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Institute for Infection Prevention and Hospital Epidemiology

Microbial genome analysis

Whole genome sequencing of nosocomial pathogens

Project:

We use whole genome sequencing (WGS) to look at the very makings of each bacterium. By deducing its genetic code we have the ultimate resolution to inform us about putative transmission events on hospital wards, which allows us to investigate outbreaks. Furthermore, we can use the data generated to learn about antibiotic resistance. We are also involved in a number of projects with internal and external collaborators. One of our main interests is the spread of Gram-negative multidrug resistant clones through hospital networks. For this, we collaborate closely with colleagues at the Wellcome Trust Sanger Institute, Cambridge, UK, Imperial College London, London, UK, University Medical Center Groningen, Groningen, Netherlands, Charité Berlin, Berlin, Germany, and Justus-Liebig-University Hospital, Gießen, Germany.

Dr. Sandra Reuter

Evolution of bacteria in hospital settings, their adaptation and survival strategies; WGS can help us to understand long as well as short term evolutionary dynamics shaping bacterial populations.

  • MiSeq & expertise in bacterial WGS
  • Compute & bioinformatics expertise

David, S., Reuter, S., Harris, S.R., Glasner, C., Feltwell, T., Argimon, S., Abudahab, K., Goater, R., Giani, T., Errico, G., Aspbury, M., Sjunnebo, S., Feil, E.J., Rossolini, G.M., Aanensen, D.M., and Grundmann, H. (2019): Epidemic of carbapenem-resistant Klebsiella pneumoniae in Europe is driven by nosocomial spread. Nat Microbiol. online

Harrison, E.M., Ba, X., Coll, F., Blane, B., Restif, O., Carvell, H., Köser, C.U., Jamrozy, D., Reuter, S., Lovering, A., Gleadall, N., Bellis, K.L., Uhlemann, A.-C., Lowy, F.D., Massey, R.C., Grilo, I.R., Sobral, R., Larsen, J., Larsen, A.R., Vingsbo Lundberg, C., Parkhill, J., Paterson, G.K., Holden, M.T.G., Peacock, S.J., and Holmes, M.A. (2019): Genomic identification of cryptic susceptibility to penicillins and β-lactamase inhibitors in methicillin-resistant Staphylococcus aureus. Nat Microbiol. online

Reuter, S., Ludden, C., Judge, K., Gouliouris, T., Blane, B., Coll, F., Naydenova, P., Hunt, M., Tracey, A., Hopkins, K.L., Brown, N.M., Woodford, N., Parkhill, J., and Peacock, S.J. (2017): Sharing of carbapenemase-encoding plasmids between Enterobacteriaceae in UK sewage uncovered by MinION sequencing. MGen, 3 (7): e000114. online

Coll, F., Harrison, E.M., Toleman, M.S., Reuter, S., Raven, K.E., Blane, B., Palmer, B., Kappeler, A.R.M., Brown, N.M., Török, M.E., Parkhill, J., and Peacock, S.J. (2017): Longitudinal genomic surveillance of MRSA in the UK reveals transmission patterns in hospitals and the community. Sci Trans Med, 9 (413): eaak9745. online

Reuter, S., Török, M.E., Holden, M.T.G., Reynolds, R., Raven, K.E., Blane, B., Donker, T., Bentley, S.D., Aanensen, D.M., Grundmann, H., Feil, E.J., Spratt, B.G., Parkhill, J., and Peacock, S.J. (2016): Building a genomic framework for prospective MRSA surveillance in the United Kingdom and the Republic of Ireland. Genome Res, 26 (2): 263 – 270.   pubmed/26672018

Page, A.J., Cummins, C.A., Hunt, M., Wong, V.K., Reuter, S., Holden, M.T.G., Fookes, M., Falush, D., Keane, J.A., and Parkhill, J. (2015): Roary: Rapid large-scale prokaryote pan genome analysis. Bioinformatics, 31 (22): 3691 – 3693.  pubmed/26198102

Reuter, S., Connor, T.R., Barquist, L., Walker, D., Feltwell, T., Harris, S.R., Fookes, M., Hall, M.E., Fuchs, T.M., Corander, J., DuFour, M., Ringwood, T., Savin, C., Bouchier, C., Martin, L., Miettinen, M., Shubin, M., Riehm, J., Laukkanen-Ninios, R., Sihvonen, L.M., Siitonen, A., Skurnik, M., Falcao, J.P., Fukushima, H., Scholz, H.C., Prentice, M.B., Wren, B.W., Parkhill, J., Carniel, E., Achtman, M., McNally, A., and Thomson, N.R. (2014): Parallel independent evolution of pathogenicity within the genus Yersinia. Proc Nat Acad Sci USA, 111(8): 6768 – 73.  Online

Reuter, S., Ellington, M.J., Cartwright, E.J.P., Köser, C.U., Török, M.E., Gouliouris, T., Harris, S.R., Brown, N.M., Holden, M.T.G., Quail, M., Parkhill, J., Smith, G.P., Bentley, S.D., and Peacock, S.J. (2013): Rapid whole genome sequencing to improve diagnostic and public health microbiology. JAMA Int Med, 173 (15): 1397 – 1404. Online

Project Leader:

Dr. biol. Sandra Reuter

Tel.: ++49 (0) 7 61 / 2 70 82 35 0

 Fax: ++49 (0) 7 61 / 2 70 83 03 0

sandra.reuter@uniklinik-freiburg.de

Curriculum vitae