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The introduction of high throughput genomics technologies is proving transformative for infectious disease research and clinical microbiology. Significant investments in this field have enabled the institute to establish a state- of-the-art genome sequencing facility with bioinformatics infrastructure and expertise. The team collaborate across the university and NHS Trust, as well as externally with a range of both clinical and research focused projects..

Applications include the sequencing of isolates from patients with difficult-to-treat tuberculosis in order to identify resistance mutations to assist clinicians with the development of personalised drug regimens. In addition, genome sequencing can quickly identify possible transmission events, which can further direct public health investigations and inform the appropriate public health response.

Hospital acquired infections such as MRSA, E. coli and Pseudomonas are a continually developing problem. In collaboration with clinical colleagues from St George’s NHS Trust, the genomics and bioinformatics team have applied sequencing to better understand both the mechanisms driving this resistance, as well as the role of carriage by otherwise healthy individuals and processes by which organisms can be transmitted within the hospital environment .

Further research focused projects include those aiming to understand how bacteria gain resistance through the exchange of mobile genetic elements such as plasmids or bacteriophages, as well as sequencing Streptococcus isolates to confirm molecular types.


  • Witney, A. A. et al. Clinical Application of Whole-Genome Sequencing To Inform Treatment for Multidrug-Resistant Tuberculosis Cases. J. Clin. Microbiol. 53, 1473–1483 (2015).

  • Pond, M. J. et al. Accurate detection of Neisseria gonorrhoeae ciprofloxacin susceptibility directly from genital and extragenital clinical samples: towards genotype-guided antimicrobial therapy. J. Antimicrob. Chemother. 71, 897–902 (2016).

  • Witney, A. A. a et al. Genome sequencing and characterization of an extensively drug-resistant sequence type 111 serotype O12 hospital outbreak strain of Pseudomonas aeruginosa. Clin. Microbiol. Infect. 20, (2014).

  • McCarthy, A. J. et al. Extensive horizontal gene transfer during staphylococcus aureus co-colonization in vivo. Genome Biol. Evol. 6, (2014).

  • Stanczak-Mrozek, K. I., Laing, K. G. & Lindsay, J. A. Resistance gene transfer: induction of transducing phage by sub-inhibitory concentrations of antimicrobials is not correlated to induction of lytic phage. J. Antimicrob. Chemother. 72, 1624–1631 (2017).

  • Tall, H. et al. Identification of Streptococcus suis Meningitis through Population-Based Surveillance, Togo, 2010-2014. Emerg. Infect. Dis. 22, 1262–4 (2016).


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