Publications from the Genomic Epidemiology Research Group

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 | Year: 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 | Year: 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 | Year: 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 | Year: 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 | Year: 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 | Year: 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 | Year: 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 | Year: 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

Type: Journal article (Peer reviewed)

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

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 | Year: 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 | Year: 2020 | DOI: https://doi.org/10.1093/jac/dkaa390

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

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 | Year: 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 | Year: 2020 | DOI: https://doi.org/10.1093/ofid/ofaa410

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 | Year: 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 | 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, vol: 147, issue: 7, pages: 1953-1962

Type: Journal article (Peer reviewed)

Status: Published | Year: 2020 | DOI: https://doi.org/10.1002/ijc.32942

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 | Year: 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 | Year: 2020 | DOI: https://doi.org/10.1007/s12560-020-09441-1