Center for Genomic Epidemiology

Publications

  • 77. Kirstahler P, Bjerrum SS, Friis-Møller A, la Cour M, Aarestrup FM, Westh H, Pamp SJ. Genomics-Based Identification of Microorganisms in Human Ocular Body Fluid. Nature Research Journal. 2018 Mar 7;8(1):4126. doi: 10.1038/s41598-018-22416-4. Link to publication...
  • 76. Petersen, TN., Lukjancenko, O., Thomsen, MCF., Sperotto, MM., Lund, O., Aarestrup, FM., Sicheritz-Pontén, T. MGmapper: Reference based mapping and taxonomy annotation of metagenomics sequence reads. PLoS One. 2017. Link to publication...
  • 75. Berg, E. S; Wester, A. L; 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. Norwegian patients and retail chicken meat share cephalosporin-resistant Escherichia coli and IncK/blaCMY-2 resistance plasmids. 2017. Clinical Microbiology and Infection.Infection (ISSN: 1198-743X) (DOI: http://dx.doi.org/10.1016/j.cmi.2016.12.035) E-pub ahead of print.
  • 74. Ahrenfeldt, J; Skaarup, C; Hasman, H; Pedersen, AG; Aarestrup, FM; Lund, O. Bacterial whole genome-based phylogeny: construction of a new benchmarking dataset and assessment of some existing methods. 2017. BMC Genomics. Link to publication...
  • 73. Jurtz VI, Villarroel J, Lund O, Voldby Larsen M, Nielsen. MetaPhinder - Identifying Bacteriophage Sequences in Metagenomic Data Sets,PLoS One. 2016; 11(9): e0163111.. Link to publication...
  • 72. Clausen, PTL, Zankari, E, Aarestrup, FM. Benchmarking of methods for identification of antimicrobial resistance genes in bacterial whole genome data. Journal of antimicrobial chemotherapy; 71(9): 2484-2488. Link to publication...
  • 71. Kumburu HH, Sonda T, Mmbaga BT, Alifrangis M, Lund O, Kibiki G, Aarestrup FM. Patterns of infections, aetiological agents, and antimicrobial resistance at a tertiary care hospital in northern Tanzania. Trop Med Int Health. 2017 Jan 10. doi: 10.1111/tmi.12836.. Link to publication...
  • 70. 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. Norwegian patients and retail chicken meat share cephalosporin-resistant Escherichia coli and IncK/blaCMY-2 resistance plasmids. Clin Microbiol Infect. 2017 Jan 7. pii: S1198-743X(17)30006-X. Link to publication...
  • 69. Joensen KG, Engsbro AL, Lukjancenko O, Kaas RS, Lund O, Westh H, Aarestrup FM. Evaluating next-generation sequencing for direct clinical diagnostics in diarrhoeal disease. Eur J Clin Microbiol Infect Dis. 2017 Mar 11. doi: 10.1007/s10096-017-2947-2. [Epub ahead of print]. Link to publication...
  • 68. Espinoza-Valles I, Vora GJ, Lin B, Leekitcharoenphon P, González-Castillo A, Ussery D, Høj L, Gomez-Gil B. Unique and conserved genome regions in Vibrio harveyi and related species in comparison with the shrimp pathogen Vibrio harveyi CAIM 1792. Microbiology. 2015 Sep;161(9):1762-79. Link to publication...
  • 67. Leekitcharoenphon P, Pamp SJ, Andresen LO, Aarestrup FM, Comparative genomics of toxigenic and non-toxigenic Staphylococcus hyicus, Veterinary Microbiology, Volume 185, 15 March 2016, Pages 34-40, ISSN 0378-1135. Link to publication...
  • 66. Leekitcharoenphon P, Hendriksen RS, Le Hello S, Weill F-X, Baggesen DL, Jun S-R, Ussery DW, Lund O, Crook DW, Wilson DJ, Aarestrup FM. Global genomic epidemiology of Salmonella enterica serovar Typhimurium DT104. Appl Environ Microbiol 82:000 - 000. February 2016. doi:10.1128/AEM.03821-15. Link to publication...
  • 65. Leekitcharoenphon P, Raufu I, Nielsen MT, Rosenqvist Lund BS, Ameh JA, Ambali AG, Sørensen G, Le Hello S, Aarestrup FM, Hendriksen RS. Investigating Salmonella Eko from Various Sources in Nigeria by Whole Genome Sequencing to Identify the Source of Human Infections. 2016. PLoS One. 2016. 11(5):e0156212. Link to publication...
  • 64. Henri C, Félix B, Guillier L, Leekitcharoenphon P, Michelon D, Mariet JF, Aarestrup FM, Mistou MY, Hendriksen RS, Roussel S. Population genetic structure of Listeria monocytogenes strains determined by pulsed-field gel electrophoresis and multilocus sequence typing. Appl Environ Microbiol. 2016. pii: AEM.00583-16. Link to publication...
  • 63. Roer L, Hendriksen RS, Leekitcharoenphon P, Lukjancenko O, Kaas RS, Hasman H, Aarestrup FM. Is the Evolution of Salmonella enterica subsp. enterica Linked to Restriction- Modification Systems?. mSystems. 2016. DOI: 10.1128/mSystems.00009-16. Link to publication...
  • 62. Siriphap A, Leekitcharoenphon P, Kaas RS, Theethakaew C, Aarestrup FM, Sutheinkul O, Hendriksen RS. Characterization and Genetic Variation of Vibrio cholerae Isolated from Clinical and Environmental Sources in Thailand. PLoS One. 2017 Jan 19;12(1):e0169324 Link to publication...
  • 61. Cavaco LM, Bernal JF, Zankari E, Léon M, Hendriksen RS, Perez-Gutierrez E, Aarestrup FM, Donado-Godoy P. Detection of linezolid resistance due to the optrA gene in Enterococcus faecalis from poultry meat from the American continent (Colombia). J Antimicrob Chemother. 2016 Dec 20. pii: dkw490. doi: 10.1093/jac/dkw490. Link to publication...
  • 60. Ahrenfeldt J, Skaarup C, Hasman H, Pedersen AG, Aarestrup FM, Lund O. Bacterial whole genome-based phylogeny: construction of a new benchmarking dataset and assessment of some existing methods. BMC Genomics. 2017 Jan 5;18(1):19. doi: 10.1186/s12864-016-3407-6. Link to publication...
  • 59. Thomsen MCF, Ahrenfeldt J, Cisneros JLB, Jurtz V, Larsen MV, Hasman H, Aarestrup FM, Lund O. A Bacterial Analysis Platform: An Integrated System for Analysing Bacterial Whole Genome Sequencing Data for Clinical Diagnostics and Surveillance. PLoS ONE 2016, 11(6): e0157718. doi:10.1371/journal.pone.0157718 Link to publication...
  • 58. Hasman H, Hammerum AM, Hansen F, Hendriksen RS, Olesen B, Agersø Y, Zankari E, Leekitcharoenphon P, Stegger M, Kaas RS, Cavaco LM, Hansen DS, Aarestrup FM, Skov RL. Detection of mcr-1 encoding plasmid-mediated colistin-resistant Escherichia coli isolates from human bloodstream infection and imported chicken meat, Denmark 2015. Euro Surveill. 2015 Dec 10;20(49). doi: 10.2807/1560-7917.ES.2015.20.49.30085. PubMed PMID: 26676364 Read more...
  • 57. Franco A, Leekitcharoenphon P, Feltrin F, Alba P, Cordaro G, Iurescia M, Tolli R, D'Incau M, Staffolani M, Di Giannatale E, Hendriksen RS, Battisti A. Emergence of a Clonal Lineage of Multidrug-Resistant ESBL-Producing Salmonella Infantis Transmitted from Broilers and Broiler Meat to Humans in Italy between 2011 and 2014. PLoS One. 2015 Dec 30;10(12):e0144802. doi: 10.1371/journal.pone.0144802. eCollection 2015 Read more...
  • 56. Saputra D, Rasmussen S, Larsen MV, Haddad N, Sperotto MM, Aarestrup FM, Lund O, Sicheritz-Pontén T. Reads2Type: a web application for rapid microbial taxonomy identification. BMC Bioinformatics. 2015 Nov 25;16(1):398. doi: 10.1186/s12859-015-0829-0 Read more...
  • 55. Zschach H, Joensen KG, Lindhard B, Lund O, Goderdzishvili M, Chkonia I, Jgenti G, Kvatadze N, Alavidze Z, Kutter EM, Hasman H, Larsen MV. What Can We Learn from a Metagenomic Analysis of a Georgian Bacteriophage Cocktail?Viruses 2015, 7(12), 6570-6589; doi:10.3390/v7122958 Read more...
  • 54. Jensen MB, Schumacher H, Hasman H, Aarestrup FM. [Pasteurella multocida septicaemia and pneumonia after chemotherapy in a patient who had no known contact with animals.]. Ugeskr Laeger. 2014 Dec 15;176(25A). pii: V01130015 Read more...
  • 53. Joensen KG, Tetzschner AM, Iguchi A, Aarestrup FM, Scheutz F. Rapid and Easy In Silico Serotyping of Escherichia coli Isolates by Use of Whole-Genome Sequencing Data. J Clin Microbiol. 2015 Aug;53(8):2410-26. doi: 10.1128/JCM.00008-15. Epub 2015 May 13. PubMed PMID: 25972421; PubMed Central PMCID: PMC4508402. Read more...
  • 52. Pedersen K, Soerensen G, Loefstroem C, Leekitcharoenphon P, Nielsen B, Wingstrand A, Aarestrup FM, Hendriksen RS, Baggesen DL. Reappearance of Salmonella serovar Choleraesuis var. Kunzendorf in Danish pig herds. Vet Microbiol. 2015 Apr 17;176(3-4):282-91. doi: 10.1016/j.vetmic.2015.01.004. Epub 2015 Jan 27. PubMed PMID: 25703158 Read more...
  • 51. Antilles N, Garcia-Migura L, Joensen KG, Leekitcharoenphon P, Aarestrup FM, Cerdà-Cuéllar M, Hendriksen RS. Audouin's gull, a potential vehicle of an extended spectrum ß-lactamase producing Salmonella Agona. FEMS Microbiol Lett. 2015 Jan;362(3):1-4. doi: 10.1093/femsle/fnu039. Epub 2014 Dec 4. PubMed PMID: 25673651 Read more...
  • 50. Wang M, Borris L, Aarestrup FM, Hasman H. Identification of a Pseudomonas aeruginosa co-producing NDM-1, VIM-5 and VIM-6 metallo-ß-lactamases in Denmark using whole-genome sequencing. Int J Antimicrob Agents. 45:324-5. Marts 2015. Read more...
  • 49. Spoor L. E., P. R. McAdam, L. A. Weinert, A. Rambaut, H. Hasman, F. M. Aarestrup, A. M. Kearns, A. R. Larsen, R. L. Skov and J. R. Fitzgerald. Livestock origin for a human pandemic clone of community-associated methicillin-resistant Staphylococcus aureus. MBio. 13;4, August 2013. Read more...
  • 48. Qin Y, Hasman H, Aarestrup FM, Alwathnani HA, Rensing C. Genome Sequences of Three Highly Copper-Resistant Salmonella enterica subsp. I Serovar Typhimurium Strains Isolated from Pigs in Denmark. Genome Announc December 2014. Read more...
  • 47. Luthje F. L., Hasman H., Aarestrup FM, Alwathnani HA, Rensing C. Genome Sequences of Two Copper-Resistant Escherichia coli Strains Isolated from Copper-Fed Pigs. Genome Announc. December 2014. Read more...
  • 46. Christiansen M. T., R. S. Kaas, R. R. Chaudhuri, M. A. Holmes, H. Hasman, F. M. Aarestrup. Genome-wide high-throughput screening to investigate essential genes involved in methicillin-resistant Staphylococcus aureus Sequence Type 398 survival. PLoS One. 9:e89018. February 2014. Read more...
  • 45. Carattoli A, E. Zankari, A. Garcìa-Fernandez, M. Volby Larsen, O. Lund, L. Villa, F.M. Aarestrup, H. Hasman. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother. 58:3895-903. July 2014. Read more...
  • 44. Abdelbary M. M., A. Wittenberg, C. Cuny, F. Layer, K. Kurt, L. H. Wieler, B. Walther, R. Skov, J. Larsen, H. Hasman, J. R. Fitzgerald, T. C. Smith, J. A. Wagenaar, A. Pantosti, M. Hallin, M. J. Struelens, G. Edwards, R. Böse, U. Nübel, W. Witte. Phylogenetic analysis of Staphylococcus aureus CC398 reveals a sub-lineage epidemiologically associated with infections in horses. 2014. PLoS One. 9:e88083. Read more...
  • 43. Kaas RS, Leekitcharoenphon P, Aarestrup FM, Lund O. Solving the problem of comparing whole bacterial genomes across different sequencing platforms. PLoS One. 2014 Aug 11;9(8):e104984. doi: 10.1371/journal.pone.0104984. eCollection 2014. PubMed PMID: 25110940; PubMed Central PMCID: PMC4128722. Read more...
  • 42. Hendriksen RS, Leekitcharoenphon P, Lukjancenko O, Lukwesa-Musyani C,Tambatamba B, Mwaba J, Kalonda A, Nakazwe R, Kwenda G, Jensen JD, Svendsen CA,Dittmann KK, Kaas RS, Cavaco LM, Aarestrup FM, Hasman H, Mwansa JC. Genomic Signature of Multi-Drug Resistant Salmonella Typhi related to a Massive Outbreak in Zambia during 2010 - 2012. J Clin Microbiol. 2014 Nov 12. pii: JCM.02026-14 [Epub ahead of print]. Read more...
  • 41. Hendriksen RS, Leekitcharoenphon P, Mikoleit M, Jensen JD, Kaas RS, Roer L,Joshi HB, Pornruangmong S, Pulsrikarn C, Gonzalez-Aviles GD, Reuland EA, Nashwan AN, Wester AL, Aarestrup FM, Hasman H. A genomic dissection of travel associated SBL-producing Salmonella Typhi originating from the Philippines - A one-off occurrence or threat to the effective treatment of typhoid fever? J Clin, Microbiol. 2014 Nov 26. pii: JCM.03104-14, Epub ahead of print. Read more...
  • 40. Joensen KG, Scheutz F, Lund O, Hasman H, Kaas RS, Nielsen EM, Aarestrup FM. Evaluation of Real-Time WGS for Routine Typing, Surveillance and Outbreak Detection of Verotoxigenic Escherichia coli. Published: J Clin Microbiol. 2014 Feb 26. [Epub ahead of print]. Read more...
  • 39. Larsen MV, Cosentino S, Lukjancenko O, Saputra D, Rasmussen S, Hasman H, Sicheritz-Pontén T, Aarestrup FM, Ussery DW, Lund O. Benchmarking of Methods for Genomic Taxonomy. Published: J Clin Microbiol. 2014 Feb 26. [Epub ahead of print]. Read more...
  • 38. Kleinheinz KA, Joensen KG, Larsen MV. Applying the ResFinder and VirulenceFinder web-services for easy identification of acquired antibiotic resistance and E. coli virulence genes in bacteriophage and prophage nucleotide sequences. Published: Bacteriophage 2014 Jan 1;4(1):e27943. Epub 2014 Jan 22. Read more...
  • 37. Lukjancenko O, Ussery DW. Vibrio chromosome-specific families. Published: Front. Microbiol., 18 March 2014 | doi: 10.3389/fmicb.2014.00073. Read more...
  • 36. Leekitcharoenphon P, Nielsen EM, Kaas RS, Lund O, Aarestrup FM. Evaluation of Whole Genome Sequencing for Outbreak Detection of Salmonella enterica. Published: February 04, 2014, DOI: 10.1371/journal.pone.0087991. Read more...
  • 35. Cosentino S, Voldby Larsen M, Møller Aarestrup F, Lund O. PathogenFinder - Distinguishing Friend from Foe Using Bacterial Whole Genome Sequence Data. PLoS One. 2013 Oct 28;8(10):e77302. doi: 10.1371/journal.pone.0077302. PubMed PMID: 24204795; PubMed Central PMCID: PMC3810466. Read more...
  • 34. Gautier L, Lund O. Low-bandwidth and non-compute intensive remote identification of microbes from raw sequencing reads. PLoS One. 2013 Dec 31;8(12):e83784. doi: 10.1371/journal.pone.0083784. PubMed PMID: 24391826; PubMed Central PMCID: PMC3877093. Read more...
  • 33. Hasman H, Saputra D, Sicheritz-Ponten T, Lund O, Svendsen CA, Frimodt-Møller N, Aarestrup FM. Rapid whole genome sequencing for the detection and characterization of microorganisms directly from clinical samples. J Clin Microbiol. 2013 Oct 30. Epub ahead of print. Read more...
  • 32. Domingues AR, Vieira AR, Hendriksen RS, Pulsrikarn C, Aarestrup FM. Spatio-temporal analysis of Salmonella surveillance data in Thailand. Epidemiol Infect. 2013 Oct 9:1-11. Epub ahead of print. Read more...
  • 31. Pimlapas Leekitcharoenphon, Carsten Friis, Ea Zankari, Christina Aaby Svendsen, Lance B. Price, Maral Rahmani, Ana Herrero-Fresno, Kayode Fashae, Olivier Vandenberg, Frank M. Aarestrup, Rene S. Hendriksen.Genomics of an emerging clone of Salmonella serovar Typhimurium ST313 from Nigeria and the Democratic Republic of Congo. J Infect Dev Ctries 2013. Read more...
  • 30. Leon Eyrich Jessen, Ilka Hoof, Ole Lund, Morten Nielsen. SigniSite: Identification of residue-level genotype-phenotype correlations in protein multiple sequence alignments. Nucleic Acids Research, Volume 41, Issue W1, 2013. Read more...
  • 29. Larsen, MV. Internet-Based Solutions for Analysis of Next-Generation Sequence Data. J. Clin. Microbiol, 2013. Read more...
  • 28. Leekitcharoenphon P, Kaas RS, Thomsen MC, Friis C, Rasmussen S, Aarestrup FM. snpTree--a web-server to identify and construct SNP trees from whole genome sequence data. BMC Genomics. 2012:13 Suppl 7:S6. Read more...
  • 27. Hendriksen RS, Joensen KG, Lukwesa-Musyani C, Kalondaa A, Leekitcharoenphon P, Nakazwe R, Aarestrup FM, Hasman H, Mwansa JC. Extremely drug-resistat Salmonella enterica serovar Senftenberg infections in patients in Zambia. J Clin Microbiol. 2013 Jan; 51(1):284-6. Read more...
  • 26. Zankari E, Hasman H, Kaas RS, Seyfarth AM, Agersø Y, Lund O, Larsen MV, Aarestrup FM. Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing. J Antimicrob Chemother. 2012 Dec Read more...
  • 25. Kaas RS, Friis C, Ussery DW, Aarestrup FM. Estimating variation within the genes and inferring the phylogeny of 186 sequenced diverse Escherichia coli genomes. BMC Genomics. 2012 Oct 31;13(1):577E-published ahead of print. Read more...
  • 24. Frank M. Aarestrup, Eric W. Brown, Chris Detter, Peter Gerner-Smidt, Matthew W. Gilmour, Dag Harmsen, Rene S. Hendriksen, Roger Hewson, David L. Heymann, Karin Johansson, Kashef Ijaz, Paul S. Keim, Marion Koopmans, Annelies Kroneman, Danilo Lo Fo Wong, Ole Lund, Daniel Palm, Pathom Sawanpanyalert, Jeremy Sobel, and Jørgen Schlundt. Integrating Genome-based Informatics to Modernize Global Disease Monitoring, Information Sharing, and Response. E-published ahead of print. Read more...
  • 23. Zankari E, Hasman H, Cosentine S, Vestergaard M, Rasmussen S, Lund O, Aarestrup FM, Larsen MV. Identification of acquired antimicrobial resistance genes. J. Antimicrob. Chemother. (2012) doi: 10.1093/jac/dks261. 2012, June. Read more...
  • 22. Kröger C, Dillon S, Cameron A, Papenfort K, Sivasankaran SK, Hokamp K, Chao Y, Sittka A, Hébrard M, Händler K, Colgan A, Leekitcharoenphon P, Langridge G, Lohan AJ, Loftus B, Lucchini S, Ussery DW, Dorman CJ, Thomson NR, Vogel J, Hintonc JCD. The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium. PNAS. 2012, May 29. Read more...
  • 21. Leekitcharoenphon P, Lukjancenko O, Friis C, Aarestrup FM, Ussery DW. Genomic variation in Salmonella enterica core genes for epidemiological typing. BMC Genomics. 2012 Mar12;13(1):88. Read more...
  • 20. Price LB, Stegger M, Hasman H, Aziz M, Larsen J, Andersen PS, Pearson T, Waters AE, Foster JT, Schupp J, Gillece J, Driebe E, Liu CM, Springer B, Zdovc I, Battisti A, Franco A, Zmudzki J, Schwarz S, Butaye P, Jouy E, Pomba C, Porrero MC, Ruimy R, Smith TC, Robinson DA, Weese JS, Arriola CS, Yu F, Laurent F, Keim P, Skov R, Aarestrup FM. Staphylococcus aureus CC398. Host Adaptation and Emergence of Methicillin Resistance in Livestock. MBio. 2012 Feb 21;3(1). Read more...
  • 19. Karlsson FH, Ussery DW, Nielsen J, Nookaew I. "A closer look at bacteroides: phylogenetic relationship and genomic implications of a life in the human gut.", Microb Ecol. 61:473-485 (2011(2011). Read more...
  • 18. Brede DA, Snipen LG, Ussery DW, Nederbragt AJ, Nes IF. "Complete genome sequence of the commensal Enterococcus faecalis 62, isolated from a healthy Norwegian infant.", J Bacteriol. 2011 May;193(9):2377-8. (2011). Read more...
  • 17. Field D, Amaral-Zettler L, Cochrane G, Cole JR, Dawyndt P, Garrity GM, Gilbert J, Glöckner FO, Hirschman L, Karsch-Mizrachi I, Klenk HP, Knight R, Kottmann R, Kyrpides N, Meyer F, San Gil I, Sansone SA, Schriml LM, Sterk P, Tatusova T, Ussery DW, White O, Wooley J. The Genomic Standards Consortium. PLoS Biology, 9:(6) e1001088, (2011). Read more...
  • 16. Takamiya M, Ozen A, Rasmussen M, Alter T, Gilbert T, Ussery DW, and Knøchel S. Genome Sequence of Campylobacter jejuni strain 327, a strain isolated from a turkey slaughterhouse.Stand Genomic Sci. 2011 Apr 29;4(2):113-22. Epub 2011 Apr 25 Read more...
  • 15. Takamiya M, Ozen A, Rasmussen M, Alter T, Gilbert T, Ussery DW, and Knøchel S. Genome sequences of two stress-tolerant Campylobacter jejuni poultry strains, 305 and DFVF1099. J. Bacteriol. 193:5546-5547, (2011). Read more...
  • 14. Larsen MV, Cosentino S, Rasmussen S, Friis C, Hasman H, Marvig RL, Jelsbak L, Pontén TS, Ussery DW, Aarestrup FM, Lund O. Multilocus Sequence Typing of Total Genome Sequenced Bacteria. J Clin Microbiol. 2012 Jan 11. Read more...
  • 13. Lukjancenko O, Ussery DW, Wassenaar TM. Comparative Genomics of Bifidobacterium, Lactobacillus and Related Probiotic Genera. Microb Ecol. 2011 October Read more...
  • 12. Keim PS, Aarestrup FM, Shakya G, Price LB, Hendriksen RS, Engelthaler DM, Pearson T. Reply to "South Asia instead of Nepal may be the origin of the Haitian cholera outbreak strain". MBio. 2011 November Read more...
  • 11. Concepción Porrero M, Hasman H, Vela AI, Fernández-Garayzábal JF, Domínguez L, Aarestrup FM. Clonal diversity of Staphylococcus aureus originating from the small ruminants goats and sheep. Vet Microbiol. 2011 October Read more...
  • 10. Hendriksen RS, Le Hello S, Bortolaia V, Pulsrikarn C, Nielsen EM, Pornruangwong S, Chaichana P, Svendsen CA, Weill FX, Aarestrup FM. Characterization of Salmonella enterica serovar Stanley isolates; a serovar endemic to Asia and associated with travel. J Clin Microbiol. 2011 December Read more...
  • 9. Hendriksen RS, Price LB, Schupp JM. Population Genetics of Vibrio cholerae from Nepal in 2010: Evidence on the Origin of the Haitian Outbreak. mBio, 2011 August . Read more...
  • 8. Ozen Al, Ussery DW,. Defining the Pseudomonas Genus: Where Do We Draw the Line with Azotobacter?. Microbial Ecology, 2011 August . Read more...
  • 7. Cao X, Cavaco LM, Lv Y, Li Y, Zheng B, Wang P, Hasman H, Liu Y, Aarestrup FM. Molecular Characterization and Antimicrobial Susceptibility Testing of Escherichia coli Isolates from Patients with Urinary Tract Infections in 20 Chinese Hospitals. J Clin Microbiol. 2011 Jul;49(7):2496-501. Read more...
  • 6. Jacobsen A, Hendriksen RS, Aaresturp FM, Ussery DW, Friis C. The Salmonella enterica Pan-genome. Microbial Ecology, 2011 Jun 4. Read more...
  • 5. Lukjancenko O, Wassenaar TM, Ussery DW. Comparison of 61 Sequenced Escherichia coli Genomes. Microbial Ecology, 60:708-720, (2010). Read more...
  • 4. Friis C, Wassenaar TM, Javed MA, Snipen L, Lagesen K, Hallin PF, Newell DG, Toszeghy M, Ridley A, Manning G, Ussery DW. Genomic Characterization of Campylobacter jejuni strain M1. PLoS ONE, 5: e12253. (2010). Read more...
  • 3. Lukjancenko O, Ussery DW. Design of an Enterobacteriaceae Pan-genome Microarray Chip. CSBio 2010. Proceedings. CCIS , 115: 174-189.
  • 2. Qureshi M, Rotenberg E, Stærfeldt HH, Hansson L, Ussery D. The Genome Atlas Resource. CSBio 2010. Proceedings. CCIS, 115:149-158.
  • 1. Andreatta M, Nielsen M, Møller Aarestrup F, Lund O. In Silico Prediction of Human Pathogenicity in the gamma-Proteobacteria. PLoS One. 2010 Oct. Read more...