We are still waiting for widespread health-care improvements resulting from sequencing of the human genome (Nature 470, 140; 2011), but microbial genome sequences are already generating important clinical applications.

Hospital laboratory sequencing is set to become an invaluable tool for the delineation, tracking and control of infections such as methicillin-resistant Staphylococcus aureus (MRSA) and Streptococcus pneumoniae (see, for example, S. R.Harris et al. Science 327, 469–474; 2010, and N. J. Croucher et al. Science 331, 430–434; 2011). It will also be crucial for monitoring antibiotic resistance and emerging pathogens such as those responsible for severe acute respiratory syndrome (SARS), H5N1 and H1N1 influenza.

The use of routine sequencing in diagnostic laboratories will revolutionize our understanding of infectious diseases. By reducing the need for microbiological reference laboratories, there will be fewer delays in delivering information. Sequencing will provide the ultimate source of clinically relevant information on responses to vaccines and microbial drug resistance, for example, as well as useful public-health data. It will also help to direct research by enabling real-time tracking of pathogens.