Publications from the Genomic Epidemiology Research Group

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

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

Clades of huge phages from across Earth's ecosystems

Al-Shayeb, Basem ; Sachdeva, Rohan ; Chen, Lin-Xing ; Ward, Fred ; Munk, Patrick ; Devoto, Audra ; Castelle, Cindy J ; Olm, Matthew R ; Bouma-Gregson, Keith ; Amano, Yuki ; He, Christine ; Méheust, Raphaël ; Brooks, Brandon ; Thomas, Alex ; Lavy, Adi ; Matheus-Carnevali, Paula ; Sun, Christine ; Goltsman, Daniela S A ; Borton, Mikayla A ; Sharrar, Allison ; Jaffe, Alexander L ; Nelson, Tara C ; Kantor, Rose ; Keren, Ray ; Lane, Katherine R ; Farag, Ibrahim F ; Lei, Shufei ; Finstad, Kari ; Amundson, Ronald ; Anantharaman, Karthik ; Zhou, Jinglie ; Probst, Alexander J ; Power, Mary E ; Tringe, Susannah G ; Li, Wen-Jun ; Wrighton, Kelly ; Harrison, Sue ; Morowitz, Michael ; Relman, David A ; Doudna, Jennifer A ; Lehours, Anne-Catherine ; Warren, Lesley ; Cate, Jamie H D ; Santini, Joanne M ; Banfield, Jillian F
in: Nature, vol: 578, pages: 425-431

Type: Journal article (Peer reviewed)

Status: Published | Year: 2020 | DOI: https://doi.org/10.1038/s41586-020-2007-4

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, vol: 17, pages: 55–67

Type: Journal article (Peer reviewed)

Status: Published | Year: 2020 | DOI: https://doi.org/10.1007/s10433-019-00523-z

Four European Salmonella Typhimurium datasets collected to develop WGS-based source attribution methods

Munck, Nanna Sophia Mucha ; Leekitcharoenphon, Pimlapas ; Litrup, Eva ; Kaas, Rolf Sommer ; Meinen, Anika ; Guillier, Laurent ; Tang, Yue ; Malorny, Burkhard ; Palma, Federica ; Borowiak, Maria ; Gourmelon, Michèle ; Simon, Sandra ; Banerji, Sangeeta ; Petrovska, Liljana ; Dallman, Timothy J ; Hald, Tine
in: Scientific Data, vol: 7, issue: 1

Type: Journal article (Peer reviewed)

Status: Published | Year: 2020 | DOI: https://doi.org/10.1038/s41597-020-0417-7

Gastrointestinal toxicity during induction treatment for childhood acute lymphoblastic leukemia: The impact of the gut microbiota

De Pietri, Silvia ; Ingham, Anna Cäcilia ; Frandsen, Thomas L. ; Rathe, Mathias ; Krych, Lukasz ; Castro‐Mejía, Josue L. ; Nielsen, Dennis S. ; Nersting, Jacob ; Wehner, Peder S. ; Schmiegelow, Kjeld ; Hasle, Henrik ; Pamp, Sünje Johanna ; Müller, Klaus
in: International Journal of Cancer

Type: Journal article (Peer reviewed)

Status: Accepted/In press | Year: 2020 | DOI: https://doi.org/10.1002/ijc.32942

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

Szarvas, Judit ; Ahrenfeldt, Johanne ; Bellod Cisneros, Jose Luis ; Thomsen, Martin Christen Frølund ; Aarestrup, Frank Møller ; Lund, Ole
in: Communications Biology, vol: 3, issue: 1

Type: Journal article (Peer reviewed)

Status: Published | Year: 2020 | DOI: https://doi.org/10.1038/s42003-020-0869-5

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

Ahrenfeldt, Johanne ; Waisi, Madina ; Loft, Isabella Charlotte ; Clausen, Philip Thomas Lanken Conradsen ; Allesøe, Rosa Lundbye ; Szarvas, Judit ; Hendriksen, Rene S. ; Aarestrup, Frank Møller ; Lund, Ole
in: Scientific Reports, vol: 10

Type: Journal article (Peer reviewed)

Status: Published | Year: 2020 | DOI: https://doi.org/10.1038/s41598-020-59292-w

Occupational Exposure and Carriage of Antimicrobial Resistance Genes (tetW, ermB) in Pig Slaughterhouse Workers

Van Gompel, Liese ; Dohmen, Wietske ; Luiken, Roosmarijn E. C. ; Bouwknegt, Martijn ; Heres, Lourens ; Van Heijnsbergen, Eri ; Jongerius-Gortemaker, Betty G M ; Scherpenisse, Peter ; Greve, Gerdit D ; Tersteeg-Zijderveld, Monique H G ; Wadepohl, Katharina ; Ribeiro Duarte, Ana Sofia ; Muñoz-Gómez, Violeta ; Fischer, Jennie ; Skarżyńska, Magdalena ; Wasyl, Dariusz ; Wagenaar, Jaap A ; Urlings, Bert A P ; Dorado-García, Alejandro ; Wouters, Inge M ; Heederik, Dick J J ; Schmitt, Heike ; Smit, Lidwien A M
in: Annals of Work Exposures and Health, vol: 64, issue: 2, pages: 125-137

Type: Journal article (Peer reviewed)

Status: Published | Year: 2020 | DOI: https://doi.org/10.1093/annweh/wxz098

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

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

Aytan, Derya ; Clausen, Philip Thomas Lanken Conradsen ; Bortolaia, Valeria ; Aarestrup, Frank Møller ; Lund, Ole
in: mSystems, vol: 5, issue: 1

Type: Journal article (Peer reviewed)

Status: Published | Year: 2020 | DOI: https://doi.org/10.1128/msystems.00774-19

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

Munck, Nanna Sophia Mucha ; Smith, James ; Bates, John ; Glass, Kathryn ; Hald, Tine ; Kirk, Martyn D
in: Foodborne pathogens and disease

Type: Journal article (Peer reviewed)

Status: Accepted/In press | Year: 2020 | DOI: https://doi.org/10.1089/fpd.2019.2706

Symposium report: One Health meets sequencing

Egli, Adrian ; Koch, Daniel ; Danuser, Jürg ; Hendriksen, Rene S. ; Driesen, Susanne ; Schmid, Diana Coman ; Neher, Richard ; Mäusezahl, Mirjam ; Seth-Smith, Helena Mb ; Bloemberg, Guido ; Tschudin-Sutter, Sarah ; Endimiani, Andrea ; Perreten, Vincent ; Greub, Gilbert ; Schrenzel, Jacques ; Stephan, Roger
in: Microbes and Infection, vol: 22, issue: 1, pages: 1-7

Type: Journal article (Peer reviewed)

Status: Published | Year: 2020 | DOI: https://doi.org/10.1016/j.micinf.2019.07.004

Towards a European health research and innovation cloud (HRIC)

Aarestrup, Frank Møller ; Albeyatti, A. ; Armitage, W. J. ; Auffray, C. ; Augello, L. ; Balling, R. ; Benhabiles, N. ; Bertolini, G. ; Bjaalie, J. G. ; Black, M. ; Blomberg, N. ; Bogaert, P. ; Bubak, M. ; Claerhout, B. ; Clarke, L. ; De Meulder, B. ; D'Errico, G. ; Di Meglio, A. ; Forgo, N. ; Gans-Combe, C. ; Gray, A. E. ; Gut, I. ; Gyllenberg, A. ; Hemmrich-Stanisak, G. ; Hjorth, L. ; Ioannidis, Y. ; Jarmalaite, S. ; Kel, A. ; Kherif, F. ; Korbel, J. O. ; Larue, C. ; Laszlo, M. ; Maas, A. ; Magalhaes, L. ; Manneh-Vangramberen, I. ; Morley-Fletcher, E. ; Ohmann, C. ; Oksvold, P. ; Oxtoby, N. P. ; Perseil, I. ; Pezoulas, V. ; Riess, O. ; Riper, H. ; Roca, J. ; Rosenstiel, P. ; Sabatier, P. ; Sanz, F. ; Tayeb, M. ; Thomassen, G. ; Van Bussel, J. ; Van Den Bulcke, M. ; Van Oyen, H.
in: Genome Medicine, vol: 12, issue: 1

Type: Journal article (Peer reviewed)

Status: Published | Year: 2020 | DOI: https://doi.org/10.1186/s13073-020-0713-z

Using sewage for surveillance of antimicrobial resistance

Aarestrup, Frank Møller ; Woolhouse, Mark E.J.
in: Science, vol: 367, issue: 6478, pages: 630-632

Type: Journal article (Peer reviewed)

Status: Published | Year: 2020 | DOI: https://doi.org/10.1126/science.aba3432

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

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