Publications from the Genomic Epidemiology Research Group

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

Type: Journal article (Peer reviewed)

Status: Accepted/In press | Year: 2019 | DOI: https://doi.org/10.1111/1758-2229.12728

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, University of Copenhagen, Frederiksberg C
Presented at: 13th DWF Water Research Conference

Type: Conference abstract in proceedings (Peer reviewed)

Status: Published | Year: 2019

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 | Year: 2019 | DOI: https://doi.org/10.1016/j.ijfoodmicro.2018.11.016

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

Type: Journal article (Peer reviewed)

Status: Accepted/In press | Year: 2019 | DOI: https://doi.org/10.1038/s41564-018-0338-9

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 | Year: 2019 | DOI: https://doi.org/10.1371/journal.pone.0210368

Modelling the Impact of Migration on HIV Persistency in Ghana

Apenteng, Ofosuhene Okofrobour ; Ismail, Noor Azina
in: Statistics, Optimization and Information Computing, vol: 7, issue: 1, pages: 55-65

Type: Journal article (Peer reviewed)

Status: Published | Year: 2019 | DOI: https://doi.org/10.19139/soic.v7i1.552

Plasmid ATLAS: plasmid visual analytics and identification in high-throughput sequencing data

Jesus, Tiago F. ; Ribeiro-Gonçalves, Bruno ; Silva, Diogo N. ; Bortolaia, Valeria ; Ramirez, Mário ; Carriço, João A
in: Nucleic Acids Research, vol: 47, issue: D1, pages: 188-194

Type: Journal article (Peer reviewed)

Status: Published | Year: 2019 | DOI: https://doi.org/10.1093/nar/gky1073

The antimicrobial resistome in relation to antimicrobial use and biosecurity in pig farming, a metagenome-wide association study in nine European countries

Van Gompel, Liese ; Luiken, Roosmarijn E C ; Sarrazin, Steven ; Munk, Patrick ; Knudsen, Berith Elkær ; Hansen, Rasmus B ; Bossers, Alex ; Aarestrup, Frank Møller ; Dewulf, Jeroen ; Wagenaar, Jaap A ; Mevius, Dik J ; Schmitt, Heike ; Heederik, Dick J J ; Dorado-García, Alejandro ; Smit, Lidwien A M ; consortium, EFFORT
in: Journal of Antimicrobial Chemotherapy

Type: Journal article (Peer reviewed)

Status: Accepted/In press | Year: 2019 | DOI: https://doi.org/10.1093/jac/dky518

The External Quality Assurance System of the WHO Global Foodborne Infections Network, 2017

Karlsmose Pedersen, Susanne ; Frimann, Jens-Ole Marinus ; Aarestrup, Frank Møller ; Hendriksen, Rene S.

Type: Report

Status: Published | Year: 2019

Zoonoses in the Bolivian Amazon: alarming initial results from an NGO-led one health initiative

Robles, E. Alandia ; Martinez, E. ; Voigt, D. Arteaga ; Durán, P. ; Hald, Tine ; Quispe, E. ; Salazar, C. ; Salas, A. ; Nielsen, L. R.
in: International Journal of Infectious Diseases, vol: 79, issue: Suppl. 1, pages: 5-6
Presented at: International Meeting on Emerging Diseases and Surveillance (IMED) 2016

Type: Conference abstract in journal (Peer reviewed)

Status: Published | Year: 2019 | DOI: https://doi.org/10.1016/j.ijid.2018.11.032

The role of outer membrane proteins and lipopolysaccharides for the sensitivity of escherichia coli to antimicrobial peptides

Ebbensgaard, Anna Elisabeth ; Mordhorst, Hanne ; Møller Aarestrup, Frank ; Bech Hansen, Egon
in: Frontiers in Microbiology, vol: 9

Type: Journal article (Peer reviewed)

Status: Published | Year: 2018 | DOI: https://doi.org/10.3389/fmicb.2018.02153

Abundance and diversity of the faecal resistome in slaughter pigs and broilers in nine European countries

Munk, Patrick ; Knudsen, Berith Elkær ; Lukjacenko, Oksana ; Duarte, Ana Sofia Ribeiro ; Van Gompel, Liese ; Luiken, Roosmarijn E.C. ; Smit, Lidwien A.M. ; Schmitt, Heike ; Garcia, Alejandro Dorado ; Hansen, Rasmus Borup ; Petersen, Thomas Nordahl ; Bossers, Alex ; Ruppé, Etienne ; Graveland, Haitske ; van Essen, Alieda ; Gonzalez-Zorn, Bruno ; Moyano, Gabriel ; Sanders, Pascal ; Chauvin, Claire ; David, Julie ; Battisti, Antonio ; Caprioli, Andrea ; Dewulf, Jeroen ; Blaha, Thomas ; Wadepohl, Katharina ; Brandt, Maximiliane ; Wasyl, Dariusz ; Skarzyńska, Magdalena ; Zajac, Magdalena ; Daskalov, Hristo ; Saatkamp, Helmut W. ; Stärk, Katharina D.C. ; Lund, Ole ; Hald, Tine ; Pamp, Sünje Johanna ; Vigre, Håkan ; Heederik, Dick ; Wagenaar, Jaap A. ; Mevius, Dik ; Møller Aarestrup, Frank ; ,
in: Nature Microbiology, vol: 3, issue: 8, pages: 898-908

Type: Journal article (Peer reviewed)

Status: Published | Year: 2018 | DOI: https://doi.org/10.1038/s41564-018-0192-9

Dissection of the antimicrobial and hemolytic activity of Cap18: Generation of Cap18 derivatives with enhanced specificity

Ebbensgaard, Anna Elisabeth ; Mordhorst, Hanne ; Overgaard, Michael Toft ; Aarestrup, Frank Møller ; Hansen, Egon Bech
in: PLoS ONE, vol: 13, issue: 5

Type: Journal article (Peer reviewed)

Status: Published | Year: 2018 | DOI: https://doi.org/10.1371/journal.pone.0197742

Microbial contamination level profiles attributed to contamination of beef carcasses, personnel, and equipment: case of small and medium enterprise slaughterhouses

Wambui, Joseph ; Lamuka, Peter ; Karuri, Edward ; Matofari, Joseph ; Njage, Patrick Murigu Kamau
in: Journal of Food Protection, vol: 81, issue: 4, pages: 684-691

Type: Journal article (Peer reviewed)

Status: Published | Year: 2018 | DOI: https://doi.org/10.4315/0362-028X.JFP-17-402

High diversity of genes and plasmids encoding resistance to third-generation cephalosporins and quinolones in clinical Escherichia coli from commercial poultry flocks in Italy

Niero, Giulia ; Bortolaia, Valeria ; Vanni, Michele ; Intorre, Luigi ; Guardabassi, Luca ; Piccirillo, Alessandra
in: Veterinary Microbiology, vol: 216, pages: 93-98

Type: Journal article (Peer reviewed)

Status: Published | Year: 2018 | DOI: https://doi.org/10.1016/j.vetmic.2018.02.012

Direct whole-genome sequencing of Plasmodium falciparum specimens from dried erythrocyte spots

Nag, Sidsel ; Kofoed, Poul Erik ; Ursing, Johan ; Lemvigh, Camilla Koldbæk ; Allesøe, Rosa Lundbye ; Rodrigues, Amabelia ; Svendsen, Christina Aaby ; Jensen, Jacob Dyring ; Alifrangis, Michael ; Lund, Ole ; Møller Aarestrup, Frank
in: Malaria Journal, vol: 17, issue: 1

Type: Journal article (Peer reviewed)

Status: Published | Year: 2018 | DOI: https://doi.org/10.1186/s12936-018-2232-6

Prevalence and risk factors for CTX-M gram-negative bacteria in hospitalized patients at a tertiary care hospital in Kilimanjaro, Tanzania

Sonda, Tolbert ; Kumburu, Happiness ; van Zwetselaar, Marco ; Alifrangis, Michael ; Mmbaga, Blandina T. ; Lund, Ole ; Møller Aarestrup, Frank ; Kibiki, Gibson
in: European Journal of Clinical Microbiology and Infectious Diseases, vol: 37, issue: 5, pages: 897-906

Type: Journal article (Peer reviewed)

Status: Published | Year: 2018 | DOI: https://doi.org/10.1007/s10096-018-3196-8

Multiplex PCR for detection of plasmid-mediated colistin resistance determinants, mcr-1, mcr-2, mcr-3, mcr-4 and mcr-5 for surveillance purposes

Rebelo, Ana Rita ; Bortolaia, Valeria ; Kjeldgaard, Jette S. ; Karlsmose Pedersen, Susanne ; Leekitcharoenphon, Pimlapas ; Hansen, Inge M. ; Guerra, Beatriz ; Malorny, Burkhard ; Borowiak, Maria ; Hammerl, Jens Andre ; Battisti, Antonio ; Franco, Alessia ; Alba, Patricia ; Perrin-Guyomard, Agnes ; Granier, Sophie A. ; de Frutos, Cristina ; Escobar, ; Malhotra-Kumar, Surbhi ; Villa, Laura ; Carattoli, Alessandra ; Hendriksen, Rene S.
in: Eurosurveillance, vol: 23, issue: 6

Type: Journal article (Peer reviewed)

Status: Published | Year: 2018 | DOI: https://doi.org/10.2807/1560-7917.ES.2018.23.6.17-00672

Accurate genotyping across variant classes and lengths using variant graphs

Sibbesen, Jonas Andreas ; Maretty, Lasse ; Jensen, Jacob Malte ; Petersen, Bent ; Liu, Siyang ; Villesen, Palle ; Skov, Laurits ; Belling, Kirstine ; Theil Have, Christian ; Gonzalez-Izarzugaza, Jose Maria ; Grosjean, Marie ; Bork-Jensen, Jette ; Grove, Jakob ; Dam-Als, Thomas ; Huang, Shujia ; Chang, Yuqi ; Xu, Ruiqi ; Ye, Weijian ; Rao, Junhua ; Guo, Xiaosen ; Sun, Jihua ; Cao, Hongzhi ; Ye, Chen ; van Beusekom, Johan ; Espeseth, Thomas ; Flindt, Esben ; Friborg, Rune M. ; Halager, Anders Egerup ; Le Hellard, Stephanie ; Hultman, Christina M. ; Lescai, Francesco ; Li, Shengting ; Lund, Ole ; Løngren, Peter ; Mailund, Thomas ; Matey-Hernandez, María Luisa ; Mors, Ole ; Pedersen, Christian N. S. ; Sicheritz-Pontén, Thomas ; Sullivan, Patrick ; Ali , Syed ; Westergaard, David ; Yadav, Rachita ; Li, Ning ; Xu, Xun ; Hansen, Torben ; Krogh, Anders ; Bolund, Lars ; Sørensen, Thorkild I. A. ; Pedersen, Oluf ; Gupta, Ramneek ; Rasmussen, Simon ; Besenbacher, Søren ; Børglum, Anders D. ; Wang, Jun ; Eiberg, Hans ; Kristiansen, Karsten ; Brunak, Søren ; Schierup, Mikkel Heide
in: Nature Genetics

Type: Journal article (Peer reviewed)

Status: Published | Year: 2018 | DOI: https://doi.org/10.1038/s41588-018-0145-5

A culture-independent method for studying transfer of IncI1 plasmids from wild-type Escherichia coli in complex microbial communities

Anjum, Mehreen ; Madsen, Jonas Stenløkke ; Espinosa-Gongora, Carmen ; Jana, Bimal ; Wiese, Maria ; Nielsen, Dennis Sandris ; Sørensen, Søren Johannes ; Moodley, Arshnee ; Bortolaia, Valeria ; Guardabassi, Luca
in: Journal of Microbiological Methods, vol: 152, pages: 18-26

Type: Journal article (Peer reviewed)

Status: Published | Year: 2018 | DOI: https://doi.org/10.1016/j.mimet.2018.07.009

AnOxPe-pred: Using deep learning for the prediction of antioxidative properties of peptides.

Olsen, Tobias Hegelund ; Pertseva, Margarita ; García Moreno, Pedro Jesús ; Jacobsen, Charlotte ; Lund, Ole ; Hansen, Egon Bech ; Marcatili, Paolo
part of: Sustain Conference 2018, 2018, Technical University of Denmark (DTU), Lyngby, Denmark
Presented at: Sustain conference 2018: Creating Technology for a Sustainable Society

Type: Conference abstract in proceedings (Peer reviewed)

Status: Published | Year: 2018

Antibody Cross-Reactivity in Antivenom Research

Ledsgaard, Line ; Jenkins, Timothy P ; Davidsen, Kristian ; Krause, Kamille Elvstrøm ; Martos-Esteban, Andrea ; Engmark, Mikael ; Andersen, Mikael Rørdam ; Lund, Ole ; Laustsen, Andreas Hougaard
in: Toxins, vol: 10, issue: 10

Type: Journal article (Peer reviewed)

Status: Published | Year: 2018 | DOI: https://doi.org/10.3390/toxins10100393

Benchmarking the HLA typing performance of Polysolver and Optitype in 50 Danish parental trios

Matey-Hernandez, María Luisa ; Maretty, Lasse ; Jensen, Jacob Malte ; Petersen, Bent ; Andreas Sibbesen, Jonas ; Liu, Siyang ; Villesen, Palle ; Skov, Laurits ; Belling, Kirstine ; Theil Have, Christian ; Gonzalez-Izarzugaza, Jose Maria ; Grosjean, Marie ; Bork-Jensen, Jette ; Grove, Jakob ; Als, Thomas D. ; Huang, Shujia ; Chang, Yuqi ; Xu, Ruiqi ; Ye, Weijian ; Rao, Junhua ; Guo, Xiaosen ; Sun, Jihua ; Cao, Hongzhi ; Ye, Chen ; Beusekom, Johan v. ; Espeseth, Thomas ; Flindt, Esben N. ; Friborg, Rune M. ; Halager, Anders Egerup ; Le Hellard, Stephanie ; Hultman, Christina M. ; Lescai, Francesco ; Li, Shengting ; Lund, Ole ; Løngren, Peter ; Mailund, Thomas ; Mors, Ole ; Pedersen, Christian N. S. ; Sicheritz-Pontén, Thomas ; Sullivan, Patrick F. ; Ali , Syed ; Westergaard, David ; Yadav, Rachita ; Li, Ning ; Xu, Xun ; Hansen, Torben ; Krogh, Anders ; Bolund, Lars ; Sørensen, Thorkild I. A. ; Pedersen, Oluf ; Gupta, Ramneek ; Besenbacher, Søren ; Børglum, Anders D. ; Wang, Jun ; Eiberg, Hans ; Kristiansen, Karsten ; Brunak, Søren ; Schierup, Mikkel Heide ; Izarzugaza, Jose M. G.
in: B M C Bioinformatics, vol: 19

Type: Journal article (Peer reviewed)

Status: Published | Year: 2018 | DOI: https://doi.org/10.1186/s12859-018-2239-6

Cephalosporin-resistant Escherichia coli isolated from farm-workers and pigs in northern Vietnam

Dang, Son T T ; Bortolaia, Valeria ; Thi, Nhat T ; Quang, Huan L ; Dalsgaard, Anders
in: Tropical Medicine & International Health, vol: 23, issue: 4, pages: 415-424

Type: Journal article (Peer reviewed)

Status: Published | Year: 2018 | DOI: https://doi.org/10.1111/tmi.13054

CHTyper, a Web Tool for Subtyping of Extraintestinal Pathogenic Escherichia coli based on the fumC and fimH Alleles

Roer, Louise ; Johannesen, Thor Bech ; Hansen, Frank ; Stegger, Marc ; Tchesnokova, Veronika ; Sokurenko, Evgeni ; Garibay, Natasha ; Allesøe, Rosa Lundbye ; Thomsen, Martin C. F. ; Lund, Ole ; Hasman, Henrik ; Hammerum, Anette M.
in: Journal of Clinical Microbiology, vol: 56, issue: 4

Type: Journal article (Peer reviewed)

Status: Published | Year: 2018 | DOI: https://doi.org/10.1128/JCM.00063-18