Publications from the Genomic Epidemiology Research Group

Predicting effects of changed antimicrobial usage on the abundance of antimicrobial resistance genes in finisher’ gut microbiomes

Dalhoff Andersen, Vibe ; Møller Aarestrup, Frank ; Munk, Patrick ; Stengaard Jensen, Marie ; de Knegt, Leonardo ; Bortolaia, Valeria ; nudsen, B. E. ; Lukjancenko, Oksana ; Birkegård, A. C. ; Vigre, Håkan
in: Preventive Veterinary Medicine, vol: 174

Type: Journal article (Peer reviewed)

Status: Published | Year: 2020 | DOI: https://doi.org/10.1016/j.prevetmed.2019.104853

Multimorbidity, healthcare utilization and socioeconomic status

Frølich, Anne ; Ghith, Nermin ; Schiøtz, Michaela ; Jacobsen, Ramune ; Stockmarr, Anders
in: PLOS ONE, vol: 14, issue: 8

Type: Journal article (Peer reviewed)

Status: Published | Year: 2019 | DOI: https://doi.org/10.1371/journal.pone.0214183

An outbreak of monophasic Salmonella Typhimurium associated with raw pork sausage and other pork products, Denmark 2018-19

Helmuth, I G ; Espenhain, L ; Ethelberg, S ; Jensen, T ; Kjeldgaard, Jette Sejer ; Litrup, E ; Schjørring, S ; Muller, L
in: Epidemiology and Infection, vol: 147

Type: Journal article (Peer reviewed)

Status: Published | Year: 2019 | DOI: https://doi.org/10.1017/s0950268819002073

Antibiotic-Induced, Increased Conjugative Transfer Is Common to Diverse Naturally Occurring ESBL Plasmids in Escherichia coli

Liu, Gang ; Bogaj, Karolina ; Bortolaia, Valeria ; Olsen, John Elmerdahl ; Thomsen, Line Elnif
in: Frontiers in Microbiology, vol: 10

Type: Journal article (Peer reviewed)

Status: Published | Year: 2019 | DOI: https://doi.org/10.3389/fmicb.2019.02119

Antimicrobial resistance in hospital wastewater in Scotland: a cross-sectional metagenomics study

Perry, Meghan ; van Bunnik, Bram ; McNally, Luke ; Wee, Bryan ; Munk, Patrick ; Warr, Amanda ; Moore, Barbara ; Kalima, Pota ; Philip, Carol ; de Roda Husman, Ana Maria ; Aarestrup, Frank Møller ; Woolhouse, Mark
in: Lancet, vol: 394, pages: S1

Type: Conference abstract in journal (Peer reviewed)

Status: Published | Year: 2019 | DOI: https://doi.org/10.1016/s0140-6736(19)32798-9

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

Type: Journal article (Peer reviewed)

Status: Accepted/In press | Year: 2019 | DOI: https://doi.org/10.1016/j.foodcont.2019.106958

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

Pasquali, F. ; Do Valle, I. ; Palma, F. ; Remondini, D. ; Manfreda, G. ; Castellani, G. ; Hendriksen, Rene S. ; De Cesare, A.
in: Heliyon, vol: 5, issue: 10

Type: Journal article (Peer reviewed)

Status: Published | Year: 2019 | DOI: https://doi.org/10.1016/j.heliyon.2019.e02745

Associations between antimicrobial use and the faecal resistome on broiler farms from nine European countries

Luiken, Roosmarijn E C ; Van Gompel, Liese ; Munk, Patrick ; Sarrazin, Steven ; Joosten, Philip ; Dorado-García, Alejandro ; Borup Hansen, Rasmus ; Knudsen, Berith Elkær ; Bossers, Alex ; Wagenaar, Jaap A ; Aarestrup, Frank Møller ; Dewulf, Jeroen ; Mevius, Dik J ; Heederik, Dick J J ; Smit, Lidwien A M ; Schmitt, Heike ; consortium, EFFORT
in: Journal of Antimicrobial Chemotherapy, vol: 74, issue: 9, pages: 2596–2604

Type: Journal article (Peer reviewed)

Status: Published | Year: 2019 | DOI: https://doi.org/10.1093/jac/dkz235

Attributable sources of community-acquired carriage of Escherichia coli containing β-lactam antibiotic resistance genes

, ; Mughini-Gras, Lapo ; Dorado-García, Alejandro ; van Duijkeren, Engeline ; van den Bunt, Gerrita ; Dierikx, Cindy M. ; Bonten, Marc J.M. ; Bootsma, Martin C.J. ; Schmitt, Heike ; Hald, Tine ; Evers, Eric G. ; de Koeijer, Aline ; van Pelt, Wilfrid ; Franz, Eelco ; Mevius, Dik J. ; Heederik, Dick J.J.
in: The Lancet Planetary Health, vol: 3, issue: 8, pages: e357-e369

Type: Journal article (Peer reviewed)

Status: Published | Year: 2019 | DOI: https://doi.org/10.1016/S2542-5196(19)30130-5

Ceftriaxone use in a tertiary care hospital in Kilimanjaro, Tanzania

Sonda, Tolbert B. ; Horumpende, Pius G. ; Kumburu, Happiness H. ; van Zwetselaar, Marco ; Mshana, Stephen E. ; Alifrangis, Michael ; Lund, Ole ; Møller Aarestrup, Frank ; Chilongola, Jaffu O. ; Mmbaga, Blandina T. ; Kibiki, Gibson S.
in: PLOS ONE, vol: 14, issue: 8

Type: Journal article (Peer reviewed)

Status: Published | Year: 2019 | DOI: https://doi.org/10.1371/journal.pone.0220261

Comparison of Gene Expression Profiles of Uropathogenic Escherichia Coli CFT073 after Prolonged Exposure to Subinhibitory Concentrations of Different Biocides

Ligowska-Marzęta, Małgorzata Anna ; Hancock, Viktoria ; Ingmer, Hanne ; Aarestrup, Frank Møller
in: Antibiotics, vol: 8, issue: 4

Type: Journal article (Peer reviewed)

Status: Published | Year: 2019 | DOI: https://doi.org/10.3390/antibiotics8040167

Contaminating viral sequences in high-throughput sequencing viromics: a linkage study of 700 sequencing libraries

Asplund, Maria ; Kjartansdóttir, Kristín Rós ; Mollerup, Sarah ; Vinner, Lasse ; Fridholm, Helena ; Herrera, José A. R. ; Friis-Nielsen, Jens ; Hansen, Thomas Arn ; Jensen, Randi Holm ; Nielsen, Ida Broman ; Richter, Stine Raith ; Rey-Iglesia, Alba ; Matey-Hernandez, Maria Luisa ; Alquezar-Planas, David E. ; Olsen, Pernille V. S. ; Sicheritz-Pontén, Thomas ; Willerslev, Eske ; Lund, Ole ; Brunak, Søren ; Mourier, Tobias ; Nielsen, Lars Peter ; Izarzugaza, Jose M. G. ; Hansen, Anders Johannes
in: Clinical Microbiology and Infection, vol: 25, issue: 10, pages: 1277-1285

Type: Journal article (Peer reviewed)

Status: Published | Year: 2019 | DOI: https://doi.org/10.1016/j.cmi.2019.04.028

Cross-Border Transmission of Salmonella Choleraesuis var. Kunzendorf in European Pigs and Wild Boar: Infection, Genetics, and Evolution

Leekitcharoenphon, Pimlapas ; Sørensen, Gitte ; Lofstrom, Charlotta ; Battisti, Antonio ; Szabo, Istvan ; Wasyl, Dariusz ; Slowey, Rosemarie ; Zhao, Shaohua ; Brisabois, Anne ; Kornschober, Christian ; Karssin, Age ; Szilard, Janosi ; Cerny, Tomas ; Svendsen, Christina Aaby ; Pedersen, Karl ; Aarestrup, Frank Møller ; Hendriksen, Rene S.
in: Frontiers in Microbiology, vol: 10

Type: Journal article (Peer reviewed)

Status: Published | Year: 2019 | DOI: https://doi.org/10.3389/fmicb.2019.00179

Data science in healthcare

Abedjan, Ziawasch ; Boujemaa, Nozha ; Campbell, Stuart ; Casla, Patricia ; Chatterjea, Supriyo ; Consoli, Sergio ; Costa-Soria, Cristobal ; Czech, Paul ; Despenic, Marija ; Garattini, Chiara ; Hamelinck, Dirk ; Heinrich, Adrienne ; Kraaij, Wessel ; Kustra, Jacek ; Lojo, Aizea ; Sanchez, Marga Martin ; Mayer, Miguel A. ; Melideo, Matteo ; Menasalvas, Ernestina ; Møller Aarestrup, Frank ; Artigot, Elvira Narro ; Petković, Milan ; Recupero, Diego Reforgiato ; Gonzalez, Alejandro Rodriguez ; Kerremans, Gisele Roesems ; Roller, Roland ; Romao, Mario ; Ruping, Stefan ; Sasaki, Felix ; Spek, Wouter ; Stojanovic, Nenad ; Thoms, Jack ; Vasiljevs, Andrejs ; Verachtert, Wilfried ; Wuyts, Roel
part of: Data Science for Healthcare, pages: 3-38, 2019, Springer

Type: Book chapter (Peer reviewed)

Status: Published | Year: 2019 | DOI: https://doi.org/10.1007/978-3-030-05249-2_1

Development of a simplified on-farm animal health and welfare benchmarking tool for pig herds

Wadepohl, K. ; Blaha, T. ; Van Gompel, L. ; Duarte, A. S. R. ; Nielsen, Cecilie Liv ; Saatkamp, H. ; Wagenaar, J. A. ; Meemken, D. ; Graveland, H. ; Schmitt, H. ; Heederik, D. ; Luiken, R. E. C. ; Mevius, D. ; van Essen, A. ; Gonzalez-Zorn, B. ; Moyano, G. ; Saunders, P. ; Chauvin, C. ; David, J. ; Battisti, A. ; Caprioli, A. ; Dewulf, J. ; Brandt, M. ; Aarestrup, Frank Møller ; Hald, Tine ; Wasyl, D. ; Skarzynska, M. ; Zajac, M. ; Daskalov, H. ; Staerk, K.
in: Berliner und Munchener Tierarztliche Wochenschrift, vol: 132, issue: 11-12, pages: 504-512

Type: Journal article (Peer reviewed)

Status: Published | Year: 2019 | DOI: https://doi.org/10.2376/0005-9366-18088

Disease-free monoculture farming by fungus-growing termites

Otani, Saria ; Challinor, Victoria L. ; Kreuzenbeck, Nina B. ; Kildgaard, Sara ; Krath Christensen, Søren ; Larsen, Louise Lee Munk ; Aanen, Duur K. ; Rasmussen, Silas Anselm ; Beemelmanns, Christine ; Poulsen, Michael
in: Scientific Reports, vol: 9, issue: 1

Type: Journal article (Peer reviewed)

Status: Published | Year: 2019 | DOI: https://doi.org/10.1038/s41598-019-45364-z

DTU Fødevareinstituttet i front for at forebygge sygdomme

Kornholt, Heidi ; Svingen, Terje ; Aarestrup, Frank Møller ; Poulsen, Morten
in: Miljø og sundhed, vol: 25, issue: 2, pages: 13-17

Type: Journal article (Peer reviewed)

Status: Published | Year: 2019

Economic hardship over twenty-two consecutive years of adult life and markers of early ageing

Foverskov, E. ; Petersen, G. L. ; Pedersen, Jolene Lee Masters ; Rod, N . H. ; Mortensen, E. L. ; Bruunsgaard, H. ; Lund, R.
in: European Journal of Public Health, vol: 29, issue: Supplement 4, pages: 38-38
Presented at: 12th European Public Health Conference

Type: Conference abstract in journal (Peer reviewed)

Status: Published | Year: 2019 | DOI: https://doi.org/10.1093/eurpub/ckz185.085

Economic hardship over twenty-two consecutive years of adult life and markers of early ageing: physical capability, cognitive function and inflammation

Foverskov, Else ; Petersen, Gitte Lindved ; Pedersen, Jolene Lee Masters ; Rod, Naja Hulvej ; Mortensen, Erik Lykke ; Bruunsgaard, Helle ; Lund, Rikke
in: European Journal of Ageing

Type: Journal article (Peer reviewed)

Status: Accepted/In press | Year: 2019 | DOI: https://doi.org/10.1007/s10433-019-00523-z

Environmental surveillance and genomic characterization of Vibrio cholerae O1 from fish, phytoplankton and water in Lake Victoria

Hounmanou, Y. M. G. ; Leekitcharoenphon, Pimlapas ; Hendriksen, Rene S. ; Dougnon, T. V. ; Mdegela, R. H. ; Olsen, John ; Dalsgaard, Anders
part of: 13th DWF Water Research Conference - Abstracts, pages: 52-52, 2019, University of Copenhagen, Frederiksberg C
Presented at: 13th Annual Water Research Conference

Type: Conference abstract in proceedings (Peer reviewed)

Status: Published | Year: 2019

Evaluation of temocillin for phenotypic carbapenemase screening of Escherichia coli and Salmonella enterica isolates in relation to the presence of genes encoding ESBLs and carbapenemase production

Cavaco, Lina M ; Hansen, Frank ; Mushtaq, Shazad ; Hill, Robert L R ; Woodford, Neil ; Le Hello, Simon ; Hendriksen, Rene S. ; Hammerum, Anette Marie ; Hasman, Henrik
in: Journal of Antimicrobial Chemotherapy, vol: 74, issue: 3, pages: 639-644

Type: Journal article (Peer reviewed)

Status: Published | Year: 2019 | DOI: https://doi.org/10.1093/jac/dky493

Exit tunnel modulation as resistance mechanism of S. aureus erythromycin resistant mutant

Halfon, Yehuda ; Matzov, Donna ; Eyal, Zohar ; Bashan, Anat ; Zimmerman, Ella ; Kjeldgaard, Jette Sejer ; Ingmer, Hanne ; Yonath, Ada
in: Scientific Reports, vol: 9, issue: 1

Type: Journal article (Peer reviewed)

Status: Published | Year: 2019 | DOI: https://doi.org/10.1038/s41598-019-48019-1

Fate of CMY-2-encoding plasmids introduced into the human fecal microbiota by exogenous Escherichia coli

Anjum, Mehreen ; Madsen, Jonas Stenløkke ; Nesme, Joseph ; Jana, Bimal ; Wiese, Maria ; Jasinskytė, Džiuginta ; Nielsen, Dennis Sandris ; Sørensen, Søren Johannes ; Dalsgaard, Anders ; Moodley, Arshnee ; Bortolaia, Valeria ; Guardabassi, Luca
in: Antimicrobial Agents and Chemotherapy, vol: 63, issue: 5

Type: Journal article (Peer reviewed)

Status: Published | Year: 2019 | DOI: https://doi.org/10.1128/AAC.02528-18

Global disease burden of pathogens in animal source foods, 2010

Li, Min ; Havelaar, Arie H. ; Hoffmann, Sandra ; Hald, Tine ; Kirk, Martyn D. ; Torgerson, Paul R. ; Devleesschauwer, Brecht
in: PLOS ONE, vol: 14, issue: 6

Type: Journal article (Peer reviewed)

Status: Published | Year: 2019 | DOI: https://doi.org/10.1371/journal.pone.0216545

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

Hendriksen, Rene S. ; Munk, Patrick ; Njage, Patrick Murigu Kamau ; van Bunnik, Bram ; McNally, Luke ; Lukjancenko, Oksana ; Röder, Timo ; Nieuwenhuijse, David ; Karlsmose Pedersen, Susanne ; Kjeldgaard, Jette Sejer ; Kaas, Rolf Sommer ; Clausen, Philip Thomas Lanken Conradsen ; Vogt, Josef Korbinian ; Leekitcharoenphon, Pimlapas ; van de Schans, Milou G M ; Zuidema, Tina ; de Roda Husman, Ana Maria ; Rasmussen, Simon ; Petersen, Bent ; Global, Sewage Surveillance project consortium ; Amid, Clara ; Cochrane, Guy ; Sicheritz-Pontén, Thomas ; Schmitt, Heike ; Alvarez, Jorge Raul Matheu ; Aidara-Kane, Awa ; Pamp, Sünje Johanna ; Lund, Ole ; Hald, Tine ; Woolhouse, Mark ; Koopmans, Marion P ; Vigre, Håkan ; Petersen, Thomas Nordahl ; Aarestrup, Frank Møller
in: Nature Communications, vol: 10

Type: Journal article (Peer reviewed)

Status: Published | Year: 2019 | DOI: https://doi.org/10.1038/s41467-019-08853-3