Whole genome sequencing and infection prevention

While attending a HICPAC meeting this week, I had a chance to chat with David Henderson about the use of whole genome sequencing (WGS) to help investigate an Acinetobacter outbreak at the NIH Clinical Center. I’m sure you’ll hear more about this at IDWeek (yet another reason to attend!). In the meantime you can check out the report in this week’s NEJM describing use of rapid WGS to investigate a NICU MRSA outbreak. My Journal Watch summary is here, if you want an abbreviated version. I’m a little surprised the paper made it into the NEJM, as it isn’t clear how the WGS contributed much to control of this particular outbreak. The work is most useful as an example of how WGS is now rapid and inexpensive enough to contribute to patient care and infection prevention work in real time (rather than only in retrospect, or as a research tool).

However, there are a couple reasons that you won’t see WGS coming to many labs in the near future. First, analysis and interpretation of the enormous amount of resulting data (the entire bacterial genome sequence) is not simple, requiring substantial local expertise. Second, we have a very incomplete understanding of which genetic differences and mutations are clinically important. Until we expand our knowledge base and bring some automation to the analysis and interpretation, bacterial WGS to inform outbreak and transmission investigations will remain limited to a few large centers that have in-house capacity.