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Items: 1 to 50 of 422

1.

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.

2.

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.

3.

High-throughput sequencing-based investigation of viruses in human cancers by multi-enrichment approach.

Mollerup S, Asplund M, Friis-Nielsen J, Kjartansdóttir KR, Fridholm H, Hansen TA, Herrera JAR, Barnes CJ, Jensen RH, Richter SR, Nielsen IB, Pietroni C, Alquezar-Planas DE, Rey-Iglesia A, Olsen PVS, De Meyts ER, Groth-Pedersen L, von Buchwald C, Jensen DH, Gniadecki R, Høgdall E, Langhoff JL, Pete I, Vereczkey I, Baranyai Z, Dybkaer K, Johnsen HE, Steiniche T, Hokland P, Rosenberg J, Baandrup U, Sicheritz-Pontén T, Willerslev E, Brunak S, Lund O, Mourier T, Vinner L, Izarzugaza JMG, Nielsen LP, Hansen AJ.

J Infect Dis. 2019 Jun 28. pii: jiz318. doi: 10.1093/infdis/jiz318. [Epub ahead of print]

PMID:
31253993
4.

Contaminating viral sequences in high-throughput sequencing viromics: a linkage study of 700 sequencing libraries.

Asplund M, Kjartansdóttir KR, Mollerup S, Vinner L, Fridholm H, Herrera JAR, Friis-Nielsen J, Hansen TA, Jensen RH, Nielsen IB, Richter SR, Rey-Iglesia A, Matey-Hernandez ML, Alquezar-Planas DE, Olsen PVS, Sicheritz-Pontén T, Willerslev E, Lund O, Brunak S, Mourier T, Nielsen LP, Izarzugaza JMG, Hansen AJ.

Clin Microbiol Infect. 2019 May 4. pii: S1198-743X(19)30206-X. doi: 10.1016/j.cmi.2019.04.028. [Epub ahead of print]

5.

LRE-Finder, a Web tool for detection of the 23S rRNA mutations and the optrA, cfr, cfr(B) and poxtA genes encoding linezolid resistance in enterococci from whole-genome sequences.

Hasman H, Clausen PTLC, Kaya H, Hansen F, Knudsen JD, Wang M, Holzknecht BJ, Samulioniené J, Røder BL, Frimodt-Møller N, Lund O, Hammerum AM.

J Antimicrob Chemother. 2019 Jun 1;74(6):1473-1476. doi: 10.1093/jac/dkz092.

PMID:
30863844
6.

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.

7.

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.

8.

Antibody Cross-Reactivity in Antivenom Research.

Ledsgaard L, Jenkins TP, Davidsen K, Krause KE, Martos-Esteban A, Engmark M, Rørdam Andersen M, Lund O, Laustsen AH.

Toxins (Basel). 2018 Sep 27;10(10). pii: E393. doi: 10.3390/toxins10100393. Review.

9.

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.

10.

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
11.

Transient Posttranscriptional Gene Silencing in Medicago truncatula: Virus-Induced Gene Silencing (VIGS).

Serwatowska J, Lund OS, Johansen IE.

Methods Mol Biol. 2018;1822:115-122. doi: 10.1007/978-1-4939-8633-0_8.

PMID:
30043300
12.

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
13.

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
14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

19.

CHTyper, a Web Tool for Subtyping of Extraintestinal Pathogenic Escherichia coli Based on the fumC and fimH Alleles.

Roer L, Johannesen TB, Hansen F, Stegger M, Tchesnokova V, Sokurenko E, Garibay N, Allesøe R, Thomsen MCF, Lund O, Hasman H, Hammerum AM.

J Clin Microbiol. 2018 Mar 26;56(4). pii: e00063-18. doi: 10.1128/JCM.00063-18. Print 2018 Apr. No abstract available.

20.

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.

21.

Multidrug-resistant Neisseria gonorrhoeae infection with ceftriaxone resistance and intermediate resistance to azithromycin, Denmark, 2017.

Terkelsen D, Tolstrup J, Johnsen CH, Lund O, Larsen HK, Worning P, Unemo M, Westh H.

Euro Surveill. 2017 Oct;22(42). doi: 10.2807/1560-7917.ES.2017.22.42.17-00659.

22.

RUCS: rapid identification of PCR primers for unique core sequences.

Thomsen MCF, Hasman H, Westh H, Kaya H, Lund O.

Bioinformatics. 2017 Dec 15;33(24):3917-3921. doi: 10.1093/bioinformatics/btx526.

23.

Qualitative analysis of MMI raters' scorings of medical school candidates: A matter of taste?

Christensen MK, Lykkegaard E, Lund O, O'Neill LD.

Adv Health Sci Educ Theory Pract. 2018 May;23(2):289-310. doi: 10.1007/s10459-017-9794-x. Epub 2017 Sep 27.

PMID:
28956195
24.

High-density peptide microarray exploration of the antibody response in a rabbit immunized with a neurotoxic venom fraction.

Engmark M, Jespersen MC, Lomonte B, Lund O, Laustsen AH.

Toxicon. 2017 Nov;138:151-158. doi: 10.1016/j.toxicon.2017.08.028. Epub 2017 Sep 1.

PMID:
28867663
25.

Sequencing and de novo assembly of 150 genomes from Denmark as a population reference.

Maretty L, Jensen JM, Petersen B, Sibbesen JA, Liu S, Villesen P, Skov L, Belling K, Theil Have C, Izarzugaza JMG, Grosjean M, Bork-Jensen J, Grove J, Als TD, Huang S, Chang Y, Xu R, Ye W, Rao J, Guo X, Sun J, Cao H, Ye C, van Beusekom J, Espeseth T, Flindt E, Friborg RM, Halager AE, Le Hellard S, Hultman CM, Lescai F, Li S, Lund O, Løngren P, Mailund T, Matey-Hernandez ML, Mors O, Pedersen CNS, Sicheritz-Pontén T, Sullivan P, Syed A, Westergaard D, Yadav R, Li N, Xu X, Hansen T, Krogh A, Bolund L, Sørensen TIA, Pedersen O, Gupta R, Rasmussen S, Besenbacher S, Børglum AD, Wang J, Eiberg H, Kristiansen K, Brunak S, Schierup MH.

Nature. 2017 Aug 3;548(7665):87-91. doi: 10.1038/nature23264. Epub 2017 Jul 26.

PMID:
28746312
26.

Cross-recognition of a pit viper (Crotalinae) polyspecific antivenom explored through high-density peptide microarray epitope mapping.

Engmark M, Lomonte B, Gutiérrez JM, Laustsen AH, De Masi F, Andersen MR, Lund O.

PLoS Negl Trop Dis. 2017 Jul 14;11(7):e0005768. doi: 10.1371/journal.pntd.0005768. eCollection 2017 Jul.

27.

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.

28.

Development of a Web Tool for Escherichia coli Subtyping Based on fimH Alleles.

Roer L, Tchesnokova V, Allesøe R, Muradova M, Chattopadhyay S, Ahrenfeldt J, Thomsen MCF, Lund O, Hansen F, Hammerum AM, Sokurenko E, Hasman H.

J Clin Microbiol. 2017 Aug;55(8):2538-2543. doi: 10.1128/JCM.00737-17. Epub 2017 Jun 7.

29.

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.

30.

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
31.

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.

32.

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;:.

33.

ArrayPitope: Automated Analysis of Amino Acid Substitutions for Peptide Microarray-Based Antibody Epitope Mapping.

Hansen CS, Østerbye T, Marcatili P, Lund O, Buus S, Nielsen M.

PLoS One. 2017 Jan 17;12(1):e0168453. doi: 10.1371/journal.pone.0168453. eCollection 2017.

34.

Perturbed CD8+ T cell TIGIT/CD226/PVR axis despite early initiation of antiretroviral treatment in HIV infected individuals.

Tauriainen J, Scharf L, Frederiksen J, Naji A, Ljunggren HG, Sönnerborg A, Lund O, Reyes-Terán G, Hecht FM, Deeks SG, Betts MR, Buggert M, Karlsson AC.

Sci Rep. 2017 Jan 13;7:40354. doi: 10.1038/srep40354.

35.

Norwegian patients and retail chicken meat share cephalosporin-resistant Escherichia coli and IncK/blaCMY-2 resistance plasmids.

Berg ES, Wester AL, Ahrenfeldt J, Mo SS, Slettemeås JS, Steinbakk M, Samuelsen Ø, Grude N, Simonsen GS, Løhr IH, Jørgensen SB, Tofteland S, Lund O, Dahle UR, Sunde M.

Clin Microbiol Infect. 2017 Jun;23(6):407.e9-407.e15. doi: 10.1016/j.cmi.2016.12.035. Epub 2017 Jan 7.

36.

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.

37.

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.

38.

New Genome-Wide Algorithm Identifies Novel In-Vivo Expressed Mycobacterium Tuberculosis Antigens Inducing Human T-Cell Responses with Classical and Unconventional Cytokine Profiles.

Coppola M, van Meijgaarden KE, Franken KL, Commandeur S, Dolganov G, Kramnik I, Schoolnik GK, Comas I, Lund O, Prins C, van den Eeden SJ, Korsvold GE, Oftung F, Geluk A, Ottenhoff TH.

Sci Rep. 2016 Nov 28;6:37793. doi: 10.1038/srep37793.

39.

High-throughput immuno-profiling of mamba (Dendroaspis) venom toxin epitopes using high-density peptide microarrays.

Engmark M, Andersen MR, Laustsen AH, Patel J, Sullivan E, de Masi F, Hansen CS, Kringelum JV, Lomonte B, Gutiérrez JM, Lund O.

Sci Rep. 2016 Nov 8;6:36629. doi: 10.1038/srep36629.

40.

CD4+ T cells with an activated and exhausted phenotype distinguish immunodeficiency during aviremic HIV-2 infection.

Buggert M, Frederiksen J, Lund O, Betts MR, Biague A, Nielsen M, Tauriainen J, Norrgren H, Medstrand P, Karlsson AC, Jansson M; SWEGUB CORE group.

AIDS. 2016 Oct 23;30(16):2415-2426.

41.

MetaPhinder-Identifying Bacteriophage Sequences in Metagenomic Data Sets.

Jurtz VI, Villarroel J, Lund O, Voldby Larsen M, Nielsen M.

PLoS One. 2016 Sep 29;11(9):e0163111. doi: 10.1371/journal.pone.0163111. eCollection 2016.

42.

Old habits die hard: a case study on how new ways of teaching colonoscopy affect the habitus of experienced clinicians.

Lund O, Andersen B, Christensen MK.

Int J Med Educ. 2016 Sep 19;7:297-308. doi: 10.5116/ijme.57d5.5693.

43.

DNA barcoding and isolation of vertically transmitted ascomycetes in sorghum from Burkina Faso: Epicoccum sorghinum is dominant in seedlings and appears as a common root pathogen.

Stokholm MS, Wulff EG, Zida EP, Thio IG, Néya JB, Soalla RW, Głazowska SE, Andresen M, Topbjerg HB, Boelt B, Lund OS.

Microbiol Res. 2016 Oct;191:38-50. doi: 10.1016/j.micres.2016.05.004. Epub 2016 May 21.

44.

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.

PMID:
27365186
45.

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.

46.

Meta-analysis of proportion estimates of Extended-Spectrum-Beta-Lactamase-producing Enterobacteriaceae in East Africa hospitals.

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

Antimicrob Resist Infect Control. 2016 May 14;5:18. doi: 10.1186/s13756-016-0117-4. eCollection 2016. Review.

47.

HostPhinder: A Phage Host Prediction Tool.

Villarroel J, Kleinheinz KA, Jurtz VI, Zschach H, Lund O, Nielsen M, Larsen MV.

Viruses. 2016 May 4;8(5). pii: E116. doi: 10.3390/v8050116.

48.

Synthesis and Biological Evaluations of Cytotoxic and Antiangiogenic Triterpenoids-Jacaranone Conjugates.

Sun H, Yue PY, Wang SR, Huo L, Zhao Y, Xie S, Kringelum JV, Lund O, Taboureau O, Zhou J, Wong RN, Fang WS.

Med Chem. 2016;12(8):775-785.

PMID:
27140183
49.

Application of Whole-Genome Sequencing Data for O-Specific Antigen Analysis and In Silico Serotyping of Pseudomonas aeruginosa Isolates.

Thrane SW, Taylor VL, Lund O, Lam JS, Jelsbak L.

J Clin Microbiol. 2016 Jul;54(7):1782-1788. doi: 10.1128/JCM.00349-16. Epub 2016 Apr 20.

50.

Global Genomic Epidemiology of Salmonella enterica Serovar Typhimurium DT104.

Leekitcharoenphon P, Hendriksen RS, Le Hello S, Weill FX, Baggesen DL, Jun SR, Ussery DW, Lund O, Crook DW, Wilson DJ, Aarestrup FM.

Appl Environ Microbiol. 2016 Apr 4;82(8):2516-26. doi: 10.1128/AEM.03821-15. Print 2016 Apr.

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