The general approach in their pilot studies is to isolate the bacteria responsible for the outbreak, sequence the genome, and based on the information produces they determine what the bug is and whether there are any features (like SNPs) it carries that make it unique.
They then develop a quicker, PCR based test capable of detecting the specific strain around the hospital and use it to collect data and make decisions to manage that unique outbreak.
There are still some cases where characterizing drug resistance patterns of the bacteria is involved, involving slower, intentional, experimentation and microbiology lab based detective work. Eventually, you might be able to dispense with this and predict (with excellent accuracy) what the bugs are resistant to using sequencing.
Nevertheless, it's pretty clear that the genomics approach is paying off for them in terms of speed:
It's quicker, indeed. That's one of the very important reasons to do the pilot. We're screening the intensive care unit two times a week and sometimes samples arrive on Thursday and when you finally get the results [using conventional culture techniques] it might be six days later. With Pathogenica, we are able to get the results in a shorter time.And just how fast is that? Rossen claims that they can go from having a bug isolated from the first patient to an RT-PCR based test in about a week. That includes all the sample collection, handling, sequencing, bioinformatics, and decision making on the screening test.
That's pretty fast.
While he's optimistic that they can still shorten the time further to three or four days with improved sample preparation, faster sequencing, and better bioinformatics, developing better methods is still limited by having the right people and expertise available, a statement very similar to what I said a few months ago; the critical resource for this level of medicine is the people.
This work is definitely something to keep an eye on as their experience develops.