A multi-hospital, clinician-initiated bacterial genomics program to investigate treatment failure in severe Staphylococcus aureus infections
Giulieri, S. G.; Leroi, M.; Daniel, D.; Chean, R.; Bond, K.; Walker, H.; Holmes, N.; Mothobi, N.; Alexander, A.; Jenney, A.; Beckett, C.; Mahony, A.; Stevens, K.; Sherry, N.; Howden, B. P.
Show abstract
Bacterial genomics is increasingly used for infectious diseases surveillance, outbreak control and prediction of antibiotic resistance. With expanding availability of rapid whole-genome sequencing, bacterial genomics data could become a valuable tool for clinicians managing bacterial infections, driving precision medicine strategies. Here, we present a novel clinician-driven bacterial genomics framework that applies within-patient evolutionary analysis to identify in real-time microbial genetic changes that have an impact on the outcome of severe Staphylococcus aureus infections, a strategy that is increasingly used in cancer genomics. Our approach uses a combination of bacterial genomics and novel microbiological testing to identify and track bacterial adaptive mutations that underlie antibiotic treatment failure. We show real-life examples of the impact of our approach and propose a roadmap for the use of bacterial genomics to advance the management of severe bacterial infections.
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