Publikationer fra forskningsgruppen for Genetisk epidemiologi

Predicting effects of changed antimicrobial usage on the abundance of antimicrobial resistance genes in finisher’ gut microbiomes

Dalhoff Andersen, Vibe ; Møller Aarestrup, Frank ; Munk, Patrick ; Stengaard Jensen, Marie ; de Knegt, Leonardo ; Bortolaia, Valeria ; nudsen, B. E. ; Lukjancenko, Oksana ; Birkegård, A. C. ; Vigre, Håkan
in: Preventive Veterinary Medicine, vol: 174

Type: Journal article (Peer reviewed)

Status: Published | År: 2020 | DOI: https://doi.org/10.1016/j.prevetmed.2019.104853

Multimorbidity, healthcare utilization and socioeconomic status

Frølich, Anne ; Ghith, Nermin ; Schiøtz, Michaela ; Jacobsen, Ramune ; Stockmarr, Anders
in: PLOS ONE, vol: 14, issue: 8

Type: Journal article (Peer reviewed)

Status: Published | År: 2019 | DOI: https://doi.org/10.1371/journal.pone.0214183

Antibiotic-Induced, Increased Conjugative Transfer Is Common to Diverse Naturally Occurring ESBL Plasmids in Escherichia coli

Liu, Gang ; Bogaj, Karolina ; Bortolaia, Valeria ; Olsen, John Elmerdahl ; Thomsen, Line Elnif
in: Frontiers in Microbiology, vol: 10

Type: Journal article (Peer reviewed)

Status: Published | År: 2019 | DOI: https://doi.org/10.3389/fmicb.2019.02119

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

Perry, Meghan ; van Bunnik, Bram ; McNally, Luke ; Wee, Bryan ; Munk, Patrick ; Warr, Amanda ; Moore, Barbara ; Kalima, Pota ; Philip, Carol ; de Roda Husman, Ana Maria ; Aarestrup, Frank Møller ; Woolhouse, Mark
in: Lancet, vol: 394, pages: S1

Type: Conference abstract in journal (Peer reviewed)

Status: Published | År: 2019 | DOI: https://doi.org/10.1016/s0140-6736(19)32798-9

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, Rene S. ; De Cesare, A.
in: Heliyon, vol: 5, issue: 10

Type: Journal article (Peer reviewed)

Status: Published | År: 2019 | DOI: https://doi.org/10.1016/j.heliyon.2019.e02745

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, vol: 74, issue: 9, pages: 2596–2604

Type: Journal article (Peer reviewed)

Status: Published | År: 2019 | DOI: https://doi.org/10.1093/jac/dkz235

Attributable sources of community-acquired carriage of Escherichia coli containing β-lactam antibiotic resistance genes

, ; Mughini-Gras, Lapo ; Dorado-García, Alejandro ; van Duijkeren, Engeline ; van den Bunt, Gerrita ; Dierikx, Cindy M. ; Bonten, Marc J.M. ; Bootsma, Martin C.J. ; Schmitt, Heike ; Hald, Tine ; Evers, Eric G. ; de Koeijer, Aline ; van Pelt, Wilfrid ; Franz, Eelco ; Mevius, Dik J. ; Heederik, Dick J.J.
in: The Lancet Planetary Health, vol: 3, issue: 8, pages: e357-e369

Type: Journal article (Peer reviewed)

Status: Published | År: 2019 | DOI: https://doi.org/10.1016/S2542-5196(19)30130-5

Ceftriaxone use in a tertiary care hospital in Kilimanjaro, Tanzania

Sonda, Tolbert B. ; Horumpende, Pius G. ; Kumburu, Happiness H. ; van Zwetselaar, Marco ; Mshana, Stephen E. ; Alifrangis, Michael ; Lund, Ole ; Møller Aarestrup, Frank ; Chilongola, Jaffu O. ; Mmbaga, Blandina T. ; Kibiki, Gibson S.
in: PLOS ONE, vol: 14, issue: 8

Type: Journal article (Peer reviewed)

Status: Published | År: 2019 | DOI: https://doi.org/10.1371/journal.pone.0220261

Comparison of Gene Expression Profiles of Uropathogenic Escherichia Coli CFT073 after Prolonged Exposure to Subinhibitory Concentrations of Different Biocides

Ligowska-Marzęta, Małgorzata Anna ; Hancock, Viktoria ; Ingmer, Hanne ; Aarestrup, Frank Møller
in: Antibiotics, vol: 8, issue: 4

Type: Journal article (Peer reviewed)

Status: Published | År: 2019 | DOI: https://doi.org/10.3390/antibiotics8040167

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, vol: 25, issue: 10, pages: 1277-1285

Type: Journal article (Peer reviewed)

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

Data science in healthcare

Abedjan, Ziawasch ; Boujemaa, Nozha ; Campbell, Stuart ; Casla, Patricia ; Chatterjea, Supriyo ; Consoli, Sergio ; Costa-Soria, Cristobal ; Czech, Paul ; Despenic, Marija ; Garattini, Chiara ; Hamelinck, Dirk ; Heinrich, Adrienne ; Kraaij, Wessel ; Kustra, Jacek ; Lojo, Aizea ; Sanchez, Marga Martin ; Mayer, Miguel A. ; Melideo, Matteo ; Menasalvas, Ernestina ; Møller Aarestrup, Frank ; Artigot, Elvira Narro ; Petković, Milan ; Recupero, Diego Reforgiato ; Gonzalez, Alejandro Rodriguez ; Kerremans, Gisele Roesems ; Roller, Roland ; Romao, Mario ; Ruping, Stefan ; Sasaki, Felix ; Spek, Wouter ; Stojanovic, Nenad ; Thoms, Jack ; Vasiljevs, Andrejs ; Verachtert, Wilfried ; Wuyts, Roel
part of: Data Science for Healthcare, pages: 3-38, 2019, Springer

Type: Book chapter (Peer reviewed)

Status: Published | År: 2019 | DOI: https://doi.org/10.1007/978-3-030-05249-2_1

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 | År: 2019 | DOI: https://doi.org/10.1038/s41598-019-45364-z

DTU Fødevareinstituttet i front for at forebygge sygdomme

Kornholt, Heidi ; Svingen, Terje ; Aarestrup, Frank Møller ; Poulsen, Morten
in: Miljø og sundhed, vol: 25, issue: 2, pages: 13-17

Type: Journal article (Peer reviewed)

Status: Published | År: 2019

Economic hardship over twenty-two consecutive years of adult life and markers of early ageing

Foverskov, E. ; Petersen, G. L. ; Pedersen, Jolene Lee Masters ; Rod, N . H. ; Mortensen, E. L. ; Bruunsgaard, H. ; Lund, R.
in: European Journal of Public Health, vol: 29, issue: Supplement 4, pages: 38-38
Presented at: 12th European Public Health Conference

Type: Conference abstract in journal (Peer reviewed)

Status: Published | År: 2019 | DOI: https://doi.org/10.1093/eurpub/ckz185.085

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 | År: 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 | År: 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 | År: 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 | År: 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 | År: 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 | År: 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 | År: 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 | År: 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, vol: 4, pages: 1727-1736

Type: Journal article (Peer reviewed)

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

Improved Resistance Prediction in Mycobacterium tuberculosis by Better Handling of Insertions and Deletions, Premature Stop Codons, and Filtering of Non-informative Sites

Johnsen, Camilla Hundahl ; Clausen, Philip Thomas Lanken Conradsen ; Aarestrup, Frank Møller ; Lund, Ole
in: Frontiers in Microbiology, vol: 10

Type: Journal article (Peer reviewed)

Status: Published | År: 2019 | DOI: https://doi.org/10.3389/fmicb.2019.02464

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 | År: 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 | År: 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 | År: 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 | År: 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 | År: 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 | År: 2019 | DOI: https://doi.org/10.1038/s41564-018-0338-9

Meta-Analysis and Meta-Regression Indicate Dynamic Prevalence and Moderators of Foodborne Pathogens in African Indigenous Fermented Milk

Wambui, Joseph M. ; Njage, Patrick Murigu Kamau ; Tasara, Taurai ; Buys, Elna Maria
in: Microorganisms, vol: 7, issue: 11

Type: Journal article (Peer reviewed)

Status: Published | År: 2019 | DOI: https://doi.org/10.3390/microorganisms7110563

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 | År: 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 | År: 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 | År: 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 | År: 2019 | DOI: https://doi.org/10.3389/fmicb.2019.01753

Organic Complexity in Protostellar Disk Candidates

Bergner, Jennifer B. ; Martín-Doménech, Rafael ; Öberg, Karin I. ; Jørgensen, Jes K. ; Artur De La Villarmois, Elizabeth ; Brinch, Christian
in: Acs Earth and Space Chemistry, vol: 3, issue: 8, pages: 1564-1575

Type: Journal article (Peer reviewed)

Status: Published | År: 2019 | DOI: https://doi.org/10.1021/acsearthspacechem.9b00059

Pathogen surveillance in the informal settlement, Kibera, Kenya, using a metagenomics approach

Hendriksen, Rene S. ; Lukjancenko, Oksana ; Munk, Patrick ; Hjort Hjelmsø, Mathis ; Verani, Jennifer R. ; Ng'eno, Eric ; Bigogo, Godfrey ; Kiplangat, Samuel ; Oumar, Traoré ; Bergmark, Lasse ; Röder, Timo ; Neatherlin, John C. ; Clayton, Onyango ; Hald, Tine ; Karlsmose, Susanne ; Pamp, Sünje Johanna ; Fields, Barry ; Montgomery, Joel M. ; Møller Aarestrup, Frank
in: P L o S One, vol: 14, issue: 10

Type: Journal article (Peer reviewed)

Status: Published | År: 2019 | DOI: https://doi.org/10.1371/journal.pone.0222531

Plasmid ATLAS: plasmid visual analytics and identification in high-throughput sequencing data

Jesus, Tiago F. ; Ribeiro-Gonçalves, Bruno ; Silva, Diogo N. ; Bortolaia, Valeria ; Ramirez, Mário ; Carriço, João A
in: Nucleic acids research, vol: 47, issue: D1, pages: 188-194

Type: Journal article (Peer reviewed)

Status: Published | År: 2019 | DOI: https://doi.org/10.1093/nar/gky1073

Probabilistic modeling for an integrated temporary acquired immunity with norovirus epidemiological data

Owusu-Ansah, Emmanuel de-Graft Johnson ; Barnes, Benedict ; Abaidoo, Robert ; Tine, Hald ; Dalsgaard, Anders ; Permin, Anders ; Schou, Torben Wilde
in: Infectious Disease Modelling, vol: 4, pages: 99-114

Type: Journal article (Peer reviewed)

Status: Published | År: 2019 | DOI: https://doi.org/10.1016/j.idm.2019.04.005

Proficiency testing of virus diagnostics based on bioinformatics analysis of simulated in silico high-throughput sequencing datasets

Brinkmann, Annika ; Andrusch, Andreas ; Belka, Ariane ; Wylezich, Claudia ; Höper, Dirk ; Pohlmann, Anne ; Petersen, Thomas Nordahl ; Lucas, Pierrick ; Blanchard, Yannick ; Papa, Anna ; Melidou, Angeliki ; Oude Munnink, Bas B ; Matthijnssens, Jelle ; Deboutte, Ward ; Ellis, Richard J ; Hansmann, Florian ; Baumgärtner, Wolfgang ; van der Vries, Erhard ; Osterhaus, Albert ; Camma, Cesare ; Mangone, Iolanda ; Lorusso, Alessio ; Maracci, Maurilia ; Nunes, Alexandra ; Pinto, Miguel ; Borges, Vítor ; Kroneman, Annelies ; Schmitz, Dennis ; Corman, Victor Max ; Drosten, Christian ; Jones, Terry C ; Hendriksen, Rene S. ; Aarestrup, Frank Møller ; Koopmans, Marion ; Beer, Martin ; Nitsche, Andreas
in: Journal of Clinical Microbiology, vol: 57, issue: 8

Type: Journal article (Peer reviewed)

Status: Published | År: 2019 | DOI: https://doi.org/10.1128/JCM.00466-19

Proof of concept: used malaria rapid diagnostic tests applied for parallel sequencing for surveillance of molecular markers of anti-malarial resistance in Bissau, Guinea-Bissau during 2014-2017

Nag, Sidsel ; Ursing, Johan ; Rodrigues, Amabelia ; Crespo, Marina ; Krogsgaard, Camilla ; Lund, Ole ; Aarestrup, Frank Møller ; Alifrangis, Michael ; Kofoed, PouL-Erik
in: Malaria Journal, vol: 18, issue: 1

Type: Journal article (Peer reviewed)

Status: Published | År: 2019 | DOI: https://doi.org/10.1186/s12936-019-2894-8

SignalP 5.0 improves signal peptide predictions using deep neural networks

Almagro Armenteros, Jose Juan ; Tsirigos, Konstantinos D. ; Sønderby, Casper Kaae ; Petersen, Thomas Nordahl ; Winther, Ole ; Brunak, Søren ; von Heijne, Gunnar ; Nielsen, Henrik
in: Nature Biotechnology, vol: 37, pages: 420-423

Type: Journal article (Peer reviewed)

Status: Published | År: 2019 | DOI: https://doi.org/10.1038/s41587-019-0036-z

Specific gut microbiome members are associated with distinct immune markers in pediatric allogeneic hematopoietic stem cell transplantation

Ingham, Anna Cäcilia ; Kielsen, Katrine ; Cilieborg, Malene Skovsted ; Lund, Ole ; Holmes, Susan ; Møller Aarestrup, Frank ; Müller, Klaus Gottlob ; Pamp, Sünje Johanna
in: Microbiome, vol: 7, issue: 1

Type: Journal article (Peer reviewed)

Status: Published | År: 2019 | DOI: https://doi.org/10.1186/s40168-019-0745-z

ST131 fimH22 Escherichia coli isolate with a blaCMY-2/IncI1/ST12 plasmid obtained from a patient with bloodstream infection: highly similar to E. coli isolates of broiler origin

Roer, Louise ; Overballe-Petersen, Søren ; Hansen, Frank ; Johannesen, Thor B ; Stegger, Marc ; Bortolaia, Valeria ; Leekitcharoenphon, Pimlapas ; Bisgaard Korsgaard, Helle ; Seyfarth, Anne Mette ; Mossong, Joël ; Wattiau, Pierre ; Boland, Cécile ; Hansen, Dennis S ; Hasman, Henrik ; Hammerum, Anette M ; Hendriksen, Rene S.
in: Journal of Antimicrobial Chemotherapy, vol: 74, issue: 3, pages: 557-560

Type: Journal article (Peer reviewed)

Status: Published | År: 2019 | DOI: https://doi.org/10.1093/jac/dky484

Surveillance and Genomics of Toxigenic Vibrio cholerae O1 From Fish, Phytoplankton and Water in Lake Victoria, Tanzania

Hounmanou, Yaovi M. Glides ; Leekitcharoenphon, Pimlapas ; Hendriksen, Rene S. ; Dougnon, Tamegnon ; Mdegela, Robinson H. ; Olsen, John E. ; Dalsgaard, Anders
in: Frontiers in Microbiology, vol: 10

Type: Journal article (Peer reviewed)

Status: Published | År: 2019 | DOI: https://doi.org/10.3389/fmicb.2019.00901

Symposium report: One Health meets sequencing

Egli, Adrian ; Koch, Daniel ; Danuser, Jürg ; Hendriksen, Rene S. ; Driesen, Susanne ; Schmid, Diana Coman ; Neher, Richard ; Mäusezahl, Mirjam ; Seth-Smith, Helena Mb ; Bloemberg, Guido ; Tschudin-Sutter, Sarah ; Endimiani, Andrea ; Perreten, Vincent ; Greub, Gilbert ; Schrenzel, Jacques ; Stephan, Roger
in: Microbes and Infection

Type: Journal article (Peer reviewed)

Status: Accepted/In press | År: 2019 | DOI: https://doi.org/10.1016/j.micinf.2019.07.004

The 24th EURL-AR Proficiency Test - Enterococci, Staphylococci and Escherichia coli 2018

Bortolaia, Valeria ; Karlsmose Pedersen, Susanne ; Hendriksen, Rene S. ; Aarestrup, Frank Møller

Type: Report

Status: Published | År: 2019

The 25th EURL-AR Proficiency Test Salmonella, Campylobacter and genotypic characterisation 2018

Karlsmose Pedersen, Susanne ; Hendriksen, Rene S. ; Bortolaia, Valeria

Type: Report

Status: Published | År: 2019

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

Van Gompel, Liese ; Luiken, Roosmarijn E C ; Sarrazin, Steven ; Munk, Patrick ; Knudsen, Berith Elkær ; Hansen, Rasmus B ; Bossers, Alex ; Aarestrup, Frank Møller ; Dewulf, Jeroen ; Wagenaar, Jaap A ; Mevius, Dik J ; Schmitt, Heike ; Heederik, Dick J J ; Dorado-García, Alejandro ; Smit, Lidwien A M ; consortium, EFFORT
in: Journal of Antimicrobial Chemotherapy, vol: 74, issue: 4, pages: 865-876

Type: Journal article (Peer reviewed)

Status: Published | År: 2019 | DOI: https://doi.org/10.1093/jac/dky518

The External Quality Assurance System of the WHO Global Foodborne Infections Network, 2017

Karlsmose Pedersen, Susanne ; Frimann, Jens-Ole Marinus ; Aarestrup, Frank Møller ; Hendriksen, Rene S.

Type: Report

Status: Published | År: 2019

Using Genomics to Track Global Antimicrobial Resistance

Hendriksen, Rene S. ; Bortolaia, Valeria ; Tate, Heather ; Tyson, Gregory H ; Aarestrup, Frank Møller ; McDermott, Patrick F.
in: Frontiers in Public Health, vol: 7

Type: Journal article (Peer reviewed)

Status: Published | År: 2019 | DOI: https://doi.org/10.3389/fpubh.2019.00242

Using WGS to identify antibiotic resistance genes and predict antimicrobial resistance phenotypes in MDR Acinetobacter baumannii in Tanzania

Kumburu, Happiness H ; Sonda, Tolbert ; van Zwetselaar, Marco ; Leekitcharoenphon, Pimlapas ; Lukjancenko, Oksana ; Mmbaga, Blandina Theophil ; Alifrangis, Michael ; Lund, Ole ; Aarestrup, Frank Møller ; Kibiki, Gibson S
in: Journal of Antimicrobial Chemotherapy, vol: 74, issue: 6, pages: 1484-1493

Type: Journal article (Peer reviewed)

Status: Published | År: 2019 | DOI: https://doi.org/10.1093/jac/dkz055

Whole Genome Sequencing Analysis of Nontyphoidal Salmonella enterica of Chicken Meat and Human Origin Under Surveillance in Sri Lanka

Tay, Moon Y F ; Pathirage, Sujatha ; Chandrasekaran, Lakshmi ; Wickramasuriya, Uddami ; Sadeepanie, Nirasha ; Waidyarathna, Kaushalya D K ; Liyanage, Liyanaralalage Dilini Chathurika ; Seow, Kelyn L G ; Hendriksen, Rene S. ; Takeuchi, Masami T ; Schlundt, Jørgen
in: Foodborne pathogens and disease, vol: 16, issue: 7

Type: Journal article (Peer reviewed)

Status: Published | År: 2019 | DOI: https://doi.org/10.1089/fpd.2018.2604

Worldwide human mitochondrial haplogroup distribution from urban sewage

Pipek, Orsolya Anna ; Medgyes-Horváth, Anna ; Dobos, László ; Stéger, József ; Szalai-Gindl, János ; Visontai, Dávid ; Kaas, Rolf Sommer ; Koopmans, Marion ; Hendriksen, Rene S. ; Møller Aarestrup, Frank ; Csabai, István
in: Scientific Reports, vol: 9, issue: 1

Type: Journal article (Peer reviewed)

Status: Published | År: 2019 | DOI: https://doi.org/10.1038/s41598-019-48093-5

Zoonoses in the Bolivian Amazon: alarming initial results from an NGO-led one health initiative

Robles, E. Alandia ; Martinez, E. ; Voigt, D. Arteaga ; Durán, P. ; Hald, Tine ; Quispe, E. ; Salazar, C. ; Salas, A. ; Nielsen, L. R.
in: International Journal of Infectious Diseases, vol: 79, issue: Suppl. 1, pages: 5-6
Presented at: International Meeting on Emerging Diseases and Surveillance (IMED) 2016

Type: Conference abstract in journal (Peer reviewed)

Status: Published | År: 2019 | DOI: https://doi.org/10.1016/j.ijid.2018.11.032

The role of outer membrane proteins and lipopolysaccharides for the sensitivity of escherichia coli to antimicrobial peptides

Ebbensgaard, Anna Elisabeth ; Mordhorst, Hanne ; Møller Aarestrup, Frank ; Bech Hansen, Egon
in: Frontiers in Microbiology, vol: 9

Type: Journal article (Peer reviewed)

Status: Published | År: 2018 | DOI: https://doi.org/10.3389/fmicb.2018.02153

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

Munk, Patrick ; Knudsen, Berith Elkær ; Lukjacenko, Oksana ; Duarte, Ana Sofia Ribeiro ; Van Gompel, Liese ; Luiken, Roosmarijn E.C. ; Smit, Lidwien A.M. ; Schmitt, Heike ; Garcia, Alejandro Dorado ; Hansen, Rasmus Borup ; Petersen, Thomas Nordahl ; Bossers, Alex ; Ruppé, Etienne ; Graveland, Haitske ; van Essen, Alieda ; Gonzalez-Zorn, Bruno ; Moyano, Gabriel ; Sanders, Pascal ; Chauvin, Claire ; David, Julie ; Battisti, Antonio ; Caprioli, Andrea ; Dewulf, Jeroen ; Blaha, Thomas ; Wadepohl, Katharina ; Brandt, Maximiliane ; Wasyl, Dariusz ; Skarzyńska, Magdalena ; Zajac, Magdalena ; Daskalov, Hristo ; Saatkamp, Helmut W. ; Stärk, Katharina D.C. ; Lund, Ole ; Hald, Tine ; Pamp, Sünje Johanna ; Vigre, Håkan ; Heederik, Dick ; Wagenaar, Jaap A. ; Mevius, Dik ; Møller Aarestrup, Frank ; ,
in: Nature Microbiology, vol: 3, issue: 8, pages: 898-908

Type: Journal article (Peer reviewed)

Status: Published | År: 2018 | DOI: https://doi.org/10.1038/s41564-018-0192-9

Dissection of the antimicrobial and hemolytic activity of Cap18: Generation of Cap18 derivatives with enhanced specificity

Ebbensgaard, Anna Elisabeth ; Mordhorst, Hanne ; Overgaard, Michael Toft ; Aarestrup, Frank Møller ; Hansen, Egon Bech
in: PLOS ONE, vol: 13, issue: 5

Type: Journal article (Peer reviewed)

Status: Published | År: 2018 | DOI: https://doi.org/10.1371/journal.pone.0197742

Microbial contamination level profiles attributed to contamination of beef carcasses, personnel, and equipment: case of small and medium enterprise slaughterhouses

Wambui, Joseph ; Lamuka, Peter ; Karuri, Edward ; Matofari, Joseph ; Njage, Patrick Murigu Kamau
in: Journal of Food Protection, vol: 81, issue: 4, pages: 684-691

Type: Journal article (Peer reviewed)

Status: Published | År: 2018 | DOI: https://doi.org/10.4315/0362-028X.JFP-17-402

High diversity of genes and plasmids encoding resistance to third-generation cephalosporins and quinolones in clinical Escherichia coli from commercial poultry flocks in Italy

Niero, Giulia ; Bortolaia, Valeria ; Vanni, Michele ; Intorre, Luigi ; Guardabassi, Luca ; Piccirillo, Alessandra
in: Veterinary Microbiology, vol: 216, pages: 93-98

Type: Journal article (Peer reviewed)

Status: Published | År: 2018 | DOI: https://doi.org/10.1016/j.vetmic.2018.02.012

Direct whole-genome sequencing of Plasmodium falciparum specimens from dried erythrocyte spots

Nag, Sidsel ; Kofoed, Poul Erik ; Ursing, Johan ; Lemvigh, Camilla Koldbæk ; Allesøe, Rosa Lundbye ; Rodrigues, Amabelia ; Svendsen, Christina Aaby ; Jensen, Jacob Dyring ; Alifrangis, Michael ; Lund, Ole ; Møller Aarestrup, Frank
in: Malaria Journal, vol: 17, issue: 1

Type: Journal article (Peer reviewed)

Status: Published | År: 2018 | DOI: https://doi.org/10.1186/s12936-018-2232-6

Prevalence and risk factors for CTX-M gram-negative bacteria in hospitalized patients at a tertiary care hospital in Kilimanjaro, Tanzania

Sonda, Tolbert ; Kumburu, Happiness ; van Zwetselaar, Marco ; Alifrangis, Michael ; Mmbaga, Blandina T. ; Lund, Ole ; Møller Aarestrup, Frank ; Kibiki, Gibson
in: European Journal of Clinical Microbiology and Infectious Diseases, vol: 37, issue: 5, pages: 897-906

Type: Journal article (Peer reviewed)

Status: Published | År: 2018 | DOI: https://doi.org/10.1007/s10096-018-3196-8

Multiplex PCR for detection of plasmid-mediated colistin resistance determinants, mcr-1, mcr-2, mcr-3, mcr-4 and mcr-5 for surveillance purposes

Rebelo, Ana Rita ; Bortolaia, Valeria ; Kjeldgaard, Jette S. ; Karlsmose Pedersen, Susanne ; Leekitcharoenphon, Pimlapas ; Hansen, Inge M. ; Guerra, Beatriz ; Malorny, Burkhard ; Borowiak, Maria ; Hammerl, Jens Andre ; Battisti, Antonio ; Franco, Alessia ; Alba, Patricia ; Perrin-Guyomard, Agnes ; Granier, Sophie A. ; de Frutos, Cristina ; Escobar, ; Malhotra-Kumar, Surbhi ; Villa, Laura ; Carattoli, Alessandra ; Hendriksen, Rene S.
in: Eurosurveillance, vol: 23, issue: 6

Type: Journal article (Peer reviewed)

Status: Published | År: 2018 | DOI: https://doi.org/10.2807/1560-7917.ES.2018.23.6.17-00672

Accurate genotyping across variant classes and lengths using variant graphs

Sibbesen, Jonas Andreas ; Maretty, Lasse ; Jensen, Jacob Malte ; Petersen, Bent ; Liu, Siyang ; Villesen, Palle ; Skov, Laurits ; Belling, Kirstine ; Theil Have, Christian ; Gonzalez-Izarzugaza, Jose Maria ; Grosjean, Marie ; Bork-Jensen, Jette ; Grove, Jakob ; Dam-Als, Thomas ; Huang, Shujia ; Chang, Yuqi ; Xu, Ruiqi ; Ye, Weijian ; Rao, Junhua ; Guo, Xiaosen ; Sun, Jihua ; Cao, Hongzhi ; Ye, Chen ; van Beusekom, Johan ; Espeseth, Thomas ; Flindt, Esben ; Friborg, Rune M. ; Halager, Anders Egerup ; Le Hellard, Stephanie ; Hultman, Christina M. ; Lescai, Francesco ; Li, Shengting ; Lund, Ole ; Løngren, Peter ; Mailund, Thomas ; Matey-Hernandez, María Luisa ; Mors, Ole ; Pedersen, Christian N. S. ; Sicheritz-Pontén, Thomas ; Sullivan, Patrick ; Ali , Syed ; Westergaard, David ; Yadav, Rachita ; Li, Ning ; Xu, Xun ; Hansen, Torben ; Krogh, Anders ; Bolund, Lars ; Sørensen, Thorkild I. A. ; Pedersen, Oluf ; Gupta, Ramneek ; Rasmussen, Simon ; Besenbacher, Søren ; Børglum, Anders D. ; Wang, Jun ; Eiberg, Hans ; Kristiansen, Karsten ; Brunak, Søren ; Schierup, Mikkel Heide
in: Nature Genetics

Type: Journal article (Peer reviewed)

Status: Published | År: 2018 | DOI: https://doi.org/10.1038/s41588-018-0145-5

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

Anjum, Mehreen ; Madsen, Jonas Stenløkke ; Espinosa-Gongora, Carmen ; Jana, Bimal ; Wiese, Maria ; Nielsen, Dennis Sandris ; Sørensen, Søren Johannes ; Moodley, Arshnee ; Bortolaia, Valeria ; Guardabassi, Luca
in: Journal of Microbiological Methods, vol: 152, pages: 18-26

Type: Journal article (Peer reviewed)

Status: Published | År: 2018 | DOI: https://doi.org/10.1016/j.mimet.2018.07.009

AnOxPe-pred: Using deep learning for the prediction of antioxidative properties of peptides.

Olsen, Tobias Hegelund ; Pertseva, Margarita ; García Moreno, Pedro Jesús ; Jacobsen, Charlotte ; Lund, Ole ; Hansen, Egon Bech ; Marcatili, Paolo
part of: Sustain Conference 2018, 2018, Technical University of Denmark, Lyngby, Denmark
Presented at: Sustain conference 2018: Creating Technology for a Sustainable Society

Type: Conference abstract in proceedings (Peer reviewed)

Status: Published | År: 2018

Antibody Cross-Reactivity in Antivenom Research

Ledsgaard, Line ; Jenkins, Timothy P ; Davidsen, Kristian ; Krause, Kamille Elvstrøm ; Martos-Esteban, Andrea ; Engmark, Mikael ; Andersen, Mikael Rørdam ; Lund, Ole ; Laustsen, Andreas Hougaard
in: Toxins, vol: 10, issue: 10

Type: Journal article (Peer reviewed)

Status: Published | År: 2018 | DOI: https://doi.org/10.3390/toxins10100393

Benchmarking the HLA typing performance of Polysolver and Optitype in 50 Danish parental trios

Matey-Hernandez, María Luisa ; Maretty, Lasse ; Jensen, Jacob Malte ; Petersen, Bent ; Andreas Sibbesen, Jonas ; Liu, Siyang ; Villesen, Palle ; Skov, Laurits ; Belling, Kirstine ; Theil Have, Christian ; Gonzalez-Izarzugaza, Jose Maria ; Grosjean, Marie ; Bork-Jensen, Jette ; Grove, Jakob ; Als, Thomas D. ; Huang, Shujia ; Chang, Yuqi ; Xu, Ruiqi ; Ye, Weijian ; Rao, Junhua ; Guo, Xiaosen ; Sun, Jihua ; Cao, Hongzhi ; Ye, Chen ; Beusekom, Johan v. ; Espeseth, Thomas ; Flindt, Esben N. ; Friborg, Rune M. ; Halager, Anders Egerup ; Le Hellard, Stephanie ; Hultman, Christina M. ; Lescai, Francesco ; Li, Shengting ; Lund, Ole ; Løngren, Peter ; Mailund, Thomas ; Mors, Ole ; Pedersen, Christian N. S. ; Sicheritz-Pontén, Thomas ; Sullivan, Patrick F. ; Ali , Syed ; Westergaard, David ; Yadav, Rachita ; Li, Ning ; Xu, Xun ; Hansen, Torben ; Krogh, Anders ; Bolund, Lars ; Sørensen, Thorkild I. A. ; Pedersen, Oluf ; Gupta, Ramneek ; Besenbacher, Søren ; Børglum, Anders D. ; Wang, Jun ; Eiberg, Hans ; Kristiansen, Karsten ; Brunak, Søren ; Schierup, Mikkel Heide ; Izarzugaza, Jose M. G.
in: B M C Bioinformatics, vol: 19

Type: Journal article (Peer reviewed)

Status: Published | År: 2018 | DOI: https://doi.org/10.1186/s12859-018-2239-6

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

Dang, Son T T ; Bortolaia, Valeria ; Thi, Nhat T ; Quang, Huan L ; Dalsgaard, Anders
in: Tropical Medicine & International Health, vol: 23, issue: 4, pages: 415-424

Type: Journal article (Peer reviewed)

Status: Published | År: 2018 | DOI: https://doi.org/10.1111/tmi.13054

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

Roer, Louise ; Johannesen, Thor Bech ; Hansen, Frank ; Stegger, Marc ; Tchesnokova, Veronika ; Sokurenko, Evgeni ; Garibay, Natasha ; Allesøe, Rosa Lundbye ; Thomsen, Martin C. F. ; Lund, Ole ; Hasman, Henrik ; Hammerum, Anette M.
in: Journal of Clinical Microbiology, vol: 56, issue: 4

Type: Journal article (Peer reviewed)

Status: Published | År: 2018 | DOI: https://doi.org/10.1128/JCM.00063-18

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

Carfora, Virginia ; Alba, Patricia ; Leekitcharoenphon, Pimlapas ; Ballaro, Daniele ; Cordaro, Gessica ; Di Matteo, Paola ; Donati, Valentina ; Ianzano, Angela ; Iurescia, Manuela ; Stravino, Fiorentino ; Tagliaferri, Tania ; Battisti, Antonio ; Franco, Alessia
in: Frontiers in Microbiology, vol: 9

Type: Journal article (Peer reviewed)

Status: Published | År: 2018 | DOI: https://doi.org/10.3389/fmicb.2018.01880

Comparative genomics of quinolone‐resistant and susceptible Campylobacter jejuni of poultry origin from major poultry producing European countries (GENCAMP)

Leekitcharoenphon, Pimlapas ; Garcia‐Graells, Cristina ; Botteldoorn, Nadine ; Dierick, Katelijne ; Kempf, Isabelle ; Olkkola, Satu ; Rossi, Mirko ; Nykäsenoja, Suvi ; Malorny, Burkhard ; Stingl, Kerstin ; Battisti, Antonio ; Franco, Alessia ; Mossong, Joël ; Veldman, Kees ; Mevius, Dik ; Wasyl, Dariusz ; Wieczorek, Kinga ; Osek, Jacek ; Clemente, Lurdes ; Lacatus, Angela ; Nicorescu, Isabela ; García, Monserrat Agüero ; Escobar, Cristina De Frutos ; Ferrer, Manuel Duran ; Ugarte‐Ruiz, María ; Anjum, Muna F ; Teale, Christopher ; Ågren, Joakim ; Hendriksen, Rene S. ; Aarestrup, Frank Møller
in: EFSA Supporting Publications, vol: 15, issue: 5

Type: Journal article (Peer reviewed)

Status: Published | År: 2018 | DOI: https://doi.org/10.2903/sp.efsa.2018.EN-1398

Comparative genomics of Vibrio cholerae O1 isolated from cholera patients in Bangladesh

Hossain, Zenat Zebin ; Leekitcharoenphon, Pimlapas ; Dalsgaard, Anders ; Sultana, Rokaia ; Begum, Anowara ; Jensen, Peter Kjær Mackie ; Hendriksen, Rene S.
in: Letters in Applied Microbiology, vol: 67, issue: 4, pages: 329-336

Type: Journal article (Peer reviewed)

Status: Published | År: 2018 | DOI: https://doi.org/10.1111/lam.13046

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

Carfora, Virginia ; Alba, Patricia ; Leekitcharoenphon, Pimlapas ; Ballaro, Daniele ; Cordaro, Gessica ; Di Matteo, Paola ; Donati, Valentina ; Ianzano, Angela ; Iurescia, Manuela ; Stravino, Fiorentino ; Tagliaferri, Tania ; Battisti, Antonio ; Franco, Alessia
in: Frontiers in Microbiology, vol: 9

Type: Journal article (Peer reviewed)

Status: Published | År: 2018 | DOI: https://doi.org/10.3389/fmicb.2018.02395

DANMAP 2017 - Use of antimicrobial agents and occurrence of antimicrobial resistance in bacteria from food animals, food and humans in Denmark

Borck Høg, Birgitte ; Bager, Flemming ; Korsgaard, Helle Bisgaard ; Ellis-Iversen, Johanne ; Pedersen, Karl ; Jensen, Lars Bogø ; Hendriksen, Rene S. ; Bortolaia, Valeria ; Rhod Larsen, Anders ; Petersen, Andreas ; Hammerich, Anette M. ; Nielsen, Eva Møller ; Slotved, Hans-Christian ; Hasman, Henrik ; Boel, Jeppe ; Skov Jensen, Jørgen ; Skjold Selle Pedersen, Karoline ; Roer, Louise ; Torpdahl, Mia ; Skovgaard, Sissel ; Hoffmann, Steen ; Schytte Olsen, Stefan ; Dalby, Tine ; Wolff Sönksen, Ute ; Vorobieva, Veronika

Type: Report

Status: Published | År: 2018

Draft Genome Sequence of Salmonella enterica subsp. enterica Serotype Typhimurium Sequence Type 313, Isolated from India

Bangera, Sohan Rodney ; Umakanth, Shashikiran ; Mukhopadhyay, Asish K. ; Leekitcharoenphon, Pimlapas ; Chowdhury, Goutam ; Hendriksen, Rene S. ; Ballal, Mamatha
in: Microbiology Resource Announcements, vol: 7, issue: 8

Type: Journal article (Peer reviewed)

Status: Published | År: 2018 | DOI: https://doi.org/10.1128/MRA.00990-18

Draft Genome Sequences of Enterococcus mundtii Strains Isolated from Beef Slaughterhouses in Kenya

Wambui, Joseph ; Stevens, Marc ; Njage, Patrick Murigu Kamau ; Wüthrich, Daniel ; Egli, Adrian ; Stephan, Roger ; Tasara, Taurai
in: Genome Announcements, vol: 6, issue: 21

Type: Journal article (Peer reviewed)

Status: Published | År: 2018 | DOI: https://doi.org/10.1128/genomeA.00446-18

Drivers and Dynamics of Methicillin-Resistant Livestock-Associated Staphylococcus aureus CC398 in Pigs and Humans in Denmark

Sieber, Raphael N ; Skov, Robert L ; Nielsen, Jens ; Schulz, Jana ; Price, Lance B ; Møller Aarestrup, Frank ; Larsen, Anders R ; Stegger, Marc ; Larsen, Jesper
in: mBio, vol: 9, issue: 6

Type: Journal article (Peer reviewed)

Status: Published | År: 2018 | DOI: https://doi.org/10.1128/mBio.02142-18

Environmental sustainable decision making – The need and obstacles for integration of LCA into decision analysis

Dong, Yan ; Miraglia, Simona ; Manzo, Stefano ; Georgiadis, Stylianos ; Sørup, Hjalte Jomo Danielsen ; Boriani, Elena ; Hald, Tine ; Thöns, Sebastian ; Hauschild, Michael Zwicky
in: Environmental Science and Policy, vol: 87, pages: 33-44

Type: Journal article (Peer reviewed)

Status: Published | År: 2018 | DOI: https://doi.org/10.1016/j.envsci.2018.05.018

Final report of ENGAGE ‐ Establishing Next Generation sequencing Ability for Genomic analysis in Europe

Hendriksen, Rene S. ; Karlsmose Pedersen, Susanne ; Leekitcharoenphon, Pimlapas ; Malorny, Burkhard ; Borowiak, Maria ; Battisti, Antonio ; Franco, Alessia ; Alba, Patricia ; Carfora, Virginia ; Ricci, Antonia ; Mastrorilli, Eleonora ; Losasso, Carmen ; Longo, Alessandra ; Petrin, Sara ; Barco, Lisa ; Wołkowicz, Tomasz ; Gierczyński, Rafał ; Zacharczuk, Katarzyna ; Wolaniuk, Natalia ; Wasyl, Dariusz ; Zajac, Magdalena ; Wieczorek, Kinga ; Pόłtorak, Katarzyna ; Petrovska‐Holmes, Liljana ; Davies, Rob ; Tang, Yue ; Grant, Kathie ; Underwood, Anthony ; Dallman, Timothy ; Painset, Anaïs ; Hartman, Hassan ; Al‐Shabib, Ali ; Cowley, Lauren
in: EFSA Supporting Publications, vol: 15, issue: 6

Type: Journal article (Peer reviewed)

Status: Published | År: 2018 | DOI: https://doi.org/10.2903/sp.efsa.2018.EN-1431

Genomics-Based Identifcation of Microorganisms in Human Ocular Body Fluid

Kirstahler, Philipp ; Solborg Bjerrum, Søren ; Friis-Møller, Alice ; Dornonville de la Cour, Morten ; Aarestrup, Frank Møller ; Westh, Henrik T. ; Pamp, Sünje Johanna
in: Scientific Reports, vol: 8

Type: Journal article (Peer reviewed)

Status: Published | År: 2018 | DOI: https://doi.org/10.1038/s41598-018-22416-4

Global Antimicrobial Resistance Surveillance System (GLASS) - The detection and reporting of colistin resistance

Bortolaia, Valeria ; Dekhnich, Andrey ; Hendriksen, Rene S. ; Kozlov, Roman ; Patel, Jean ; Paveenkittiporn, Wantana ; Perovic, Olga ; Rebelo, Ana Rita ; Woodford, Neil

Type: Report

Status: Published | År: 2018

Growth potential of pathogens in reverse osmosis filtrated whey intended for water re-use in cheese production

Hellmér, Maria ; Buschhardt, Tasja ; Njage, Patrick Murigu Kamau ; Hansen, Tina Beck ; Aabo, Søren
part of: The Danish Microbiological Society Annual Congress 2018 - programme & abstracts, pages: 50-50, 2018, Danish Microbiological Society, Copenhagen, Denmark
Presented at: The Danish Microbiological Society Annual Congress 2018

Type: Conference abstract in proceedings (Peer reviewed)

Status: Published | År: 2018

Håndbog i opklaring af fødevare- eller vandbårne sygdomsudbrud

Jensen, Tenna ; Müller, Luise ; Sørensen, Gitte ; Kjeldgaard, Jette Sejer

Type: Book

Status: Published | År: 2018

Hospital Epidemiology of Methicillin-Resistant Staphylococcus aureus in a Tertiary Care Hospital in Moshi, Tanzania, as Determined by Whole Genome Sequencing

Kumburu, Happiness H. ; Sonda, Tolbert ; Leekitcharoenphon, Pimlapas ; van Zwetselaar, Marco ; Lukjancenko, Oksana ; Alifrangis, Michael ; Lund, Ole ; Mmbaga, Blandina T. ; Kibiki, Gibson ; Aarestrup, Frank Møller
in: Journal of Biomedicine and Biotechnology, vol: 2018

Type: Journal article (Peer reviewed)

Status: Published | År: 2018 | DOI: https://doi.org/10.1155/2018/2087693

Improved ontology for eukaryotic single-exon coding sequences in biological databases

Jorquera, Roddy ; González, Carolina ; Clausen, Philip ; Petersen, Bent ; Holmes, David S
in: Database, vol: 2018, issue: 1

Type: Journal article (Peer reviewed)

Status: Published | År: 2018 | DOI: https://doi.org/10.1093/database/bay089

Microbiological Safety of Fresh Tilapia ( Oreochromis niloticus) from Kenyan Fresh Water Fish Value Chains

Onjong, Hillary Adawo ; Ngayo, Musa Otieno ; Mwaniki, Mercy ; Wambui, Joseph ; Njage, Patrick Murigu Kamau
in: Journal of Food Protection, vol: 81, issue: 12, pages: 1973-1981

Type: Journal article (Peer reviewed)

Status: Published | År: 2018 | DOI: https://doi.org/10.4315/0362-028X.JFP-18-078

Molecular Epidemiology of mcr-Encoded Colistin Resistance in Enterobacteriaceae From Food-Producing Animals in Italy Revealed Through the EU Harmonized Antimicrobial Resistance Monitoring

Alba, Patricia ; Leekitcharoenphon, Pimlapas ; Franco, Alessia ; Feltrin, Fabiola ; Ianzano, Angela ; Caprioli, Andrea ; Stravino, Fiorentino ; Hendriksen, Rene S. ; Bortolaia, Valeria ; Battisti, Antonio
in: Frontiers in Microbiology, vol: 9

Type: Journal article (Peer reviewed)

Status: Published | År: 2018 | DOI: https://doi.org/10.3389/fmicb.2018.01217

Molecular epidemiology of virulence and antimicrobial resistance determinants in Klebsiella pneumoniae from hospitalised patients in Kilimanjaro, Tanzania

Sonda, Tolbert ; Kumburu, Happiness ; van Zwetselaar, Marco ; Alifrangis, Michael ; Mmbaga, Blandina T. ; Lund, Ole ; Kibiki, Gibson S. ; Møller Aarestrup, Frank
in: European Journal of Clinical Microbiology and Infectious Diseases, vol: 37, issue: 10, pages: 1901-1914

Type: Journal article (Peer reviewed)

Status: Published | År: 2018 | DOI: https://doi.org/10.1007/s10096-018-3324-5

Phenotypic and genotypic comparison of salmonellae from diarrhoeic and healthy humans and cattle, Nigeria

Fashae, K. ; Leekitcharoenphon, Pimlapas ; Hendriksen, Rene S.
in: Zoonoses and Public Health, vol: 65, issue: 1, pages: e185-e195

Type: Review (Peer reviewed)

Status: Published | År: 2018 | DOI: https://doi.org/10.1111/zph.12427

Presence of extended-spectrum cephalosporin (ESC) resistance Escherichia coli in two Danish poultry slaughterhouses

Jensen, Lars Bogø ; Birk, Tina ; Hendriksen, Rene S. ; Leekitcharoenphon, Pimlapas ; Ortved, Gitte ; Lundsby, Katrine ; Jørgensen, Bettina ; Aabo, Søren
part of: The Danish Microbiological Society Annual Congress 2018 - programme & abstracts, pages: 78-78, 2018, Danish Microbiological Society, Copenhagen, Denmark
Presented at: The Danish Microbiological Society Annual Congress 2018

Type: Conference abstract in proceedings (Peer reviewed)

Status: Published | År: 2018

Probabilistic approach for assessing cancer risk due to benzo[a]pyrene in barbecued meat: Informing advice for population groups

Jakobsen, Lea Sletting ; Georgiadis, Stylianos ; Nielsen, Bo Friis ; Bokkers, Bas G H ; Boriani, Elena ; Duedahl-Olesen, Lene ; Hald, Tine ; Nauta, Maarten J ; Stockmarr, Anders ; Pires, Sara Monteiro
in: PLOS ONE, vol: 13, issue: 11

Type: Journal article (Peer reviewed)

Status: Published | År: 2018 | DOI: https://doi.org/10.1371/journal.pone.0207032

Proficiency of WHO Global Foodborne Infections Network External Quality Assurance System participants in the identification and susceptibility testing of thermo-tolerant Campylobacter spp. from 2003-2012

Karlsmose Pedersen, Susanne ; Wagenaar, Jaap A ; Vigre, Håkan ; Roer, Louise ; Mikoleit, Matthew ; Aidara-Kane, Awa ; Cawthorne, Amy L ; Aarestrup, Frank Møller ; Hendriksen, Rene S.
in: Journal of Clinical Microbiology, vol: 56, issue: 11

Type: Journal article (Peer reviewed)

Status: Published | År: 2018 | DOI: https://doi.org/10.1128/JCM.01066-18

Public Health Surveillance using Decentralized Technologies

Bellod Cisneros, Jose Luis ; Aarestrup, Frank Møller ; Lund, Ole
in: Blockchain in Healthcare Today, vol: 1

Type: Journal article (Peer reviewed)

Status: Published | År: 2018 | DOI: https://doi.org/10.30953/bhty.v1.17

Quantitative risk assessment of hemolytic uremic syndrome associated with consumption of bulk milk sold directly from producer to consumer in South Africa

Ntuli, Victor ; Njage, Patrick Murigu Kamau ; Bonilauri, Paolo ; Serraino, Andrea ; Buys, Elna M.
in: Journal of Food Protection, vol: 81, issue: 3, pages: 472-481

Type: Journal article (Peer reviewed)

Status: Published | År: 2018 | DOI: https://doi.org/10.4315/0362-028X.JFP-17-199