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3. Laboratory capability and surveillance testing for middle east respiratory syndrome coronavirus infection in the who European region, June 2013

Author

Pereyaslov, D., Rosin, P., Palm, D., Zeller, H., Gross, D., Brown, C. S., Struelens, M. J., Robo, A., Hatibi, I. H., Alis, J. C., Sargsyan, S., Gurbanov, S., Gribkova, N., Ranst, M., Ieven, G., Patteet, S., Tomic, S., Korsun, N., Drazenovic, V., Pieridou-Bagkatzouni, D., Jirincova, H., Havlickova, M., Fomsgaard, A., Rae, K., Lappalainen, M., Ikonen, N., Lina, B., Sylvie van der WERF, Manuguerra, J. -C, Machablishvili, A., Eickmann, M., Wolff, T., Dobler, G., Schmidt-Chanasit, J., Drosten, C., Papa, A., Mentis, A. F., Kis, Z., Löve, A., Coughlan, S., Mandelboim, M., Capobianchi, M. R., Landini, M. P., Baldanti, F., Palu, G., Ghisetti, V., Donatelli, I., Nusupbayeva, G., Tokhtabakiyeva, Z., Kasymbekova, K., Storozenko, J., Erne, S., Griskevicius, A., Opp, M., Barbara, C., Vratnica, Z., Reusken, C., Dudman, S. G., Hungnes, O., Pancer, K., Guiomar, R., Eder, V., Lupulescu, E., Yatsyshina, S., Pisareva, M., Buzitskaya, Z., Sergeev, A., Nedeljković, J., Staroňová, E., Županc, T. A., Petrovec, M., Korva, M., Prosenc, K., Casas, I., Gaines, H., Cherpillod, P., Zakirova, N., Bosevska, G., Altas, B., Ciblak, M., Mironenko, A., Dykhanovska, T., Demchyshyna, I., Bermingham, A., Rakhimov, R., Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), European Centre for Disease Prevention and Control [Stockholm, Sweden] (ECDC), Experts of the MERS-CoV Working Group Members of this working group who provided survey data: Albania: Alma Robo, Iris Hasibra (Hatibi), Institute of Public Health, Tirana Andorra: Josep Casals Alis, Ministry of Health, Welfare and Labour, Andorra la Vella Armenia: Shushan Sargsyan, Virology Laboratory, Centre for Diseases Control and Prevention, Yerevan Austria: Stephan Aberle, Department of Virology, Medical University of Vienna, Vienna Azerbaijan: Sadraddin Gurbanov, National Virology Laboratory, National Anti-Plague Station, Baku Belarus: Natalia Gribkova, Laboratory for Influenza and Influenza-like Diseases, Republican Research and Practical Center for Epidemiology and Microbiology, Minsk Belgium: Marc Van Ranst, Greet Ieven and Sophie Patteet, National Reference Centre of Respiratory Viruses, University Hospital Leuven and UZA Antwerpen, Antwerpen Bosnia and Herzegovina: Stanka Tomic, Microbiology Department, Institute of Public Health of the Republic of Srpska, Banja Luka Bulgaria: Neli Korsun, National Laboratory 'Influenza and ARD', Department of Virology, National Centre of Infectious and Parasitic Diseases, Sofia Croatia: Vladimir Drazenovic, National Influenza Centre, Croatian National Institute of Public Health, Zagreb Cyprus: Despo Pieridou-Bagkatzouni, Microbiology Department, Nicosia General Hospital, Nicosia Czech Republic: Helena Jirincova, Martina Havlickova, National Reference Laboratory for Influenza, National Institute for Public Health, Prague Denmark: Anders Fomsgaard, Virus Research and Development Laboratory, Department Microbiology Diagnostic and Virology, Statens Serum Institut, Copenhagen Estonia: Külli Rae, Laboratory of Communicable Diseases, Health Board, Tallinn Finland: Maija Lappalainen, Department of Virology and Immunology, Helsinki University Hospital, Laboratory Services (HUSLAB) and Niina Ikonen, Virology Unit, National Institute for Health and Welfare, Helsinki France: Bruno Lina, Centre National de Référence des Virus Influenza – HCL, Lyon and Sylvie van der Werf, Unit of Molecular Genetics of RNA viruses, Institut Pasteur and Jean-Claude Manuguerra, Cellule d’Intervention Biologique d’Urgence (CIBU), Institut Pasteur, Paris Georgia: Ann Machablishvili, National Influenza Centre, National Centre for Disease Control and Public Health, Tbilisi Germany: Markus Eickmann, Institut für Virologie der Philipps-Universität in Marburg and Thorsten Wolff, Div of Influenza and other Respiratory viruses, Robert Koch-Institut, and Dr. Gerhard Dobler, Bundeswehr Instittue of Microbiology, and Jonas Schmidt-Chanasit, WHOCC for Arbovirus and Haemorrhagic Fever Reference and Research at Bernhard Nocht Institute for Tropical Medicine, Hamburg, and Christian Drosten, Virology Institute, Bonn Greece: Anna Papa, National Reference Laboratory for Arboviruses and Hemorrhagic Fever viruses, Aristotle University of Thessaloniki, Thessaloniki and Andreas F. Mentis, National Influenza Reference Laboratory of Southern Greece/Hellenic Pasteur Institute, Athens Hungary: Zoltan Kis, Department for Respiratory Viruses / National Biosafety Laboratory, B. Johan National Center for Epidemiology, Budapest Iceland: Arthur Löve, Department of Virology, Landspitali- National University Hospital, Reykjavik Ireland: Suzie Coughlan, National Virus Reference Laboratory/University College Dublin, Dublin Israel: Michal Mandelboim, Central Virology Laboratory, Sheba Medical Center, Tel Hashomer Italy: Maria R. Capobianchi, Laboratory of Virology/National Institute for Infectious Diseases Lazzaro Spallanzani, and Maria Paola Landini, Regional Center for Emerging Infections (CRREM)/ Unit of Clinical Microbiology, St. Orsola General Hospital, Bologna, and Fausto Baldanti, Molecular Virology Unit, Department of Microbiology and Virology, Fondazione IRCCS Policlinico San Matteo, Pavia, and Giorgio Palu, Microbiology and Virology/Padova University Hospital, and Valeria Ghisetti, Laboratory of Microbiology and Virology, Amedeo di Savoia Hospital, Torino, and Isabella Donatelli, National Influenza Centre, Instituto Superiore di Sanita, Kazakhstan: Gaukhar Nusupbayeva, Zarina Tokhtabakiyeva, National Reference Laboratory on Control of Viral Infections, Scientifical-Practical Center of Sanitary and Epidemiological Expertise and Monitoring, Almaty Kyrgyzstan: Kaliya Kasymbekova, Centre of Molecular-Genetic and Microbiological Investigations, Department of State Sanitary Epidemiological Surveillance, Bishkek Latvia: Jelena Storozenko, Riga East University Hospital, Latvian Centre of Infectious Diseases, National Microbiology Reference Laboratory, Riga Liechtenstein: Sabine Erne, Office of Public Health, Country Administration of Principality of Liechtenstein Lithuania: Algirdas Griskevicius, National Public Health Surveillance Laboratory, Vilnius Luxembourg: Matthias Opp, Laboratoire National de Santé, Luxembourg Malta: Christopher Barbara, Pathology Department, Mater Dei Hospital, Msida Montenegro: Zoran Vratnica, Centre for Medical Microbiology, Public Health Institute of Montenegro, Podgorica Netherlands: Chantal Reusken, Centre for Infectious Disease Research, Diagnostics and Screening, National Institute for Public Health and the Environment, Bilthoven Norway: Susanne Gjeruldsen Dudman and Olav Hungnes, Department of Virology, Norwegian Institute of Public Health, Oslo Poland: Katarzyna Pancer, National Institute of Public Health- National Institute of Hygiene, Department of Virology, Warsaw Portugal: Raquel Guiomar, National Influenza Reference Laboratory, Infectious Diseases Department, National Institute of Health, Lisboa Republic of Moldova: Veronica Eder, Laboratory of Viral Respiratory Infections, National Center for Public Health, Chisinau Romania: Emilia Lupulescu, Laboratory for Respiratory Viruses/ NIRDMI Cantacuzino, Bucharest Russian Federation: Svetlana Yatsyshina, Reference Centre for Infection Agents, Central Research Institute of Epidemiology (CRIE), Rospotrebnadzor, Moscow, and Maria Pisareva and Zhanna Buzitskaya, Laboratory of Molecular Virology and Genetic Engineering, Research Institute of Influenza, St Petersburg, and Alexander Sergeev, State Research Center of Virology and Biotechnology VECTOR, Novosibirsk Serbia: Jasminka Nedeljković, Respiratory Department, Torlak Institute of Immunology and Virology, Belgrade Slovakia: Edita Staroňová, National Influenza Center/Public Health Authority, Bratislava Slovenia: Tatjana Avšič Županc, Miroslav Petrovec, Miša Korva, University of Ljubljana, Faculty of Medicine, Institute of Microbiology and Immunology, and Katarina Prosenc, Laboratory for Virology, National Public Health Institute Slovenia, Ljubljana Spain: Inmaculada Casas, Influenza National Reference Laboratory, National Influenza Center-Madrid, Instituto de Salud Carlos III, Majadahonda, Madrid and Ramon Cisterna Clinical microbiology and infection control, Hospital Basurto Bilbao Spain Sweden: Hans Gaines, Swedish Institute for Communicable Disease Control, Stockholm Switzerland: Pascal Cherpillod, National Reference Centre for Emerging Viral Infections, Laboratory of Virology, Division of Infectious Diseases University of Geneva Hospitals, Geneva Tajikistan: Niginamo Zakirova, Virology Laboratory, State Sanitary-Epidemiological Surveillance, Dushanbe The former Yugoslav Republic of Macedonia: Golubinka Bosevska, Laboratory for Virology and Molecular Diagnostics, Institute of Public Health, Skopje Turkey: Basak Altas, National Influenza Centre, Virology Reference and Research Laboratory, Public Health Institutions of Turkey, Ankara, and Meral Ciblak, National Influenza Reference Laboratory, Faculty of Medicine, University of Istanbul, Istanbul Turkmenistan: Central Reference Laboratory, Sanitary Epidemiologic Service, Ashgabat Ukraine: Alla Mironenko, National Influenza Centre, L.V.Gromashevsky Institute of Epidemiology & Infectious diseases NAMS, and Tetiana Dykhanovska and Iryna Demchyshyna, Centre of influenza and ARVI, Central Sanitary and Epidemiological Station, Kiev United Kingdom: Alison Bermingham, Respiratory Virus Unit, Virus Reference Department, Public Health England, London Uzbekistan: Ravshan Rakhimov, National Influenza Centre, Institute of Virology, Tashkent., and We thank the ECDC National Microbiology Focal Points in EU/EEA countries, focal points from laboratories of the EuroFlu and ENIVD networks for coordinating data collection and for dedicated and rapid responses to the surveys.

Subjects
Epidemiology, Middle East respiratory syndrome coronavirus, [SDV]Life Sciences [q-bio], SARS (Disease), MERS (Disease), medicine.disease_cause, World Health Organization, Communicable Diseases, Emerging, World health, Viral genetics, Coronavirus infections -- Laboratory manuals, Environmental protection, Virology, Environmental health, medicine, media_common.cataloged_instance, Humans, European Union, European union, Coronavirus, media_common, Middle East, business.industry, Reverse Transcriptase Polymerase Chain Reaction, Public Health, Environmental and Occupational Health, Reference Standards, European region, Health Surveys, Diseases -- Causes and theories of causation, Middle East Respiratory Syndrome Coronavirus, RNA, Viral, Disease prevention, business, Coronavirus Infections, Laboratories, Sentinel Surveillance, Sequence Analysis
Abstract

Since September 2012, over 90 cases of respiratory disease caused by a novel coronavirus, now named Middle East respiratory syndrome coronavirus (MERS-CoV), have been reported in the Middle East and Europe. To ascertain the capabilities and testing experience of national reference laboratories across the World Health Organization (WHO) European Region to detect this virus, the European Centre for Disease Prevention and Control (ECDC) and the WHO Regional Office for Europe conducted a joint survey in November 2012 and a follow-up survey in June 2013. In 2013, 29 of 52 responding WHO European Region countries and 24 of 31 countries of the European Union/European Economic Area (EU/EEA) had laboratory capabilities to detect and confirm MERS-CoV cases, compared with 22 of 46 and 18 of 30 countries, respectively, in 2012. By June 2013, more than 2,300 patients had been tested in 23 countries in the WHO European Region with nine laboratory-confirmed MERS-CoV cases. These data indicate that the Region has developed significant capability to detect this emerging virus in accordance with WHO and ECDC guidance. However, not all countries had developed capabilities, and the needs to do so should be addressed. This includes enhancing collaborations between countries to ensure diagnostic capabilities for surveillance of MERS-CoV infections across the European Region., peer-reviewed

Published
2014
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5. Zoonoses et maladies à transmission vectorielle - Surveillance épidémiologique en Belgique: Rapport 2013-2014

Author

Rebolledo, J, Lernout, Tinne, Litzroth, A, Van Beckhoven, D, Brochier, Bernard, Delaere, Bénédicte, Fretin, David, Heuninckx, W, Hing, M, Jacobs, J, Kabamba-Mukadi, Benoît, Maes, P, Mori, M, Patteet, S, Quoilin, S, Saegeman, Veroniek S M V., Suin, V., Truyens, Carine, Vanrompay, D, Van-Esbroeck, Marjan, Van Gucht, Steven, Wattiau, P, Rebolledo, J, Lernout, Tinne, Litzroth, A, Van Beckhoven, D, Brochier, Bernard, Delaere, Bénédicte, Fretin, David, Heuninckx, W, Hing, M, Jacobs, J, Kabamba-Mukadi, Benoît, Maes, P, Mori, M, Patteet, S, Quoilin, S, Saegeman, Veroniek S M V., Suin, V., Truyens, Carine, Vanrompay, D, Van-Esbroeck, Marjan, Van Gucht, Steven, and Wattiau, P

Abstract

info:eu-repo/semantics/published

Published
2015

6. Culture-Based Methods and Molecular Tools for Azole-Resistant Aspergillus fumigatusDetection in a Belgian University Hospital

Author

Montesinos, I., Argudín, M. A., Hites, M., Ahajjam, F., Dodémont, M., Dagyaran, C., Bakkali, M., Etienne, I., Jacobs, F., Knoop, C., Patteet, S., and Lagrou, K.

Abstract

ABSTRACTAzole-resistant Aspergillus fumigatusis an increasing worldwide problem with major clinical implications. Surveillance is warranted to guide clinicians to provide optimal treatment to patients. To investigate azole resistance in clinical Aspergillusisolates in our institution, a Belgian university hospital, we conducted a laboratory-based surveillance between June 2015 and October 2016. Two different approaches were used: a prospective culture-based surveillance using VIPcheck on unselected A. fumigatus(n= 109 patients, including 19 patients with proven or probable invasive aspergillosis [IA]), followed by molecular detection of mutations conferring azole resistance, and a retrospective detection of azole-resistant A. fumigatusin bronchoalveolar lavage fluid using the commercially available AsperGenius PCR (n= 100 patients, including 29 patients with proven or probable IA). By VIPcheck, 25 azole-resistant A. fumigatusspecimens were isolated from 14 patients (12.8%). Of these 14 patients, only 2 had proven or probable IA (10.5%). Mutations at the cyp51Agene were observed in 23 of the 25 A. fumigatusisolates; TR34/L98H was the most prevalent mutation (46.7%), followed by TR46/Y121F/T289A (26.7%). Twenty-seven (27%) patients were positive for the presence of Aspergillusspecies by AsperGenius PCR. A. fumigatuswas detected by AsperGenius in 20 patients, and 3 of these patients carried cyp51Amutations. Two patients had proven or probable IA and cyp51Amutation (11.7%). Our study has shown that the detection of azole-resistant A. fumigatusin clinical isolates was a frequent finding in our institution. Hence, a rapid method for resistance detection may be useful to improve patient management. Centers that care for immunocompromised patients should perform routine surveillance to determine their local epidemiology.

Published
2017
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7. Performance of the new ID-fungi plate using two types of reference libraries (Bruker and MSI) to identify fungi with the Bruker MALDI Biotyper.

Author

Heireman L, Patteet S, and Steyaert S

Subjects
Mycological Typing Techniques, Reference Standards, Arthrodermataceae classification, Arthrodermataceae growth & development, Arthrodermataceae isolation & purification, Culture Media, Fungi classification, Fungi growth & development, Fungi isolation & purification
Abstract

During the last decade, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has revolutionized the diagnosis of fungal infections. Recently, a new Conidia ID-fungi plate (IDFP) medium was introduced to facilitate growth and sampling of fungi. This study aimed to evaluate the IDFP for fungal MALDI-TOF MS identification by comparison with a standard fungal growth medium using two reference libraries. A total of 75 filamentous fungal isolates (including 32 dermatophytes) were inoculated on IDFP and Sabouraud-gentamicin-chloramphenicol (SGC) agar and identified by MALDI-TOF MS using formic acid/acetonitrile extraction. Both the commercially available Bruker library (version 2.0) and the public available MSI web application (version 2018) were applied. For 15% of the isolates, a faster growth was noticed on IDFP compared to SGC. IDFP enhanced the performance of fungal identification compared to SGC for both MSI (increase of 16% identifications to genus and 5% to species level) and Bruker library (increase of 22% identifications to genus and 8% to species level). In total, only 73% of the tested isolates were present in the Bruker library compared to 92% for MSI library. No significant difference (P = 0.46) in MALDI score between IDFP and SGC was observed for the MSI library, but scores were significantly (P = 0.03) higher for IDFP when using Bruker library, potentially explained by the prevention of agar contamination by using IDFP since the Bruker database was created from liquid media. IDFP is a promising alternative growth medium for MALDI-TOF MS fungal identification which would strongly benefit from optimizing the Bruker reference library., (© The Author(s) 2020. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology.)

Published
2020
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8. Beta-d-Glucan for Diagnosing Pneumocystis Pneumonia: a Direct Comparison between the Wako β-Glucan Assay and the Fungitell Assay.

Author

Mercier T, Guldentops E, Patteet S, Beuselinck K, Lagrou K, and Maertens J

Subjects
Biomarkers, Case-Control Studies, Humans, Pneumocystis carinii classification, Pneumocystis carinii genetics, Pneumonia, Pneumocystis microbiology, ROC Curve, Reproducibility of Results, Sensitivity and Specificity, Molecular Diagnostic Techniques methods, Molecular Diagnostic Techniques standards, Pneumonia, Pneumocystis blood, Pneumonia, Pneumocystis diagnosis, beta-Glucans blood
Abstract

Measuring serum beta-d-glucan (BDG) is a useful tool for supporting a quantitative PCR (qPCR)-based diagnosis of suspected Pneumocystis pneumonia (PCP) with bronchoalveolar lavage (BAL) fluid. Since the 2000s, the Fungitell assay was the only BDG assay which was FDA cleared and Conformité Européenne (CE) marked. However, the Wako β-glucan test was also recently CE marked and commercialized. We analyzed archived sera from 116 PCP cases (who were considered to have PCP based on compatible clinical and radiological findings plus a BAL fluid qPCR threshold cycle value of ≤28) and 114 controls (those with a BAL fluid qPCR threshold cycle value of >45 and no invasive fungal infection) using the Fungitell and Wako assays in parallel and assessed their diagnostic performance using the manufacturer's proposed cutoffs of 80 pg/ml and 11 pg/ml, respectively. We found the Wako assay to be more specific (0.98 versus 0.87, P  < 0.001) and the Fungitell assay to be more sensitive (0.78 versus 0.85, P  = 0.039) at the proposed cutoffs. Overall performance, as determined by the area under the receiver operating characteristic curve, was similar for both assays. We determined a new Wako assay cutoff (3.616 pg/ml) to match the sensitivity of the Fungitell assay (0.88 at a cutoff of ≥60 pg/ml). Using this newly proposed cutoff, the specificity of the Wako assay was significantly better than that of the Fungitell assay (0.89 versus 0.82, P  = 0.011). In conclusion, the Wako assay performed excellently compared to the Fungitell assay for the diagnosis of presumed PCP based on qPCR. In addition, contrary to the Fungitell assay, the Wako assay allows for single-sample testing with lower inter- and intrarun variability. Finally, we propose an optimized cutoff for the Wako assay to reliably exclude PCP., (Copyright © 2019 American Society for Microbiology.)

Published
2019
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9. Comparison of two automated immunoassays for the determination of Puumalavirus IgM and IgG.

Author

Muyldermans A, Lagrou K, Patteet S, Van Esbroeck M, Van Ranst M, and Saegeman V

Subjects
Enzyme-Linked Immunosorbent Assay methods, Humans, Sensitivity and Specificity, Antibodies, Viral blood, Automation, Laboratory methods, Diagnostic Tests, Routine methods, Hemorrhagic Fever with Renal Syndrome diagnosis, Immunoglobulin G blood, Immunoglobulin M blood, Puumala virus immunology
Abstract

Background: Puumala virus (PUUV), a member of the genus hantavirus, can cause nephropathia epidemica, a mild form of haemorrhagic fever with renal syndrome. The method of choice for the serodiagnosis of hantavirus infections are enzyme-linked immunosorbent assays (ELISAs)., Objectives: Two commercially available PUUV ELISA kits were compared: Hantavirus (Puumala) IgM/IgG ELISA (Progen, Heidelberg, Germany) and PUUMALA IgM and IgG EIA AutoM (Reagena, Toivala, Finland)., Study Design: The sensitivity of the ELISA kits was evaluated with a panel of 55 serum samples from patients with an acute (n=27) or past (n=28) infection based on Progen or Reagena. A panel of 56 serum samples was composed to evaluate the specificity: samples with potentially false positive Progen Puumala IgM results (n=12), seronegative samples for Puumala IgG/IgM with Progen (n=20), and potentially cross reacting samples (n=24). Discrepancies between the two assays were resolved with strip immunoblot. As measure of agreement between Progen and Reagena results, Cohen kappa coefficient was calculated., Results: Reagena showed a higher specificity (IgM 100%, IgG 100%) than Progen Puumala (IgM 73.21%, IgG 100%). However, Reagena showed a slightly lower sensitivity (IgM 96.15%, IgG 97.78%) compared with Progen (IgM 100%, IgG 100%). Substantial agreement with a Cohen kappa of 0.67 and 0.76 was found between the two assays for Puumala IgM and IgG respectively., Conclusions: This study showed a higher specificity of Reagena in comparison to Progen with a lower sensitivity, probably caused by selection bias. In spite of Reagena's lower sensitivity, no acute infection was missed with this assay., (Copyright © 2014 Elsevier B.V. All rights reserved.)

Published
2014
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