Research group for Genomic Epidemiology

  • Kemitorvet, Bygning 202

    DK-2800 Kgs Lyngby

    Denmark

Research Output

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Journal article
2016

Whole genome sequencing as a tool for phylogenetic analysis of clinical strains of Mitis group streptococci

Rasmusen, L. H., Dargis, R., Iversen, K. H., Christensen, J. J., Skovgaard, O., Justesen, U. S., Rosenvinge, F. S., Moser, C., Lukjancenko, O., Rasmussen, S. & Nielsen, X. C., 2016, In : European Journal of Clinical Microbiology & Infectious Diseases. 35, 10, p. 1615-1625 11 p.

Research output: Contribution to journalJournal articleResearchpeer-review

1 Downloads (Pure)

Whole-genome Sequencing Used to Investigate a Nationwide Outbreak of Listeriosis Caused by Ready-to-eat Delicatessen Meat, Denmark, 2014

Kvistholm Jensen, A., Nielsen, E. M., Björkman, J. T., Jensen, T., Müller, L., Persson, S., Bjerager, G., Perge, A., Krause, T. G., Kiil, K., Sørensen, G., Andersen, J. K., Mølbak, K. & Ethelberg, S., 2016, In : Clinical Infectious Diseases. 63, 1, p. 64-70 7 p.

Research output: Contribution to journalJournal articleResearchpeer-review

World Health Organization Estimates of the Relative Contributions of Food to the Burden of Disease Due to Selected Foodborne Hazards: A Structured Expert Elicitation

Hald, T., Aspinall, W., Devleesschauwer, B., Cooke, R., Corrigan, T., Havelaar, A. H., Gibb, H. J., Torgerson, P. R., Kirk, M. D., Angulo, F. J., Lake, R. J., Speybroeck, N. & Hoffmann, S., 2016, In : P L o S One. 11, 1, 35 p., e0145839.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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166 Downloads (Pure)
2015

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.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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247 Downloads (Pure)

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.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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187 Downloads (Pure)

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

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

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

Comparative Evaluation of the Antimicrobial Activity of Different Antimicrobial Peptides against a Range of Pathogenic Bacteria

Ebbensgaard, A. E., Mordhorst, H., Overgaard, M. T., Nielsen, C. G., Aarestrup, F. M., Hansen, E. B. & Mergaert, P. (ed.), 2015, In : P L o S One. 10, 12, 18 p., e0144611.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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269 Downloads (Pure)

Detection of mcr-1 encoding plasmid-mediated colistin-resistant Escherichia coli isolates from human bloodstream infection and imported chicken meat, Denmark 2015

Hasman, H., Hammerum, A. M., Hansen, F., Hendriksen, R. S., Olesen, B., Agersø, Y., Zankari, E., Leekitcharoenphon, P., Stegger, M., Kaas, R. S., Cavaco, L., Hansen, D. S., Aarestrup, F. M. & Skov, R. L., 2015, In : Eurosurveillance (Online Edition). 20, 49, p. 1-5 5 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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2421 Downloads (Pure)

Development of Spatial Distribution Patterns by Biofilm Cells

Haagensen, J. A. J., Hansen, S. K., Bak Christensen, B., Pamp, S. J. & Molin, S., 2015, In : Applied and Environmental Microbiology. 81, 18, p. 6120-6128 9 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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280 Downloads (Pure)

Draft Genome Sequences of Sanguibacteroides justesenii, gen. nov., sp. nov., Strains OUH 308042T (= ATCC BAA-2681T) and OUH 334697 (= ATCC BAA-2682), Isolated from Blood Cultures from Two Different Patients

Sydenham, T. V., Hasman, H. & Justesen, U. S., 2015, In : Genome Announcements. 3, 2, p. e00005-15

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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99 Downloads (Pure)

Emergence of a Clonal Lineage of Multidrug-Resistant ESBL-Producing Salmonella Infantis Transmitted from Broilers and Broiler Meat to Humans in Italy between 2011 and 2014

Franco, A., Leekitcharoenphon, P., Feltrin, F., Alba, P., Cordaro, G., Iurescia, M., Tolli, R., D'Incau, M., Staffolani, M., Di Giannatale, E., Hendriksen, R. S., Battisti, A. & Cloeckaert, A. (ed.), 2015, In : P L o S One. 10, 12, 15 p., e0144802.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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176 Downloads (Pure)

Genome sequences of copper resistant and sensitive Enterococcus faecalis strains isolated from copper-fed pigs in Denmark

Zhang, S., Wang, D., Wang, Y., Hasman, H., Aarestrup, F. M., Alwathnani, H. A., Zhu, Y-G. & Rensing, C., 2015, In : Standards in Genomic Sciences. 10, 1, 10 p., 35.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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260 Downloads (Pure)

Identification and Antimicrobial Resistance of Bacteria Isolated from Probiotic Products Used in Shrimp Culture

Noor Uddin, G. M., Larsen, M. H., Christensen, H., Aarestrup, F. M., Phu, T. M. & Dalsgaard, A., 2015, In : P L o S One. 10, 7, 21 p., e0132338.

Research output: Contribution to journalJournal articleResearchpeer-review

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415 Downloads (Pure)

Limited similarity between plasmids encoding CTX-M-1 β-lactamase in Escherichia coli from humans, pigs, cattle, organic poultry layers and horses in Denmark

Jakobsen, L., Bortolaia, V., Bielak, E. M., Moodley, A., Olsen, S. S., Hansen, D. S., Frimodt-Møller, N., Guardabassi, L. & Hasman, H., 2015, In : Journal of Global Antimicrobial Resistance. 3, 2, p. 132-136

Research output: Contribution to journalJournal articleResearchpeer-review

Meta-genomic analysis of toilet waste from long distance flights; a step towards global surveillance of infectious diseases and antimicrobial resistance

Petersen, T. N., Rasmussen, S., Hasman, H., Carøe, C., Bælum, J., Schultz, A. C., Bergmark, L., Svendsen, C. A., Lund, O., Sicheritz-Pontén, T. & Aarestrup, F. M., 2015, In : Scientific Reports. 5, 9 p., 11444.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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378 Downloads (Pure)

Methodological Framework for World Health Organization Estimates of the Global Burden of Foodborne Disease

Devleesschauwer, B., Haagsma, J. A., Angulo, F. J., Bellinger, D. C., Cole, D., Döpfer, D., Fazil, A., Fèvre, E. M., Gibb, H. J., Hald, T., Kirk, M. D., Lake, R. J., Maertens de Noordhout, C., Mathers, C. D., McDonald, S. A., Pires, S. M., Speybroeck, N., Thomas, M. K., Torgerson, P. R., Wu, F. & 3 others, Havelaar, A. H., Praet, N. & Kretzschmar, M. E. E. (ed.), 2015, In : P L o S One. 10, 12, 20 p., e0142498.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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165 Downloads (Pure)

Performance, compliance and reliability of Waste stabilization pond: Effluent discharge quality and environmental protection agency standards in Ghana

Owusu-Ansah, E. D-G. J., Sampson, A., Amponsah, S. K., Abaidoo, R. C. & Hald, T., 2015, In : Research Journal of Applied Science, Engineering and Technology. 10, 11, p. 1293-1302 10 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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421 Downloads (Pure)

Rapid and Easy In Silico Serotyping of Escherichia coli Isolates by Use of Whole-Genome Sequencing Data

Joensen, K. G., Tetzschner, A. M. M., Iguchi, A., Aarestrup, F. M. & Scheutz, F., 2015, In : Journal of Clinical Microbiology. 53, 8, p. 2410-2426 17 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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199 Downloads (Pure)

Reads2Type: a web application for rapid microbial taxonomy identification

Saputra, D., Rasmussen, S., Larsen, M. V., Haddad, N., Sperotto, M. M., Aarestrup, F. M., Lund, O. & Sicheritz-Pontén, T., 2015, In : B M C Bioinformatics. 16, 1, 10 p., 398.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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334 Downloads (Pure)

The use of third and fourth generation cephalosporins affects the occurrence of extended-spectrum cephalosporinase-producing Escherichia coli in Danish pig herds

Dalhoff Andersen, V., Jensen, V. F., Vigre, H., Andreasen, M. & Agersø, Y., 2015, In : Veterinary Journal. 204, 3, p. 345-350 6 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Threat of multidrug resistant Staphylococcus aureus in Western Nepal

Bhatta, D. R., Cavaco, L., Nath, G., Gaur, A., Gokhale, S. & Bhatta, D. R., 2015, In : Asian Pacific Journal of Tropical Disease. 5, 8, p. 617-621 5 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Unique and conserved genome regions in Vibrio harveyi and related species in comparison with the shrimp pathogen Vibrio harveyi CAIM 1792

Valles, I. E., Vora, G. J., Lin, B., Leekitcharoenphon, P., González-Castillo, A., Ussery, D., Høj, L. & Gomez-Gil, B., 2015, In : Microbiology. 161, 9, p. 1762-1779 18 p.

Research output: Contribution to journalJournal articleResearchpeer-review

What Can We Learn from a Metagenomic Analysis of a Georgian Bacteriophage Cocktail?

Zschach, H., Joensen, K. G., Lindhard, B., Lund, O., Goderdzishvili, M., Chkonia, I., Jgenti, G., Kvatadze, N., Alavidze, Z., Kutter, E. M., Hasman, H. & Larsen, M. V., 2015, In : Viruses. 7, 12, p. 6570-6589 20 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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185 Downloads (Pure)
2014

Quality scores for 32,000 genomes

Land, M. L., Hyatt, D., Jun, S-R., Kora, G. H., Hauser, L. J., Lukjancenko, O. & Ussery, D., 2014, In : Standards in Genomic Sciences. 9, 20, 10 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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233 Downloads (Pure)
2013

The global establishment of a highly-fluoroquinolone resistant Salmonella enterica serotype Kentucky ST198 strain

Le Hello, S., Bekhit, A., Granier, S. A., Barua, H., Beutlich, J., Zaja̧c, M., Münch, S., Sintchenko, V., Bouchrif, B., Fashae, K., Pinsard, J. L., Sontag, L., Fabre, L., Garnier, M., Guibert, V., Howard, P., Hendriksen, R. S., Christensen, J. P., Biswas, P. K., Cloeckaert, A. & 4 others, Rabsch, W., Wasyl, D., Doublet, B. & Weill, F. X., 2013, In : Frontiers in Microbiology. 4, p. 395 1 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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114 Downloads (Pure)