Research group for Genomic Epidemiology

  • Kemitorvet, Bygning 202

    DK-2800 Kgs Lyngby

    Denmark

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A Bacterial Analysis Platform: An Integrated System for Analysing Bacterial Whole Genome Sequencing Data for Clinical Diagnostics and Surveillance

Thomsen, M. C. F., Ahrenfeldt, J., Bellod Cisneros, J. L., Jurtz, V. I., Larsen, M. V., Hasman, H., Aarestrup, F. M. & Lund, O., 2016, In : P L o S One. 11, 6, 14 p., e0157718.

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Abundance and diversity of the faecal resistome in slaughter pigs and broilers in nine European countries

Munk, P., Knudsen, B. E., Lukjacenko, O., Duarte, A. S. R., Van Gompel, L., Luiken, R. E. C., Smit, L. A. M., Schmitt, H., Garcia, A. D., Hansen, R. B., Petersen, T. N., Bossers, A., Ruppé, E., Graveland, H., van Essen, A., Gonzalez-Zorn, B., Moyano, G., Sanders, P., Chauvin, C., David, J. & 21 others, Battisti, A., Caprioli, A., Dewulf, J., Blaha, T., Wadepohl, K., Brandt, M., Wasyl, D., Skarzyńska, M., Zajac, M., Daskalov, H., Saatkamp, H. W., Stärk, K. D. C., Lund, O., Hald, T., Pamp, S. J., Vigre, H., Heederik, D., Wagenaar, J. A., Mevius, D., Møller Aarestrup, F. & EFFORT Group, 1 Aug 2018, In : Nature Microbiology. 3, 8, p. 898-908

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Accuracy of qPCR and bacterial culture for the diagnosis of bovine intramammary infections and teat skin colonisation with Streptococcus agalactiae and Staphylococcus aureus using Bayesian analysis

Svennesen, L., Mahmmod, Y. S., Skjølstrup, N. K., Mathiasen, L. R., Katholm, J., Pedersen, K., Klaas, I. C. & Nielsen, S. S., 2018, In : Preventive Veterinary Medicine. 161, p. 69-74 6 p.

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A culture-independent method for studying transfer of IncI1 plasmids from wild-type Escherichia coli in complex microbial communities

Anjum, M., Madsen, J. S., Espinosa-Gongora, C., Jana, B., Wiese, M., Nielsen, D. S., Sørensen, S. J., Moodley, A., Bortolaia, V. & Guardabassi, L., 2018, In : Journal of Microbiological Methods. 152, p. 18-26

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Adaptation and mitigation options to manage aflatoxin contamination in food with a climate change perspective

Wambui, J. M., Karuri, E. G., Ojiambo, J. A. & Njage, P. M. K., 2016, In : World Mycotoxin Journal. 9, 5, p. 875-888 14 p.

Research output: Contribution to journalJournal articleResearchpeer-review

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

Ribeiro Duarte, A. S., Stärk, K. D. C., Munk, P., Leekitcharoenphon, P., Bossers, A., Luiken, R., Sarrazin, S., Lukjancenko, O., Pamp, S. J., Bortolaia, V., Nissen, J. N., Kirstahler, P., Van Gompel, L., Poulsen, C. S., Kaas, R. S., Hellmér, M., Hansen, R. B., Gomez, V. M. & Hald, T., 2020, In : Frontiers in Public Health. 8, 10 p., 38.

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A decision support system for the control of Campylobacter in chickens at farm level using data from Denmark

Garcia, A. B., Madsen, A. L. & Vigre, H., 2016, In : The Journal of Agricultural Science. 154, 4, p. 720-731

Research output: Contribution to journalJournal articleResearchpeer-review

A detailed investigation of the porcine skin and nose microbiome using universal and Staphylococcus specific primers

Strube, M. L., Hansen, J. E., Rasmussen, S. & Pedersen, K., 2018, In : Scientific Reports. 8, 9 p., 12751.

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Adhesion of Escherichia coli under flow conditions reveals potential novel effects of FimH mutations

Feenstra, T., Schmidt Thøgersen, M., Wieser, E., Peschel, A., Ball, M. J., Brandes, R., Satchell, S. C., Stockner, T., Aarestrup, F. M., Rees, A. J. & Kain, R., 2017, In : European Journal of Clinical Microbiology & Infectious Diseases. 36, 3, p. 467-478 12 p.

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Aetiology-Specific Estimates of the Global and Regional Incidence and Mortality of Diarrhoeal Diseases Commonly Transmitted through Food

Pires, S. M., Fischer-Walker, C. L., Lanata, C. F., Devleesschauwer, B., Hall, A. J., Kirk, M. D., Ribeiro Duarte, A. S., Black, R. E. & Angulo, F. J., 2015, In : P L o S One. 10, 12, 17 p., e0142927.

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247 Downloads (Pure)
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A Livestock-Associated, Multidrug-Resistant, Methicillin-Resistant Staphylococcus aureus Clonal Complex 97 Lineage Spreading in Dairy Cattle and Pigs in Italy

Feltrin, F., Alba, P., Kraushaar, B., Ianzano, A., Argudíín, M. A., Di Matteo, P., Porrero, M. C., Aarestrup, F. M., Butaye, P., Franco, A. & Battisti, A., 2016, In : APPLIED AND ENVIRONMENTAL MICROBIOLOGY. 82, 3, p. 816-821 6 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Analytical Profiling of Airplane Wastewater - a New Matrix for Mapping Worldwide Patterns of Drug Use and Abuse

Mardal, M., Aarestrup, F. M., Rasmussen, B. S., Mollerup, C. B., Dalsgaard, P. W. & Linnet, K., 2017, In : Scandinavian Journal of Forensic Science. 23, 1, p. 1-6

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An Approach to Cluster EU Member States into Groups According to Pathways of Salmonella in the Farm‐to‐Consumption Chain for Pork Products

Vigre, H., Coutinho Calado Domingues, A. R., Pedersen, U. B. & Hald, T., 2016, In : Risk Analysis. 36, 3, p. 450-460 11 p.

Research output: Contribution to journalJournal articleResearchpeer-review

An Assessment of Different Genomic Approaches for Inferring Phylogeny of Listeria monocytogenes

Henri, C., Leekitcharoenphon, P., Carleton, H. A., Radomski, N., Kaas, R. S., Mariet, J-F., Felten, A., Aarestrup, F. M., Smidt, P. G., Roussel, S., Guillier, L., Mistou, M-Y. & Hendriksen, R. S., 2017, In : Frontiers in Microbiology. 8, 13 p., 2351.

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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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An OXA-48-producing Escherichia coli isolated from a Danish patient with no hospitalization abroad

Gedebjerg, A., Hasman, H., Sorensen, C. M. & Wang, M., 2015, In : B M C Infectious Diseases. 47, 8, p. 593-595 3 p.

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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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Antibody Cross-Reactivity in Antivenom Research

Ledsgaard, L., Jenkins, T. P., Davidsen, K., Krause, K. E., Martos-Esteban, A., Engmark, M., Andersen, M. R., Lund, O. & Laustsen, A. H., 2018, In : Toxins. 10, 10, 19 p., 393.

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217 Downloads (Pure)

Antimicrobial peptide CAP18 and its effect on Yersinia ruckeri infections in rainbow trout Oncorhynchus mykiss (Walbaum): comparing administration by injection and oral routes

Chettri, J. K., Mehrdana, F., Hansen, E. B., Ebbensgaard, A. E., Overgaard, M. T., Lauritsen, A. H., Dalsgaard, I. & Buchmann, K., 2017, In : Journal of Fish Diseases. 40, 1, p. 97-104

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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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Antimikrobielle stoffer Forbrug og resistensmønstre

Nikolaisen, N. K., Chriél, M., Jensen, V. F., Larsen, G., Pedersen, K. & Struve, T., 2017, In : Faglig Årsberetning. 2017, p. 83-88

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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.

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Application of Molecular Typing Results in Source Attribution Models: The Case of Multiple Locus Variable Number Tandem Repeat Analysis (MLVA) of Salmonella Isolates Obtained from Integrated Surveillance in Denmark

de Knegt, L., Pires, S. M., Löfström, C., Sørensen, G., Pedersen, K., Torpdahl, M., Nielsen, E. M. & Hald, T., 2016, In : Risk Analysis. 36, 3, p. 571-588 18 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Application of Probabilistic Modeling to Quantify the Reduction Levels of Hepatocellular Carcinoma Risk Attributable to Chronic Aflatoxins Exposure

Wambui, J. M., Karuri, E. G., Ojiambo, J. A. & Njage, P. M. K., 2017, In : NUTRITION AND CANCER-AN INTERNATIONAL JOURNAL. 69, 1, p. 1-13 13 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Apramycin treatment affects selection and spread of a multidrug-resistant Escherichia coli strain able to colonize the human gut in the intestinal microbiota of pigs

Herrero-Fresno, A., Zachariasen, C., Hansen, M. H., Hendriksen, R. S., Nielsen, S. S. & Olsen, J. E., 2016, In : Veterinary Research. 47, 1, 10 p., 12.

Research output: Contribution to journalJournal articleResearchpeer-review

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A Quantitative Microbiological Risk Assessment for Salmonella in Pigs for the European Union

Snary, E. L., Swart, A. N., Simons, R. R. L., Coutinho Calado Domingues, A. R., Vigre, H., Evers, E. G., Hald, T. & Hill, A. A., 2016, In : Risk Analysis. 36, 3, p. 437-449 13 p.

Research output: Contribution to journalJournal articleResearchpeer-review

A risk-based approach for evaluation of hygiene performance at pig slaughter

Bollerslev, A. M., Nauta, M., Hald, T., Hansen, T. B. & Aabo, S., 2016, In : Food Control. 75, p. 116-125 10 p.

Research output: Contribution to journalJournal articleResearchpeer-review

A sampling and metagenomic sequencing-based methodology for monitoring antimicrobial resistance in swine herds

Munk, P., Dalhoff Andersen, V., de Knegt, L., Jensen, M. S., Knudsen, B. E., Lukjancenko, O., Mordhorst, H., Clasen, J., Agersø, Y., Folkesson, A., Pamp, S. J., Vigre, H. & Aarestrup, F. M., 2016, In : Journal of Antimicrobial Chemotherapy. 72, p. 385-392 8 p., dkw415.

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Assessing low quality water use policy framework: Case study from Ghana

Amponsah, O., Vigre, H., Wilde Schou, T., Boateng, E. S., Braimah, I. & Abaidoo, R. C., 2015, In : Resources, Conservation and Recycling. 97, p. 1-15 15 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Assessing the Effectiveness of On‐Farm and Abattoir Interventions in Reducing Pig Meat–Borne Salmonellosis within E.U. Member States

Hill, A. A., Simons, R. L., Swart, A. N., Kelly, L., Hald, T. & Snary, E. L., 2016, In : Risk Analysis. 36, 3, p. 546-560 15 p.

Research output: Contribution to journalJournal articleResearchpeer-review

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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Association of Panton Valentine Leukocidin (PVL) genes with methicillin resistant Staphylococcus aureus (MRSA) in Western Nepal: a matter of concern for community infections (a hospital based prospective study)

Bhatta, D. R., Cavaco, L., Nath, G., Kumar, K., Gaur, A., Gokhale, S. & Bhatta, D. R., 2016, In : B M C Infectious Diseases. 16, 1, 6 p., 199.

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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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A Systems Approach to Evaluate One Health Initiatives

Rüegg, S. R., Nielsen, L. R., Buttigieg, S. C., Santa, M., Aragrande, M., Canali, M., Ehlinger, T., Chantziaras, I., Boriani, E., Radeski, M., Bruce, M., Queenan, K. & Häsler, B., 2018, In : Frontiers in Veterinary Science. 5, 19 p., 23.

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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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Attribution of global foodborne disease to specific foods: Findings from a World Health Organization structured expert elicitation

Hoffmann, S., Devleesschauwer, B., Aspinall, W., Cooke, R., Corrigan, T., Havelaar, A., Angulo, F., Gibb, H., Kirk, M., Lake, R., Speybroeck, N., Torgerson, P. & Hald, T., 2017, In : PLOS ONE. 12, 9, 26 p., e0183641.

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Audouin's gull, a potential vehicle of an extended spectrum beta-lactamase producing Salmonella Agona

Antilles, N., Garcia-Migura, L., Joensen, K. G., Leekitcharoenphon, P., Aarestrup, F. M., Cerda-Cuellar, M. & Hendriksen, R. S., 2015, In : FEMS Microbiology Letters. 362, 3, p. 1-4 4 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Bacterial whole genome-based phylogeny: construction of a new benchmarking dataset and assessment of some existing methods

Ahrenfeldt, J., Skaarup, C., Hasman, H., Pedersen, A. G., Aarestrup, F. M. & Lund, O., 2017, In : BMC Genomics. 18, 13 p., 19.

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Benchmarking of methods for identification of antimicrobial resistance genes in bacterial whole genome data

Clausen, P. T. L. C., Zankari, E., Aarestrup, F. M. & Lund, O., 2016, In : Journal of Antimicrobial Chemotherapy. 71, 9, p. 2484-2488 5 p.

Research output: Contribution to journalJournal articleResearchpeer-review

2 Downloads (Pure)

Biocide Susceptibility of Staphylococcus aureus CC398 and CC30 Isolates from Pigs and Identification of the Biocide Resistance Genes, qacG and qacC

Seier-Petersen, M. A., Nielsen, L. N., Ingmer, H., Aarestrup, F. M. & Agersø, Y., 2015, In : Microbial Drug Resistance. 21, 5, p. 527-536 10 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Carbapenemase VCC-1-Producing Vibrio cholerae in Coastal Waters of Germany

Hammerl, J. A., Jaeckel, C., Bortolaia, V., Schwartz, K., Bier, N., Hendriksen, R. S., Guerra, B. & Strauch, E., 2017, In : Emerging Infectious Diseases . 23, 10, p. 1735-1737 3 p.

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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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Cephalosporin-resistant Escherichia coli isolated from farm-workers and pigs in northern Vietnam

Dang, S. T. T., Bortolaia, V., Thi, N. T., Quang, H. L. & Dalsgaard, A., 2018, In : Tropical Medicine & International Health. 23, 4, p. 415-424

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Characterization and genetic variation of vibrio cholerae isolated from clinical and environmental sources in Thailand

Siriphap, A., Leekitcharoenphon, P., Kaas, R. S., Theethakaew, C., Aarestrup, F. M., Sutheinkul, O. & Hendriksen, R. S., 2017, In : P L o S One. 12, 1, 17 p., e0169324.

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Characterization of the Human Risk of Salmonellosis Related to Consumption of Pork Products in Different E.U. Countries Based on a QMRA

Vigre, H., Barfoed, K., Swart, A. N., Simons, R. R. L., Hill, A. A., Snary, E. L. & Hald, T., 2016, In : Risk Analysis. 36, 3, p. 531-545 15 p.

Research output: Contribution to journalJournal articleResearchpeer-review

CHROMagar COL-APSE: a selective bacterial culture medium for the isolation and differentiation of colistin-resistant Gram-negative pathogens

Abdul Momin, M. H. F., Bean, D. C., Hendriksen, R. S., Haenni, M., Phee, L. M. & Wareham, D. W., 2017, In : Journal of Medical Microbiology. 66, p. 1554-1561

Research output: Contribution to journalJournal articleResearchpeer-review

CHTyper, a Web Tool for Subtyping of Extraintestinal Pathogenic Escherichia coli based on the fumC and fimH Alleles

Roer, L., Johannesen, T. B., Hansen, F., Stegger, M., Tchesnokova, V., Sokurenko, E., Garibay, N., Allesøe, R. L., Thomsen, M. C. F., Lund, O., Hasman, H. & Hammerum, A. M., 2018, In : Journal of Clinical Microbiology. 56, 4, 7 p., e00063.

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Clades of huge phages from across Earth's ecosystems

Al-Shayeb, B., Sachdeva, R., Chen, L-X., Ward, F., Munk, P., Devoto, A., Castelle, C. J., Olm, M. R., Bouma-Gregson, K., Amano, Y., He, C., Méheust, R., Brooks, B., Thomas, A., Lavy, A., Matheus-Carnevali, P., Sun, C., Goltsman, D. S. A., Borton, M. A., Sharrar, A. & 25 others, Jaffe, A. L., Nelson, T. C., Kantor, R., Keren, R., Lane, K. R., Farag, I. F., Lei, S., Finstad, K., Amundson, R., Anantharaman, K., Zhou, J., Probst, A. J., Power, M. E., Tringe, S. G., Li, W-J., Wrighton, K., Harrison, S., Morowitz, M., Relman, D. A., Doudna, J. A., Lehours, A-C., Warren, L., Cate, J. H. D., Santini, J. M. & Banfield, J. F., 2020, In : Nature. 578, p. 425-431

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Colistin Resistance Mediated by mcr-1 in ESBL-Producing, Multidrug Resistant Salmonella Infantis in Broiler Chicken Industry, Italy (2016-2017)

Carfora, V., Alba, P., Leekitcharoenphon, P., Ballaro, D., Cordaro, G., Di Matteo, P., Donati, V., Ianzano, A., Iurescia, M., Stravino, F., Tagliaferri, T., Battisti, A. & Franco, A., 2018, In : Frontiers in Microbiology. 9, 6 p., 1880.

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