Publications from the Genomic Epidemiology Research Group

A compartmental model to investigate the dynamics of the COVID-19 pandemic: A case study in five countries

Apenteng, Ofosuhene Okofrobour ; Oduro, Bismark ; Owusu-Mensah, Isaac
in: International Journal of Biomathematics

Type: Journal article (Peer reviewed)

Status: Accepted/In press | Year: 2021 | DOI: https://doi.org/10.1142/S1793524521500273

A roadmap for the generation of benchmarking resources for antimicrobial resistance detection using next generation sequencing

Petrillo, Mauro ; Fabbri, Marco ; Kagkli, Dafni Maria ; Querci, Maddalena ; Van den Eede, Guy ; Alm, Erik ; Aytan, Derya ; Capella-Gutierrez, Salvador ; Carrillo, Catherine ; Cestaro, Alessandro ; Chan, Kok-Gan ; Coque, Teresa ; Endrullat, Christoph ; Gut, Ivo ; Hammer, Paul ; Kay, Gemma L. ; Madec, Jean-Yves ; Mather, Alison E. ; McHardy, Alice Carolyn ; Naas, Thierry ; Paracchini, Valentina ; Peter, Silke ; Pightling, Arthur ; Raffael, Barbara ; Rossen, John ; Ruppé, Etienne ; Schlaberg, Robert ; Vanneste, Kevin ; Weber, Lukas ; Westh, Henrik ; Angers-Loustau, Alexandre
in: F1000Research, vol: 10

Type: Journal article (Peer reviewed)

Status: Accepted/In press | Year: 2021 | DOI: https://doi.org/10.12688/f1000research.39214.1

Article outcome of different sequencing and assembly approaches on the detection of plasmids and localization of antimicrobial resistance genes in commensal escherichia coli

Juraschek, Katharina ; Borowiak, Maria ; Tausch, Simon H. ; Malorny, Burkhard ; Käsbohrer, Annemarie ; Otani, Saria ; Schwarz, Stefan ; Meemken, Diana ; Deneke, Carlus ; Hammerl, Jens Andre
in: Microorganisms, vol: 9, issue: 3

Type: Journal article (Peer reviewed)

Status: Published | Year: 2021 | DOI: https://doi.org/10.3390/microorganisms9030598

Attribution of illnesses transmitted by food and water to comprehensive transmission pathways using structured expert judgment, United States

Beshearse, Elizabeth ; Bruce, Beau B. ; Nane, Gabriela F. ; Cooke, Roger M. ; Aspinall, Willy ; Hald, Tine ; Crim, Stacy M. ; Griffin, Patricia M. ; Fullerton, Kathleen E. ; Collier, Sarah A. ; Benedict, Katharine M. ; Beach, Michael J. ; Hall, Aron J. ; Havelaar, Arie H.
in: Emerging Infectious Diseases , vol: 27, issue: 1, pages: 182-195

Type: Journal article (Peer reviewed)

Status: Published | Year: 2021 | DOI: https://doi.org/10.3201/eid2701.200316

Automated download and clean-up of family specific databases for kmer-based virus identification

Allesøe, Rosa Lundbye ; Lemvigh, Camilla Koldbæk ; Phan, My V T ; Clausen, Philip Thomas Lanken Conradsen ; Florensa, Alfred Ferrer ; Koopmans, Marion P G ; Lund, Ole ; Cotten, Matthew
in: Bioinformatics

Type: Journal article (Peer reviewed)

Status: Accepted/In press | Year: 2021 | DOI: https://doi.org/10.1093/bioinformatics/btaa857

Burden of foodborne diseases

Pires, Sara Monteiro ; Desta, Binyam N. ; Mughini-Gras, Lapo ; Mmbaga, Blandina T. ; Fayemi, Olanrewaju E. ; Salvador, Elsa M. ; Gobena, Tesfaye ; Majowicz, Shannon E. ; Hald, Tine ; Hoejskov, Peter S. ; Minato, Yuki ; Devleesschauwer, Brecht
in: Current Opinion in Food Science, vol: 39, pages: 152-159

Type: Review (Peer reviewed)

Status: Published | Year: 2021 | DOI: https://doi.org/10.1016/j.cofs.2021.01.006

Detection of mobile genetic elements associated with antibiotic resistance in Salmonella enterica using a newly developed web tool: MobileElementFinder

Johansson, Markus Hans Kristofer ; Bortolaia, Valeria ; Tansirichaiya, Supathep ; Aarestrup, Frank Møller ; Roberts, Adam P ; Petersen, Thomas Nordahl
in: Journal of Antimicrobial Chemotherapy, vol: 76, issue: 1, pages: 101–109

Type: Journal article (Peer reviewed)

Status: Published | Year: 2021 | DOI: https://doi.org/10.1093/jac/dkaa390

Economic evaluation of whole genome sequencing for pathogen identification and surveillance - results of case studies in Europe and the Americas 2016 to 2019

Alleweldt, Frank ; Kara, Şenda ; Best, Kris ; Aarestrup, Frank Møller ; Beer, Martin ; Bestebroer, Theo M. ; Campos, Josefina ; Casadei, Gabriele ; Chinen, Isabel ; Van Domselaar, Gary ; Dominguez, Catherine ; Everett, Helen E. ; Fouchier, Ron Am ; Grant, Kathie ; Green, Jonathan ; Höper, Dirk ; Johnston, Jonathan ; Koopmans, Marion Pg ; Oude Munnink, Bas B. ; Myers, Robert ; Nadon, Celine ; Patel, Ami ; Pohlmann, Anne ; Pongolini, Stefano ; Reimer, Aleisha ; Thiessen, Shane ; Wylezich, Claudia
in: Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin, vol: 26, issue: 9

Type: Journal article (Peer reviewed)

Status: Published | Year: 2021 | DOI: https://doi.org/10.2807/1560-7917.ES.2021.26.9.1900606