Research group for Genomic Epidemiology

  • Kemitorvet, Bygning 202

    DK-2800 Kgs Lyngby

    Denmark

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2020

AB_SA: Accessory genes-Based Source Attribution – tracing the source of Salmonella enterica Typhimurium environmental strains

Guillier, L., Gourmelon, M., Lozach, S., Cadel-Six, S., Vignaud, M-L., Munck, N. S. M., Hald, T. & Palma, F., 2020, (Accepted/In press) In : Microbial Genomics. 10 p.

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Accelerating surveillance and research of antimicrobial resistance - an online repository for sharing of antimicrobial susceptibility data associated with whole-genome sequences

Matamoros, S., Hendriksen, R. S., Pataki, B. Á., Pakseresht, N., Rossello, M., Silvester, N., Amid, C., Aarestrup, F. M., Koopmans, M., Cochrane, G., Csabai, I., Lund, O., Schultsz, C. & Group, T. C. M-A., 2020, In : Microbial Genomics. 6, 5, 6 p.

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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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An interactive database for the investigation of high-density peptide microarray guided interaction patterns and antivenom cross-reactivity

Krause, K. E., Jenkins, T. P., Skaarup, C., Engmark, M., Casewell, N. R., Ainsworth, S., Lomonte, B., Fernández, J., Gutiérrez, J. M., Lund, O. & Laustsen, A. H., 2020, In : PLOS Neglected Tropical Diseases . 14, 6, 20 p., e0008366.

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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, In : Food Control. 114, 106958.

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Application of Whole-Genome Sequences and Machine Learning in Source Attribution of Salmonella Typhimurium

Munck, N. S. M., Njage, P. M. K., Leekitcharoenphon, P., Litrup, E. & Hald, T., 2020, (Accepted/In press) In : Risk Analysis.

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Assessing the Effect of Fungicide Treatment on Cocoa Black Pod Disease in Ghana

Oduro, B., Apenteng, O. O. & Nkansah, H., 2020, In : Statistics, Optimization & Information Computing. 8, 2, p. 374–385

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CCMetagen: comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data

Marcelino, V. R., Clausen, P. T. L. C., Buchmann, J. P., Wille, M., Iredell, J. R., Meyer, W., Lund, O., Sorrell, T. C. & Holmes, E. C., 2020, In : Genome Biology (Online Edition). 21, 15 p., 103.

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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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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, In : European Journal of Ageing. 17, p. 55–67

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access

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

Munck, N. S. M., Leekitcharoenphon, P., Litrup, E., Kaas, R. S., Meinen, A., Guillier, L., Tang, Y., Malorny, B., Palma, F., Borowiak, M., Gourmelon, M., Simon, S., Banerji, S., Petrovska, L., Dallman, T. J. & Hald, T., 2020, In : Scientific Data. 7, 1, 12 p., 75.

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

De Pietri, S., Ingham, A. C., Frandsen, T. L., Rathe, M., Krych, L., Castro‐Mejía, J. L., Nielsen, D. S., Nersting, J., Wehner, P. S., Schmiegelow, K., Hasle, H., Pamp, S. J. & Müller, K., 2020, (Accepted/In press) In : International Journal of Cancer. 11 p.

Research output: Contribution to journalJournal articleResearchpeer-review

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

Szarvas, J., Ahrenfeldt, J., Bellod Cisneros, J. L., Thomsen, M. C. F., Aarestrup, F. M. & Lund, O., 2020, In : Communications Biology. 3, 1, 10 p., 137.

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

Ahrenfeldt, J., Waisi, M., Loft, I. C., Clausen, P. T. L. C., Allesøe, R. L., Szarvas, J., Hendriksen, R. S., Aarestrup, F. M. & Lund, O., 2020, In : Scientific Reports. 10, 11 p., 3033.

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Molecular epidemiology of Salmonella Infantis in Europe: insights into the success of the bacterial host and its parasitic pESI-like megaplasmid

Alba, P., Leekitcharoenphon, P., Carfora, V., Amoruso, R., Cordaro, G., Di Matteo, P., Ianzano, A., Iurescia, M., Diaconu, E. L., Study Group, E-E-A. N., Karlsmose Pedersen, S., Guerra, B., Hendriksen, R. S., Franco, A. & Battisti, A., 2020, In : Microbial Genomics. 6, 5, 12 p.

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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, In : Annals of Work Exposures and Health. 64, 2, p. 125-137

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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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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, In : Foodborne pathogens and disease. 17, 5, p. 357-364

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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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The gut microbiome but not the resistome is associated with urogenital schistosomiasis in preschool-aged children

Osakunor, D. N. M., Munk, P., Mduluza, T., Petersen, T. N., Brinch, C., Ivens, A., Chimponda, T., Amanfo, S. A., Murray, J., Woolhouse, M. E. J., Aarestrup, F. M. & Mutapi, F., 2020, In : Communications Biology. 3, 1, 11 p., 155.

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Towards a European health research and innovation cloud (HRIC)

Aarestrup, F. M., 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. & 32 others, 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., 2020, In : Genome Medicine. 12, 1, 14 p., 18.

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Using sewage for surveillance of antimicrobial resistance

Aarestrup, F. M. & Woolhouse, M. E. J., 2020, In : Science. 367, 6478, p. 630-632

Research output: Contribution to journalJournal articleResearchpeer-review

2019

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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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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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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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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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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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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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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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

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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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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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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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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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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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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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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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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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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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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

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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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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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