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Items: 1 to 50 of 359

1.

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

Ingham AC, Kielsen K, Cilieborg MS, Lund O, Holmes S, Aarestrup FM, Müller KG, Pamp SJ.

Microbiome. 2019 Sep 13;7(1):131. doi: 10.1186/s40168-019-0745-z.

2.

Worldwide human mitochondrial haplogroup distribution from urban sewage.

Pipek OA, Medgyes-Horváth A, Dobos L, Stéger J, Szalai-Gindl J, Visontai D, Kaas RS, Koopmans M, Hendriksen RS, Aarestrup FM, Csabai I.

Sci Rep. 2019 Aug 12;9(1):11624. doi: 10.1038/s41598-019-48093-5.

3.

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

Sonda TB, Horumpende PG, Kumburu HH, van Zwetselaar M, Mshana SE, Alifrangis M, Lund O, Aarestrup FM, Chilongola JO, Mmbaga BT, Kibiki GS.

PLoS One. 2019 Aug 5;14(8):e0220261. doi: 10.1371/journal.pone.0220261. eCollection 2019.

4.

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.

Nag S, Ursing J, Rodrigues A, Crespo M, Krogsgaard C, Lund O, Aarestrup FM, Alifrangis M, Kofoed PE.

Malar J. 2019 Jul 26;18(1):252. doi: 10.1186/s12936-019-2894-8.

5.

Global phylogeography and ancient evolution of the widespread human gut virus crAssphage.

Edwards RA, Vega AA, Norman HM, Ohaeri M, Levi K, Dinsdale EA, Cinek O, Aziz RK, McNair K, Barr JJ, Bibby K, Brouns SJJ, Cazares A, de Jonge PA, Desnues C, Díaz Muñoz SL, Fineran PC, Kurilshikov A, Lavigne R, Mazankova K, McCarthy DT, Nobrega FL, Reyes Muñoz A, Tapia G, Trefault N, Tyakht AV, Vinuesa P, Wagemans J, Zhernakova A, Aarestrup FM, Ahmadov G, Alassaf A, Anton J, Asangba A, Billings EK, Cantu VA, Carlton JM, Cazares D, Cho GS, Condeff T, Cortés P, Cranfield M, Cuevas DA, De la Iglesia R, Decewicz P, Doane MP, Dominy NJ, Dziewit L, Elwasila BM, Eren AM, Franz C, Fu J, Garcia-Aljaro C, Ghedin E, Gulino KM, Haggerty JM, Head SR, Hendriksen RS, Hill C, Hyöty H, Ilina EN, Irwin MT, Jeffries TC, Jofre J, Junge RE, Kelley ST, Khan Mirzaei M, Kowalewski M, Kumaresan D, Leigh SR, Lipson D, Lisitsyna ES, Llagostera M, Maritz JM, Marr LC, McCann A, Molshanski-Mor S, Monteiro S, Moreira-Grez B, Morris M, Mugisha L, Muniesa M, Neve H, Nguyen NP, Nigro OD, Nilsson AS, O'Connell T, Odeh R, Oliver A, Piuri M, Prussin Ii AJ, Qimron U, Quan ZX, Rainetova P, Ramírez-Rojas A, Raya R, Reasor K, Rice GAO, Rossi A, Santos R, Shimashita J, Stachler EN, Stene LC, Strain R, Stumpf R, Torres PJ, Twaddle A, Ugochi Ibekwe M, Villagra N, Wandro S, White B, Whiteley A, Whiteson KL, Wijmenga C, Zambrano MM, Zschach H, Dutilh BE.

Nat Microbiol. 2019 Oct;4(10):1727-1736. doi: 10.1038/s41564-019-0494-6. Epub 2019 Jul 8.

PMID:
31285584
6.

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

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

J Antimicrob Chemother. 2019 Sep 1;74(9):2596-2604. doi: 10.1093/jac/dkz235.

PMID:
31199864
7.

Proficiency Testing of Virus Diagnostics Based on Bioinformatics Analysis of Simulated In Silico High-Throughput Sequencing Data Sets.

Brinkmann A, Andrusch A, Belka A, Wylezich C, Höper D, Pohlmann A, Nordahl Petersen T, Lucas P, Blanchard Y, Papa A, Melidou A, Oude Munnink BB, Matthijnssens J, Deboutte W, Ellis RJ, Hansmann F, Baumgärtner W, van der Vries E, Osterhaus A, Camma C, Mangone I, Lorusso A, Marcacci M, Nunes A, Pinto M, Borges V, Kroneman A, Schmitz D, Corman VM, Drosten C, Jones TC, Hendriksen RS, Aarestrup FM, Koopmans M, Beer M, Nitsche A.

J Clin Microbiol. 2019 Jul 26;57(8). pii: e00466-19. doi: 10.1128/JCM.00466-19. Print 2019 Aug.

8.

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

Hendriksen RS, Munk P, Njage P, van Bunnik B, McNally L, Lukjancenko O, Röder T, Nieuwenhuijse D, Pedersen SK, Kjeldgaard J, Kaas RS, Clausen PTLC, Vogt JK, Leekitcharoenphon P, van de Schans MGM, Zuidema T, de Roda Husman AM, Rasmussen S, Petersen B; Global Sewage Surveillance project consortium, Amid C, Cochrane G, Sicheritz-Ponten T, Schmitt H, Alvarez JRM, Aidara-Kane A, Pamp SJ, Lund O, Hald T, Woolhouse M, Koopmans MP, Vigre H, Petersen TN, Aarestrup FM.

Nat Commun. 2019 Mar 8;10(1):1124. doi: 10.1038/s41467-019-08853-3.

9.

Using WGS to identify antibiotic resistance genes and predict antimicrobial resistance phenotypes in MDR Acinetobacter baumannii in Tanzania.

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

J Antimicrob Chemother. 2019 Jun 1;74(6):1484-1493. doi: 10.1093/jac/dkz055.

10.

Cross-Border Transmission of Salmonella Choleraesuis var. Kunzendorf in European Pigs and Wild Boar: Infection, Genetics, and Evolution.

Leekitcharoenphon P, Sørensen G, Löfström C, Battisti A, Szabo I, Wasyl D, Slowey R, Zhao S, Brisabois A, Kornschober C, Kärssin A, Szilárd J, Černý T, Svendsen CA, Pedersen K, Aarestrup FM, Hendriksen RS.

Front Microbiol. 2019 Feb 6;10:179. doi: 10.3389/fmicb.2019.00179. eCollection 2019.

11.

Megaphages infect Prevotella and variants are widespread in gut microbiomes.

Devoto AE, Santini JM, Olm MR, Anantharaman K, Munk P, Tung J, Archie EA, Turnbaugh PJ, Seed KD, Blekhman R, Aarestrup FM, Thomas BC, Banfield JF.

Nat Microbiol. 2019 Apr;4(4):693-700. doi: 10.1038/s41564-018-0338-9. Epub 2019 Jan 28.

PMID:
30692672
12.

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 Apr 1;74(4):865-876. doi: 10.1093/jac/dky518.

PMID:
30649386
13.

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.

14.

COMPARISON BETWEEN THE ENDOSCOPIC FINDINGS AND THE HISTOLOGICAL DIAGNOSIS OF ANTRAL GASTRITES.

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.

15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

PMID:
30131524
21.

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.

PMID:
30038308
22.

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.

PMID:
30030694
23.

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.

24.

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.

25.

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.

26.

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.

27.

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.

28.

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.

29.

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.

30.

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.

31.

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.

32.

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.

PMID:
29409561
33.

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.

PMID:
29309339
34.

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.

35.

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.

36.

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.

37.

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.

PMID:
28926006
38.

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.

PMID:
28651652
39.

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.

40.

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.

41.

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.

PMID:
28488022
42.

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.

PMID:
28463791
43.

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.

44.

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;:.

45.

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.

46.

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.

PMID:
28115502
47.

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.

48.

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.

49.

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.

50.

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.

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