Publications from the Genomic Epidemiology Research Group

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

Type: Journal article (Peer reviewed)

Status: Accepted/In press | 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

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

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

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

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

Type: Journal article (Peer reviewed)

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

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

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

Type: Journal article (Peer reviewed)

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

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 | Year: 2020 | DOI: https://doi.org/10.1038/s42003-020-0869-5

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 | Year: 2020 | DOI: https://doi.org/10.1038/s41598-020-59292-w

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 | Year: 2020 | DOI: https://doi.org/10.1099/mgen.0.000365

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

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

Type: Journal article (Peer reviewed)

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

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 | Year: 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 | Year: 2020 | DOI: https://doi.org/10.1128/msystems.00774-19

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 | Year: 2020 | DOI: https://doi.org/10.1002/aah.10093

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

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 | Year: 2020 | DOI: https://doi.org/10.1038/s42003-020-0859-7