Publikationer fra forskningsgruppen for Genetisk epidemiologi

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2019
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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     |    År: 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     |    År: 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     |    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

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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     |    År: 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     |    År: 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     |    År: 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     |    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

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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     |    År: 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     |    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

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

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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     |    År: 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     |    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

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

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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

Type: Journal article (Peer reviewed)

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


https://www.food.dtu.dk/forskning/genetisk-epidemiologi/publikationer?dtulistcode=National%20Food%20Instit-33440&fr=26&mr=25&ptype=all&qt=DtuPublicationQuery
7 DECEMBER 2019