CORDIS

EU research results

CORDIS

COllaborative Management Platform for detection and Analyses of (Re-)emerging and foodborne outbreaks in Europe

Fact Sheet

Reporting

Results

News & Multimedia

Objective

COMPARE aims to harness the rapid advances in molecular technology to improve identification and mitigation of emerging infectious diseases and foodborne outbreaks. To this purpose COMPARE will establish a “One serves all” analytical framework and data exchange platform that will allow real time analysis and interpretation of sequence-based pathogen data in combination with associated data (e.g. clinical, epidemiological data) in an integrated inter-sectorial, interdisciplinary, international, “one health” approach.
The framework will link research, clinical and public health organisations active in human health, animal health, and food safety in Europe and beyond, to develop (i) integrated risk assessment and risk based collection of samples and data, (ii) harmonised workflows for generating comparable sequence and associated data, (iii) state-of-the-art analytical workflows and tools for generating actionable information for support of patient diagnosis, treatment, outbreak detection and -investigation and (iv) risk communication tools.

The analytical workflows will be linked to a flexible, scalable and open-source data- and information platform supporting rapid sharing, interrogation and analysis of sequence-based pathogen data in combination with other associated data. The system will be linked to existing and future complementary systems, networks and databases such as those used by ECDC, NCBI and EFSA. The functionalities of the system will be tested and fine tuned through underpinning research studies on priority pathogens covering healthcare-associated infections, food-borne disease, and (zoonotic) (re-) emerging diseases with epidemic or pandemic potential. Throughout the project, extensive consultations with future users, studies into the barriers to open data sharing, dissemination and training activities and studies on the cost-effectiveness of the system will support future sustainable user uptake.

Programme(s)

H2020-EU.3.1.2. - Preventing disease

Topic(s)

PHC-07-2014 - Improving the control of infectious epidemics and foodborne outbreaks through rapid identification of pathogens

Call for proposal

H2020-PHC-2014-single-stage

See other projects for this call

Funding Scheme

RIA - Research and Innovation action

Leaflet | Map data © OpenStreetMap contributors, Credit: EC-GISCO, © EuroGeographics for the administrative boundaries

Coordinator

DANMARKS TEKNISKE UNIVERSITET

Address

Anker Engelundsvej 1 Bygning 101 A
2800 Kgs Lyngby

Denmark

Activity type

Higher or Secondary Education Establishments

EU Contribution

€ 3 006 000

Website

Contact the organisation

Participants (30)

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ERASMUS UNIVERSITAIR MEDISCH CENTRUM ROTTERDAM

Netherlands

EU Contribution

€ 2 656 641

STATENS SERUM INSTITUT

Denmark

EU Contribution

€ 919 750

FRIEDRICH LOEFFLER INSTITUT - BUNDESFORSCHUNGSINSTITUT FUER TIERGESUNDHEIT

Germany

EU Contribution

€ 1 000 000

AGENCE NATIONALE DE LA SECURITE SANITAIRE DE L ALIMENTATION DE L ENVIRONNEMENT ET DU TRAVAIL

France

EU Contribution

€ 601 250

ROBERT KOCH-INSTITUT

Germany

EU Contribution

€ 718 000

EUROPEAN MOLECULAR BIOLOGY LABORATORY

Germany

EU Contribution

€ 1 950 000

ISTITUTO SUPERIORE DI SANITA

Italy

EU Contribution

€ 603 125

RIJKSINSTITUUT VOOR VOLKSGEZONDHEID EN MILIEU

Netherlands

EU Contribution

€ 759 500

THE SECRETARY OF STATE FOR ENVIRONMENT, FOOD AND RURAL AFFAIRS

United Kingdom

EU Contribution

€ 971 361,25

THE UNIVERSITY OF EDINBURGH

United Kingdom

EU Contribution

€ 697 258,75

UNIVERSITAETSKLINIKUM BONN

Germany

EU Contribution

€ 172 675,30

Academisch Medisch Centrum bij de Universiteit van Amsterdam

Netherlands

EU Contribution

€ 602 795

UNIVERSITEIT ANTWERPEN

Belgium

EU Contribution

€ 402 500

ARTEMIS ONE HEALTH RESEARCH BV

Netherlands

EU Contribution

€ 306 250

THE CHANCELLOR MASTERS AND SCHOLARS OF THE UNIVERSITY OF CAMBRIDGE

United Kingdom

EU Contribution

€ 504 057,50

STIFTUNG TIERAERZTLICHE HOCHSCHULE HANNOVER

Germany

EU Contribution

€ 403 750

UNIVERSIDAD DE CASTILLA - LA MANCHA

Spain

EU Contribution

€ 400 750

FONDATION MERIEUX

France

EU Contribution

€ 428 830

ARISTOTELIO PANEPISTIMIO THESSALONIKIS

Greece

EU Contribution

€ 353 750

INSTITUT FRANCAIS DE RECHERCHE POUR L'EXPLOITATION DE LA MER

France

EU Contribution

€ 401 807,50

ERASMUS UNIVERSITEIT ROTTERDAM

Netherlands

EU Contribution

€ 438 516,25

THE AUSTRALIAN NATIONAL UNIVERSITY

Australia

MAGYAR TUDOMANYOS AKADEMIA WIGNER FIZIKAI KUTATOKOZPONT

Hungary

EU Contribution

€ 403 750

CIVIC CONSULTING GMBH

Germany

EU Contribution

€ 434 531,25

CIVIC CONSULTING ALLEWELDT & KARA GBR

Germany

RESPONSIBLE TECHNOLOGY

France

EU Contribution

€ 411 387,50

ALMA MATER STUDIORUM - UNIVERSITA DI BOLOGNA

Italy

EU Contribution

€ 434 181,25

LEIBNIZ-INSTITUT DSMZ-DEUTSCHE SAMMLUNG VON MIKROORGANISMEN UND ZELLKULTUREN GMBH

Germany

EU Contribution

€ 403 770

GENOME RESEARCH LIMITED

United Kingdom

EU Contribution

€ 200 000

CHARITE - UNIVERSITAETSMEDIZIN BERLIN

Germany

EU Contribution

€ 231 583,45

Project information

COMPARE

Grant agreement ID: 643476

Project website

Status

Ongoing project

Start date

1 December 2014
End date

30 November 2019

Funded under:

H2020-EU.3.1.2.

Overall budget:

€ 20 847 771
EU contribution

€ 20 817 771

Coordinated by:

DANMARKS TEKNISKE UNIVERSITET

Denmark

Periodic Reporting for period 2 - COMPARE (COllaborative Management Platform for detection and Analyses of (Re-)emerging and foodborne outbreaks in Europe)

Reporting period: 2016-06-01 to 2017-11-30

Summary of the context and overall objectives of the project

COMPARE is a multidisciplinary research network that envisions a globally linked data and information sharing platform system for the rapid identification, containment and mitigation of emerging infectious diseases and foodborne outbreaks. The system will collect, process and analyse sequence-based pathogen data in combination with associated (clinical, epidemiological and other) data for the generation of actionable information to relevant authorities and other users in the human health, animal health and food safety domains. COMPARE aims to make as much data as possible publicly available and will thus, contribute significantly to global Open Science.

The Specific Objectives of COMPARE include the following:
A. Risk-assessment models and risk-based sampling and data collection strategies that enhance our capacity to detect potential disease outbreaks;
B. From samples and associated metadata to comparable data: harmonised standards for sample processing and sequencing to obtain high quality and comparable sequence data from and metadata associated with a specimen;
C. From comparable data to actionable information: designing analytical workflows for turning comparable data into actionable information for addressing questions in frontline diagnostics, foodborne infections and (re-) emerging infections.
o Frontline diagnostics
o Public health
o (Re)-emerging infections research
D. Designing and building a common data and information platform supporting rapid sharing, integration and analysis of sequence-based pathogen data in combination with other contextual metadata; The system will be linked to existing and future complementary systems, networks and databases such as those used by ECDC, NCBI and EFSA.
E. Risk communication tools will be developed enabling authorities in the human and animal health and food safety sectors to effectively communicate the results obtained.
F. Studies on the barriers (ethical, regulatory, administrative, logistical, political) to the implementation and widespread use of open-data sharing platforms
G. Development of a framework for estimating the cost-effectiveness of the COMPARE system, including the value of safety.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

Genomic information as the pathogen-independent language

Project information

COMPARE

Grant agreement ID: 643476

Project website

Status

Ongoing project

Start date

1 December 2014
End date

30 November 2019

Funded under:

H2020-EU.3.1.2.

Overall budget:

€ 20 847 771
EU contribution

€ 20 817 771

Coordinated by:

DANMARKS TEKNISKE UNIVERSITET

Deliverables

Documents, reports (6)

Matrix-dependent sample handling protocols

D2.1 Matrix-dependent sample handling protocols for human, animal, wildlife/vectors and food samples (M12)

Algorithm for detection of informative (sub)types

D4.2 Algorithm for detection of informative (sub)types for epidemiological analysis and RA for the main foodborne pathogens (M32)

Prediction algorithm AMR markers

D3.2 Prediction algorithm for antimicrobial resistance markers in sequence data (M24)

Sequencing workflow

D2.3 Sequencing workflow including relevant NGS platforms (M36)

Methodologies report

D14.2 State-of-the-art methodologies for the measurement and valuation of the elements specified in the framework. This will include a section on the system itself and on the wider framework (Month 30);

Standard protocol sample processing

D2.2 Standard protocol for sample processing (M24)

Other (5)

CE Framework

D14.1 Framework for assessing cost-effectiveness of COMPARE in which key costs and benefits are highlighted. This will include a section on the system itself and on the wider framework (Month 18);

Phylogenetic and phylogeographic tools

D5.3 Phylogenetic and phylogeographic tools for epidemiological investigations and rapid risk assessment (M30)

Analytical workflow for clinical diagnostic application

D3.1 Analytical workflow for clinical diagnostic application (M18)

Automated tools for rapid assessment of key transmission parameters

D1.1 Automated tools for rapid assessment of key transmission parameters and rates of spread estimates (M24)

Data analysis pipeline

D2.4 Evaluated and documented data analysis pipeline (M24 and onwards)

Websites, patent fillings, videos etc. (2)

Public website

D13.3 COMPARE public website (month 3);

Leaflet and templates

D13.2 Leaflet and templates for promotional material in COMPARE corporate style (month 3);

Publications

Peer reviewed articles (158)

Next-generation sequencing of five new avian paramyxoviruses 8 isolates from Kazakhstan indicates a low genetic evolution rate over four decades

Author(s): Sasan Fereidouni, M. Jenckel, A. Seidalina, K. Karamendin, M. Beer, E. Starick, S. Asanova, E. Kasymbekov, M. Sayatov, A. Kydyrmanov

Published in: Archives of Virology, Issue 163/2, 2018, Page(s) 331-336, ISSN 0304-8608

DOI: 10.1007/s00705-017-3593-9

Complete Genome Sequence of a Porcine Epidemic Diarrhea S Gene Indel Strain Isolated in France in December 2014

Author(s): Béatrice Grasland, Lionel Bigault, Cécilia Bernard, Hélène Quenault, Olivier Toulouse, Christelle Fablet, Nicolas Rose, Fabrice Touzain, Yannick Blanchard

Published in: Genome Announcements, Issue 3/3, 2015, Page(s) e00535-15, ISSN 2169-8287

DOI: 10.1128/genomeA.00535-15

Comparative Genomics of Field Isolates of Mycobacterium bovis and M. caprae Provides Evidence for Possible Correlates with Bacterial Viability and Virulence

Author(s): José de la Fuente, Iratxe Díez-Delgado, Marinela Contreras, Joaquín Vicente, Alejandro Cabezas-Cruz, Raquel Tobes, Marina Manrique, Vladimir López, Beatriz Romero, Javier Bezos, Lucas Dominguez, Iker A. Sevilla, Joseba M. Garrido, Ramón Juste, Guillermo Madico, Edward Jones-López, Christian Gortazar

Published in: PLOS Neglected Tropical Diseases, Issue 9/11, 2015, Page(s) e0004232, ISSN 1935-2735

DOI: 10.1371/journal.pntd.0004232

Meta-genomic analysis of toilet waste from long distance flights; a step towards global surveillance of infectious diseases and antimicrobial resistance

Author(s): Thomas Nordahl Petersen, Simon Rasmussen, Henrik Hasman, Christian Carøe, Jacob Bælum, Anna Charlotte Schultz, Lasse Bergmark, Christina A. Svendsen, Ole Lund, Thomas Sicheritz-Pontén, Frank M. Aarestrup

Published in: Scientific Reports, Issue 5, 2015, Page(s) 11444, ISSN 2045-2322

DOI: 10.1038/srep11444

Evaluating next-generation sequencing for direct clinical diagnostics in diarrhoeal disease

Author(s): K. G. Joensen, A. L. Ø. Engsbro, O. Lukjancenko, R. S. Kaas, O. Lund, H. Westh, F. M. Aarestrup

Published in: European Journal of Clinical Microbiology & Infectious Diseases, Issue 36/7, 2017, Page(s) 1325-1338, ISSN 0934-9723

DOI: 10.1007/s10096-017-2947-2

Comparison of six commercial kits to extract bacterial chromosome and plasmid DNA for MiSeq sequencing

Author(s): Laura Becker, Matthias Steglich, Stephan Fuchs, Guido Werner, Ulrich Nübel

Published in: Scientific Reports, Issue 6, 2016, Page(s) 28063, ISSN 2045-2322

DOI: 10.1038/srep28063

Porcine Epidemic Diarrhea in Europe: In-Detail Analyses of Disease Dynamics and Molecular Epidemiology

Author(s): Dennis Hanke, Anne Pohlmann, Carola Sauter-Louis, Dirk Höper, Julia Stadler, Mathias Ritzmann, Adi Steinrigl, Bernd-Andreas Schwarz, Valerij Akimkin, Robert Fux, Sandra Blome, Martin Beer

Published in: Viruses, Issue 9/7, 2017, Page(s) 177, ISSN 1999-4915

DOI: 10.3390/v9070177

Virus genomes reveal factors that spread and sustained the Ebola epidemic

Author(s): Gytis Dudas, Luiz Max Carvalho, Trevor Bedford, Andrew J. Tatem, Guy Baele, Nuno R. Faria, Daniel J. Park, Jason T. Ladner, Armando Arias, Danny Asogun, Filip Bielejec, Sarah L. Caddy, Matthew Cotten, Jonathan D’Ambrozio, Simon Dellicour, Antonino Di Caro, Joseph W. Diclaro, Sophie Duraffour, Michael J. Elmore, Lawrence S. Fakoli, Ousmane Faye, Merle L. Gilbert, Sahr M. Gevao, Stephen Gire, Adrianne Gladden-Young, Andreas Gnirke, Augustine Goba, Donald S. Grant, Bart L. Haagmans, Julian A. Hiscox, Umaru Jah, Jeffrey R. Kugelman, Di Liu, Jia Lu, Christine M. Malboeuf, Suzanne Mate, David A. Matthews, Christian B. Matranga, Luke W. Meredith, James Qu, Joshua Quick, Suzan D. Pas, My V. T. Phan, Georgios Pollakis, Chantal B. Reusken, Mariano Sanchez-Lockhart, Stephen F. Schaffner, John S. Schieffelin, Rachel S. Sealfon, Etienne Simon-Loriere, Saskia L. Smits, Kilian Stoecker, Lucy Thorne, Ekaete Alice Tobin, Mohamed A. Vandi, Simon J. Watson, Kendra West, Shannon Whitmer, Michael R. Wiley, Sarah M. Winnicki, Shirlee Wohl, Roman Wölfel, Nathan L. Yozwiak, Kristian G. Andersen, Sylvia O. Blyden, Fatorma Bolay, Miles W. Carroll, Bernice Dahn, Boubacar Diallo, Pierre Formenty, Christophe Fraser, George F. Gao, Robert F. Garry, Ian Goodfellow, Stephan Günther, Christian T. Happi, Edward C. Holmes, Brima Kargbo, Sakoba Keïta, Paul Kellam, Marion P. G. Koopmans, Jens H. Kuhn, Nicholas J. Loman, N’Faly Magassouba, Dhamari Naidoo, Stuart T. Nichol, Tolbert Nyenswah, Gustavo Palacios, Oliver G. Pybus, Pardis C. Sabeti, Amadou Sall, Ute Ströher, Isatta Wurie, Marc A. Suchard, Philippe Lemey, Andrew Rambaut

Published in: Nature, Issue 544/7650, 2017, Page(s) 309-315, ISSN 0028-0836

DOI: 10.1038/nature22040

PulseNet International: Vision for the implementation of whole genome sequencing (WGS) for global food-borne disease surveillance

Author(s): Celine Nadon, Ivo Van Walle, Peter Gerner-Smidt, Josefina Campos, Isabel Chinen, Jeniffer Concepcion-Acevedo, Brent Gilpin, Anthony M. Smith, Kai Man Kam, Enrique Perez, Eija Trees, Kristy Kubota, Johanna Takkinen, Eva Møller Nielsen, Heather Carleton

Published in: Eurosurveillance, Issue 22/23, 2017, ISSN 1025-496X

DOI: 10.2807/1560-7917.ES.2017.22.23.30544

Dissemination of the mcr-1 colistin resistance gene

Author(s): Maris S Arcilla, Jarne M van Hattem, Sebastien Matamoros, Damian C Melles, John Penders, Menno D de Jong, Constance Schultsz

Published in: The Lancet Infectious Diseases, Issue 16/2, 2016, Page(s) 147-149, ISSN 1473-3099

DOI: 10.1016/S1473-3099(15)00541-1

Genome Target Evaluator (GTEvaluator): A workflow exploiting genome dataset to measure the sensitivity and specificity of genetic markers

Author(s): Arnaud Felten, Laurent Guillier, Nicolas Radomski, Michel-Yves Mistou, Renaud Lailler, Sabrina Cadel-Six

Published in: PLOS ONE, Issue 12/7, 2017, Page(s) e0182082, ISSN 1932-6203

DOI: 10.1371/journal.pone.0182082

Machine Learning Methods as a Tool for Predicting Risk of Illness Applying Next‐Generation Sequencing Data

Author(s): Patrick Murigu Kamau Njage Clementine Henri Pimlapas Leekitcharoenphon Michel‐Yves Mistou Rene S. Hendriksen Tine Hald

Published in: Risk Analysis, Issue 2018, 2018, ISSN 0272-4332

DOI: 10.1111/risa.13239

Influenza A (H10N7) Virus Causes Respiratory Tract Disease in Harbor Seals and Ferrets

Author(s): Judith M. A. van den Brand, Peter Wohlsein, Sander Herfst, Rogier Bodewes, Vanessa M. Pfankuche, Marco W. G. van de Bildt, Frauke Seehusen, Christina Puff, Mathilde Richard, Ursula Siebert, Kristina Lehnert, Theo Bestebroer, Pascal Lexmond, Ron A. M. Fouchier, Ellen Prenger-Berninghoff, Werner Herbst, Marion Koopmans, Albert D. M. E. Osterhaus, Thijs Kuiken, Wolfgang Baumgärtner

Published in: PLOS ONE, Issue 11/7, 2016, Page(s) e0159625, ISSN 1932-6203

DOI: 10.1371/journal.pone.0159625

Fatal Encephalitic Borna Disease Virus 1 in Solid-Organ Transplant Recipients

Author(s): Kore Schlottau, Leonie Forth, Klemens Angstwurm, Dirk Höper, Daniel Zecher, Friederike Liesche, Bernd Hoffmann, Victoria Kegel, Daniel Seehofer, Sabine Platen, Bernd Salzberger, Uwe G. Liebert, Hans-Helmut Niller, Barbara Schmidt, Kaspar Matiasek, Markus J. Riemenschneider, Christoph Brochhausen, Bernhard Banas, Lutz Renders, Philipp Moog, Silke Wunderlich, Christian L. Seifert, Ana Barreiros, Axel Rahmel, Jutta Weiss, Dennis Tappe, Christiane Herden, Jonas Schmidt-Chanasit, Martin Schwemmle, Dennis Rubbenstroth, Jürgen Schlegel, Corinna Pietsch, Donata Hoffmann, Jonathan Jantsch, Martin Beer

Published in: New England Journal of Medicine, Issue 379/14, 2018, Page(s) 1377-1379, ISSN 0028-4793

DOI: 10.1056/NEJMc1803115

Discovery and diagnosis of new viral pathogens: proposal for a generic workflow based on next-generation sequencing and new integrated data analysis approaches

Author(s): Dirk Höper, Anne Pohlmann

Published in: Euroreference, Issue Euroreference 1 - June 2016 METHOD, 2016, Page(s) 58-62, ISSN 2110-5294

The evolution of Ebola virus: Insights from the 2013–2016 epidemic

Author(s): Edward C. Holmes, Gytis Dudas, Andrew Rambaut, Kristian G. Andersen

Published in: Nature, Issue 538/7624, 2016, Page(s) 193-200, ISSN 0028-0836

DOI: 10.1038/nature19790

Cross host transmission in the emergence of MERS coronavirus

Author(s): Chantal BEM Reusken, V Stalin Raj, Marion P Koopmans, Bart L Haagmans

Published in: Current Opinion in Virology, Issue 16, 2016, Page(s) 55-62, ISSN 1879-6257

DOI: 10.1016/j.coviro.2016.01.004

Using genomics data to reconstruct transmission trees during disease outbreaks

Author(s): M.D. HALL, M.E.J. WOOLHOUSE, A. RAMBAUT

Published in: Revue Scientifique et Technique de l'OIE, Issue 35/1, 2016, Page(s) 287-296, ISSN 0253-1933

DOI: 10.20506/rst.35.1.2433

A generic framework for spatial quantitative risk assessments of infectious diseases: Lumpy skin disease case study

Author(s): Rachel A. Taylor, Alexander D. C. Berriman, Paul Gale, Louise A. Kelly, Emma L. Snary

Published in: Transboundary and Emerging Diseases, 2018, ISSN 1865-1674

DOI: 10.1111/tbed.12993

Metagenomic approaches to identifying infectious agents

Author(s): D. HÖPER, T.C. METTENLEITER, M. BEER

Published in: Revue Scientifique et Technique de l'OIE, Issue 35/1, 2016, Page(s) 83-93, ISSN 0253-1933

DOI: 10.20506/rst.35.1.2419

Low Virulence and Lack of Airborne Transmission of the Dutch Highly Pathogenic Avian Influenza Virus H5N8 in Ferrets

Author(s): Mathilde Richard, Sander Herfst, Judith M. A. van den Brand, Pascal Lexmond, Theo M. Bestebroer, Guus F. Rimmelzwaan, Marion Koopmans, Thijs Kuiken, Ron A. M. Fouchier

Published in: PLOS ONE, Issue 10/6, 2015, Page(s) e0129827, ISSN 1932-6203

DOI: 10.1371/journal.pone.0129827

Molecular epidemiology of Crimean-Congo hemorrhagic fever in Bulgaria-An update

Author(s): Anna Papa, Styliani Pappa, Elitsa Panayotova, Elpida Papadopoulou, Iva Christova

Published in: Journal of Medical Virology, Issue 88/5, 2016, Page(s) 769-773, ISSN 0146-6615

DOI: 10.1002/jmv.24400

Fast and accurate mutation detection in whole genome sequences of multiple isogenic samples with IsoMut

Author(s): O. Pipek, D. Ribli, J. Molnár, Á. Póti, M. Krzystanek, A. Bodor, G. E. Tusnády, Z. Szallasi, I. Csabai, D. Szüts

Published in: BMC Bioinformatics, Issue 18/1, 2017, ISSN 1471-2105

DOI: 10.1186/s12859-017-1492-4

Dual Emergence of Usutu Virus in Common Blackbirds, Eastern France, 2015

Author(s): Sylvie Lecollinet, Yannick Blanchard, Christine Manson, Steeve Lowenski, Eve Laloy, Hélène Quenault, Fabrice Touzain, Pierrick Lucas, Cyril Eraud, Céline Bahuon, Stéphan Zientara, Cécile Beck, Anouk Decors

Published in: Emerging Infectious Diseases, Issue 22/12, 2016, Page(s) 2225-2225, ISSN 1080-6040

DOI: 10.3201/eid2212.161272

Comparison of norovirus genogroup I, II and IV seroprevalence among children in the Netherlands, 1963, 1983 and 2006

Author(s): Janko van Beek, Miranda de Graaf, Ming Xia, Xi Jiang, Jan Vinjé, Mathias Beersma, Erwin de Bruin, David van de Vijver, Melle Holwerda, Marlies van Houten, Annemarie M. Buisman, Rob van Binnendijk, Albert D. M. E. Osterhaus, Fiona van der Klis, Harry Vennema, Marion P. G. Koopmans

Published in: Journal of General Virology, Issue 97/9, 2016, Page(s) 2255-2264, ISSN 0022-1317

DOI: 10.1099/jgv.0.000533

A single amino acid change in the non-structural NV protein impacts the virulence phenotype of Viral hemorrhagic septicemia virus in trout

Author(s): Laury Baillon, Emilie Mérour, Joëlle Cabon, Lénaïg Louboutin, Hélène Quenault, Fabrice Touzain, Thierry Morin, Yannick Blanchard, Stéphane Biacchesi, Michel Brémont

Published in: Journal of General Virology, Issue 98/6, 2017, Page(s) 1181-1184, ISSN 0022-1317

DOI: 10.1099/jgv.0.000830

Zika virus evolution and spread in the Americas

Author(s): Hayden C. Metsky, Christian B. Matranga, Shirlee Wohl, Stephen F. Schaffner, Catherine A. Freije, Sarah M. Winnicki, Kendra West, James Qu, Mary Lynn Baniecki, Adrianne Gladden-Young, Aaron E. Lin, Christopher H. Tomkins-Tinch, Simon H. Ye, Daniel J. Park, Cynthia Y. Luo, Kayla G. Barnes, Rickey R. Shah, Bridget Chak, Giselle Barbosa-Lima, Edson Delatorre, Yasmine R. Vieira, Lauren M. Paul, Amanda L. Tan, Carolyn M. Barcellona, Mario C. Porcelli, Chalmers Vasquez, Andrew C. Cannons, Marshall R. Cone, Kelly N. Hogan, Edgar W. Kopp, Joshua J. Anzinger, Kimberly F. Garcia, Leda A. Parham, Rosa M. Gélvez Ramírez, Maria C. Miranda Montoya, Diana P. Rojas, Catherine M. Brown, Scott Hennigan, Brandon Sabina, Sarah Scotland, Karthik Gangavarapu, Nathan D. Grubaugh, Glenn Oliveira, Refugio Robles-Sikisaka, Andrew Rambaut, Lee Gehrke, Sandra Smole, M. Elizabeth Halloran, Luis Villar, Salim Mattar, Ivette Lorenzana, Jose Cerbino-Neto, Clarissa Valim, Wim Degrave, Patricia T. Bozza, Andreas Gnirke, Kristian G. Andersen, Sharon Isern, Scott F. Michael, Fernando A. Bozza, Thiago M. L. Souza, Irene Bosch, Nathan L. Yozwiak, Bronwyn L. MacInnis, Pardis C. Sabeti

Published in: Nature, Issue 546/7658, 2017, Page(s) 411-415, ISSN 0028-0836

DOI: 10.1038/nature22402

Ιnfluenza A(H3N2) genetic variants in vaccinated patients in northern Greece

Author(s): A. Melidou, G. Gioula, M. Exindari, E. Ioannou, K. Gkolfinopoulou, T. Georgakopoulou, S. Tsiodras, A. Papa

Published in: Journal of Clinical Virology, Issue 94, 2017, Page(s) 29-32, ISSN 1386-6532

DOI: 10.1016/j.jcv.2017.07.003

A retrospective molecular study of Cryptosporidium species and genotypes in HIV-infected patients from Thailand

Author(s): Anna Rosa Sannella, Yupin Suputtamongkol, Ekkarat Wongsawat, Simone M. Cacciò

Published in: Parasites & Vectors, Issue 12/1, 2019, ISSN 1756-3305

DOI: 10.1186/s13071-019-3348-4

Pathological findings in the red fox (Vulpes vulpes), stone marten (Martes foina) and raccoon dog (Nyctereutes procyonoides), with special emphasis on infectious and zoonotic agents in Northern Germany

Author(s): Charlotte Lempp, Nicole Jungwirth, Miguel L. Grilo, Anja Reckendorf, Arlena Ulrich, Abbo van Neer, Rogier Bodewes, Vanessa M. Pfankuche, Christian Bauer, Albert D. M. E. Osterhaus, Wolfgang Baumgärtner, Ursula Siebert

Published in: PLOS ONE, Issue 12/4, 2017, Page(s) e0175469, ISSN 1932-6203

DOI: 10.1371/journal.pone.0175469

Assessing the Epidemic Potential of RNA and DNA Viruses

Author(s): Mark E.J. Woolhouse, Liam Brierley, Chris McCaffery, Sam Lycett

Published in: Emerging Infectious Diseases, Issue 22/12, 2016, Page(s) 2037-2044, ISSN 1080-6040

DOI: 10.3201/eid2212.160123

Improving hazard characterization in microbial risk assessment using next generation sequencing data and machine learning: Predicting clinical outcomes in shigatoxigenic Escherichia coli

Author(s): Patrick Murigu Kamau Njage, Pimlapas Leekitcharoenphon, Tine Hald

Published in: International Journal of Food Microbiology, Issue 292, 2019, Page(s) 72-82, ISSN 0168-1605

DOI: 10.1016/j.ijfoodmicro.2018.11.016

Genomic epidemiology reveals multiple introductions of Zika virus into the United States

Author(s): Nathan D. Grubaugh, Jason T. Ladner, Moritz U. G. Kraemer, Gytis Dudas, Amanda L. Tan, Karthik Gangavarapu, Michael R. Wiley, Stephen White, Julien Thézé, Diogo M. Magnani, Karla Prieto, Daniel Reyes, Andrea M. Bingham, Lauren M. Paul, Refugio Robles-Sikisaka, Glenn Oliveira, Darryl Pronty, Carolyn M. Barcellona, Hayden C. Metsky, Mary Lynn Baniecki, Kayla G. Barnes, Bridget Chak, Catherine A. Freije, Adrianne Gladden-Young, Andreas Gnirke, Cynthia Luo, Bronwyn MacInnis, Christian B. Matranga, Daniel J. Park, James Qu, Stephen F. Schaffner, Christopher Tomkins-Tinch, Kendra L. West, Sarah M. Winnicki, Shirlee Wohl, Nathan L. Yozwiak, Joshua Quick, Joseph R. Fauver, Kamran Khan, Shannon E. Brent, Robert C. Reiner, Paola N. Lichtenberger, Michael J. Ricciardi, Varian K. Bailey, David I. Watkins, Marshall R. Cone, Edgar W. Kopp, Kelly N. Hogan, Andrew C. Cannons, Reynald Jean, Andrew J. Monaghan, Robert F. Garry, Nicholas J. Loman, Nuno R. Faria, Mario C. Porcelli, Chalmers Vasquez, Elyse R. Nagle, Derek A. T. Cummings, Danielle Stanek, Andrew Rambaut, Mariano Sanchez-Lockhart, Pardis C. Sabeti, Leah D. Gillis, Scott F. Michael, Trevor Bedford, Oliver G. Pybus, Sharon Isern, Gustavo Palacios, Kristian G. Andersen

Published in: Nature, Issue 546/7658, 2017, Page(s) 401-405, ISSN 0028-0836

DOI: 10.1038/nature22400

Development and preliminary evaluation of a multiplexed amplification and next generation sequencing method for viral hemorrhagic fever diagnostics

Author(s): Annika Brinkmann, Koray Ergünay, Aleksandar Radonić, Zeliha Kocak Tufan, Cristina Domingo, Andreas Nitsche

Published in: PLOS Neglected Tropical Diseases, Issue 11/11, 2017, Page(s) e0006075, ISSN 1935-2727

DOI: 10.1371/journal.pntd.0006075

Emerging arboviral human diseases in Southern Europe

Author(s): Anna Papa

Published in: Journal of Medical Virology, Issue 89/8, 2017, Page(s) 1315-1322, ISSN 0146-6615

DOI: 10.1002/jmv.24803

Transmission patterns and evolution of respiratory syncytial virus in a community outbreak identified by genomic analysis

Author(s): Charles N. Agoti, Patrick K. Munywoki, My V. T. Phan, James R. Otieno, Everlyn Kamau, Anne Bett, Ivy Kombe, George Githinji, Graham F. Medley, Patricia A. Cane, Paul Kellam, Matthew Cotten, D. James Nokes

Published in: Virus Evolution, Issue 3/1, 2017, ISSN 2057-1577

DOI: 10.1093/ve/vex006

Human Clade 2.3.4.4 A/H5N6 Influenza Virus Lacks Mammalian Adaptation Markers and Does Not Transmit via the Airborne Route between Ferrets

Author(s): Sander Herfst, Chris K. P. Mok, Judith M. A. van den Brand, Stefan van der Vliet, Miruna E. Rosu, Monique I. Spronken, Zifeng Yang, Dennis de Meulder, Pascal Lexmond, Theo M. Bestebroer, J. S. Malik Peiris, Ron A. M. Fouchier, Mathilde Richard

Published in: mSphere, Issue 3/1, 2018, Page(s) e00405-17, ISSN 2379-5042

DOI: 10.1128/mSphere.00405-17

Lack of virological and serological evidence for continued circulation of highly pathogenic avian influenza H5N8 virus in wild birds in the Netherlands, 14 November 2014 to 31 January 2016

Author(s): Marjolein J Poen, Josanne H Verhagen, Ruth J Manvell, Ian Brown, Theo M Bestebroer, Stefan van der Vliet, Oanh Vuong, Rachel D Scheuer, Henk P van der Jeugd, Bart A Nolet, Erik Kleyheeg, Gerhard J D M Müskens, Frank A Majoor, Christian Grund, Ron A M Fouchier

Published in: Eurosurveillance, Issue 21/38, 2016, ISSN 1025-496X

DOI: 10.2807/1560-7917.ES.2016.21.38.30349

One Health training and research activities in Western Europe

Author(s): Reina Sikkema, Marion Koopmans

Published in: Infection Ecology & Epidemiology, Issue 6/1, 2016, Page(s) 33703, ISSN 2000-8686

DOI: 10.3402/iee.v6.33703

Detection of mcr-1 encoding plasmid-mediated colistin-resistant Escherichia coli isolates from human bloodstream infection and imported chicken meat, Denmark 2015

Author(s): Henrik Hasman, Anette M. Hammerum, Frank Hansen, Rene S. Hendriksen, Bente Olesen, Yvonne Agersø, Ea Zankari, Pimlapas Leekitcharoenphon, Marc Stegger, Rolf S. Kaas, Lina M. Cavaco, Dennis S. Hansen, Frank M. Aarestrup, Robert L. Skov

Published in: Eurosurveillance, Issue 20/49, 2015, ISSN 1025-496X

DOI: 10.2807/1560-7917.ES.2015.20.49.30085

Identification of a novel plasmid-mediated colistin-resistance gene, mcr-2 , in Escherichia coli , Belgium, June 2016

Author(s): Basil Britto Xavier, Christine Lammens, Rohit Ruhal, Samir Kumar-Singh, Patrick Butaye, Herman Goossens, Surbhi Malhotra-Kumar

Published in: Eurosurveillance, Issue 21/27, 2016, ISSN 1025-496X

DOI: 10.2807/1560-7917.ES.2016.21.27.30280

A novel alphaherpesvirus associated with fatal diseases in banded Penguins

Author(s): Florian Pfaff, Christoph Schulze, Patricia König, Kati Franzke, Sabine Bock, Andreas Hlinak, Jens Kämmerling, Andreas Ochs, André Schüle, Thomas C. Mettenleiter, Dirk Höper1, Martin Beer

Published in: Journal of General Virology, Issue 98/1, 2017, Page(s) 89-95, ISSN 0022-1317

DOI: 10.1099/jgv.0.000698

Prevalence of Staphylococcus aureus and of methicillin-resistant S. aureus (MRSA) along the production chain of dairy products in north-western Greece

Author(s): Panagiotis Papadopoulos, Theofilos Papadopoulos, Apostolos S. Angelidis, Evridiki Boukouvala, Antonios Zdragas, Anna Papa, Christos Hadjichristodoulou, Daniel Sergelidis

Published in: Food Microbiology, Issue 69, 2018, Page(s) 43-50, ISSN 0740-0020

DOI: 10.1016/j.fm.2017.07.016

Presence of atypical porcine pestivirus (APPV) genomes in newborn piglets correlates with congenital tremor

Author(s): Alexander Postel, Florian Hansmann, Christine Baechlein, Nicole Fischer, Malik Alawi, Adam Grundhoff, Sarah Derking, Jörg Tenhündfeld, Vanessa Maria Pfankuche, Vanessa Herder, Wolfgang Baumgärtner, Michael Wendt, Paul Becher

Published in: Scientific Reports, Issue 6, 2016, Page(s) 27735, ISSN 2045-2322

DOI: 10.1038/srep27735

Role for migratory wild birds in the global spread of avian influenza H5N8

Author(s): The Global Consortium for H5N8 and Related Influenza Viruses

Published in: Science, Issue 354/6309, 2016, Page(s) 213-217, ISSN 0036-8075

DOI: 10.1126/science.aaf8852

Wild bird surveillance around outbreaks of highly pathogenic avian influenza A(H5N8) virus in the Netherlands, 2014, within the context of global flyways

Author(s): J Verhagen, H van der Jeugd, B Nolet, R Slaterus, S Kharitonov, P de Vries, O Vuong, F Majoor, T Kuiken, R Fouchier

Published in: Eurosurveillance, Issue 20/12, 2015, Page(s) 21069, ISSN 1560-7917

DOI: 10.2807/1560-7917.ES2015.20.12.21069

Outbreaks among Wild Birds and Domestic Poultry Caused by Reassorted Influenza A(H5N8) Clade 2.3.4.4 Viruses, Germany, 2016

Author(s): Anne Pohlmann, Elke Starick, Timm Harder, Christian Grund, Dirk Höper, Anja Globig, Christoph Staubach, Klaas Dietze, Günter Strebelow, Reiner G. Ulrich, Jan Schinköthe, Jens P. Teifke, Franz J. Conraths, Thomas C. Mettenleiter, Martin Beer

Published in: Emerging Infectious Diseases, Issue 23/4, 2017, Page(s) 633-636, ISSN 1080-6040

DOI: 10.3201/eid2304.161949

Developing a framework to assess the costeffectiveness of COMPARE – a global platform for the exchange of sequence-based pathogen data

Author(s): F. ALLEWELDT, S. KARA, A. OSINSKI, P. VAN BAAL, K. KELLERBORG, F.M. AARESTRUP, M. KOOPMANS

Published in: Revue Scientifique et Technique de l'OIE, Issue 36/1, 2017, Page(s) 311-322, ISSN 0253-1933

DOI: 10.20506/rst.36.1.2631

The challenge of detecting indels in bacterial genomes from short-read sequencing data

Author(s): Matthias Steglich, Ulrich Nübel

Published in: Journal of Biotechnology, Issue 250, 2017, Page(s) 11-15, ISSN 0168-1656

DOI: 10.1016/j.jbiotec.2017.02.026

Human influence and biotic homogenization drive the distribution of Escherichia coli virulence genes in natural habitats

Author(s): Adriana Cabal, Joaquin Vicente, Julio Alvarez, Jose Angel Barasona, Mariana Boadella, Lucas Dominguez, Christian Gortazar

Published in: MicrobiologyOpen, Issue 6/3, 2017, Page(s) e00445, ISSN 2045-8827

DOI: 10.1002/mbo3.445

SpreaD3: Interactive Visualization of Spatiotemporal History and Trait Evolutionary Processes

Author(s): Filip Bielejec, Guy Baele, Bram Vrancken, Marc A. Suchard, Andrew Rambaut, Philippe Lemey

Published in: Molecular Biology and Evolution, Issue 33/8, 2016, Page(s) 2167-2169, ISSN 0737-4038

DOI: 10.1093/molbev/msw082

Deletion Variants of Middle East Respiratory Syndrome Coronavirus from Humans, Jordan, 2015

Author(s): Mart M. Lamers, V. Stalin Raj, Mah’d Shafei, Sami Sheikh Ali, Sultan M. Abdallh, Mahmoud Gazo, Samer Nofal, Xiaoyan Lu, Dean D. Erdman, Marion P. Koopmans, Mohammad Abdallat, Aktham Haddadin, Bart L. Haagmans

Published in: Emerging Infectious Diseases, Issue 22/4, 2016, Page(s) 716-719, ISSN 1080-6040

DOI: 10.3201/eid2204.152065

Bacterial pathogens and endosymbionts in ticks

Author(s): Anna Papa, Katerina Tsioka, Anastasia Kontana, Christos Papadopoulos, Nektarios Giadinis

Published in: Ticks and Tick-borne Diseases, Issue 8/1, 2017, Page(s) 31-35, ISSN 1877-959X

DOI: 10.1016/j.ttbdis.2016.09.011

Microbiological profile of chicken carcasses: A comparative analysis using shotgun metagenomic sequencing

Author(s): Alessandra De Cesare, Federica Palma, Alex Lucchi, Frederique Pasquali, Gerardo Manfreda

Published in: Italian Journal of Food Safety, Issue 7/1, 2018, ISSN 2239-7132

DOI: 10.4081/ijfs.2018.6923

Crimean-Congo Hemorrhagic Fever: Tick-Host-Virus Interactions

Author(s): Anna Papa, Katerina Tsergouli, Katerina Tsioka, Ali Mirazimi

Published in: Frontiers in Cellular and Infection Microbiology, Issue 7, 2017, ISSN 2235-2988

DOI: 10.3389/fcimb.2017.00213

Multiple detection of zoonotic variegated squirrel bornavirus 1 RNA in different squirrel species suggests a possible unknown origin for the virus

Author(s): Kore Schlottau, Bernd Hoffmann, Timo Homeier-Bachmann, Christine Fast, Rainer G. Ulrich, Martin Beer, Donata Hoffmann

Published in: Archives of Virology, Issue 162/9, 2017, Page(s) 2747-2754, ISSN 0304-8608

DOI: 10.1007/s00705-017-3432-z

Canine Bocavirus Type 2 Infection Associated With Intestinal Lesions

Author(s): Chutchai Piewbang, Wendy K. Jo, Christina Puff, Martin Ludlow, Erhard van der Vries, Wijit Banlunara, Anudep Rungsipipat, Jochen Kruppa, Klaus Jung, Somporn Techangamsuwan, Wolfgang Baumgärtner, Albert D. M. E. Osterhaus

Published in: Veterinary Pathology, Issue 55/3, 2018, Page(s) 434-441, ISSN 0300-9858

DOI: 10.1177/0300985818755253

Characterization of the bacterial microbiota in wild-caught Ixodes ventalloi

Author(s): Sandra Díaz-Sánchez, Angélica Hernández-Jarguín, Alessandra Torina, Isabel G. Fernández de Mera, Valeria Blanda, Santo Caracappa, Christian Gortazar, José de la Fuente

Published in: Ticks and Tick-borne Diseases, Issue 10/2, 2019, Page(s) 336-343, ISSN 1877-959X

DOI: 10.1016/j.ttbdis.2018.11.014

Variegated Squirrel Bornavirus 1 in Squirrels, Germany and the Netherlands

Author(s): Kore Schlottau, Maria Jenckel, Judith van den Brand, Christine Fast, Christiane Herden, Dirk Höper, Timo Homeier-Bachmann, Jens Thielebein, Niels Mensing, Bert Diender, Donata Hoffmann, Rainer G. Ulrich, Thomas C. Mettenleiter, Marion Koopmans, Dennis Tappe, Jonas Schmidt-Chanasit, Chantal B.E.M. Reusken, Martin Beer, Bernd Hoffmann

Published in: Emerging Infectious Diseases, Issue 23/3, 2017, Page(s) 477-481, ISSN 1080-6040

DOI: 10.3201/eid2303.161061

Global Spread of Norovirus GII.17 Kawasaki 308, 2014–2016

Author(s): Martin C.W. Chan, Yunwen Hu, Haili Chen, Alexander T. Podkolzin, Ekaterina V. Zaytseva, Jun Komano, Naomi Sakon, Yong Poovorawan, Sompong Vongpunsawad, Thanundorn Thanusuwannasak, Joanne Hewitt, Dawn Croucher, Nikail Collins, Jan Vinjé, Xiaoli L. Pang, Bonita E. Lee, Miranda de Graaf, Janko van Beek, Harry Vennema, Marion P.G. Koopmans, Sandra Niendorf, Mateja Poljsak-Prijatelj, Andrej Steyer, Peter A. White, Jennifer H. Lun, Janet Mans, Tin-Nok Hung, Kirsty Kwok, Kelton Cheung, Nelson Lee, Paul K.S. Chan

Published in: Emerging Infectious Diseases, Issue 23/8, 2017, Page(s) 1359-1354, ISSN 1080-6040

DOI: 10.3201/eid2308.161138

Chronic norovirus infection among solid organ recipients in a tertiary care hospital, the Netherlands, 2006–2014

Author(s): J. van Beek, A.A. van der Eijk, P.L.A. Fraaij, K. Caliskan, K. Cransberg, M. Dalinghaus, R.A.S. Hoek, H.J. Metselaar, J. Roodnat, H. Vennema, M.P.G. Koopmans

Published in: Clinical Microbiology and Infection, Issue 23/4, 2017, Page(s) 265.e9-265.e13, ISSN 1198-743X

DOI: 10.1016/j.cmi.2016.12.010

Severe acute respiratory infection caused by swine influenza virus in a child necessitating extracorporeal membrane oxygenation (ECMO), the Netherlands, October 2016

Author(s): Pieter L A Fraaij, Enno D Wildschut, Robert J Houmes, Corien M Swaan, Christian J Hoebe, H C C de Jonge, Paulien Tolsma, Isme de Kleer, Suzan D Pas, Bas B Oude Munnink, My V T Phan, Theo M Bestebroer, R Shanty Roosenhoff, Jeroen J A van Kampen, Matthew Cotten, Nancy Beerens, Ron A M Fouchier, Johannes H van den Kerkhof, Aura Timen, Marion P Koopmans

Published in: Eurosurveillance, Issue 21/48, 2016, ISSN 1025-496X

DOI: 10.2807/1560-7917.ES.2016.21.48.30416

A Versatile Sample Processing Workflow for Metagenomic Pathogen Detection

Author(s): Claudia Wylezich, Anna Papa, Martin Beer, Dirk Höper

Published in: Scientific Reports, Issue 8/1, 2018, ISSN 2045-2322

DOI: 10.1038/s41598-018-31496-1

Immunolabelling of non-phosphorylated neurofilament indicates damage of spinal cord axons in TSE-infected goats

Author(s): M. Nadeem, I. Spitzbarth, V. Haist, K. Rohn, K. Tauscher, K. Rohn, A. Bossers, J. Langeveld, P. Papasavva-Stylianou, M. H. Groschup, W. Baumgärtner, I. Gerhauser, C. Fast

Published in: Veterinary Record, Issue 178/6, 2016, Page(s) 141.1-141, ISSN 0042-4900

DOI: 10.1136/vr.103425

Ancient hepatitis B viruses from the Bronze Age to the Medieval period

Author(s): Barbara Mühlemann, Terry C. Jones, Peter de Barros Damgaard, Morten E. Allentoft, Irina Shevnina, Andrey Logvin, Emma Usmanova, Irina P. Panyushkina, Bazartseren Boldgiv, Tsevel Bazartseren, Kadicha Tashbaeva, Victor Merz, Nina Lau, Václav Smrčka, Dmitry Voyakin, Egor Kitov, Andrey Epimakhov, Dalia Pokutta, Magdolna Vicze, T. Douglas Price, Vyacheslav Moiseyev, Anders J. Hansen, Ludovic Orlando, Simon Rasmussen, Martin Sikora, Lasse Vinner, Albert D. M. E. Osterhaus, Derek J. Smith, Dieter Glebe, Ron A. M. Fouchier, Christian Drosten, Karl-Göran Sjögren, Kristian Kristiansen, Eske Willerslev

Published in: Nature, Issue 557/7705, 2018, Page(s) 418-423, ISSN 0028-0836

DOI: 10.1038/s41586-018-0097-z

Rapid cell division of Staphylococcus aureus during colonization of the human nose

Author(s): Anna K. Szafrańska, Vera Junker, Matthias Steglich, Ulrich Nübel

Published in: BMC Genomics, Issue 20/1, 2019, ISSN 1471-2164

DOI: 10.1186/s12864-019-5604-6

Atypical Cowpox Virus Infection in a Series of Cats

Author(s): N. Jungwirth, C. Puff, K. Köster, R. Mischke, H. Meyer, A. Stark, B. Thoma, G. Zöller, F. Seehusen, M. Hewicker-Trautwein, A. Beineke, W. Baumgärtner, P. Wohlsein

Published in: Journal of Comparative Pathology, Issue 158, 2018, Page(s) 71-76, ISSN 0021-9975

DOI: 10.1016/j.jcpa.2017.12.003

Evaluation of Methods for the Concentration and Extraction of Viruses from Sewage in the Context of Metagenomic Sequencing

Author(s): Mathis Hjort Hjelmsø, Maria Hellmér, Xavier Fernandez-Cassi, Natàlia Timoneda, Oksana Lukjancenko, Michael Seidel, Dennis Elsässer, Frank M. Aarestrup, Charlotta Löfström, Sílvia Bofill-Mas, Josep F. Abril, Rosina Girones, Anna Charlotte Schultz

Published in: PLOS ONE, Issue 12/1, 2017, Page(s) e0170199, ISSN 1932-6203

DOI: 10.1371/journal.pone.0170199

Epidemiological characteristics of human-infective RNA viruses

Author(s): Mark E. J. Woolhouse, Liam Brierley

Published in: Scientific Data, Issue 5, 2018, Page(s) 180017, ISSN 2052-4463

DOI: 10.1038/sdata.2018.17

Loeffler 4.0: Diagnostic Metagenomics

Author(s): Dirk Höper, Claudia Wylezich, Martin Beer

Published in: Advances in Virus Research, Issue volume 99, 2017, Page(s) 17-37, ISSN 0065-3527

DOI: 10.1016/bs.aivir.2017.08.001

Prevalence, antimicrobial susceptibility and characterization of Staphylococcus aureus and methicillin-resistant Staphylococcus aureus isolated from dairy industries in north-central and north-eastern Greece

Author(s): Panagiotis Papadopoulos, Theofilos Papadopoulos, Apostolos S. Angelidis, Charalampos Kotzamanidis, Antonios Zdragas, Anna Papa, George Filioussis, Daniel Sergelidis

Published in: International Journal of Food Microbiology, Issue 291, 2019, Page(s) 35-41, ISSN 0168-1605

DOI: 10.1016/j.ijfoodmicro.2018.11.007

Unbiased whole-genome deep sequencing of human and porcine stool samples reveals circulation of multiple groups of rotaviruses and a putative zoonotic infection

Author(s): My V. T. Phan, Pham Hong Anh, Nguyen Van Cuong, Bas B. Oude Munnink, Lia van der Hoek, Phuc Tran My, Tue Ngo Tri, Juliet E. Bryant, Stephen Baker, Guy Thwaites, Mark Woolhouse, Paul Kellam, Maia A. Rabaa, Matthew Cotten

Published in: Virus Evolution, Issue 2/2, 2016, Page(s) vew027, ISSN 2057-1577

DOI: 10.1093/ve/vew027

Quantifying the contribution of four resistance mechanisms to ciprofloxacin MIC in Escherichia coli : a systematic review

Author(s): Boas C L van der Putten, Daniel Remondini, Giovanni Pasquini, Victoria A Janes, Sébastien Matamoros, Constance Schultsz

Published in: Journal of Antimicrobial Chemotherapy, Issue 74/2, 2018, Page(s) 298-310, ISSN 0305-7453

DOI: 10.1093/jac/dky417

High Prevalence of Highly Variable Atypical Porcine Pestiviruses Found in Germany

Author(s): M. Beer, K. Wernike, C. Dräger, D. Höper, A. Pohlmann, C. Bergermann, C. Schröder, S. Klinkhammer, S. Blome, B. Hoffmann

Published in: Transboundary and Emerging Diseases, 2016, ISSN 1865-1674

DOI: 10.1111/tbed.12532

Full-length genome sequences of porcine epidemic diarrhoea virus strain CV777; Use of NGS to analyse genomic and sub-genomic RNAs

Author(s): Thomas Bruun Rasmussen, Maria Beatrice Boniotti, Alice Papetti, Béatrice Grasland, Jean-Pierre Frossard, Akbar Dastjerdi, Marcel Hulst, Dennis Hanke, Anne Pohlmann, Sandra Blome, Wim H. M. van der Poel, Falko Steinbach, Yannick Blanchard, Antonio Lavazza, Anette Bøtner, Graham J. Belsham

Published in: PLOS ONE, Issue 13/3, 2018, Page(s) e0193682, ISSN 1932-6203

DOI: 10.1371/journal.pone.0193682

Neurotropic virus infections as the cause of immediate and delayed neuropathology

Author(s): Martin Ludlow, Jeroen Kortekaas, Christiane Herden, Bernd Hoffmann, Dennis Tappe, Corinna Trebst, Diane E. Griffin, Hannah E. Brindle, Tom Solomon, Alan S. Brown, Debby van Riel, Katja C. Wolthers, Dasja Pajkrt, Peter Wohlsein, Byron E. E. Martina, Wolfgang Baumgärtner, Georges M. Verjans, Albert D. M. E. Osterhaus

Published in: Acta Neuropathologica, Issue 131/2, 2016, Page(s) 159-184, ISSN 0001-6322

DOI: 10.1007/s00401-015-1511-3

Genome Sequences of a Novel Vietnamese Bat Bunyavirus

Author(s): Bas B. Oude Munnink, My V. T. Phan, Lia van der Hoek, Paul Kellam, Matthew Cotten

Published in: Genome Announcements, Issue 4/6, 2016, Page(s) e01366-16, ISSN 2169-8287

DOI: 10.1128/genomeA.01366-16

Establishment and cryptic transmission of Zika virus in Brazil and the Americas

Author(s): N. R. Faria, J. Quick, I.M. Claro, J. Thézé, J. G. de Jesus, M. Giovanetti, M. U. G. Kraemer, S. C. Hill, A. Black, A. C. da Costa, L. C. Franco, S. P. Silva, C.-H. Wu, J. Raghwani, S. Cauchemez, L. du Plessis, M. P. Verotti, W. K. de Oliveira, E. H. Carmo, G. E. Coelho, A. C. F. S. Santelli, L. C. Vinhal, C. M. Henriques, J. T. Simpson, M. Loose, K. G. Andersen, N. D. Grubaugh, S. Somasekar, C. Y. Chiu, J. E. Muñoz-Medina, C. R. Gonzalez-Bonilla, C. F. Arias, L. L. Lewis-Ximenez, S. A. Baylis, A. O. Chieppe, S. F. Aguiar, C. A. Fernandes, P. S. Lemos, B. L. S. Nascimento, H. A. O. Monteiro, I. C. Siqueira, M. G. de Queiroz, T. R. de Souza, J. F. Bezerra, M. R. Lemos, G. F. Pereira, D. Loudal, L. C. Moura, R. Dhalia, R. F. França, T. Magalhães, E. T. Marques, T. Jaenisch, G. L. Wallau, M. C. de Lima, V. Nascimento, E. M. de Cerqueira, M. M. de Lima, D. L. Mascarenhas, J. P. Moura Neto, A. S. Levin, T. R. Tozetto-Mendoza, S. N. Fonseca, M. C. Mendes-Correa, F. P. Milagres, A. Segurado, E. C. Holmes, A. Rambaut, T. Bedford, M. R. T. Nunes, E. C. Sabino, L. C. J. Alcantara, N. J. Loman, O. G. Pybus

Published in: Nature, Issue 546/7658, 2017, Page(s) 406-410, ISSN 0028-0836

DOI: 10.1038/nature22401

Biocuration of functional annotation at the European nucleotide archive

Author(s): Richard Gibson, Blaise Alako, Clara Amid, Ana Cerdeño-Tárraga, Iain Cleland, Neil Goodgame, Petra ten Hoopen, Suran Jayathilaka, Simon Kay, Rasko Leinonen, Xin Liu, Swapna Pallreddy, Nima Pakseresht, Jeena Rajan, Marc Rosselló, Nicole Silvester, Dmitriy Smirnov, Ana Luisa Toribio, Daniel Vaughan, Vadim Zalunin, Guy Cochrane

Published in: Nucleic Acids Research, Issue 44/D1, 2016, Page(s) D58-D66, ISSN 0305-1048

DOI: 10.1093/nar/gkv1311

Listeria monocytogenes Sequence Types 121 and 14 Repeatedly Isolated Within One Year of Sampling in a Rabbit Meat Processing Plant: Persistence and Ecophysiology

Author(s): Frédérique Pasquali, Federica Palma, Laurent Guillier, Alex Lucchi, Alessandra De Cesare, Gerardo Manfreda

Published in: Frontiers in Microbiology, Issue 9, 2018, ISSN 1664-302X

DOI: 10.3389/fmicb.2018.00596

Spatiotemporal analysis of the genetic diversity of seal influenza A(H10N7) virus, Northwestern Europe

Author(s): Rogier Bodewes, Siamak Zohari, Jesper S. Krog, Matthew D. Hall, Timm C. Harder, Theo M. Bestebroer, Marco W.G. van de Bildt, Monique I. Spronken, Lars E. Larsen, Ursula Siebert, Peter Wohlsein, Christina Puff, Frauke Seehusen, Wolfgang Baumgärtner, Tero Härkönen, Saskia L. Smits, Sander Herfst, Albert D.M.E. Osterhaus, Ron A.M. Fouchier, Marion P. Koopmans, Thijs Kuiken

Published in: Journal of Virology, 2016, Page(s) JVI.03046-15, ISSN 0022-538X

DOI: 10.1128/JVI.03046-15

Novel canine circovirus strains from Thailand: Evidence for genetic recombination

Author(s): Chutchai Piewbang, Wendy K. Jo, Christina Puff, Erhard van der Vries, Sawang Kesdangsakonwut, Anudep Rungsipipat, Jochen Kruppa, Klaus Jung, Wolfgang Baumgärtner, Somporn Techangamsuwan, Martin Ludlow, Albert D. M. E. Osterhaus

Published in: Scientific Reports, Issue 8/1, 2018, ISSN 2045-2322

DOI: 10.1038/s41598-018-25936-1

One health, multiple challenges: The inter-species transmission of influenza A virus

Author(s): Kirsty R. Short, Mathilde Richard, Josanne H. Verhagen, Debby van Riel, Eefje J.A. Schrauwen, Judith M.A. van den Brand, Benjamin Mänz, Rogier Bodewes, Sander Herfst

Published in: One Health, Issue 1, 2015, Page(s) 1-13, ISSN 2352-7714

DOI: 10.1016/j.onehlt.2015.03.001

Genomics-Based Identification of Microorganisms in Human Ocular Body Fluid

Author(s): Philipp Kirstahler, Søren Solborg Bjerrum, Alice Friis-Møller, Morten la Cour, Frank M. Aarestrup, Henrik Westh, Sünje Johanna Pamp

Published in: Scientific Reports, Issue 8/1, 2018, ISSN 2045-2322

DOI: 10.1038/s41598-018-22416-4

Acute viral infections of the central nervous system, 2014-2016, Greece

Author(s): Anna Papa, Elpida Papadopoulou

Published in: Journal of Medical Virology, Issue 90/4, 2018, Page(s) 644-647, ISSN 0146-6615

DOI: 10.1002/jmv.24997

Virus detection in high-throughput sequencing data without a reference genome of the host

Author(s): Jochen Kruppa, Wendy K. Jo, Erhard van der Vries, Martin Ludlow, Albert Osterhaus, Wolfgang Baumgaertner, Klaus Jung

Published in: Infection, Genetics and Evolution, Issue 66, 2018, Page(s) 180-187, ISSN 1567-1348

DOI: 10.1016/j.meegid.2018.09.026

Isolation and whole-genome sequencing of a Crimean-Congo hemorrhagic fever virus strain, Greece

Author(s): Anna Papa, Elpida Papadopoulou, Katerina Tsioka, Anastasia Kontana, Styliani Pappa, Ageliki Melidou, Nektarios D. Giadinis

Published in: Ticks and Tick-borne Diseases, Issue 9/4, 2018, Page(s) 788-791, ISSN 1877-959X

DOI: 10.1016/j.ttbdis.2018.02.024

Zoonotic Transmission of mcr-1 Colistin Resistance Gene from Small-Scale Poultry Farms, Vietnam

Author(s): Nguyen Vinh Trung, Sébastien Matamoros, Juan J. Carrique-Mas, Nguyen Huu Nghia, Nguyen Thi Nhung, Tran Thi Bich Chieu, Ho Huynh Mai, Willemien van Rooijen, James Campbell, Jaap A. Wagenaar, Anita Hardon, Nguyen Thi Nhu Mai, Thai Quoc Hieu, Guy Thwaites, Menno D. de Jong, Constance Schultsz, Ngo Thi Hoa

Published in: Emerging Infectious Diseases, Issue 23/3, 2017, Page(s) 529-532, ISSN 1080-6040

DOI: 10.3201/eid2303.161553

Hepatitis E Virus Infection in Dromedaries, North and East Africa, United Arab Emirates, and Pakistan, 1983–2015

Author(s): Andrea Rasche, Muhammad Saqib, Anne M. Liljander, Set Bornstein, Ali Zohaib, Stefanie Renneker, Katja Steinhagen, Renate Wernery, Mario Younan, Ilona Gluecks, Mosaad Hilali, Bakri E. Musa, Joerg Jores, Ulrich Wernery, Jan Felix Drexer, Christian Drosten, Victor Max Corman

Published in: Emerging Infectious Diseases, Issue 22/7, 2016, Page(s) 1249-1252, ISSN 1080-6040

DOI: 10.3201/eid2207.160168

Global outbreak of severe Mycobacterium chimaera disease after cardiac surgery: a molecular epidemiological study

Author(s): Jakko van Ingen, Thomas A Kohl, Katharina Kranzer, Barbara Hasse, Peter M Keller, Anna Katarzyna Szafrańska, Doris Hillemann, Meera Chand, Peter Werner Schreiber, Rami Sommerstein, Christoph Berger, Michele Genoni, Christian Rüegg, Nicolas Troillet, Andreas F Widmer, Sören L Becker, Mathias Herrmann, Tim Eckmanns, Sebastian Haller, Christiane Höller, Sylvia B Debast, Maurice J Wolfhagen, Joost Hopman, Jan Kluytmans, Merel Langelaar, Daan W Notermans, Jaap ten Oever, Peter van den Barselaar, Alexander B A Vonk, Margreet C Vos, Nada Ahmed, Timothy Brown, Derrick Crook, Theresa Lamagni, Nick Phin, E Grace Smith, Maria Zambon, Annerose Serr, Tim Götting, Winfried Ebner, Alexander Thürmer, Christian Utpatel, Cathrin Spröer, Boyke Bunk, Ulrich Nübel, Guido V Bloemberg, Erik C Böttger, Stefan Niemann, Dirk Wagner, Hugo Sax

Published in: The Lancet Infectious Diseases, Issue 17/10, 2017, Page(s) 1033-1041, ISSN 1473-3099

DOI: 10.1016/S1473-3099(17)30324-9

Recovering full-length viral genomes from metagenomes

Author(s): Saskia L. Smits, Rogier Bodewes, Aritz Ruiz-González, Wolfgang Baumgärtner, Marion P. Koopmans, Albert D. M. E. Osterhaus, Anita C. Schürch

Published in: Frontiers in Microbiology, Issue 6, 2015, ISSN 1664-302X

DOI: 10.3389/fmicb.2015.01069

Lessons from Ebola: Improving infectious disease surveillance to inform outbreak management

Author(s): M. E. J. Woolhouse, A. Rambaut, P. Kellam

Published in: Science Translational Medicine, Issue 7/307, 2015, Page(s) 307rv5-307rv5, ISSN 1946-6234

DOI: 10.1126/scitranslmed.aab0191

Evolutionary origins of hepatitis A virus in small mammals

Author(s): Jan Felix Drexler, Victor M. Corman, Alexander N. Lukashev, Judith M. A. van den Brand, Anatoly P. Gmyl, Sebastian Brünink, Andrea Rasche, Nicole Seggewiβ, Hui Feng, Lonneke M. Leijten, Peter Vallo, Thijs Kuiken, Andreas Dotzauer, Rainer G. Ulrich, Stanley M. Lemon, Christian Drosten

Published in: Proceedings of the National Academy of Sciences, Issue 112/49, 2015, Page(s) 15190-15195, ISSN 0027-8424

DOI: 10.1073/pnas.1516992112

Use of Next Generation Sequencing to study two cowpox virus outbreaks

Author(s): Markus H. Antwerpen, Enrico Georgi, Alexandra Nikolic, Gudrun Zoeller, Peter Wohlsein, Wolfgang Baumgärtner, Christophe Peyrefitte, Remi Charrel, Hermann Meyer

Published in: PeerJ, Issue 7, 2019, Page(s) e6561, ISSN 2167-8359

DOI: 10.7717/peerj.6561

Human norovirus transmission and evolution in a changing world

Author(s): Miranda de Graaf, Janko van Beek, Marion P. G. Koopmans

Published in: Nature Reviews Microbiology, Issue 14/7, 2016, Page(s) 421-433, ISSN 1740-1526

DOI: 10.1038/nrmicro.2016.48

Comparative Proteomics Identifies Host Immune System Proteins Affected by Infection with Mycobacterium bovis

Author(s): Vladimir López, Margarita Villar, João Queirós, Joaquín Vicente, Lourdes Mateos-Hernández, Iratxe Díez-Delgado, Marinela Contreras, Paulo C. Alves, Pilar Alberdi, Christian Gortázar, José de la Fuente

Published in: PLOS Neglected Tropical Diseases, Issue 10/3, 2016, Page(s) e0004541, ISSN 1935-2735

DOI: 10.1371/journal.pntd.0004541

Microarray-Based Gene Expression Analysis for Veterinary Pathologists: A Review

Author(s): Barbara B. Raddatz, Ingo Spitzbarth, Katja A. Matheis, Arno Kalkuhl, Ulrich Deschl, Wolfgang Baumgärtner, Reiner Ulrich

Published in: Veterinary Pathology, Issue 54/5, 2017, Page(s) 734-755, ISSN 0300-9858

DOI: 10.1177/0300985817709887

Rapid and Consistent Evolution of Colistin Resistance in Extensively Drug-Resistant Pseudomonas aeruginosa during Morbidostat Culture

Author(s): Bianca Dößelmann, Matthias Willmann, Matthias Steglich, Boyke Bunk, Ulrich Nübel, Silke Peter, Richard A. Neher

Published in: Antimicrobial Agents and Chemotherapy, Issue 61/9, 2017, Page(s) e00043-17, ISSN 0066-4804

DOI: 10.1128/AAC.00043-17

Challenges in laboratory diagnosis of acute viral central nervous system infections in the era of emerging infectious diseases: the syndromic approach

Author(s): Anna Papa, Tzimoula Kotrotsiou, Elpida Papadopoulou, Chantal Reusken, Corine GeurtsvanKessel, Marion Koopmans

Published in: Expert Review of Anti-infective Therapy, Issue 14/9, 2016, Page(s) 829-836, ISSN 1478-7210

DOI: 10.1080/14787210.2016.1215914

Second International Conference on Crimean-Congo Hemorrhagic Fever

Author(s): Jessica R. Spengler, Dennis A. Bente, Mike Bray, Felicity Burt, Roger Hewson, Gülay Korukluoglu, Ali Mirazimi, Friedemann Weber, Anna Papa

Published in: Antiviral Research, Issue 150, 2018, Page(s) 137-147, ISSN 0166-3542

DOI: 10.1016/j.antiviral.2017.11.019

Sharing Data for Global Infectious Disease Surveillance and Outbreak Detection

Author(s): Frank M. Aarestrup, Marion G. Koopmans

Published in: Trends in Microbiology, Issue 24/4, 2016, Page(s) 241-245, ISSN 0966-842X

DOI: 10.1016/j.tim.2016.01.009

Detection of Hepatitis E Virus in Sewage After an Outbreak on a French Island

Author(s): Takayuki Miura, Sébastien Lhomme, Jean-Claude Le Saux, Philippe Le Mehaute, Yvonnick Guillois, Elizabeth Couturier, Jacques Izopet, Florence Abranavel, Françoise S. Le Guyader

Published in: Food and Environmental Virology, 2016, ISSN 1867-0334

DOI: 10.1007/s12560-016-9241-9

Wild ducks excrete highly pathogenic avian influenza virus H5N8 (2014–2015) without clinical or pathological evidence of disease

Author(s): Judith M. A. van den Brand, Josanne H. Verhagen, Edwin J. B. Veldhuis Kroeze, Marco W. G. van de Bildt, Rogier Bodewes, Sander Herfst, Mathilde Richard, Pascal Lexmond, Theo M. Bestebroer, Ron A. M. Fouchier, Thijs Kuiken

Published in: Emerging Microbes & Infections, Issue 7/1, 2018, ISSN 2222-1751

DOI: 10.1038/s41426-018-0070-9

Drivers of MERS-CoV Emergence in Qatar

Author(s): Elmoubasher Farag, Reina Sikkema, Tinka Vinks, Md Islam, Mohamed Nour, Hamad Al-Romaihi, Mohammed Al Thani, Muzzamil Atta, Farhoud Alhajri, Salih Al-Marri, Mohd AlHajri, Chantal Reusken, Marion Koopmans

Published in: Viruses, Issue 11/1, 2019, Page(s) 22, ISSN 1999-4915

DOI: 10.3390/v11010022

Widespread activity of multiple lineages of Usutu virus, western Europe, 2016

Author(s): Daniel Cadar, Renke Lühken, Henk van der Jeugd, Mutien Garigliany, Ute Ziegler, Markus Keller, Jennifer Lahoreau, Lars Lachmann, Norbert Becker, Marja Kik, Bas B Oude Munnink, Stefan Bosch, Egbert Tannich, Annick Linden, Volker Schmidt, Marion P Koopmans, Jolianne Rijks, Daniel Desmecht, Martin H Groschup, Chantal Reusken, Jonas Schmidt-Chanasit

Published in: Eurosurveillance, Issue 22/4, 2017, ISSN 1025-496X

DOI: 10.2807/1560-7917.ES.2017.22.4.30452

Genome-wide identification of geographical segregated genetic markers in Salmonella enterica serovar Typhimurium variant 4,[5],12:i:-

Author(s): Federica Palma, Gerardo Manfreda, Mickael Silva, Antonio Parisi, Dillon O. R. Barker, Eduardo N. Taboada, Frédérique Pasquali, Mirko Rossi

Published in: Scientific Reports, Issue 8/1, 2018, ISSN 2045-2322

DOI: 10.1038/s41598-018-33266-5

Identification and molecular characterization of spotted fever group rickettsiae in ticks collected from farm ruminants in Lebanon

Author(s): Isabel G. Fernández de Mera, Valeria Blanda, Alessandra Torina, Mayssaa Fawaz Dabaja, Ali El Romeh, Alejandro Cabezas-Cruz, José de la Fuente

Published in: Ticks and Tick-borne Diseases, Issue 9/1, 2018, Page(s) 104-108, ISSN 1877-959X

DOI: 10.1016/j.ttbdis.2017.10.001

Emergence of a Clonal Lineage of Multidrug-Resistant ESBL-Producing Salmonella Infantis Transmitted from Broilers and Broiler Meat to Humans in Italy between 2011 and 2014

Author(s): Alessia Franco, Pimlapas Leekitcharoenphon, Fabiola Feltrin, Patricia Alba, Gessica Cordaro, Manuela Iurescia, Rita Tolli, Mario D’Incau, Monica Staffolani, Elisabetta Di Giannatale, Rene S. Hendriksen, Antonio Battisti

Published in: PLOS ONE, Issue 10/12, 2015, Page(s) e0144802, ISSN 1932-6203

DOI: 10.1371/journal.pone.0144802

Crimean-Congo hemorrhagic fever virus in ticks collected from livestock in Albania

Author(s): Anna Papa, Enkeleda Velo, Perparim Kadiaj, Katerina Tsioka, Anastasia Kontana, Majlinda Kota, Silvia Bino

Published in: Infection, Genetics and Evolution, Issue 54, 2017, Page(s) 496-500, ISSN 1567-1348

DOI: 10.1016/j.meegid.2017.08.017

Global status of Middle East respiratory syndrome coronavirus in dromedary camels: a systematic review

Author(s): R. S. Sikkema, E. A. B. A. Farag, Mazharul Islam, Muzzamil Atta, C. B. E. M. Reusken, Mohd M. Al-Hajri, M. P. G. Koopmans

Published in: Epidemiology and Infection, Issue 147, 2019, ISSN 0950-2688

DOI: 10.1017/s095026881800345x

Global phylogenetic analysis of Escherichia coli and plasmids carrying the mcr-1 gene indicates bacterial diversity but plasmid restriction

Author(s): Sébastien Matamoros, Jarne M. van Hattem, Maris S. Arcilla, Niels Willemse, Damian C. Melles, John Penders, Trung Nguyen Vinh, Ngo Thi Hoa, Menno D. de Jong, Constance Schultsz

Published in: Scientific Reports, Issue 7/1, 2017, ISSN 2045-2322

DOI: 10.1038/s41598-017-15539-7

Bluetongue virus serotype 27: Detection and characterization of two novel variants in Corsica, France

Author(s): Claudia Schulz, Cyril Viarouge, Corinne Sailleau, Martin Beer, Damien Vitour, Dirk Höper, Massimo Palmarini, Maria Jenckel, Stéphan Zientara, Bernd Hoffmann, Emmanuel Bréard, Mélanie Gallois

Published in: Journal of General Virology, 2016, ISSN 0022-1317

DOI: 10.1099/jgv.0.000557

Colistin resistance gene mcr-1 harboured on a multidrug resistant plasmid

Author(s): Surbhi Malhotra-Kumar, Basil Britto Xavier, Anupam J Das, Christine Lammens, Patrick Butaye, Herman Goossens

Published in: The Lancet Infectious Diseases, Issue 16/3, 2016, Page(s) 283-284, ISSN 1473-3099

DOI: 10.1016/S1473-3099(16)00012-8

Colistin-resistant Escherichia coli harbouring mcr-1 isolated from food animals in Hanoi, Vietnam

Author(s): Surbhi Malhotra-Kumar, Basil Britto Xavier, Anupam J Das, Christine Lammens, Ha Thi Thu Hoang, Ngoc Thi Pham, Herman Goossens

Published in: The Lancet Infectious Diseases, Issue 16/3, 2016, Page(s) 286-287, ISSN 1473-3099

DOI: 10.1016/S1473-3099(16)00014-1

Emergence of a novel GII.17 norovirus – End of the GII.4 era?

Author(s): M de Graaf, J van Beek, H Vennema, A Podkolzin, J Hewitt, F Bucardo, K Templeton, J Mans, J Nordgren, G Reuter, M Lynch, L Rasmussen, N Iritani, M Chan, V Martella, K Ambert-Balay, J Vinjé, P White, M Koopmans

Published in: Eurosurveillance, Issue 20/26, 2015, Page(s) 21178, ISSN 1560-7917

DOI: 10.2807/1560-7917.ES2015.20.26.21178

Swarm incursions of reassortants of highly pathogenic avian influenza virus strains H5N8 and H5N5, clade 2.3.4.4b, Germany, winter 2016/17

Author(s): Anne Pohlmann, Elke Starick, Christian Grund, Dirk Höper, Günter Strebelow, Anja Globig, Christoph Staubach, Franz J. Conraths, Thomas C. Mettenleiter, Timm Harder, Martin Beer

Published in: Scientific Reports, Issue 8/1, 2018, ISSN 2045-2322

DOI: 10.1038/s41598-017-16936-8

Adaptive MCMC in Bayesian phylogenetics: an application to analyzing partitioned data in BEAST

Author(s): Guy Baele, Philippe Lemey, Andrew Rambaut, Marc A. Suchard

Published in: Bioinformatics, Issue 33/12, 2017, Page(s) 1798-1805, ISSN 1367-4803

DOI: 10.1093/bioinformatics/btx088

Influenza A(H5N8) Virus Similar to Strain in Korea Causing Highly Pathogenic Avian Influenza in Germany

Author(s): Timm Harder, Sebastian Maurer-Stroh, Anne Pohlmann, Elke Starick, Detlef Höreth-Böntgen, Karin Albrecht, Gunter Pannwitz, Jens Teifke, Vithiagaran Gunalan, Raphael T.C. Lee, Carola Sauter-Louis, Timo Homeier, Christoph Staubach, Carola Wolf, Günter Strebelow, Dirk Höper, Christian Grund, Franz J. Conraths, Thomas C. Mettenleiter, Martin Beer

Published in: Emerging Infectious Diseases, Issue 21/5, 2015, Page(s) 860-863, ISSN 1080-6040

DOI: 10.3201/eid2105.141897

Detection of Circovirus in Foxes with Meningoencephalitis, United Kingdom, 2009–2013

Author(s): Steve Bexton, Lidewij C. Wiersma, Sarah Getu, Peter R. van Run, Georges M.G.M. Verjans, Debby Schipper, Claudia M.E. Schapendonk, Rogier Bodewes, Lucy Oldroyd, Bart L. Haagmans, Marion M.P. Koopmans, Saskia L. Smits

Published in: Emerging Infectious Diseases, Issue 21/7, 2015, Page(s) 1205-1208, ISSN 1080-6040

DOI: 10.3201/eid2107.150228

Draft Genome Sequences of Anaplasma phagocytophilum , A. marginale , and A. ovis Isolates from Different Hosts

Author(s): Sandra Diaz-Sanchez, Angélica Hernández-Jarguín, Isabel G. Fernández de Mera, Pilar Alberdi, Erich Zweygarth, Christian Gortazar, José de la Fuente

Published in: Genome Announcements, Issue 6/5, 2018, Page(s) e01503-17, ISSN 2169-8287

DOI: 10.1128/genomeA.01503-17

Lleida Bat Lyssavirus isolation in Miniopterus schreibersii in France

Author(s): Evelyne Picard-Meyer, Veronique Beven, Edouard Hirchaud, Cédric Guillaume, Gérald Larcher, Emmanuelle Robardet, Alexandre Servat, Yannick Blanchard, Florence Cliquet

Published in: Zoonoses and Public Health, Issue 66/2, 2019, Page(s) 254-258, ISSN 1863-1959

DOI: 10.1111/zph.12535

Infections shared with wildlife: an updated perspective

Author(s): C. Gortázar, J. F. Ruiz-Fons, U. Höfle

Published in: European Journal of Wildlife Research, Issue 62/5, 2016, Page(s) 511-525, ISSN 1612-4642

DOI: 10.1007/s10344-016-1033-x

Complete sequence of an IncFII plasmid harbouring the colistin resistance gene mcr-1 isolated from Belgian pig farms

Author(s): B. B. Xavier, C. Lammens, P. Butaye, H. Goossens, S. Malhotra-Kumar

Published in: Journal of Antimicrobial Chemotherapy, 2016, Page(s) dkw191, ISSN 0305-7453

DOI: 10.1093/jac/dkw191

The effects of sampling strategy on the quality of reconstruction of viral population dynamics using Bayesian skyline family coalescent methods: A simulation study

Author(s): Matthew D. Hall, Mark E. J. Woolhouse, and Andrew Rambaut

Published in: Virus Evolution, Issue 2016, 2(1), 2016, Page(s) 1-14, ISSN 2057-1577

DOI: 10.1093/ve/vew003

Ancient human parvovirus B19 in Eurasia reveals its long-term association with humans

Author(s): Barbara Mühlemann, Ashot Margaryan, Peter de Barros Damgaard, Morten E. Allentoft, Lasse Vinner, Anders J. Hansen, Andrzej Weber, Vladimir I. Bazaliiskii, Martyna Molak, Jette Arneborg, Wieslaw Bogdanowicz, Ceri Falys, Mikhail Sablin, Václav Smrčka, Sabine Sten, Kadicha Tashbaeva, Niels Lynnerup, Martin Sikora, Derek J. Smith, Ron A. M. Fouchier, Christian Drosten, Karl-Göran Sjögren, Kristian Kristiansen, Eske Willerslev, Terry C. Jones

Published in: Proceedings of the National Academy of Sciences, Issue 115/29, 2018, Page(s) 7557-7562, ISSN 0027-8424

DOI: 10.1073/pnas.1804921115

Epidemiological and Molecular Analysis of an Outbreak of Highly Pathogenic Avian Influenza H5N8 clade 2.3.4.4 in a German Zoo: Effective Disease Control with Minimal Culling

Author(s): A. Globig, E. Starick, T. Homeier, A. Pohlmann, C. Grund, P. Wolf, A. Zimmermann, C. Wolf, D. Heim, H. Schlößer, S. Zander, M. Beer, F. J. Conraths, T. C. Harder

Published in: Transboundary and Emerging Diseases, 2016, ISSN 1865-1674

DOI: 10.1111/tbed.12570

Genetic detection of hantaviruses in rodents, Albania

Author(s): Anna Papa, Elton Rogozi, Enkelejda Velo, Evangelia Papadimitriou, Silvia Bino

Published in: Journal of Medical Virology, 2016, Page(s) n/a-n/a, ISSN 0146-6615

DOI: 10.1002/jmv.24486

Cross-border outbreak of listeriosis caused by cold-smoked salmon, revealed by integrated surveillance and whole genome sequencing (WGS), Denmark and France, 2015 to 2017

Author(s): Susanne Schjørring, Sofie Gillesberg Lassen, Tenna Jensen, Alexandra Moura, Jette S Kjeldgaard, Luise Müller, Stine Thielke, Alexandre Leclercq, Mylene M Maury, Mathieu Tourdjman, Marie-Pierre Donguy, Marc Lecuit, Steen Ethelberg, Eva M Nielsen

Published in: Eurosurveillance, Issue 22/50, 2017, ISSN 1560-7917

DOI: 10.2807/1560-7917.ES.2017.22.50.17-00762

New Avian Hepadnavirus in Palaeognathous Bird, Germany

Author(s): Wendy K. Jo, Vanessa M. Pfankuche, Henning Petersen, Samuel Frei, Maya Kummrow, Stephan Lorenzen, Martin Ludlow, Julia Metzger, Wolfgang Baumgärtner, Albert Osterhaus, Erhard van der Vries

Published in: Emerging Infectious Diseases, Issue 23/12, 2017, Page(s) 2089-2091, ISSN 1080-6040

DOI: 10.3201/eid2312.161634

First molecular investigation of Cryptosporidium spp. in young calves in Algeria

Author(s): Djahida Benhouda, Ahcène Hakem, Anna Rosa Sannella, Afaf Benhouda, Simone M. Cacciò

Published in: Parasite, Issue 24, 2017, Page(s) 15, ISSN 1776-1042

DOI: 10.1051/parasite/2017014

Modelling the impact of curtailing antibiotic usage in food animals on antibiotic resistance in humans

Author(s): B. A. D. van Bunnik, M. E. J. Woolhouse

Published in: Royal Society Open Science, Issue 4/4, 2017, Page(s) 161067, ISSN 2054-5703

DOI: 10.1098/rsos.161067

Complete Genome Sequences of Field Isolates of Mycobacterium bovis and Mycobacterium caprae

Author(s): José de la Fuente, Iratxe Díez-Delgado, Marinela Contreras, Joaquín Vicente, Alejandro Cabezas-Cruz, Marina Manrique, Raquel Tobes, Vladimir López, Beatriz Romero, Lucas Domínguez, Joseba M. Garrido, Ramón Juste, Christian Gortazar

Published in: Genome Announcements, Issue 3/3, 2015, Page(s) e00247-15, ISSN 2169-8287

DOI: 10.1128/genomeA.00247-15

Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage

Author(s): Rene S. Hendriksen, Patrick Munk, Patrick Njage, Bram van Bunnik, Luke McNally, Oksana Lukjancenko, Timo Röder, David Nieuwenhuijse, Susanne Karlsmose Pedersen, Jette Kjeldgaard, Rolf S. Kaas, Philip Thomas Lanken Conradsen Clausen, Josef Korbinian Vogt, Pimlapas Leekitcharoenphon, Milou G. M. van de Schans, Tina Zuidema, Ana Maria de Roda Husman, Simon Rasmussen, Bent Petersen, Clara Amid, Guy Cochrane, Thomas Sicheritz-Ponten, Heike Schmitt, Jorge Raul Matheu Alvarez, Awa Aidara-Kane, Sünje J. Pamp, Ole Lund, Tine Hald, Mark Woolhouse, Marion P. Koopmans, Håkan Vigre, Thomas Nordahl Petersen, Frank M. Aarestrup

Published in: Nature Communications, Issue 10/1, 2019, ISSN 2041-1723

DOI: 10.1038/s41467-019-08853-3

Next-generation sequencing and norovirus

Author(s): Matthew Cotten, Marion Koopmans

Published in: Future Virology, Issue 11/11, 2016, Page(s) 719-722, ISSN 1746-0794

DOI: 10.2217/fvl-2016-0099

LVQ-KNN: Composition-based DNA/RNA binning of short nucleotide sequences utilizing a prototype-based k-nearest neighbor approach

Author(s): Ariane Belka, Mareike Fischer, Anne Pohlmann, Martin Beer, Dirk Höper

Published in: Virus Research, Issue 258, 2018, Page(s) 55-63, ISSN 0168-1702

DOI: 10.1016/j.virusres.2018.10.002

Consolidating and Exploring Antibiotic Resistance Gene Data Resources

Author(s): Basil Britto Xavier, Anupam J. Das, Guy Cochrane, Sandra De Ganck, Samir Kumar-Singh, Frank Møller Aarestrup, Herman Goossens, Surbhi Malhotra-Kumar

Published in: Journal of Clinical Microbiology, Issue 54/4, 2016, Page(s) 851-859, ISSN 0095-1137

DOI: 10.1128/JCM.02717-15

Genotypic anomaly in Ebola virus strains circulating in Magazine Wharf area, Freetown, Sierra Leone, 2015

Author(s): Saskia L Smits, Suzan D Pas, Chantal B Reusken, Bart L Haagmans, Peirro Pertile, Corrado Cancedda, Kerry Dierberg, Isata Wurie, Abdul Kamara, David Kargbo, Sarah L Caddy, Armando Arias, Lucy Thorne, Jia Lu, Umaru Jah, Ian Goodfellow, Marion P Koopmans

Published in: Eurosurveillance, Issue 20/40, 2015, ISSN 1025-496X

DOI: 10.2807/1560-7917.ES.2015.20.40.30035

Metagenomic Sequencing for Surveillance of Food- and Waterborne Viral Diseases

Author(s): David F. Nieuwenhuijse, Marion P. G. Koopmans

Published in: Frontiers in Microbiology, Issue 8, 2017, ISSN 1664-302X

DOI: 10.3389/fmicb.2017.00230

Discordant detection of avian influenza virus subtypes in time and space between poultry and wild birds; Towards improvement of surveillance programs

Author(s): Josanne H. Verhagen, Pascal Lexmond, Oanh Vuong, Martin Schutten, Judith Guldemeester, Albert D. M. E. Osterhaus, Armin R. W. Elbers, Roy Slaterus, Menno Hornman, Guus Koch, Ron A. M. Fouchier

Published in: PLOS ONE, Issue 12/3, 2017, Page(s) e0173470, ISSN 1932-6203

DOI: 10.1371/journal.pone.0173470

Norovirus Infection in Harbor Porpoises

Author(s): Miranda de Graaf, Rogier Bodewes, Cornelis E. van Elk, Marco van de Bildt, Sarah Getu, Georgina I. Aron, Georges M.G.M. Verjans, Albert D.M.E. Osterhaus, Judith M.A. van den Brand, Thijs Kuiken, Marion P.G. Koopmans

Published in: Emerging Infectious Diseases, Issue 23/1, 2017, Page(s) 87-91, ISSN 1080-6040

DOI: 10.3201/eid2301.161081

Rapid and precise alignment of raw reads against redundant databases with KMA

Author(s): Philip T. L. C. Clausen, Frank M. Aarestrup, Ole Lund

Published in: BMC Bioinformatics, Issue 19/1, 2018, ISSN 1471-2105

DOI: 10.1186/s12859-018-2336-6

Digital PCR for Quantifying Norovirus in Oysters Implicated in Outbreaks, France

Author(s): David Polo, Julien Schaeffer, Nelly Fournet, Jean-Claude Le Saux, Sylvain Parnaudeau, Catherine McLeod, Françoise S. Le Guyader

Published in: Emerging Infectious Diseases, Issue 22/12, 2016, Page(s) 2189-2191, ISSN 1080-6040

DOI: 10.3201/eid2212.160841

Whole genome sequencing for typing and characterisation of Listeria monocytogenes isolated in a rabbit meat processing plant

Author(s): Federica Palma, Frédérique Pasquali, Alex Lucchi, Alessandra De Cesare, Gerardo Manfreda

Published in: Italian Journal of Food Safety, Issue 6/3, 2017, ISSN 2239-7132

DOI: 10.4081/ijfs.2017.6879

Seroprevalence of Antibodies against Seal Influenza A(H10N7) Virus in Harbor Seals and Gray Seals from the Netherlands

Author(s): Rogier Bodewes, Ana Rubio García, Sophie M. Brasseur, Guillermo J. Sanchez Conteras, Marco W. G. van de Bildt, Marion P. G. Koopmans, Albert D. M. E. Osterhaus, Thijs Kuiken

Published in: PLOS ONE, Issue 10/12, 2015, Page(s) e0144899, ISSN 1932-6203

DOI: 10.1371/journal.pone.0144899

Porcine Bocavirus Infection Associated with Encephalomyelitis in a Pig, Germany1

Author(s): Vanessa M. Pfankuche, Rogier Bodewes, Kerstin Hahn, Christina Puff, Andreas Beineke, André Habierski, Albert D.M.E. Osterhaus, Wolfgang Baumgärtner

Published in: Emerging Infectious Diseases, Issue 22/7, 2016, Page(s) 1310-1312, ISSN 1080-6040

DOI: 10.3201/eid2207.152049

Yellow fever in a traveller returning from Suriname to the Netherlands, March 2017

Author(s): Marjan Wouthuyzen-Bakker, Marjolein Knoester, Aad P van den Berg, Corine H GeurtsvanKessel, Marion PG Koopmans, Coretta Van Leer-Buter, Bob Oude Velthuis, Suzan D Pas, Wilhelmina LM Ruijs, Jonas Schmidt-Chanasit, Stephen GS Vreden, Tjip S van der Werf, Chantal BEM Reusken, Wouter FW Bierman

Published in: Eurosurveillance, Issue 22/11, 2017, ISSN 1025-496X

DOI: 10.2807/1560-7917.ES.2017.22.11.30488

A novel astrovirus associated with encephalitis and ganglionitis in domestic sheep

Author(s): F. Pfaff, K. Schlottau, S. Scholes, A. Courtenay, B. Hoffmann, D. Höper, M. Beer

Published in: Transboundary and Emerging Diseases, Issue 64/3, 2017, Page(s) 677-682, ISSN 1865-1674

DOI: 10.1111/tbed.12623

A Bacterial Analysis Platform: An Integrated System for Analysing Bacterial Whole Genome Sequencing Data for Clinical Diagnostics and Surveillance

Author(s): Martin Christen Frølund Thomsen, Johanne Ahrenfeldt, Jose Luis Bellod Cisneros, Vanessa Jurtz, Mette Voldby Larsen, Henrik Hasman, Frank Møller Aarestrup, Ole Lund

Published in: PLOS ONE, Issue 11/6, 2016, Page(s) e0157718, ISSN 1932-6203

DOI: 10.1371/journal.pone.0157718

European Nucleotide Archive in 2016

Author(s): Ana Luisa Toribio, Blaise Alako, Clara Amid, Ana Cerdeño-Tarrága, Laura Clarke, Iain Cleland, Susan Fairley, Richard Gibson, Neil Goodgame, Petra ten Hoopen, Suran Jayathilaka, Simon Kay, Rasko Leinonen, Xin Liu, Josué Martínez-Villacorta, Nima Pakseresht, Jeena Rajan, Kethi Reddy, Marc Rosello, Nicole Silvester, Dmitriy Smirnov, Daniel Vaughan, Vadim Zalunin, Guy Cochrane

Published in: Nucleic Acids Research, Issue 45/D1, 2017, Page(s) D32-D36, ISSN 0305-1048

DOI: 10.1093/nar/gkw1106

How ownership rights over microorganisms affect infectious disease control and innovation: A root-cause analysis of barriers to data sharing as experienced by key stakeholders

Author(s): Carolina dos S. Ribeiro, Martine Y. van Roode, George B. Haringhuizen, Marion P. Koopmans, Eric Claassen, Linda H. M. van de Burgwal

Published in: PLOS ONE, Issue 13/5, 2018, Page(s) e0195885, ISSN 1932-6203

DOI: 10.1371/journal.pone.0195885

Novel phlebovirus detected in Haemaphysalis parva ticks in a Greek island

Author(s): Anna Papa, Anastasia Kontana, Katerina Tsioka, Anastasios Saratsis, Smaragda Sotiraki

Published in: Ticks and Tick-borne Diseases, Issue 8/1, 2017, Page(s) 157-160, ISSN 1877-959X

DOI: 10.1016/j.ttbdis.2016.10.012

Local amplification of highly pathogenic avian influenza H5N8 viruses in wild birds in the Netherlands, 2016 to 2017

Author(s): Marjolein J. Poen, Theo M. Bestebroer, Oanh Vuong, Rachel D. Scheuer, Henk P. van der Jeugd, Erik Kleyheeg, Dirk Eggink, Pascal Lexmond, Judith M.A. van den Brand, Lineke Begeman, Stefan van der Vliet, Gerhard J.D.M. Müskens, Frank A. Majoor, Marion P.G. Koopmans, Thijs Kuiken, Ron A.M. Fouchier

Published in: Eurosurveillance, Issue 23/4, 2018, ISSN 1025-496x

DOI: 10.2807/1560-7917.ES.2018.23.4.17-00449

Effect of blood type on anti-α-Gal immunity and the incidence of infectious diseases

Author(s): Alejandro Cabezas-Cruz, Lourdes Mateos-Hernández, Pilar Alberdi, Margarita Villar, Gilles Riveau, Emmanuel Hermann, Anne-Marie Schacht, Jamal Khalife, Margarida Correia-Neves, Christian Gortazar, José de la Fuente

Published in: Experimental & Molecular Medicine, Issue 49/3, 2017, Page(s) e301, ISSN 1226-3613

DOI: 10.1038/emm.2016.164

Threats to timely sharing of pathogen sequence data

Author(s): Carolina dos S. Ribeiro, Marion P. Koopmans, George B. Haringhuizen

Published in: Science, Issue Vol. 362, Issue 6413,, 2018, Page(s) pp. 404-406, ISSN 1095-9203

DOI: 10.1126/science.aau5229

Vaccines, Apes, and Conspiracy

Author(s): Emilio Mordini

Published in: The American Journal of Bioethics, Issue 18/10, 2018, Page(s) 55-57, ISSN 1526-5161

DOI: 10.1080/15265161.2018.1516001

Interactomics and tick vaccine development: new directions for the control of tick-borne diseases

Author(s): Sara Artigas-Jerónimo, José De La Fuente, Margarita Villar

Published in: Expert Review of Proteomics, Issue 15/8, 2018, Page(s) 627-635, ISSN 1478-9450

DOI: 10.1080/14789450.2018.1506701

First gene-ontology enrichment analysis based on bacterial coregenome variants: insights into adaptations of Salmonella serovars to mammalian- and avian-hosts

Author(s): Arnaud Felten, Meryl Vila Nova, Kevin Durimel, Laurent Guillier, Michel-Yves Mistou, Nicolas Radomski

Published in: BMC Microbiology, Issue 17/1, 2017, ISSN 1471-2180

DOI: 10.1186/s12866-017-1132-1

Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases

Author(s): Armando Arias, Simon J. Watson, Danny Asogun, Ekaete Alice Tobin, Jia Lu, My V. T. Phan, Umaru Jah, Raoul Emeric Guetiya Wadoum, Luke Meredith, Lucy Thorne, Sarah Caddy, Alimamy Tarawalie, Pinky Langat, Gytis Dudas, Nuno R. Faria, Simon Dellicour, Abdul Kamara, Brima Kargbo, Brima Osaio Kamara, Sahr Gevao, Daniel Cooper, Matthew Newport, Peter Horby, Jake Dunning, Foday Sahr, Tim Brooks, Andrew J.H. Simpson, Elisabetta Groppelli, Guoying Liu, Nisha Mulakken, Kate Rhodes, James Akpablie, Zabulon Yoti, Margaret Lamunu, Esther Vitto, Patrick Otim, Collins Owilli, Isaac Boateng, Lawrence Okoror, Emmanuel Omomoh, Jennifer Oyakhilome, Racheal Omiunu, Ighodalo Yemisis, Donatus Adomeh, Solomon Ehikhiametalor, Patience Akhilomen, Chris Aire, Andreas Kurth, Nicola Cook, Jan Baumann, Martin Gabriel, Roman Wölfel, Antonino Di Caro, Miles W. Carroll, Stephan Günther, John Redd, Dhamari Naidoo, Oliver G. Pybus, Andrew Rambaut, Paul Kellam, Ian Goodfellow, Matthew Cotten

Published in: Virus Evolution, Issue 2/1, 2016, Page(s) vew016, ISSN 2057-1577

DOI: 10.1093/ve/vew016

Project information

COMPARE

Grant agreement ID: 643476

Project website

Status

Ongoing project

Start date

1 December 2014
End date

30 November 2019

Funded under:

H2020-EU.3.1.2.

Overall budget:

€ 20 847 771
EU contribution

€ 20 817 771

Coordinated by:

DANMARKS TEKNISKE UNIVERSITET

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Last update: 10 June 2019

Record number: 194068

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Periodic Reporting for period 2 - COMPARE (COllaborative Management Platform for detection and Analyses of (Re-)emerging and foodborne outbreaks in Europe)

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