Publications from the Genomic Epidemiology Research Group

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

Type: Journal article (Peer reviewed)

Status: Accepted/In press | Year: 2019 | DOI: https://doi.org/10.1093/nar/gky1073

Whole grain-rich diet reduces body weight and systemic low-grade inflammation without inducing major changes of the gut microbiome: a randomised cross-over trial

Roager, Henrik Munch ; Vogt, Josef Korbinian ; Kristensen, Mette ; Hansen, Lea Benedicte S ; Ibrügger, Sabine ; Mærkedahl, Rasmus B ; Bahl, Martin Iain ; Lind, Mads Vendelbo ; Nielsen, Rikke Linnemann ; Frøkiær, Hanne ; Gøbel, Rikke Juul ; Landberg, Rikard ; Ross, Alastair B ; Brix, Susanne ; Holck, Jesper ; Meyer, Anne S. ; Sparholt, Morten H ; Christensen, Anders F ; Carvalho, Vera ; Holst, Jens Juul ; Rumessen, Jüri Johannes ; Linneberg, Allan ; Sicheritz-Pontén, Thomas ; Dalgaard, Marlene Danner ; Blennow, Andreas ; Frandsen, Henrik Lauritz ; Villas-Bôas, Silas Granato ; Kristiansen, Karsten ; Vestergaard, Henrik ; Hansen, Torben ; Ekstrøm, Claus T ; Ritz, Christian ; Nielsen, Henrik Bjørn ; Pedersen, Oluf Borbye ; Gupta, Ramneek ; Lauritzen, Lotte ; Licht, Tine Rask
in: Gut, vol: 68, issue: 1, pages: 83-93

Type: Journal article (Peer reviewed)

Status: Published | Year: 2019 | DOI: https://doi.org/10.1136/gutjnl-2017-314786

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

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

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

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

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

Colistin Resistance Mediated by mcr-1 in ESBL-Producing, Multidrug Resistant Salmonella Infantis in Broiler Chicken Industry, Italy (2016-2017)

Carfora, Virginia ; Alba, Patricia ; Leekitcharoenphon, Pimlapas ; Ballaro, Daniele ; Cordaro, Gessica ; Di Matteo, Paola ; Donati, Valentina ; Ianzano, Angela ; Iurescia, Manuela ; Stravino, Fiorentino ; Tagliaferri, Tania ; Battisti, Antonio ; Franco, Alessia
in: Frontiers in Microbiology, vol: 9

Type: Journal article (Peer reviewed)

Status: Published | Year: 2018 | DOI: https://doi.org/10.3389/fmicb.2018.01880

Comparative genomics of quinolone‐resistant and susceptible Campylobacter jejuni of poultry origin from major poultry producing European countries (GENCAMP)

Leekitcharoenphon, Pimlapas ; Garcia‐Graells, Cristina ; Botteldoorn, Nadine ; Dierick, Katelijne ; Kempf, Isabelle ; Olkkola, Satu ; Rossi, Mirko ; Nykäsenoja, Suvi ; Malorny, Burkhard ; Stingl, Kerstin ; Battisti, Antonio ; Franco, Alessia ; Mossong, Joël ; Veldman, Kees ; Mevius, Dik ; Wasyl, Dariusz ; Wieczorek, Kinga ; Osek, Jacek ; Clemente, Lurdes ; Lacatus, Angela ; Nicorescu, Isabela ; García, Monserrat Agüero ; Escobar, Cristina De Frutos ; Ferrer, Manuel Duran ; Ugarte‐Ruiz, María ; Anjum, Muna F ; Teale, Christopher ; Ågren, Joakim ; Hendriksen, Rene S. ; Aarestrup, Frank Møller
in: EFSA Supporting Publications, vol: 15, issue: 5

Type: Journal article (Peer reviewed)

Status: Published | Year: 2018 | DOI: https://doi.org/10.2903/sp.efsa.2018.EN-1398

Comparative genomics of Vibrio cholerae O1 isolated from cholera patients in Bangladesh

Hossain, Zenat Zebin ; Leekitcharoenphon, Pimlapas ; Dalsgaard, Anders ; Sultana, Rokaia ; Begum, Anowara ; Jensen, Peter Kjær Mackie ; Hendriksen, Rene S.
in: Letters in Applied Microbiology, vol: 67, issue: 4, pages: 329-336

Type: Journal article (Peer reviewed)

Status: Published | Year: 2018 | DOI: https://doi.org/10.1111/lam.13046

Corrigendum: Colistin Resistance Mediated by mcr-1 in ESBL-Producing, Multidrug Resistant Salmonella Infantis in Broiler Chicken Industry, Italy (2016-2017)

Carfora, Virginia ; Alba, Patricia ; Leekitcharoenphon, Pimlapas ; Ballaro, Daniele ; Cordaro, Gessica ; Di Matteo, Paola ; Donati, Valentina ; Ianzano, Angela ; Iurescia, Manuela ; Stravino, Fiorentino ; Tagliaferri, Tania ; Battisti, Antonio ; Franco, Alessia
in: Frontiers in Microbiology, vol: 9

Type: Journal article (Peer reviewed)

Status: Published | Year: 2018 | DOI: https://doi.org/10.3389/fmicb.2018.02395

DANMAP 2017 - Use of antimicrobial agents and occurrence of antimicrobial resistance in bacteria from food animals, food and humans in Denmark

Borck Høg, Birgitte ; Bager, Flemming ; Korsgaard, Helle Bisgaard ; Ellis-Iversen, Johanne ; Pedersen, Karl ; Jensen, Lars Bogø ; Hendriksen, Rene S. ; Bortolaia, Valeria ; Rhod Larsen, Anders ; Petersen, Andreas ; Hammerich, Anette M. ; Nielsen, Eva Møller ; Slotved, Hans-Christian ; Hasman, Henrik ; Boel, Jeppe ; Skov Jensen, Jørgen ; Skjold Selle Pedersen, Karoline ; Roer, Louise ; Torpdahl, Mia ; Skovgaard, Sissel ; Hoffmann, Steen ; Schytte Olsen, Stefan ; Dalby, Tine ; Wolff Sönksen, Ute ; Vorobieva, Veronika

Type: Report

Status: Published | Year: 2018

Draft Genome Sequence of Salmonella enterica subsp. enterica Serotype Typhimurium Sequence Type 313, Isolated from India

Bangera, Sohan Rodney ; Umakanth, Shashikiran ; Mukhopadhyay, Asish K. ; Leekitcharoenphon, Pimlapas ; Chowdhury, Goutam ; Hendriksen, Rene S. ; Ballal, Mamatha
in: Microbiology Resource Announcements, vol: 7, issue: 8

Type: Journal article (Peer reviewed)

Status: Published | Year: 2018 | DOI: https://doi.org/10.1128/MRA.00990-18

Final report of ENGAGE ‐ Establishing Next Generation sequencing Ability for Genomic analysis in Europe

Hendriksen, Rene S. ; Karlsmose Pedersen, Susanne ; Leekitcharoenphon, Pimlapas ; Malorny, Burkhard ; Borowiak, Maria ; Battisti, Antonio ; Franco, Alessia ; Alba, Patricia ; Carfora, Virginia ; Ricci, Antonia ; Mastrorilli, Eleonora ; Losasso, Carmen ; Longo, Alessandra ; Petrin, Sara ; Barco, Lisa ; Wołkowicz, Tomasz ; Gierczyński, Rafał ; Zacharczuk, Katarzyna ; Wolaniuk, Natalia ; Wasyl, Dariusz ; Zajac, Magdalena ; Wieczorek, Kinga ; Pόłtorak, Katarzyna ; Petrovska‐Holmes, Liljana ; Davies, Rob ; Tang, Yue ; Grant, Kathie ; Underwood, Anthony ; Dallman, Timothy ; Painset, Anaïs ; Hartman, Hassan ; Al‐Shabib, Ali ; Cowley, Lauren
in: EFSA Supporting Publications, vol: 15, issue: 6

Type: Journal article (Peer reviewed)

Status: Published | Year: 2018 | DOI: https://doi.org/10.2903/sp.efsa.2018.EN-1431

Hospital Epidemiology of Methicillin-Resistant Staphylococcus aureus in a Tertiary Care Hospital in Moshi, Tanzania, as Determined by Whole Genome Sequencing

Kumburu, Happiness H. ; Sonda, Tolbert ; Leekitcharoenphon, Pimlapas ; van Zwetselaar, Marco ; Lukjancenko, Oksana ; Alifrangis, Michael ; Lund, Ole ; Mmbaga, Blandina T. ; Kibiki, Gibson ; Aarestrup, Frank Møller
in: Journal of Biomedicine and Biotechnology, vol: 2018

Type: Journal article (Peer reviewed)

Status: Published | Year: 2018 | DOI: https://doi.org/10.1155/2018/2087693

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

Type: Journal article (Peer reviewed)

Status: Accepted/In press | Year: 2018 | DOI: https://doi.org/10.1111/risa.13239

Molecular Epidemiology of mcr-Encoded Colistin Resistance in Enterobacteriaceae From Food-Producing Animals in Italy Revealed Through the EU Harmonized Antimicrobial Resistance Monitoring

Alba, Patricia ; Leekitcharoenphon, Pimlapas ; Franco, Alessia ; Feltrin, Fabiola ; Ianzano, Angela ; Caprioli, Andrea ; Stravino, Fiorentino ; Hendriksen, Rene S. ; Bortolaia, Valeria ; Battisti, Antonio
in: Frontiers in Microbiology, vol: 9

Type: Journal article (Peer reviewed)

Status: Published | Year: 2018 | DOI: https://doi.org/10.3389/fmicb.2018.01217

Pathology and bacteria related to digital dermatitis in dairy cattle in all year round grazing system in Brazil

Moreira, Tiago F. ; Facury Filho, Elias J. ; Carvalho, Antônio U. ; Strube, Mikael L. ; Nielsen, Martin W. ; Klitgaard, Kirstine ; Jensen, Tim K. ; te Pas, Marinus F. W. (Editor)
in: P L o S One, vol: 13, issue: 3

Type: Journal article (Peer reviewed)

Status: Published | Year: 2018 | DOI: https://doi.org/10.1371/journal.pone.0193870

Phenotypic and genotypic comparison of salmonellae from diarrhoeic and healthy humans and cattle, Nigeria

Fashae, K. ; Leekitcharoenphon, Pimlapas ; Hendriksen, Rene S.
in: Zoonoses and Public Health, vol: 65, issue: 1, pages: e185-e195

Type: Review (Peer reviewed)

Status: Published | Year: 2018 | DOI: https://doi.org/10.1111/zph.12427

Presence of extended-spectrum cephalosporin (ESC) resistance Escherichia coli in two Danish poultry slaughterhouses

Jensen, Lars Bogø ; Birk, Tina ; Hendriksen, Rene S. ; Leekitcharoenphon, Pimlapas ; Ortved, Gitte ; Lundsby, Katrine ; Jørgensen, Bettina ; Aabo, Søren
part of: The Danish Microbiological Society Annual Congress 2018 - programme & abstracts, pages: 78-78, 2018, Danish Microbiological Society, Copenhagen, Denmark
Presented at: The Danish Microbiological Society Annual Congress 2018

Type: Conference abstract in proceedings (Peer reviewed)

Status: Published | Year: 2018

Source Attribution and Risk Assessment of Antimicrobial Resistance

Pires, Sara Monteiro ; Riberio Duarte, Ana Sofia ; Hald, Tine
in: Microbiology Spectrum, vol: 6, issue: 3

Type: Journal article (Peer reviewed)

Status: Published | Year: 2018 | DOI: https://doi.org/10.1128/microbiolspec.ARBA-0027-2017

Source Attribution and Risk Assessment of Antimicrobial Resistance

Pires, Sara Monteiro ; Ribeiro Duarte, Ana Sofia ; Hald, Tine
part of: Antimicrobial Resistance in Bacteria from Livestock and Companion Animals, pages: 619-635, 2018, ASM Press, Washington, DC

Type: Book chapter (Peer reviewed)

Status: Published | Year: 2018 | DOI: https://doi.org/10.1128/microbiolspec.ARBA-0027-2017

Streptococcus sanguinis and Streptococcus gordonii: virulence factors in the pan and core-genomes of clinical strains isolated from patients with infective endocarditis

Iversen, Katrine Højholt ; Hesselbjerg Rasmussen, Louise ; Jensen, Christian Salgård ; Chen Nielsen, Xiaohui ; Rasmussen, Simon ; Dargis, Rimtas ; Justesen, Ulrik Stenz ; Lukjancenko, Oksana ; Moser, Claus Ernst ; Christensen, Jens Jørgen
Presented at: 28th European Congress of Clinical Microbiology and Infectious Diseases

Type: Poster

Status: Published | Year: 2018