Publications from the Genomic Epidemiology Research Group

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

Luiken, Roosmarijn E C ; Van Gompel, Liese ; Munk, Patrick ; Sarrazin, Steven ; Joosten, Philip ; Dorado-García, Alejandro ; Borup Hansen, Rasmus ; Knudsen, Berith Elkær ; Bossers, Alex ; Wagenaar, Jaap A ; Aarestrup, Frank Møller ; Dewulf, Jeroen ; Mevius, Dik J ; Heederik, Dick J J ; Smit, Lidwien A M ; Schmitt, Heike ; consortium, EFFORT
in: Journal of Antimicrobial Chemotherapy

Type: Journal article (Peer reviewed)

Status: Accepted/In press | Year: 2019 | DOI: https://doi.org/10.1093/jac/dkz235

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

Asplund, Maria ; Kjartansdóttir, Kristín Rós ; Mollerup, Sarah ; Vinner, Lasse ; Fridholm, Helena ; Herrera, José A. R. ; Friis-Nielsen, Jens ; Hansen, Thomas Arn ; Jensen, Randi Holm ; Nielsen, Ida Broman ; Richter, Stine Raith ; Rey-Iglesia, Alba ; Matey-Hernandez, Maria Luisa ; Alquezar-Planas, David E. ; Olsen, Pernille V. S. ; Sicheritz-Pontén, Thomas ; Willerslev, Eske ; Lund, Ole ; Brunak, Søren ; Mourier, Tobias ; Nielsen, Lars Peter ; Izarzugaza, Jose M. G. ; Hansen, Anders Johannes
in: Clinical Microbiology and Infection

Type: Journal article (Peer reviewed)

Status: Accepted/In press | Year: 2019 | DOI: https://doi.org/10.1016/j.cmi.2019.04.028

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

Leekitcharoenphon, Pimlapas ; Sørensen, Gitte ; Lofstrom, Charlotta ; Battisti, Antonio ; Szabo, Istvan ; Wasyl, Dariusz ; Slowey, Rosemarie ; Zhao, Shaohua ; Brisabois, Anne ; Kornschober, Christian ; Karssin, Age ; Szilard, Janosi ; Cerny, Tomas ; Svendsen, Christina Aaby ; Pedersen, Karl ; Aarestrup, Frank Møller ; Hendriksen, Rene S.
in: Frontiers in Microbiology, vol: 10

Type: Journal article (Peer reviewed)

Status: Published | Year: 2019 | DOI: https://doi.org/10.3389/fmicb.2019.00179

Disease-free monoculture farming by fungus-growing termites

Otani, Saria ; Challinor, Victoria L. ; Kreuzenbeck, Nina B. ; Kildgaard, Sara ; Krath Christensen, Søren ; Larsen, Louise Lee Munk ; Aanen, Duur K. ; Rasmussen, Silas Anselm ; Beemelmanns, Christine ; Poulsen, Michael
in: Scientific Reports, vol: 9, issue: 1

Type: Journal article (Peer reviewed)

Status: Published | Year: 2019 | DOI: https://doi.org/10.1038/s41598-019-45364-z

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

Foverskov, Else ; Petersen, Gitte Lindved ; Pedersen, Jolene Lee Masters ; Rod, Naja Hulvej ; Mortensen, Erik Lykke ; Bruunsgaard, Helle ; Lund, Rikke
in: European Journal of Ageing

Type: Journal article (Peer reviewed)

Status: Accepted/In press | Year: 2019 | DOI: https://doi.org/10.1007/s10433-019-00523-z

Environmental surveillance and genomic characterization of Vibrio cholerae O1 from fish, phytoplankton and water in Lake Victoria

Hounmanou, Y. M. G. ; Leekitcharoenphon, Pimlapas ; Hendriksen, Rene S. ; Dougnon, T. V. ; Mdegela, R. H. ; Olsen, John ; Dalsgaard, Anders
part of: 13th DWF Water Research Conference - Abstracts, pages: 52-52, 2019, University of Copenhagen, Frederiksberg C
Presented at: 13th Annual Water Research Conference

Type: Conference abstract in proceedings (Peer reviewed)

Status: Published | Year: 2019

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, Lina M ; Hansen, Frank ; Mushtaq, Shazad ; Hill, Robert L R ; Woodford, Neil ; Le Hello, Simon ; Hendriksen, Rene S. ; Hammerum, Anette Marie ; Hasman, Henrik
in: Journal of Antimicrobial Chemotherapy, vol: 74, issue: 3, pages: 639-644

Type: Journal article (Peer reviewed)

Status: Published | Year: 2019 | DOI: https://doi.org/10.1093/jac/dky493

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

Halfon, Yehuda ; Matzov, Donna ; Eyal, Zohar ; Bashan, Anat ; Zimmerman, Ella ; Kjeldgaard, Jette Sejer ; Ingmer, Hanne ; Yonath, Ada
in: Scientific Reports, vol: 9, issue: 1

Type: Journal article (Peer reviewed)

Status: Published | Year: 2019 | DOI: https://doi.org/10.1038/s41598-019-48019-1

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

Anjum, Mehreen ; Madsen, Jonas Stenløkke ; Nesme, Joseph ; Jana, Bimal ; Wiese, Maria ; Jasinskytė, Džiuginta ; Nielsen, Dennis Sandris ; Sørensen, Søren Johannes ; Dalsgaard, Anders ; Moodley, Arshnee ; Bortolaia, Valeria ; Guardabassi, Luca
in: Antimicrobial Agents and Chemotherapy, vol: 63, issue: 5

Type: Journal article (Peer reviewed)

Status: Published | Year: 2019 | DOI: https://doi.org/10.1128/AAC.02528-18

Global disease burden of pathogens in animal source foods, 2010

Li, Min ; Havelaar, Arie H. ; Hoffmann, Sandra ; Hald, Tine ; Kirk, Martyn D. ; Torgerson, Paul R. ; Devleesschauwer, Brecht
in: PLOS ONE, vol: 14, issue: 6

Type: Journal article (Peer reviewed)

Status: Published | Year: 2019 | DOI: https://doi.org/10.1371/journal.pone.0216545

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

Hendriksen, Rene S. ; Munk, Patrick ; Njage, Patrick Murigu Kamau ; van Bunnik, Bram ; McNally, Luke ; Lukjancenko, Oksana ; Röder, Timo ; Nieuwenhuijse, David ; Karlsmose Pedersen, Susanne ; Kjeldgaard, Jette Sejer ; Kaas, Rolf Sommer ; Clausen, Philip Thomas Lanken Conradsen ; Vogt, Josef Korbinian ; Leekitcharoenphon, Pimlapas ; van de Schans, Milou G M ; Zuidema, Tina ; de Roda Husman, Ana Maria ; Rasmussen, Simon ; Petersen, Bent ; Global, Sewage Surveillance project consortium ; Amid, Clara ; Cochrane, Guy ; Sicheritz-Pontén, Thomas ; Schmitt, Heike ; Alvarez, Jorge Raul Matheu ; Aidara-Kane, Awa ; Pamp, Sünje Johanna ; Lund, Ole ; Hald, Tine ; Woolhouse, Mark ; Koopmans, Marion P ; Vigre, Håkan ; Petersen, Thomas Nordahl ; Aarestrup, Frank Møller
in: Nature Communications, vol: 10

Type: Journal article (Peer reviewed)

Status: Published | Year: 2019 | DOI: https://doi.org/10.1038/s41467-019-08853-3

Global phylogenomics of multidrug-resistant Salmonella enterica serotype Kentucky ST198

Hawkey, Jane ; Le Hello, Simon ; Doublet, Benoît ; Granier, Sophie A ; Hendriksen, Rene S. ; Fricke, W Florian ; Ceyssens, Pieter-Jan ; Gomart, Camille ; Billman-Jacobe, Helen ; Holt, Kathryn E ; Weill, François-Xavier
in: Microbial Genomics, vol: 5, issue: 7

Type: Journal article (Peer reviewed)

Status: Published | Year: 2019 | DOI: https://doi.org/10.1099/mgen.0.000269

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

Edwards, Robert A. ; Vega, Alejandro A. ; Norman, Holly M. ; Ohaeri, Maria ; Levi, Kyle ; Dinsdale, Elizabeth A. ; Cinek, Ondrej ; Aziz, Ramy K. ; McNair, Katelyn ; Barr, Jeremy J. ; Bibby, Kyle ; Brouns, Stan J.J. ; Cazares, Adrian ; de Jonge, Patrick A. ; Desnues, Christelle ; Díaz Muñoz, Samuel L. ; Fineran, Peter C. ; Kurilshikov, Alexander ; Lavigne, Rob ; Mazankova, Karla ; McCarthy, David T. ; Nobrega, Franklin L. ; Reyes Muñoz, Alejandro ; Tapia, German ; Trefault, Nicole ; Tyakht, Alexander V. ; Vinuesa, Pablo ; Wagemans, Jeroen ; Zhernakova, Alexandra ; Møller Aarestrup, Frank ; Ahmadov, Gunduz ; Alassaf, Abeer ; Anton, Josefa ; Asangba, Abigail ; Billings, Emma K. ; Cantu, Vito Adrian ; Carlton, Jane M. ; Cazares, Daniel ; Cho, Gyu Sung ; Condeff, Tess ; Cortés, Pilar ; Cranfield, Mike ; Cuevas, Daniel A. ; De la Iglesia, Rodrigo ; Decewicz, Przemyslaw ; Doane, Michael P. ; Dominy, Nathaniel J. ; Dziewit, Lukasz ; Elwasila, Bashir Mukhtar ; Eren, A. Murat ; Franz, Charles ; Fu, Jingyuan ; Garcia-Aljaro, Cristina ; Ghedin, Elodie ; Gulino, Kristen M. ; Haggerty, John M. ; Head, Steven R. ; Hendriksen, Rene S. ; Hill, Colin ; Hyöty, Heikki ; Ilina, Elena N. ; Irwin, Mitchell T. ; Jeffries, Thomas C. ; Jofre, Juan ; Junge, Randall E. ; Kelley, Scott T. ; Khan Mirzaei, Mohammadali ; Kowalewski, Martin ; Kumaresan, Deepak ; Leigh, Steven R. ; Lipson, David ; Lisitsyna, Eugenia S. ; Llagostera, Montserrat ; Maritz, Julia M. ; Marr, Linsey C. ; McCann, Angela ; Molshanski-Mor, Shahar ; Monteiro, Silvia ; Moreira-Grez, Benjamin ; Morris, Megan ; Mugisha, Lawrence ; Muniesa, Maite ; Neve, Horst ; Nguyen, Nam phuong ; Nigro, Olivia D. ; Nilsson, Anders S. ; O’Connell, Taylor ; Odeh, Rasha ; Oliver, Andrew ; Piuri, Mariana ; Prussin, Aaron J. ; Qimron, Udi ; Quan, Zhe Xue ; Rainetova, Petra ; Ramírez-Rojas, Adán ; Raya, Raul ; Reasor, Kim ; Rice, Gillian A.O. ; Rossi, Alessandro ; Santos, Ricardo ; Shimashita, John ; Stachler, Elyse N. ; Stene, Lars C. ; Strain, Ronan ; Stumpf, Rebecca ; Torres, Pedro J. ; Twaddle, Alan ; Ugochi Ibekwe, Mary Ann ; Villagra, Nicolás ; Wandro, Stephen ; White, Bryan ; Whiteley, Andy ; Whiteson, Katrine L. ; Wijmenga, Cisca ; Zambrano, Maria M. ; Zschach, Henrike ; Dutilh, Bas E.
in: Nature Microbiology

Type: Journal article (Peer reviewed)

Status: Accepted/In press | Year: 2019 | DOI: https://doi.org/10.1038/s41564-019-0494-6

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

Otani, Saria ; Zhukova, Mariya ; Koné, N'golo Abdoulaye ; da Costa, Rafael Rodrigues ; Mikaelyan, Aram ; Sapountzis, Panagiotis ; Poulsen, Michael
in: Environmental Microbiology Reports, vol: 11, issue: 2, pages: 196-205

Type: Journal article (Peer reviewed)

Status: Published | Year: 2019 | DOI: https://doi.org/10.1111/1758-2229.12728

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

Holguín, Angela Victoria ; Cárdenas, Pablo ; Prada-Peñaranda, Catalina ; Rabelo Leite, Laura ; Buitrago, Camila ; Clavijo, Viviana ; Oliveira, Guilherme ; Leekitcharoenphon, Pimlapas ; Møller Aarestrup, Frank ; Vives, Martha J.
in: Viruses, vol: 11, issue: 2

Type: Journal article (Peer reviewed)

Status: Published | Year: 2019 | DOI: https://doi.org/10.3390/v11020188

Improving hazard characterization in microbial risk assessment using next generation sequencing data and machine learning: Predicting clinical outcomes in shigatoxigenic Escherichia coli

Njage, Patrick Murigu Kamau ; Leekitcharoenphon, Pimlapas ; Hald, Tine
in: International Journal of Food Microbiology, vol: 292, pages: 72-82

Type: Journal article (Peer reviewed)

Status: Published | Year: 2019 | DOI: https://doi.org/10.1016/j.ijfoodmicro.2018.11.016

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, Adam ; Roer, Louise ; Overballe-Petersen, Søren ; Hansen, Frank ; Bortolaia, Valeria ; Leekitcharoenphon, Pimlapas ; Korsgaard, Helle Bisgaard ; Seyfarth, Anne Mette ; Hendriksen, Rene S. ; Hasman, Henrik ; Hammerum, Anette Marie
in: Journal of Antimicrobial Chemotherapy, vol: 74, issue: 8, pages: 2171-2175

Type: Journal article (Peer reviewed)

Status: Published | Year: 2019 | DOI: https://doi.org/10.1093/jac/dkz199

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

Apruzzese, Isabella ; Song, Eunyeong ; Bonah, Ernest ; Sanidad, Vernadette S. ; Leekitcharoenphon, Pimlapas ; Medardus, Julius John ; Abdalla, Nagmeldin ; Hosseini, Hedayat ; Takeuchi, Masami
in: Foodborne pathogens and disease, vol: 16, issue: 7

Type: Journal article (Peer reviewed)

Status: Published | Year: 2019 | DOI: https://doi.org/10.1089/fpd.2018.2599

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, Henrik ; Clausen, Philip Thomas Lanken Conradsen ; Kaya, Hülya ; Hansen, Frank ; Knudsen, Jenny Dahl ; Wang, Mikala ; Holzknecht, Barbara Juliane ; Samulioniené, Jurgita ; Røder, Bent L ; Frimodt-Møller, Niels ; Lund, Ole ; Hammerum, Anette Marie
in: Journal of Antimicrobial Chemotherapy, vol: 74, issue: 6, pages: 1473-1476

Type: Journal article (Peer reviewed)

Status: Published | Year: 2019 | DOI: https://doi.org/10.1093/jac/dkz092

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

Njage, Patrick Murigu Kamau ; Henri, Clementine ; Leekitcharoenphon, Pimlapas ; Mistou, Michel-Yves ; Hendriksen, Rene S. ; Hald, Tine
in: Risk Analysis, vol: 39, issue: 6, pages: 1397-1413

Type: Journal article (Peer reviewed)

Status: Published | Year: 2019 | DOI: https://doi.org/10.1111/risa.13239

Megaphages infect Prevotella and variants are widespread in gut microbiomes

Devoto, Audra E. ; Santini, Joanne M. ; Olm, Matthew R. ; Anantharaman, Karthik ; Munk, Patrick ; Tung, Jenny ; Archie, Elizabeth A. ; Turnbaugh, Peter J. ; Seed, Kimberley D. ; Blekhman, Ran ; Møller Aarestrup, Frank ; Thomas, Brian C. ; Banfield, Jillian F.
in: Nature Microbiology, vol: 4, pages: 693-700

Type: Journal article (Peer reviewed)

Status: Published | Year: 2019 | DOI: https://doi.org/10.1038/s41564-018-0338-9

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

Hjelmsø, Mathis Hjort ; Mollerup, Sarah ; Jensen, Randi Holm ; Pietroni, Carlotta ; Lukjancenko, Oksana ; Schultz, Anna Charlotte ; Møller Aarestrup, Frank ; Hansen, Anders Johannes
in: PLOS ONE, vol: 14, issue: 1

Type: Journal article (Peer reviewed)

Status: Published | Year: 2019 | DOI: https://doi.org/10.1371/journal.pone.0210368

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

Lauritsen, Camilla Vester ; Sejer Kjeldgaard, Jette ; Ingmer, Hanne ; Bisgaard, Magne ; Christensen, Henrik
in: International Journal of Food Microbiology, vol: 300, pages: 14-21

Type: Journal article (Peer reviewed)

Status: Published | Year: 2019 | DOI: https://doi.org/10.1016/j.ijfoodmicro.2019.04.003

Modelling the Impact of Migration on HIV Persistency in Ghana

Apenteng, Ofosuhene Okofrobour ; Ismail, Noor Azina
in: Statistics, Optimization & Information Computing, vol: 7, issue: 1, pages: 55-65

Type: Journal article (Peer reviewed)

Status: Published | Year: 2019 | DOI: https://doi.org/10.19139/soic.v7i1.552

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

Zajac, Magdalena ; Sztromwasser, Pawel ; Bortolaia, Valeria ; Leekitcharoenphon, Pimlapas ; Cavaco, Lina ; Zietek-Barszcz, Anna ; Hendriksen, Rene S. ; Wasyl, Dariusz
in: Frontiers in Microbiology, vol: 10

Type: Journal article (Peer reviewed)

Status: Published | Year: 2019 | DOI: https://doi.org/10.3389/fmicb.2019.01753