“Although genomics has already begun to improve diagnostics and treatments in a few circumstances, profound improvements in the effectiveness of healthcare cannot realistically be expected for many years.” (Nature 470, 140; 2011)
While this certainly applies to human sequencing, the immediate clinical applications of genomics are already being seen in infectious diseases, as exemplified by recent studies of MRSA and C. difficile (S. R. Harris et al. Science 327, 469-474; 2010 & N. J. Croucher et al. Science 331, 430-434; 2011). However, the fascinating series of articles from this journal marking 10 years of the Human Genome Project made no mention of the use of genomics in clinical microbiology, despite the fact that over 13 million people die due to infectious diseases every year (WHO: The global burden of disease: 2004 update; 2008).
Hospital laboratory sequencing is destined to become a vital tool for the delineation, tracking and control of hospital-acquired infections, rising rates of antibiotic resistance, and the threat of new and emerging pathogens such as SARS, H5N1 and H1N1 influenza. The use of routine sequencing for specific sample types or cultured pathogens processed through diagnostic laboratories will provide a paradigm shift in our understanding of infectious diseases. Sequencing will also reduce the need for microbiological reference laboratories and the associated time delays, provide the ultimate source of additional clinically relevant information (such as drug resistance and response to vaccines), and generate public health data and direct research by enabling real-time tracking of pathogens.