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COMPARE SIGNED

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

Total Cost €

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EC-Contrib. €

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Partnership

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Project "COMPARE" data sheet

The following table provides information about the project.

Coordinator
DANMARKS TEKNISKE UNIVERSITET 

Organization address
address: ANKER ENGELUNDSVEJ 1 BYGNING 101 A
city: KGS LYNGBY
postcode: 2800
website: www.dtu.dk

contact info
title: n.a.
name: n.a.
surname: n.a.
function: n.a.
email: n.a.
telephone: n.a.
fax: n.a.

 Coordinator Country Denmark [DK]
 Project website http://www.compare-europe.eu/
 Total cost 20˙847˙771 €
 EC max contribution 20˙817˙771 € (100%)
 Programme 1. H2020-EU.3.1.2. (Preventing disease)
 Code Call H2020-PHC-2014-single-stage
 Funding Scheme RIA
 Starting year 2014
 Duration (year-month-day) from 2014-12-01   to  2019-11-30

 Partnership

Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 
1    DANMARKS TEKNISKE UNIVERSITET DK (KGS LYNGBY) coordinator 3˙006˙000.00
2    ERASMUS UNIVERSITAIR MEDISCH CENTRUM ROTTERDAM NL (ROTTERDAM) participant 2˙656˙641.00
3    EUROPEAN MOLECULAR BIOLOGY LABORATORY DE (HEIDELBERG) participant 1˙950˙000.00
4    FRIEDRICH LOEFFLER INSTITUT - BUNDESFORSCHUNGSINSTITUT FUER TIERGESUNDHEIT DE (GREIFSWALD-INSEL RIEMS) participant 1˙000˙000.00
5    THE SECRETARY OF STATE FOR ENVIRONMENT, FOOD AND RURAL AFFAIRS UK (LONDON) participant 971˙361.00
6    STATENS SERUM INSTITUT DK (KOBENHAVN S) participant 919˙750.00
7    RIJKSINSTITUUT VOOR VOLKSGEZONDHEID EN MILIEU NL (BILTHOVEN) participant 759˙500.00
8    ROBERT KOCH-INSTITUT DE (Berlin) participant 718˙000.00
9    THE UNIVERSITY OF EDINBURGH UK (EDINBURGH) participant 697˙258.00
10    ISTITUTO SUPERIORE DI SANITA IT (ROMA) participant 603˙125.00
11    ACADEMISCH MEDISCH CENTRUM BIJ DE UNIVERSITEIT VAN AMSTERDAM NL (AMSTERDAM) participant 602˙795.00
12    AGENCE NATIONALE DE LA SECURITE SANITAIRE DE L ALIMENTATION DE L ENVIRONNEMENT ET DU TRAVAIL FR (MAISONS ALFORT) participant 601˙250.00
13    THE CHANCELLOR MASTERS AND SCHOLARSOF THE UNIVERSITY OF CAMBRIDGE UK (CAMBRIDGE) participant 504˙057.00
14    ERASMUS UNIVERSITEIT ROTTERDAM NL (ROTTERDAM) participant 438˙516.00
15    CIVIC CONSULTING GMBH DE (BERLIN) participant 434˙531.00
16    ALMA MATER STUDIORUM - UNIVERSITA DI BOLOGNA IT (BOLOGNA) participant 434˙181.00
17    FONDATION MERIEUX FR (LYON) participant 428˙830.00
18    RESPONSIBLE TECHNOLOGY FR (PARIS) participant 411˙387.00
19    LEIBNIZ-INSTITUT DSMZ-DEUTSCHE SAMMLUNG VON MIKROORGANISMEN UND ZELLKULTUREN GMBH DE (BRAUNSCHWEIG) participant 403˙770.00
20    STIFTUNG TIERAERZTLICHE HOCHSCHULE HANNOVER DE (HANNOVER) participant 403˙750.00
21    WIGNER FIZIKAI KUTATOKOZPONT HU (Budapest) participant 403˙750.00
22    UNIVERSITEIT ANTWERPEN BE (ANTWERPEN) participant 402˙500.00
23    INSTITUT FRANCAIS DE RECHERCHE POUR L'EXPLOITATION DE LA MER FR (PLOUZANE) participant 401˙807.00
24    UNIVERSIDAD DE CASTILLA - LA MANCHA ES (CIUDAD REAL) participant 400˙750.00
25    ARISTOTELIO PANEPISTIMIO THESSALONIKIS EL (THESSALONIKI) participant 353˙750.00
26    ARTEMIS BIO-SUPPORT B.V. NL (DELFT) participant 306˙250.00
27    CHARITE - UNIVERSITAETSMEDIZIN BERLIN DE (BERLIN) participant 231˙583.00
28    GENOME RESEARCH LIMITED UK (LONDON) participant 200˙000.00
29    UNIVERSITATSKLINIKUM BONN DE (BONN) participant 172˙675.00
30    CIVIC CONSULTING ALLEWELDT & KARA GBR DE (Berlin) participant 0.00
31    THE AUSTRALIAN NATIONAL UNIVERSITY AU (CANBERRA) participant 0.00

Map

 Project 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.

 Deliverables

List of deliverables.
Data analysis pipeline Other 2020-04-25 06:39:05
Analytical workflow for clinical diagnostic application Other 2020-04-25 06:39:05
Prediction algorithm AMR markers Documents, reports 2020-04-25 06:39:05
Public website Websites, patent fillings, videos etc. 2020-04-25 06:39:05
Sequencing workflow Documents, reports 2020-04-25 06:39:05
Methodologies report Documents, reports 2020-04-25 06:39:05
Automated tools for rapid assessment of key transmission parameters Other 2020-04-25 06:39:05
Leaflet and templates Websites, patent fillings, videos etc. 2020-04-25 06:39:05
Matrix-dependent sample handling protocols Documents, reports 2020-04-25 06:39:05
Phylogenetic and phylogeographic tools Other 2020-04-25 06:39:05
CE Framework Other 2020-04-25 06:39:05
Standard protocol sample processing Documents, reports 2020-04-25 06:39:05
Algorithm for detection of informative (sub)types Documents, reports 2020-04-25 06:39:05
Risk based surveillance plans, sampling algorithms and protocols Documents, reports 2019-10-15 13:18:33
Validated RA model for NGS data Other 2019-10-15 13:18:15
Tools for rapid sequence based detection of strain specific clusters Other 2019-10-15 13:18:32
Analytical workflow Other 2019-10-15 13:18:09
Generic workflow engine Other 2019-10-15 13:18:07
Methods for prediction of pathogen phenotype from genotype) Other 2019-10-15 13:18:20
Generic RA framework Other 2019-10-15 13:17:30
Case study cost-effectiveness report Documents, reports 2019-10-15 13:18:03
Paper on methodology and results of estimating the value of safety Documents, reports 2019-10-15 13:18:06

Take a look to the deliverables list in detail:  detailed list of COMPARE deliverables.

 Publications

year authors and title journal last update
List of publications.
2020 Anna Papa, Sandra Gewehr, Katerina Tsioka, Stella Kalaitzopoulou, Styliani Pappa, Spiros Mourelatos
Detection of flaviviruses and alphaviruses in mosquitoes in Central Macedonia, Greece, 2018
published pages: 105278, ISSN: 0001-706X, DOI: 10.1016/j.actatropica.2019.105278
Acta Tropica 202 2020-04-25
2019 Sofia Strubbia, My V. T. Phan, Julien Schaeffer, Marion Koopmans, Matthew Cotten, Françoise S. Le Guyader
Characterization of Norovirus and Other Human Enteric Viruses in Sewage and Stool Samples Through Next-Generation Sequencing
published pages: 400-409, ISSN: 1867-0334, DOI: 10.1007/s12560-019-09402-3
Food and Environmental Virology 11/4 2020-04-25
2020 D. Aytan-Aktug, P. T. L. C. Clausen, V. Bortolaia, F. M. Aarestrup, O. Lund
Prediction of Acquired Antimicrobial Resistance for Multiple Bacterial Species Using Neural Networks
published pages: , ISSN: 2379-5077, DOI: 10.1128/msystems.00774-19
mSystems 5/1 2020-04-25
2020 Johanne Ahrenfeldt, Madina Waisi, Isabella C. Loft, Philip T. L. C. Clausen, Rosa Allesøe, Judit Szarvas, Rene S. Hendriksen, Frank M. Aarestrup, Ole Lund
Metaphylogenetic analysis of global sewage reveals that bacterial strains associated with human disease show less degree of geographic clustering
published pages: , ISSN: 2045-2322, DOI: 10.1038/s41598-020-59292-w
Scientific Reports 10/1 2020-04-25
2018 Doreen Muth, Victor Max Corman, Hanna Roth, Tabea Binger, Ronald Dijkman, Lina Theresa Gottula, Florian Gloza-Rausch, Andrea Balboni, Mara Battilani, Danijela Rihtarič, Ivan Toplak, Ramón Seage Ameneiros, Alexander Pfeifer, Volker Thiel, Jan Felix Drexler, Marcel Alexander Müller, Christian Drosten
Attenuation of replication by a 29 nucleotide deletion in SARS-coronavirus acquired during the early stages of human-to-human transmission
published pages: , ISSN: 2045-2322, DOI: 10.1038/s41598-018-33487-8
Scientific Reports 8/1 2020-04-25
2019 Sofia Strubbia, Julien Schaeffer, Bas B. Oude Munnink, Alban Besnard, My V. T. Phan, David F. Nieuwenhuijse, Miranda de Graaf, Claudia M. E. Schapendonk, Candice Wacrenier, Matthew Cotten, Marion P. G. Koopmans, Françoise S. Le Guyader
Metavirome Sequencing to Evaluate Norovirus Diversity in Sewage and Related Bioaccumulated Oysters
published pages: , ISSN: 1664-302X, DOI: 10.3389/fmicb.2019.02394
Frontiers in Microbiology 10 2020-04-25
2019 Katerina Tsergouli, Theodoros Karampatakis, Anna-Bettina Haidich, Symeon Metallidis, Anna Papa
Nosocomial infections caused by Crimean-Congo haemorrhagic fever virus
published pages: , ISSN: 0195-6701, DOI: 10.1016/j.jhin.2019.12.001
Journal of Hospital Infection 2020-04-25
2018 Alessandra De Cesare, Antonio Parisi, Alex Lucchi, Loredana Capozzi, Angela Bianco, Frederique Pasquali, Gerardo Manfreda
Microbiota analysis and microbiological hazard assessment in poultry carcasses from conventional and antibiotic free farms
published pages: , ISSN: 2239-7132, DOI: 10.4081/ijfs.2018.7706
Italian Journal of Food Safety 7/4 2020-04-25
2019 Sandra Díaz-Sánchez, Agustín Estrada-Peña, Alejandro Cabezas-Cruz, José de la Fuente
Evolutionary Insights into the Tick Hologenome
published pages: 725-737, ISSN: 1471-4922, DOI: 10.1016/j.pt.2019.06.014
Trends in Parasitology 35/9 2020-04-25
2019 Nicolas Radomski, Sabrina Cadel-Six, Emeline Cherchame, Arnaud Felten, Pauline Barbet, Federica Palma, Ludovic Mallet, Simon Le Hello, François-Xavier Weill, Laurent Guillier, Michel-Yves Mistou
A Simple and Robust Statistical Method to Define Genetic Relatedness of Samples Related to Outbreaks at the Genomic Scale – Application to Retrospective Salmonella Foodborne Outbreak Investigations
published pages: , ISSN: 1664-302X, DOI: 10.3389/fmicb.2019.02413
Frontiers in Microbiology 10 2020-04-25
2019 Rene S. Hendriksen, Oksana Lukjancenko, Patrick Munk, Mathis H. Hjelmsø, Jennifer R. Verani, Eric Ng’eno, Godfrey Bigogo, Samuel Kiplangat, Traoré Oumar, Lasse Bergmark, Timo Röder, John C. Neatherlin, Onyango Clayton, Tine Hald, Susanne Karlsmose, Sünje J. Pamp, Barry Fields, Joel M. Montgomery, Frank M. Aarestrup
Pathogen surveillance in the informal settlement, Kibera, Kenya, using a metagenomics approach
published pages: e0222531, ISSN: 1932-6203, DOI: 10.1371/journal.pone.0222531
PLOS ONE 14/10 2020-04-25
2019 Nicholas Costa Barroso Lima, Arif M. Tanmoy, Emilie Westeel, Luiz Gonzaga Paula de Almeida, Alain Rajoharison, Maksuda Islam, Hubert P. Endtz, Samir K. Saha, Ana Tereza Ribeiro de Vasconcelos, Florence Komurian-Pradel
Analysis of isolates from Bangladesh highlights multiple ways to carry resistance genes in Salmonella Typhi
published pages: , ISSN: 1471-2164, DOI: 10.1186/s12864-019-5916-6
BMC Genomics 20/1 2020-04-25
2019 Serafeim C. Chaintoutis, Anna Papa, Danai Pervanidou, Chrysostomos I. Dovas
Evolutionary dynamics of lineage 2 West Nile virus in Europe, 2004–2018: Phylogeny, selection pressure and phylogeography
published pages: 106617, ISSN: 1055-7903, DOI: 10.1016/j.ympev.2019.106617
Molecular Phylogenetics and Evolution 141 2020-04-25
2019 Nanna Munck, James Smith, John Bates, Kathryn Glass, Tine Hald, Martyn D. Kirk
Source Attribution of Salmonella in Macadamia Nuts to Animal and Environmental Reservoirs in Queensland, Australia
published pages: , ISSN: 1535-3141, DOI: 10.1089/fpd.2019.2706
Foodborne Pathogens and Disease 2020-04-25
2019 Sarah Fourour, Pierrick Lucas, Fabrice Touzain, Véronique Tocqueville, Anne V. Gautier-Bouchardon, Isabelle Kempf, Corinne Marois-Créhan
Genomic polymorphism of Mycoplasma flocculare revealed by a newly developed multilocus sequence typing scheme
published pages: 108422, ISSN: 0378-1135, DOI: 10.1016/j.vetmic.2019.108422
Veterinary Microbiology 237 2020-04-25
2019 Sherif A El-Kafrawy, Victor M Corman, Ahmed M Tolah, Saad B Al Masaudi, Ahmed M Hassan, Marcel A Müller, Tobias Bleicker, Steve M Harakeh, Abdulrahman A Alzahrani, Ghaleb A Alsaaidi, Abdulaziz N Alagili, Anwar M Hashem, Alimuddin Zumla, Christian Drosten, Esam I Azhar
Enzootic patterns of Middle East respiratory syndrome coronavirus in imported African and local Arabian dromedary camels: a prospective genomic study
published pages: e521-e528, ISSN: 2542-5196, DOI: 10.1016/s2542-5196(19)30243-8
The Lancet Planetary Health 3/12 2020-04-25
2019 Clara Amid, Nima Pakseresht, Nicole Silvester, Suran Jayathilaka, Ole Lund, Lukasz D Dynovski, Bálint Á Pataki, Dávid Visontai, Basil Britto Xavier, Blaise T F Alako, Ariane Belka, Jose L B Cisneros, Matthew Cotten, George B Haringhuizen, Peter W Harrison, Dirk Höper, Sam Holt, Camilla Hundahl, Abdulrahman Hussein, Rolf S Kaas, Xin Liu, Rasko Leinonen, Surbhi Malhotra-Kumar, David F Nieuwenhui
The COMPARE Data Hubs
published pages: , ISSN: 1758-0463, DOI: 10.1093/database/baz136
Database 2019 2020-04-25
2019 Panagiotis Papadopoulos, Apostolos S. Angelidis, Theofilos Papadopoulos, Charalampos Kotzamanidis, Antonios Zdragas, Anna Papa, George Filioussis, Daniel Sergelidis
Staphylococcus aureus and methicillin-resistant S. aureus (MRSA) in bulk tank milk, livestock and dairy-farm personnel in north-central and north-eastern Greece: Prevalence, characterization and genetic relatedness
published pages: 103249, ISSN: 0740-0020, DOI: 10.1016/j.fm.2019.103249
Food Microbiology 84 2020-04-25
2019 F. Pasquali, I. Do Valle, F. Palma, D. Remondini, G. Manfreda, G. Castellani, R.S. Hendriksen, A. De Cesare
Application of different DNA extraction procedures, library preparation protocols and sequencing platforms: impact on sequencing results
published pages: e02745, ISSN: 2405-8440, DOI: 10.1016/j.heliyon.2019.e02745
Heliyon 5/10 2020-04-25
2017 Anna Papa, Anastasia Kontana, Katerina Tsioka, Ilias Chaligiannis, Smaragda Sotiraki
Molecular detection of Crimean-Congo hemorrhagic fever virus in ticks, Greece, 2012–2014
published pages: 3057-3063, ISSN: 0932-0113, DOI: 10.1007/s00436-017-5616-6
Parasitology Research 116/11 2020-04-25
2019 Joaquín Vicente, Marco Apollonio, Jose A. Blanco-Aguiar, Tomasz Borowik, Francesca Brivio, Jim Casaer, Simon Croft, Göran Ericsson, Ezio Ferroglio, Dolores Gavier-Widen, Christian Gortázar, Patrick A. Jansen, Oliver Keuling, Rafał Kowalczyk, Karolina Petrovic, Radim Plhal, Tomasz Podgórski, Marie Sange, Massimo Scandura, Krzysztof Schmidt, Graham C. Smith, Ramon Soriguer, Hans-Hermann Thulke,
Science-based wildlife disease response
published pages: 943.2-944, ISSN: 0036-8075, DOI: 10.1126/science.aax4310
Science 364/6444 2020-04-25
2018 Jasmine Coppens, Basil Britto Xavier, Lavanya Vanjari, Sarah De Backer, Christine Lammens, Lakshmi Vemu, Herman Goossens, Surbhi Malhotra-Kumar
Novel composite SCCmec type III element in ST239 MRSA isolated from an Indian hospital
published pages: , ISSN: 0305-7453, DOI: 10.1093/JAC/DKY399
Journal of Antimicrobial Chemotherapy 2020-04-25
2019 Claudia Wylezich, Ariane Belka, Dennis Hanke, Martin Beer, Sandra Blome, Dirk Höper
Metagenomics for broad and improved parasite detection: a proof-of-concept study using swine faecal samples
published pages: 769-777, ISSN: 0020-7519, DOI: 10.1016/j.ijpara.2019.04.007
International Journal for Parasitology 49/10 2020-04-25
2019 Wendy K. Jo, Cornelis van Elk, Marco van de Bildt, Peter van Run, Monique Petry, Sonja T. Jesse, Klaus Jung, Martin Ludlow, Thijs Kuiken, Albert Osterhaus
An evolutionary divergent pestivirus lacking the N pro gene systemically infects a whale species
published pages: 1383-1392, ISSN: 2222-1751, DOI: 10.1080/22221751.2019.1664940
Emerging Microbes & Infections 8/1 2020-04-25
2019 Yann Sévellec, Arnaud Felten, Nicolas Radomski, Sophie Granier, Simon Le Hello, Liljana Petrovska, Michel-Yves Mistou, Sabrina Cadel-Six
Genetic Diversity of Salmonella Derby from the Poultry Sector in Europe
published pages: 46, ISSN: 2076-0817, DOI: 10.3390/pathogens8020046
Pathogens 8/2 2020-04-25
2019 Meryl Vila Nova, Kévin Durimel, Kévin La, Arnaud Felten, Philippe Bessières, Michel-Yves Mistou, Mahendra Mariadassou, Nicolas Radomski
Genetic and metabolic signatures of Salmonella enterica subsp. enterica associated with animal sources at the pangenomic scale
published pages: , ISSN: 1471-2164, DOI: 10.1186/s12864-019-6188-x
BMC Genomics 20/1 2020-04-25
2019 Robert E. Weber, Michael Pietsch, Andre Frühauf, Yvonne Pfeifer, Maria Martin, Dirk Luft, Sören Gatermann, Niels Pfennigwerth, Martin Kaase, Guido Werner, Stephan Fuchs
IS26-Mediated Transfer of blaNDM–1 as the Main Route of Resistance Transmission During a Polyclonal, Multispecies Outbreak in a German Hospital
published pages: , ISSN: 1664-302X, DOI: 10.3389/fmicb.2019.02817
Frontiers in Microbiology 10 2020-04-25
2019 Amélie Chastagner, Vincent Enouf, David Peroz, Séverine Hervé, Pierrick Lucas, Stéphane Quéguiner, Stéphane Gorin, Véronique Beven, Sylvie Behillil, Philippe Leneveu, Emmanuel Garin, Yannick Blanchard, Sylvie van der Werf, Gaëlle Simon
Bidirectional Human–Swine Transmission of Seasonal Influenza A(H1N1)pdm09 Virus in Pig Herd, France, 2018
published pages: 1940-1943, ISSN: 1080-6040, DOI: 10.3201/eid2510.190068
Emerging Infectious Diseases 25/10 2020-04-25
2019 Jan Forth, Leonie Forth, Jacqueline King, Oxana Groza, Alexandra Hübner, Ann Olesen, Dirk Höper, Linda Dixon, Christopher Netherton, Thomas Rasmussen, Sandra Blome, Anne Pohlmann, Martin Beer
A Deep-Sequencing Workflow for the Fast and Efficient Generation of High-Quality African Swine Fever Virus Whole-Genome Sequences
published pages: 846, ISSN: 1999-4915, DOI: 10.3390/v11090846
Viruses 11/9 2020-04-25
2019 Anne Pohlmann, Donata Hoffmann, Christian Grund, Susanne Koethe, Daniela Hüssy, Simone M. Meier, Jacqueline King, Jan Schinköthe, Reiner Ulrich, Timm Harder, Martin Beer
Genetic Characterization and Zoonotic Potential of Highly Pathogenic Avian Influenza Virus A(H5N6/H5N5), Germany, 2017–2018
published pages: 1973-1976, ISSN: 1080-6040, DOI: 10.3201/eid2510.181931
Emerging Infectious Diseases 25/10 2020-04-25
2019 Anna Cäcilia Ingham, Katrine Kielsen, Malene Skovsted Cilieborg, Ole Lund, Susan Holmes, Frank M. Aarestrup, Klaus Gottlob Müller, Sünje Johanna Pamp
Specific gut microbiome members are associated with distinct immune markers in pediatric allogeneic hematopoietic stem cell transplantation
published pages: , ISSN: 2049-2618, DOI: 10.1186/s40168-019-0745-z
Microbiome 7/1 2020-04-25
2019 Julie Eclercy, Patricia Renson, Arnaud Lebret, Edouard Hirchaud, Valérie Normand, Mathieu Andraud, Frédéric Paboeuf, Yannick Blanchard, Nicolas Rose, Olivier Bourry
A Field Recombinant Strain Derived from Two Type 1 Porcine Reproductive and Respiratory Syndrome Virus (PRRSV-1) Modified Live Vaccines Shows Increased Viremia and Transmission in SPF Pigs
published pages: 296, ISSN: 1999-4915, DOI: 10.3390/v11030296
Viruses 11/3 2020-04-25
2020 Rachel A. Taylor, Roberto Condoleo, Robin R. L. Simons, Paul Gale, Louise A. Kelly, Emma L. Snary
The Risk of Infection by African Swine Fever Virus in European Swine Through Boar Movement and Legal Trade of Pigs and Pig Meat
published pages: , ISSN: 2297-1769, DOI: 10.3389/fvets.2019.00486
Frontiers in Veterinary Science 6 2020-04-25
2019 Danielle J. Ingle, Satheesh Nair, Hassan Hartman, Philip M. Ashton, Zoe A. Dyson, Martin Day, Joanne Freedman, Marie A. Chattaway, Kathryn E. Holt, Timothy J. Dallman
Informal genomic surveillance of regional distribution of Salmonella Typhi genotypes and antimicrobial resistance via returning travellers
published pages: e0007620, ISSN: 1935-2727, DOI: 10.1371/journal.pntd.0007620
PLOS Neglected Tropical Diseases 13/9 2020-04-25
2019 Amélie Chastagner, Emilie Bonin, Christelle Fablet, Stéphane Quéguiner, Edouard Hirchaud, Pierrick Lucas, Stéphane Gorin, Nicolas Barbier, Véronique Béven, Emmanuel Garin, Yannick Blanchard, Nicolas Rose, Séverine Hervé, Gaëlle Simon
Virus persistence in pig herds led to successive reassortment events between swine and human influenza A viruses, resulting in the emergence of a novel triple-reassortant swine influenza virus
published pages: , ISSN: 1297-9716, DOI: 10.1186/s13567-019-0699-y
Veterinary Research 50/1 2020-04-25
2020 Anita Puranik, Marek J. Slomka, Caroline J. Warren, Saumya S. Thomas, Sahar Mahmood, Alexander M.P. Byrne, Andrew M. Ramsay, Paul Skinner, Samantha Watson, Helen E. Everett, Alejandro Núñez, Ian H. Brown, Sharon M. Brookes
Transmission dynamics between infected waterfowl and terrestrial poultry: Differences between the transmission and tropism of H5N8 highly pathogenic avian influenza virus (clade 2.3.4.4a) among ducks, chickens and turkeys
published pages: 113-123, ISSN: 0042-6822, DOI: 10.1016/j.virol.2019.10.014
Virology 541 2020-04-25
2019 Robert A. Edwards, Alejandro A. Vega, Holly M. Norman, Maria Ohaeri, Kyle Levi, Elizabeth A. Dinsdale, Ondrej Cinek, Ramy K. Aziz, Katelyn McNair, Jeremy J. Barr, Kyle Bibby, Stan J. J. Brouns, Adrian Cazares, Patrick A. de Jonge, Christelle Desnues, Samuel L. Díaz Muñoz, Peter C. Fineran, Alexander Kurilshikov, Rob Lavigne, Karla Mazankova, David T. McCarthy, Franklin L. Nobrega, Alejandro Reye
Global phylogeography and ancient evolution of the widespread human gut virus crAssphage
published pages: , ISSN: 2058-5276, DOI: 10.1038/s41564-019-0494-6
Nature Microbiology 2020-04-25
2019 Orsolya Anna Pipek, Anna Medgyes-Horváth, László Dobos, József Stéger, János Szalai-Gindl, Dávid Visontai, Rolf S. Kaas, Marion Koopmans, Rene S. Hendriksen, Frank M. Aarestrup, István Csabai
Worldwide human mitochondrial haplogroup distribution from urban sewage
published pages: , ISSN: 2045-2322, DOI: 10.1038/s41598-019-48093-5
Scientific Reports 9/1 2020-04-25
2016 David Polo, Julien Schaeffer, Nelly Fournet, Jean-Claude Le Saux, Sylvain Parnaudeau, Catherine McLeod, Françoise S. Le Guyader
Digital PCR for Quantifying Norovirus in Oysters Implicated in Outbreaks, France
published pages: 2189-2191, ISSN: 1080-6040, DOI: 10.3201/eid2212.160841
Emerging Infectious Diseases 22/12 2020-04-25
2017 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
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
published pages: e0175469, ISSN: 1932-6203, DOI: 10.1371/journal.pone.0175469
PLOS ONE 12/4 2020-04-25
2017 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
Porcine Epidemic Diarrhea in Europe: In-Detail Analyses of Disease Dynamics and Molecular Epidemiology
published pages: 177, ISSN: 1999-4915, DOI: 10.3390/v9070177
Viruses 9/7 2020-04-25
2016 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
Severe acute respiratory infection caused by swine influenza virus in a child necessitating extracorporeal membrane oxygenation (ECMO), the Netherlands, October 2016
published pages: , ISSN: 1025-496X, DOI: 10.2807/1560-7917.ES.2016.21.48.30416
Eurosurveillance 21/48 2020-04-25
2016 Laura Becker, Matthias Steglich, Stephan Fuchs, Guido Werner, Ulrich Nübel
Comparison of six commercial kits to extract bacterial chromosome and plasmid DNA for MiSeq sequencing
published pages: 28063, ISSN: 2045-2322, DOI: 10.1038/srep28063
Scientific Reports 6 2020-04-25
2015 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
Comparative Genomics of Field Isolates of Mycobacterium bovis and M. caprae Provides Evidence for Possible Correlates with Bacterial Viability and Virulence
published pages: e0004232, ISSN: 1935-2735, DOI: 10.1371/journal.pntd.0004232
PLOS Neglected Tropical Diseases 9/11 2020-04-25
2016 B. B. Xavier, C. Lammens, P. Butaye, H. Goossens, S. Malhotra-Kumar
Complete sequence of an IncFII plasmid harbouring the colistin resistance gene mcr-1 isolated from Belgian pig farms
published pages: dkw191, ISSN: 0305-7453, DOI: 10.1093/jac/dkw191
Journal of Antimicrobial Chemotherapy 2020-04-25
2018 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
Human Clade 2.3.4.4 A/H5N6 Influenza Virus Lacks Mammalian Adaptation Markers and Does Not Transmit via the Airborne Route between Ferrets
published pages: e00405-17, ISSN: 2379-5042, DOI: 10.1128/mSphere.00405-17
mSphere 3/1 2020-04-25
2018 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
Wild ducks excrete highly pathogenic avian influenza virus H5N8 (2014–2015) without clinical or pathological evidence of disease
published pages: , ISSN: 2222-1751, DOI: 10.1038/s41426-018-0070-9
Emerging Microbes & Infections 7/1 2020-04-25
2016 Martin Christen Frølund Thomsen, Johanne Ahrenfeldt, Jose Luis Bellod Cisneros, Vanessa Jurtz, Mette Voldby Larsen, Henrik Hasman, Frank Møller Aarestrup, Ole Lund
A Bacterial Analysis Platform: An Integrated System for Analysing Bacterial Whole Genome Sequencing Data for Clinical Diagnostics and Surveillance
published pages: e0157718, ISSN: 1932-6203, DOI: 10.1371/journal.pone.0157718
PLOS ONE 11/6 2020-04-25
2016 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
Influenza A (H10N7) Virus Causes Respiratory Tract Disease in Harbor Seals and Ferrets
published pages: e0159625, ISSN: 1932-6203, DOI: 10.1371/journal.pone.0159625
PLOS ONE 11/7 2020-04-25
2015 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
Low Virulence and Lack of Airborne Transmission of the Dutch Highly Pathogenic Avian Influenza Virus H5N8 in Ferrets
published pages: e0129827, ISSN: 1932-6203, DOI: 10.1371/journal.pone.0129827
PLOS ONE 10/6 2020-04-25
2016 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
Neurotropic virus infections as the cause of immediate and delayed neuropathology
published pages: 159-184, ISSN: 0001-6322, DOI: 10.1007/s00401-015-1511-3
Acta Neuropathologica 131/2 2020-04-25
2017 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
Yellow fever in a traveller returning from Suriname to the Netherlands, March 2017
published pages: , ISSN: 1025-496X, DOI: 10.2807/1560-7917.ES.2017.22.11.30488
Eurosurveillance 22/11 2020-04-25
2018 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
Novel canine circovirus strains from Thailand: Evidence for genetic recombination
published pages: , ISSN: 2045-2322, DOI: 10.1038/s41598-018-25936-1
Scientific Reports 8/1 2020-04-25
2016 Takayuki Miura, Sébastien Lhomme, Jean-Claude Le Saux, Philippe Le Mehaute, Yvonnick Guillois, Elizabeth Couturier, Jacques Izopet, Florence Abranavel, Françoise S. Le Guyader
Detection of Hepatitis E Virus in Sewage After an Outbreak on a French Island
published pages: , ISSN: 1867-0334, DOI: 10.1007/s12560-016-9241-9
Food and Environmental Virology 2020-04-25
2018 Sasan Fereidouni, M. Jenckel, A. Seidalina, K. Karamendin, M. Beer, E. Starick, S. Asanova, E. Kasymbekov, M. Sayatov, A. Kydyrmanov
Next-generation sequencing of five new avian paramyxoviruses 8 isolates from Kazakhstan indicates a low genetic evolution rate over four decades
published pages: 331-336, ISSN: 0304-8608, DOI: 10.1007/s00705-017-3593-9
Archives of Virology 163/2 2020-04-25
2016 Bas B. Oude Munnink, My V. T. Phan, Lia van der Hoek, Paul Kellam, Matthew Cotten
Genome Sequences of a Novel Vietnamese Bat Bunyavirus
published pages: e01366-16, ISSN: 2169-8287, DOI: 10.1128/genomeA.01366-16
Genome Announcements 4/6 2020-04-25
2016 M.D. HALL, M.E.J. WOOLHOUSE, A. RAMBAUT
Using genomics data to reconstruct transmission trees during disease outbreaks
published pages: 287-296, ISSN: 0253-1933, DOI: 10.20506/rst.35.1.2433
Revue Scientifique et Technique de l\'OIE 35/1 2020-04-25
2017 Arnaud Felten, Meryl Vila Nova, Kevin Durimel, Laurent Guillier, Michel-Yves Mistou, Nicolas Radomski
First gene-ontology enrichment analysis based on bacterial coregenome variants: insights into adaptations of Salmonella serovars to mammalian- and avian-hosts
published pages: , ISSN: 1471-2180, DOI: 10.1186/s12866-017-1132-1
BMC Microbiology 17/1 2020-04-25
2016 Vanessa M. Pfankuche, Rogier Bodewes, Kerstin Hahn, Christina Puff, Andreas Beineke, André Habierski, Albert D.M.E. Osterhaus, Wolfgang Baumgärtner
Porcine Bocavirus Infection Associated with Encephalomyelitis in a Pig, Germany1
published pages: 1310-1312, ISSN: 1080-6040, DOI: 10.3201/eid2207.152049
Emerging Infectious Diseases 22/7 2020-04-25
2017 F. ALLEWELDT, S. KARA, A. OSINSKI, P. VAN BAAL, K. KELLERBORG, F.M. AARESTRUP, M. KOOPMANS
Developing a framework to assess the costeffectiveness of COMPARE – a global platform for the exchange of sequence-based pathogen data
published pages: 311-322, ISSN: 0253-1933, DOI: 10.20506/rst.36.1.2631
Revue Scientifique et Technique de l\'OIE 36/1 2020-04-25
2018 Anna Papa, Elpida Papadopoulou
Acute viral infections of the central nervous system, 2014-2016, Greece
published pages: 644-647, ISSN: 0146-6615, DOI: 10.1002/jmv.24997
Journal of Medical Virology 90/4 2020-04-25
2017 Bianca Dößelmann, Matthias Willmann, Matthias Steglich, Boyke Bunk, Ulrich Nübel, Silke Peter, Richard A. Neher
Rapid and Consistent Evolution of Colistin Resistance in Extensively Drug-Resistant Pseudomonas aeruginosa during Morbidostat Culture
published pages: e00043-17, ISSN: 0066-4804, DOI: 10.1128/AAC.00043-17
Antimicrobial Agents and Chemotherapy 61/9 2020-04-25
2017 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
Zoonotic Transmission of mcr-1 Colistin Resistance Gene from Small-Scale Poultry Farms, Vietnam
published pages: 529-532, ISSN: 1080-6040, DOI: 10.3201/eid2303.161553
Emerging Infectious Diseases 23/3 2020-04-25
2018 Carolina dos S. Ribeiro, Martine Y. van Roode, George B. Haringhuizen, Marion P. Koopmans, Eric Claassen, Linda H. M. van de Burgwal
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
published pages: e0195885, ISSN: 1932-6203, DOI: 10.1371/journal.pone.0195885
PLOS ONE 13/5 2020-04-25
2017 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
Variegated Squirrel Bornavirus 1 in Squirrels, Germany and the Netherlands
published pages: 477-481, ISSN: 1080-6040, DOI: 10.3201/eid2303.161061
Emerging Infectious Diseases 23/3 2020-04-25
2017 A. Melidou, G. Gioula, M. Exindari, E. Ioannou, K. Gkolfinopoulou, T. Georgakopoulou, S. Tsiodras, A. Papa
Ιnfluenza A(H3N2) genetic variants in vaccinated patients in northern Greece
published pages: 29-32, ISSN: 1386-6532, DOI: 10.1016/j.jcv.2017.07.003
Journal of Clinical Virology 94 2020-04-25
2018 Claudia Wylezich, Anna Papa, Martin Beer, Dirk Höper
A Versatile Sample Processing Workflow for Metagenomic Pathogen Detection
published pages: , ISSN: 2045-2322, DOI: 10.1038/s41598-018-31496-1
Scientific Reports 8/1 2020-04-25
2017 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
Norovirus Infection in Harbor Porpoises
published pages: 87-91, ISSN: 1080-6040, DOI: 10.3201/eid2301.161081
Emerging Infectious Diseases 23/1 2020-04-25
2017 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
A novel alphaherpesvirus associated with fatal diseases in banded Penguins
published pages: 89-95, ISSN: 0022-1317, DOI: 10.1099/jgv.0.000698
Journal of General Virology 98/1 2020-04-25
2018 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
Local amplification of highly pathogenic avian influenza H5N8 viruses in wild birds in the Netherlands, 2016 to 2017
published pages: , ISSN: 1025-496x, DOI: 10.2807/1560-7917.ES.2018.23.4.17-00449
Eurosurveillance 23/4 2020-04-25
2017 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
Transmission patterns and evolution of respiratory syncytial virus in a community outbreak identified by genomic analysis
published pages: , ISSN: 2057-1577, DOI: 10.1093/ve/vex006
Virus Evolution 3/1 2020-04-25
2015 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
One health, multiple challenges: The inter-species transmission of influenza A virus
published pages: 1-13, ISSN: 2352-7714, DOI: 10.1016/j.onehlt.2015.03.001
One Health 1 2020-04-25
2015 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
Seroprevalence of Antibodies against Seal Influenza A(H10N7) Virus in Harbor Seals and Gray Seals from the Netherlands
published pages: e0144899, ISSN: 1932-6203, DOI: 10.1371/journal.pone.0144899
PLOS ONE 10/12 2020-04-25
2015 M. E. J. Woolhouse, A. Rambaut, P. Kellam
Lessons from Ebola: Improving infectious disease surveillance to inform outbreak management
published pages: 307rv5-307rv5, ISSN: 1946-6234, DOI: 10.1126/scitranslmed.aab0191
Science Translational Medicine 7/307 2020-04-25
2017 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
Global outbreak of severe Mycobacterium chimaera disease after cardiac surgery: a molecular epidemiological study
published pages: 1033-1041, ISSN: 1473-3099, DOI: 10.1016/S1473-3099(17)30324-9
The Lancet Infectious Diseases 17/10 2020-04-25
2017 Dirk Höper, Claudia Wylezich, Martin Beer
Loeffler 4.0: Diagnostic Metagenomics
published pages: 17-37, ISSN: 0065-3527, DOI: 10.1016/bs.aivir.2017.08.001
Advances in Virus Research volume 99 2020-04-25
2017 Matthias Steglich, Ulrich Nübel
The challenge of detecting indels in bacterial genomes from short-read sequencing data
published pages: 11-15, ISSN: 0168-1656, DOI: 10.1016/j.jbiotec.2017.02.026
Journal of Biotechnology 250 2020-04-25
2017 Adriana Cabal, Joaquin Vicente, Julio Alvarez, Jose Angel Barasona, Mariana Boadella, Lucas Dominguez, Christian Gortazar
Human influence and biotic homogenization drive the distribution of Escherichia coli virulence genes in natural habitats
published pages: e00445, ISSN: 2045-8827, DOI: 10.1002/mbo3.445
MicrobiologyOpen 6/3 2020-04-25
2018 Panagiotis Papadopoulos, Theofilos Papadopoulos, Apostolos S. Angelidis, Evridiki Boukouvala, Antonios Zdragas, Anna Papa, Christos Hadjichristodoulou, Daniel Sergelidis
Prevalence of Staphylococcus aureus and of methicillin-resistant S. aureus (MRSA) along the production chain of dairy products in north-western Greece
published pages: 43-50, ISSN: 0740-0020, DOI: 10.1016/j.fm.2017.07.016
Food Microbiology 69 2020-04-25
2017 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
Discordant detection of avian influenza virus subtypes in time and space between poultry and wild birds; Towards improvement of surveillance programs
published pages: e0173470, ISSN: 1932-6203, DOI: 10.1371/journal.pone.0173470
PLOS ONE 12/3 2020-04-25
2017 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
Chronic norovirus infection among solid organ recipients in a tertiary care hospital, the Netherlands, 2006–2014
published pages: 265.e9-265.e13, ISSN: 1198-743X, DOI: 10.1016/j.cmi.2016.12.010
Clinical Microbiology and Infection 23/4 2020-04-25
2017 Anna Papa, Anastasia Kontana, Katerina Tsioka, Anastasios Saratsis, Smaragda Sotiraki
Novel phlebovirus detected in Haemaphysalis parva ticks in a Greek island
published pages: 157-160, ISSN: 1877-959X, DOI: 10.1016/j.ttbdis.2016.10.012
Ticks and Tick-borne Diseases 8/1 2020-04-25
2017 K. G. Joensen, A. L. Ø. Engsbro, O. Lukjancenko, R. S. Kaas, O. Lund, H. Westh, F. M. Aarestrup
Evaluating next-generation sequencing for direct clinical diagnostics in diarrhoeal disease
published pages: 1325-1338, ISSN: 0934-9723, DOI: 10.1007/s10096-017-2947-2
European Journal of Clinical Microbiology & Infectious Diseases 36/7 2020-04-25
2017 David F. Nieuwenhuijse, Marion P. G. Koopmans
Metagenomic Sequencing for Surveillance of Food- and Waterborne Viral Diseases
published pages: , ISSN: 1664-302X, DOI: 10.3389/fmicb.2017.00230
Frontiers in Microbiology 8 2020-04-25
2017 Kore Schlottau, Bernd Hoffmann, Timo Homeier-Bachmann, Christine Fast, Rainer G. Ulrich, Martin Beer, Donata Hoffmann
Multiple detection of zoonotic variegated squirrel bornavirus 1 RNA in different squirrel species suggests a possible unknown origin for the virus
published pages: 2747-2754, ISSN: 0304-8608, DOI: 10.1007/s00705-017-3432-z
Archives of Virology 162/9 2020-04-25
2016 Matthew Cotten, Marion Koopmans
Next-generation sequencing and norovirus
published pages: 719-722, ISSN: 1746-0794, DOI: 10.2217/fvl-2016-0099
Future Virology 11/11 2020-04-25
2016 Claudia Schulz, Cyril Viarouge, Corinne Sailleau, Martin Beer, Damien Vitour, Dirk Höper, Massimo Palmarini, Maria Jenckel, Stéphan Zientara, Bernd Hoffmann, Emmanuel Bréard, Mélanie Gallois
Bluetongue virus serotype 27: Detection and characterization of two novel variants in Corsica, France
published pages: , ISSN: 0022-1317, DOI: 10.1099/jgv.0.000557
Journal of General Virology 2020-04-25
2016 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
Dual Emergence of Usutu Virus in Common Blackbirds, Eastern France, 2015
published pages: 2225-2225, ISSN: 1080-6040, DOI: 10.3201/eid2212.161272
Emerging Infectious Diseases 22/12 2020-04-25
2017 O. Pipek, D. Ribli, J. Molnár, Á. Póti, M. Krzystanek, A. Bodor, G. E. Tusnády, Z. Szallasi, I. Csabai, D. Szüts
Fast and accurate mutation detection in whole genome sequences of multiple isogenic samples with IsoMut
published pages: , ISSN: 1471-2105, DOI: 10.1186/s12859-017-1492-4
BMC Bioinformatics 18/1 2020-04-25
2017 Djahida Benhouda, Ahcène Hakem, Anna Rosa Sannella, Afaf Benhouda, Simone M. Cacciò
First molecular investigation of Cryptosporidium spp. in young calves in Algeria
published pages: 15, ISSN: 1776-1042, DOI: 10.1051/parasite/2017014
Parasite 24 2020-04-25
2017 Laury Baillon, Emilie Mérour, Joëlle Cabon, Lénaïg Louboutin, Hélène Quenault, Fabrice Touzain, Thierry Morin, Yannick Blanchard, Stéphane Biacchesi, Michel Brémont
A single amino acid change in the non-structural NV protein impacts the virulence phenotype of Viral hemorrhagic septicemia virus in trout
published pages: 1181-1184, ISSN: 0022-1317, DOI: 10.1099/jgv.0.000830
Journal of General Virology 98/6 2020-04-25
2017 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
Outbreaks among Wild Birds and Domestic Poultry Caused by Reassorted Influenza A(H5N8) Clade 2.3.4.4 Viruses, Germany, 2016
published pages: 633-636, ISSN: 1080-6040, DOI: 10.3201/eid2304.161949
Emerging Infectious Diseases 23/4 2020-04-25
2016 Maris S Arcilla, Jarne M van Hattem, Sebastien Matamoros, Damian C Melles, John Penders, Menno D de Jong, Constance Schultsz
Dissemination of the mcr-1 colistin resistance gene
published pages: 147-149, ISSN: 1473-3099, DOI: 10.1016/S1473-3099(15)00541-1
The Lancet Infectious Diseases 16/2 2020-04-25
2017 Anna Papa, Enkeleda Velo, Perparim Kadiaj, Katerina Tsioka, Anastasia Kontana, Majlinda Kota, Silvia Bino
Crimean-Congo hemorrhagic fever virus in ticks collected from livestock in Albania
published pages: 496-500, ISSN: 1567-1348, DOI: 10.1016/j.meegid.2017.08.017
Infection, Genetics and Evolution 54 2020-04-25
2016 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
Spatiotemporal analysis of the genetic diversity of seal influenza A(H10N7) virus, Northwestern Europe
published pages: JVI.03046-15, ISSN: 0022-538X, DOI: 10.1128/JVI.03046-15
Journal of Virology 2020-04-25
2017 Guy Baele, Philippe Lemey, Andrew Rambaut, Marc A. Suchard
Adaptive MCMC in Bayesian phylogenetics: an application to analyzing partitioned data in BEAST
published pages: 1798-1805, ISSN: 1367-4803, DOI: 10.1093/bioinformatics/btx088
Bioinformatics 33/12 2020-04-25
2018 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
Canine Bocavirus Type 2 Infection Associated With Intestinal Lesions
published pages: 434-441, ISSN: 0300-9858, DOI: 10.1177/0300985818755253
Veterinary Pathology 55/3 2020-04-25
2016 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
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
published pages: , ISSN: 1865-1674, DOI: 10.1111/tbed.12570
Transboundary and Emerging Diseases 2020-04-25
2016 Anna Papa, Elton Rogozi, Enkelejda Velo, Evangelia Papadimitriou, Silvia Bino
Genetic detection of hantaviruses in rodents, Albania
published pages: n/a-n/a, ISSN: 0146-6615, DOI: 10.1002/jmv.24486
Journal of Medical Virology 2020-04-25
2015 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
Complete Genome Sequences of Field Isolates of Mycobacterium bovis and Mycobacterium caprae
published pages: e00247-15, ISSN: 2169-8287, DOI: 10.1128/genomeA.00247-15
Genome Announcements 3/3 2020-04-25
2016 Anna Papa, Styliani Pappa, Elitsa Panayotova, Elpida Papadopoulou, Iva Christova
Molecular epidemiology of Crimean-Congo hemorrhagic fever in Bulgaria-An update
published pages: 769-773, ISSN: 0146-6615, DOI: 10.1002/jmv.24400
Journal of Medical Virology 88/5 2020-04-25
2016 Matthew D. Hall, Mark E. J. Woolhouse, and Andrew Rambaut
The effects of sampling strategy on the quality of reconstruction of viral population dynamics using Bayesian skyline family coalescent methods: A simulation study
published pages: 1-14, ISSN: 2057-1577, DOI: 10.1093/ve/vew003
Virus Evolution 2016, 2(1) 2020-04-25
2016 Filip Bielejec, Guy Baele, Bram Vrancken, Marc A. Suchard, Andrew Rambaut, Philippe Lemey
SpreaD3: Interactive Visualization of Spatiotemporal History and Trait Evolutionary Processes
published pages: 2167-2169, ISSN: 0737-4038, DOI: 10.1093/molbev/msw082
Molecular Biology and Evolution 33/8 2020-04-25
2017 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
Effect of blood type on anti-α-Gal immunity and the incidence of infectious diseases
published pages: e301, ISSN: 1226-3613, DOI: 10.1038/emm.2016.164
Experimental & Molecular Medicine 49/3 2020-04-25
2015 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
Emergence of a novel GII.17 norovirus – End of the GII.4 era?
published pages: 21178, ISSN: 1560-7917, DOI: 10.2807/1560-7917.ES2015.20.26.21178
Eurosurveillance 20/26 2020-04-25
2018 Jessica R. Spengler, Dennis A. Bente, Mike Bray, Felicity Burt, Roger Hewson, Gülay Korukluoglu, Ali Mirazimi, Friedemann Weber, Anna Papa
Second International Conference on Crimean-Congo Hemorrhagic Fever
published pages: 137-147, ISSN: 0166-3542, DOI: 10.1016/j.antiviral.2017.11.019
Antiviral Research 150 2020-04-25
2016 Reina Sikkema, Marion Koopmans
One Health training and research activities in Western Europe
published pages: 33703, ISSN: 2000-8686, DOI: 10.3402/iee.v6.33703
Infection Ecology & Epidemiology 6/1 2020-04-25
2015 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
Meta-genomic analysis of toilet waste from long distance flights; a step towards global surveillance of infectious diseases and antimicrobial resistance
published pages: 11444, ISSN: 2045-2322, DOI: 10.1038/srep11444
Scientific Reports 5 2020-04-25
2017 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
PulseNet International: Vision for the implementation of whole genome sequencing (WGS) for global food-borne disease surveillance
published pages: , ISSN: 1025-496X, DOI: 10.2807/1560-7917.ES.2017.22.23.30544
Eurosurveillance 22/23 2020-04-25
2016 Basil Britto Xavier, Anupam J. Das, Guy Cochrane, Sandra De Ganck, Samir Kumar-Singh, Frank Møller Aarestrup, Herman Goossens, Surbhi Malhotra-Kumar
Consolidating and Exploring Antibiotic Resistance Gene Data Resources
published pages: 851-859, ISSN: 0095-1137, DOI: 10.1128/JCM.02717-15
Journal of Clinical Microbiology 54/4 2020-04-25
2018 Frédérique Pasquali, Federica Palma, Laurent Guillier, Alex Lucchi, Alessandra De Cesare, Gerardo Manfreda
Listeria monocytogenes Sequence Types 121 and 14 Repeatedly Isolated Within One Year of Sampling in a Rabbit Meat Processing Plant: Persistence and Ecophysiology
published pages: , ISSN: 1664-302X, DOI: 10.3389/fmicb.2018.00596
Frontiers in Microbiology 9 2020-04-25
2016 Chantal BEM Reusken, V Stalin Raj, Marion P Koopmans, Bart L Haagmans
Cross host transmission in the emergence of MERS coronavirus
published pages: 55-62, ISSN: 1879-6257, DOI: 10.1016/j.coviro.2016.01.004
Current Opinion in Virology 16 2020-04-25
2017 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
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
published pages: , ISSN: 1560-7917, DOI: 10.2807/1560-7917.ES.2017.22.50.17-00762
Eurosurveillance 22/50 2020-04-25
2017 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
Widespread activity of multiple lineages of Usutu virus, western Europe, 2016
published pages: , ISSN: 1025-496X, DOI: 10.2807/1560-7917.ES.2017.22.4.30452
Eurosurveillance 22/4 2020-04-25
2017 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
Global phylogenetic analysis of Escherichia coli and plasmids carrying the mcr-1 gene indicates bacterial diversity but plasmid restriction
published pages: , ISSN: 2045-2322, DOI: 10.1038/s41598-017-15539-7
Scientific Reports 7/1 2020-04-25
2015 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
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
published pages: e0144802, ISSN: 1932-6203, DOI: 10.1371/journal.pone.0144802
PLOS ONE 10/12 2020-04-25
2017 Arnaud Felten, Laurent Guillier, Nicolas Radomski, Michel-Yves Mistou, Renaud Lailler, Sabrina Cadel-Six
Genome Target Evaluator (GTEvaluator): A workflow exploiting genome dataset to measure the sensitivity and specificity of genetic markers
published pages: e0182082, ISSN: 1932-6203, DOI: 10.1371/journal.pone.0182082
PLOS ONE 12/7 2020-04-25
2017 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
Zika virus evolution and spread in the Americas
published pages: 411-415, ISSN: 0028-0836, DOI: 10.1038/nature22402
Nature 546/7658 2020-04-25
2016 The Global Consortium for H5N8 and Related Influenza Viruses
Role for migratory wild birds in the global spread of avian influenza H5N8
published pages: 213-217, ISSN: 0036-8075, DOI: 10.1126/science.aaf8852
Science 354/6309 2020-04-25
2016 Edward C. Holmes, Gytis Dudas, Andrew Rambaut, Kristian G. Andersen
The evolution of Ebola virus: Insights from the 2013–2016 epidemic
published pages: 193-200, ISSN: 0028-0836, DOI: 10.1038/nature19790
Nature 538/7624 2020-04-25
2016 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
Biocuration of functional annotation at the European nucleotide archive
published pages: D58-D66, ISSN: 0305-1048, DOI: 10.1093/nar/gkv1311
Nucleic Acids Research 44/D1 2020-04-25
2016 Dirk Höper, Anne Pohlmann
Discovery and diagnosis of new viral pathogens: proposal for a generic workflow based on next-generation sequencing and new integrated data analysis approaches
published pages: 58-62, ISSN: 2110-5294, DOI:
Euroreference Euroreference 1 - June 2016 MET 2020-04-25
2017 Anna Papa
Emerging arboviral human diseases in Southern Europe
published pages: 1315-1322, ISSN: 0146-6615, DOI: 10.1002/jmv.24803
Journal of Medical Virology 89/8 2020-04-25
2017 F. Pfaff, K. Schlottau, S. Scholes, A. Courtenay, B. Hoffmann, D. Höper, M. Beer
A novel astrovirus associated with encephalitis and ganglionitis in domestic sheep
published pages: 677-682, ISSN: 1865-1674, DOI: 10.1111/tbed.12623
Transboundary and Emerging Diseases 64/3 2020-04-25
2016 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
Deletion Variants of Middle East Respiratory Syndrome Coronavirus from Humans, Jordan, 2015
published pages: 716-719, ISSN: 1080-6040, DOI: 10.3201/eid2204.152065
Emerging Infectious Diseases 22/4 2020-04-25
2015 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
Detection of Circovirus in Foxes with Meningoencephalitis, United Kingdom, 2009–2013
published pages: 1205-1208, ISSN: 1080-6040, DOI: 10.3201/eid2107.150228
Emerging Infectious Diseases 21/7 2020-04-25
2015 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
Detection of mcr-1 encoding plasmid-mediated colistin-resistant Escherichia coli isolates from human bloodstream infection and imported chicken meat, Denmark 2015
published pages: , ISSN: 1025-496X, DOI: 10.2807/1560-7917.ES.2015.20.49.30085
Eurosurveillance 20/49 2020-04-25
2018 Anna Papa, Elpida Papadopoulou, Katerina Tsioka, Anastasia Kontana, Styliani Pappa, Ageliki Melidou, Nektarios D. Giadinis
Isolation and whole-genome sequencing of a Crimean-Congo hemorrhagic fever virus strain, Greece
published pages: 788-791, ISSN: 1877-959X, DOI: 10.1016/j.ttbdis.2018.02.024
Ticks and Tick-borne Diseases 9/4 2020-04-25
2016 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
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
published pages: , ISSN: 1025-496X, DOI: 10.2807/1560-7917.ES.2016.21.38.30349
Eurosurveillance 21/38 2020-04-25
2018 Anne Pohlmann, Elke Starick, Christian Grund, Dirk Höper, Günter Strebelow, Anja Globig, Christoph Staubach, Franz J. Conraths, Thomas C. Mettenleiter, Timm Harder, Martin Beer
Swarm incursions of reassortants of highly pathogenic avian influenza virus strains H5N8 and H5N5, clade 2.3.4.4b, Germany, winter 2016/17
published pages: , ISSN: 2045-2322, DOI: 10.1038/s41598-017-16936-8
Scientific Reports 8/1 2020-04-25
2018 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
Full-length genome sequences of porcine epidemic diarrhoea virus strain CV777; Use of NGS to analyse genomic and sub-genomic RNAs
published pages: e0193682, ISSN: 1932-6203, DOI: 10.1371/journal.pone.0193682
PLOS ONE 13/3 2020-04-25
2017 Anna Papa, Katerina Tsergouli, Katerina Tsioka, Ali Mirazimi
Crimean-Congo Hemorrhagic Fever: Tick-Host-Virus Interactions
published pages: , ISSN: 2235-2988, DOI: 10.3389/fcimb.2017.00213
Frontiers in Cellular and Infection Microbiology 7 2020-04-25
2016 Anna Papa, Tzimoula Kotrotsiou, Elpida Papadopoulou, Chantal Reusken, Corine GeurtsvanKessel, Marion Koopmans
Challenges in laboratory diagnosis of acute viral central nervous system infections in the era of emerging infectious diseases: the syndromic approach
published pages: 829-836, ISSN: 1478-7210, DOI: 10.1080/14787210.2016.1215914
Expert Review of Anti-infective Therapy 14/9 2020-04-25
2016 Surbhi Malhotra-Kumar, Basil Britto Xavier, Anupam J Das, Christine Lammens, Patrick Butaye, Herman Goossens
Colistin resistance gene mcr-1 harboured on a multidrug resistant plasmid
published pages: 283-284, ISSN: 1473-3099, DOI: 10.1016/S1473-3099(16)00012-8
The Lancet Infectious Diseases 16/3 2020-04-25
2016 D. HÖPER, T.C. METTENLEITER, M. BEER
Metagenomic approaches to identifying infectious agents
published pages: 83-93, ISSN: 0253-1933, DOI: 10.20506/rst.35.1.2419
Revue Scientifique et Technique de l\'OIE 35/1 2020-04-25
2016 M. Beer, K. Wernike, C. Dräger, D. Höper, A. Pohlmann, C. Bergermann, C. Schröder, S. Klinkhammer, S. Blome, B. Hoffmann
High Prevalence of Highly Variable Atypical Porcine Pestiviruses Found in Germany
published pages: , ISSN: 1865-1674, DOI: 10.1111/tbed.12532
Transboundary and Emerging Diseases 2020-04-25
2018 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
Ancient human parvovirus B19 in Eurasia reveals its long-term association with humans
published pages: 7557-7562, ISSN: 0027-8424, DOI: 10.1073/pnas.1804921115
Proceedings of the National Academy of Sciences 115/29 2020-04-25
2018 Philipp Kirstahler, Søren Solborg Bjerrum, Alice Friis-Møller, Morten la Cour, Frank M. Aarestrup, Henrik Westh, Sünje Johanna Pamp
Genomics-Based Identification of Microorganisms in Human Ocular Body Fluid
published pages: , ISSN: 2045-2322, DOI: 10.1038/s41598-018-22416-4
Scientific Reports 8/1 2020-04-25
2016 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
Immunolabelling of non-phosphorylated neurofilament indicates damage of spinal cord axons in TSE-infected goats
published pages: 141.1-141, ISSN: 0042-4900, DOI: 10.1136/vr.103425
Veterinary Record 178/6 2020-04-25
2016 Frank M. Aarestrup, Marion G. Koopmans
Sharing Data for Global Infectious Disease Surveillance and Outbreak Detection
published pages: 241-245, ISSN: 0966-842X, DOI: 10.1016/j.tim.2016.01.009
Trends in Microbiology 24/4 2020-04-25
2015 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
Evolutionary origins of hepatitis A virus in small mammals
published pages: 15190-15195, ISSN: 0027-8424, DOI: 10.1073/pnas.1516992112
Proceedings of the National Academy of Sciences 112/49 2020-04-25
2016 Mark E.J. Woolhouse, Liam Brierley, Chris McCaffery, Sam Lycett
Assessing the Epidemic Potential of RNA and DNA Viruses
published pages: 2037-2044, ISSN: 1080-6040, DOI: 10.3201/eid2212.160123
Emerging Infectious Diseases 22/12 2020-04-25
2016 Miranda de Graaf, Janko van Beek, Marion P. G. Koopmans
Human norovirus transmission and evolution in a changing world
published pages: 421-433, ISSN: 1740-1526, DOI: 10.1038/nrmicro.2016.48
Nature Reviews Microbiology 14/7 2020-04-25
2018 Philip T. L. C. Clausen, Frank M. Aarestrup, Ole Lund
Rapid and precise alignment of raw reads against redundant databases with KMA
published pages: , ISSN: 1471-2105, DOI: 10.1186/s12859-018-2336-6
BMC Bioinformatics 19/1 2020-04-25
2016 Surbhi Malhotra-Kumar, Basil Britto Xavier, Anupam J Das, Christine Lammens, Ha Thi Thu Hoang, Ngoc Thi Pham, Herman Goossens
Colistin-resistant Escherichia coli harbouring mcr-1 isolated from food animals in Hanoi, Vietnam
published pages: 286-287, ISSN: 1473-3099, DOI: 10.1016/S1473-3099(16)00014-1
The Lancet Infectious Diseases 16/3 2020-04-25
2018 Mark E. J. Woolhouse, Liam Brierley
Epidemiological characteristics of human-infective RNA viruses
published pages: 180017, ISSN: 2052-4463, DOI: 10.1038/sdata.2018.17
Scientific Data 5 2020-04-25
2017 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
European Nucleotide Archive in 2016
published pages: D32-D36, ISSN: 0305-1048, DOI: 10.1093/nar/gkw1106
Nucleic Acids Research 45/D1 2020-04-25
2017 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
Evaluation of Methods for the Concentration and Extraction of Viruses from Sewage in the Context of Metagenomic Sequencing
published pages: e0170199, ISSN: 1932-6203, DOI: 10.1371/journal.pone.0170199
PLOS ONE 12/1 2020-04-25
2017 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
Global Spread of Norovirus GII.17 Kawasaki 308, 2014–2016
published pages: 1359-1354, ISSN: 1080-6040, DOI: 10.3201/eid2308.161138
Emerging Infectious Diseases 23/8 2020-04-25
2017 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
Genomic epidemiology reveals multiple introductions of Zika virus into the United States
published pages: 401-405, ISSN: 0028-0836, DOI: 10.1038/nature22400
Nature 546/7658 2020-04-25
2015 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
Influenza A(H5N8) Virus Similar to Strain in Korea Causing Highly Pathogenic Avian Influenza in Germany
published pages: 860-863, ISSN: 1080-6040, DOI: 10.3201/eid2105.141897
Emerging Infectious Diseases 21/5 2020-04-25
2017 Federica Palma, Frédérique Pasquali, Alex Lucchi, Alessandra De Cesare, Gerardo Manfreda
Whole genome sequencing for typing and characterisation of Listeria monocytogenes isolated in a rabbit meat processing plant
published pages: , ISSN: 2239-7132, DOI: 10.4081/ijfs.2017.6879
Italian Journal of Food Safety 6/3 2020-04-25
2017 Barbara B. Raddatz, Ingo Spitzbarth, Katja A. Matheis, Arno Kalkuhl, Ulrich Deschl, Wolfgang Baumgärtner, Reiner Ulrich
Microarray-Based Gene Expression Analysis for Veterinary Pathologists: A Review
published pages: 734-755, ISSN: 0300-9858, DOI: 10.1177/0300985817709887
Veterinary Pathology 54/5 2020-04-25
2015 Saskia L. Smits, Rogier Bodewes, Aritz Ruiz-González, Wolfgang Baumgärtner, Marion P. Koopmans, Albert D. M. E. Osterhaus, Anita C. Schürch
Recovering full-length viral genomes from metagenomes
published pages: , ISSN: 1664-302X, DOI: 10.3389/fmicb.2015.01069
Frontiers in Microbiology 6 2020-04-25
2017 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
Virus genomes reveal factors that spread and sustained the Ebola epidemic
published pages: 309-315, ISSN: 0028-0836, DOI: 10.1038/nature22040
Nature 544/7650 2020-04-25
2016 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
Unbiased whole-genome deep sequencing of human and porcine stool samples reveals circulation of multiple groups of rotaviruses and a putative zoonotic infection
published pages: vew027, ISSN: 2057-1577, DOI: 10.1093/ve/vew027
Virus Evolution 2/2 2020-04-25
2015 J Verhagen, H van der Jeugd, B Nolet, R Slaterus, S Kharitonov, P de Vries, O Vuong, F Majoor, T Kuiken, R Fouchier
Wild bird surveillance around outbreaks of highly pathogenic avian influenza A(H5N8) virus in the Netherlands, 2014, within the context of global flyways
published pages: 21069, ISSN: 1560-7917, DOI: 10.2807/1560-7917.ES2015.20.12.21069
Eurosurveillance 20/12 2020-04-25
2016 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
Comparison of norovirus genogroup I, II and IV seroprevalence among children in the Netherlands, 1963, 1983 and 2006
published pages: 2255-2264, ISSN: 0022-1317, DOI: 10.1099/jgv.0.000533
Journal of General Virology 97/9 2020-04-25
2016 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
Hepatitis E Virus Infection in Dromedaries, North and East Africa, United Arab Emirates, and Pakistan, 1983–2015
published pages: 1249-1252, ISSN: 1080-6040, DOI: 10.3201/eid2207.160168
Emerging Infectious Diseases 22/7 2020-04-25
2016 C. Gortázar, J. F. Ruiz-Fons, U. Höfle
Infections shared with wildlife: an updated perspective
published pages: 511-525, ISSN: 1612-4642, DOI: 10.1007/s10344-016-1033-x
European Journal of Wildlife Research 62/5 2020-04-25
2016 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
Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases
published pages: vew016, ISSN: 2057-1577, DOI: 10.1093/ve/vew016
Virus Evolution 2/1 2020-04-25
2017 B. A. D. van Bunnik, M. E. J. Woolhouse
Modelling the impact of curtailing antibiotic usage in food animals on antibiotic resistance in humans
published pages: 161067, ISSN: 2054-5703, DOI: 10.1098/rsos.161067
Royal Society Open Science 4/4 2020-04-25
2017 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
Establishment and cryptic transmission of Zika virus in Brazil and the Americas
published pages: 406-410, ISSN: 0028-0836, DOI: 10.1038/nature22401
Nature 546/7658 2020-04-25
2016 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
Presence of atypical porcine pestivirus (APPV) genomes in newborn piglets correlates with congenital tremor
published pages: 27735, ISSN: 2045-2322, DOI: 10.1038/srep27735
Scientific Reports 6 2020-04-25
2015 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
Genotypic anomaly in Ebola virus strains circulating in Magazine Wharf area, Freetown, Sierra Leone, 2015
published pages: , ISSN: 1025-496X, DOI: 10.2807/1560-7917.ES.2015.20.40.30035
Eurosurveillance 20/40 2020-04-25
2016 Basil Britto Xavier, Christine Lammens, Rohit Ruhal, Samir Kumar-Singh, Patrick Butaye, Herman Goossens, Surbhi Malhotra-Kumar
Identification of a novel plasmid-mediated colistin-resistance gene, mcr-2 , in Escherichia coli , Belgium, June 2016
published pages: , ISSN: 1025-496X, DOI: 10.2807/1560-7917.ES.2016.21.27.30280
Eurosurveillance 21/27 2020-04-25
2016 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
Comparative Proteomics Identifies Host Immune System Proteins Affected by Infection with Mycobacterium bovis
published pages: e0004541, ISSN: 1935-2735, DOI: 10.1371/journal.pntd.0004541
PLOS Neglected Tropical Diseases 10/3 2020-04-25
2018 Rachel A. Taylor, Alexander D. C. Berriman, Paul Gale, Louise A. Kelly, Emma L. Snary
A generic framework for spatial quantitative risk assessments of infectious diseases: Lumpy skin disease case study
published pages: , ISSN: 1865-1674, DOI: 10.1111/tbed.12993
Transboundary and Emerging Diseases 2020-04-25
2015 Béatrice Grasland, Lionel Bigault, Cécilia Bernard, Hélène Quenault, Olivier Toulouse, Christelle Fablet, Nicolas Rose, Fabrice Touzain, Yannick Blanchard
Complete Genome Sequence of a Porcine Epidemic Diarrhea S Gene Indel Strain Isolated in France in December 2014
published pages: e00535-15, ISSN: 2169-8287, DOI: 10.1128/genomeA.00535-15
Genome Announcements 3/3 2020-04-25
2018 Sandra Diaz-Sanchez, Angélica Hernández-Jarguín, Isabel G. Fernández de Mera, Pilar Alberdi, Erich Zweygarth, Christian Gortazar, José de la Fuente
Draft Genome Sequences of Anaplasma phagocytophilum , A. marginale , and A. ovis Isolates from Different Hosts
published pages: e01503-17, ISSN: 2169-8287, DOI: 10.1128/genomeA.01503-17
Genome Announcements 6/5 2020-04-25
2017 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
New Avian Hepadnavirus in Palaeognathous Bird, Germany
published pages: 2089-2091, ISSN: 1080-6040, DOI: 10.3201/eid2312.161634
Emerging Infectious Diseases 23/12 2020-04-25
2018 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
Ancient hepatitis B viruses from the Bronze Age to the Medieval period
published pages: 418-423, ISSN: 0028-0836, DOI: 10.1038/s41586-018-0097-z
Nature 557/7705 2020-04-25
2017 Annika Brinkmann, Koray Ergünay, Aleksandar Radonić, Zeliha Kocak Tufan, Cristina Domingo, Andreas Nitsche
Development and preliminary evaluation of a multiplexed amplification and next generation sequencing method for viral hemorrhagic fever diagnostics
published pages: e0006075, ISSN: 1935-2727, DOI: 10.1371/journal.pntd.0006075
PLOS Neglected Tropical Diseases 11/11 2020-04-25
2017 Anna Papa, Katerina Tsioka, Anastasia Kontana, Christos Papadopoulos, Nektarios Giadinis
Bacterial pathogens and endosymbionts in ticks
published pages: 31-35, ISSN: 1877-959X, DOI: 10.1016/j.ttbdis.2016.09.011
Ticks and Tick-borne Diseases 8/1 2020-04-25
2019 Markus H. Antwerpen, Enrico Georgi, Alexandra Nikolic, Gudrun Zoeller, Peter Wohlsein, Wolfgang Baumgärtner, Christophe Peyrefitte, Remi Charrel, Hermann Meyer
Use of Next Generation Sequencing to study two cowpox virus outbreaks
published pages: e6561, ISSN: 2167-8359, DOI: 10.7717/peerj.6561
PeerJ 7 2020-04-25
2019 Sandra Díaz-Sánchez, Angélica Hernández-Jarguín, Alessandra Torina, Isabel G. Fernández de Mera, Valeria Blanda, Santo Caracappa, Christian Gortazar, José de la Fuente
Characterization of the bacterial microbiota in wild-caught Ixodes ventalloi
published pages: 336-343, ISSN: 1877-959X, DOI: 10.1016/j.ttbdis.2018.11.014
Ticks and Tick-borne Diseases 10/2 2020-04-25
2018 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
Atypical Cowpox Virus Infection in a Series of Cats
published pages: 71-76, ISSN: 0021-9975, DOI: 10.1016/j.jcpa.2017.12.003
Journal of Comparative Pathology 158 2020-04-25
2018 Patrick Murigu Kamau Njage Clementine Henri Pimlapas Leekitcharoenphon Michel‐Yves Mistou Rene S. Hendriksen Tine Hald
Machine Learning Methods as a Tool for Predicting Risk of Illness Applying Next‐Generation Sequencing Data
published pages: , ISSN: 0272-4332, DOI: 10.1111/risa.13239
Risk Analysis 2018 2020-04-25
2019 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
Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage
published pages: , ISSN: 2041-1723, DOI: 10.1038/s41467-019-08853-3
Nature Communications 10/1 2020-04-25
2018 Jochen Kruppa, Wendy K. Jo, Erhard van der Vries, Martin Ludlow, Albert Osterhaus, Wolfgang Baumgaertner, Klaus Jung
Virus detection in high-throughput sequencing data without a reference genome of the host
published pages: 180-187, ISSN: 1567-1348, DOI: 10.1016/j.meegid.2018.09.026
Infection, Genetics and Evolution 66 2020-04-25
2019 Panagiotis Papadopoulos, Theofilos Papadopoulos, Apostolos S. Angelidis, Charalampos Kotzamanidis, Antonios Zdragas, Anna Papa, George Filioussis, Daniel Sergelidis
Prevalence, antimicrobial susceptibility and characterization of Staphylococcus aureus and methicillin-resistant Staphylococcus aureus isolated from dairy industries in north-central and north-eastern Greece
published pages: 35-41, ISSN: 0168-1605, DOI: 10.1016/j.ijfoodmicro.2018.11.007
International Journal of Food Microbiology 291 2020-04-25
2019 Anna K. Szafrańska, Vera Junker, Matthias Steglich, Ulrich Nübel
Rapid cell division of Staphylococcus aureus during colonization of the human nose
published pages: , ISSN: 1471-2164, DOI: 10.1186/s12864-019-5604-6
BMC Genomics 20/1 2020-04-25
2018 Isabel G. Fernández de Mera, Valeria Blanda, Alessandra Torina, Mayssaa Fawaz Dabaja, Ali El Romeh, Alejandro Cabezas-Cruz, José de la Fuente
Identification and molecular characterization of spotted fever group rickettsiae in ticks collected from farm ruminants in Lebanon
published pages: 104-108, ISSN: 1877-959X, DOI: 10.1016/j.ttbdis.2017.10.001
Ticks and Tick-borne Diseases 9/1 2020-04-25
2018 Federica Palma, Gerardo Manfreda, Mickael Silva, Antonio Parisi, Dillon O. R. Barker, Eduardo N. Taboada, Frédérique Pasquali, Mirko Rossi
Genome-wide identification of geographical segregated genetic markers in Salmonella enterica serovar Typhimurium variant 4,[5],12:i:-
published pages: , ISSN: 2045-2322, DOI: 10.1038/s41598-018-33266-5
Scientific Reports 8/1 2020-04-25
2019 Anna Rosa Sannella, Yupin Suputtamongkol, Ekkarat Wongsawat, Simone M. Cacciò
A retrospective molecular study of Cryptosporidium species and genotypes in HIV-infected patients from Thailand
published pages: , ISSN: 1756-3305, DOI: 10.1186/s13071-019-3348-4
Parasites & Vectors 12/1 2020-04-25
2018 Boas C L van der Putten, Daniel Remondini, Giovanni Pasquini, Victoria A Janes, Sébastien Matamoros, Constance Schultsz
Quantifying the contribution of four resistance mechanisms to ciprofloxacin MIC in Escherichia coli : a systematic review
published pages: 298-310, ISSN: 0305-7453, DOI: 10.1093/jac/dky417
Journal of Antimicrobial Chemotherapy 74/2 2020-04-25
2019 Evelyne Picard-Meyer, Veronique Beven, Edouard Hirchaud, Cédric Guillaume, Gérald Larcher, Emmanuelle Robardet, Alexandre Servat, Yannick Blanchard, Florence Cliquet
Lleida Bat Lyssavirus isolation in Miniopterus schreibersii in France
published pages: 254-258, ISSN: 1863-1959, DOI: 10.1111/zph.12535
Zoonoses and Public Health 66/2 2020-04-25
2019 Patrick Murigu Kamau Njage, Pimlapas Leekitcharoenphon, Tine Hald
Improving hazard characterization in microbial risk assessment using next generation sequencing data and machine learning: Predicting clinical outcomes in shigatoxigenic Escherichia coli
published pages: 72-82, ISSN: 0168-1605, DOI: 10.1016/j.ijfoodmicro.2018.11.016
International Journal of Food Microbiology 292 2020-04-25
2018 Sara Artigas-Jerónimo, José De La Fuente, Margarita Villar
Interactomics and tick vaccine development: new directions for the control of tick-borne diseases
published pages: 627-635, ISSN: 1478-9450, DOI: 10.1080/14789450.2018.1506701
Expert Review of Proteomics 15/8 2020-04-25
2019 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
Drivers of MERS-CoV Emergence in Qatar
published pages: 22, ISSN: 1999-4915, DOI: 10.3390/v11010022
Viruses 11/1 2020-04-25
2019 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
Global status of Middle East respiratory syndrome coronavirus in dromedary camels: a systematic review
published pages: , ISSN: 0950-2688, DOI: 10.1017/s095026881800345x
Epidemiology and Infection 147 2020-04-25
2018 Emilio Mordini
Vaccines, Apes, and Conspiracy
published pages: 55-57, ISSN: 1526-5161, DOI: 10.1080/15265161.2018.1516001
The American Journal of Bioethics 18/10 2020-04-25
2018 Ariane Belka, Mareike Fischer, Anne Pohlmann, Martin Beer, Dirk Höper
LVQ-KNN: Composition-based DNA/RNA binning of short nucleotide sequences utilizing a prototype-based k-nearest neighbor approach
published pages: 55-63, ISSN: 0168-1702, DOI: 10.1016/j.virusres.2018.10.002
Virus Research 258 2020-04-25
2018 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
Fatal Encephalitic Borna Disease Virus 1 in Solid-Organ Transplant Recipients
published pages: 1377-1379, ISSN: 0028-4793, DOI: 10.1056/NEJMc1803115
New England Journal of Medicine 379/14 2020-04-25
2018 Carolina dos S. Ribeiro, Marion P. Koopmans, George B. Haringhuizen
Threats to timely sharing of pathogen sequence data
published pages: pp. 404-406, ISSN: 1095-9203, DOI: 10.1126/science.aau5229
Science Vol. 362, Issue 6413, 2020-04-25
2018 Sam Nooij, Dennis Schmitz, Harry Vennema, Annelies Kroneman, Marion P. G. Koopmans
Overview of Virus Metagenomic Classification Methods and Their Biological Applications
published pages: , ISSN: 1664-302X, DOI: 10.3389/fmicb.2018.00749
Frontiers in Microbiology 9 2020-04-25
2018 Angélica Hernández-Jarguín, Sandra Díaz-Sánchez, Margarita Villar, José de la Fuente
Integrated metatranscriptomics and metaproteomics for the characterization of bacterial microbiota in unfed Ixodes ricinus
published pages: 1241-1251, ISSN: 1877-959X, DOI: 10.1016/j.ttbdis.2018.04.020
Ticks and Tick-borne Diseases 9/5 2020-04-25
2018 Matthias Steglich, Julia D. Hofmann, Julia Helmecke, Johannes Sikorski, Cathrin Spröer, Thomas Riedel, Boyke Bunk, Jörg Overmann, Meina Neumann-Schaal, Ulrich Nübel
Convergent Loss of ABC Transporter Genes From Clostridioides difficile Genomes Is Associated With Impaired Tyrosine Uptake and p-Cresol Production
published pages: , ISSN: 1664-302X, DOI: 10.3389/fmicb.2018.00901
Frontiers in Microbiology 9 2020-04-25
2018 Klaas Dietze, Annika Graaf, Timo Homeier-Bachmann, Christian Grund, Leonie Forth, Anne Pohlmann, Christa Jeske, Mattis Wintermann, Martin Beer, Franz J. Conraths, Timm Harder
From low to high pathogenicity-Characterization of H7N7 avian influenza viruses in two epidemiologically linked outbreaks
published pages: , ISSN: 1865-1674, DOI: 10.1111/tbed.12906
Transboundary and Emerging Diseases 2020-04-25
2018 Christine Baechlein, Anna Lena Baron, Denise Meyer, Lara Gorriz-Martin, Vanessa Maria Pfankuche, Wolfgang Baumgärtner, Susanne Polywka, Sven Peine, Nicole Fischer, Jürgen Rehage, Paul Becher
Further characterization of bovine hepacivirus: Antibody response, course of infection, and host tropism
published pages: , ISSN: 1865-1674, DOI: 10.1111/tbed.12999
Transboundary and Emerging Diseases 2020-04-25
2018 Katerina Tsergouli, Elpida Papadopoulou, Katerina Tsioka, Anna Papa
Molecular epidemiology of Dobrava-Belgrade virus in Greece
published pages: 9-12, ISSN: 1567-1348, DOI: 10.1016/j.meegid.2018.06.007
Infection, Genetics and Evolution 64 2020-04-25
2018 Anna Papa, Hana Zelená, Elpida Papadopoulou, Jakub Mrázek
Uukuniemi virus, Czech Republic
published pages: 1129-1132, ISSN: 1877-959X, DOI: 10.1016/j.ttbdis.2018.04.011
Ticks and Tick-borne Diseases 9/5 2020-04-25
2017 Ea Zankari, Rosa Allesøe, Katrine G Joensen, Lina M Cavaco, Ole Lund, Frank M Aarestrup
PointFinder: a novel web tool for WGS-based detection of antimicrobial resistance associated with chromosomal point mutations in bacterial pathogens
published pages: 2764-2768, ISSN: 0305-7453, DOI: 10.1093/jac/dkx217
Journal of Antimicrobial Chemotherapy 72/10 2020-04-25
2018 Adam Meijer, Corien M Swaan, Martin Voerknecht, Edin Jusic, Sharon van den Brink, Lisa A Wijsman, Bettie CG Voordouw, Gé A Donker, Jacqueline Sleven, Wendelien W Dorigo-Zetsma, Sanela Svraka, Michiel van Boven, Manon R Haverkate, Aura Timen, Jaap T van Dissel, Marion PG Koopmans, Theo M Bestebroer, Ron AM Fouchier
Case of seasonal reassortant A(H1N2) influenza virus infection, the Netherlands, March 2018
published pages: , ISSN: 1560-7917, DOI: 10.2807/1560-7917.ES.2018.23.15.18-00160
Eurosurveillance 23/15 2020-04-25
2018 F.X. Briand, E. Niqueux, A. Schmitz, E. Hirchaud, H. Quenault, C. Allée, A. Le Prioux, C. Guillou-Cloarec, K. Ogor, M.O. Le Bras, H. Gares, P. Daniel, A. Fediaevsky, C. Martenot, P. Massin, S. Le Bouquin, Y. Blanchard, N. Eterradossi
Emergence and multiple reassortments of French 2015–2016 highly pathogenic H5 avian influenza viruses
published pages: 208-214, ISSN: 1567-1348, DOI: 10.1016/j.meegid.2018.04.007
Infection, Genetics and Evolution 61 2020-04-25
2018 Amélie Chastagner, Séverine Hervé, Emilie Bonin, Stéphane Quéguiner, Edouard Hirchaud, Dinah Henritzi, Véronique Béven, Stéphane Gorin, Nicolas Barbier, Yannick Blanchard, Gaëlle Simon
Spatio-temporal distribution and evolution of the A/H1N1 2009 pandemic virus in pigs in France from 2009 to 2017: identification of a potential swine-specific lineage
published pages: , ISSN: 0022-538X, DOI: 10.1128/JVI.00988-18
Journal of Virology 2020-04-25
2018 S. Díaz-Sánchez, A. Hernández-Jarguín, A. Torina, I. G. Fernández de Mera, A. Estrada-Peña, M. Villar, F. La Russa, V. Blanda, J. Vicente, S. Caracappa, C. Gortazar, J. de la Fuente
Biotic and abiotic factors shape the microbiota of wild-caught populations of the arbovirus vector Culicoides imicola
published pages: , ISSN: 0962-1075, DOI: 10.1111/imb.12526
Insect Molecular Biology 2020-04-25
2018 Laura Becker, Stephan Fuchs, Yvonne Pfeifer, Torsten Semmler, Tim Eckmanns, Gerit Korr, Dagmar Sissolak, Michael Friedrichs, Edith Zill, Mei-Lin Tung, Christian Dohle, Martin Kaase, Sören Gatermann, Holger Rüssmann, Matthias Steglich, Sebastian Haller, Guido Werner
Whole Genome Sequence Analysis of CTX-M-15 Producing Klebsiella Isolates Allowed Dissecting a Polyclonal Outbreak Scenario
published pages: , ISSN: 1664-302X, DOI: 10.3389/fmicb.2018.00322
Frontiers in Microbiology 9 2020-04-25
2018 Wendy K. Jo, Vanessa M. Pfankuche, Annika Lehmbecker, Byron Martina, Ana Rubio-Garcia, Stefanie Becker, Jochen Kruppa, Klaus Jung, Daniela Klotz, Julia Metzger, Martin Ludlow, Wolfgang Baumgärtner, Erhard van der Vries, Albert Osterhaus
Association of Batai Virus Infection and Encephalitis in Harbor Seals, Germany, 2016
published pages: 1691-1695, ISSN: 1080-6040, DOI: 10.3201/eid2409.171829
Emerging Infectious Diseases 24/9 2020-04-25
2018 Thijs Kuiken, Mya Breitbart, Martin Beer, Christian Grund, Dirk Höper, Bernadette van den Hoogen, Jean-Louis H Kerkhoffs, Aloys C M Kroes, Karyna Rosario, Peter van Run, Matthias Schwarz, Sanela Svraka, Jens Teifke, Marion Koopmans
Zoonotic Infection With Pigeon Paramyxovirus Type 1 Linked to Fatal Pneumonia
published pages: 1037-1044, ISSN: 0022-1899, DOI: 10.1093/infdis/jiy036
The Journal of Infectious Diseases 218/7 2020-04-25
2018 Anna Papa, Filothei Markatou, Helena C. Maltezou, Elpida Papadopoulou, Eirini Terzi, Sarantoula Ventouri, Danai Pervanidou, Sotirios Tsiodras, Efstratios Maltezos
Crimean-Congo haemorrhagic fever in a Greek worker returning from Bulgaria, June 2018
published pages: , ISSN: 1560-7917, DOI: 10.2807/1560-7917.ES.2018.23.35.1800432
Eurosurveillance 23/35 2020-04-25
2017 Oude Munnink, Bas B; Phan, My V T; VIZIONS, Consortium; Simmonds, Peter; Koopmans, Marion P G; Kellam, Paul; van der Hoek, Lia; Cotten, Matthew
OUP accepted manuscript
published pages: , ISSN: 2057-1577, DOI: 10.1093/ve/vex022
Virus Evolution 2020-04-25
2018 Vanessa Pfankuche, Kerstin Hahn, Rogier Bodewes, Florian Hansmann, André Habierski, Ann-Kathrin Haverkamp, Stephanie Pfaender, Stephanie Walter, Christine Baechlein, Alexander Postel, Eike Steinmann, Paul Becher, Albert Osterhaus, Wolfgang Baumgärtner, Christina Puff
Comparison of Different In Situ Hybridization Techniques for the Detection of Various RNA and DNA Viruses
published pages: 384, ISSN: 1999-4915, DOI: 10.3390/v10070384
Viruses 10/7 2020-04-25
2018 David Polo, Julien Schaeffer, Peter Teunis, Vincent Buchet, Françoise S. Le Guyader
Infectivity and RNA Persistence of a Norovirus Surrogate, the Tulane Virus, in Oysters
published pages: , ISSN: 1664-302X, DOI: 10.3389/fmicb.2018.00716
Frontiers in Microbiology 9 2020-04-25
2018 Rueshandra Roosenhoff, Erhard van der Vries, Anne van der Linden, Geert van Amerongen, Koert J. Stittelaar, Saskia L. Smits, Martin Schutten, Ron A. M. Fouchier
Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance
published pages: e0200849, ISSN: 1932-6203, DOI: 10.1371/journal.pone.0200849
PLOS ONE 13/7 2020-04-25
2018 Alessandra De Cesare, Federica Palma, Alex Lucchi, Frederique Pasquali, Gerardo Manfreda
Microbiological profile of chicken carcasses: A comparative analysis using shotgun metagenomic sequencing
published pages: , ISSN: 2239-7132, DOI: 10.4081/ijfs.2018.6923
Italian Journal of Food Safety 7/1 2020-04-25
2018 Hülya Kaya, Henrik Hasman, Jesper Larsen, Marc Stegger, Thor Bech Johannesen, Rosa Lundbye Allesøe, Camilla Koldbæk Lemvigh, Frank Møller Aarestrup, Ole Lund, Anders Rhod Larsen
SCC mec Finder, a Web-Based Tool for Typing of Staphylococcal Cassette Chromosome mec in Staphylococcus aureus Using Whole-Genome Sequence Data
published pages: , ISSN: 2379-5042, DOI: 10.1128/mSphere.00612-17
mSphere 3/1 2020-04-25
2019 Marjolein J Poen, Divya Venkatesh, Theo M Bestebroer, Oanh Vuong, Rachel D Scheuer, Bas B Oude Munnink, Dennis de Meulder, Mathilde Richard, Thijs Kuiken, Marion P G Koopmans, Leon Kelder, Yong-Joo Kim, Youn-Jeong Lee, Mieke Steensels, Benedicte Lambrecht, Adam Dan, Anne Pohlmann, Martin Beer, Vladimir Savic, Ian H Brown, Ron A M Fouchier, Nicola S Lewis
Co-circulation of genetically distinct highly pathogenic avian influenza A clade 2.3.4.4 (H5N6) viruses in wild waterfowl and poultry in Europe and East Asia, 2017–18
published pages: , ISSN: 2057-1577, DOI: 10.1093/ve/vez004
Virus Evolution 5/1 2020-04-25
2017 Johanne Ahrenfeldt, Carina Skaarup, Henrik Hasman, Anders Gorm Pedersen, Frank Møller Aarestrup, Ole Lund
Bacterial whole genome-based phylogeny: construction of a new benchmarking dataset and assessment of some existing methods
published pages: , ISSN: 1471-2164, DOI: 10.1186/s12864-016-3407-6
BMC Genomics 18/1 2020-04-25
2019 Sasan Fereidouni, Graham L. Freimanis, Mukhit Orynbayev, Paolo Ribeca, John Flannery, Donald P. King, Steffen Zuther, Martin Beer, Dirk Höper, Aidyn Kydyrmanov, Kobey Karamendin, Richard Kock
Mass Die-Off of Saiga Antelopes, Kazakhstan, 2015
published pages: 1169-1176, ISSN: 1080-6040, DOI: 10.3201/eid2506.180990
Emerging Infectious Diseases 25/6 2020-04-25
2019 Johanna Kennedy, Vanessa Maria Pfankuche, Doris Hoeltig, Alexander Postel, Oliver Keuling, Malgorzata Ciurkiewicz, Wolfgang Baumgärtner, Paul Becher, Christine Baechlein
Genetic variability of porcine pegivirus in pigs from Europe and China and insights into tissue tropism
published pages: , ISSN: 2045-2322, DOI: 10.1038/s41598-019-44642-0
Scientific Reports 9/1 2020-04-25
2019 Meg Perry-Duxbury, Job van Exel, Werner Brouwer
How to value safety in economic evaluations in health care? A review of applications in different sectors
published pages: , ISSN: 1618-7598, DOI: 10.1007/s10198-019-01076-9
The European Journal of Health Economics 2020-04-25
2019 Sergio García-Fernández, Martinique Frentrup, Matthias Steglich, Aitor Gonzaga, Marta Cobo, Nieves López-Fresneña, Javier Cobo, María-Isabel Morosini, Rafael Cantón, Rosa del Campo, Ulrich Nübel
Whole-genome sequencing reveals nosocomial Clostridioides difficile transmission and a previously unsuspected epidemic scenario
published pages: , ISSN: 2045-2322, DOI: 10.1038/s41598-019-43464-4
Scientific Reports 9/1 2020-04-25
2019 Anna Papa, Elpida Papadopoulou, Charikleia Chatzixanthouliou, Petros Glouftsios, Styliani Pappa, Danai Pervanidou, Loukas Georgiou
Emergence of West Nile virus lineage 2 belonging to the Eastern European subclade, Greece
published pages: 1673-1675, ISSN: 0304-8608, DOI: 10.1007/s00705-019-04243-8
Archives of Virology 164/6 2020-04-25
2019 Annika Brinkmann, Andreas Andrusch, Ariane Belka, Claudia Wylezich, Dirk Höper, Anne Pohlmann, Thomas Nordahl Petersen, Pierrick Lucas, Yannick Blanchard, Anna Papa, Angeliki Melidou, Bas B. Oude Munnink, Jelle Matthijnssens, Ward Deboutte, Richard J. Ellis, Florian Hansmann, Wolfgang Baumgärtner, Erhard van der Vries, Albert Osterhaus, Cesare Camma, Iolanda Mangone, Alessio Lorusso, Maurilia Ma
Proficiency testing of virus diagnostics based on bioinformatics analysis of simulated in silico high-throughput sequencing datasets
published pages: , ISSN: 0095-1137, DOI: 10.1128/jcm.00466-19
Journal of Clinical Microbiology 2020-04-25
2018 Pierrick Lucas, Eric Jouy, Laetitia Le Devendec, Claire de Boisséson, Agnès Perrin-Guyomard, Thomas Jové, Yannick Blanchard, Fabrice Touzain, Isabelle Kempf
Characterization of plasmids harboring blaCTX-M genes in Escherichia coli from French pigs
published pages: 100-106, ISSN: 0378-1135, DOI: 10.1016/j.vetmic.2018.08.005
Veterinary Microbiology 224 2020-04-25
2019 Danielle J. Ingle, Anders Gonçalves da Silva, Mary Valcanis, Susan A. Ballard, Torsten Seemann, Amy V. Jennison, Ivan Bastian, Rolf Wise, Martyn D. Kirk, Benjamin P. Howden, Deborah A. Williamson
Emergence and divergence of major lineages of Shiga-toxin-producing Escherichia coli in Australia
published pages: , ISSN: 2057-5858, DOI: 10.1099/mgen.0.000268
Microbial Genomics 5/5 2020-04-25
2019 Nele Villabruna, Marion P. G. Koopmans, Miranda de Graaf
Animals as Reservoir for Human Norovirus
published pages: 478, ISSN: 1999-4915, DOI: 10.3390/v11050478
Viruses 11/5 2020-04-25
2019 Danielle J Ingle, Marion Easton, Mary Valcanis, Torsten Seemann, Jason C Kwong, Nicola Stephens, Glen P Carter, Anders Gonçalves da Silva, James Adamopoulos, Sarah L Baines, Kathryn E Holt, Eric P F Chow, Christopher K Fairley, Marcus Y Chen, Martyn D Kirk, Benjamin P Howden, Deborah A Williamson
Co-circulation of Multidrug-resistant Shigella Among Men Who Have Sex With Men in Australia
published pages: , ISSN: 1058-4838, DOI: 10.1093/cid/ciz005
Clinical Infectious Diseases 2020-04-25
2019 João Queirós, Margarita Villar, Angélica Hernández-Jarguín, Vladimir López, Isabel Fernández de Mera, Joaquín Vicente, Paulo C. Alves, Christian Gortazar, José de la Fuente
A metaproteomics approach reveals changes in mandibular lymph node microbiota of wild boar naturally exposed to an increasing trend of Mycobacterium tuberculosis complex infection
published pages: 103-112, ISSN: 1472-9792, DOI: 10.1016/j.tube.2018.12.003
Tuberculosis 114 2020-04-25
2019 Serafeim C. Chaintoutis, Elpida Papadopoulou, Angeliki Melidou, Anna Papa, Chrysostomos I. Dovas
A PCR-based NGS protocol for whole genome sequencing of West Nile virus lineage 2 directly from biological specimens
published pages: , ISSN: 0890-8508, DOI: 10.1016/j.mcp.2019.06.002
Molecular and Cellular Probes 2020-04-25
2019 B.B. Oude Munnink, M. Kik, N.D. de Bruijn, R. Kohl, A. van der Linden, C.B.E.M. Reusken, M. Koopmans
Towards high quality real-time whole genome sequencing during outbreaks using Usutu virus as example
published pages: 49-54, ISSN: 1567-1348, DOI: 10.1016/j.meegid.2019.04.015
Infection, Genetics and Evolution 73 2020-04-25
2018 Stella Kiambi, Victor M. Corman, Rina Sitawa, Jane Githinji, James Ngoci, Abdullahi S. Ozomata, Emma Gardner, Sophie von Dobschuetz, Subhash Morzaria, Joshua Kimutai, Simon Schroeder, Obadiah Njagi, Piers Simpkin, Gabriel Rugalema, Zelalem Tadesse, Juan Lubroth, Yilma Makonnen, Christian Drosten, Marcel A. Müller, Folorunso O. Fasina
Detection of distinct MERS-Coronavirus strains in dromedary camels from Kenya, 2017
published pages: 1-4, ISSN: 2222-1751, DOI: 10.1038/s41426-018-0193-z
Emerging Microbes & Infections 7/1 2020-04-25
2019 Fabian K. Berger, Sabine Gfrörer, Sören L. Becker, Rossella Baldan, Daniela Maria Cirillo, Martinique Frentrup, Matthias Steglich, Pit Engling, Ulrich Nübel, Alexander Mellmann, Markus Bischoff, Barbara Gärtner, Lutz von Müller
Hospital outbreak due to Clostridium difficile ribotype 018 (RT018) in Southern Germany
published pages: 189-193, ISSN: 1438-4221, DOI: 10.1016/j.ijmm.2019.03.001
International Journal of Medical Microbiology 309/3-4 2020-04-25
2019 Manuela Tietgen, Jan S Kramer, Steffen Brunst, Bardya Djahanschiri, Sonali Wohra, Paul G Higgins, Marko Weidensdorfer, Sara Riedel-Christ, Klaas M Pos, Aitor Gonzaga, Matthias Steglich, Ulrich Nübel, Ingo Ebersberger, Ewgenij Proschak, Stephan Göttig
Identification of the novel class D β-lactamase OXA-679 involved in carbapenem resistance in Acinetobacter calcoaceticus
published pages: 1494-1502, ISSN: 0305-7453, DOI: 10.1093/jac/dkz080
Journal of Antimicrobial Chemotherapy 74/6 2020-04-25
2019 Frederique Pasquali, Federica Palma, Marcello Trevisani, Antonio Parisi, Alex Lucchi, Alessandra De Cesare, Gerardo Manfreda
Whole genome sequencing based typing and characterisation of Shiga-toxin producing Escherichia coli strains belonging to O157 and O26 serotypes and isolated in dairy farms
published pages: , ISSN: 2239-7132, DOI: 10.4081/ijfs.2018.7673
Italian Journal of Food Safety 7/4 2020-04-25
2018 Arif M. Tanmoy, Emilie Westeel, Katrien De Bruyne, Johan Goris, Alain Rajoharison, Mohammad S. I. Sajib, Alex van Belkum, Samir K. Saha, Florence Komurian-Pradel, Hubert P. Endtz
Salmonella enterica Serovar Typhi in Bangladesh: Exploration of Genomic Diversity and Antimicrobial Resistance
published pages: , ISSN: 2161-2129, DOI: 10.1128/mbio.02112-18
mBio 9/6 2020-04-25
2019 Anna Papa
Diagnostic approaches for Crimean-Congo hemorrhagic fever virus
published pages: 531-536, ISSN: 1473-7159, DOI: 10.1080/14737159.2019.1615450
Expert Review of Molecular Diagnostics 19/6 2020-04-25

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