Publications from the Genomic Epidemiology Research Group

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

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

Exposure assessment to staphylococcus enterotoxins in Nile tilapia (Oreochromis niloticus) supplied through semi-regulated and unregulated value chains

Onjong, Hillary Adawo ; Ntuli, Victor ; Mwaniki, Mercy ; Njage, Patrick Murigu Kamau
in: Food Control, vol: 119

Type: Journal article (Peer reviewed)

Status: Published | Year: 2021 | DOI: https://doi.org/10.1016/j.foodcont.2020.107487

Extended-spectrum beta-lactamase-producing Escherichia coli and antimicrobial resistance in municipal and hospital wastewaters in Czech Republic

Kutilova, Iva ; Medvecky, Matej ; Leekitcharoenphon, Pimlapas ; Munk, Patrick ; Masarikova, Martina ; Davidova-Gerzova, Lenka ; Jamborova, Ivana ; Bortolaia, Valeria ; Pamp, Sünje Johanna ; Dolejska, Monika
in: Environmental Research, vol: 193

Type: Journal article (Peer reviewed)

Status: Published | Year: 2021 | DOI: https://doi.org/10.1016/j.envres.2020.110487

Global Food-source Identifier (GFI)

Ribeiro Duarte, Ana Sofia ; Nielsen, Cecilie Liv ; Candela, Leonardo ; Valentin, Lars ; Aarestrup, Frank Møller ; Vigre, Håkan
in: Food Control, vol: 121

Type: Journal article (Peer reviewed)

Status: Published | Year: 2021 | DOI: https://doi.org/10.1016/j.foodcont.2020.107623

Improved metagenome binning and assembly using deep variational autoencoders

Nissen, Jakob Nybo ; Johansen, Joachim ; Allesøe, Rosa Lundbye ; Sønderby, Casper Kaae ; Armenteros, Jose Juan Almagro ; Grønbech, Christopher Heje ; Jensen, Lars Juhl ; Nielsen, Henrik Bjørn ; Petersen, Thomas Nordahl ; Winther, Ole ; Rasmussen, Simon
in: Nature Biotechnology

Type: Journal article (Peer reviewed)

Status: Accepted/In press | Year: 2021 | DOI: https://doi.org/10.1038/s41587-020-00777-4

Non-typhoidal human salmonellosis in Rio Grande do Sul, Brazil: A combined source attribution study of microbial subtyping and outbreak data

Neto, Waldemir Santiago ; Leotti, Vanessa Bielefeldt ; Pires, Sara Monteiro ; Hald, Tine ; Corbellini, Luis Gustavo
in: International Journal of Food Microbiology, vol: 338

Type: Journal article (Peer reviewed)

Status: Published | Year: 2021 | DOI: https://doi.org/10.1016/j.ijfoodmicro.2020.108992

Prevalence and genomic analysis of ESBL-producing Escherichia coli in retail raw meats in Singapore

Guo, Siyao ; Aung, Kyaw Thu ; Leekitcharoenphon, Pimlapas ; Tay, Moon Y F ; Seow, Kelyn L G ; Zhong, Yang ; Ng, Lee Ching ; Aarestrup, Frank Møller ; Schlundt, Joergen
in: Journal of Antimicrobial Chemotherapy

Type: Journal article (Peer reviewed)

Status: Accepted/In press | Year: 2021 | DOI: https://doi.org/10.1093/jac/dkaa461

Salmonella enterica serovar Typhi H58 clone has been endemic in Zimbabwe from 2012 to 2019

Mashe, Tapfumanei ; Leekitcharoenphon, Pimlapas ; Mtapuri-Zinyowera, Sekesai ; Kingsley, Robert A ; Robertson, V ; Tarupiwa, Andrew ; Kock, Marleen M ; Makombe, Evidence P ; Chaibva, Blessmore V ; Manangazira, Portia ; Phiri, Isaac ; Nyadundu, Simon ; Chigwena, Chriswell T ; Mufoya, Last P ; Thilliez, Gaetan ; Midzi, Stanely ; Mwamakamba, Lusubilo W ; Hamblion, Esther L ; Matheu, Jorge ; Jensen, Jacob Dyring ; Aarestrup, Frank Møller ; Hendriksen, Rene S. ; Ehlers, Marthie M
in: Journal of Antimicrobial Chemotherapy

Type: Journal article (Peer reviewed)

Status: Accepted/In press | Year: 2021 | DOI: https://doi.org/10.1093/jac/dkaa519

Trichinella spp. in Wild Boars (Sus scrofa), Brown Bears (Ursus arctos), Eurasian Lynxes (Lynx lynx) and Badgers (Meles meles) in Estonia, 2007–2014

Karssin, Age ; Häkkinen, Liidia ; Vilem, Annika ; Jokelainen, Pikka ; Lassen, Brian
in: Animals, vol: 11

Type: Journal article (Peer reviewed)

Status: Published | Year: 2021 | DOI: https://doi.org//10.3390/ani11010183

Variation in post-smolt growth pattern of wild one sea-winter salmon (Salmo salar L.), and its linkage to surface warming in the eastern North Atlantic Ocean

Todd, Christopher D ; Hanson, Nora N ; Boehme, Lars ; Revie, Crawford W ; Marques, Ana Rita Pinheiro
in: Journal of Fish Biology

Type: Journal article (Peer reviewed)

Status: Accepted/In press | Year: 2021 | DOI: https://doi.org/10.1111/jfb.14552

AB_SA: Accessory genes-Based Source Attribution – tracing the source of Salmonella enterica Typhimurium environmental strains

Guillier, Laurent ; Gourmelon, Michèle ; Lozach, Solen ; Cadel-Six, Sabrina ; Vignaud, Marie-Léone ; Munck, Nanna Sophia Mucha ; Hald, Tine ; Palma, Federica
in: Microbial Genomics, vol: 6, issue: 7

Type: Journal article (Peer reviewed)

Status: Published | Year: 2020 | DOI: https://doi.org/10.1099/mgen.0.000366

Accelerating surveillance and research of antimicrobial resistance - an online repository for sharing of antimicrobial susceptibility data associated with whole-genome sequences

Matamoros, Sébastien ; Hendriksen, Rene S. ; Pataki, Bálint Ármin ; Pakseresht, Nima ; Rossello, Marc ; Silvester, Nicole ; Amid, Clara ; Aarestrup, Frank Møller ; Koopmans, Marion ; Cochrane, Guy ; Csabai, Istvan ; Lund, Ole ; Schultsz, Constance ; Group, The Compare Ml-Amr
in: Microbial Genomics, vol: 6, issue: 5

Type: Journal article (Peer reviewed)

Status: Published | Year: 2020 | DOI: https://doi.org/10.1099/mgen.0.000342

Addressing Learning Needs on the Use of Metagenomics in Antimicrobial Resistance Surveillance

Ribeiro Duarte, Ana Sofia ; Stärk, Katharina D. C. ; Munk, Patrick ; Leekitcharoenphon, Pimlapas ; Bossers, Alex ; Luiken, Roosmarijn ; Sarrazin, Steven ; Lukjancenko, Oksana ; Pamp, Sünje Johanna ; Bortolaia, Valeria ; Nissen, Jakob Nybo ; Kirstahler, Philipp ; Van Gompel, Liese ; Poulsen, Casper Sahl ; Kaas, Rolf Sommer ; Hellmér, Maria ; Hansen, Rasmus Borup ; Gomez, Violeta Munoz ; Hald, Tine
in: Frontiers in Public Health, vol: 8

Type: Journal article (Peer reviewed)

Status: Published | Year: 2020 | DOI: https://doi.org/10.3389/fpubh.2020.00038

A High Resolution DNA Melting Curve Analysis for the Rapid and Efficient Molecular Diagnostics of Extended Spectrum β-Lactamase Determinants from Foodborne Escherichia coli

Njage, Patrick Murigu Kamau ; Buys, Elna M.
in: Microorganisms, vol: 8, issue: 1

Type: Journal article (Peer reviewed)

Status: Published | Year: 2020 | DOI: https://doi.org/10.3390/microorganisms8010090

A metagenomic glimpse into the gut of wild and domestic animals

Skarżyńska, Magdalena ; Leekitcharoenphon, Pimlapas ; Hendriksen, Rene S. ; Aarestrup, Frank Møller ; Wasyl, Dariusz
in: PLOS ONE, vol: 15, issue: 12

Type: Journal article (Peer reviewed)

Status: Published | Year: 2020 | DOI: https://doi.org/10.1371/journal.pone.0242987

An interactive database for the investigation of high-density peptide microarray guided interaction patterns and antivenom cross-reactivity

Krause, Kamille E. ; Jenkins, Timothy P. ; Skaarup, Carina ; Engmark, Mikael ; Casewell, Nicholas R. ; Ainsworth, Stuart ; Lomonte, Bruno ; Fernández, Julián ; Gutiérrez, José M. ; Lund, Ole ; Laustsen, Andreas H.
in: PLOS Neglected Tropical Diseases , vol: 14, issue: 6

Type: Journal article (Peer reviewed)

Status: Published | Year: 2020 | DOI: https://doi.org/10.1371/journal.pntd.0008366

Annual Report on Zoonoses in Denmark 2019

Helwigh, Birgitte ; Petersen, Channie Kahl ; Torpdahl, Mia (Editor)

Type: Report

Status: Published | Year: 2020

AnOxPePred

Olsen, Tobias Hegelund ; Yesiltas, Betül ; Marin, Frederikke Isa ; Pertseva, Margarita ; García-Moreno, Pedro J ; Gregersen, Simon ; Overgaard, Michael Toft ; Jacobsen, Charlotte ; Lund, Ole ; Hansen, Egon Bech ; Marcatili, Paolo
in: Scientific Reports, vol: 10, issue: 1

Type: Journal article (Peer reviewed)

Status: Published | Year: 2020 | DOI: https://doi.org/10.1038/s41598-020-78319-w

Antimicrobial resistant E. coli and enterococci in pangasius fillets and prawns in Danish retail imported from Asia

Ellis-Iversen, Johanne ; Seyfarth, Anne Mette ; Korsgaard, Helle Bisgaard ; Bortolaia, Valeria ; Munck, Nanna Sophia Mucha ; Dalsgaard, Anders
in: Food Control, vol: 114

Type: Journal article (Peer reviewed)

Status: Published | Year: 2020 | DOI: https://doi.org/10.1016/j.foodcont.2019.106958

Application of Whole-Genome Sequences and Machine Learning in Source Attribution of Salmonella Typhimurium

Munck, Nanna Sophia Mucha ; Njage, Patrick Murigu Kamau ; Leekitcharoenphon, Pimlapas ; Litrup, Eva ; Hald, Tine
in: Risk Analysis, vol: 40, issue: 9, pages: 1693-1705

Type: Journal article (Peer reviewed)

Status: Published | Year: 2020 | DOI: https://doi.org/10.1111/risa.13510

Assessing the Effect of Fungicide Treatment on Cocoa Black Pod Disease in Ghana

Oduro, Bismark ; Apenteng, Ofosuhene Okofrobour ; Nkansah, Henrietta
in: Statistics, Optimization & Information Computing, vol: 8, issue: 2, pages: 374–385

Type: Journal article (Peer reviewed)

Status: Published | Year: 2020 | DOI: https://doi.org/10.19139/soic-2310-5070-686

Base protocol for real time active random surveillance of coronavirus disease (COVID-19) – Adapting veterinary methodology to public health

Foddai, Alessandro ; Lubroth, Juan ; Ellis-Iversen, Johanne
in: One Health, vol: 9

Type: Journal article (Peer reviewed)

Status: Published | Year: 2020 | DOI: https://doi.org/10.1016/j.onehlt.2020.100129

Burden of Disease Estimates of Seven Pathogens Commonly Transmitted Through Foods in Denmark, 2017

Pires, Sara Monteiro ; Jakobsen, Lea Sletting ; Ellis-Iversen, Johanne ; Pessoa, Joana ; Ethelberg, Steen
in: Foodborne pathogens and disease, vol: 17, issue: 5

Type: Journal article (Peer reviewed)

Status: Published | Year: 2020 | DOI: https://doi.org/10.1089/fpd.2019.2705