A New Way of Understanding What Might Kill Us

It has been more than half a century since the discovery of penicillin revolutionized our ability to control communicable disease. Since that time a lot of progress has been made on all kinds of diseases, although the emphasis has been more on degenerative diseases--treatments for cardiovascular conditions, cancer, and other issues that are associated especially with an aging population. But, a story in today's New York Times puts the control of bacteria and viruses back in the spotlight. The story focuses on the work of Dr. James M. Musser, chairman of pathology and genomic medicine at the Methodist Hospital System in Houston.

It is the start of a new age in microbiology, Dr. Musser and others say. And the sort of molecular epidemiology he and his colleagues wanted to do is only a small part of it. New methods of quickly sequencing entire microbial genomes are revolutionizing the field.

The first bacterial genome was sequenced in 1995 — a triumph at the time, requiring 13 months of work. Today researchers can sequence the DNA that constitutes a micro-organism’s genome in a few days or even, with the latest equipment, a day. (Analyzing it takes a bit longer, though.) They can simultaneously get sequences of all the microbes on a tooth or in saliva or in a sample of sewage. And the cost has dropped to about $1,000 per genome, from more than $1 million.

With rapid genome sequencing, “we are able to look at the master blueprint of a microbe,” Dr. Relman [from Stanford University] said in a telephone interview. It is “like being given the operating manual for your car after you have been trying to trouble-shoot a problem with it for some time.” Dr. Matthew K. Waldor of Harvard Medical School said the new technology “is changing all aspects of microbiology — it’s just transformative.”

One group is starting to develop what it calls disease weather maps. The idea is to get swabs or samples from sewage treatment plants or places like subways or hospitals and quickly sequence the genomes of all the micro-organisms. That will tell them exactly what bacteria and viruses are present and how prevalent they are.

Knowledge is power and we seem to be gaining at an increasing rate on these bugs that still can kill us.