20132020

Research output per year

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Research Output

  • 14 Journal article
  • 1 Conference abstract in journal
2020

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.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
82 Downloads (Pure)

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

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
133 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.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
281 Downloads (Pure)

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.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
29 Downloads (Pure)
2019

Antimicrobial resistance in hospital wastewater in Scotland: a cross-sectional metagenomics study

Perry, M., van Bunnik, B., McNally, L., Wee, B., Munk, P., Warr, A., Moore, B., Kalima, P., Philip, C., de Roda Husman, A. M., Aarestrup, F. M. & Woolhouse, M., 2019, In : Lancet. 394, p. S1

Research output: Contribution to journalConference abstract in journalResearchpeer-review

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

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
227 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.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
379 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

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
210 Downloads (Pure)

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.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
104 Downloads (Pure)

The antimicrobial resistome in relation to antimicrobial use and biosecurity in pig farming, a metagenome-wide association study in nine European countries

Van Gompel, L., Luiken, R. E. C., Sarrazin, S., Munk, P., Knudsen, B. E., Hansen, R. B., Bossers, A., Aarestrup, F. M., Dewulf, J., Wagenaar, J. A., Mevius, D. J., Schmitt, H., Heederik, D. J. J., Dorado-García, A., Smit, L. A. M. & consortium, EFFORT., 2019, In : Journal of Antimicrobial Chemotherapy. 74, 4, p. 865-876

Research output: Contribution to journalJournal articleResearchpeer-review

2018

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

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
457 Downloads (Pure)
2017

The association between measurements of antimicrobial use and resistance in the faeces microbiota of finisher batches

Dalhoff Andersen, V., de Knegt, L., Munk, P., Jensen, M. S., Agersø, Y., Aarestrup, F. M. & Vigre, H., 2017, In : Epidemiology and Infection. 145, 13, p. 2827-2837 11 p.

Research output: Contribution to journalJournal articleResearchpeer-review

2016

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.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
290 Downloads (Pure)

Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition

Knudsen, B. E., Bergmark, L., Munk, P., Lukjancenko, O., Priemé, A., Aarestrup, F. M. & Pamp, S. J., 2016, In : mSystems. 1, 5, 15 p., e00095-16.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
312 Downloads (Pure)