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

Van Gompel L, Luiken REC, Sarrazin S, Munk P, Knudsen BE, Hansen RB, Bossers A, Aarestrup FM, Dewulf J, Wagenaar JA, Mevius DJ, Schmitt H, Heederik DJJ, Dorado-García A, Smit LAM; EFFORT consortium .

J Antimicrob Chemother. 2019 Jan 14. doi: 10.1093/jac/dky518. [Epub ahead of print]


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

Hjelmsø MH, Mollerup S, Jensen RH, Pietroni C, Lukjancenko O, Schultz AC, Aarestrup FM, Hansen AJ.

PLoS One. 2019 Jan 14;14(1):e0210368. doi: 10.1371/journal.pone.0210368. eCollection 2019.



Bertges LC, Dibai FN, Bezerra G, Oliveira ES, Aarestrup FM, Bertges KR.

Arq Gastroenterol. 2018 Jul-Sep;55(3):212-215. doi: 10.1590/S0004-2803.201800000-56.


Drivers and Dynamics of Methicillin-Resistant Livestock-Associated Staphylococcus aureus CC398 in Pigs and Humans in Denmark.

Sieber RN, Skov RL, Nielsen J, Schulz J, Price LB, Aarestrup FM, Larsen AR, Stegger M, Larsen J.

MBio. 2018 Nov 13;9(6). pii: e02142-18. doi: 10.1128/mBio.02142-18.


Brazilian experience with atopy patch tests for Dermatophagoides pteronyssinus, Dermatophagoides farinae and Blomia tropicalis.

Souza Lima IPCM, Aarestrup BJ, Souza Lima EM, Souza Lima MC, Souza Lima EC, Aarestrup FM.

World Allergy Organ J. 2018 Oct 24;11(1):27. doi: 10.1186/s40413-018-0206-3. eCollection 2018.


The Role of Outer Membrane Proteins and Lipopolysaccharides for the Sensitivity of Escherichia coli to Antimicrobial Peptides.

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

Front Microbiol. 2018 Sep 7;9:2153. doi: 10.3389/fmicb.2018.02153. eCollection 2018.


Proficiency of WHO Global Foodborne Infections Network External Quality Assurance System Participants in Identification and Susceptibility Testing of Thermotolerant Campylobacter spp. from 2003 to 2012.

Pedersen SK, Wagenaar JA, Vigre H, Roer L, Mikoleit M, Aidara-Kane A, Cawthorne AL, Aarestrup FM, Hendriksen RS.

J Clin Microbiol. 2018 Oct 25;56(11). pii: e01066-18. doi: 10.1128/JCM.01066-18. Print 2018 Nov.


Rapid and precise alignment of raw reads against redundant databases with KMA.

Clausen PTLC, Aarestrup FM, Lund O.

BMC Bioinformatics. 2018 Aug 29;19(1):307. doi: 10.1186/s12859-018-2336-6.


Author Correction: Abundance and diversity of the faecal resistome in slaughter pigs and broilers in nine European countries.

Munk P, Knudsen BE, Lukjancenko O, Duarte ASR, Van Gompel L, Luiken REC, Smit LAM, Schmitt H, Garcia AD, Hansen RB, Petersen TN, Bossers A, Ruppé E, Lund O, Hald T, Pamp SJ, Vigre H, Heederik D, Wagenaar JA, Mevius D, Aarestrup FM; EFFORT Group.

Nat Microbiol. 2018 Oct;3(10):1186. doi: 10.1038/s41564-018-0241-4.


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

Munk P, Knudsen BE, Lukjancenko O, Duarte ASR, Van Gompel L, Luiken REC, Smit LAM, Schmitt H, Garcia AD, Hansen RB, Petersen TN, Bossers A, Ruppé E; EFFORT Group, Lund O, Hald T, Pamp SJ, Vigre H, Heederik D, Wagenaar JA, Mevius D, Aarestrup FM.

Nat Microbiol. 2018 Aug;3(8):898-908. doi: 10.1038/s41564-018-0192-9. Epub 2018 Jul 23. Erratum in: Nat Microbiol. 2018 Oct;3(10):1186.


Molecular epidemiology of virulence and antimicrobial resistance determinants in Klebsiella pneumoniae from hospitalised patients in Kilimanjaro, Tanzania.

Sonda T, Kumburu H, van Zwetselaar M, Alifrangis M, Mmbaga BT, Lund O, Kibiki GS, Aarestrup FM.

Eur J Clin Microbiol Infect Dis. 2018 Oct;37(10):1901-1914. doi: 10.1007/s10096-018-3324-5. Epub 2018 Jul 20.


Pemphigus Vulgaris in the Mouth and Esophageal Mucosa.

de Macedo AG, Bertges ER, Bertges LC, Mendes RA, Bertges TABS, Bertges KR, Aarestrup FM.

Case Rep Gastroenterol. 2018 Jun 15;12(2):260-265. doi: 10.1159/000489299. eCollection 2018 May-Aug.


Whole genome sequencing reveals high clonal diversity of Escherichia coli isolated from patients in a tertiary care hospital in Moshi, Tanzania.

Sonda T, Kumburu H, van Zwetselaar M, Alifrangis M, Mmbaga BT, Aarestrup FM, Kibiki G, Lund O.

Antimicrob Resist Infect Control. 2018 Jun 8;7:72. doi: 10.1186/s13756-018-0361-x. eCollection 2018.


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.


Does Knowing Someone with Breast Cancer Influence the Prevalence of Adherence to Breast and Cervical Cancer Screening?

Brum IV, Rodrigues TCGF, Laporte EGJ, Aarestrup FM, Vitral GSF, Laporte BEP.

Rev Bras Ginecol Obstet. 2018 Apr;40(4):203-208. doi: 10.1055/s-0038-1623512. Epub 2018 Apr 2.


Genomics-Based Identification of Microorganisms in Human Ocular Body Fluid.

Kirstahler P, Bjerrum SS, Friis-Møller A, la Cour M, Aarestrup FM, Westh H, Pamp SJ.

Sci Rep. 2018 Mar 7;8(1):4126. doi: 10.1038/s41598-018-22416-4.


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

Kumburu HH, Sonda T, Leekitcharoenphon P, van Zwetselaar M, Lukjancenko O, Alifrangis M, Lund O, Mmbaga BT, Kibiki G, Aarestrup FM.

Biomed Res Int. 2018 Jan 2;2018:2087693. doi: 10.1155/2018/2087693. eCollection 2018.


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

Nag S, Kofoed PE, Ursing J, Lemvigh CK, Allesøe RL, Rodrigues A, Svendsen CA, Jensen JD, Alifrangis M, Lund O, Aarestrup FM.

Malar J. 2018 Feb 23;17(1):91. doi: 10.1186/s12936-018-2232-6.


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.


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

Sonda T, Kumburu H, van Zwetselaar M, Alifrangis M, Mmbaga BT, Lund O, Aarestrup FM, Kibiki G.

Eur J Clin Microbiol Infect Dis. 2018 May;37(5):897-906. doi: 10.1007/s10096-018-3196-8. Epub 2018 Feb 20.


Validation of the register-based lifetime antimicrobial usage measurement for finisher batches based on comparison with recorded antimicrobial usage at farm level.

Andersen VD, Munk P, de Knegt LV, Jensen MS, Aarestrup FM, Vigre H.

Epidemiol Infect. 2018 Mar;146(4):515-523. doi: 10.1017/S0950268818000134. Epub 2018 Feb 7.


Punctuated 88% Phenol Peeling for the Treatment of Facial Photoaging: A Clinical and Histopathological Study.

de Mendonça MCC, Segheto NN, Aarestrup FM, Aarestrup BJV.

Dermatol Surg. 2018 Feb;44(2):241-247. doi: 10.1097/DSS.0000000000001357.


Epidemiology of Danish Aeromonas salmonicida subsp. salmonicida in Fish Farms Using Whole Genome Sequencing.

Bartkova S, Leekitcharoenphon P, Aarestrup FM, Dalsgaard I.

Front Microbiol. 2017 Dec 5;8:2411. doi: 10.3389/fmicb.2017.02411. eCollection 2017.


An Assessment of Different Genomic Approaches for Inferring Phylogeny of Listeria monocytogenes.

Henri C, Leekitcharoenphon P, Carleton HA, Radomski N, Kaas RS, Mariet JF, Felten A, Aarestrup FM, Gerner Smidt P, Roussel S, Guillier L, Mistou MY, Hendriksen RS.

Front Microbiol. 2017 Nov 29;8:2351. doi: 10.3389/fmicb.2017.02351. eCollection 2017.


PointFinder: a novel web tool for WGS-based detection of antimicrobial resistance associated with chromosomal point mutations in bacterial pathogens.

Zankari E, Allesøe R, Joensen KG, Cavaco LM, Lund O, Aarestrup FM.

J Antimicrob Chemother. 2017 Oct 1;72(10):2764-2768. doi: 10.1093/jac/dkx217.


Developing a framework to assess the costeffectiveness of COMPARE - a global platform for the exchange of sequence-based pathogen data.

Alleweldt F, Kara S, Osinski A, Van Baal P, Kellerborg K, Aarestrup FM, Koopmans M.

Rev Sci Tech. 2017 Apr;36(1):311-322. doi: 10.20506/rst.36.1.2631. Review.


The association between measurements of antimicrobial use and resistance in the faeces microbiota of finisher batches.

Andersen VD, DE Knegt LV, Munk P, Jensen MS, Agersø Y, Aarestrup FM, Vigre H.

Epidemiol Infect. 2017 Oct;145(13):2827-2837. doi: 10.1017/S0950268817001285. Epub 2017 Jun 27.


Emergence of Livestock-Associated Methicillin-Resistant Staphylococcus aureus Bloodstream Infections in Denmark.

Larsen J, Petersen A, Larsen AR, Sieber RN, Stegger M, Koch A, Aarestrup FM, Price LB, Skov RL; Danish MRSA Study Group .

Clin Infect Dis. 2017 Oct 1;65(7):1072-1076. doi: 10.1093/cid/cix504.


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.


Erratum to: Evaluating next-generation sequencing for direct clinical diagnostics in diarrhoeal disease.

Joensen KG, Engsbro ALØ, Lukjancenko O, Kaas RS, Lund O, Westh H, Aarestrup FM.

Eur J Clin Microbiol Infect Dis. 2017 Jul;36(7):1339-1342. doi: 10.1007/s10096-017-2993-9. No abstract available.


β-Caryophyllene ameliorates the development of experimental autoimmune encephalomyelitis in C57BL/6 mice.

Fontes LBA, Dias DDS, Aarestrup BJV, Aarestrup FM, Da Silva Filho AA, Corrêa JODA.

Biomed Pharmacother. 2017 Jul;91:257-264. doi: 10.1016/j.biopha.2017.04.092. Epub 2017 May 2.


Perioperative Anaphylaxis to Chlorhexidine during Surgery and Septoplasty.

Teixeira de Abreu AP, Ribeiro de Oliveira LR, Teixeira de Abreu AF, Ribeiro de Oliveira E, Santos de Melo Ireno M, Aarestrup FM, Aarestrup MF, Aarestrup PF.

Case Rep Otolaryngol. 2017;2017:9605804. doi: 10.1155/2017/9605804. Epub 2017 Mar 19.


Evaluating next-generation sequencing for direct clinical diagnostics in diarrhoeal disease.

Joensen KG, Engsbro ALØ, Lukjancenko O, Kaas RS, Lund O, Westh H, Aarestrup FM.

Eur J Clin Microbiol Infect Dis. 2017 Jul;36(7):1325-1338. doi: 10.1007/s10096-017-2947-2. Epub 2017 Mar 11. Erratum in: Eur J Clin Microbiol Infect Dis. 2017 May 9;:.


Commentary: Benefits and risks of antimicrobial use in food-producing animals.

Schlundt J, Aarestrup FM.

Front Microbiol. 2017 Feb 7;8:181. doi: 10.3389/fmicb.2017.00181. eCollection 2017. No abstract available.


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.


Characterization and Genetic Variation of Vibrio cholerae Isolated from Clinical and Environmental Sources in Thailand.

Siriphap A, Leekitcharoenphon P, Kaas RS, Theethakaew C, Aarestrup FM, Sutheinkul O, Hendriksen RS.

PLoS One. 2017 Jan 19;12(1):e0169324. doi: 10.1371/journal.pone.0169324. eCollection 2017.


Evaluation of Methods for the Concentration and Extraction of Viruses from Sewage in the Context of Metagenomic Sequencing.

Hjelmsø MH, Hellmér M, Fernandez-Cassi X, Timoneda N, Lukjancenko O, Seidel M, Elsässer D, Aarestrup FM, Löfström C, Bofill-Mas S, Abril JF, Girones R, Schultz AC.

PLoS One. 2017 Jan 18;12(1):e0170199. doi: 10.1371/journal.pone.0170199. eCollection 2017.


Patterns of infections, aetiological agents and antimicrobial resistance at a tertiary care hospital in northern Tanzania.

Kumburu HH, Sonda T, Mmbaga BT, Alifrangis M, Lund O, Kibiki G, Aarestrup FM.

Trop Med Int Health. 2017 Apr;22(4):454-464. doi: 10.1111/tmi.12836. Epub 2017 Feb 3.


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.


Detection of linezolid resistance due to the optrA gene in Enterococcus faecalis from poultry meat from the American continent (Colombia).

Cavaco LM, Bernal JF, Zankari E, Léon M, Hendriksen RS, Perez-Gutierrez E, Aarestrup FM, Donado-Godoy P.

J Antimicrob Chemother. 2017 Mar 1;72(3):678-683. doi: 10.1093/jac/dkw490.


The role of whole genome sequencing in antimicrobial susceptibility testing of bacteria: report from the EUCAST Subcommittee.

Ellington MJ, Ekelund O, Aarestrup FM, Canton R, Doumith M, Giske C, Grundman H, Hasman H, Holden MTG, Hopkins KL, Iredell J, Kahlmeter G, Köser CU, MacGowan A, Mevius D, Mulvey M, Naas T, Peto T, Rolain JM, Samuelsen Ø, Woodford N.

Clin Microbiol Infect. 2017 Jan;23(1):2-22. doi: 10.1016/j.cmi.2016.11.012. Epub 2016 Nov 23. Review.


Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition.

Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM, Pamp SJ.

mSystems. 2016 Oct 18;1(5). pii: e00095-16. eCollection 2016 Sep-Oct.


Is the Evolution of Salmonella enterica subsp. enterica Linked to Restriction-Modification Systems?

Roer L, Hendriksen RS, Leekitcharoenphon P, Lukjancenko O, Kaas RS, Hasman H, Aarestrup FM.

mSystems. 2016 Jun 21;1(3). pii: e00009-16. eCollection 2016 May-Jun.


Adhesion of Escherichia coli under flow conditions reveals potential novel effects of FimH mutations.

Feenstra T, Thøgersen MS, Wieser E, Peschel A, Ball MJ, Brandes R, Satchell SC, Stockner T, Aarestrup FM, Rees AJ, Kain R.

Eur J Clin Microbiol Infect Dis. 2017 Mar;36(3):467-478. doi: 10.1007/s10096-016-2820-8. Epub 2016 Nov 5.


Benchmarking of methods for identification of antimicrobial resistance genes in bacterial whole genome data.

Clausen PT, Zankari E, Aarestrup FM, Lund O.

J Antimicrob Chemother. 2016 Sep;71(9):2484-8. doi: 10.1093/jac/dkw184. Epub 2016 Jun 30.


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.


Fraction of exhaled nitric oxide measurements in the diagnoses of asthma in elderly patients.

Godinho Netto AC, Dos Reis TG, Matheus CF, Aarestrup BJ, Aarestrup FM.

Clin Interv Aging. 2016 May 12;11:623-9. doi: 10.2147/CIA.S94741. eCollection 2016.


Population Genetic Structure of Listeria monocytogenes Strains as Determined by Pulsed-Field Gel Electrophoresis and Multilocus Sequence Typing.

Henri C, Félix B, Guillier L, Leekitcharoenphon P, Michelon D, Mariet JF, Aarestrup FM, Mistou MY, Hendriksen RS, Roussel S.

Appl Environ Microbiol. 2016 Aug 30;82(18):5720-8. doi: 10.1128/AEM.00583-16. Print 2016 Sep 15.


Investigating Salmonella Eko from Various Sources in Nigeria by Whole Genome Sequencing to Identify the Source of Human Infections.

Leekitcharoenphon P, Raufu I, Nielsen MT, Rosenqvist Lund BS, Ameh JA, Ambali AG, Sørensen G, Le Hello S, Aarestrup FM, Hendriksen RS.

PLoS One. 2016 May 26;11(5):e0156212. doi: 10.1371/journal.pone.0156212. eCollection 2016.


The Lake Chad Basin, an Isolated and Persistent Reservoir of Vibrio cholerae O1: A Genomic Insight into the Outbreak in Cameroon, 2010.

Kaas RS, Ngandjio A, Nzouankeu A, Siriphap A, Fonkoua MC, Aarestrup FM, Hendriksen RS.

PLoS One. 2016 May 18;11(5):e0155691. doi: 10.1371/journal.pone.0155691. eCollection 2016.

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