Publikationer fra forskningsgruppen for Genetisk epidemiologi

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

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

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

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

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

A High Resolution DNA Melting Curve Analysis for the Rapid and Efficient Molecular Diagnostics of Extended Spectrum β-Lactamase Determinants from Foodborne Escherichia coli

Njage, Patrick Murigu Kamau ; Buys, Elna M.
in: Microorganisms, vol: 8, issue: 1

Type: Journal article (Peer reviewed)

Status: Published | År: 2020 | DOI: https://doi.org/10.3390/microorganisms8010090

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

Antimicrobial resistant E. coli and enterococci in pangasius fillets and prawns in Danish retail imported from Asia

Ellis-Iversen, Johanne ; Seyfarth, Anne Mette ; Korsgaard, Helle Bisgaard ; Bortolaia, Valeria ; Munck, Nanna Sophia Mucha ; Dalsgaard, Anders
in: Food Control, vol: 114

Type: Journal article (Peer reviewed)

Status: Published | År: 2020 | DOI: https://doi.org/10.1016/j.foodcont.2019.106958

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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 | År: 2020 | DOI: https://doi.org/10.1038/s41597-020-0417-7

Global, regional, and national burden of chronic kidney disease, 1990–2017

Bikbov, Boris ; Purcell, Caroline A. ; Levey, Andrew S. ; Smith, Mari ; Abdoli, Amir ; Abebe, Molla ; Adebayo, Oladimeji M. ; Afarideh, Mohsen ; Agarwal, Sanjay Kumar ; Agudelo-Botero, Marcela ; Ahmadian, Elham ; Al-Aly, Ziyad ; Alipour, Vahid ; Almasi-Hashiani, Amir ; Al-Raddadi, Rajaa M. ; Alvis-Guzman, Nelson ; Amini, Saeed ; Andrei, Tudorel ; Andrei, Catalina Liliana ; Andualem, Zewudu ; Anjomshoa, Mina ; Arabloo, Jalal ; Ashagre, Alebachew Fasil ; Asmelash, Daniel ; Ataro, Zerihun ; Atout, Maha Moh d.Wahbi ; Ayanore, Martin Amogre ; Badawi, Alaa ; Bakhtiari, Ahad ; Ballew, Shoshana H. ; Balouchi, Abbas ; Banach, Maciej ; Barquera, Simon ; Basu, Sanjay ; Bayih, Mulat Tirfie ; Bedi, Neeraj ; Bello, Aminu K. ; Bensenor, Isabela M. ; Bijani, Ali ; Boloor, Archith ; Borzì, Antonio M. ; Cámera, Luis Alberto ; Carrero, Juan J. ; Carvalho, Félix ; Castro, Franz ; Catalá-López, Ferrán ; Chang, Alex R. ; Chin, Ken Lee ; Chung, Sheng Chia ; Cirillo, Massimo ; Cousin, Ewerton ; Dandona, Lalit ; Dandona, Rakhi ; Daryani, Ahmad ; Das Gupta, Rajat ; Demeke, Feleke Mekonnen ; Demoz, Gebre Teklemariam ; Desta, Desilu Mahari ; Do, Huyen Phuc ; Duncan, Bruce B. ; Eftekhari, Aziz ; Esteghamati, Alireza ; Fatima, Syeda Sadia ; Fernandes, João C. ; Fernandes, Eduarda ; Fischer, Florian ; Freitas, Marisa ; Gad, Mohamed M. ; Gebremeskel, Gebreamlak Gebremedhn ; Gebresillassie, Begashaw Melaku ; Geta, Birhanu ; Ghafourifard, Mansour ; Ghajar, Alireza ; Ghith, Nermin ; Gill, Paramjit Singh ; Ginawi, Ibrahim Abdelmageed ; Gupta, Rajeev ; Hafezi-Nejad, Nima ; Haj-Mirzaian, Arvin ; Haj-Mirzaian, Arya ; Hariyani, Ninuk ; Hasan, Mehedi ; Hasankhani, Milad ; Hasanzadeh, Amir ; Hassen, Hamid Yimam ; Hay, Simon I. ; Heidari, Behnam ; Herteliu, Claudiu ; Hoang, Chi Linh ; Hosseini, Mostafa ; Hostiuc, Mihaela ; Irvani, Seyed Sina Naghibi ; Islam, Sheikh Mohammed Shariful ; Jafari Balalami, Nader ; James, Spencer L. ; Jassal, Simerjot K. ; Jha, Vivekanand ; Jonas, Jost B. ; Joukar, Farahnaz ; Jozwiak, Jacek Jerzy ; Kabir, Ali ; Kahsay, Amaha ; Kasaeian, Amir ; Kassa, Tesfaye Dessale ; Kassaye, Hagazi Gebremedhin ; Khader, Yousef Saleh ; Khalilov, Rovshan ; Khan, Ejaz Ahmad ; Khan, Mohammad Saud ; Khang, Young Ho ; Kisa, Adnan ; Kovesdy, Csaba P. ; Kuate Defo, Barthelemy ; Kumar, G. Anil ; Larsson, Anders O. ; Lim, Lee Ling ; Lopez, Alan D. ; Lotufo, Paulo A. ; Majeed, Azeem ; Malekzadeh, Reza ; März, Winfried ; Masaka, Anthony ; Meheretu, Hailemariam Abiy Alemu ; Miazgowski, Tomasz ; Mirica, Andreea ; Mirrakhimov, Erkin M. ; Mithra, Prasanna ; Moazen, Babak ; Mohammad, Dara K. ; Mohammadpourhodki, Reza ; Mohammed, Shafiu ; Mokdad, Ali H. ; Morales, Linda ; Moreno Velasquez, Ilais ; Mousavi, Seyyed Meysam ; Mukhopadhyay, Satinath ; Nachega, Jean B. ; Nadkarni, Girish N. ; Nansseu, Jobert Richie ; Natarajan, Gopalakrishnan ; Nazari, Javad ; Neal, Bruce ; Negoi, Ruxandra Irina ; Nguyen, Cuong Tat ; Nikbakhsh, Rajan ; Noubiap, Jean Jacques ; Nowak, Christoph ; Olagunju, Andrew T. ; Ortiz, Alberto ; Owolabi, Mayowa Ojo ; Palladino, Raffaele ; Pathak, Mona ; Poustchi, Hossein ; Prakash, Swayam ; Prasad, Narayan ; Rafiei, Alireza ; Raju, Sree Bhushan ; Ramezanzadeh, Kiana ; Rawaf, Salman ; Rawaf, David Laith ; Rawal, Lal ; Reiner, Robert C. ; Rezapour, Aziz ; Ribeiro, Daniel Cury ; Roever, Leonardo ; Rothenbacher, Dietrich ; Rwegerera, Godfrey M. ; Saadatagah, Seyedmohammad ; Safari, Saeed ; Sahle, Berhe Weldearegawi ; Salem, Hosni ; Sanabria, Juan ; Santos, Itamar S. ; Sarveazad, Arash ; Sawhney, Monika ; Schaeffner, Elke ; Schmidt, Maria Inês ; Schutte, Aletta Elisabeth ; Sepanlou, Sadaf G. ; Shaikh, Masood Ali ; Sharafi, Zeinab ; Sharif, Mehdi ; Sharifi, Amrollah ; Silva, Diego Augusto Santos ; Singh, Jasvinder A. ; Singh, Narinder Pal ; Sisay, Malede Mequanent M. ; Soheili, Amin ; Sutradhar, Ipsita ; Teklehaimanot, Berhane Fseha ; Tesfay, Berhe etsay ; Teshome, Getnet Fetene ; Thakur, Jarnail Singh ; Tonelli, Marcello ; Tran, Khanh Bao ; Tran, Bach Xuan ; Tran Ngoc, Candide ; Ullah, Irfan ; Valdez, Pascual R. ; Varughese, Santosh ; Vos, Theo ; Vu, Linh Gia ; Waheed, Yasir ; Werdecker, Andrea ; Wolde, Haileab Fekadu ; Wondmieneh, Adam Belay ; Wulf Hanson, Sarah ; Yamada, Tomohide ; Yeshaw, Yigizie ; Yonemoto, Naohiro ; Yusefzadeh, Hasan ; Zaidi, Zoubida ; Zaki, Leila ; Zaman, Sojib Bin ; Zamora, Nelson ; Zarghi, Afshin ; Zewdie, Kaleab Alemayehu ; Ärnlöv, Johan ; Coresh, Josef ; Perico, Norberto ; Remuzzi, Giuseppe ; Murray, Chris J.L.
in: The Lancet, vol: 395, issue: 10225, pages: 709-733

Type: Journal article (Peer reviewed)

Status: Published | År: 2020 | DOI: https://doi.org/10.1016/S0140-6736(20)30045-3

Inactivation of hepatitis A virus and murine norovirus on surfaces of plastic, steel and raspberries using steam-ultrasound treatment

Rajiuddin, Sheikh Md ; Vigre, Håkan ; Musavian, Hanieh Sadat ; Kohle, Simon ; Krebs, Niels ; Hansen, Tina Beck ; Gantzer, Christophe ; Schultz, Anna Charlotte
in: Food and Environmental Virology

Type: Journal article (Peer reviewed)

Status: Accepted/In press | År: 2020 | DOI: https://doi.org/10.1007/s12560-020-09441-1

In Silico Genotyping of Escherichia coli Isolates for Extraintestinal Virulence Genes by Use of Whole-Genome Sequencing Data

Malberg Tetzschner, Anna Maria ; Johnson, James R. ; Johnston, Brian D. ; Lund, Ole ; Scheutz, Flemming
in: Journal of Clinical Microbiology, vol: 58, issue: 10

Type: Journal article (Peer reviewed)

Status: Published | År: 2020 | DOI: https://doi.org/10.1128/JCM.01269-20

Large scale automated phylogenomic analysis of bacterial isolates and the Evergreen Online platform

Szarvas, Judit ; Ahrenfeldt, Johanne ; Bellod Cisneros, Jose Luis ; Thomsen, Martin Christen Frølund ; Aarestrup, Frank Møller ; Lund, Ole
in: Communications Biology, vol: 3, issue: 1

Type: Journal article (Peer reviewed)

Status: Published | År: 2020 | DOI: https://doi.org/10.1038/s42003-020-0869-5

Long-Term Temporal Stability of the Resistome in Sewage from Copenhagen

Brinch, Christian ; Leekitcharoenphon, Pimlapas ; Duarte, Ana Sofia Ribeiro ; Svendsen, Christina Aaby ; Jensen, Jacob Dyring ; Aarestrup, Frank Møller
in: mSystems, vol: 5, issue: 5

Type: Journal article (Peer reviewed)

Status: Published | År: 2020 | DOI: https://doi.org/10.1128/mSystems.00841-20

Measuring universal health coverage based on an index of effective coverage of health services in 204 countries and territories, 1990–2019

Lozano, Rafael ; Fullman, Nancy ; Mumford, John Everett ; Knight, Megan ; Barthelemy, Celine M. ; Abbafati, Cristiana ; Abbastabar, Hedayat ; Abd-Allah, Foad ; Abdollahi, Mohammad ; Abedi, Aidin ; Abolhassani, Hassan ; Abosetugn, Akine Eshete ; Abreu, Lucas Guimarães ; Abrigo, Michael R.M. ; Abu Haimed, Abdulaziz Khalid ; Abushouk, Abdelrahman I. ; Adabi, Maryam ; Adebayo, Oladimeji M. ; Adekanmbi, Victor ; Adelson, Jaimie ; Adetokunboh, Olatunji O. ; Adham, Davoud ; Advani, Shailesh M. ; Afshin, Ashkan ; Agarwal, Gina ; Agasthi, Pradyumna ; Aghamir, Seyed Mohammad Kazem ; Agrawal, Anurag ; Ahmad, Tauseef ; Akinyemi, Rufus Olusola ; Alahdab, Fares ; Al-Aly, Ziyad ; Alam, Khurshid ; Albertson, Samuel B. ; Alemu, Yihun Mulugeta ; Alhassan, Robert Kaba ; Ali, Muhammad ; Ali, Saqib ; Alipour, Vahid ; Aljunid, Syed Mohamed ; Alla, François ; Almadi, Majid Abdulrahman Hamad ; Almasi, Ali ; Almasi-Hashiani, Amir ; Almasri, Nihad A. ; Al-Mekhlafi, Hesham M. ; Almulhim, Abdulaziz M. ; Alonso, Jordi ; Al-Raddadi, Rajaa M. ; Altirkawi, Khalid A. ; Alvis-Guzman, Nelson ; Alvis-Zakzuk, Nelson J. ; Amini, Saeed ; Amini-Rarani, Mostafa ; Amiri, Fatemeh ; Amit, Arianna Maever L. ; Amugsi, Dickson A. ; Ancuceanu, Robert ; Anderlini, Deanna ; Andrei, Catalina Liliana ; Androudi, Sofia ; Ansari, Fereshteh ; Ansari-Moghaddam, Alireza ; Antonio, Carl Abelardo T. ; Antony, Catherine M. ; Antriyandarti, Ernoiz ; Anvari, Davood ; Anwer, Razique ; Arabloo, Jalal ; Arab-Zozani, Morteza ; Aravkin, Aleksandr Y. ; Aremu, Olatunde ; Ärnlöv, Johan ; Asaad, Malke ; Asadi-Aliabadi, Mehran ; Asadi-Pooya, Ali A. ; Ashbaugh, Charlie ; Athari, Seyyed Shamsadin ; Atout, Maha Moh d.Wahbi ; Ausloos, Marcel ; Avila-Burgos, Leticia ; Ayala Quintanilla, Beatriz Paulina ; Ayano, Getinet ; Ayanore, Martin Amogre ; Aynalem, Yared Asmare ; Aynalem, Getie Lake ; Ayza, Muluken Altaye ; Azari, Samad ; Azzopardi, Peter S. ; B, Darshan B. ; Babaee, Ebrahim ; Badiye, Ashish D. ; Bahrami, Mohammad Amin ; Baig, Atif Amin ; Bakhshaei, Mohammad Hossein ; Bakhtiari, Ahad ; Bakkannavar, Shankar M. ; Balachandran, Arun ; Balassyano, Shelly ; Banach, Maciej ; Banerjee, Srikanta K. ; Banik, Palash Chandra ; Bante, Agegnehu Bante ; Bante, Simachew Animen ; Barker-Collo, Suzanne Lyn ; Bärnighausen, Till Winfried ; Barrero, Lope H. ; Bassat, Quique ; Basu, Sanjay ; Baune, Bernhard T. ; Bayati, Mohsen ; Baye, Bayisa Abdissa ; Bedi, Neeraj ; Beghi, Ettore ; Behzadifar, Masoud ; Bekuma, Tariku Tesfaye Tesfaye ; Bell, Michelle L. ; Bensenor, Isabela M. ; Berman, Adam E. ; Bernabe, Eduardo ; Bernstein, Robert S. ; Bhagavathula, Akshaya Srikanth ; Bhandari, Dinesh ; Bhardwaj, Pankaj ; Bhat, Anusha Ganapati ; Bhattacharyya, Krittika ; Bhattarai, Suraj ; Bhutta, Zulfiqar A. ; Bijani, Ali ; Bikbov, Boris ; Bilano, Ver ; Biondi, Antonio ; Birihane, Binyam Minuye ; Bockarie, Moses John ; Bohlouli, Somayeh ; Bojia, Hunduma Amensisa ; Bolla, Srinivasa Rao Rao ; Boloor, Archith ; Brady, Oliver J. ; Braithwaite, Dejana ; Briant, Paul Svitil ; Briggs, Andrew M. ; Briko, Nikolay Ivanovich ; Burugina Nagaraja, Sharath ; Busse, Reinhard ; Butt, Zahid A. ; Caetano dos Santos, Florentino Luciano ; Cahuana-Hurtado, Lucero ; Cámera, Luis Alberto ; Cárdenas, Rosario ; Carreras, Giulia ; Carrero, Juan J. ; Carvalho, Felix ; Castaldelli-Maia, Joao Mauricio ; Castañeda-Orjuela, Carlos A. ; Castelpietra, Giulio ; Castro, Franz ; Catalá-López, Ferrán ; Causey, Kate ; Cederroth, Christopher R. ; Cercy, Kelly M. ; Cerin, Ester ; Chandan, Joht Singh ; Chang, Angela Y. ; Charan, Jaykaran ; Chattu, Vijay Kumar ; Chaturvedi, Sarika ; Chin, Ken Lee ; Cho, Daniel Youngwhan ; Choi, Jee Young Jasmine ; Christensen, Hanne ; Chu, Dinh Toi ; Chung, Michael T. ; Ciobanu, Liliana G. ; Cirillo, Massimo ; Comfort, Haley ; Compton, Kelly ; Cortesi, Paolo Angelo ; Costa, Vera Marisa ; Cousin, Ewerton ; Dahlawi, Saad M.A. ; Damiani, Giovanni ; Dandona, Lalit ; Dandona, Rakhi ; Darega Gela, Jiregna ; Darwesh, Aso Mohammad ; Daryani, Ahmad ; Dash, Aditya Prasad ; Davey, Gail ; Dávila-Cervantes, Claudio Alberto ; Davletov, Kairat ; De Neve, Jan Walter ; Denova-Gutiérrez, Edgar ; Deribe, Kebede ; Dervenis, Nikolaos ; Desai, Rupak ; Dharmaratne, Samath Dhamminda ; Dhungana, Govinda Prasad ; Dianatinasab, Mostafa ; Dias da Silva, Diana ; Diaz, Daniel ; Dippenaar, Ilse N. ; Do, Hoa Thi ; Dorostkar, Fariba ; Doshmangir, Leila ; Duncan, Bruce B. ; Duraes, Andre Rodrigues ; Eagan, Arielle Wilder ; Edvardsson, David ; El Sayed, Iman ; El Tantawi, Maha ; Elgendy, Islam Y. ; Elyazar, Iqbal RF ; Eskandari, Khalil ; Eskandarieh, Sharareh ; Esmaeilnejad, Saman ; Esteghamati, Alireza ; Ezekannagha, Oluchi ; Farag, Tamer ; Farahmand, Mohammad ; Faraon, Emerito Jose A. ; Farinha, Carla Sofia e.Sá ; Farioli, Andrea ; Faris, Pawan Sirwan ; Faro, Andre ; Fazlzadeh, Mehdi ; Feigin, Valery L. ; Fernandes, Eduarda ; Ferrara, Pietro ; Feyissa, Garumma Tolu ; Filip, Irina ; Fischer, Florian ; Fisher, James L. ; Flor, Luisa Sorio ; Foigt, Nataliya A. ; Folayan, Morenike Oluwatoyin ; Fomenkov, Artem Alekseevich ; Foroutan, Masoud ; 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in: The Lancet, vol: 396, issue: 10258, pages: 1250-1284

Type: Journal article (Peer reviewed)

Status: Published | År: 2020 | DOI: https://doi.org/10.1016/S0140-6736(20)30750-9

Metaphylogenetic analysis of global sewage reveals that bacterial strains associated with human disease show less degree of geographic clustering

Ahrenfeldt, Johanne ; Waisi, Madina ; Loft, Isabella Charlotte ; Clausen, Philip Thomas Lanken Conradsen ; Allesøe, Rosa Lundbye ; Szarvas, Judit ; Hendriksen, Rene S. ; Aarestrup, Frank Møller ; Lund, Ole
in: Scientific Reports, vol: 10

Type: Journal article (Peer reviewed)

Status: Published | År: 2020 | DOI: https://doi.org/10.1038/s41598-020-59292-w

Molecular Characteristics and Zoonotic Potential of Salmonella Weltevreden From Cultured Shrimp and Tilapia in Vietnam and China

Hounmanou, Yaovi M.G. ; Dalsgaard, Anders ; Sopacua, Tirzania Frannetta ; Uddin, Gazi Md Noor ; Leekitcharoenphon, Pimlapas ; Hendriksen, Rene S. ; Olsen, John E. ; Larsen, Marianne Halberg
in: Frontiers in Microbiology, vol: 11

Type: Journal article (Peer reviewed)

Status: Published | År: 2020 | DOI: https://doi.org/10.3389/fmicb.2020.01985

Molecular epidemiology of Salmonella Infantis in Europe: insights into the success of the bacterial host and its parasitic pESI-like megaplasmid

Alba, Patricia ; Leekitcharoenphon, Pimlapas ; Carfora, Virginia ; Amoruso, Roberta ; Cordaro, Gessica ; Di Matteo, Paola ; Ianzano, Angela ; Iurescia, Manuela ; Diaconu, Elena L ; Study Group, Engage-Eurl-Ar Network ; Karlsmose Pedersen, Susanne ; Guerra, Beatriz ; Hendriksen, Rene S. ; Franco, Alessia ; Battisti, Antonio
in: Microbial Genomics, vol: 6, issue: 5

Type: Journal article (Peer reviewed)

Status: Published | År: 2020 | DOI: https://doi.org/10.1099/mgen.0.000365

Monitoring of Farm-Level Antimicrobial Use to Guide Stewardship

Sanders, Pim ; Vanderhaeghen, Wannes ; Fertner, Mette Ely ; Fuchs, Klemens ; Obritzhauser, Walter ; Agunos, Agnes ; Carson, Carolee ; Borck Høg, Birgitte ; Dalhoff Andersen, Vibe ; Chauvin, Claire ; Hémonic, Anne ; Käsbohrer, Annemarie ; Merle, Roswitha ; Alborali, Giovanni L. ; Scali, Federico ; Stärk, Katharina D.C. ; Muentener, Cedric ; van Geijlswijk, Ingeborg ; Broadfoot, Fraser ; Pokludová, Lucie ; Firth, Clair L. ; Carmo, Luís P. ; Manzanilla, Edgar Garcia ; Jensen, Laura Mark ; Sjölund, Marie ; Pinto Ferreira, Jorge ; Brown, Stacey ; Heederik, Dick ; Dewulf, Jeroen
in: Frontiers in Veterinary Science, vol: 7

Type: Review (Peer reviewed)

Status: Published | År: 2020 | DOI: https://doi.org/10.3389/fvets.2020.00540

Network Approach to Source Attribution of Salmonella enterica Serovar Typhimurium and Its Monophasic Variant

Merlotti, Alessandra ; Manfreda, Gerardo ; Munck, Nanna Sophia Mucha ; Hald, Tine ; Litrup, Eva ; Nielsen, Eva Møller ; Remondini, Daniel ; Pasquali, Frédérique
in: Frontiers in Microbiology, vol: 11

Type: Journal article (Peer reviewed)

Status: Published | År: 2020 | DOI: https://doi.org/10.3389/fmicb.2020.01205

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 | År: 2020 | DOI: https://doi.org/10.1093/annweh/wxz098

Phylogenetic Investigation of Norovirus Transmission between Humans and Animals

Villabruna, Nele ; Izquierdo Lara, Ray W. ; Szarvas, Judit ; Koopmans, Marion P. G. ; de Graaf, Miranda
in: Viruses, vol: 12, issue: 11

Type: Journal article (Peer reviewed)

Status: Published | År: 2020 | DOI: https://doi.org/10.3390/v12111287

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

Prediction of Acquired Antimicrobial Resistance for Multiple Bacterial Species Using Neural Networks

Aytan, Derya ; Clausen, Philip Thomas Lanken Conradsen ; Bortolaia, Valeria ; Aarestrup, Frank Møller ; Lund, Ole
in: mSystems, vol: 5, issue: 1

Type: Journal article (Peer reviewed)

Status: Published | År: 2020 | DOI: https://doi.org/10.1128/msystems.00774-19

Proficiency Testing of Metagenomics-Based Detection of Food-Borne Pathogens Using a Complex Artificial Sequencing Dataset

Höper, Dirk ; Grützke, Josephine ; Brinkmann, Annika ; Mossong, Joël ; Matamoros, Sébastien ; Ellis, Richard J. ; Deneke, Carlus ; Tausch, Simon H. ; Cuesta, Isabel ; Monzón, Sara ; Juliá, Miguel ; Petersen, Thomas Nordahl ; Hendriksen, Rene S. ; Pamp, Sünje Joanna ; Leijon, Mikael ; Hakhverdyan, Mikhayil ; Walsh, Aaron M. ; Cotter, Paul D. ; Chandrasekaran, Lakshmi ; Tay, Moon Y.F. ; Schlundt, Joergen ; Sala, Claudia ; De Cesare, Alessandra ; Nitsche, Andreas ; Beer, Martin ; Wylezich, Claudia
in: Frontiers in Microbiology, vol: 11

Type: Journal article (Peer reviewed)

Status: Published | År: 2020 | DOI: https://doi.org/10.3389/fmicb.2020.575377

Quantitative Microbial Risk Assessment Based on Whole Genome Sequencing Data

Njage, Patrick Murigu Kamau ; Leekitcharoenphon, Pimlapas ; Hansen, Lisbeth Truelstrup ; Hendriksen, Rene S. ; Faes, Christel ; Aerts, Marc ; Hald, Tine
in: Microorganisms, vol: 8, issue: 11

Type: Journal article (Peer reviewed)

Status: Published | År: 2020 | DOI: https://doi.org/10.3390/microorganisms8111772

Sequence Analysis of Plasmids in Vibrio anguillarum from Different Fish and Locations

Akter, Tasmina ; Lindegaard, Mikkel ; Pedersen, Karl ; Strube, Mikael Lenz ; Ronco, Troels ; Dalsgaard, Inger
in: Journal of Aquatic Animal Health, vol: 32, issue: 1, pages: 21-27

Type: Journal article

Status: Published | År: 2020 | DOI: https://doi.org/10.1002/aah.10093

Setting a baseline for global urban virome surveillance in sewage

, ; Nieuwenhuijse, David F. ; Oude Munnink, Bas B. ; Phan, My V.T. ; Hendriksen, Rene S. ; Bego, Artan ; Rees, Catherine ; Neilson, Elizabeth Heather ; Coventry, Kris ; Collignon, Peter ; Allerberger, Franz ; Rahube, Teddie O. ; Oliveira, Guilherme ; Ivanov, Ivan ; Sopheak, Thet ; Vuthy, Yith ; Yost, Christopher K. ; Tabo, Djim adjim ; Cuadros-Orellana, Sara ; Ke, Changwen ; Zheng, Huanying ; Baisheng, Li ; Jiao, Xiaoyang ; Donado-Godoy, Pilar ; Coulibaly, Kalpy Julien ; Hrenovic, Jasna ; Jergović, Matijana ; Karpíšková, Renáta ; Elsborg, Bodil ; Legesse, Mengistu ; Eguale, Tadesse ; Heikinheimo, Annamari ; Villacis, Jose Eduardo ; Sanneh, Bakary ; Malania, Lile ; Nitsche, Andreas ; Brinkmann, Annika ; Saba, Courage Kosi Setsoafia ; Kocsis, Bela ; Solymosi, Norbert ; Thorsteinsdottir, Thorunn R. ; Hatha, Abdulla Mohamed ; Alebouyeh, Masoud ; Morris, Dearbhaile ; O’Connor, Louise ; Cormican, Martin ; Moran-Gilad, Jacob ; Battisti, Antonio ; Alba, Patricia ; Munk, Patrick ; Aarestrup, Frank Møller
in: Scientific Reports, vol: 10, issue: 1

Type: Journal article (Peer reviewed)

Status: Published | År: 2020 | DOI: https://doi.org/10.1038/s41598-020-69869-0

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, vol: 17, issue: 5, pages: 357-364

Type: Journal article (Peer reviewed)

Status: Published | År: 2020 | DOI: https://doi.org/10.1089/fpd.2019.2706

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 | År: 2020 | DOI: https://doi.org/10.1016/j.micinf.2019.07.004

The 24th Proficiency Testing, 2018 – Enterococci, staphyloccci and E. coli

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

Type: Report

Status: Published | År: 2020

The Analysis of Field Strains Isolated From Food, Animal and Clinical Sources Uncovers Natural Mutations in Listeria monocytogenes Nisin Resistance Genes

Wambui, Joseph ; Eshwar, Athmanya K. ; Aalto-Araneda, Mariella ; Pöntinen, Anna ; Stevens, Marc J.A. ; Njage, Patrick Murigu Kamau ; Tasara, Taurai
in: Frontiers in Microbiology, vol: 11

Type: Journal article (Peer reviewed)

Status: Published | År: 2020 | DOI: https://doi.org/10.3389/fmicb.2020.549531

The association between meat inspection codes, footpad lesions and thinning of broiler flocks in the Danish broiler production

Alfifi, Ahmed ; Dalsgaard, Anders ; Christensen, Jens P. ; Larsen, Marianne Halberg ; Sandberg, Marianne
in: Preventive Veterinary Medicine, vol: 185

Type: Journal article (Peer reviewed)

Status: Published | År: 2020 | DOI: https://doi.org/10.1016/j.prevetmed.2020.105205

The gut microbiome but not the resistome is associated with urogenital schistosomiasis in preschool-aged children

Osakunor, Derick N. M. ; Munk, Patrick ; Mduluza, Takafira ; Petersen, Thomas Nordahl ; Brinch, Christian ; Ivens, Alasdair ; Chimponda, Theresa ; Amanfo, Seth A. ; Murray, Janice ; Woolhouse, Mark E. J. ; Aarestrup, Frank Møller ; Mutapi, Francisca
in: Communications Biology, vol: 3, issue: 1

Type: Journal article (Peer reviewed)

Status: Published | År: 2020 | DOI: https://doi.org/10.1038/s42003-020-0859-7

The impact of implementing HIV prevention policies therapy and control strategy among HIV and AIDS incidence cases in Malaysia

Apenteng, Ofosuhene Okofrobour ; Osei, Prince P. ; Oduro, Bismark ; Kwabla, Mavis Pearl ; Ismail, Noor Azina
in: Infectious Disease Modelling, vol: 5, pages: 755-765

Type: Journal article (Peer reviewed)

Status: Published | År: 2020 | DOI: https://doi.org/10.1016/j.idm.2020.09.009

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 | År: 2020 | DOI: https://doi.org/10.1186/s13073-020-0713-z

Understanding and predicting ciprofloxacin minimum inhibitory concentration in Escherichia coli with machine learning

Pataki, Bálint Ármin ; Matamoros, Sébastien ; van der Putten, Boas C L ; Remondini, Daniel ; Giampieri, Enrico ; Aytan-Aktug, Derya ; Hendriksen, Rene S. ; Lund, Ole ; Csabai, Istvan ; Schultsz, Constance ; COMPARE ML-AMR group, SPS
in: Scientific Reports, vol: 10, issue: 1

Type: Journal article (Peer reviewed)

Status: Published | År: 2020 | DOI: https://doi.org/10.1038/s41598-020-71693-5

Using novel methodologies to support burden of disease estimates

Hald, Tine
in: European Journal of Public Health, vol: 30, issue: Suppl. 5, pages: 350-351
Presented at: 16th World Congress on Public Health 2020

Type: Conference abstract in journal (Peer reviewed)

Status: Published | År: 2020 | DOI: https://doi.org/10.1093/eurpub/ckaa165.951

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 | År: 2020 | DOI: https://doi.org/10.1126/science.aba3432

Using stochastic dynamic modelling to estimate the sensitivity of current and alternative surveillance program of Salmonella in conventional broiler production

Apenteng, Ofosuhene Okofrobour ; Arnold, Mark E. ; Vigre, Håkan
in: Scientific Reports, vol: 10, issue: 1

Type: Journal article (Peer reviewed)

Status: Published | År: 2020 | DOI: https://doi.org/10.1038/s41598-020-76514-3

Variation in post-smolt growth pattern of wild one sea-winter salmon (Salmo salar L.), and its linkage to surface warming in the eastern North Atlantic Ocean

Todd, Christopher D ; Hanson, Nora N ; Boehme, Lars ; Revie, Crawford W ; Marques, Ana Rita Pinheiro
in: Journal of Fish Biology

Type: Journal article (Peer reviewed)

Status: Accepted/In press | År: 2020 | DOI: https://doi.org/10.1111/jfb.14552

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 | År: 2019 | DOI: https://doi.org/10.1017/s0950268819002073

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

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 | År: 2019 | DOI: https://doi.org/10.3389/fmicb.2019.02816

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 | År: 2019 | DOI: https://doi.org/10.3389/fmicb.2019.02974

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

DANMAP 2018

Borck Høg, Birgitte ; Ellis-Iversen, Johanne ; Wolf Sönksen, Ute (Editor) ; Bortolaia, Valeria ; Hendriksen, Rene S. ; Korsgaard, Helle Bisgaard ; Petersen, Channie Kahl ; 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 ; Rhod Larsen, Anders ; Møller, Eva ; Schytte Olsen, Stefan ; Skjold Selle Pedersen, Karoline ; Petersen, Andreas ; Porsbo, Lone Jannok ; Roer, Louise ; Skovgaard, Sissel ; Slotved, Hans-Christian ; Wolf Sönksen, Ute ; Torpdahl, Mia

Type: Report

Status: Published | År: 2019

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

Type: Book chapter (Peer reviewed)

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

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 | År: 2019 | DOI: https://doi.org/10.2376/0005-9366-18088

Diversity and Population Overlap between Avian and Human Escherichia coli Belonging to Sequence Type 95

Jørgensen, Steffen L. ; Stegger, Marc ; Kudirkiene, Eglé ; Lilje, Berit ; Poulsen, Louise L. ; Ronco, Troels ; Pires Dos Santos, Teresa ; Kiil, Kristoffer ; Bisgaard, Magne ; Pedersen, Karl ; Nolan, Lisa K. ; Price, Lance B. ; Olsen, Rikke H. ; Andersen, Paal S. ; Christensen, Henrik
in: mSphere, vol: 4, issue: 1

Type: Journal article (Peer reviewed)

Status: Published | År: 2019 | DOI: https://doi.org/10.1128/mSphere.00333-18

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

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

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, 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

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 | År: 2019 | DOI: https://doi.org/10.1371/journal.pntd.0007934

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

LA-MRSA CC398 in Dairy Cattle and Veal Calf Farms Indicates Spillover From Pig Production

Hansen, Julie Elvekjær ; Ronco, Troels ; Stegger, Marc ; Sieber, Raphael N. ; Fertner, Mette Ely ; Læssøe Martin, Henrik ; Farre, Michael ; Toft, Nils ; Larsen, Anders R. ; Pedersen, Karl
in: Frontiers in Microbiology, vol: 10

Type: Journal article (Peer reviewed)

Status: Published | År: 2019 | DOI: https://doi.org/10.3389/fmicb.2019.02733

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

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

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

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 | År: 2019