Publikationer fra forskningsgruppen for Genetisk epidemiologi

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2021
 

Exposure assessment to staphylococcus enterotoxins in Nile tilapia (Oreochromis niloticus) supplied through semi-regulated and unregulated value chains

Onjong, Hillary Adawo ; Ntuli, Victor ; Mwaniki, Mercy ; Njage, Patrick Murigu Kamau
in: Food Control, vol: 119

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2021     |    DOI: https://doi.org/10.1016/j.foodcont.2020.107487

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Global Food-source Identifier (GFI)

Ribeiro Duarte, Ana Sofia ; Nielsen, Cecilie Liv ; Candela, Leonardo ; Valentin, Lars ; Aarestrup, Frank Møller ; Vigre, Håkan
in: Food Control, vol: 121

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2021     |    DOI: https://doi.org/10.1016/j.foodcont.2020.107623

2020
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AB_SA: Accessory genes-Based Source Attribution – tracing the source of Salmonella enterica Typhimurium environmental strains

Guillier, Laurent ; Gourmelon, Michèle ; Lozach, Solen ; Cadel-Six, Sabrina ; Vignaud, Marie-Léone ; Munck, Nanna Sophia Mucha ; Hald, Tine ; Palma, Federica
in: Microbial Genomics, vol: 6, issue: 7

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2020     |    DOI: https://doi.org/10.1099/mgen.0.000366

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Accelerating surveillance and research of antimicrobial resistance - an online repository for sharing of antimicrobial susceptibility data associated with whole-genome sequences

Matamoros, Sébastien ; Hendriksen, Rene S. ; Pataki, Bálint Ármin ; Pakseresht, Nima ; Rossello, Marc ; Silvester, Nicole ; Amid, Clara ; Aarestrup, Frank Møller ; Koopmans, Marion ; Cochrane, Guy ; Csabai, Istvan ; Lund, Ole ; Schultsz, Constance ; Group, The Compare Ml-Amr
in: Microbial Genomics, vol: 6, issue: 5

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2020     |    DOI: https://doi.org/10.1099/mgen.0.000342

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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     |    År: 2020     |    DOI: https://doi.org/10.3389/fpubh.2020.00038

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An interactive database for the investigation of high-density peptide microarray guided interaction patterns and antivenom cross-reactivity

Krause, Kamille E. ; Jenkins, Timothy P. ; Skaarup, Carina ; Engmark, Mikael ; Casewell, Nicholas R. ; Ainsworth, Stuart ; Lomonte, Bruno ; Fernández, Julián ; Gutiérrez, José M. ; Lund, Ole ; Laustsen, Andreas H.
in: PLOS Neglected Tropical Diseases , vol: 14, issue: 6

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2020     |    DOI: https://doi.org/10.1371/journal.pntd.0008366

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Application of Whole-Genome Sequences and Machine Learning in Source Attribution of Salmonella Typhimurium

Munck, Nanna Sophia Mucha ; Njage, Patrick Murigu Kamau ; Leekitcharoenphon, Pimlapas ; Litrup, Eva ; Hald, Tine
in: Risk Analysis, vol: 40, issue: 9, pages: 1693-1705

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2020     |    DOI: https://doi.org/10.1111/risa.13510

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Assessing the Effect of Fungicide Treatment on Cocoa Black Pod Disease in Ghana

Oduro, Bismark ; Apenteng, Ofosuhene Okofrobour ; Nkansah, Henrietta
in: Statistics, Optimization & Information Computing, vol: 8, issue: 2, pages: 374–385

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2020     |    DOI: https://doi.org/10.19139/soic-2310-5070-686

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Automated download and clean-up of family specific databases for kmer-based virus identification

Allesøe, Rosa Lundbye ; Lemvigh, Camilla Koldbæk ; Phan, My V T ; Clausen, Philip Thomas Lanken Conradsen ; Florensa, Alfred Ferrer ; Koopmans, Marion P G ; Lund, Ole ; Cotten, Matthew
in: Bioinformatics

Type: Journal article (Peer reviewed)

Status: Accepted/In press     |    År: 2020     |    DOI: https://doi.org/10.1093/bioinformatics/btaa857

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CCMetagen: comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data

Marcelino, Vanessa R. ; Clausen, Philip Thomas Lanken Conradsen ; Buchmann, Jan P. ; Wille, Michelle ; Iredell, Jonathan R. ; Meyer, Wieland ; Lund, Ole ; Sorrell, Tania C. ; Holmes, Edward C.
in: Genome Biology (Online Edition), vol: 21

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2020     |    DOI: https://doi.org/10.1186/s13059-020-02014-2

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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     |    År: 2020     |    DOI: https://doi.org/10.1038/s41586-020-2007-4

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Comment on: Gross national income and antibiotic resistance in invasive isolates: analysis of the top-ranked antibiotic-resistant bacteria on the 2017 WHO priority list

Aarestrup, Frank Møller ; van Bunnik, Bram
in: Journal of Antimicrobial Chemotherapy, vol: 75, issue: 7, pages: 2017-2018

Type: Comment/debate (Peer reviewed)

Status: Published     |    År: 2020     |    DOI: https://doi.org/10.1093/jac/dkz551

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CRHP Finder, a webtool for the detection of clarithromycin resistance in Helicobacter pylori from whole-genome sequencing data

Yusibova, Melodi ; Hasman, Henrik ; Clausen, Philip Thomas Lanken Conradsen ; Imkamp, Frank ; Wagner, Karoline ; Andersen, Leif Percival
in: Helicobacter

Type: Journal article (Peer reviewed)

Status: Accepted/In press     |    År: 2020     |    DOI: https://doi.org/10.1111/hel.12752

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DANMAP 2019 - Use of antimicrobial agents and occurrence of antimicrobial resistance in bacteria from food animals, food and humans in Denmark

Korsgaard, Helle Bisgaard ; Ellis-Iversen, Johanne ; Hendriksen, Rene S. ; Borck Høg, Birgitte ; Ronco, Troels ; Attauabi, Majda ; Boel, Jeppe ; Dalby, Tine ; Hammerum, Anette M. ; Hansen, Frank ; Hasman, Henrik ; Henius, Anna Emilie ; Hoffmann, Steen ; Ilan, Mette Bar ; Kaya, Hülya ; Kjerulf, Anne ; Kristensen, Brian ; Kähler, Jonas ; Rhod Larsen, Anders ; Nielsen, Eva Møller ; Schytte Olsen, Stefan ; Petersen, Andreas ; Porsbo, Lone Jannok ; Roer, Louise ; Skovgaard, Sissel ; Slotved, Hans-Christian ; Wolff Sönksen, Ute ; Torpdahl, Mia ; Laursen, Maja

Type: Report

Status: Published     |    År: 2020

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Data integration for prediction of weight loss in randomized controlled dietary trials

Nielsen, Rikke Linnemann ; Helenius, Marianne ; Garcia, Sara L. ; Roager, Henrik M. ; Aytan-Aktug, Derya ; Hansen, Lea Benedicte Skov ; Lind, Mads Vendelbo ; Vogt, Josef Korbinian ; Dalgaard, Marlene Danner ; Bahl, Martin I. ; Jensen, Cecilia Bang ; Muktupavela, Rasa ; Warinner, Christina ; Aaskov, Vincent ; Gøbel, Rikke ; Kristensen, Mette ; Frøkiær, Hanne ; Sparholt, Morten H. ; Christensen, Anders F. ; Vestergaard, Henrik ; Hansen, Torben ; Kristiansen, Karsten ; Brix, Susanne ; Petersen, Thomas Nordahl ; Lauritzen, Lotte ; Licht, Tine Rask ; Pedersen, Oluf ; Gupta, Ramneek
in: Scientific Reports, vol: 10, issue: 1

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2020     |    DOI: https://doi.org/10.1038/s41598-020-76097-z

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Description and determinants of the faecal resistome and microbiome of farmers and slaughterhouse workers: A metagenome-wide cross-sectional study

Van Gompel, Liese ; Luiken, Roosmarijn E.C. ; Hansen, Rasmus B. ; Munk, Patrick ; Bouwknegt, Martijn ; Heres, Lourens ; Greve, Gerdit D. ; Scherpenisse, Peter ; Jongerius-Gortemaker, Betty G.M. ; Tersteeg-Zijderveld, Monique H.G. ; García-Cobos, Silvia ; Dohmen, Wietske ; Dorado-García, Alejandro ; Wagenaar, Jaap A. ; Urlings, Bert A.P. ; Aarestrup, Frank Møller ; Mevius, Dik J. ; Heederik, Dick J.J. ; Schmitt, Heike ; Bossers, Alex ; Smit, Lidwien A.M.
in: Environment International, vol: 143

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2020     |    DOI: https://doi.org/10.1016/j.envint.2020.105939

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Detection of mobile genetic elements associated with antibiotic resistance in Salmonella enterica using a newly developed web tool: MobileElementFinder

Johansson, Markus Hans Kristofer ; Bortolaia, Valeria ; Tansirichaiya, Supathep ; Aarestrup, Frank Møller ; Roberts, Adam P ; Petersen, Thomas Nordahl
in: Journal of Antimicrobial Chemotherapy

Type: Journal article (Peer reviewed)

Status: Accepted/In press     |    År: 2020     |    DOI: https://doi.org/10.1093/jac/dkaa390

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Draft Genome Sequences of Lactococcus lactis Strains MS22314, MS22333, MS22336, and MS22337, Isolated from Fermented Camel Milk in Ethiopia

Bragason, Esben ; Svendsen, Christina Aaby ; Guya, Mitiku Eshetu ; Berhe, Tesfemariam ; Hansen, Egon Bech
in: Microbiology Resource Announcements, vol: 9, issue: 47

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2020     |    DOI: https://doi.org/10.1128/MRA.00862-20

 

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     |    År: 2020     |    DOI: https://doi.org/10.1007/s10433-019-00523-z

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Erratum: Application of shotgun metagenomics to smoked salmon experimentally spiked: Comparison between sequencing and microbiological data using different bioinformatic approaches (Italian Journal of Food Safety, (2019), 8, 4)

De Cesare, Alessandra ; Oliveri, Chiara ; Lucchi, Alex ; Pasquali, Frederique ; Pamp, Sünje Johanna ; Mordhorst, Hanne ; Wylezich, Claudia ; Poulsen, Casper Sahl ; Manfreda, Gerardo
in: Italian Journal of Food Safety, vol: 9, issue: 1

Type: Comment/debate (Peer reviewed)

Status: Published     |    År: 2020     |    DOI: https://doi.org/10.4081/ijfs.2020.8991

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Expansion of a subset within C2 subclade of Escherichia coli sequence type 131 (ST131) is driving the increasing rates of Aminoglycoside resistance

Hojabri, Zoya ; Darabi, Narges ; Mirmohammadkhani, Majid ; Rahimi, Hamzeh ; Hemmati, Romina ; Saeedi, Zahra ; Roustaee, Kiarash ; Leekitcharoenphon, Pimlapas ; Pajand, Omid ; Aarestrup, Frank Møller
in: Open Forum Infectious Diseases

Type: Journal article (Peer reviewed)

Status: Accepted/In press     |    År: 2020     |    DOI: https://doi.org/10.1093/ofid/ofaa410

 

Extended-spectrum beta-lactamase-producing Escherichia coli and antimicrobial resistance in municipal and hospital wastewaters in Czech Republic

Kutilova, Iva ; Medvecky, Matej ; Leekitcharoenphon, Pimlapas ; Munk, Patrick ; Masarikova, Martina ; Davidova-Gerzova, Lenka ; Jamborova, Ivana ; Bortolaia, Valeria ; Pamp, Sünje Johanna ; Dolejska, Monika
in: Environmental Research

Type: Journal article (Peer reviewed)

Status: Accepted/In press     |    År: 2020     |    DOI: https://doi.org/10.1016/j.envres.2020.110487

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Farm dust resistomes and bacterial microbiomes in European poultry and pig farms

, ; Luiken, Roosmarijn E.C. ; Van Gompel, Liese ; Bossers, Alex ; Munk, Patrick ; Joosten, Philip ; Hansen, Rasmus Borup ; Knudsen, Berith Elkær ; García-Cobos, Silvia ; Dewulf, Jeroen ; Aarestrup, Frank Møller ; Wagenaar, Jaap A. ; Smit, Lidwien A.M. ; Mevius, Dik J. ; Heederik, Dick J.J. ; Schmitt, Heike
in: Environment International, vol: 143

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2020     |    DOI: https://doi.org/10.1016/j.envint.2020.105971