Publications from the Genomic Epidemiology Research Group

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2020
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Addressing Learning Needs on the Use of Metagenomics in Antimicrobial Resistance Surveillance

Ribeiro Duarte, Ana Sofia ; Stärk, Katharina D. C. ; Munk, Patrick ; Leekitcharoenphon, Pimlapas ; Bossers, Alex ; Luiken, Roosmarijn ; Sarrazin, Steven ; Lukjancenko, Oksana ; Pamp, Sünje Johanna ; Bortolaia, Valeria ; Nissen, Jakob Nybo ; Kirstahler, Philipp ; Van Gompel, Liese ; Poulsen, Casper Sahl ; Kaas, Rolf Sommer ; Hellmér, Maria ; Hansen, Rasmus Borup ; Gomez, Violeta Munoz ; Hald, Tine
in: Frontiers in Public Health, vol: 8

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2020     |    DOI: https://doi.org/10.3389/fpubh.2020.00038

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Clades of huge phages from across Earth's ecosystems

Al-Shayeb, Basem ; Sachdeva, Rohan ; Chen, Lin-Xing ; Ward, Fred ; Munk, Patrick ; Devoto, Audra ; Castelle, Cindy J ; Olm, Matthew R ; Bouma-Gregson, Keith ; Amano, Yuki ; He, Christine ; Méheust, Raphaël ; Brooks, Brandon ; Thomas, Alex ; Lavy, Adi ; Matheus-Carnevali, Paula ; Sun, Christine ; Goltsman, Daniela S A ; Borton, Mikayla A ; Sharrar, Allison ; Jaffe, Alexander L ; Nelson, Tara C ; Kantor, Rose ; Keren, Ray ; Lane, Katherine R ; Farag, Ibrahim F ; Lei, Shufei ; Finstad, Kari ; Amundson, Ronald ; Anantharaman, Karthik ; Zhou, Jinglie ; Probst, Alexander J ; Power, Mary E ; Tringe, Susannah G ; Li, Wen-Jun ; Wrighton, Kelly ; Harrison, Sue ; Morowitz, Michael ; Relman, David A ; Doudna, Jennifer A ; Lehours, Anne-Catherine ; Warren, Lesley ; Cate, Jamie H D ; Santini, Joanne M ; Banfield, Jillian F
in: Nature, vol: 578, pages: 425-431

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2020     |    DOI: https://doi.org/10.1038/s41586-020-2007-4

 

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, vol: 17, pages: 55–67

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2020     |    DOI: https://doi.org/10.1007/s10433-019-00523-z

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

Munck, Nanna Sophia Mucha ; Leekitcharoenphon, Pimlapas ; Litrup, Eva ; Kaas, Rolf Sommer ; Meinen, Anika ; Guillier, Laurent ; Tang, Yue ; Malorny, Burkhard ; Palma, Federica ; Borowiak, Maria ; Gourmelon, Michèle ; Simon, Sandra ; Banerji, Sangeeta ; Petrovska, Liljana ; Dallman, Timothy J ; Hald, Tine
in: Scientific Data, vol: 7, issue: 1

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2020     |    DOI: https://doi.org/10.1038/s41597-020-0417-7

 

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

De Pietri, Silvia ; Ingham, Anna Cäcilia ; Frandsen, Thomas L. ; Rathe, Mathias ; Krych, Lukasz ; Castro‐Mejía, Josue L. ; Nielsen, Dennis S. ; Nersting, Jacob ; Wehner, Peder S. ; Schmiegelow, Kjeld ; Hasle, Henrik ; Pamp, Sünje Johanna ; Müller, Klaus
in: International Journal of Cancer

Type: Journal article (Peer reviewed)

Status: Accepted/In press     |    Year: 2020     |    DOI: https://doi.org/10.1002/ijc.32942

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Occupational Exposure and Carriage of Antimicrobial Resistance Genes (tetW, ermB) in Pig Slaughterhouse Workers

Van Gompel, Liese ; Dohmen, Wietske ; Luiken, Roosmarijn E. C. ; Bouwknegt, Martijn ; Heres, Lourens ; Van Heijnsbergen, Eri ; Jongerius-Gortemaker, Betty G M ; Scherpenisse, Peter ; Greve, Gerdit D ; Tersteeg-Zijderveld, Monique H G ; Wadepohl, Katharina ; Ribeiro Duarte, Ana Sofia ; Muñoz-Gómez, Violeta ; Fischer, Jennie ; Skarżyńska, Magdalena ; Wasyl, Dariusz ; Wagenaar, Jaap A ; Urlings, Bert A P ; Dorado-García, Alejandro ; Wouters, Inge M ; Heederik, Dick J J ; Schmitt, Heike ; Smit, Lidwien A M
in: Annals of Work Exposures and Health, vol: 64, issue: 2, pages: 125-137

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2020     |    DOI: https://doi.org/10.1093/annweh/wxz098

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Source Attribution of Salmonella in Macadamia Nuts to Animal and Environmental Reservoirs in Queensland, Australia

Munck, Nanna Sophia Mucha ; Smith, James ; Bates, John ; Glass, Kathryn ; Hald, Tine ; Kirk, Martyn D
in: Foodborne pathogens and disease

Type: Journal article (Peer reviewed)

Status: Accepted/In press     |    Year: 2020     |    DOI: https://doi.org/10.1089/fpd.2019.2706

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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, vol: 22, issue: 1, pages: 1-7

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2020     |    DOI: https://doi.org/10.1016/j.micinf.2019.07.004

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Towards a European health research and innovation cloud (HRIC)

Aarestrup, Frank Møller ; 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. ; 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.
in: Genome Medicine, vol: 12, issue: 1

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2020     |    DOI: https://doi.org/10.1186/s13073-020-0713-z

 

Using sewage for surveillance of antimicrobial resistance

Aarestrup, Frank Møller ; Woolhouse, Mark E.J.
in: Science, vol: 367, issue: 6478, pages: 630-632

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2020     |    DOI: https://doi.org/10.1126/science.aba3432

2019
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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     |    Year: 2019     |    DOI: https://doi.org/10.1371/journal.pone.0214183

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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, Jette Sejer ; Litrup, E ; Schjørring, S ; Muller, L
in: Epidemiology and Infection, vol: 147

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1017/s0950268819002073

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

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

Type: Journal article (Peer reviewed)

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

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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     |    Year: 2019     |    DOI: https://doi.org/10.1093/jac/dkz235

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

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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     |    Year: 2019     |    DOI: https://doi.org/10.1371/journal.pone.0220261

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

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 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     |    Year: 2019     |    DOI: https://doi.org/10.1016/j.cmi.2019.04.028

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Corrigendum: 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.2019.02816

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

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.3389/fmicb.2019.02974

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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

 

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

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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, Cecilie Liv ; 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. ; Caprioli, A. ; Dewulf, J. ; Brandt, M. ; Aarestrup, Frank Møller ; Hald, Tine ; Wasyl, D. ; Skarzynska, M. ; Zajac, M. ; Daskalov, H. ; Staerk, K.
in: Berliner und Munchener Tierarztliche Wochenschrift, vol: 132, issue: 11-12, pages: 504-512

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.2376/0005-9366-18088

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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

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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     |    Year: 2019

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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     |    Year: 2019     |    DOI: https://doi.org/10.1093/eurpub/ckz185.085

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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

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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

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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

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Genomic insights into Vibrio cholerae O1 responsible for cholera epidemics in Tanzania between 1993 and 2017

Hounmanou, Yaovi Mahuton Gildas ; Leekitcharoenphon, Pimlapas ; Kudirkiene, Egle ; Mdegela, Robinson H. ; Hendriksen, Rene S. ; Olsen, John Elmerdahl ; Dalsgaard, Anders
in: PLOS Neglected Tropical Diseases , vol: 13, issue: 12

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1371/journal.pntd.0007934

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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

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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

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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, vol: 4, pages: 1727-1736

Type: Journal article (Peer reviewed)

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

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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

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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

 

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

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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

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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

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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

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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     |    Year: 2019     |    DOI: https://doi.org/10.3390/microorganisms7110563

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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

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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

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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

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One day in Denmark to evaluate the applicability of whole-genome sequencing in clinical microbiology diagnostics

Bastos Rebelo, Ana Rita ; Aarestrup, Frank Møller ; Bortolaia, Valeria ; Leekitcharoenphon, Pimlapas ; Hansen, Dennis Schrøder ; Westh, Henrik ; Nørskov-Lauritsen, Niels ; Nielsen, Hans Linde ; Kemp, Michael ; Røder, Bent Løwe ; Frimodt-Møller, Niels ; Dzajic, Esad ; Søndergaard, Turid Snekloth ; Østergaard, Claus
Presented at:
29th 29 ECCMID

Type: Conference abstract for conference (Peer reviewed)

Status: Published     |    Year: 2019

 

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     |    Year: 2019     |    DOI: https://doi.org/10.1021/acsearthspacechem.9b00059

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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     |    Year: 2019     |    DOI: https://doi.org/10.1371/journal.pone.0222531

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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     |    Year: 2019     |    DOI: https://doi.org/10.1093/nar/gky1073

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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     |    Year: 2019     |    DOI: https://doi.org/10.1016/j.idm.2019.04.005

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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     |    Year: 2019     |    DOI: https://doi.org/10.1128/JCM.00466-19

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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     |    Year: 2019     |    DOI: https://doi.org/10.1186/s12936-019-2894-8

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Salmonella control in poultry flocks and its public health impact

, ; Koutsoumanis, Kostas ; Allende, Ana ; Alvarez-Ordóñez, Avelino ; Bolton, Declan ; Bover-Cid, Sara ; Chemaly, Marianne ; Cesare, Alessandra De ; Herman, Lieve ; Hilbert, Friederike ; Lindqvist, Roland ; Nauta, Maarten ; Peixe, Luisa ; Ru, Giuseppe ; Simmons, Marion ; Skandamis, Panagiotis ; Suffredini, Elisabetta ; Dewulf, Jeroen ; Hald, Tine ; Michel, Virginie ; Niskanen, Taina ; Ricci, Antonia ; Snary, Emma ; Boelaert, Frank ; Messens, Winy ; Davies, Robert
in: EFSA Journal, vol: 17, issue: 2

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.2903/j.efsa.2019.5596

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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     |    Year: 2019     |    DOI: https://doi.org/10.1038/s41587-019-0036-z

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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     |    Year: 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     |    Year: 2019     |    DOI: https://doi.org/10.1093/jac/dky484

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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     |    Year: 2019     |    DOI: https://doi.org/10.3389/fmicb.2019.00901

 

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     |    Year: 2019     |    DOI: https://doi.org/10.1093/jac/dky518

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The COMPARE Data Hubs

Amid, Clara ; Pakseresht, Nima ; Silvester, Nicole ; Jayathilaka, Suran ; Lund, Ole ; Dynovski, Lukasz D. ; Pataki, Bálint ; Visontai, Dávid ; Xavier, Basil Britto ; Alako, Blaise T.F. ; Belka, Ariane ; Cisneros, Jose L.B. ; Cotten, Matthew ; Haringhuizen, George B. ; Harrison, Peter W. ; Höper, Dirk ; Holt, Sam ; Hundahl, Camilla ; Hussein, Abdulrahman ; Kaas, Rolf Sommer ; Liu, Xin ; Leinonen, Rasko ; Malhotra-Kumar, Surbhi ; Nieuwenhuijse, David F. ; Rahman, Nadim ; Dos S Ribeiro, Carolina ; Skiby, Jeffrey Edward ; Schmitz, Dennis ; Stéger, József ; Szalai-Gindl, János M. ; Thomsen, Martin Christen Frølund ; Cacciò, Simone M. ; Csabai, István ; Kroneman, Annelies ; Koopmans, Marion ; Aarestrup, Frank Møller ; Cochrane, Guy
in: Database : the journal of biological databases and curation, vol: 2019, pages: 1-14

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1093/database/baz136

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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     |    Year: 2019     |    DOI: https://doi.org/10.3389/fpubh.2019.00242

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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     |    Year: 2019     |    DOI: https://doi.org/10.1093/jac/dkz055

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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     |    Year: 2019     |    DOI: https://doi.org/10.1089/fpd.2018.2604

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Whole genome sequencing and metagenomics for outbreak investigation, source attribution and risk assessment of food-borne microorganisms

, ; Koutsoumanis, Kostas ; Allende, Ana ; Alvarez‐Ordoňez, Avelino ; Bolton, Declan ; Bover-Cid, Sara ; Chemaly, Marianne ; Davies, Robert ; De Cesare, Alessandra ; Hilbert, Friederike ; Lindqvist, Roland ; Nauta, Maarten ; Peixe, Luisa ; Ru, Giuseppe ; Simmons, Marion ; Skandamis, Panagiotis N. ; Suffredini, Elisabetta ; Jenkins, Claire ; Malorny, Burkhard ; Ribeiro Duarte, Ana Sofia ; Torpdahl, Mia ; da Silva Felicio, Maria Teresa ; Guerra, Beatriz ; Rossi, Mirko ; Herman, Lieve
in: E F S A Journal, vol: 17, issue: 12

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.2903/j.efsa.2019.5898

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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     |    Year: 2019     |    DOI: https://doi.org/10.1038/s41598-019-48093-5

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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     |    Year: 2019     |    DOI: https://doi.org/10.1016/j.ijid.2018.11.032

2018
  PDF

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     |    Year: 2018     |    DOI: https://doi.org/10.1038/s41564-018-0192-9

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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     |    Year: 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     |    Year: 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     |    Year: 2018     |    DOI: https://doi.org/10.1016/j.vetmic.2018.02.012

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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     |    Year: 2018     |    DOI: https://doi.org/10.1186/s12936-018-2232-6

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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     |    Year: 2018     |    DOI: https://doi.org/10.1007/s10096-018-3196-8

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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     |    Year: 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     |    Year: 2018     |    DOI: https://doi.org/10.1038/s41588-018-0145-5

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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     |    Year: 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     |    Year: 2018

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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     |    Year: 2018     |    DOI: https://doi.org/10.3390/toxins10100393

 

A One Health evaluation framework

Rüegg, Simon R ; Häsler, Barbara ; Nielsen, Liza Rosenbaum ; Buttigieg, Sandra C ; Santa, Mijalche ; Aragrande, Maurizio ; Canali, Massimo ; Ehlinger, Timothy ; Queenan, Kevin ; Chantziaras, Ilias ; Boriani, Elena ; Radeski, Miroslav ; Bruce, Mieghan ; Keune, Hans ; Bennani, Houda ; Ifejika Speranza, Chinwe ; Carmo, Luis Pedro ; Esposito, Roberto ; Filippitzi, Maria-Eleni ; McIntyre, K. Marie ; McMahon, Barry J ; Peyre, Marisa ; Falzon, Laura C. ; Bardosh, Kevin L. ; Frazzoli, Chiara ; Hald, Tine ; Marcus, Grace ; Zinsstag, Jakob
part of: Integrated approaches to health - A handbook for the evaluation of One Health, pages: 38-85, 2019, Wageningen Academic Publishers, The Netherlands

Type: Book chapter (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.3920/978-90-8686-875-9

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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     |    Year: 2018     |    DOI: https://doi.org/10.1186/s12859-018-2239-6

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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     |    Year: 2018     |    DOI: https://doi.org/10.1111/tmi.13054

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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     |    Year: 2018     |    DOI: https://doi.org/10.1128/JCM.00063-18

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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     |    Year: 2018     |    DOI: https://doi.org/10.3389/fmicb.2018.01880

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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     |    Year: 2018     |    DOI: https://doi.org/10.2903/sp.efsa.2018.EN-1398

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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     |    Year: 2018     |    DOI: https://doi.org/10.1111/lam.13046

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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     |    Year: 2018     |    DOI: https://doi.org/10.3389/fmicb.2018.02395


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28 MARCH 2020