Research group for Genomic Epidemiology

  • Kemitorvet, Bygning 202

    DK-2800 Kgs Lyngby

    Denmark

Research Output 2013 2020

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2020
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Antimicrobial resistant E. coli and enterococci in pangasius fillets and prawns in Danish retail imported from Asia

Ellis-Iversen, J., Seyfarth, A. M., Korsgaard, H. B., Bortolaia, V., Munck, N. S. M. & Dalsgaard, A., 2020, (Accepted/In press) In : Food Control. 106958.

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

Foverskov, E., Petersen, G. L., Pedersen, J. L. M., Rod, N. H., Mortensen, E. L., Bruunsgaard, H. & Lund, R., 2020, (Accepted/In press) In : European Journal of Ageing.

Research output: Contribution to journalJournal articleResearchpeer-review

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4 Downloads (Pure)

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

Van Gompel, L., Dohmen, W., Luiken, R. E. C., Bouwknegt, M., Heres, L., Van Heijnsbergen, E., Jongerius-Gortemaker, B. G. M., Scherpenisse, P., Greve, G. D., Tersteeg-Zijderveld, M. H. G., Wadepohl, K., Ribeiro Duarte, A. S., Muñoz-Gómez, V., Fischer, J., Skarżyńska, M., Wasyl, D., Wagenaar, J. A., Urlings, B. A. P., Dorado-García, A., Wouters, I. M. & 3 others, Heederik, D. J. J., Schmitt, H. & Smit, L. A. M., 2020, (Accepted/In press) In : Annals of Work Exposures and Health. p. 1-13 wxz098.

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48 Downloads (Pure)

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

Dalhoff Andersen, V., Møller Aarestrup, F., Munk, P., Stengaard Jensen, M., de Knegt, L., Bortolaia, V., nudsen, B. E., Lukjancenko, O., Birkegård, A. C. & Vigre, H., 2020, In : Preventive Veterinary Medicine. 174, 10 p., 104853.

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7 Downloads (Pure)

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

Aytan, D., Clausen, P. T. L. C., Bortolaia, V., Aarestrup, F. M. & Lund, O., 2020, In : mSystems. 5, 1, 15 p., e00774-19.

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

Munck, N. S. M., Smith, J., Bates, J., Glass, K., Hald, T. & Kirk, M. D., 2020, (Accepted/In press) In : Foodborne pathogens and disease.

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18 Downloads (Pure)

Symposium report: One Health meets sequencing

Egli, A., Koch, D., Danuser, J., Hendriksen, R. S., Driesen, S., Schmid, D. C., Neher, R., Mäusezahl, M., Seth-Smith, H. M., Bloemberg, G., Tschudin-Sutter, S., Endimiani, A., Perreten, V., Greub, G., Schrenzel, J. & Stephan, R., 2020, In : Microbes and Infection. 22, 1, p. 1-7

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2019
16 Downloads (Pure)

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, J. S., Litrup, E., Schjørring, S. & Muller, L., 2019, In : Epidemiology and Infection. 147, 7 p., e315.

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56 Downloads (Pure)

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

Liu, G., Bogaj, K., Bortolaia, V., Olsen, J. E. & Thomsen, L. E., 2019, In : Frontiers in Microbiology. 10, 12 p., 2119.

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27 Downloads (Pure)

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, R. S. & De Cesare, A., 2019, In : Heliyon. 5, 10, 9 p., e02745.

Research output: Contribution to journalJournal articleResearchpeer-review

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162 Downloads (Pure)

Association between teat skin colonization and intramammary infection with Staphylococcus aureus and Streptococcus agalactiae in herds with automatic milking systems

Svennesen, L., Nielsen, S. S., Mahmmod, Y. S., Krömker, V., Pedersen, K. & Klaas, I. C., 2019, In : Journal Of Dairy Science. 102, 1, p. 629-639

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64 Downloads (Pure)

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

Luiken, R. E. C., Van Gompel, L., Munk, P., Sarrazin, S., Joosten, P., Dorado-García, A., Borup Hansen, R., Knudsen, B. E., Bossers, A., Wagenaar, J. A., Aarestrup, F. M., Dewulf, J., Mevius, D. J., Heederik, D. J. J., Smit, L. A. M., Schmitt, H. & consortium, EFFORT., 2019, In : Journal of Antimicrobial Chemotherapy. 74, 9, p. 2596–2604

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55 Downloads (Pure)

Attributable sources of community-acquired carriage of Escherichia coli containing β-lactam antibiotic resistance genes: a population-based modelling study

ESBL Attribution Consortium, 2019, In : The Lancet Planetary Health. 3, 8, p. e357-e369

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66 Downloads (Pure)

Ceftriaxone use in a tertiary care hospital in Kilimanjaro, Tanzania: A need for a hospital antibiotic stewardship programme

Sonda, T. B., Horumpende, P. G., Kumburu, H. H., van Zwetselaar, M., Mshana, S. E., Alifrangis, M., Lund, O., Møller Aarestrup, F., Chilongola, J. O., Mmbaga, B. T. & Kibiki, G. S., 2019, In : PLOS ONE. 14, 8, 11 p., e0220261.

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42 Downloads (Pure)

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

Ligowska-Marzęta, M. A., Hancock, V., Ingmer, H. & Aarestrup, F. M., 2019, In : Antibiotics. 8, 4, 19 p., 167.

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

Asplund, M., Kjartansdóttir, K. R., Mollerup, S., Vinner, L., Fridholm, H., Herrera, J. A. R., Friis-Nielsen, J., Hansen, T. A., Jensen, R. H., Nielsen, I. B., Richter, S. R., Rey-Iglesia, A., Matey-Hernandez, M. L., Alquezar-Planas, D. E., Olsen, P. V. S., Sicheritz-Pontén, T., Willerslev, E., Lund, O., Brunak, S., Mourier, T. & 3 others, Nielsen, L. P., Izarzugaza, J. M. G. & Hansen, A. J., 2019, In : Clinical Microbiology and Infection. 25, 10, p. 1277-1285

Research output: Contribution to journalJournal articleResearchpeer-review

18 Downloads (Pure)

Corrigendum: Occurrence and Characterization of mcr-1-Positive Escherichia coli Isolated From Food-Producing Animals in Poland, 2011-2016

Zajac, M., Sztromwasser, P., Bortolaia, V., Leekitcharoenphon, P., Cavaco, L., Zietek-Barszcz, A., Hendriksen, R. S. & Wasyl, D., 2019, In : Frontiers in Microbiology. 10, 2816.

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3 Downloads (Pure)

Corrigendum: Surveillance and Genomics of Toxigenic Vibrio cholerae O1 From Fish, Phytoplankton and Water in Lake Victoria, Tanzania (Frontiers in Microbiology, (2019), 10, (901), 10.3389/fmicb.2019.00901)

Hounmanou, Y. M. G., Leekitcharoenphon, P., Hendriksen, R. S., Dougnon, T. V., Mdegela, R. H., Olsen, J. E. & Dalsgaard, A., 2019, In : Frontiers in Microbiology. 10, 2 p., 2974.

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166 Downloads (Pure)

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

Leekitcharoenphon, P., Sørensen, G., Lofstrom, C., Battisti, A., Szabo, I., Wasyl, D., Slowey, R., Zhao, S., Brisabois, A., Kornschober, C., Karssin, A., Szilard, J., Cerny, T., Svendsen, C. A., Pedersen, K., Aarestrup, F. M. & Hendriksen, R. S., 2019, In : Frontiers in Microbiology. 10, 12 p., 179.

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8 Downloads (Pure)

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, C. L., 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. & 10 others, Caprioli, A., Dewulf, J., Brandt, M., Aarestrup, F. M., Hald, T., Wasyl, D., Skarzynska, M., Zajac, M., Daskalov, H. & Staerk, K., 2019, In : Berliner und Munchener Tierarztliche Wochenschrift. 132, 11-12, p. 504-512

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62 Downloads (Pure)

Disease-free monoculture farming by fungus-growing termites

Otani, S., Challinor, V. L., Kreuzenbeck, N. B., Kildgaard, S., Krath Christensen, S., Larsen, L. L. M., Aanen, D. K., Rasmussen, S. A., Beemelmanns, C. & Poulsen, M., 2019, In : Scientific Reports. 9, 1, 10 p., 8819.

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30 Downloads (Pure)

DTU Fødevareinstituttet i front for at forebygge sygdomme

Kornholt, H., Svingen, T., Aarestrup, F. M. & Poulsen, M., 2019, In : Miljø og sundhed. 25, 2, p. 13-17

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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, L. M., Hansen, F., Mushtaq, S., Hill, R. L. R., Woodford, N., Le Hello, S., Hendriksen, R. S., Hammerum, A. M. & Hasman, H., 2019, In : Journal of Antimicrobial Chemotherapy. 74, 3, p. 639-644

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53 Downloads (Pure)

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

Halfon, Y., Matzov, D., Eyal, Z., Bashan, A., Zimmerman, E., Kjeldgaard, J. S., Ingmer, H. & Yonath, A., 2019, In : Scientific Reports. 9, 1, 8 p., 11460.

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

Anjum, M., Madsen, J. S., Nesme, J., Jana, B., Wiese, M., Jasinskytė, D., Nielsen, D. S., Sørensen, S. J., Dalsgaard, A., Moodley, A., Bortolaia, V. & Guardabassi, L., 2019, In : Antimicrobial Agents and Chemotherapy. 63, 5, 13 p., e02528.

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15 Downloads (Pure)

Genomic insights into Vibrio cholerae O1 responsible for cholera epidemics in Tanzania between 1993 and 2017

Hounmanou, Y. M. G., Leekitcharoenphon, P., Kudirkiene, E., Mdegela, R. H., Hendriksen, R. S., Olsen, J. E. & Dalsgaard, A., 2019, In : PLOS Neglected Tropical Diseases . 13, 12, 14 p., e0007934.

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82 Downloads (Pure)

Global disease burden of pathogens in animal source foods, 2010

Li, M., Havelaar, A. H., Hoffmann, S., Hald, T., Kirk, M. D., Torgerson, P. R. & Devleesschauwer, B., 2019, In : PLOS ONE. 14, 6, 18 p., e0216545.

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294 Downloads (Pure)

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

Hendriksen, R. S., Munk, P., Njage, P. M. K., van Bunnik, B., McNally, L., Lukjancenko, O., Röder, T., Nieuwenhuijse, D., Karlsmose Pedersen, S., Kjeldgaard, J. S., Kaas, R. S., Clausen, P. T. L. C., Vogt, J. K., Leekitcharoenphon, P., van de Schans, M. G. M., Zuidema, T., de Roda Husman, A. M., Rasmussen, S., Petersen, B., Global, S. S. P. C. & 14 others, Amid, C., Cochrane, G., Sicheritz-Pontén, T., Schmitt, H., Alvarez, J. R. M., Aidara-Kane, A., Pamp, S. J., Lund, O., Hald, T., Woolhouse, M., Koopmans, M. P., Vigre, H., Petersen, T. N. & Aarestrup, F. M., 2019, In : Nature Communications. 10, 12 p., 1124.

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44 Downloads (Pure)

Global phylogenomics of multidrug-resistant Salmonella enterica serotype Kentucky ST198

Hawkey, J., Le Hello, S., Doublet, B., Granier, S. A., Hendriksen, R. S., Fricke, W. F., Ceyssens, P-J., Gomart, C., Billman-Jacobe, H., Holt, K. E. & Weill, F-X., 2019, In : Microbial Genomics. 5, 7, 12 p.

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

Edwards, R. A., Vega, A. A., Norman, H. M., Ohaeri, M., Levi, K., Dinsdale, E. A., Cinek, O., Aziz, R. K., McNair, K., Barr, J. J., Bibby, K., Brouns, S. J. J., Cazares, A., de Jonge, P. A., Desnues, C., Díaz Muñoz, S. L., Fineran, P. C., Kurilshikov, A., Lavigne, R., Mazankova, K. & 97 others, McCarthy, D. T., Nobrega, F. L., Reyes Muñoz, A., Tapia, G., Trefault, N., Tyakht, A. V., Vinuesa, P., Wagemans, J., Zhernakova, A., Møller Aarestrup, F., Ahmadov, G., Alassaf, A., Anton, J., Asangba, A., Billings, E. K., Cantu, V. A., Carlton, J. M., Cazares, D., Cho, G. S., Condeff, T., Cortés, P., Cranfield, M., Cuevas, D. A., De la Iglesia, R., Decewicz, P., Doane, M. P., Dominy, N. J., Dziewit, L., Elwasila, B. M., Eren, A. M., Franz, C., Fu, J., Garcia-Aljaro, C., Ghedin, E., Gulino, K. M., Haggerty, J. M., Head, S. R., Hendriksen, R. S., Hill, C., Hyöty, H., Ilina, E. N., Irwin, M. T., Jeffries, T. C., Jofre, J., Junge, R. E., Kelley, S. T., Khan Mirzaei, M., Kowalewski, M., Kumaresan, D., Leigh, S. R., Lipson, D., Lisitsyna, E. S., Llagostera, M., Maritz, J. M., Marr, L. C., McCann, A., Molshanski-Mor, S., Monteiro, S., Moreira-Grez, B., Morris, M., Mugisha, L., Muniesa, M., Neve, H., Nguyen, N. P., Nigro, O. D., Nilsson, A. S., O’Connell, T., Odeh, R., Oliver, A., Piuri, M., Prussin, A. J., Qimron, U., Quan, Z. X., Rainetova, P., Ramírez-Rojas, A., Raya, R., Reasor, K., Rice, G. A. O., Rossi, A., Santos, R., Shimashita, J., Stachler, E. N., Stene, L. C., Strain, R., Stumpf, R., Torres, P. J., Twaddle, A., Ugochi Ibekwe, M. A., Villagra, N., Wandro, S., White, B., Whiteley, A., Whiteson, K. L., Wijmenga, C., Zambrano, M. M., Zschach, H. & Dutilh, B. E., 2019, In : Nature Microbiology. 4, p. 1727-1736

Research output: Contribution to journalJournal articleResearchpeer-review

143 Downloads (Pure)

Gut microbial compositions mirror caste-specific diets in a major lineage of social insects

Otani, S., Zhukova, M., Koné, N. A., da Costa, R. R., Mikaelyan, A., Sapountzis, P. & Poulsen, M., 2019, In : Environmental Microbiology Reports. 11, 2, p. 196-205

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155 Downloads (Pure)

Host Resistance, Genomics and Population Dynamics in a Salmonella Enteritidis and Phage System

Holguín, A. V., Cárdenas, P., Prada-Peñaranda, C., Rabelo Leite, L., Buitrago, C., Clavijo, V., Oliveira, G., Leekitcharoenphon, P., Møller Aarestrup, F. & Vives, M. J., 2019, In : Viruses. 11, 2, 22 p., 188.

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37 Downloads (Pure)
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IncI1 ST3 and IncI1 ST7 plasmids from CTX-M-1-producing Escherichia coli obtained from patients with bloodstream infections are closely related to plasmids from E. coli of animal origin

Valcek, A., Roer, L., Overballe-Petersen, S., Hansen, F., Bortolaia, V., Leekitcharoenphon, P., Korsgaard, H. B., Seyfarth, A. M., Hendriksen, R. S., Hasman, H. & Hammerum, A. M., 2019, In : Journal of Antimicrobial Chemotherapy. 74, 8, p. 2171-2175

Research output: Contribution to journalJournal articleResearchpeer-review

108 Downloads (Pure)

Investing in Food Safety for Developing Countries: Opportunities and Challenges in Applying Whole-Genome Sequencing for Food Safety Management

Apruzzese, I., Song, E., Bonah, E., Sanidad, V. S., Leekitcharoenphon, P., Medardus, J. J., Abdalla, N., Hosseini, H. & Takeuchi, M., 2019, In : Foodborne pathogens and disease. 16, 7, 11 p.

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LRE-Finder, a Web tool for detection of the 23S rRNA mutations and the optrA, cfr, cfr(B) and poxtA genes encoding linezolid resistance in enterococci from whole-genome sequences

Hasman, H., Clausen, P. T. L. C., Kaya, H., Hansen, F., Knudsen, J. D., Wang, M., Holzknecht, B. J., Samulioniené, J., Røder, B. L., Frimodt-Møller, N., Lund, O. & Hammerum, A. M., 2019, In : Journal of Antimicrobial Chemotherapy. 74, 6, p. 1473-1476

Research output: Contribution to journalJournal articleResearchpeer-review

70 Downloads (Pure)

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

Njage, P. M. K., Henri, C., Leekitcharoenphon, P., Mistou, M-Y., Hendriksen, R. S. & Hald, T., 2019, In : Risk Analysis. 39, 6, p. 1397-1413 17 p.

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145 Downloads (Pure)

Megaphages infect Prevotella and variants are widespread in gut microbiomes

Devoto, A. E., Santini, J. M., Olm, M. R., Anantharaman, K., Munk, P., Tung, J., Archie, E. A., Turnbaugh, P. J., Seed, K. D., Blekhman, R., Møller Aarestrup, F., Thomas, B. C. & Banfield, J. F., 2019, In : Nature Microbiology. 4, p. 693-700

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Meta-Analysis and Meta-Regression Indicate Dynamic Prevalence and Moderators of Foodborne Pathogens in African Indigenous Fermented Milk

Wambui, J. M., Njage, P. M. K., Tasara, T. & Buys, E. M., 2019, In : Microorganisms. 7, 11, 19 p., 563.

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Metagenomic analysis of viruses in toilet waste from long distance flights—A new procedure for global infectious disease surveillance

Hjelmsø, M. H., Mollerup, S., Jensen, R. H., Pietroni, C., Lukjancenko, O., Schultz, A. C., Møller Aarestrup, F. & Hansen, A. J., 2019, In : PLOS ONE. 14, 1, 15 p., e0210368.

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Microbiota encompassing putative spoilage bacteria in retail packaged broiler meat and commercial broiler abattoir

Lauritsen, C. V., Sejer Kjeldgaard, J., Ingmer, H., Bisgaard, M. & Christensen, H., 2019, In : International Journal of Food Microbiology. 300, p. 14-21

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202 Downloads (Pure)

Modelling the Impact of Migration on HIV Persistency in Ghana

Apenteng, O. O. & Ismail, N. A., 2019, In : Statistics, Optimization & Information Computing. 7, 1, p. 55-65

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72 Downloads (Pure)

Occurrence and Characterization of mcr-1-Positive Escherichia coli Isolated From Food-Producing Animals in Poland, 2011-2016

Zajac, M., Sztromwasser, P., Bortolaia, V., Leekitcharoenphon, P., Cavaco, L., Zietek-Barszcz, A., Hendriksen, R. S. & Wasyl, D., 2019, In : Frontiers in Microbiology. 10, 14 p., 1753.

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Organic Complexity in Protostellar Disk Candidates

Bergner, J. B., Martín-Doménech, R., Öberg, K. I., Jørgensen, J. K., Artur De La Villarmois, E. & Brinch, C., 2019, In : Acs Earth and Space Chemistry. 3, 8, p. 1564-1575

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

Hendriksen, R. S., Lukjancenko, O., Munk, P., Hjort Hjelmsø, M., Verani, J. R., Ng'eno, E., Bigogo, G., Kiplangat, S., Oumar, T., Bergmark, L., Röder, T., Neatherlin, J. C., Clayton, O., Hald, T., Karlsmose, S., Pamp, S. J., Fields, B., Montgomery, J. M. & Møller Aarestrup, F., 2019, In : P L o S One. 14, 10, 15 p., e0222531.

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Plasmid ATLAS: plasmid visual analytics and identification in high-throughput sequencing data

Jesus, T. F., Ribeiro-Gonçalves, B., Silva, D. N., Bortolaia, V., Ramirez, M. & Carriço, J. A., 2019, In : Nucleic acids research. 47, D1, p. 188-194

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Probabilistic modeling for an integrated temporary acquired immunity with norovirus epidemiological data

Owusu-Ansah, E. D-G. J., Barnes, B., Abaidoo, R., Tine, H., Dalsgaard, A., Permin, A. & Schou, T. W., 2019, In : Infectious Disease Modelling. 4, p. 99-114

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

Brinkmann, A., Andrusch, A., Belka, A., Wylezich, C., Höper, D., Pohlmann, A., Petersen, T. N., Lucas, P., Blanchard, Y., Papa, A., Melidou, A., Oude Munnink, B. B., Matthijnssens, J., Deboutte, W., Ellis, R. J., Hansmann, F., Baumgärtner, W., van der Vries, E., Osterhaus, A., Camma, C. & 16 others, Mangone, I., Lorusso, A., Maracci, M., Nunes, A., Pinto, M., Borges, V., Kroneman, A., Schmitz, D., Corman, V. M., Drosten, C., Jones, T. C., Hendriksen, R. S., Aarestrup, F. M., Koopmans, M., Beer, M. & Nitsche, A., 2019, In : Journal of Clinical Microbiology. 57, 8, 12 p., e00466-19.

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