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

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Deliverables

Matrix-dependent sample handling protocols

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

Paper on methodology and results of estimating the value of safety

D14.3 A scientific paper describing the methodology and results of estimating the value of safety, with the results from several European countries (Month 45);

Report on NGS based diagnostics in comparison to gold standard methods

D6.1 Report on NGS based diagnostics in comparison to gold standard methods (month 42)

Standardized protocols

D3.3 Standardized protocols for detection of clusters of healthcare associated infections (M42)

Risk based surveillance plans, sampling algorithms and protocols

D1.2 Risk based surveillance plans, sampling algorithms and protocols for surveillance of emerging and foodborne diseases and pathogens not covered by existing surveillance (M40)

Publications and presentations

D13.6 COMPARE acknowledged publications and presentations (month 60).

Algorithm for detection of informative (sub)types

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

Cost-effectiveness report

D14.5 A report on the assessment of options for refining selected elements of COMPARE in view of improving the overall cost-effectiveness of the system, with recommendations (Month 60)

Case study cost-effectiveness report

D14.4 Report on the (potential) cost-effectiveness of COMPARE, based on the case studies (scenario/pilot/retrospective studies). Each case study presented will include a section on elements related to the system and on the wider framework (Month 54);

Workshop programme

D13.5 COMPARE workshop programme (10 planned, continuously updated) (month 12);

Prediction algorithm AMR markers

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

Sequencing workflow

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

Full technical specifications

D9.5 Full technical specifications and publication submission (Month 60)

Methodologies report

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

Standard protocol sample processing

D2.2 Standard protocol for sample processing (M24)

CE Framework

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

Initial version COMPARE RCT box V1

D10.3: Initial version COMPARE Risk Communication Tool box V1 (crct box V1) – Month 36

Integrated analytical workflows

D9.4 Integrated analytical workflows from WPs 2, 3, 4 and 5 (Month 48)

Phylogenetic and phylogeographic tools

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

Analytical workflow for clinical diagnostic application

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

Automated tools for rapid assessment of key transmission parameters

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

Analytical workflow

D4.3 Analytical workflow for epidemiological handling of and response to food-borne outbreaks in Europe (M48)

Generic RA framework

D1.3 Generic risk assessment framework to target surveillance activities and outbreak investigations (M46)

Methods for prediction of pathogen phenotype from genotype)

D5.5 Methods for prediction of pathogen phenotype from genotype data and structure models (M42)

Beta version COMPARE RCT box V2

D10.4: Beta version COMPARE Risk Communication Tool box V2 integrated and interoperable with the COMPARE platform (crct box V2) – Month 48

Integration with map / tree / network visualisation components to the COMPARE data portal

This deliverable relates to WP9 task 4, and represents the utility of the existing MicroReact map/tree/phylogeny interface, as appropriate, for use within the COMPARE data portal. The work will involve the linking of MicroReact, to the output of db searching within the COMPARE data portal and the extension of APIs to allow the tools to be ‘launched’ in remote servers (eg VMs within the cloud infrastructure) if appropriate.

Tools for rapid sequence based detection of strain specific clusters

D5.2 Tools for rapid sequence based detection of strain specific clusters in time, place and host for the main emerging pathogen classes (M30)

Tools for detecting SNPs

D5.4 Tools for detecting single nucleotide polymorphisms and analyses within and between hosts (M36)

Validated RA model for NGS data

D4.4 Validated SA model for NGS data (M48)

Generic workflow engine

D9.3 Generic workflow engine supporting assembly and functional annotation workflows (Month 36)

Data analysis pipeline

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

E-learning materials

D13.4 e-learning materials (continuously updated) (month 12);

Public website

D13.3 COMPARE public website (month 3);

Leaflet and templates

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

Publications

Crimean-Congo hemorrhagic fever virus lineages Europe 1 and Europe 2 in Bulgarian ticks

Author(s): Elitsa Panayotova, Anna Papa, Iva Trifonova, Iva Christova
Published in: Ticks and Tick-borne Diseases, 2016, ISSN 1877-959X
Publisher: Elsevier BV
DOI: 10.1016/j.ttbdis.2016.05.010

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

Author(s): Takayuki Miura, Sébastien Lhomme, Jean-Claude Le Saux, Philippe Le Mehaute, Yvonnick Guillois, Elizabeth Couturier, Jacques Izopet, Florence Abranavel, Françoise S. Le Guyader
Published in: Food and Environmental Virology, 2016, ISSN 1867-0334
Publisher: Springer Verlag
DOI: 10.1007/s12560-016-9241-9

Human norovirus transmission and evolution in a changing world

Author(s): Miranda de Graaf, Janko van Beek, Marion P. G. Koopmans
Published in: Nature Reviews Microbiology, Issue 14/7, 2016, Page(s) 421-433, ISSN 1740-1526
Publisher: Nature Publishing Group
DOI: 10.1038/nrmicro.2016.48

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

Author(s): M de Graaf, J van Beek, H Vennema, A Podkolzin, J Hewitt, F Bucardo, K Templeton, J Mans, J Nordgren, G Reuter, M Lynch, L Rasmussen, N Iritani, M Chan, V Martella, K Ambert-Balay, J Vinjé, P White, M Koopmans
Published in: Eurosurveillance, Issue 20/26, 2015, Page(s) 21178, ISSN 1560-7917
Publisher: European Centre for Disease Prevention and Control (ECDC)
DOI: 10.2807/1560-7917.ES2015.20.26.21178

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

Author(s): B. B. Xavier, C. Lammens, P. Butaye, H. Goossens, S. Malhotra-Kumar
Published in: Journal of Antimicrobial Chemotherapy, 2016, Page(s) dkw191, ISSN 0305-7453
Publisher: Oxford University Press
DOI: 10.1093/jac/dkw191

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

Author(s): B. A. D. van Bunnik, M. E. J. Woolhouse
Published in: Royal Society Open Science, Issue 4/4, 2017, Page(s) 161067, ISSN 2054-5703
Publisher: Royal Society Open Science
DOI: 10.1098/rsos.161067

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

Author(s): Laury Baillon, Emilie Mérour, Joëlle Cabon, Lénaïg Louboutin, Hélène Quenault, Fabrice Touzain, Thierry Morin, Yannick Blanchard, Stéphane Biacchesi, Michel Brémont
Published in: Journal of General Virology, Issue 98/6, 2017, Page(s) 1181-1184, ISSN 0022-1317
Publisher: Society for General Microbiology
DOI: 10.1099/jgv.0.000830

Virus genomes reveal factors that spread and sustained the Ebola epidemic

Author(s): Gytis Dudas, Luiz Max Carvalho, Trevor Bedford, Andrew J. Tatem, Guy Baele, Nuno R. Faria, Daniel J. Park, Jason T. Ladner, Armando Arias, Danny Asogun, Filip Bielejec, Sarah L. Caddy, Matthew Cotten, Jonathan D’Ambrozio, Simon Dellicour, Antonino Di Caro, Joseph W. Diclaro, Sophie Duraffour, Michael J. Elmore, Lawrence S. Fakoli, Ousmane Faye, Merle L. Gilbert, Sahr M. Gevao, Stephen Gire, Adri
Published in: Nature, Issue 544/7650, 2017, Page(s) 309-315, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/nature22040

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

Author(s): Bianca Dößelmann, Matthias Willmann, Matthias Steglich, Boyke Bunk, Ulrich Nübel, Silke Peter, Richard A. Neher
Published in: Antimicrobial Agents and Chemotherapy, Issue 61/9, 2017, Page(s) e00043-17, ISSN 0066-4804
Publisher: American Society for Microbiology
DOI: 10.1128/AAC.00043-17

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

Author(s): Dennis Hanke, Anne Pohlmann, Carola Sauter-Louis, Dirk Höper, Julia Stadler, Mathias Ritzmann, Adi Steinrigl, Bernd-Andreas Schwarz, Valerij Akimkin, Robert Fux, Sandra Blome, Martin Beer
Published in: Viruses, Issue 9/7, 2017, Page(s) 177, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v9070177

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

Author(s): Anna Papa, Enkeleda Velo, Perparim Kadiaj, Katerina Tsioka, Anastasia Kontana, Majlinda Kota, Silvia Bino
Published in: Infection, Genetics and Evolution, Issue 54, 2017, Page(s) 496-500, ISSN 1567-1348
Publisher: Elsevier BV
DOI: 10.1016/j.meegid.2017.08.017

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

Author(s): Kore Schlottau, Bernd Hoffmann, Timo Homeier-Bachmann, Christine Fast, Rainer G. Ulrich, Martin Beer, Donata Hoffmann
Published in: Archives of Virology, Issue 162/9, 2017, Page(s) 2747-2754, ISSN 0304-8608
Publisher: Springer Verlag
DOI: 10.1007/s00705-017-3432-z

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

Author(s): Jakko van Ingen, Thomas A Kohl, Katharina Kranzer, Barbara Hasse, Peter M Keller, Anna Katarzyna Szafrańska, Doris Hillemann, Meera Chand, Peter Werner Schreiber, Rami Sommerstein, Christoph Berger, Michele Genoni, Christian Rüegg, Nicolas Troillet, Andreas F Widmer, Sören L Becker, Mathias Herrmann, Tim Eckmanns, Sebastian Haller, Christiane Höller, Sylvia B Debast, Maurice J Wolfhagen, Joost
Published in: The Lancet Infectious Diseases, Issue 17/10, 2017, Page(s) 1033-1041, ISSN 1473-3099
Publisher: The Lancet Publishing Group
DOI: 10.1016/S1473-3099(17)30324-9

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

Author(s): A. Melidou, G. Gioula, M. Exindari, E. Ioannou, K. Gkolfinopoulou, T. Georgakopoulou, S. Tsiodras, A. Papa
Published in: Journal of Clinical Virology, Issue 94, 2017, Page(s) 29-32, ISSN 1386-6532
Publisher: Elsevier BV
DOI: 10.1016/j.jcv.2017.07.003

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

Author(s): Charlotte Lempp, Nicole Jungwirth, Miguel L. Grilo, Anja Reckendorf, Arlena Ulrich, Abbo van Neer, Rogier Bodewes, Vanessa M. Pfankuche, Christian Bauer, Albert D. M. E. Osterhaus, Wolfgang Baumgärtner, Ursula Siebert
Published in: PLOS ONE, Issue 12/4, 2017, Page(s) e0175469, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0175469

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

Author(s): Martin C.W. Chan, Yunwen Hu, Haili Chen, Alexander T. Podkolzin, Ekaterina V. Zaytseva, Jun Komano, Naomi Sakon, Yong Poovorawan, Sompong Vongpunsawad, Thanundorn Thanusuwannasak, Joanne Hewitt, Dawn Croucher, Nikail Collins, Jan Vinjé, Xiaoli L. Pang, Bonita E. Lee, Miranda de Graaf, Janko van Beek, Harry Vennema, Marion P.G. Koopmans, Sandra Niendorf, Mateja Poljsak-Prijatelj, Andrej Steyer, Pe
Published in: Emerging Infectious Diseases, Issue 23/8, 2017, Page(s) 1359-1354, ISSN 1080-6040
Publisher: US National Center for Infectious Diseases
DOI: 10.3201/eid2308.161138

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

Author(s): Panagiotis Papadopoulos, Theofilos Papadopoulos, Apostolos S. Angelidis, Evridiki Boukouvala, Antonios Zdragas, Anna Papa, Christos Hadjichristodoulou, Daniel Sergelidis
Published in: Food Microbiology, Issue 69, 2018, Page(s) 43-50, ISSN 0740-0020
Publisher: Academic Press
DOI: 10.1016/j.fm.2017.07.016

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

Author(s): N. R. Faria, J. Quick, I.M. Claro, J. Thézé, J. G. de Jesus, M. Giovanetti, M. U. G. Kraemer, S. C. Hill, A. Black, A. C. da Costa, L. C. Franco, S. P. Silva, C.-H. Wu, J. Raghwani, S. Cauchemez, L. du Plessis, M. P. Verotti, W. K. de Oliveira, E. H. Carmo, G. E. Coelho, A. C. F. S. Santelli, L. C. Vinhal, C. M. Henriques, J. T. Simpson, M. Loose, K. G. Andersen, N. D. Grubaugh, S. Somasekar, C.
Published in: Nature, Issue 546/7658, 2017, Page(s) 406-410, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/nature22401

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

Author(s): Nathan D. Grubaugh, Jason T. Ladner, Moritz U. G. Kraemer, Gytis Dudas, Amanda L. Tan, Karthik Gangavarapu, Michael R. Wiley, Stephen White, Julien Thézé, Diogo M. Magnani, Karla Prieto, Daniel Reyes, Andrea M. Bingham, Lauren M. Paul, Refugio Robles-Sikisaka, Glenn Oliveira, Darryl Pronty, Carolyn M. Barcellona, Hayden C. Metsky, Mary Lynn Baniecki, Kayla G. Barnes, Bridget Chak, Catherine A. F
Published in: Nature, Issue 546/7658, 2017, Page(s) 401-405, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/nature22400

Zika virus evolution and spread in the Americas

Author(s): Hayden C. Metsky, Christian B. Matranga, Shirlee Wohl, Stephen F. Schaffner, Catherine A. Freije, Sarah M. Winnicki, Kendra West, James Qu, Mary Lynn Baniecki, Adrianne Gladden-Young, Aaron E. Lin, Christopher H. Tomkins-Tinch, Simon H. Ye, Daniel J. Park, Cynthia Y. Luo, Kayla G. Barnes, Rickey R. Shah, Bridget Chak, Giselle Barbosa-Lima, Edson Delatorre, Yasmine R. Vieira, Lauren M. Paul, Amanda
Published in: Nature, Issue 546/7658, 2017, Page(s) 411-415, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/nature22402

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

Author(s): Anna Papa, Katerina Tsergouli, Katerina Tsioka, Ali Mirazimi
Published in: Frontiers in Cellular and Infection Microbiology, Issue 7, 2017, ISSN 2235-2988
Publisher: Frontiers Media S. A.
DOI: 10.3389/fcimb.2017.00213

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

Author(s): J. van Beek, A.A. van der Eijk, P.L.A. Fraaij, K. Caliskan, K. Cransberg, M. Dalinghaus, R.A.S. Hoek, H.J. Metselaar, J. Roodnat, H. Vennema, M.P.G. Koopmans
Published in: Clinical Microbiology and Infection, Issue 23/4, 2017, Page(s) 265.e9-265.e13, ISSN 1198-743X
Publisher: Blackwell Publishing Inc.
DOI: 10.1016/j.cmi.2016.12.010

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

Author(s): F. ALLEWELDT, S. KARA, A. OSINSKI, P. VAN BAAL, K. KELLERBORG, F.M. AARESTRUP, M. KOOPMANS
Published in: Revue Scientifique et Technique de l'OIE, Issue 36/1, 2017, Page(s) 311-322, ISSN 0253-1933
Publisher: Office International des Epizooties (OIE)
DOI: 10.20506/rst.36.1.2631

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

Author(s): Arnaud Felten, Laurent Guillier, Nicolas Radomski, Michel-Yves Mistou, Renaud Lailler, Sabrina Cadel-Six
Published in: PLOS ONE, Issue 12/7, 2017, Page(s) e0182082, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0182082

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

Author(s): Djahida Benhouda, Ahcène Hakem, Anna Rosa Sannella, Afaf Benhouda, Simone M. Cacciò
Published in: Parasite, Issue 24, 2017, Page(s) 15, ISSN 1776-1042
Publisher: EDP SCIENCES S A
DOI: 10.1051/parasite/2017014

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

Author(s): Daniel Cadar, Renke Lühken, Henk van der Jeugd, Mutien Garigliany, Ute Ziegler, Markus Keller, Jennifer Lahoreau, Lars Lachmann, Norbert Becker, Marja Kik, Bas B Oude Munnink, Stefan Bosch, Egbert Tannich, Annick Linden, Volker Schmidt, Marion P Koopmans, Jolianne Rijks, Daniel Desmecht, Martin H Groschup, Chantal Reusken, Jonas Schmidt-Chanasit
Published in: Eurosurveillance, Issue 22/4, 2017, ISSN 1025-496X
Publisher: Centre Europeen pour la Surveillance Epidemiologique du SIDA
DOI: 10.2807/1560-7917.ES.2017.22.4.30452

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

Author(s): Marjan Wouthuyzen-Bakker, Marjolein Knoester, Aad P van den Berg, Corine H GeurtsvanKessel, Marion PG Koopmans, Coretta Van Leer-Buter, Bob Oude Velthuis, Suzan D Pas, Wilhelmina LM Ruijs, Jonas Schmidt-Chanasit, Stephen GS Vreden, Tjip S van der Werf, Chantal BEM Reusken, Wouter FW Bierman
Published in: Eurosurveillance, Issue 22/11, 2017, ISSN 1025-496X
Publisher: Centre Europeen pour la Surveillance Epidemiologique du SIDA
DOI: 10.2807/1560-7917.ES.2017.22.11.30488

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

Author(s): Mathis Hjort Hjelmsø, Maria Hellmér, Xavier Fernandez-Cassi, Natàlia Timoneda, Oksana Lukjancenko, Michael Seidel, Dennis Elsässer, Frank M. Aarestrup, Charlotta Löfström, Sílvia Bofill-Mas, Josep F. Abril, Rosina Girones, Anna Charlotte Schultz
Published in: PLOS ONE, Issue 12/1, 2017, Page(s) e0170199, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0170199

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

Author(s): O. Pipek, D. Ribli, J. Molnár, Á. Póti, M. Krzystanek, A. Bodor, G. E. Tusnády, Z. Szallasi, I. Csabai, D. Szüts
Published in: BMC Bioinformatics, Issue 18/1, 2017, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-017-1492-4

Norovirus Infection in Harbor Porpoises

Author(s): Miranda de Graaf, Rogier Bodewes, Cornelis E. van Elk, Marco van de Bildt, Sarah Getu, Georgina I. Aron, Georges M.G.M. Verjans, Albert D.M.E. Osterhaus, Judith M.A. van den Brand, Thijs Kuiken, Marion P.G. Koopmans
Published in: Emerging Infectious Diseases, Issue 23/1, 2017, Page(s) 87-91, ISSN 1080-6040
Publisher: US National Center for Infectious Diseases
DOI: 10.3201/eid2301.161081

European Nucleotide Archive in 2016

Author(s): Ana Luisa Toribio, Blaise Alako, Clara Amid, Ana Cerdeño-Tarrága, Laura Clarke, Iain Cleland, Susan Fairley, Richard Gibson, Neil Goodgame, Petra ten Hoopen, Suran Jayathilaka, Simon Kay, Rasko Leinonen, Xin Liu, Josué Martínez-Villacorta, Nima Pakseresht, Jeena Rajan, Kethi Reddy, Marc Rosello, Nicole Silvester, Dmitriy Smirnov, Daniel Vaughan, Vadim Zalunin, Guy Cochrane
Published in: Nucleic Acids Research, Issue 45/D1, 2017, Page(s) D32-D36, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkw1106

Cross host transmission in the emergence of MERS coronavirus

Author(s): Chantal BEM Reusken, V Stalin Raj, Marion P Koopmans, Bart L Haagmans
Published in: Current Opinion in Virology, Issue 16, 2016, Page(s) 55-62, ISSN 1879-6257
Publisher: Elsevier BV
DOI: 10.1016/j.coviro.2016.01.004

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

Author(s): Janko van Beek, Miranda de Graaf, Ming Xia, Xi Jiang, Jan Vinjé, Mathias Beersma, Erwin de Bruin, David van de Vijver, Melle Holwerda, Marlies van Houten, Annemarie M. Buisman, Rob van Binnendijk, Albert D. M. E. Osterhaus, Fiona van der Klis, Harry Vennema, Marion P. G. Koopmans
Published in: Journal of General Virology, Issue 97/9, 2016, Page(s) 2255-2264, ISSN 0022-1317
Publisher: Society for General Microbiology
DOI: 10.1099/jgv.0.000533

Infections shared with wildlife: an updated perspective

Author(s): C. Gortázar, J. F. Ruiz-Fons, U. Höfle
Published in: European Journal of Wildlife Research, Issue 62/5, 2016, Page(s) 511-525, ISSN 1612-4642
Publisher: Springer Verlag
DOI: 10.1007/s10344-016-1033-x

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

Author(s): Mathilde Richard, Sander Herfst, Judith M. A. van den Brand, Pascal Lexmond, Theo M. Bestebroer, Guus F. Rimmelzwaan, Marion Koopmans, Thijs Kuiken, Ron A. M. Fouchier
Published in: PLOS ONE, Issue 10/6, 2015, Page(s) e0129827, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0129827

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

Author(s): José de la Fuente, Iratxe Díez-Delgado, Marinela Contreras, Joaquín Vicente, Alejandro Cabezas-Cruz, Marina Manrique, Raquel Tobes, Vladimir López, Beatriz Romero, Lucas Domínguez, Joseba M. Garrido, Ramón Juste, Christian Gortazar
Published in: Genome Announcements, Issue 3/3, 2015, Page(s) e00247-15, ISSN 2169-8287
Publisher: Journals ASM
DOI: 10.1128/genomeA.00247-15

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

Author(s): José de la Fuente, Iratxe Díez-Delgado, Marinela Contreras, Joaquín Vicente, Alejandro Cabezas-Cruz, Raquel Tobes, Marina Manrique, Vladimir López, Beatriz Romero, Javier Bezos, Lucas Dominguez, Iker A. Sevilla, Joseba M. Garrido, Ramón Juste, Guillermo Madico, Edward Jones-López, Christian Gortazar
Published in: PLOS Neglected Tropical Diseases, Issue 9/11, 2015, Page(s) e0004232, ISSN 1935-2735
Publisher: PUBLIC LIBRARY SCIENCE
DOI: 10.1371/journal.pntd.0004232

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

Author(s): Vladimir López, Margarita Villar, João Queirós, Joaquín Vicente, Lourdes Mateos-Hernández, Iratxe Díez-Delgado, Marinela Contreras, Paulo C. Alves, Pilar Alberdi, Christian Gortázar, José de la Fuente
Published in: PLOS Neglected Tropical Diseases, Issue 10/3, 2016, Page(s) e0004541, ISSN 1935-2735
Publisher: PUBLIC LIBRARY SCIENCE
DOI: 10.1371/journal.pntd.0004541

Neurotropic virus infections as the cause of immediate and delayed neuropathology

Author(s): Martin Ludlow, Jeroen Kortekaas, Christiane Herden, Bernd Hoffmann, Dennis Tappe, Corinna Trebst, Diane E. Griffin, Hannah E. Brindle, Tom Solomon, Alan S. Brown, Debby van Riel, Katja C. Wolthers, Dasja Pajkrt, Peter Wohlsein, Byron E. E. Martina, Wolfgang Baumgärtner, Georges M. Verjans, Albert D. M. E. Osterhaus
Published in: Acta Neuropathologica, Issue 131/2, 2016, Page(s) 159-184, ISSN 0001-6322
Publisher: Springer Verlag
DOI: 10.1007/s00401-015-1511-3

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

Author(s): Laura Becker, Matthias Steglich, Stephan Fuchs, Guido Werner, Ulrich Nübel
Published in: Scientific Reports, Issue 6, 2016, Page(s) 28063, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/srep28063

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

Author(s): Mart M. Lamers, V. Stalin Raj, Mah’d Shafei, Sami Sheikh Ali, Sultan M. Abdallh, Mahmoud Gazo, Samer Nofal, Xiaoyan Lu, Dean D. Erdman, Marion P. Koopmans, Mohammad Abdallat, Aktham Haddadin, Bart L. Haagmans
Published in: Emerging Infectious Diseases, Issue 22/4, 2016, Page(s) 716-719, ISSN 1080-6040
Publisher: US National Center for Infectious Diseases
DOI: 10.3201/eid2204.152065

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

Author(s): Alexander Postel, Florian Hansmann, Christine Baechlein, Nicole Fischer, Malik Alawi, Adam Grundhoff, Sarah Derking, Jörg Tenhündfeld, Vanessa Maria Pfankuche, Vanessa Herder, Wolfgang Baumgärtner, Michael Wendt, Paul Becher
Published in: Scientific Reports, Issue 6, 2016, Page(s) 27735, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/srep27735

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

Author(s): Alessia Franco, Pimlapas Leekitcharoenphon, Fabiola Feltrin, Patricia Alba, Gessica Cordaro, Manuela Iurescia, Rita Tolli, Mario D’Incau, Monica Staffolani, Elisabetta Di Giannatale, Rene S. Hendriksen, Antonio Battisti
Published in: PLOS ONE, Issue 10/12, 2015, Page(s) e0144802, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0144802

Biocuration of functional annotation at the European nucleotide archive

Author(s): Richard Gibson, Blaise Alako, Clara Amid, Ana Cerdeño-Tárraga, Iain Cleland, Neil Goodgame, Petra ten Hoopen, Suran Jayathilaka, Simon Kay, Rasko Leinonen, Xin Liu, Swapna Pallreddy, Nima Pakseresht, Jeena Rajan, Marc Rosselló, Nicole Silvester, Dmitriy Smirnov, Ana Luisa Toribio, Daniel Vaughan, Vadim Zalunin, Guy Cochrane
Published in: Nucleic Acids Research, Issue 44/D1, 2016, Page(s) D58-D66, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkv1311

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

Author(s): Rogier Bodewes, Ana Rubio García, Sophie M. Brasseur, Guillermo J. Sanchez Conteras, Marco W. G. van de Bildt, Marion P. G. Koopmans, Albert D. M. E. Osterhaus, Thijs Kuiken
Published in: PLOS ONE, Issue 10/12, 2015, Page(s) e0144899, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0144899

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

Author(s): Sébastien Matamoros, Jarne M. van Hattem, Maris S. Arcilla, Niels Willemse, Damian C. Melles, John Penders, Trung Nguyen Vinh, Ngo Thi Hoa, Menno D. de Jong, Constance Schultsz
Published in: Scientific Reports, Issue 7/1, 2017, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-017-15539-7

High Prevalence of Highly Variable Atypical Porcine Pestiviruses Found in Germany

Author(s): M. Beer, K. Wernike, C. Dräger, D. Höper, A. Pohlmann, C. Bergermann, C. Schröder, S. Klinkhammer, S. Blome, B. Hoffmann
Published in: Transboundary and Emerging Diseases, 2016, ISSN 1865-1674
Publisher: Blackwell-Wiss.-Verl
DOI: 10.1111/tbed.12532

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

Author(s): Armando Arias, Simon J. Watson, Danny Asogun, Ekaete Alice Tobin, Jia Lu, My V. T. Phan, Umaru Jah, Raoul Emeric Guetiya Wadoum, Luke Meredith, Lucy Thorne, Sarah Caddy, Alimamy Tarawalie, Pinky Langat, Gytis Dudas, Nuno R. Faria, Simon Dellicour, Abdul Kamara, Brima Kargbo, Brima Osaio Kamara, Sahr Gevao, Daniel Cooper, Matthew Newport, Peter Horby, Jake Dunning, Foday Sahr, Tim Brooks, Andrew J.
Published in: Virus Evolution, Issue 2/1, 2016, Page(s) vew016, ISSN 2057-1577
Publisher: Oxford University Press
DOI: 10.1093/ve/vew016

Metagenomic approaches to identifying infectious agents

Author(s): D. HÖPER, T.C. METTENLEITER, M. BEER
Published in: Revue Scientifique et Technique de l'OIE, Issue 35/1, 2016, Page(s) 83-93, ISSN 0253-1933
Publisher: Office International des Epizooties (OIE)
DOI: 10.20506/rst.35.1.2419

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

Author(s): Claudia Schulz, Cyril Viarouge, Corinne Sailleau, Martin Beer, Damien Vitour, Dirk Höper, Massimo Palmarini, Maria Jenckel, Stéphan Zientara, Bernd Hoffmann, Emmanuel Bréard, Mélanie Gallois
Published in: Journal of General Virology, 2016, ISSN 0022-1317
Publisher: Society for General Microbiology
DOI: 10.1099/jgv.0.000557

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

Author(s): Andrea Rasche, Muhammad Saqib, Anne M. Liljander, Set Bornstein, Ali Zohaib, Stefanie Renneker, Katja Steinhagen, Renate Wernery, Mario Younan, Ilona Gluecks, Mosaad Hilali, Bakri E. Musa, Joerg Jores, Ulrich Wernery, Jan Felix Drexer, Christian Drosten, Victor Max Corman
Published in: Emerging Infectious Diseases, Issue 22/7, 2016, Page(s) 1249-1252, ISSN 1080-6040
Publisher: US National Center for Infectious Diseases
DOI: 10.3201/eid2207.160168

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

Author(s): Anna Papa, Tzimoula Kotrotsiou, Elpida Papadopoulou, Chantal Reusken, Corine GeurtsvanKessel, Marion Koopmans
Published in: Expert Review of Anti-infective Therapy, Issue 14/9, 2016, Page(s) 829-836, ISSN 1478-7210
Publisher: Future Drugs Ltd.
DOI: 10.1080/14787210.2016.1215914

Using genomics data to reconstruct transmission trees during disease outbreaks

Author(s): M.D. HALL, M.E.J. WOOLHOUSE, A. RAMBAUT
Published in: Revue Scientifique et Technique de l'OIE, Issue 35/1, 2016, Page(s) 287-296, ISSN 0253-1933
Publisher: Office International des Epizooties (OIE)
DOI: 10.20506/rst.35.1.2433

Porcine Bocavirus Infection Associated with Encephalomyelitis in a Pig, Germany1

Author(s): Vanessa M. Pfankuche, Rogier Bodewes, Kerstin Hahn, Christina Puff, Andreas Beineke, André Habierski, Albert D.M.E. Osterhaus, Wolfgang Baumgärtner
Published in: Emerging Infectious Diseases, Issue 22/7, 2016, Page(s) 1310-1312, ISSN 1080-6040
Publisher: US National Center for Infectious Diseases
DOI: 10.3201/eid2207.152049

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

Author(s): Judith M. A. van den Brand, Peter Wohlsein, Sander Herfst, Rogier Bodewes, Vanessa M. Pfankuche, Marco W. G. van de Bildt, Frauke Seehusen, Christina Puff, Mathilde Richard, Ursula Siebert, Kristina Lehnert, Theo Bestebroer, Pascal Lexmond, Ron A. M. Fouchier, Ellen Prenger-Berninghoff, Werner Herbst, Marion Koopmans, Albert D. M. E. Osterhaus, Thijs Kuiken, Wolfgang Baumgärtner
Published in: PLOS ONE, Issue 11/7, 2016, Page(s) e0159625, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0159625

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

Author(s): Basil Britto Xavier, Christine Lammens, Rohit Ruhal, Samir Kumar-Singh, Patrick Butaye, Herman Goossens, Surbhi Malhotra-Kumar
Published in: Eurosurveillance, Issue 21/27, 2016, ISSN 1025-496X
Publisher: Centre Europeen pour la Surveillance Epidemiologique du SIDA
DOI: 10.2807/1560-7917.ES.2016.21.27.30280

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

Author(s): Matthew D. Hall, Mark E. J. Woolhouse, and Andrew Rambaut
Published in: Virus Evolution, Issue 2016, 2(1), 2016, Page(s) 1-14, ISSN 2057-1577
Publisher: Oxford University Press
DOI: 10.1093/ve/vew003

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

Author(s): Dirk Höper, Anne Pohlmann
Published in: Euroreference, Issue Euroreference 1 - June 2016 METHOD, 2016, Page(s) 58-62, ISSN 2110-5294
Publisher: ANSES

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

Author(s): Sasan Fereidouni, M. Jenckel, A. Seidalina, K. Karamendin, M. Beer, E. Starick, S. Asanova, E. Kasymbekov, M. Sayatov, A. Kydyrmanov
Published in: Archives of Virology, Issue 163/2, 2018, Page(s) 331-336, ISSN 0304-8608
Publisher: Springer Verlag
DOI: 10.1007/s00705-017-3593-9

Genomics-Based Identification of Microorganisms in Human Ocular Body Fluid

Author(s): Philipp Kirstahler, Søren Solborg Bjerrum, Alice Friis-Møller, Morten la Cour, Frank M. Aarestrup, Henrik Westh, Sünje Johanna Pamp
Published in: Scientific Reports, Issue 8/1, 2018, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-018-22416-4

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

Author(s): Thomas Bruun Rasmussen, Maria Beatrice Boniotti, Alice Papetti, Béatrice Grasland, Jean-Pierre Frossard, Akbar Dastjerdi, Marcel Hulst, Dennis Hanke, Anne Pohlmann, Sandra Blome, Wim H. M. van der Poel, Falko Steinbach, Yannick Blanchard, Antonio Lavazza, Anette Bøtner, Graham J. Belsham
Published in: PLOS ONE, Issue 13/3, 2018, Page(s) e0193682, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0193682

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

Author(s): Anna Papa, Elpida Papadopoulou
Published in: Journal of Medical Virology, Issue 90/4, 2018, Page(s) 644-647, ISSN 0146-6615
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/jmv.24997

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

Author(s): Barbara B. Raddatz, Ingo Spitzbarth, Katja A. Matheis, Arno Kalkuhl, Ulrich Deschl, Wolfgang Baumgärtner, Reiner Ulrich
Published in: Veterinary Pathology, Issue 54/5, 2017, Page(s) 734-755, ISSN 0300-9858
Publisher: SAGE Publications
DOI: 10.1177/0300985817709887

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

Author(s): Federica Palma, Frédérique Pasquali, Alex Lucchi, Alessandra De Cesare, Gerardo Manfreda
Published in: Italian Journal of Food Safety, Issue 6/3, 2017, ISSN 2239-7132
Publisher: PagePress
DOI: 10.4081/ijfs.2017.6879

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

Author(s): Frédérique Pasquali, Federica Palma, Laurent Guillier, Alex Lucchi, Alessandra De Cesare, Gerardo Manfreda
Published in: Frontiers in Microbiology, Issue 9, 2018, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2018.00596

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

Author(s): Susanne Schjørring, Sofie Gillesberg Lassen, Tenna Jensen, Alexandra Moura, Jette S Kjeldgaard, Luise Müller, Stine Thielke, Alexandre Leclercq, Mylene M Maury, Mathieu Tourdjman, Marie-Pierre Donguy, Marc Lecuit, Steen Ethelberg, Eva M Nielsen
Published in: Eurosurveillance, Issue 22/50, 2017, ISSN 1560-7917
Publisher: European Centre for Disease Control and Prevention
DOI: 10.2807/1560-7917.ES.2017.22.50.17-00762

Canine Bocavirus Type 2 Infection Associated With Intestinal Lesions

Author(s): Chutchai Piewbang, Wendy K. Jo, Christina Puff, Martin Ludlow, Erhard van der Vries, Wijit Banlunara, Anudep Rungsipipat, Jochen Kruppa, Klaus Jung, Somporn Techangamsuwan, Wolfgang Baumgärtner, Albert D. M. E. Osterhaus
Published in: Veterinary Pathology, Issue 55/3, 2018, Page(s) 434-441, ISSN 0300-9858
Publisher: SAGE Publications
DOI: 10.1177/0300985818755253

New Avian Hepadnavirus in Palaeognathous Bird, Germany

Author(s): Wendy K. Jo, Vanessa M. Pfankuche, Henning Petersen, Samuel Frei, Maya Kummrow, Stephan Lorenzen, Martin Ludlow, Julia Metzger, Wolfgang Baumgärtner, Albert Osterhaus, Erhard van der Vries
Published in: Emerging Infectious Diseases, Issue 23/12, 2017, Page(s) 2089-2091, ISSN 1080-6040
Publisher: US National Center for Infectious Diseases
DOI: 10.3201/eid2312.161634

Epidemiological characteristics of human-infective RNA viruses

Author(s): Mark E. J. Woolhouse, Liam Brierley
Published in: Scientific Data, Issue 5, 2018, Page(s) 180017, ISSN 2052-4463
Publisher: Springer
DOI: 10.1038/sdata.2018.17

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

Author(s): Sandra Diaz-Sanchez, Angélica Hernández-Jarguín, Isabel G. Fernández de Mera, Pilar Alberdi, Erich Zweygarth, Christian Gortazar, José de la Fuente
Published in: Genome Announcements, Issue 6/5, 2018, Page(s) e01503-17, ISSN 2169-8287
Publisher: American Society for Microbiology
DOI: 10.1128/genomeA.01503-17

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

Author(s): Sander Herfst, Chris K. P. Mok, Judith M. A. van den Brand, Stefan van der Vliet, Miruna E. Rosu, Monique I. Spronken, Zifeng Yang, Dennis de Meulder, Pascal Lexmond, Theo M. Bestebroer, J. S. Malik Peiris, Ron A. M. Fouchier, Mathilde Richard
Published in: mSphere, Issue 3/1, 2018, Page(s) e00405-17, ISSN 2379-5042
Publisher: American Society for Microbiology
DOI: 10.1128/mSphere.00405-17

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

Author(s): Marjolein J. Poen, Theo M. Bestebroer, Oanh Vuong, Rachel D. Scheuer, Henk P. van der Jeugd, Erik Kleyheeg, Dirk Eggink, Pascal Lexmond, Judith M.A. van den Brand, Lineke Begeman, Stefan van der Vliet, Gerhard J.D.M. Müskens, Frank A. Majoor, Marion P.G. Koopmans, Thijs Kuiken, Ron A.M. Fouchier
Published in: Eurosurveillance, Issue 23/4, 2018, ISSN 1025-496x
Publisher: Centre Europeen pour la Surveillance Epidemiologique du SIDA
DOI: 10.2807/1560-7917.ES.2018.23.4.17-00449

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

Author(s): Anna Papa, Elpida Papadopoulou, Katerina Tsioka, Anastasia Kontana, Styliani Pappa, Ageliki Melidou, Nektarios D. Giadinis
Published in: Ticks and Tick-borne Diseases, Issue 9/4, 2018, Page(s) 788-791, ISSN 1877-959X
Publisher: Elsevier BV
DOI: 10.1016/j.ttbdis.2018.02.024

Second International Conference on Crimean-Congo Hemorrhagic Fever

Author(s): Jessica R. Spengler, Dennis A. Bente, Mike Bray, Felicity Burt, Roger Hewson, Gülay Korukluoglu, Ali Mirazimi, Friedemann Weber, Anna Papa
Published in: Antiviral Research, Issue 150, 2018, Page(s) 137-147, ISSN 0166-3542
Publisher: Elsevier BV
DOI: 10.1016/j.antiviral.2017.11.019

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

Author(s): Barbara Mühlemann, Terry C. Jones, Peter de Barros Damgaard, Morten E. Allentoft, Irina Shevnina, Andrey Logvin, Emma Usmanova, Irina P. Panyushkina, Bazartseren Boldgiv, Tsevel Bazartseren, Kadicha Tashbaeva, Victor Merz, Nina Lau, Václav Smrčka, Dmitry Voyakin, Egor Kitov, Andrey Epimakhov, Dalia Pokutta, Magdolna Vicze, T. Douglas Price, Vyacheslav Moiseyev, Anders J. Hansen, Ludovic Orlando
Published in: Nature, Issue 557/7705, 2018, Page(s) 418-423, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-018-0097-z

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

Author(s): Carolina dos S. Ribeiro, Martine Y. van Roode, George B. Haringhuizen, Marion P. Koopmans, Eric Claassen, Linda H. M. van de Burgwal
Published in: PLOS ONE, Issue 13/5, 2018, Page(s) e0195885, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0195885

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

Author(s): Annika Brinkmann, Koray Ergünay, Aleksandar Radonić, Zeliha Kocak Tufan, Cristina Domingo, Andreas Nitsche
Published in: PLOS Neglected Tropical Diseases, Issue 11/11, 2017, Page(s) e0006075, ISSN 1935-2727
Publisher: Public Library of Science
DOI: 10.1371/journal.pntd.0006075

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

Author(s): Arnaud Felten, Meryl Vila Nova, Kevin Durimel, Laurent Guillier, Michel-Yves Mistou, Nicolas Radomski
Published in: BMC Microbiology, Issue 17/1, 2017, ISSN 1471-2180
Publisher: BioMed Central
DOI: 10.1186/s12866-017-1132-1

Loeffler 4.0: Diagnostic Metagenomics

Author(s): Dirk Höper, Claudia Wylezich, Martin Beer
Published in: Advances in Virus Research, Issue volume 99, 2017, Page(s) 17-37, ISSN 0065-3527
Publisher: Academic Press
DOI: 10.1016/bs.aivir.2017.08.001

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

Author(s): Celine Nadon, Ivo Van Walle, Peter Gerner-Smidt, Josefina Campos, Isabel Chinen, Jeniffer Concepcion-Acevedo, Brent Gilpin, Anthony M. Smith, Kai Man Kam, Enrique Perez, Eija Trees, Kristy Kubota, Johanna Takkinen, Eva Møller Nielsen, Heather Carleton
Published in: Eurosurveillance, Issue 22/23, 2017, ISSN 1025-496X
Publisher: Centre Europeen pour la Surveillance Epidemiologique du SIDA
DOI: 10.2807/1560-7917.ES.2017.22.23.30544

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

Author(s): Anne Pohlmann, Elke Starick, Christian Grund, Dirk Höper, Günter Strebelow, Anja Globig, Christoph Staubach, Franz J. Conraths, Thomas C. Mettenleiter, Timm Harder, Martin Beer
Published in: Scientific Reports, Issue 8/1, 2018, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-017-16936-8

A Versatile Sample Processing Workflow for Metagenomic Pathogen Detection

Author(s): Claudia Wylezich, Anna Papa, Martin Beer, Dirk Höper
Published in: Scientific Reports, Issue 8/1, 2018, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-018-31496-1

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

Author(s): Philip T. L. C. Clausen, Frank M. Aarestrup, Ole Lund
Published in: BMC Bioinformatics, Issue 19/1, 2018, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-018-2336-6

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

Author(s): Judith M. A. van den Brand, Josanne H. Verhagen, Edwin J. B. Veldhuis Kroeze, Marco W. G. van de Bildt, Rogier Bodewes, Sander Herfst, Mathilde Richard, Pascal Lexmond, Theo M. Bestebroer, Ron A. M. Fouchier, Thijs Kuiken
Published in: Emerging Microbes & Infections, Issue 7/1, 2018, ISSN 2222-1751
Publisher: Nature Publishing Group
DOI: 10.1038/s41426-018-0070-9

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

Author(s): Barbara Mühlemann, Ashot Margaryan, Peter de Barros Damgaard, Morten E. Allentoft, Lasse Vinner, Anders J. Hansen, Andrzej Weber, Vladimir I. Bazaliiskii, Martyna Molak, Jette Arneborg, Wieslaw Bogdanowicz, Ceri Falys, Mikhail Sablin, Václav Smrčka, Sabine Sten, Kadicha Tashbaeva, Niels Lynnerup, Martin Sikora, Derek J. Smith, Ron A. M. Fouchier, Christian Drosten, Karl-Göran Sjögren, Kristia
Published in: Proceedings of the National Academy of Sciences, Issue 115/29, 2018, Page(s) 7557-7562, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.1804921115

Novel canine circovirus strains from Thailand: Evidence for genetic recombination

Author(s): Chutchai Piewbang, Wendy K. Jo, Christina Puff, Erhard van der Vries, Sawang Kesdangsakonwut, Anudep Rungsipipat, Jochen Kruppa, Klaus Jung, Wolfgang Baumgärtner, Somporn Techangamsuwan, Martin Ludlow, Albert D. M. E. Osterhaus
Published in: Scientific Reports, Issue 8/1, 2018, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-018-25936-1

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

Author(s): Kirsty R. Short, Mathilde Richard, Josanne H. Verhagen, Debby van Riel, Eefje J.A. Schrauwen, Judith M.A. van den Brand, Benjamin Mänz, Rogier Bodewes, Sander Herfst
Published in: One Health, Issue 1, 2015, Page(s) 1-13, ISSN 2352-7714
Publisher: Elsevier
DOI: 10.1016/j.onehlt.2015.03.001

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

Author(s): The Global Consortium for H5N8 and Related Influenza Viruses
Published in: Science, Issue 354/6309, 2016, Page(s) 213-217, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.aaf8852

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

Author(s): Marjolein J Poen, Josanne H Verhagen, Ruth J Manvell, Ian Brown, Theo M Bestebroer, Stefan van der Vliet, Oanh Vuong, Rachel D Scheuer, Henk P van der Jeugd, Bart A Nolet, Erik Kleyheeg, Gerhard J D M Müskens, Frank A Majoor, Christian Grund, Ron A M Fouchier
Published in: Eurosurveillance, Issue 21/38, 2016, ISSN 1025-496X
Publisher: Centre Europeen pour la Surveillance Epidemiologique du SIDA
DOI: 10.2807/1560-7917.ES.2016.21.38.30349

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

Author(s): Rachel A. Taylor, Alexander D. C. Berriman, Paul Gale, Louise A. Kelly, Emma L. Snary
Published in: Transboundary and Emerging Diseases, 2018, ISSN 1865-1674
Publisher: Blackwell-Wiss.-Verl
DOI: 10.1111/tbed.12993

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

Author(s): Alessandra De Cesare, Federica Palma, Alex Lucchi, Frederique Pasquali, Gerardo Manfreda
Published in: Italian Journal of Food Safety, Issue 7/1, 2018, ISSN 2239-7132
Publisher: PagePress
DOI: 10.4081/ijfs.2018.6923

From low to high pathogenicity-Characterization of H7N7 avian influenza viruses in two epidemiologically linked outbreaks

Author(s): Klaas Dietze, Annika Graaf, Timo Homeier-Bachmann, Christian Grund, Leonie Forth, Anne Pohlmann, Christa Jeske, Mattis Wintermann, Martin Beer, Franz J. Conraths, Timm Harder
Published in: Transboundary and Emerging Diseases, 2018, ISSN 1865-1674
Publisher: Blackwell-Wiss.-Verl
DOI: 10.1111/tbed.12906

Zoonotic Infection With Pigeon Paramyxovirus Type 1 Linked to Fatal Pneumonia

Author(s): 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
Published in: The Journal of Infectious Diseases, Issue 218/7, 2018, Page(s) 1037-1044, ISSN 0022-1899
Publisher: University of Chicago Press
DOI: 10.1093/infdis/jiy036

Comparison of Different In Situ Hybridization Techniques for the Detection of Various RNA and DNA Viruses

Author(s): 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
Published in: Viruses, Issue 10/7, 2018, Page(s) 384, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v10070384

Convergent Loss of ABC Transporter Genes From Clostridioides difficile Genomes Is Associated With Impaired Tyrosine Uptake and p-Cresol Production

Author(s): Matthias Steglich, Julia D. Hofmann, Julia Helmecke, Johannes Sikorski, Cathrin Spröer, Thomas Riedel, Boyke Bunk, Jörg Overmann, Meina Neumann-Schaal, Ulrich Nübel
Published in: Frontiers in Microbiology, Issue 9, 2018, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2018.00901

Emergence and multiple reassortments of French 2015–2016 highly pathogenic H5 avian influenza viruses

Author(s): 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
Published in: Infection, Genetics and Evolution, Issue 61, 2018, Page(s) 208-214, ISSN 1567-1348
Publisher: Elsevier BV
DOI: 10.1016/j.meegid.2018.04.007

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

Author(s): Amélie Chastagner, Séverine Hervé, Emilie Bonin, Stéphane Quéguiner, Edouard Hirchaud, Dinah Henritzi, Véronique Béven, Stéphane Gorin, Nicolas Barbier, Yannick Blanchard, Gaëlle Simon
Published in: Journal of Virology, 2018, ISSN 0022-538X
Publisher: American Society for Microbiology
DOI: 10.1128/JVI.00988-18

Crimean-Congo haemorrhagic fever in a Greek worker returning from Bulgaria, June 2018

Author(s): Anna Papa, Filothei Markatou, Helena C. Maltezou, Elpida Papadopoulou, Eirini Terzi, Sarantoula Ventouri, Danai Pervanidou, Sotirios Tsiodras, Efstratios Maltezos
Published in: Eurosurveillance, Issue 23/35, 2018, ISSN 1560-7917
Publisher: ECDC
DOI: 10.2807/1560-7917.ES.2018.23.35.1800432

Further characterization of bovine hepacivirus: Antibody response, course of infection, and host tropism

Author(s): 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
Published in: Transboundary and Emerging Diseases, 2018, ISSN 1865-1674
Publisher: Blackwell-Wiss.-Verl
DOI: 10.1111/tbed.12999

Whole Genome Sequence Analysis of CTX-M-15 Producing Klebsiella Isolates Allowed Dissecting a Polyclonal Outbreak Scenario

Author(s): 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
Published in: Frontiers in Microbiology, Issue 9, 2018, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2018.00322

Association of Batai Virus Infection and Encephalitis in Harbor Seals, Germany, 2016

Author(s): 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
Published in: Emerging Infectious Diseases, Issue 24/9, 2018, Page(s) 1691-1695, ISSN 1080-6040
Publisher: US National Center for Infectious Diseases
DOI: 10.3201/eid2409.171829

Molecular epidemiology of Dobrava-Belgrade virus in Greece

Author(s): Katerina Tsergouli, Elpida Papadopoulou, Katerina Tsioka, Anna Papa
Published in: Infection, Genetics and Evolution, Issue 64, 2018, Page(s) 9-12, ISSN 1567-1348
Publisher: Elsevier BV
DOI: 10.1016/j.meegid.2018.06.007

Uukuniemi virus, Czech Republic

Author(s): Anna Papa, Hana Zelená, Elpida Papadopoulou, Jakub Mrázek
Published in: Ticks and Tick-borne Diseases, Issue 9/5, 2018, Page(s) 1129-1132, ISSN 1877-959X
Publisher: Elsevier BV
DOI: 10.1016/j.ttbdis.2018.04.011

Biotic and abiotic factors shape the microbiota of wild-caught populations of the arbovirus vector Culicoides imicola

Author(s): 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
Published in: Insect Molecular Biology, 2018, ISSN 0962-1075
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/imb.12526

Integrated metatranscriptomics and metaproteomics for the characterization of bacterial microbiota in unfed Ixodes ricinus

Author(s): Angélica Hernández-Jarguín, Sandra Díaz-Sánchez, Margarita Villar, José de la Fuente
Published in: Ticks and Tick-borne Diseases, Issue 9/5, 2018, Page(s) 1241-1251, ISSN 1877-959X
Publisher: Elsevier BV
DOI: 10.1016/j.ttbdis.2018.04.020

Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance

Author(s): 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
Published in: PLOS ONE, Issue 13/7, 2018, Page(s) e0200849, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0200849

Case of seasonal reassortant A(H1N2) influenza virus infection, the Netherlands, March 2018

Author(s): 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
Published in: Eurosurveillance, Issue 23/15, 2018, ISSN 1560-7917
Publisher: ECDC
DOI: 10.2807/1560-7917.ES.2018.23.15.18-00160

Infectivity and RNA Persistence of a Norovirus Surrogate, the Tulane Virus, in Oysters

Author(s): David Polo, Julien Schaeffer, Peter Teunis, Vincent Buchet, Françoise S. Le Guyader
Published in: Frontiers in Microbiology, Issue 9, 2018, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2018.00716

Overview of Virus Metagenomic Classification Methods and Their Biological Applications

Author(s): Sam Nooij, Dennis Schmitz, Harry Vennema, Annelies Kroneman, Marion P. G. Koopmans
Published in: Frontiers in Microbiology, Issue 9, 2018, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2018.00749

SCC mec Finder, a Web-Based Tool for Typing of Staphylococcal Cassette Chromosome mec in Staphylococcus aureus Using Whole-Genome Sequence Data

Author(s): 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
Published in: mSphere, Issue 3/1, 2018, ISSN 2379-5042
Publisher: American Society for Microbiology
DOI: 10.1128/mSphere.00612-17

PointFinder: a novel web tool for WGS-based detection of antimicrobial resistance associated with chromosomal point mutations in bacterial pathogens

Author(s): Ea Zankari, Rosa Allesøe, Katrine G Joensen, Lina M Cavaco, Ole Lund, Frank M Aarestrup
Published in: Journal of Antimicrobial Chemotherapy, Issue 72/10, 2017, Page(s) 2764-2768, ISSN 0305-7453
Publisher: Oxford University Press
DOI: 10.1093/jac/dkx217

OUP accepted manuscript

Author(s): Oude Munnink, Bas B; Phan, My V T; VIZIONS, Consortium; Simmonds, Peter; Koopmans, Marion P G; Kellam, Paul; van der Hoek, Lia; Cotten, Matthew
Published in: Virus Evolution, 2017, ISSN 2057-1577
Publisher: Oxford University Press
DOI: 10.1093/ve/vex022

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

Author(s): Kore Schlottau, Leonie Forth, Klemens Angstwurm, Dirk Höper, Daniel Zecher, Friederike Liesche, Bernd Hoffmann, Victoria Kegel, Daniel Seehofer, Sabine Platen, Bernd Salzberger, Uwe G. Liebert, Hans-Helmut Niller, Barbara Schmidt, Kaspar Matiasek, Markus J. Riemenschneider, Christoph Brochhausen, Bernhard Banas, Lutz Renders, Philipp Moog, Silke Wunderlich, Christian L. Seifert, Ana Barreiros, Ax
Published in: New England Journal of Medicine, Issue 379/14, 2018, Page(s) 1377-1379, ISSN 0028-4793
Publisher: Massachusetts Medical Society
DOI: 10.1056/NEJMc1803115

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

Author(s): Ariane Belka, Mareike Fischer, Anne Pohlmann, Martin Beer, Dirk Höper
Published in: Virus Research, Issue 258, 2018, Page(s) 55-63, ISSN 0168-1702
Publisher: Elsevier BV
DOI: 10.1016/j.virusres.2018.10.002

Vaccines, Apes, and Conspiracy

Author(s): Emilio Mordini
Published in: The American Journal of Bioethics, Issue 18/10, 2018, Page(s) 55-57, ISSN 1526-5161
Publisher: MIT Press
DOI: 10.1080/15265161.2018.1516001

Threats to timely sharing of pathogen sequence data

Author(s): Carolina dos S. Ribeiro, Marion P. Koopmans, George B. Haringhuizen
Published in: Science, Issue Vol. 362, Issue 6413,, 2018, Page(s) pp. 404-406, ISSN 1095-9203
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.aau5229

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

Author(s): Martin Christen Frølund Thomsen, Johanne Ahrenfeldt, Jose Luis Bellod Cisneros, Vanessa Jurtz, Mette Voldby Larsen, Henrik Hasman, Frank Møller Aarestrup, Ole Lund
Published in: PLOS ONE, Issue 11/6, 2016, Page(s) e0157718, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0157718

Assessing the Epidemic Potential of RNA and DNA Viruses

Author(s): Mark E.J. Woolhouse, Liam Brierley, Chris McCaffery, Sam Lycett
Published in: Emerging Infectious Diseases, Issue 22/12, 2016, Page(s) 2037-2044, ISSN 1080-6040
Publisher: US National Center for Infectious Diseases
DOI: 10.3201/eid2212.160123

One Health training and research activities in Western Europe

Author(s): Reina Sikkema, Marion Koopmans
Published in: Infection Ecology & Epidemiology, Issue 6/1, 2016, Page(s) 33703, ISSN 2000-8686
Publisher: Co-Action Publishing
DOI: 10.3402/iee.v6.33703

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

Author(s): David Polo, Julien Schaeffer, Nelly Fournet, Jean-Claude Le Saux, Sylvain Parnaudeau, Catherine McLeod, Françoise S. Le Guyader
Published in: Emerging Infectious Diseases, Issue 22/12, 2016, Page(s) 2189-2191, ISSN 1080-6040
Publisher: US National Center for Infectious Diseases
DOI: 10.3201/eid2212.160841

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

Author(s): Patrick Murigu Kamau Njage, Pimlapas Leekitcharoenphon, Tine Hald
Published in: International Journal of Food Microbiology, Issue 292, 2019, Page(s) 72-82, ISSN 0168-1605
Publisher: Elsevier BV
DOI: 10.1016/j.ijfoodmicro.2018.11.016

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

Author(s): Patrick Murigu Kamau Njage Clementine Henri Pimlapas Leekitcharoenphon Michel‐Yves Mistou Rene S. Hendriksen Tine Hald
Published in: Risk Analysis, Issue 2018, 2018, ISSN 0272-4332
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/risa.13239

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

Author(s): R. S. Sikkema, E. A. B. A. Farag, Mazharul Islam, Muzzamil Atta, C. B. E. M. Reusken, Mohd M. Al-Hajri, M. P. G. Koopmans
Published in: Epidemiology and Infection, Issue 147, 2019, ISSN 0950-2688
Publisher: Cambridge University Press
DOI: 10.1017/s095026881800345x

Drivers of MERS-CoV Emergence in Qatar

Author(s): Elmoubasher Farag, Reina Sikkema, Tinka Vinks, Md Islam, Mohamed Nour, Hamad Al-Romaihi, Mohammed Al Thani, Muzzamil Atta, Farhoud Alhajri, Salih Al-Marri, Mohd AlHajri, Chantal Reusken, Marion Koopmans
Published in: Viruses, Issue 11/1, 2019, Page(s) 22, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v11010022

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

Author(s): Rene S. Hendriksen, Patrick Munk, Patrick Njage, Bram van Bunnik, Luke McNally, Oksana Lukjancenko, Timo Röder, David Nieuwenhuijse, Susanne Karlsmose Pedersen, Jette Kjeldgaard, Rolf S. Kaas, Philip Thomas Lanken Conradsen Clausen, Josef Korbinian Vogt, Pimlapas Leekitcharoenphon, Milou G. M. van de Schans, Tina Zuidema, Ana Maria de Roda Husman, Simon Rasmussen, Bent Petersen, Clara Amid, Guy C
Published in: Nature Communications, Issue 10/1, 2019, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-019-08853-3

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

Author(s): Jochen Kruppa, Wendy K. Jo, Erhard van der Vries, Martin Ludlow, Albert Osterhaus, Wolfgang Baumgaertner, Klaus Jung
Published in: Infection, Genetics and Evolution, Issue 66, 2018, Page(s) 180-187, ISSN 1567-1348
Publisher: Elsevier BV
DOI: 10.1016/j.meegid.2018.09.026

Lleida Bat Lyssavirus isolation in Miniopterus schreibersii in France

Author(s): Evelyne Picard-Meyer, Veronique Beven, Edouard Hirchaud, Cédric Guillaume, Gérald Larcher, Emmanuelle Robardet, Alexandre Servat, Yannick Blanchard, Florence Cliquet
Published in: Zoonoses and Public Health, Issue 66/2, 2019, Page(s) 254-258, ISSN 1863-1959
Publisher: Blackwell-Wiss.-Verl
DOI: 10.1111/zph.12535

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

Author(s): Anna Rosa Sannella, Yupin Suputtamongkol, Ekkarat Wongsawat, Simone M. Cacciò
Published in: Parasites & Vectors, Issue 12/1, 2019, ISSN 1756-3305
Publisher: BioMed Central
DOI: 10.1186/s13071-019-3348-4

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

Author(s): Anna K. Szafrańska, Vera Junker, Matthias Steglich, Ulrich Nübel
Published in: BMC Genomics, Issue 20/1, 2019, ISSN 1471-2164
Publisher: BioMed Central
DOI: 10.1186/s12864-019-5604-6

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

Author(s): Federica Palma, Gerardo Manfreda, Mickael Silva, Antonio Parisi, Dillon O. R. Barker, Eduardo N. Taboada, Frédérique Pasquali, Mirko Rossi
Published in: Scientific Reports, Issue 8/1, 2018, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-018-33266-5

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

Author(s): Isabel G. Fernández de Mera, Valeria Blanda, Alessandra Torina, Mayssaa Fawaz Dabaja, Ali El Romeh, Alejandro Cabezas-Cruz, José de la Fuente
Published in: Ticks and Tick-borne Diseases, Issue 9/1, 2018, Page(s) 104-108, ISSN 1877-959X
Publisher: Elsevier BV
DOI: 10.1016/j.ttbdis.2017.10.001

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

Author(s): Boas C L van der Putten, Daniel Remondini, Giovanni Pasquini, Victoria A Janes, Sébastien Matamoros, Constance Schultsz
Published in: Journal of Antimicrobial Chemotherapy, Issue 74/2, 2018, Page(s) 298-310, ISSN 0305-7453
Publisher: Oxford University Press
DOI: 10.1093/jac/dky417

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

Author(s): Sara Artigas-Jerónimo, José De La Fuente, Margarita Villar
Published in: Expert Review of Proteomics, Issue 15/8, 2018, Page(s) 627-635, ISSN 1478-9450
Publisher: Future Drugs Ltd.
DOI: 10.1080/14789450.2018.1506701

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

Author(s): Panagiotis Papadopoulos, Theofilos Papadopoulos, Apostolos S. Angelidis, Charalampos Kotzamanidis, Antonios Zdragas, Anna Papa, George Filioussis, Daniel Sergelidis
Published in: International Journal of Food Microbiology, Issue 291, 2019, Page(s) 35-41, ISSN 0168-1605
Publisher: Elsevier BV
DOI: 10.1016/j.ijfoodmicro.2018.11.007

Characterization of the bacterial microbiota in wild-caught Ixodes ventalloi

Author(s): Sandra Díaz-Sánchez, Angélica Hernández-Jarguín, Alessandra Torina, Isabel G. Fernández de Mera, Valeria Blanda, Santo Caracappa, Christian Gortazar, José de la Fuente
Published in: Ticks and Tick-borne Diseases, Issue 10/2, 2019, Page(s) 336-343, ISSN 1877-959X
Publisher: Elsevier BV
DOI: 10.1016/j.ttbdis.2018.11.014

Atypical Cowpox Virus Infection in a Series of Cats

Author(s): N. Jungwirth, C. Puff, K. Köster, R. Mischke, H. Meyer, A. Stark, B. Thoma, G. Zöller, F. Seehusen, M. Hewicker-Trautwein, A. Beineke, W. Baumgärtner, P. Wohlsein
Published in: Journal of Comparative Pathology, Issue 158, 2018, Page(s) 71-76, ISSN 0021-9975
Publisher: W. B. Saunders Co., Ltd.
DOI: 10.1016/j.jcpa.2017.12.003

Use of Next Generation Sequencing to study two cowpox virus outbreaks

Author(s): Markus H. Antwerpen, Enrico Georgi, Alexandra Nikolic, Gudrun Zoeller, Peter Wohlsein, Wolfgang Baumgärtner, Christophe Peyrefitte, Remi Charrel, Hermann Meyer
Published in: PeerJ, Issue 7, 2019, Page(s) e6561, ISSN 2167-8359
Publisher: PeerJ
DOI: 10.7717/peerj.6561

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

Author(s): Charles N. Agoti, Patrick K. Munywoki, My V. T. Phan, James R. Otieno, Everlyn Kamau, Anne Bett, Ivy Kombe, George Githinji, Graham F. Medley, Patricia A. Cane, Paul Kellam, Matthew Cotten, D. James Nokes
Published in: Virus Evolution, Issue 3/1, 2017, ISSN 2057-1577
Publisher: Oxford University Press
DOI: 10.1093/ve/vex006

A metaproteomics approach reveals changes in mandibular lymph node microbiota of wild boar naturally exposed to an increasing trend of Mycobacterium tuberculosis complex infection

Author(s): João Queirós, Margarita Villar, Angélica Hernández-Jarguín, Vladimir López, Isabel Fernández de Mera, Joaquín Vicente, Paulo C. Alves, Christian Gortazar, José de la Fuente
Published in: Tuberculosis, Issue 114, 2019, Page(s) 103-112, ISSN 1472-9792
Publisher: Churchill Livingstone
DOI: 10.1016/j.tube.2018.12.003

Hospital outbreak due to Clostridium difficile ribotype 018 (RT018) in Southern Germany

Author(s): 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
Published in: International Journal of Medical Microbiology, Issue 309/3-4, 2019, Page(s) 189-193, ISSN 1438-4221
Publisher: Elsevier BV
DOI: 10.1016/j.ijmm.2019.03.001

Proficiency testing of virus diagnostics based on bioinformatics analysis of simulated in silico high-throughput sequencing datasets

Author(s): 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
Published in: Journal of Clinical Microbiology, 2019, ISSN 0095-1137
Publisher: American Society for Microbiology
DOI: 10.1128/jcm.00466-19

A PCR-based NGS protocol for whole genome sequencing of West Nile virus lineage 2 directly from biological specimens

Author(s): Serafeim C. Chaintoutis, Elpida Papadopoulou, Angeliki Melidou, Anna Papa, Chrysostomos I. Dovas
Published in: Molecular and Cellular Probes, 2019, ISSN 0890-8508
Publisher: Academic Press
DOI: 10.1016/j.mcp.2019.06.002

Mass Die-Off of Saiga Antelopes, Kazakhstan, 2015

Author(s): 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
Published in: Emerging Infectious Diseases, Issue 25/6, 2019, Page(s) 1169-1176, ISSN 1080-6040
Publisher: US National Center for Infectious Diseases
DOI: 10.3201/eid2506.180990

Whole-genome sequencing reveals nosocomial Clostridioides difficile transmission and a previously unsuspected epidemic scenario

Author(s): 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
Published in: Scientific Reports, Issue 9/1, 2019, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-019-43464-4

Characterization of plasmids harboring blaCTX-M genes in Escherichia coli from French pigs

Author(s): Pierrick Lucas, Eric Jouy, Laetitia Le Devendec, Claire de Boisséson, Agnès Perrin-Guyomard, Thomas Jové, Yannick Blanchard, Fabrice Touzain, Isabelle Kempf
Published in: Veterinary Microbiology, Issue 224, 2018, Page(s) 100-106, ISSN 0378-1135
Publisher: Elsevier BV
DOI: 10.1016/j.vetmic.2018.08.005

Towards high quality real-time whole genome sequencing during outbreaks using Usutu virus as example

Author(s): B.B. Oude Munnink, M. Kik, N.D. de Bruijn, R. Kohl, A. van der Linden, C.B.E.M. Reusken, M. Koopmans
Published in: Infection, Genetics and Evolution, Issue 73, 2019, Page(s) 49-54, ISSN 1567-1348
Publisher: Elsevier BV
DOI: 10.1016/j.meegid.2019.04.015

Diagnostic approaches for Crimean-Congo hemorrhagic fever virus

Author(s): Anna Papa
Published in: Expert Review of Molecular Diagnostics, Issue 19/6, 2019, Page(s) 531-536, ISSN 1473-7159
Publisher: Future Drugs Ltd.
DOI: 10.1080/14737159.2019.1615450

Emergence of West Nile virus lineage 2 belonging to the Eastern European subclade, Greece

Author(s): Anna Papa, Elpida Papadopoulou, Charikleia Chatzixanthouliou, Petros Glouftsios, Styliani Pappa, Danai Pervanidou, Loukas Georgiou
Published in: Archives of Virology, Issue 164/6, 2019, Page(s) 1673-1675, ISSN 0304-8608
Publisher: Springer Verlag
DOI: 10.1007/s00705-019-04243-8

Identification of the novel class D β-lactamase OXA-679 involved in carbapenem resistance in Acinetobacter calcoaceticus

Author(s): 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
Published in: Journal of Antimicrobial Chemotherapy, Issue 74/6, 2019, Page(s) 1494-1502, ISSN 0305-7453
Publisher: Oxford University Press
DOI: 10.1093/jac/dkz080

Genetic variability of porcine pegivirus in pigs from Europe and China and insights into tissue tropism

Author(s): Johanna Kennedy, Vanessa Maria Pfankuche, Doris Hoeltig, Alexander Postel, Oliver Keuling, Malgorzata Ciurkiewicz, Wolfgang Baumgärtner, Paul Becher, Christine Baechlein
Published in: Scientific Reports, Issue 9/1, 2019, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-019-44642-0

Salmonella enterica Serovar Typhi in Bangladesh: Exploration of Genomic Diversity and Antimicrobial Resistance

Author(s): 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
Published in: mBio, Issue 9/6, 2018, ISSN 2161-2129
Publisher: American Society for Microbiology
DOI: 10.1128/mbio.02112-18

Co-circulation of Multidrug-resistant Shigella Among Men Who Have Sex With Men in Australia

Author(s): 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
Published in: Clinical Infectious Diseases, 2019, ISSN 1058-4838
Publisher: University of Chicago Press
DOI: 10.1093/cid/ciz005

Emergence and divergence of major lineages of Shiga-toxin-producing Escherichia coli in Australia

Author(s): 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
Published in: Microbial Genomics, Issue 5/5, 2019, ISSN 2057-5858
Publisher: Microbiology Society
DOI: 10.1099/mgen.0.000268

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

Author(s): Frederique Pasquali, Federica Palma, Marcello Trevisani, Antonio Parisi, Alex Lucchi, Alessandra De Cesare, Gerardo Manfreda
Published in: Italian Journal of Food Safety, Issue 7/4, 2019, ISSN 2239-7132
Publisher: PagePress
DOI: 10.4081/ijfs.2018.7673

Animals as Reservoir for Human Norovirus

Author(s): Nele Villabruna, Marion P. G. Koopmans, Miranda de Graaf
Published in: Viruses, Issue 11/5, 2019, Page(s) 478, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v11050478

Detection of distinct MERS-Coronavirus strains in dromedary camels from Kenya, 2017

Author(s): 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
Published in: Emerging Microbes & Infections, Issue 7/1, 2018, Page(s) 1-4, ISSN 2222-1751
Publisher: Nature Publishing Group
DOI: 10.1038/s41426-018-0193-z

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

Author(s): 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
Published in: Virus Evolution, Issue 5/1, 2019, ISSN 2057-1577
Publisher: Oxford University Press (OUP)
DOI: 10.1093/ve/vez004

How to value safety in economic evaluations in health care? A review of applications in different sectors

Author(s): Meg Perry-Duxbury, Job van Exel, Werner Brouwer
Published in: The European Journal of Health Economics, 2019, ISSN 1618-7598
Publisher: Springer Verlag
DOI: 10.1007/s10198-019-01076-9

Bacterial whole genome-based phylogeny: construction of a new benchmarking dataset and assessment of some existing methods

Author(s): Johanne Ahrenfeldt, Carina Skaarup, Henrik Hasman, Anders Gorm Pedersen, Frank Møller Aarestrup, Ole Lund
Published in: BMC Genomics, Issue 18/1, 2017, ISSN 1471-2164
Publisher: BioMed Central
DOI: 10.1186/s12864-016-3407-6

Global phylogeography and ancient evolution of the widespread human gut virus crAssphage

Author(s): 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
Published in: Nature Microbiology, 2019, ISSN 2058-5276
Publisher: Nature Publishing Group
DOI: 10.1038/s41564-019-0494-6

Worldwide human mitochondrial haplogroup distribution from urban sewage

Author(s): 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
Published in: Scientific Reports, Issue 9/1, 2019, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-019-48093-5

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

Author(s): M. Nadeem, I. Spitzbarth, V. Haist, K. Rohn, K. Tauscher, K. Rohn, A. Bossers, J. Langeveld, P. Papasavva-Stylianou, M. H. Groschup, W. Baumgärtner, I. Gerhauser, C. Fast
Published in: Veterinary Record, Issue 178/6, 2016, Page(s) 141.1-141, ISSN 0042-4900
Publisher: British Veterinary Association
DOI: 10.1136/vr.103425

Sharing Data for Global Infectious Disease Surveillance and Outbreak Detection

Author(s): Frank M. Aarestrup, Marion G. Koopmans
Published in: Trends in Microbiology, Issue 24/4, 2016, Page(s) 241-245, ISSN 0966-842X
Publisher: Elsevier BV
DOI: 10.1016/j.tim.2016.01.009

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

Author(s): Béatrice Grasland, Lionel Bigault, Cécilia Bernard, Hélène Quenault, Olivier Toulouse, Christelle Fablet, Nicolas Rose, Fabrice Touzain, Yannick Blanchard
Published in: Genome Announcements, Issue 3/3, 2015, Page(s) e00535-15, ISSN 2169-8287
Publisher: American Society of Microbiologists
DOI: 10.1128/genomeA.00535-15

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

Author(s): Timm Harder, Sebastian Maurer-Stroh, Anne Pohlmann, Elke Starick, Detlef Höreth-Böntgen, Karin Albrecht, Gunter Pannwitz, Jens Teifke, Vithiagaran Gunalan, Raphael T.C. Lee, Carola Sauter-Louis, Timo Homeier, Christoph Staubach, Carola Wolf, Günter Strebelow, Dirk Höper, Christian Grund, Franz J. Conraths, Thomas C. Mettenleiter, Martin Beer
Published in: Emerging Infectious Diseases, Issue 21/5, 2015, Page(s) 860-863, ISSN 1080-6040
Publisher: US National Center for Infectious Diseases
DOI: 10.3201/eid2105.141897

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

Author(s): M. E. J. Woolhouse, A. Rambaut, P. Kellam
Published in: Science Translational Medicine, Issue 7/307, 2015, Page(s) 307rv5-307rv5, ISSN 1946-6234
Publisher: American Association for the Advancement of Science
DOI: 10.1126/scitranslmed.aab0191

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

Author(s): Surbhi Malhotra-Kumar, Basil Britto Xavier, Anupam J Das, Christine Lammens, Ha Thi Thu Hoang, Ngoc Thi Pham, Herman Goossens
Published in: The Lancet Infectious Diseases, Issue 16/3, 2016, Page(s) 286-287, ISSN 1473-3099
Publisher: The Lancet Publishing Group
DOI: 10.1016/S1473-3099(16)00014-1

Recovering full-length viral genomes from metagenomes

Author(s): Saskia L. Smits, Rogier Bodewes, Aritz Ruiz-González, Wolfgang Baumgärtner, Marion P. Koopmans, Albert D. M. E. Osterhaus, Anita C. Schürch
Published in: Frontiers in Microbiology, Issue 6, 2015, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2015.01069

Dissemination of the mcr-1 colistin resistance gene

Author(s): Maris S Arcilla, Jarne M van Hattem, Sebastien Matamoros, Damian C Melles, John Penders, Menno D de Jong, Constance Schultsz
Published in: The Lancet Infectious Diseases, Issue 16/2, 2016, Page(s) 147-149, ISSN 1473-3099
Publisher: The Lancet Publishing Group
DOI: 10.1016/S1473-3099(15)00541-1

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

Author(s): Rogier Bodewes, Siamak Zohari, Jesper S. Krog, Matthew D. Hall, Timm C. Harder, Theo M. Bestebroer, Marco W.G. van de Bildt, Monique I. Spronken, Lars E. Larsen, Ursula Siebert, Peter Wohlsein, Christina Puff, Frauke Seehusen, Wolfgang Baumgärtner, Tero Härkönen, Saskia L. Smits, Sander Herfst, Albert D.M.E. Osterhaus, Ron A.M. Fouchier, Marion P. Koopmans, Thijs Kuiken
Published in: Journal of Virology, 2016, Page(s) JVI.03046-15, ISSN 0022-538X
Publisher: American Society for Microbiology
DOI: 10.1128/JVI.03046-15

Genetic detection of hantaviruses in rodents, Albania

Author(s): Anna Papa, Elton Rogozi, Enkelejda Velo, Evangelia Papadimitriou, Silvia Bino
Published in: Journal of Medical Virology, 2016, Page(s) n/a-n/a, ISSN 0146-6615
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/jmv.24486

Evolutionary origins of hepatitis A virus in small mammals

Author(s): Jan Felix Drexler, Victor M. Corman, Alexander N. Lukashev, Judith M. A. van den Brand, Anatoly P. Gmyl, Sebastian Brünink, Andrea Rasche, Nicole Seggewiβ, Hui Feng, Lonneke M. Leijten, Peter Vallo, Thijs Kuiken, Andreas Dotzauer, Rainer G. Ulrich, Stanley M. Lemon, Christian Drosten
Published in: Proceedings of the National Academy of Sciences, Issue 112/49, 2015, Page(s) 15190-15195, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.1516992112

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

Author(s): Steve Bexton, Lidewij C. Wiersma, Sarah Getu, Peter R. van Run, Georges M.G.M. Verjans, Debby Schipper, Claudia M.E. Schapendonk, Rogier Bodewes, Lucy Oldroyd, Bart L. Haagmans, Marion M.P. Koopmans, Saskia L. Smits
Published in: Emerging Infectious Diseases, Issue 21/7, 2015, Page(s) 1205-1208, ISSN 1080-6040
Publisher: US National Center for Infectious Diseases
DOI: 10.3201/eid2107.150228

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

Author(s): Henrik Hasman, Anette M. Hammerum, Frank Hansen, Rene S. Hendriksen, Bente Olesen, Yvonne Agersø, Ea Zankari, Pimlapas Leekitcharoenphon, Marc Stegger, Rolf S. Kaas, Lina M. Cavaco, Dennis S. Hansen, Frank M. Aarestrup, Robert L. Skov
Published in: Eurosurveillance, Issue 20/49, 2015, ISSN 1025-496X
Publisher: Centre Europeen pour la Surveillance Epidemiologique du SIDA
DOI: 10.2807/1560-7917.ES.2015.20.49.30085

Consolidating and Exploring Antibiotic Resistance Gene Data Resources

Author(s): Basil Britto Xavier, Anupam J. Das, Guy Cochrane, Sandra De Ganck, Samir Kumar-Singh, Frank Møller Aarestrup, Herman Goossens, Surbhi Malhotra-Kumar
Published in: Journal of Clinical Microbiology, Issue 54/4, 2016, Page(s) 851-859, ISSN 0095-1137
Publisher: American Society for Microbiology
DOI: 10.1128/JCM.02717-15

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

Author(s): Saskia L Smits, Suzan D Pas, Chantal B Reusken, Bart L Haagmans, Peirro Pertile, Corrado Cancedda, Kerry Dierberg, Isata Wurie, Abdul Kamara, David Kargbo, Sarah L Caddy, Armando Arias, Lucy Thorne, Jia Lu, Umaru Jah, Ian Goodfellow, Marion P Koopmans
Published in: Eurosurveillance, Issue 20/40, 2015, ISSN 1025-496X
Publisher: Centre Europeen pour la Surveillance Epidemiologique du SIDA
DOI: 10.2807/1560-7917.ES.2015.20.40.30035

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

Author(s): Anna Papa, Styliani Pappa, Elitsa Panayotova, Elpida Papadopoulou, Iva Christova
Published in: Journal of Medical Virology, Issue 88/5, 2016, Page(s) 769-773, ISSN 0146-6615
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/jmv.24400

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

Author(s): Surbhi Malhotra-Kumar, Basil Britto Xavier, Anupam J Das, Christine Lammens, Patrick Butaye, Herman Goossens
Published in: The Lancet Infectious Diseases, Issue 16/3, 2016, Page(s) 283-284, ISSN 1473-3099
Publisher: The Lancet Publishing Group
DOI: 10.1016/S1473-3099(16)00012-8

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

Author(s): Thomas Nordahl Petersen, Simon Rasmussen, Henrik Hasman, Christian Carøe, Jacob Bælum, Anna Charlotte Schultz, Lasse Bergmark, Christina A. Svendsen, Ole Lund, Thomas Sicheritz-Pontén, Frank M. Aarestrup
Published in: Scientific Reports, Issue 5, 2015, Page(s) 11444, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/srep11444

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

Author(s): J Verhagen, H van der Jeugd, B Nolet, R Slaterus, S Kharitonov, P de Vries, O Vuong, F Majoor, T Kuiken, R Fouchier
Published in: Eurosurveillance, Issue 20/12, 2015, Page(s) 21069, ISSN 1560-7917
Publisher: European Commission
DOI: 10.2807/1560-7917.ES2015.20.12.21069

The Risk of Infection by African Swine Fever Virus in European Swine Through Boar Movement and Legal Trade of Pigs and Pig Meat

Author(s): Rachel A. Taylor, Roberto Condoleo, Robin R. L. Simons, Paul Gale, Louise A. Kelly, Emma L. Snary
Published in: Frontiers in Veterinary Science, Issue 6, 2020, ISSN 2297-1769
Publisher: Frontiers Media
DOI: 10.3389/fvets.2019.00486

Science-based wildlife disease response

Author(s): 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,
Published in: Science, Issue 364/6444, 2019, Page(s) 943.2-944, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.aax4310

The COMPARE Data Hubs

Author(s): 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
Published in: Database, Issue 2019, 2019, ISSN 1758-0463
Publisher: Oxford University Press
DOI: 10.1093/database/baz136

Evolutionary dynamics of lineage 2 West Nile virus in Europe, 2004–2018: Phylogeny, selection pressure and phylogeography

Author(s): Serafeim C. Chaintoutis, Anna Papa, Danai Pervanidou, Chrysostomos I. Dovas
Published in: Molecular Phylogenetics and Evolution, Issue 141, 2019, Page(s) 106617, ISSN 1055-7903
Publisher: Academic Press
DOI: 10.1016/j.ympev.2019.106617

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

Author(s): 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
Published in: Veterinary Research, Issue 50/1, 2019, ISSN 1297-9716
Publisher: BioMed Central
DOI: 10.1186/s13567-019-0699-y

Bidirectional Human–Swine Transmission of Seasonal Influenza A(H1N1)pdm09 Virus in Pig Herd, France, 2018

Author(s): 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
Published in: Emerging Infectious Diseases, Issue 25/10, 2019, Page(s) 1940-1943, ISSN 1080-6040
Publisher: US National Center for Infectious Diseases
DOI: 10.3201/eid2510.190068

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

Author(s): Julie Eclercy, Patricia Renson, Arnaud Lebret, Edouard Hirchaud, Valérie Normand, Mathieu Andraud, Frédéric Paboeuf, Yannick Blanchard, Nicolas Rose, Olivier Bourry
Published in: Viruses, Issue 11/3, 2019, Page(s) 296, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v11030296

A Deep-Sequencing Workflow for the Fast and Efficient Generation of High-Quality African Swine Fever Virus Whole-Genome Sequences

Author(s): 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
Published in: Viruses, Issue 11/9, 2019, Page(s) 846, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v11090846

Genomic polymorphism of Mycoplasma flocculare revealed by a newly developed multilocus sequence typing scheme

Author(s): Sarah Fourour, Pierrick Lucas, Fabrice Touzain, Véronique Tocqueville, Anne V. Gautier-Bouchardon, Isabelle Kempf, Corinne Marois-Créhan
Published in: Veterinary Microbiology, Issue 237, 2019, Page(s) 108422, ISSN 0378-1135
Publisher: Elsevier BV
DOI: 10.1016/j.vetmic.2019.108422

Pathogen surveillance in the informal settlement, Kibera, Kenya, using a metagenomics approach

Author(s): 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
Published in: PLOS ONE, Issue 14/10, 2019, Page(s) e0222531, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0222531

Specific gut microbiome members are associated with distinct immune markers in pediatric allogeneic hematopoietic stem cell transplantation

Author(s): Anna Cäcilia Ingham, Katrine Kielsen, Malene Skovsted Cilieborg, Ole Lund, Susan Holmes, Frank M. Aarestrup, Klaus Gottlob Müller, Sünje Johanna Pamp
Published in: Microbiome, Issue 7/1, 2019, ISSN 2049-2618
Publisher: NLM (Medline)
DOI: 10.1186/s40168-019-0745-z

Application of different DNA extraction procedures, library preparation protocols and sequencing platforms: impact on sequencing results

Author(s): F. Pasquali, I. Do Valle, F. Palma, D. Remondini, G. Manfreda, G. Castellani, R.S. Hendriksen, A. De Cesare
Published in: Heliyon, Issue 5/10, 2019, Page(s) e02745, ISSN 2405-8440
Publisher: Elsevier Ltd
DOI: 10.1016/j.heliyon.2019.e02745

Genetic Characterization and Zoonotic Potential of Highly Pathogenic Avian Influenza Virus A(H5N6/H5N5), Germany, 2017–2018

Author(s): Anne Pohlmann, Donata Hoffmann, Christian Grund, Susanne Koethe, Daniela Hüssy, Simone M. Meier, Jacqueline King, Jan Schinköthe, Reiner Ulrich, Timm Harder, Martin Beer
Published in: Emerging Infectious Diseases, Issue 25/10, 2019, Page(s) 1973-1976, ISSN 1080-6040
Publisher: US National Center for Infectious Diseases
DOI: 10.3201/eid2510.181931

Metagenomics for broad and improved parasite detection: a proof-of-concept study using swine faecal samples

Author(s): Claudia Wylezich, Ariane Belka, Dennis Hanke, Martin Beer, Sandra Blome, Dirk Höper
Published in: International Journal for Parasitology, Issue 49/10, 2019, Page(s) 769-777, ISSN 0020-7519
Publisher: Elsevier BV
DOI: 10.1016/j.ijpara.2019.04.007

IS26-Mediated Transfer of blaNDM–1 as the Main Route of Resistance Transmission During a Polyclonal, Multispecies Outbreak in a German Hospital

Author(s): Robert E. Weber, Michael Pietsch, Andre Frühauf, Yvonne Pfeifer, Maria Martin, Dirk Luft, Sören Gatermann, Niels Pfennigwerth, Martin Kaase, Guido Werner, Stephan Fuchs
Published in: Frontiers in Microbiology, Issue 10, 2019, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2019.02817

Analysis of isolates from Bangladesh highlights multiple ways to carry resistance genes in Salmonella Typhi

Author(s): 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
Published in: BMC Genomics, Issue 20/1, 2019, ISSN 1471-2164
Publisher: BioMed Central
DOI: 10.1186/s12864-019-5916-6

Nosocomial infections caused by Crimean-Congo haemorrhagic fever virus

Author(s): Katerina Tsergouli, Theodoros Karampatakis, Anna-Bettina Haidich, Symeon Metallidis, Anna Papa
Published in: Journal of Hospital Infection, 2019, ISSN 0195-6701
Publisher: W. B. Saunders Co., Ltd.
DOI: 10.1016/j.jhin.2019.12.001

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

Author(s): Panagiotis Papadopoulos, Apostolos S. Angelidis, Theofilos Papadopoulos, Charalampos Kotzamanidis, Antonios Zdragas, Anna Papa, George Filioussis, Daniel Sergelidis
Published in: Food Microbiology, Issue 84, 2019, Page(s) 103249, ISSN 0740-0020
Publisher: Academic Press
DOI: 10.1016/j.fm.2019.103249

Molecular detection of Crimean-Congo hemorrhagic fever virus in ticks, Greece, 2012–2014

Author(s): Anna Papa, Anastasia Kontana, Katerina Tsioka, Ilias Chaligiannis, Smaragda Sotiraki
Published in: Parasitology Research, Issue 116/11, 2017, Page(s) 3057-3063, ISSN 0932-0113
Publisher: Springer Verlag
DOI: 10.1007/s00436-017-5616-6

Informal genomic surveillance of regional distribution of Salmonella Typhi genotypes and antimicrobial resistance via returning travellers

Author(s): 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
Published in: PLOS Neglected Tropical Diseases, Issue 13/9, 2019, Page(s) e0007620, ISSN 1935-2727
Publisher: Public Library of Science
DOI: 10.1371/journal.pntd.0007620

Source Attribution of Salmonella in Macadamia Nuts to Animal and Environmental Reservoirs in Queensland, Australia

Author(s): Nanna Munck, James Smith, John Bates, Kathryn Glass, Tine Hald, Martyn D. Kirk
Published in: Foodborne Pathogens and Disease, 2019, ISSN 1535-3141
Publisher: Mary Ann Liebert Inc.
DOI: 10.1089/fpd.2019.2706

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

Author(s): 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
Published in: Frontiers in Microbiology, Issue 10, 2019, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2019.02413

Genetic Diversity of Salmonella Derby from the Poultry Sector in Europe

Author(s): Yann Sévellec, Arnaud Felten, Nicolas Radomski, Sophie Granier, Simon Le Hello, Liljana Petrovska, Michel-Yves Mistou, Sabrina Cadel-Six
Published in: Pathogens, Issue 8/2, 2019, Page(s) 46, ISSN 2076-0817
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/pathogens8020046

Genetic and metabolic signatures of Salmonella enterica subsp. enterica associated with animal sources at the pangenomic scale

Author(s): Meryl Vila Nova, Kévin Durimel, Kévin La, Arnaud Felten, Philippe Bessières, Michel-Yves Mistou, Mahendra Mariadassou, Nicolas Radomski
Published in: BMC Genomics, Issue 20/1, 2019, ISSN 1471-2164
Publisher: BioMed Central
DOI: 10.1186/s12864-019-6188-x

Evolutionary Insights into the Tick Hologenome

Author(s): Sandra Díaz-Sánchez, Agustín Estrada-Peña, Alejandro Cabezas-Cruz, José de la Fuente
Published in: Trends in Parasitology, Issue 35/9, 2019, Page(s) 725-737, ISSN 1471-4922
Publisher: Elsevier BV
DOI: 10.1016/j.pt.2019.06.014

An evolutionary divergent pestivirus lacking the N pro gene systemically infects a whale species

Author(s): 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
Published in: Emerging Microbes & Infections, Issue 8/1, 2019, Page(s) 1383-1392, ISSN 2222-1751
Publisher: Nature Publishing Group
DOI: 10.1080/22221751.2019.1664940

Characterization of Norovirus and Other Human Enteric Viruses in Sewage and Stool Samples Through Next-Generation Sequencing

Author(s): Sofia Strubbia, My V. T. Phan, Julien Schaeffer, Marion Koopmans, Matthew Cotten, Françoise S. Le Guyader
Published in: Food and Environmental Virology, Issue 11/4, 2019, Page(s) 400-409, ISSN 1867-0334
Publisher: Springer Verlag
DOI: 10.1007/s12560-019-09402-3

Metavirome Sequencing to Evaluate Norovirus Diversity in Sewage and Related Bioaccumulated Oysters

Author(s): 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
Published in: Frontiers in Microbiology, Issue 10, 2019, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2019.02394

Detection of flaviviruses and alphaviruses in mosquitoes in Central Macedonia, Greece, 2018

Author(s): Anna Papa, Sandra Gewehr, Katerina Tsioka, Stella Kalaitzopoulou, Styliani Pappa, Spiros Mourelatos
Published in: Acta Tropica, Issue 202, 2020, Page(s) 105278, ISSN 0001-706X
Publisher: Elsevier BV
DOI: 10.1016/j.actatropica.2019.105278

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

Author(s): 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
Published in: Virology, Issue 541, 2020, Page(s) 113-123, ISSN 0042-6822
Publisher: Academic Press
DOI: 10.1016/j.virol.2019.10.014

Enzootic patterns of Middle East respiratory syndrome coronavirus in imported African and local Arabian dromedary camels: a prospective genomic study

Author(s): 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
Published in: The Lancet Planetary Health, Issue 3/12, 2019, Page(s) e521-e528, ISSN 2542-5196
Publisher: Elsevier B.V.
DOI: 10.1016/s2542-5196(19)30243-8

Microbiota analysis and microbiological hazard assessment in poultry carcasses from conventional and antibiotic free farms

Author(s): Alessandra De Cesare, Antonio Parisi, Alex Lucchi, Loredana Capozzi, Angela Bianco, Frederique Pasquali, Gerardo Manfreda
Published in: Italian Journal of Food Safety, Issue 7/4, 2018, ISSN 2239-7132
Publisher: PagePress
DOI: 10.4081/ijfs.2018.7706

Attenuation of replication by a 29 nucleotide deletion in SARS-coronavirus acquired during the early stages of human-to-human transmission

Author(s): 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
Published in: Scientific Reports, Issue 8/1, 2018, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-018-33487-8

Novel composite SCCmec type III element in ST239 MRSA isolated from an Indian hospital

Author(s): Jasmine Coppens, Basil Britto Xavier, Lavanya Vanjari, Sarah De Backer, Christine Lammens, Lakshmi Vemu, Herman Goossens, Surbhi Malhotra-Kumar
Published in: Journal of Antimicrobial Chemotherapy, 2018, ISSN 0305-7453
Publisher: Oxford University Press
DOI: 10.1093/JAC/DKY399

Prediction of Acquired Antimicrobial Resistance for Multiple Bacterial Species Using Neural Networks

Author(s): D. Aytan-Aktug, P. T. L. C. Clausen, V. Bortolaia, F. M. Aarestrup, O. Lund
Published in: mSystems, Issue 5/1, 2020, ISSN 2379-5077
Publisher: American Society for Microbiology Journals
DOI: 10.1128/msystems.00774-19

Metaphylogenetic analysis of global sewage reveals that bacterial strains associated with human disease show less degree of geographic clustering

Author(s): Johanne Ahrenfeldt, Madina Waisi, Isabella C. Loft, Philip T. L. C. Clausen, Rosa Allesøe, Judit Szarvas, Rene S. Hendriksen, Frank M. Aarestrup, Ole Lund
Published in: Scientific Reports, Issue 10/1, 2020, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-020-59292-w

Large scale automated phylogenomic analysis of bacterial isolates and the Evergreen Online platform

Author(s): Judit Szarvas, Johanne Ahrenfeldt, Jose Luis Bellod Cisneros, Martin Christen Frølund Thomsen, Frank M. Aarestrup, Ole Lund
Published in: Communications Biology, Issue 3/1, 2020, ISSN 2399-3642
Publisher: Nature Publishing Group UK
DOI: 10.1038/s42003-020-0869-5

Emerging arboviral human diseases in Southern Europe

Author(s): Anna Papa
Published in: Journal of Medical Virology, Issue 89/8, 2017, Page(s) 1315-1322, ISSN 0146-6615
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/jmv.24803

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

Author(s): Alejandro Cabezas-Cruz, Lourdes Mateos-Hernández, Pilar Alberdi, Margarita Villar, Gilles Riveau, Emmanuel Hermann, Anne-Marie Schacht, Jamal Khalife, Margarida Correia-Neves, Christian Gortazar, José de la Fuente
Published in: Experimental & Molecular Medicine, Issue 49/3, 2017, Page(s) e301, ISSN 1226-3613
Publisher: Korean Society of Medical Biochemistry and Molecular Biology
DOI: 10.1038/emm.2016.164

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

Author(s): Adriana Cabal, Joaquin Vicente, Julio Alvarez, Jose Angel Barasona, Mariana Boadella, Lucas Dominguez, Christian Gortazar
Published in: MicrobiologyOpen, Issue 6/3, 2017, Page(s) e00445, ISSN 2045-8827
Publisher: John Wiley and Sons Inc.
DOI: 10.1002/mbo3.445

Next-generation sequencing and norovirus

Author(s): Matthew Cotten, Marion Koopmans
Published in: Future Virology, Issue 11/11, 2016, Page(s) 719-722, ISSN 1746-0794
Publisher: Future Medicine Ltd.
DOI: 10.2217/fvl-2016-0099

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

Author(s): Pieter L A Fraaij, Enno D Wildschut, Robert J Houmes, Corien M Swaan, Christian J Hoebe, H C C de Jonge, Paulien Tolsma, Isme de Kleer, Suzan D Pas, Bas B Oude Munnink, My V T Phan, Theo M Bestebroer, R Shanty Roosenhoff, Jeroen J A van Kampen, Matthew Cotten, Nancy Beerens, Ron A M Fouchier, Johannes H van den Kerkhof, Aura Timen, Marion P Koopmans
Published in: Eurosurveillance, Issue 21/48, 2016, ISSN 1025-496X
Publisher: Centre Europeen pour la Surveillance Epidemiologique du SIDA
DOI: 10.2807/1560-7917.ES.2016.21.48.30416

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

Author(s): A. Globig, E. Starick, T. Homeier, A. Pohlmann, C. Grund, P. Wolf, A. Zimmermann, C. Wolf, D. Heim, H. Schlößer, S. Zander, M. Beer, F. J. Conraths, T. C. Harder
Published in: Transboundary and Emerging Diseases, 2016, ISSN 1865-1674
Publisher: Blackwell-Wiss.-Verl
DOI: 10.1111/tbed.12570

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

Author(s): Sylvie Lecollinet, Yannick Blanchard, Christine Manson, Steeve Lowenski, Eve Laloy, Hélène Quenault, Fabrice Touzain, Pierrick Lucas, Cyril Eraud, Céline Bahuon, Stéphan Zientara, Cécile Beck, Anouk Decors
Published in: Emerging Infectious Diseases, Issue 22/12, 2016, Page(s) 2225-2225, ISSN 1080-6040
Publisher: US National Center for Infectious Diseases
DOI: 10.3201/eid2212.161272

Genome Sequences of a Novel Vietnamese Bat Bunyavirus

Author(s): Bas B. Oude Munnink, My V. T. Phan, Lia van der Hoek, Paul Kellam, Matthew Cotten
Published in: Genome Announcements, Issue 4/6, 2016, Page(s) e01366-16, ISSN 2169-8287
Publisher: American Society for Microbiology
DOI: 10.1128/genomeA.01366-16

Bacterial pathogens and endosymbionts in ticks

Author(s): Anna Papa, Katerina Tsioka, Anastasia Kontana, Christos Papadopoulos, Nektarios Giadinis
Published in: Ticks and Tick-borne Diseases, Issue 8/1, 2017, Page(s) 31-35, ISSN 1877-959X
Publisher: Elsevier BV
DOI: 10.1016/j.ttbdis.2016.09.011

A novel alphaherpesvirus associated with fatal diseases in banded Penguins

Author(s): Florian Pfaff, Christoph Schulze, Patricia König, Kati Franzke, Sabine Bock, Andreas Hlinak, Jens Kämmerling, Andreas Ochs, André Schüle, Thomas C. Mettenleiter, Dirk Höper1, Martin Beer
Published in: Journal of General Virology, Issue 98/1, 2017, Page(s) 89-95, ISSN 0022-1317
Publisher: Society for General Microbiology
DOI: 10.1099/jgv.0.000698

A novel astrovirus associated with encephalitis and ganglionitis in domestic sheep

Author(s): F. Pfaff, K. Schlottau, S. Scholes, A. Courtenay, B. Hoffmann, D. Höper, M. Beer
Published in: Transboundary and Emerging Diseases, Issue 64/3, 2017, Page(s) 677-682, ISSN 1865-1674
Publisher: Blackwell-Wiss.-Verl
DOI: 10.1111/tbed.12623

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

Author(s): My V. T. Phan, Pham Hong Anh, Nguyen Van Cuong, Bas B. Oude Munnink, Lia van der Hoek, Phuc Tran My, Tue Ngo Tri, Juliet E. Bryant, Stephen Baker, Guy Thwaites, Mark Woolhouse, Paul Kellam, Maia A. Rabaa, Matthew Cotten
Published in: Virus Evolution, Issue 2/2, 2016, Page(s) vew027, ISSN 2057-1577
Publisher: Oxford University Press
DOI: 10.1093/ve/vew027

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

Author(s): Anne Pohlmann, Elke Starick, Timm Harder, Christian Grund, Dirk Höper, Anja Globig, Christoph Staubach, Klaas Dietze, Günter Strebelow, Reiner G. Ulrich, Jan Schinköthe, Jens P. Teifke, Franz J. Conraths, Thomas C. Mettenleiter, Martin Beer
Published in: Emerging Infectious Diseases, Issue 23/4, 2017, Page(s) 633-636, ISSN 1080-6040
Publisher: US National Center for Infectious Diseases
DOI: 10.3201/eid2304.161949

Variegated Squirrel Bornavirus 1 in Squirrels, Germany and the Netherlands

Author(s): Kore Schlottau, Maria Jenckel, Judith van den Brand, Christine Fast, Christiane Herden, Dirk Höper, Timo Homeier-Bachmann, Jens Thielebein, Niels Mensing, Bert Diender, Donata Hoffmann, Rainer G. Ulrich, Thomas C. Mettenleiter, Marion Koopmans, Dennis Tappe, Jonas Schmidt-Chanasit, Chantal B.E.M. Reusken, Martin Beer, Bernd Hoffmann
Published in: Emerging Infectious Diseases, Issue 23/3, 2017, Page(s) 477-481, ISSN 1080-6040
Publisher: US National Center for Infectious Diseases
DOI: 10.3201/eid2303.161061

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

Author(s): Matthias Steglich, Ulrich Nübel
Published in: Journal of Biotechnology, Issue 250, 2017, Page(s) 11-15, ISSN 0168-1656
Publisher: Elsevier BV
DOI: 10.1016/j.jbiotec.2017.02.026

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

Author(s): K. G. Joensen, A. L. Ø. Engsbro, O. Lukjancenko, R. S. Kaas, O. Lund, H. Westh, F. M. Aarestrup
Published in: European Journal of Clinical Microbiology & Infectious Diseases, Issue 36/7, 2017, Page(s) 1325-1338, ISSN 0934-9723
Publisher: Springer Verlag
DOI: 10.1007/s10096-017-2947-2

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

Author(s): Nguyen Vinh Trung, Sébastien Matamoros, Juan J. Carrique-Mas, Nguyen Huu Nghia, Nguyen Thi Nhung, Tran Thi Bich Chieu, Ho Huynh Mai, Willemien van Rooijen, James Campbell, Jaap A. Wagenaar, Anita Hardon, Nguyen Thi Nhu Mai, Thai Quoc Hieu, Guy Thwaites, Menno D. de Jong, Constance Schultsz, Ngo Thi Hoa
Published in: Emerging Infectious Diseases, Issue 23/3, 2017, Page(s) 529-532, ISSN 1080-6040
Publisher: US National Center for Infectious Diseases
DOI: 10.3201/eid2303.161553

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

Author(s): Guy Baele, Philippe Lemey, Andrew Rambaut, Marc A. Suchard
Published in: Bioinformatics, Issue 33/12, 2017, Page(s) 1798-1805, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btx088

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

Author(s): Edward C. Holmes, Gytis Dudas, Andrew Rambaut, Kristian G. Andersen
Published in: Nature, Issue 538/7624, 2016, Page(s) 193-200, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/nature19790

SpreaD3: Interactive Visualization of Spatiotemporal History and Trait Evolutionary Processes

Author(s): Filip Bielejec, Guy Baele, Bram Vrancken, Marc A. Suchard, Andrew Rambaut, Philippe Lemey
Published in: Molecular Biology and Evolution, Issue 33/8, 2016, Page(s) 2167-2169, ISSN 0737-4038
Publisher: Oxford University Press
DOI: 10.1093/molbev/msw082

Metagenomic Sequencing for Surveillance of Food- and Waterborne Viral Diseases

Author(s): David F. Nieuwenhuijse, Marion P. G. Koopmans
Published in: Frontiers in Microbiology, Issue 8, 2017, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2017.00230

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

Author(s): Josanne H. Verhagen, Pascal Lexmond, Oanh Vuong, Martin Schutten, Judith Guldemeester, Albert D. M. E. Osterhaus, Armin R. W. Elbers, Roy Slaterus, Menno Hornman, Guus Koch, Ron A. M. Fouchier
Published in: PLOS ONE, Issue 12/3, 2017, Page(s) e0173470, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0173470

Novel phlebovirus detected in Haemaphysalis parva ticks in a Greek island

Author(s): Anna Papa, Anastasia Kontana, Katerina Tsioka, Anastasios Saratsis, Smaragda Sotiraki
Published in: Ticks and Tick-borne Diseases, Issue 8/1, 2017, Page(s) 157-160, ISSN 1877-959X
Publisher: Elsevier BV
DOI: 10.1016/j.ttbdis.2016.10.012

The Biodefense Field

Author(s): Emilio Mordini
Published in: Bioethics, Issue 30/6, 2016, Page(s) 382-383, ISSN 0269-9702
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/bioe.12269

Research Priorities and Trends in Infections Shared with Wildlife

Author(s): Christian Gortázar, Joaquín Vicente, Margarita Villar, Francisco Ruiz-Fons, Ursula Höfle, José de la Fuente
Published in: Current Trends in Wildlife Research, Issue Part of the Wildlife Research Monographs book series (WIREMO, volume 1), 2016, Page(s) 55-78, ISBN 978-3-319-27910-7
Publisher: Springer International Publishing
DOI: 10.1007/978-3-319-27912-1_3

ND-GiST: A Novel Method for Disk-Resident k-mer Indexing

Author(s): János Márk Szalai-Gindl, Attila Kiss, Gábor Halász, László Dobos, István Csabai
Published in: New Knowledge in Information Systems and Technologies - Volume 2, Issue 931, 2019, Page(s) 663-672, ISBN 978-3-030-16183-5
Publisher: Springer International Publishing
DOI: 10.1007/978-3-030-16184-2_63

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