As part of the The Genomics in Medicine Lecture Series from NHGRI, Jonathan Zenilman gave a lecture on various ways that new genome technology has aided in the ways that clinicians can diagnose, manage, and treat infectious disease. This lecture series is delivering a number of videos on various intersections of clinical medical situations and genomics, not just on the basic research in the field.
The opportunities to study previously murky microbial situations–including unculturable organisms, and mixed colonies of microbes that can be invading wounds, was really interesting (but thinking about the community in a brain abscess was…er…not suitable for lunchtime viewing perhaps). But not only were these situations nearly impossible to understand before–but they couldn’t tell whether there were resistant organisms in there. So it seriously affected treatments.
An interesting data point: in brain abscesses, using standard culturing techniques, they identified 22 bugs. Using PCR they found 72! Some were unknown, too. One patient had 16 strains. That’s quite a battle.
One side effect of these new strategies though it that it freaks out hospital administrators. Suddenly because of the increased sensitivity of the tests, there are a lot more organisms reflected on their reports.
The new techniques are really going to help in the treatment of chronic wounds. One important point was that checking the RNA-seq data is key, because it’s important to know which transcriptomes are active. Dead bugs complicate the analysis, so knowing which ones are currently alive and affecting the wound is crucial.
Another important outcome of this work would be getting pointers to more pathogen-directed therapies. Broad-spectrum treatments are causing problems of their own, and having more precise ways to target the bad bugs would really be worthwhile.
I’ve attached a sample of the kinds of data that Zenilman and colleagues have published on the types of work he describes in this lecture, but you can find many more examples. I wanted to choose an open access example though, so this is the one I include.
Price, L., Liu, C., Melendez, J., Frankel, Y., Engelthaler, D., Aziz, M., Bowers, J., Rattray, R., Ravel, J., Kingsley, C., Keim, P., Lazarus, G., & Zenilman, J. (2009). Community Analysis of Chronic Wound Bacteria Using 16S rRNA Gene-Based Pyrosequencing: Impact of Diabetes and Antibiotics on Chronic Wound Microbiota PLoS ONE, 4 (7) DOI: 10.1371/journal.pone.0006462