Clinical microbiology translation

The Pathogen genomics group is collaborating with a number of external groups to explore and enable whole genome sequencing in clinical microbiology.

About the Partnership

Bacterial whole genome sequencing provides the ultimate level of resolution for transmission tracking, and can be used to predict drug resistance. Rapid sequencing therefore has considerable potential for use in clinical mirobiology for outbreak detection and resistance analysis. We are working with groups in Cambridge and Oxford to enable this.

Sanger team partners

Partners and Funders


  • Early insights into the potential of the Oxford Nanopore MinION for the detection of antimicrobial resistance genes.

    Judge K, Harris SR, Reuter S, Parkhill J and Peacock SJ

    The Journal of antimicrobial chemotherapy 2015;70;10;2775-8

  • Evolutionary dynamics of methicillin-resistant Staphylococcus aureus within a healthcare system.

    Hsu LY, Harris SR, Chlebowicz MA, Lindsay JA, Koh TH et al.

    Genome biology 2015;16;81

  • Genome sequencing defines phylogeny and spread of methicillin-resistant Staphylococcus aureus in a high transmission setting.

    Tong SY, Holden MT, Nickerson EK, Cooper BS, Köser CU et al.

    Genome research 2015;25;1;111-8

  • Zero tolerance for healthcare-associated MRSA bacteraemia: is it realistic?

    Török ME, Harris SR, Cartwright EJ, Raven KE, Brown NM et al.

    The Journal of antimicrobial chemotherapy 2014;69;8;2238-45

  • Rapid single-colony whole-genome sequencing of bacterial pathogens.

    Köser CU, Fraser LJ, Ioannou A, Becq J, Ellington MJ et al.

    The Journal of antimicrobial chemotherapy 2014;69;5;1275-81

  • Whole-genome sequencing for rapid susceptibility testing of M. tuberculosis.

    Köser CU, Bryant JM, Becq J, Török ME, Ellington MJ et al.

    The New England journal of medicine 2013;369;3;290-2

  • Rapid bacterial whole-genome sequencing to enhance diagnostic and public health microbiology.

    Reuter S, Ellington MJ, Cartwright EJ, Köser CU, Török ME et al.

    JAMA internal medicine 2013;173;15;1397-404

  • Rapid whole-genome sequencing for investigation of a suspected tuberculosis outbreak.

    Török ME, Reuter S, Bryant J, Köser CU, Stinchcombe SV et al.

    Journal of clinical microbiology 2013;51;2;611-4

  • Routine use of microbial whole genome sequencing in diagnostic and public health microbiology.

    Köser CU, Ellington MJ, Cartwright EJ, Gillespie SH, Brown NM et al.

    PLoS pathogens 2012;8;8;e1002824

  • Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak.

    Köser CU, Holden MT, Ellington MJ, Cartwright EJ, Brown NM et al.

    The New England journal of medicine 2012;366;24;2267-75

  • Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance: a retrospective cohort study.

    Walker TM, Kohl TA, Omar SV, Hedge J, Del Ojo Elias C et al.

    The Lancet. Infectious diseases 2015;15;10;1193-202

  • Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study.

    Walker TM, Ip CL, Harrell RH, Evans JT, Kapatai G et al.

    The Lancet. Infectious diseases 2013;13;2;137-46