F M Aarestrup

Affiliations
  • The National Food Institute, Technical University of Denmark, Lyngby, Denmark. Electronic address: fmaa@food.dtu.dk.

Publications (75)

Predicting effects of changed antimicrobial usage on the abundance of antimicrobial resistance genes in finisher' gut microbiomes.

Preventive veterinary medicine
Avec: V D Andersen , F M Aarestrup , P Munk , M S Jensen , L V de Knegt , V Bortolaia , B E Knudsen , O Lukjancenko , A C Birkegård , H Vigre

Metagenomic analysis of viruses in toilet waste from long distance flights-A new procedure for global infectious disease surveillance.

PloS one
Avec: Mathis Hjort Hjelmsø , Sarah Mollerup , Randi Holm Jensen , Carlotta Pietroni , Oksana Lukjancenko , Anna Charlotte Schultz , Frank M Aarestrup , Anders Johannes Hansen

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

mSystems
Avec: D Aytan-Aktug , P T L C Clausen , V Bortolaia , F M Aarestrup , O Lund

Farm dust resistomes and bacterial microbiomes in European poultry and pig farms.

Environment international
Avec: Roosmarijn E C Luiken , Liese Van Gompel , Alex Bossers , Patrick Munk , Philip Joosten , Rasmus Borup Hansen , Berith E Knudsen , Silvia García-Cobos , Jeroen Dewulf , Frank M Aarestrup , Jaap A Wagenaar , Lidwien A M Smit , Dik J Mevius , Dick J J Heederik , Heike Schmitt , Auteur inconnu

ResFinder 4.0 for predictions of phenotypes from genotypes.

The Journal of antimicrobial chemotherapy
Avec: Valeria Bortolaia , Rolf S Kaas , Etienne Ruppe , Marilyn C Roberts , Stefan Schwarz , Vincent Cattoir , Alain Philippon , Rosa L Allesoe , Ana Rita Rebelo , Alfred Ferrer Florensa , Linda Fagelhauer , Trinad Chakraborty , Bernd Neumann , Guido Werner , Jennifer K Bender , Kerstin Stingl , Minh Nguyen , Jasmine Coppens , Basil Britto Xavier , Surbhi Malhotra-Kumar , Henrik Westh , Mette Pinholt , Muna F Anjum , Nicholas A Duggett , Isabelle Kempf , Suvi Nykäsenoja , Satu Olkkola , Kinga Wieczorek , Ana Amaro , Lurdes Clemente , Joël Mossong , Serge Losch , Catherine Ragimbeau , Ole Lund , Frank M Aarestrup

Specific gut microbiome members are associated with distinct immune markers in pediatric allogeneic hematopoietic stem cell transplantation.

Microbiome
Avec: Anna Cäcilia Ingham , Katrine Kielsen , Malene Skovsted Cilieborg , Ole Lund , Susan Holmes , Frank M Aarestrup , Klaus Gottlob Müller , Sünje Johanna Pamp

Pandemics- One Health preparedness for the next.

The Lancet regional health. Europe
Avec: Frank M Aarestrup , Marc Bonten , Marion Koopmans

Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns.

Microbiology spectrum
Avec: Casper Sahl Poulsen , Rolf Sommer Kaas , Frank M Aarestrup , Sünje Johanna Pamp

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

mSystems
Avec: Christian Brinch , Pimlapas Leekitcharoenphon , Ana S R Duarte , Christina A Svendsen , Jacob D Jensen , Frank M Aarestrup

Metagenomics analysis of bacteriophages and antimicrobial resistance from global urban sewage.

Scientific reports
Avec: Josephine E S Strange , Pimlapas Leekitcharoenphon , Frederik Duus Møller , Frank M Aarestrup

Microbiota long-term dynamics and prediction of acute graft-versus-host disease in pediatric allogeneic stem cell transplantation.

Microbiome
Avec: Anna Cäcilia Ingham , Katrine Kielsen , Hanne Mordhorst , Marianne Ifversen , Frank M Aarestrup , Klaus Gottlob Müller , Sünje Johanna Pamp

Evaluating the usefulness of next-generation sequencing for herb authentication.

Food chemistry. Molecular sciences
Avec: Anna Delgado-Tejedor , Pimlapas Leekitcharoenphon , Frank M Aarestrup , Saria Otani

The first complete genome sequence of

Microbiology resource announcements
Avec: Pimlapas Leekitcharoenphon , Saria Otani , Judit Szarvas , Tutu Mzee , Happiness Kumburu , Frederik Duus Møller , Frank M Aarestrup

Routes of dispersion of antibiotic resistance genes from the poultry farm system.

The Science of the total environment
Avec: Daniel Scicchitano , Giulia Babbi , Giorgia Palladino , Silvia Turroni , Yitagele Terefe Mekonnen , Cédric Laczny , Paul Wilmes , Pimlapas Leekitcharoenphon , Andrea Castagnetti , Federica D'Amico , Patrizia Brigidi , Castrense Savojardo , Gerardo Manfreda , Pierluigi Martelli , Alessandra De Cesare , Frank Møller Aarestrup , Marco Candela , Simone Rampelli

Is allergen immunotherapy a model of personalized treatment in pediatric respiratory allergy?

Current opinion in allergy and clinical immunology
Avec: Gustavo Falbo Wandalsen , Fernando Monteiro Aarestrup , Dirceu Solé

Plasmid characterization in bacterial isolates of public health relevance in a tertiary healthcare facility in Kilimanjaro region, Tanzania.

Journal of global antimicrobial resistance
Avec: Lameck Pashet Sengeruan , Marco van Zwetselaar , Happiness Kumburu , Frank M Aarestrup , Katharina Kreppel , Elingarami Sauli , Tolbert Sonda

Distinctive hospital and community resistomes in Scottish urban wastewater: Metagenomics of a paired wastewater sampling design.

The Science of the total environment
Avec: Hannah C Lepper , Meghan R Perry , Bryan A Wee , David Wills , Hanne Nielsen , Saria Otani , Moray Simon , Frank M Aarestrup , Mark E J Woolhouse , Bram A D van Bunnik

Association of health, nutrition, and socioeconomic variables with global antimicrobial resistance: a modelling study.

The Lancet. Planetary health
Avec: Patrick Murigu Kamau Njage , Bram van Bunnik , Patrick Munk , Ana Rita Pinheiro Marques , Frank M Aarestrup

Complete genome sequences of

Microbiology resource announcements
Avec: Judit Szarvas , Sidsel Nag , Saria Otani , Laura Elmlund Kohl Birkedahl , Frederik Duus Møller , Solomon Asante-Sefa , Denise Daley , Natalie Weiler Gustafson , Mie Møller , Anthony Onipede , Silva Tafaj , Frank M Aarestrup

NanoMGT: Marker gene typing of low complexity mono-species metagenomic samples using noisy long reads.

Biology methods & protocols
Avec: Malte B Hallgren , Philip T L C Clausen , Frank M Aarestrup

Monkeypox Clade Ib virus introduction into Burundi: first findings, July to mid-August 2024.

Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin
Avec: Néhémie Nzoyikorera , Cassien Nduwimana , Leonard Schuele , David F Nieuwenhuijse , Marion Koopmans , Saria Otani , Frank M Aarestrup , Théogène Ihorimbere , Denis Niyomwungere , Armstrong Ndihokubwayo , Idrissa Diawara , Alexis Niyomwungere , Dionis Nizigiyimana , Marie Noelle Uwineza , Bas B Oude Munnink , Joseph Nyandwi

Worldwide human mitochondrial haplogroup distribution from urban sewage.

Scientific reports
Avec: Orsolya Anna Pipek , Anna Medgyes-Horváth , László Dobos , József Stéger , János Szalai-Gindl , Dávid Visontai , Rolf S Kaas , Marion Koopmans , Rene S Hendriksen , Frank M Aarestrup , István Csabai

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

The Journal of antimicrobial chemotherapy
Avec: Liese Van Gompel , Roosmarijn E C Luiken , Steven Sarrazin , Patrick Munk , Berith E Knudsen , Rasmus B Hansen , Alex Bossers , Frank M Aarestrup , Jeroen Dewulf , Jaap A Wagenaar , Dik J Mevius , Heike Schmitt , Dick J J Heederik , Alejandro Dorado-García , Lidwien A M Smit , Auteur inconnu

Megaphages infect Prevotella and variants are widespread in gut microbiomes.

Nature microbiology
Avec: Audra E Devoto , Joanne M Santini , Matthew R Olm , Karthik Anantharaman , Patrick Munk , Jenny Tung , Elizabeth A Archie , Peter J Turnbaugh , Kimberley D Seed , Ran Blekhman , Frank M Aarestrup , Brian C Thomas , Jillian F Banfield

Associations between antimicrobial use and the faecal resistome on broiler farms from nine European countries.

The Journal of antimicrobial chemotherapy
Avec: Roosmarijn E C Luiken , Liese Van Gompel , Patrick Munk , Steven Sarrazin , Philip Joosten , Alejandro Dorado-García , Rasmus Borup Hansen , Berith E Knudsen , Alex Bossers , Jaap A Wagenaar , Frank M Aarestrup , Jeroen Dewulf , Dik J Mevius , Dick J J Heederik , Lidwien A M Smit , Heike Schmitt , Auteur inconnu

Salmonella enterica serovar Typhi H58 clone has been endemic in Zimbabwe from 2012 to 2019.

The Journal of antimicrobial chemotherapy
Avec: Tapfumanei Mashe , Pimlapas Leekitcharoenphon , Sekesai Mtapuri-Zinyowera , Robert A Kingsley , V Robertson , Andrew Tarupiwa , Marleen M Kock , Evidence P Makombe , Blessmore V Chaibva , Portia Manangazira , Isaac Phiri , Simon Nyadundu , Chriswell T Chigwena , Last P Mufoya , Gaetan Thilliez , Stanely Midzi , Lusubilo W Mwamakamba , Esther L Hamblion , Jorge Matheu , Jacob D Jensen , Frank M Aarestrup , Rene S Hendriksen , Marthie M Ehlers

Library Preparation and Sequencing Platform Introduce Bias in Metagenomic-Based Characterizations of Microbiomes.

Microbiology spectrum
Avec: Casper S Poulsen , Claus T Ekstrøm , Frank M Aarestrup , Sünje J Pamp

Metagenomic DNA sequencing for semi-quantitative pathogen detection from urine: a prospective, laboratory-based, proof-of-concept study.

The Lancet. Microbe
Avec: Victoria A Janes , Sébastien Matamoros , Patrick Munk , Philip T L C Clausen , Sylvie M Koekkoek , Linda A M Koster , Marja E Jakobs , Bob de Wever , Caroline E Visser , Frank M Aarestrup , Ole Lund , Menno D de Jong , Patrick M M Bossuyt , Daniel R Mende , Constance Schultsz

One Day in Denmark: Comparison of Phenotypic and Genotypic Antimicrobial Susceptibility Testing in Bacterial Isolates From Clinical Settings.

Frontiers in microbiology
Avec: Ana Rita Rebelo , Valeria Bortolaia , Pimlapas Leekitcharoenphon , Dennis Schrøder Hansen , Hans Linde Nielsen , Svend Ellermann-Eriksen , Michael Kemp , Bent Løwe Røder , Niels Frimodt-Møller , Turid Snekloth Søndergaard , John Eugenio Coia , Claus Østergaard , Henrik Westh , Frank M Aarestrup

Global Distribution and Diversity of Prevalent Sewage Water Plasmidomes.

mSystems
Avec: Frederik Teudt , Saria Otani , Frank M Aarestrup

Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance.

Nature communications
Avec: Patrick Munk , Christian Brinch , Frederik Duus Møller , Thomas N Petersen , Rene S Hendriksen , Anne Mette Seyfarth , Jette S Kjeldgaard , Christina Aaby Svendsen , Bram van Bunnik , Fanny Berglund , Auteur inconnu , D G Joakim Larsson , Marion Koopmans , Mark Woolhouse , Frank M Aarestrup

Rise and fall of SARS-CoV-2 variants in Rotterdam: Comparison of wastewater and clinical surveillance.

The Science of the total environment
Avec: Ray W Izquierdo-Lara , Leo Heijnen , Bas B Oude Munnink , Claudia M E Schapendonk , Goffe Elsinga , Jeroen Langeveld , Johan Post , Divyae K Prasad , Christian Carrizosa , Frederic Been , Janko van Beek , Remy Schilperoort , Rianne Vriend , Ewout Fanoy , Evelien I T de Schepper , Reina S Sikkema , Richard Molenkamp , Frank M Aarestrup , Gertjan Medema , Marion P G Koopmans , Miranda de Graaf

Antimicrobial resistance monitoring in the Danish swine production by phenotypic methods and metagenomics from 1999 to 2018.

Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin
Avec: Ana Sofia R Duarte , Ana Rita Marques , Vibe D Andersen , Helle B Korsgaard , Hanne Mordhorst , Frederik D Møller , Thomas N Petersen , Håkan Vigre , Tine Hald , Frank M Aarestrup

The quantitative effect of antimicrobial usage in Danish pig farms on the abundance of antimicrobial resistance genes in slaughter pigs.

Preventive veterinary medicine
Avec: V D Andersen , F D Møller , M S Jensen , F M Aarestrup , H Vigre

Predicting β-lactam susceptibility from the genome of

Frontiers in microbiology
Avec: Helle Brander Eriksen , Kurt Fuursted , Anders Jensen , Christian Salgård Jensen , Xiaohui Nielsen , Jens Jørgen Christensen , Patricia Shewmaker , Ana Rita Rebelo , Frank Møller Aarestrup , Kristian Schønning , Hans-Christian Slotved , Auteur inconnu

Quantitative PCR versus metagenomics for monitoring antibiotic resistance genes: balancing high sensitivity and broad coverage.

FEMS microbes
Avec: Catarina Ferreira , Saria Otani , Frank Møller Aarestrup , Célia M Manaia

The resistomes of rural and urban pigs and poultry in Ghana.

mSystems
Avec: Emilie Egholm Bruun Jensen , Victoria Sedor , Emmanuel Eshun , Patrick Njage , Saria Otani , Frank M Aarestrup

The European livestock resistome.

mSystems
Avec: Patrick Munk , Dongsheng Yang , Timo Röder , Leonie Maier , Thomas Nordahl Petersen , Ana Sofia Ribeiro Duarte , Philip T L C Clausen , Christian Brinch , Liese Van Gompel , Roosmarijn Luiken , Jaap A Wagenaar , Heike Schmitt , Dick J J Heederik , Dik J Mevius , Lidwien A M Smit , Auteur inconnu , Alex Bosser , Frank M Aarestrup

Modelling the effectiveness of surveillance based on metagenomics in detecting, monitoring, and forecasting antimicrobial resistance in livestock production under economic constraints.

Scientific reports
Avec: Ofosuhene O Apenteng , Frank M Aarestrup , Håkan Vigre

Metagenomic analysis of sewage for surveillance of bacterial pathogens: A release experiment to determine sensitivity.

PloS one
Avec: Simon Kohle , Thomas N Petersen , Håkan Vigre , Markus Hans Kristofer Johansson , Frank M Aarestrup

Real-time PCR assay to detect the novel Clade Ib monkeypox virus, September 2023 to May 2024.

Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin
Avec: Leonard Schuele , Leandre Murhula Masirika , Jean Claude Udahemuka , Freddy Belesi Siangoli , Justin Bengehya Mbiribindi , Pacifique Ndishimye , Frank M Aarestrup , Marion Koopmans , Bas B Oude Munnink , Richard Molenkamp , Auteur inconnu , Auteur inconnu

Discovery of Vibrio cholerae in Urban Sewage in Copenhagen, Denmark.

Microbial ecology
Avec: Christian Brinch , Saria Otani , Patrick Munk , Maaike van den Beld , Eelco Franz , Frank M Aarestrup

Economic evaluation of whole genome sequencing for pathogen identification and surveillance - results of case studies in Europe and the Americas 2016 to 2019.

Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin
Avec: Frank Alleweldt , Şenda Kara , Kris Best , Frank M Aarestrup , Martin Beer , Theo M Bestebroer , Josefina Campos , Gabriele Casadei , Isabel Chinen , Gary Van Domselaar , Catherine Dominguez , Helen E Everett , Ron Am Fouchier , Kathie Grant , Jonathan Green , Dirk Höper , Jonathan Johnston , Marion Pg Koopmans , Bas B Oude Munnink , Robert Myers , Celine Nadon , Ami Patel , Anne Pohlmann , Stefano Pongolini , Aleisha Reimer , Shane Thiessen , Claudia Wylezich

Detection of mobile genetic elements associated with antibiotic resistance in Salmonella enterica using a newly developed web tool: MobileElementFinder.

The Journal of antimicrobial chemotherapy
Avec: Markus H K Johansson , Valeria Bortolaia , Supathep Tansirichaiya , Frank M Aarestrup , Adam P Roberts , Thomas N Petersen

Metagenomics-Based Proficiency Test of Smoked Salmon Spiked with a Mock Community.

Microorganisms
Avec: Claudia Sala , Hanne Mordhorst , Josephine Grützke , Annika Brinkmann , Thomas N Petersen , Casper Poulsen , Paul D Cotter , Fiona Crispie , Richard J Ellis , Gastone Castellani , Clara Amid , Mikhayil Hakhverdyan , Soizick Le Guyader , Gerardo Manfreda , Jöel Mossong , Andreas Nitsche , Catherine Ragimbeau , Julien Schaeffer , Joergen Schlundt , Moon Y F Tay , Frank M Aarestrup , Rene S Hendriksen , Sünje Johanna Pamp , Alessandra De Cesare

A metagenomic glimpse into the gut of wild and domestic animals: Quantification of antimicrobial resistance and more.

PloS one
Avec: Magdalena Skarżyńska , Pimlapas Leekitcharoenphon , Rene S Hendriksen , Frank M Aarestrup , Dariusz Wasyl

Monitoring SARS-CoV-2 Circulation and Diversity through Community Wastewater Sequencing, the Netherlands and Belgium.

Emerging infectious diseases
Avec: Ray Izquierdo-Lara , Goffe Elsinga , Leo Heijnen , Bas B Oude Munnink , Claudia M E Schapendonk , David Nieuwenhuijse , Matthijs Kon , Lu Lu , Frank M Aarestrup , Samantha Lycett , Gertjan Medema , Marion P G Koopmans , Miranda de Graaf

Pathogen surveillance in the informal settlement, Kibera, Kenya, using a metagenomics approach.

PloS one
Avec: Rene S Hendriksen , Oksana Lukjancenko , Patrick Munk , Mathis H Hjelmsø , Jennifer R Verani , Eric Ng'eno , Godfrey Bigogo , Samuel Kiplangat , Traoré Oumar , Lasse Bergmark , Timo Röder , John C Neatherlin , Onyango Clayton , Tine Hald , Susanne Karlsmose , Sünje J Pamp , Barry Fields , Joel M Montgomery , Frank M Aarestrup

Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage.

Nature communications
Avec: Rene S Hendriksen , Patrick Munk , Patrick Njage , Bram van Bunnik , Luke McNally , Oksana Lukjancenko , Timo Röder , David Nieuwenhuijse , Susanne Karlsmose Pedersen , Jette Kjeldgaard , Rolf S Kaas , Philip Thomas Lanken Conradsen Clausen , Josef Korbinian Vogt , Pimlapas Leekitcharoenphon , Milou G M van de Schans , Tina Zuidema , Ana Maria de Roda Husman , Simon Rasmussen , Bent Petersen , Auteur inconnu , Clara Amid , Guy Cochrane , Thomas Sicheritz-Ponten , Heike Schmitt , Jorge Raul Matheu Alvarez , Awa Aidara-Kane , Sünje J Pamp , Ole Lund , Tine Hald , Mark Woolhouse , Marion P Koopmans , Håkan Vigre , Thomas Nordahl Petersen , Frank M Aarestrup

Improved Resistance Prediction in

Frontiers in microbiology
Avec: Camilla Hundahl Johnsen , Philip T L C Clausen , Frank M Aarestrup , Ole Lund

Setting a baseline for global urban virome surveillance in sewage.

Scientific reports
Avec: David F Nieuwenhuijse , Bas B Oude Munnink , My V T Phan , Auteur inconnu , Patrick Munk , Shweta Venkatakrishnan , Frank M Aarestrup , Matthew Cotten , Marion P G Koopmans

Description and determinants of the faecal resistome and microbiome of farmers and slaughterhouse workers: A metagenome-wide cross-sectional study.

Environment international
Avec: Liese Van Gompel , Roosmarijn E C Luiken , Rasmus B Hansen , Patrick Munk , Martijn Bouwknegt , Lourens Heres , Gerdit D Greve , Peter Scherpenisse , Betty G M Jongerius-Gortemaker , Monique H G Tersteeg-Zijderveld , Silvia García-Cobos , Wietske Dohmen , Alejandro Dorado-García , Jaap A Wagenaar , Bert A P Urlings , Frank M Aarestrup , Dik J Mevius , Dick J J Heederik , Heike Schmitt , Alex Bossers , Lidwien A M Smit

Accelerating surveillance and research of antimicrobial resistance - an online repository for sharing of antimicrobial susceptibility data associated with whole-genome sequences.

Microbial genomics
Avec: Sébastien Matamoros , Rene S Hendriksen , Bálint Ármin Pataki , Nima Pakseresht , Marc Rossello , Nicole Silvester , Clara Amid , Frank M Aarestrup , Marion Koopmans , Guy Cochrane , Istvan Csabai , Ole Lund , Constance Schultsz , The Compare Ml-Amr Group

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

Communications biology
Avec: Derick N M Osakunor , Patrick Munk , Takafira Mduluza , Thomas N Petersen , Christian Brinch , Alasdair Ivens , Theresa Chimponda , Seth A Amanfo , Janice Murray , Mark E J Woolhouse , Frank M Aarestrup , Francisca Mutapi

Prophylaxis of Upper Airway Infections in a Patient with Partial IgA Deficiency: Concurrent Use of Sublingual Immunotherapy with Inactivated Whole-Cell Bacterial Extract and Der p1.

Case reports in otolaryngology
Avec: Paula F Aarestrup , Matheus F Aarestrup , Beatriz J V Aarestrup , Fernando M Aarestrup

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

Scientific reports
Avec: Johanne Ahrenfeldt , Madina Waisi , Isabella C Loft , Philip T L C Clausen , Rosa Allesøe , Judit Szarvas , Rene S Hendriksen , Frank M Aarestrup , Ole Lund

Arrangements of Mobile Genetic Elements among Virotype E Subpopulation of

mSphere
Avec: Omid Pajand , Hamzeh Rahimi , Narges Darabi , Solaleh Roudi , Khatereh Ghassemi , Frank M Aarestrup , Pimlapas Leekitcharoenphon

Genomic evolution of antimicrobial resistance in Escherichia coli.

Scientific reports
Avec: Pimlapas Leekitcharoenphon , Markus Hans Kristofer Johansson , Patrick Munk , Burkhard Malorny , Magdalena Skarżyńska , Katharina Wadepohl , Gabriel Moyano , Ayla Hesp , Kees T Veldman , Alex Bossers , Auteur inconnu , Magdalena Zając , Dariusz Wasyl , Pascal Sanders , Bruno Gonzalez-Zorn , Michael S M Brouwer , Jaap A Wagenaar , Dick J J Heederik , Dik Mevius , Frank M Aarestrup

One Day in Denmark: Nationwide point-prevalence survey of human bacterial isolates and comparison of classical and whole-genome sequence-based species identification methods.

PloS one
Avec: Ana Rita Rebelo , Tobias Ibfelt , Valeria Bortolaia , Pimlapas Leekitcharoenphon , Dennis Schrøder Hansen , Hans Linde Nielsen , Svend Ellermann-Eriksen , Michael Kemp , Bent Løwe Røder , Niels Frimodt-Møller , Turid Snekloth Søndergaard , John Eugenio Coia , Claus Østergaard , Michael Pedersen , Henrik Westh , Frank Møller Aarestrup

ResFinder - an open online resource for identification of antimicrobial resistance genes in next-generation sequencing data and prediction of phenotypes from genotypes.

Microbial genomics
Avec: Alfred Ferrer Florensa , Rolf Sommer Kaas , Philip Thomas Lanken Conradsen Clausen , Derya Aytan-Aktug , Frank M Aarestrup

PlasmidHostFinder: Prediction of Plasmid Hosts Using Random Forest.

mSystems
Avec: Derya Aytan-Aktug , Philip T L C Clausen , Judit Szarvas , Patrick Munk , Saria Otani , Marcus Nguyen , James J Davis , Ole Lund , Frank M Aarestrup

Foodborne Pathogen Dynamics in Meat and Meat Analogues Analysed Using Traditional Microbiology and Metagenomic Sequencing.

Antibiotics (Basel, Switzerland)
Avec: Francesco Bonaldo , Baptiste Jacques Philippe Avot , Alessandra De Cesare , Frank M Aarestrup , Saria Otani

SpanSeq: similarity-based sequence data splitting method for improved development and assessment of deep learning projects.

NAR genomics and bioinformatics
Avec: Alfred Ferrer Florensa , Jose Juan Almagro Armenteros , Henrik Nielsen , Frank Møller Aarestrup , Philip Thomas Lanken Conradsen Clausen

A global phylogenomic and metabolic reconstruction of the large intestine bacterial community of domesticated cattle.

Microbiome
Avec: S Teseo , S Otani , C Brinch , S Leroy , P Ruiz , M Desvaux , E Forano , F M Aarestrup , P Sapountzis

Urticaria exacerbations and adverse reactions in patients with chronic urticaria receiving COVID-19 vaccination: Results of the UCARE COVAC-CU study.

The Journal of allergy and clinical immunology
Avec: Emek Kocatürk , Pascale Salameh , Esra Sarac , Carolina E Vera Ayala , Simon Francis Thomsen , Torsten Zuberbier , Luis Felipe Ensina , Todor A Popov , Martijn B A van Doorn , Ana Maria Giménez-Arnau , Riccardo Asero , Paulo Ricardo Criado , Fernando M Aarestrup , Zainab AbdulHameed Ansari , Salma Al Abri , Mona Al-Ahmad , Bushra Al Hinai , Anastasiia Allenova , Maryam Al-Nesf , Sabine Altrichter , Rand Arnaout , Joanna Bartosińska , Andrea Bauer , Jonathan A Bernstein , Mojca Bizjak , Hanna Bonnekoh , Laurence Bouillet , Zenon Brzoza , Ana Caroline Calvalcanti Dela Bianca Melo , Fernanda L Campinhos , Emily Carne , Saleema Cherichi Purayil , Ivan Cherrez-Ojeda , Herberto Jose Chong-Neto , George Christoff , Niall Conlon , Roberta Fachini Jardim Criado , Klara Cvenkel , Ebru Damadoglu , Inna Danilycheva , Cascia Day , Laurence de Montjoye , Semra Demir , Silvia Mariel Ferucci , Daria Fomina , Atsushi Fukunaga , Elizabeth Garcia , Asli Gelincik , Joe Hannah Göbel , Kiran Godse , Margarida Gonçalo , Maia Gotua , Clive Grattan , Agata Gugala , Carole Guillet , Ali Fuat Kalyoncu , Gul Karakaya , Alicja Kasperska-Zając , Constance H Katelaris , Maryam Khoshkhui , Andreas Kleinheinz , Marta Kolacinska-Flont , Pavel Kolkhir , Mitja Košnik , Dorota Krasowska , Muthu Sendhil Kumaran , Izabela Kuprys-Lipinska , Marcin Kurowski , Elizaveta V Kuznetsova , Désirée Larenas-Linnemann , Marina S Lebedkina , Youngsoo Lee , Michael Makris , René Maximiliano Gómez , Iman Nasr , Sophia Neisinger , Yoshiko Oda , Rabia Öztaş Kara , Esther Bastos Palitot , Niki Papapostolou , Claudio Alberto Salvador Parisi , David Pesque , Jonathan Peter , Elena Petkova , Katie Ridge , Michael Rudenko , Krzysztof Rutkowski , Sarbjit S Saini , Andac Salman , Jorge Sanchez , Bülent Şekerel , Sofia A Serdotetskova , Faradiba S Serpa , Bahar Sevimli Dikicier , Nikitas Sidiropoulos , Agnieszka Sikora , Jennifer Astrup Sørensen , Angele Soria , Ozlem Su Kucuk , Sherin Rahim Thalappil , Katarzyna Tomaszewska , Gulseren Tuncay , Derya Unal , Solange Valle , Esmee van Lindonk , Christian Vestergaard , Raisa Y Meshkova , Aleksandr Vitchuk , Paraskevi Xepapadaki , Young-Min Ye , Anna Zalewska-Janowska , Mateusz Zamlynski , Marcus Maurer

Global within-species phylogenetics of sewage microbes suggest that local adaptation shapes geographical bacterial clustering.

Communications biology
Avec: Marie Louise Jespersen , Patrick Munk , Joachim Johansen , Rolf Sommer Kaas , Henry Webel , Håkan Vigre , Henrik Bjørn Nielsen , Simon Rasmussen , Frank M Aarestrup

Importance of mobile genetic elements for dissemination of antimicrobial resistance in metagenomic sewage samples across the world.

PloS one
Avec: Markus H K Johansson , Frank M Aarestrup , Thomas N Petersen

Trends in Salmonella Dublin over time in Denmark from food and animal related isolates.

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases
Avec: Pimlapas Leekitcharoenphon , Håkan Vigre , Rolf Sommer Kaas , Frank M Aarestrup

Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses.

Microbial genomics
Avec: Nadim Rahman , Colman O'Cathail , Ahmad Zyoud , Alexey Sokolov , Bas Oude Munnink , Björn Grüning , Carla Cummins , Clara Amid , David F Nieuwenhuijse , Dávid Visontai , David Yu Yuan , Dipayan Gupta , Divyae K Prasad , Gábor Máté Gulyás , Gabriele Rinck , Jasmine McKinnon , Jeena Rajan , Jeff Knaggs , Jeffrey Edward Skiby , József Stéger , Judit Szarvas , Khadim Gueye , Krisztián Papp , Maarten Hoek , Manish Kumar , Marianna A Ventouratou , Marie-Catherine Bouquieaux , Martin Koliba , Milena Mansurova , Muhammad Haseeb , Nathalie Worp , Peter W Harrison , Rasko Leinonen , Ross Thorne , Sandeep Selvakumar , Sarah Hunt , Sundar Venkataraman , Suran Jayathilaka , Timothée Cezard , Wolfgang Maier , Zahra Waheed , Zamin Iqbal , Frank Møller Aarestrup , Istvan Csabai , Marion Koopmans , Tony Burdett , Guy Cochrane

V Brazilian Consensus on Rhinitis - 2024.

Brazilian journal of otorhinolaryngology
Avec: Dirceu Solé , Fábio Chigres Kuschnir , Antônio Carlos Pastorino , Clóvis F Constantino , Clóvis Galvão , Débora Carla Chong E Silva , Eduardo Baptistella , Ekaterini Simões Goudouris , Eulália Sakano , Fábio Ejzenbaum , Fausto Yoshio Matsumoto , Flavio Massao Mizoguchi , Fernando Monteiro Aarestrup , Gustavo F Wandalsen , Herberto José Chong Neto , João Vianney Brito de Oliveira , José Faibes Lubianca Neto , Maria Cândida V Rizzo , Maria Letícia Freitas Silva Chavarria , Marilyn Urrutia-Pereira , Nelson Augusto Rosário Filho , Norma de Paula Motta Rubini , Olavo Mion , Otávio Bejzman Piltcher , Regina Terse Ramos , Renata Di Francesco , Renato Roithmann , Wilma Terezinha Anselmo-Lima , Fabrizio Ricci Romano , João Ferreira de Mello Júnior

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

Communications biology
Avec: Judit Szarvas , Johanne Ahrenfeldt , Jose Luis Bellod Cisneros , Martin Christen Frølund Thomsen , Frank M Aarestrup , Ole Lund

Towards a European health research and innovation cloud (HRIC).

Genome medicine
Avec: F M Aarestrup , A Albeyatti , W J Armitage , C Auffray , L Augello , R Balling , N Benhabiles , G Bertolini , J G Bjaalie , M Black , N Blomberg , P Bogaert , M Bubak , B Claerhout , L Clarke , B De Meulder , G D'Errico , A Di Meglio , N Forgo , C Gans-Combe , A E Gray , I Gut , A Gyllenberg , G Hemmrich-Stanisak , L Hjorth , Y Ioannidis , S Jarmalaite , A Kel , F Kherif , J O Korbel , C Larue , M Laszlo , A Maas , L Magalhaes , I Manneh-Vangramberen , E Morley-Fletcher , C Ohmann , P Oksvold , N P Oxtoby , I Perseil , V Pezoulas , O Riess , H Riper , J Roca , P Rosenstiel , P Sabatier , F Sanz , M Tayeb , G Thomassen , J Van Bussel , M Van den Bulcke , H Van Oyen

Copaiba oil suppresses inflammation in asthmatic lungs of BALB/c mice induced with ovalbumin.

International immunopharmacology
Avec: Ludmila S Caputo , Maria Inês C Campos , Herbert J Dias , Antônio E M Crotti , Júlia B Fajardo , Chislene P Vanelli , Álvaro C D Presto , Maria S Alves , Fernando M Aarestrup , Ana Claudia C Paula , Ademar A Da Silva Filho , Beatriz J V Aarestrup , Olavo S Pereira , José Otávio do A Corrêa

Ceftriaxone use in a tertiary care hospital in Kilimanjaro, Tanzania: A need for a hospital antibiotic stewardship programme.

PloS one
Avec: Tolbert B Sonda , Pius G Horumpende , Happiness H Kumburu , Marco van Zwetselaar , Stephen E Mshana , Michael Alifrangis , Ole Lund , Frank M Aarestrup , Jaffu O Chilongola , Blandina T Mmbaga , Gibson S Kibiki

Proof of concept: used malaria rapid diagnostic tests applied for parallel sequencing for surveillance of molecular markers of anti-malarial resistance in Bissau, Guinea-Bissau during 2014-2017.

Malaria journal
Avec: Sidsel Nag , Johan Ursing , Amabelia Rodrigues , Marina Crespo , Camilla Krogsgaard , Ole Lund , Frank M Aarestrup , Michael Alifrangis , PouL-Erik Kofoed

Réseau de co-auteurs

Frank M Aarestrup 59 collaborations
Patrick Munk 17 collaborations
Pimlapas Leekitcharoenphon 13 collaborations
None None 11 collaborations
Ole Lund 11 collaborations
Saria Otani 11 collaborations
Rene S Hendriksen 9 collaborations
Marion Koopmans 7 collaborations
Thomas N Petersen 7 collaborations
Jaap A Wagenaar 6 collaborations
Dick J J Heederik 6 collaborations
Heike Schmitt 6 collaborations
Judit Szarvas 6 collaborations
Frank Møller Aarestrup 6 collaborations
Philip T L C Clausen 6 collaborations
Bas B Oude Munnink 6 collaborations
Håkan Vigre 6 collaborations
Liese Van Gompel 5 collaborations
Alex Bossers 5 collaborations
Lidwien A M Smit 5 collaborations
Dik J Mevius 5 collaborations
Christian Brinch 5 collaborations
Roosmarijn E C Luiken 4 collaborations
Valeria Bortolaia 4 collaborations
Ana Rita Rebelo 4 collaborations
Sünje Johanna Pamp 4 collaborations
Rolf Sommer Kaas 4 collaborations
Frederik Duus Møller 4 collaborations
Clara Amid 4 collaborations
Oksana Lukjancenko 3 collaborations
Berith E Knudsen 3 collaborations
Jeroen Dewulf 3 collaborations
Rolf S Kaas 3 collaborations
Alfred Ferrer Florensa 3 collaborations
Henrik Westh 3 collaborations
Hanne Mordhorst 3 collaborations
Alessandra De Cesare 3 collaborations
Bram van Bunnik 3 collaborations
David F Nieuwenhuijse 3 collaborations
Alejandro Dorado-García 3 collaborations
Sünje J Pamp 3 collaborations
Marion P G Koopmans 3 collaborations
Tine Hald 3 collaborations
Timo Röder 3 collaborations
Philip Thomas Lanken Conradsen Clausen 3 collaborations
Guy Cochrane 3 collaborations
Fernando M Aarestrup 3 collaborations
V D Andersen 2 collaborations
M S Jensen 2 collaborations
V Bortolaia 2 collaborations
H Vigre 2 collaborations
Philip Joosten 2 collaborations
Rasmus Borup Hansen 2 collaborations
Silvia García-Cobos 2 collaborations
Catherine Ragimbeau 2 collaborations
Anna Cäcilia Ingham 2 collaborations
Katrine Kielsen 2 collaborations
Klaus Gottlob Müller 2 collaborations
Jacob D Jensen 2 collaborations
Happiness Kumburu 2 collaborations
Gerardo Manfreda 2 collaborations
Fernando Monteiro Aarestrup 2 collaborations
Dirceu Solé 2 collaborations
Marco van Zwetselaar 2 collaborations
Mark E J Woolhouse 2 collaborations
Sidsel Nag 2 collaborations
Leonard Schuele 2 collaborations
József Stéger 2 collaborations
Dávid Visontai 2 collaborations
Steven Sarrazin 2 collaborations
Rasmus B Hansen 2 collaborations
Sébastien Matamoros 2 collaborations
Constance Schultsz 2 collaborations
Dennis Schrøder Hansen 2 collaborations
Hans Linde Nielsen 2 collaborations
Svend Ellermann-Eriksen 2 collaborations
Michael Kemp 2 collaborations
Bent Løwe Røder 2 collaborations
Niels Frimodt-Møller 2 collaborations
Turid Snekloth Søndergaard 2 collaborations
John Eugenio Coia 2 collaborations
Claus Østergaard 2 collaborations
Mark Woolhouse 2 collaborations
Leo Heijnen 2 collaborations
Claudia M E Schapendonk 2 collaborations
Goffe Elsinga 2 collaborations
Divyae K Prasad 2 collaborations
Richard Molenkamp 2 collaborations
Gertjan Medema 2 collaborations
Miranda de Graaf 2 collaborations
Patrick Njage 2 collaborations
Thomas Nordahl Petersen 2 collaborations
Markus Hans Kristofer Johansson 2 collaborations
Markus H K Johansson 2 collaborations
Magdalena Skarżyńska 2 collaborations
Dariusz Wasyl 2 collaborations
David Nieuwenhuijse 2 collaborations
Simon Rasmussen 2 collaborations
Istvan Csabai 2 collaborations
Beatriz J V Aarestrup 2 collaborations
Johanne Ahrenfeldt 2 collaborations
Derya Aytan-Aktug 2 collaborations
Michael Alifrangis 2 collaborations
P Munk 1 collaboration
L V de Knegt 1 collaboration
B E Knudsen 1 collaboration
O Lukjancenko 1 collaboration
A C Birkegård 1 collaboration
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Sarah Mollerup 1 collaboration
Randi Holm Jensen 1 collaboration
Carlotta Pietroni 1 collaboration
Anna Charlotte Schultz 1 collaboration
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D Aytan-Aktug 1 collaboration
P T L C Clausen 1 collaboration
O Lund 1 collaboration
Etienne Ruppe 1 collaboration
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Stefan Schwarz 1 collaboration
Vincent Cattoir 1 collaboration
Alain Philippon 1 collaboration
Rosa L Allesoe 1 collaboration
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Bernd Neumann 1 collaboration
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