have been developed for the detection of five RNA viruses that cause diseases that are notifiable to the World Organisation for Animal Health (OIE), namely: foot-and-mouth disease, classical swine fever, bluetongue disease, avian influenza and Newcastle disease. The performance of these tests for viral diagnostics and disease control and prospects for improved strategies in the future are discussed.
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Affiliation(s)
- Bernd Hoffmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
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Laczka O, Ferraz RM, Ferrer-Miralles N, Villaverde A, Muñoz FX, Campo FJD. Fast electrochemical detection of anti-HIV antibodies: Coupling allosteric enzymes and disk microelectrode arrays. Anal Chim Acta 2009; 641:1-6. [DOI: 10.1016/j.aca.2009.03.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2008] [Revised: 03/04/2009] [Accepted: 03/05/2009] [Indexed: 11/28/2022]
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Braun T, Ghatkesar MK, Backmann N, Grange W, Boulanger P, Letellier L, Lang HP, Bietsch A, Gerber C, Hegner M. Quantitative time-resolved measurement of membrane protein-ligand interactions using microcantilever array sensors. NATURE NANOTECHNOLOGY 2009; 4:179-85. [PMID: 19265848 DOI: 10.1038/nnano.2008.398] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2008] [Accepted: 12/03/2008] [Indexed: 05/17/2023]
Abstract
Membrane proteins are central to many biological processes, and the interactions between transmembrane protein receptors and their ligands are of fundamental importance in medical research. However, measuring and characterizing these interactions is challenging. Here we report that sensors based on arrays of resonating microcantilevers can measure such interactions under physiological conditions. A protein receptor--the FhuA receptor of Escherichia coli--is crystallized in liposomes, and the proteoliposomes then immobilized on the chemically activated gold-coated surface of the sensor by ink-jet spotting in a humid environment, thus keeping the receptors functional. Quantitative mass-binding measurements of the bacterial virus T5 at subpicomolar concentrations are performed. These experiments demonstrate the potential of resonating microcantilevers for the specific, label-free and time-resolved detection of membrane protein-ligand interactions in a micro-array format.
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Affiliation(s)
- Thomas Braun
- School of Physics and Centre for Research on Adaptive Nanostructures and Nanodevices, Naughton Institute, Trinity College Dublin, Dublin 2, Ireland
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Valones MAA, Guimarães RL, Brandão LAC, de Souza PRE, de Albuquerque Tavares Carvalho A, Crovela S. Principles and applications of polymerase chain reaction in medical diagnostic fields: a review. Braz J Microbiol 2009; 40:1-11. [PMID: 24031310 PMCID: PMC3768498 DOI: 10.1590/s1517-83822009000100001] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2008] [Accepted: 02/25/2009] [Indexed: 01/19/2023] Open
Abstract
Recent developments in molecular methods have revolutionized the detection and characterization of microorganisms in a broad range of medical diagnostic fields, including virology, mycology, parasitology, microbiology and dentistry. Among these methods, Polymerase Chain Reaction (PCR) has generated great benefits and allowed scientific advancements. PCR is an excellent technique for the rapid detection of pathogens, including those difficult to culture. Along with conventional PCR techniques, Real-Time PCR has emerged as a technological innovation and is playing an ever-increasing role in clinical diagnostics and research laboratories. Due to its capacity to generate both qualitative and quantitative results, Real-Time PCR is considered a fast and accurate platform. The aim of the present literature review is to explore the clinical usefulness and potential of both conventional PCR and Real-Time PCR assays in diverse medical fields, addressing its main uses and advances.
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Yoon KH, Cho JH. Detection of Respiratory Viruses in Children by Multiplex Reverse Transcriptase PCR, Direct Immunofluorescence Assay, and Shell Vial Culture. ACTA ACUST UNITED AC 2009. [DOI: 10.5145/kjcm.2009.12.3.110] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Kui Hyun Yoon
- Department of Laboratory Medicine, Wonkwang University Sanbon Hospital, Gunpo, Korea
| | - Ji Hyun Cho
- Department of Laboratory Medicine, College of Medicine, Wonkwang University, Iksan, Korea
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Cellular normalization of viral DNA loads on whole blood improves the clinical management of cytomegalovirus or Epstein Barr virus infections in the setting of pre-emptive therapy. J Med Virol 2008; 81:90-8. [PMID: 19031462 DOI: 10.1002/jmv.21334] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Two quantitative duplex real-time PCR assays were developed for co-amplification of human albumin and cytomegalovirus (CMV) or Epstein Barr virus (EBV) genes after automated extraction on whole blood, and compared two units for expressing viral DNA loads (copies per ml of blood or per 10(6) peripheral blood leukocytes (PBLs)) on 1,138 positive samples. Both PCRs were characterized by high sensitivity, reproducibility, and linear range. Automated extraction by a MagNA Pure LC Instrument was shown to be more efficient when peripheral blood cell count was inferior to 5 x 10(9) PBLs/L. Albumin co-amplification allows the detection of PCR inhibitors and normalization of viral load according to the number of cells calculated in the sample. The two ways of expressing viral load results were highly correlated, but quantitative differences varied in relation to variations of blood cell count. As these two viruses are highly cell associated, viral loads can be underestimated in patients with leucopenia. In the setting of pre-emptive strategies during CMV infection, the units in which results are expressed can influence clinical management, as illustrated in this article.
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Kumar S, Jadi RS, Anakkathil SB, Tandale BV, Mishra AC, Arankalle VA. Development and evaluation of a real-time one step reverse-transcriptase PCR for quantitation of Chandipura virus. BMC Infect Dis 2008; 8:168. [PMID: 19091082 PMCID: PMC2629476 DOI: 10.1186/1471-2334-8-168] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2008] [Accepted: 12/17/2008] [Indexed: 12/01/2022] Open
Abstract
Background Chandipura virus (CHPV), a member of family Rhabdoviridae was attributed to an explosive outbreak of acute encephalitis in children in Andhra Pradesh, India in 2003 and a small outbreak among tribal children from Gujarat, Western India in 2004. The case-fatality rate ranged from 55–75%. Considering the rapid progression of the disease and high mortality, a highly sensitive method for quantifying CHPV RNA by real-time one step reverse transcriptase PCR (real-time one step RT-PCR) using TaqMan technology was developed for rapid diagnosis. Methods Primers and probe for P gene were designed and used to standardize real-time one step RT-PCR assay for CHPV RNA quantitation. Standard RNA was prepared by PCR amplification, TA cloning and run off transcription. The optimized real-time one step RT-PCR assay was compared with the diagnostic nested RT-PCR and different virus isolation systems [in vivo (mice) in ovo (eggs), in vitro (Vero E6, PS, RD and Sand fly cell line)] for the detection of CHPV. Sensitivity and specificity of real-time one step RT-PCR assay was evaluated with diagnostic nested RT-PCR, which is considered as a gold standard. Results Real-time one step RT-PCR was optimized using in vitro transcribed (IVT) RNA. Standard curve showed linear relationship for wide range of 102-1010 (r2 = 0.99) with maximum Coefficient of variation (CV = 5.91%) for IVT RNA. The newly developed real-time RT-PCR was at par with nested RT-PCR in sensitivity and superior to cell lines and other living systems (embryonated eggs and infant mice) used for the isolation of the virus. Detection limit of real-time one step RT-PCR and nested RT-PCR was found to be 1.2 × 100 PFU/ml. RD cells, sand fly cells, infant mice, and embryonated eggs showed almost equal sensitivity (1.2 × 102 PFU/ml). Vero and PS cell-lines (1.2 × 103 PFU/ml) were least sensitive to CHPV infection. Specificity of the assay was found to be 100% when RNA from other viruses or healthy individual was used. Conclusion On account of the high sensitivity, reproducibility and specificity, the assay can be used for the rapid detection and quantitation of CHPV RNA from clinical samples during epidemics and from endemic areas. The assay may also find application in screening of antiviral compounds, understanding of pathogenesis as well as evaluation of vaccine.
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Kimura H, Ito Y, Suzuki R, Nishiyama Y. Measuring Epstein-Barr virus (EBV) load: the significance and application for each EBV-associated disease. Rev Med Virol 2008; 18:305-19. [PMID: 18494041 DOI: 10.1002/rmv.582] [Citation(s) in RCA: 112] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Because Epstein-Barr virus (EBV) is ubiquitous and persists latently in lymphocytes, simply detecting EBV is insufficient to diagnose EBV-associated diseases. Therefore, measuring the EBV load is necessary to diagnose EBV-associated diseases and to explore EBV pathogenesis. Due to the diverse biology of EBV, the significance of measuring EBV DNA and the optimal type of specimen differ among EBV-associated diseases. Recent advances in molecular technology have enabled the EBV genome to be quantitated rapidly and accurately. Real-time polymerase chain reaction (PCR) is a rapid and reliable method to quantify DNA and is widely used not only as a diagnostic tool, but also as a management tool for EBV-associated diseases. However, each laboratory currently measures EBV load with its own "homebrew" system, and there is no consensus on sample type, sample preparation protocol, or assay units. The EBV real-time PCR assay system must be standardised for large-scale studies and international comparisons.
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Affiliation(s)
- Hiroshi Kimura
- Department of Virology Nagoya University Graduate School of Medicine, Nagoya, Japan.
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Di Nicola A, Ghezzi E, Gillio F, Zerilli F, Shehi E, Maritano D, Panizzo M, Bonelli F, Adlerstein D. Anchor-based fluorescent amplicon generation assays (FLAG) for real-time measurement of human cytomegalovirus, Epstein-Barr virus, and varicella-zoster virus viral loads. Clin Chem 2008; 54:1900-7. [PMID: 18703767 DOI: 10.1373/clinchem.2008.106542] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Monitoring the human cytomegalovirus (HCMV), Epstein-Barr virus (EBV), or varicella-zoster virus (VZV) viral load is an important factor in the management of immunosuppressed patients, such as recipients of solid-organ or bone marrow transplants. The advent of real-time PCR technologies has prompted the widespread development of quantitative PCR assays for the detection of viral loads and other diagnostic purposes. METHODS The fluorescent amplicon generation (FLAG) technology uses the PspGI restriction enzyme to monitor PCR product generation. We modified the FLAG technology by introducing an accessory oligonucleotide "anchor" that stabilizes the binding of the forward primer to the target sequence (a-FLAG). We developed assays for HCMV, EBV, and VZV that incorporated an internal amplification-control reaction to validate negative results and extensively analyzed the performance of the HCMV a-FLAG assay. RESULTS The 3 assays performed similarly with respect to reaction efficiency and linear range. Compared with a commercially available kit, the HCMV a-FLAG assay results showed good correlation with calculated concentrations (r = 0.9617), excellent diagnostic sensitivity and specificity (99% and 95%, respectively), and similar values for the linear range (1-10(7) copies/microL), analytical sensitivity (0.420 copies/microL), and intra- and interassay imprecision. CONCLUSIONS The a-FLAG assay is an alternative real-time PCR technology suitable for detecting and quantifying target-DNA sequences. For clinical applications such as the measurement of viral load, a-FLAG assays provide multiplex capability, internal amplification control, and high diagnostic sensitivity and specificity.
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Whiley DM, Lambert SB, Bialasiewicz S, Goire N, Nissen MD, Sloots TP. False-negative results in nucleic acid amplification tests-do we need to routinely use two genetic targets in all assays to overcome problems caused by sequence variation? Crit Rev Microbiol 2008; 34:71-6. [PMID: 18568861 DOI: 10.1080/10408410801960913] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Nucleic acid amplification tests (NAATs) have numerous advantages over traditional diagnostic techniques and so are now widely used by diagnostic laboratories for routine detection of infectious agents. However, there is some concern over the increasing numbers of reports of NAAT false-negative results caused by sequence variation. Highly conserved NAAT target sequences have been reported for many organisms, yet sequence-related problems continue to be observed in commercial and in-house assays targeting a broad range of microbial pathogens. In light of these ongoing problems, it may be time to consider the use of two genetic targets in NAAT methods to reduce the potential for sequence-related false-negative results.
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Affiliation(s)
- D M Whiley
- Queensland Paediatric Infectious Diseases Laboratory, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital and Health Service Distric, Queensland, Australia.
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Internally controlled triplex quantitative PCR assay for human polyomaviruses JC and BK. J Clin Microbiol 2008; 46:2829-36. [PMID: 18614652 DOI: 10.1128/jcm.00844-08] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have developed a triplex TaqMan-based quantitative PCR assay for the human polyomaviruses JC (JCPyV) and BK (BKPyV). The assay simultaneously detects and quantifies both JCPyV and BKPyV in human clinical samples, and it includes an internal amplification control consisting of murine polyomavirus (MuPyV) plasmid DNA. We developed the assay for the Roche LightCycler 480 platform with the reporter dyes VIC, 6-FAM, and Cy5 for MuPyV, BKPyV, and JCPyV, respectively. The assay had a high specificity for BKPyV and JCPyV when either viral genome was present alone or in mixed samples over a range of 10(1) to 10(7) copy numbers per reaction. The analytical sensitivity was 50 copies for BKPyV and 10 copies for JCPyV. The use of the MuPyV internal control ensured monitoring of the quality of the extraction and of PCR inhibition, even in samples such as cerebrospinal fluid and plasma in which controls based on host genes cannot be effectively used. In addition, we developed a similar assay using a different dye configuration (6-FAM, VIC, and NED) that could be used on an ABI 7500 Fast platform. This assay had sensitivities similar to those of the LightCycler 480 configuration for BKPyV and JCPyV when either viral genome was present alone, but the sensitivity of detection of BKPyV was greatly decreased when an excess of JCPyV (>100-fold) was present in the sample. This internally controlled combined assay offers greater convenience and cost-effectiveness compared to separate assays for each virus and can also detect unexpected PyV activations by testing for both viruses in all samples.
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Abstract
Epstein-Barr virus (EBV) infects various cell types in a wide spectrum of benign and malignant diseases. Laboratory tests for EBV have improved and are increasingly used in diagnosis, prognosis, prediction, and prevention of diseases ranging from infectious mononucleosis to selected subtypes of lymphoma, sarcoma, and carcinoma. Indeed, the presence of EBV is among the most effective tumor markers supporting clinical management of cancer patients. In biopsies, localization of EBER transcripts by in situ hybridization remains the gold standard for identifying latent infection. Other RNA- and protein-based assays detect lytic viral replication and can distinguish carcinoma-derived from lymphocyte-derived EBV in saliva or nasopharyngeal brushings. Analysis of blood using EBV viral load and serology reflects disease status and risk of progression. This review summarizes prior research in the context of basic virologic principles to provide a rational strategy for applying and interpreting EBV tests in various clinical settings. Such assays have been incorporated into standard clinical practice in selected settings such as diagnosis of primary infection and management of patients with immune dysfunction or nasopharyngeal carcinoma. As novel therapies are developed that target virus-infected cells or overcome the adverse effects of infection, laboratory testing becomes even more critical for determining when intervention is appropriate and the extent to which it has succeeded.
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Affiliation(s)
- Margaret L Gulley
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599-7525, USA.
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The development of a qualitative real-time RT-PCR assay for the detection of hepatitis C virus. Eur J Clin Microbiol Infect Dis 2008; 27:1177-82. [PMID: 18551325 DOI: 10.1007/s10096-008-0556-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2008] [Accepted: 05/12/2008] [Indexed: 01/12/2023]
Abstract
Real-time polymerase chain reaction (PCR) represents a favourable option for the detection of hepatitis C virus (HCV). A real-time reverse transcriptase PCR (RT-PCR) assay was developed as a qualitative diagnostic screening method for the detection of HCV using the ABI PRISM 7500 Sequence Detection System. The primers and probe were designed to target the 5'-untranslated region of the hepatitis C viral genome. A second heterologous probe assay was developed for the detection of the haemagglutinin gene of phocine distemper virus (PDV) and was used as an internal control. A semi-automated HCV extraction method was also implemented using the ABI PRISM 6100 Nucleic Acid PrepStation. The HCV assay was optimised as a qualitative singleplex RT-PCR assay with parallel testing of the target and internal control. The assay results (n = 200) were compared to the COBAS AMPLICOR HCV Test v2.0 assay. The assay demonstrated a high rate of sensitivity (99%), specificity (100%) and an acceptable limit of detection (LOD) of 100 IU/ml. The development of a qualitative multiplex assay for the simultaneous detection of HCV and internal control indicates the same high rates of sensitivity and specificity. This sensitive real-time assay may prove to be a valuable method for the detection of HCV.
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Blakey GL, Luna RA, Versalovic J. Infectious diseases testing. ACTA ACUST UNITED AC 2008; Chapter 9:Unit 9.18. [PMID: 18428383 DOI: 10.1002/0471142905.hg0918s47] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Molecular methods have been applied widely for the diagnosis of infectious diseases. Beginning with solution hybridization in the early 1990s, multiple methods for nucleic acid hybridization and amplification have been introduced into the laboratory for the identification and characterization of microbial pathogens. This unit contains examples of several basic approaches for microbial detection or characterization in the laboratory. Methods in this chapter include automated nucleic acid extraction, direct detection of microbial pathogens, and characterization of pathogens by DNA sequencing or typing. Any of these methods could be customized for the characterization of bacteria, fungi, parasites, or viruses.
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Abstract
Nucleic acid amplification tests (NATs) are increasingly being used for diagnosis of respiratory virus infections. The most familiar formats use DNA or RNA target amplification methods for enhanced sensitivity above culture and antigen-based procedures. Although gel and plate-hybridisation methods are still utilised for analysis of amplified products, detection using "real-time" methods which do not require handling of amplified products are favoured in many laboratories. Assays based on nucleic acid amplification and detection can be designed against a broad range of respiratory viruses and have been particularly useful for detection of recently identified viruses such as human metapneumovirus and coronaviruses NL63 and HKU1. However, the wide range of potential pathogens which can cause similar respiratory symptomology and disease makes application of individual diagnostic assays based on detection of DNA and RNA both complex and expensive. One way to resolve this potential problem is to undertake multiplexed nucleic acid amplification reactions with analysis of amplified products by suspension microarray. The Respiratory Virus Panel (RVP) from Luminex Molecular Diagnostics is one example of such an approach which could be made available to diagnostic and public health laboratories for broad spectrum respiratory virus detection.
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Affiliation(s)
- Julie D Fox
- Provincial Laboratory for Public Health (Microbiology), University of Calgary, Calgary, Alberta, Canada.
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Renwick L, Hardie A, Girvan EK, Smith M, Leadbetter G, Claas E, Morrison D, Gibb AP, Dave J, Templeton KE. Detection of meticillin-resistant Staphylococcus aureus and Panton-Valentine leukocidin directly from clinical samples and the development of a multiplex assay using real-time polymerase chain reaction. Eur J Clin Microbiol Infect Dis 2008; 27:791-6. [DOI: 10.1007/s10096-008-0503-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2008] [Accepted: 02/20/2008] [Indexed: 10/22/2022]
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