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Host Resistance, Genomics and Population Dynamics in a Salmonella Enteritidis and Phage System.

Holguín AV, Cárdenas P, Prada-Peñaranda C, Rabelo Leite L, Buitrago C, Clavijo V, Oliveira G, Leekitcharoenphon P, Møller Aarestrup F, Vives MJ.

Viruses. 2019 Feb 22;11(2). pii: E188. doi: 10.3390/v11020188.


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

Ebbensgaard A, Mordhorst H, Overgaard MT, Aarestrup FM, Hansen EB.

PLoS One. 2018 May 31;13(5):e0197742. doi: 10.1371/journal.pone.0197742. eCollection 2018.


SCCmecFinder, a Web-Based Tool for Typing of Staphylococcal Cassette Chromosome mec in Staphylococcus aureus Using Whole-Genome Sequence Data.

Kaya H, Hasman H, Larsen J, Stegger M, Johannesen TB, Allesøe RL, Lemvigh CK, Aarestrup FM, Lund O, Larsen AR.

mSphere. 2018 Feb 14;3(1). pii: e00612-17. doi: 10.1128/mSphere.00612-17. eCollection 2018 Jan-Feb.


Correction: MGmapper: Reference based mapping and taxonomy annotation of metagenomics sequence reads.

Petersen TN, Lukjancenko O, Thomsen MCF, Maddalena Sperotto M, Lund O, Møller Aarestrup F, Sicheritz-Pontén T.

PLoS One. 2017 Jun 12;12(6):e0179778. doi: 10.1371/journal.pone.0179778. eCollection 2017.


High throughput resistance profiling of Plasmodium falciparum infections based on custom dual indexing and Illumina next generation sequencing-technology.

Nag S, Dalgaard MD, Kofoed PE, Ursing J, Crespo M, Andersen LO, Aarestrup FM, Lund O, Alifrangis M.

Sci Rep. 2017 May 25;7(1):2398. doi: 10.1038/s41598-017-02724-x.


MGmapper: Reference based mapping and taxonomy annotation of metagenomics sequence reads.

Petersen TN, Lukjancenko O, Thomsen MCF, Maddalena Sperotto M, Lund O, Møller Aarestrup F, Sicheritz-Pontén T.

PLoS One. 2017 May 3;12(5):e0176469. doi: 10.1371/journal.pone.0176469. eCollection 2017. Erratum in: PLoS One. 2017 Jun 12;12 (6):e0179778.


A sampling and metagenomic sequencing-based methodology for monitoring antimicrobial resistance in swine herds.

Munk P, Andersen VD, de Knegt L, Jensen MS, Knudsen BE, Lukjancenko O, Mordhorst H, Clasen J, Agersø Y, Folkesson A, Pamp SJ, Vigre H, Aarestrup FM.

J Antimicrob Chemother. 2017 Feb;72(2):385-392. doi: 10.1093/jac/dkw415. Epub 2016 Nov 8.


Bacterial whole genome-based phylogeny: construction of a new benchmarking dataset and assessment of some existing methods.

Ahrenfeldt J, Skaarup C, Hasman H, Pedersen AG, Aarestrup FM, Lund O.

BMC Genomics. 2017 Jan 5;18(1):19. doi: 10.1186/s12864-016-3407-6.


A Bacterial Analysis Platform: An Integrated System for Analysing Bacterial Whole Genome Sequencing Data for Clinical Diagnostics and Surveillance.

Thomsen MC, Ahrenfeldt J, Cisneros JL, Jurtz V, Larsen MV, Hasman H, Aarestrup FM, Lund O.

PLoS One. 2016 Jun 21;11(6):e0157718. doi: 10.1371/journal.pone.0157718. eCollection 2016.


Fatal Septicemia Linked to Transmission of MRSA Clonal Complex 398 in Hospital and Nursing Home, Denmark.

Nielsen RT, Kemp M, Holm A, Skov MN, Detlefsen M, Hasman H, Aarestrup FM, Kaas RS, Nielsen JB, Westh H, Kolmos HJ.

Emerg Infect Dis. 2016 May;22(5):900-2. doi: 10.3201/eid2205.151835.


Consolidating and Exploring Antibiotic Resistance Gene Data Resources.

Xavier BB, Das AJ, Cochrane G, De Ganck S, Kumar-Singh S, Aarestrup FM, Goossens H, Malhotra-Kumar S.

J Clin Microbiol. 2016 Apr;54(4):851-9. doi: 10.1128/JCM.02717-15. Epub 2016 Jan 27. Review.


Comparative Evaluation of the Antimicrobial Activity of Different Antimicrobial Peptides against a Range of Pathogenic Bacteria.

Ebbensgaard A, Mordhorst H, Overgaard MT, Nielsen CG, Aarestrup FM, Hansen EB.

PLoS One. 2015 Dec 11;10(12):e0144611. doi: 10.1371/journal.pone.0144611. eCollection 2015.


Biocide Susceptibility of Staphylococcus aureus CC398 and CC30 Isolates from Pigs and Identification of the Biocide Resistance Genes, qacG and qacC.

Seier-Petersen MA, Nielsen LN, Ingmer H, Aarestrup FM, Agersø Y.

Microb Drug Resist. 2015 Oct;21(5):527-36. doi: 10.1089/mdr.2014.0215. Epub 2015 Jun 1.


Identification of a Pseudomonas aeruginosa co-producing NDM-1, VIM-5 and VIM-6 metallo-β-lactamases in Denmark using whole-genome sequencing.

Wang M, Borris L, Aarestrup FM, Hasman H.

Int J Antimicrob Agents. 2015 Mar;45(3):324-5. doi: 10.1016/j.ijantimicag.2014.11.004. Epub 2014 Dec 5. No abstract available.


[Pasteurella multocida septicaemia and pneumonia after chemotherapy in a patient who had no known contact with animals].

Jensen MB, Schumacher H, Hasman H, Aarestrup FM.

Ugeskr Laeger. 2014 Dec 15;176(25A). pii: V01130015. Danish.


In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing.

Carattoli A, Zankari E, García-Fernández A, Voldby Larsen M, Lund O, Villa L, Møller Aarestrup F, Hasman H.

Antimicrob Agents Chemother. 2014 Jul;58(7):3895-903. doi: 10.1128/AAC.02412-14. Epub 2014 Apr 28.


PathogenFinder--distinguishing friend from foe using bacterial whole genome sequence data.

Cosentino S, Voldby Larsen M, Møller Aarestrup F, Lund O.

PLoS One. 2013 Oct 28;8(10):e77302. doi: 10.1371/journal.pone.0077302. eCollection 2013. Erratum in: PLoS One. 2013;8(12). doi:10.1371/annotation/b84e1af7-c127-45c3-be22-76abd977600f.


Expansion of a plasmid classification system for Gram-positive bacteria and determination of the diversity of plasmids in Staphylococcus aureus strains of human, animal, and food origins.

Lozano C, García-Migura L, Aspiroz C, Zarazaga M, Torres C, Aarestrup FM.

Appl Environ Microbiol. 2012 Aug;78(16):5948-55. doi: 10.1128/AEM.00870-12. Epub 2012 Jun 8.


In silico prediction of human pathogenicity in the γ-proteobacteria.

Andreatta M, Nielsen M, Møller Aarestrup F, Lund O.

PLoS One. 2010 Oct 27;5(10):e13680. doi: 10.1371/journal.pone.0013680.


Decreased susceptibility to zinc chloride is associated with methicillin resistant Staphylococcus aureus CC398 in Danish swine.

Aarestrup FM, Cavaco L, Hasman H.

Vet Microbiol. 2010 May 19;142(3-4):455-7. doi: 10.1016/j.vetmic.2009.10.021. Epub 2009 Oct 31.


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