A Microbial Census

One morning, a little over a year ago, I woke up with a very sore, and slightly swollen elbow. I remembered that I had cut my arm on a neighborhood bar table while watching a football game with some friends a few days prior, and I wondered if the cut was infected. I made an appointment with my primary care physician, who quickly diagnosed me with bursitis, an inflammation of the fluid-filled sac that pads the elbow. Since I had broken skin, the doctor wisely prescribed clindamycin, an antibiotic, to treat any tissue infection that may have seeped in. As the hours crept by, the pain in my elbow worsened, until I woke up in the middle of the night with extreme arm pain. I immediately checked the elbow that had been swollen the previous day. The swelling had doubled in size, and the skin was an angry-red color. The following morning, I was back in the clinic, and my doctor started to suspect that this was no ordinary infection on my elbow, and may in fact be a drug-resistant staph infection. Gulp. Nonetheless, he felt confident that the clindamycin should clear it up.

Under the doctor's orders, I spent the next day meticulously tracing the swollen area on my elbow with a Sharpie marker, carefully noting how much it spread. By the end of the day, my entire forearm was puffy and discolored, and my doctor said it was time for me to be admitted to the hospital. I spent 3 days there, getting intravenous treatments of vein-burning, gastrointestinal-rearranging Vancomycin pumped into my system. Not fun.

Afterward, I talked to a number of physician friends about my experience. They said my doctor's treatment plan was textbook. He had done everything right. When docs suspect drug-resistant staph, the first line of defense is typically a hearty dose of clindamycin. The problem in my case was that the staph I contracted was actually resistant to clindamycin. That explains why the infection continued to spread even though I was taking the antibiotics.

Since this little microbial foray, I've had a growing interest in infectious disease. Specifically, I like seeing smart, new ways to keep tabs on how bacterium move from place to place. I wonder, if my doctor had known that clindamycin-resistant staph was infiltrating San Francisco, would I have initially received a different antibiotic? In my opinion, this was a clear case where having more data would have aided the diagnosis, and hastened a healthy outcome.

As Thomas pointed out at The Huffington Post, the true promise of personalized medicine is more about data than specialty drugs. Data can be our personal metrics, such as blood pressure, glucose levels, or cholesterol values. But keeping medical data to ourselves would be somewhat shortsighted. The internet has taught us the power of sharing data. We share our photos on Flickr. We share our status messages on Facebook. We share links on Twitter. Likewise, we can share our health and medical data, enabling pooled statistics from large populations. In the case of infectious disease, the best preventive strategy is to know exactly what strains you're up against, and how the microbes are moving into different geographic regions over time.

Researchers recently confirmed the power of sharing microbial data in a new report, published this month in PLoS Medicine. Roughly 25% of us walk around with staph on our skin, yet not all of us get sick. That's because there's relatively few strains that cause serious symptoms. These so-called virulent strains are the ones docs want to track.

Following both methycilin-resistant (MRSA) and methycilin-susceptible (MSSA) staph strains through Europe, the authors coordinated the participation of 450 hospitals in 26 European countries, a logistic feat in its own right. When a case of staphylococcus aureus was found, the bacterium was genotyped (i.e. its DNA was analyzed to identify which strain it came from), and its location recorded. After collecting all the data, researchers could see how a particular strain of staph localized in different geographic regions. For instance, did the virulent strains stay in one hospital, or had they spread throughout the community?

The authors found that most virulent MRSA strains were contained in a health care clinic, meaning that drug-resistant staph was simply hopping from person-to-person within the hospital walls. Occasionally, that MRSA strain would show up at a different, nearby hospital, and rapidly spread in admitted patients. This implies that the carriers of the virulent MRSA strains are patients who are repeatedly admitted to different regional hospitals.

I'll leave you with a final thought: tracking microbes isn't just a task for researchers. In fact, DIYBio types should check out a cool new project called BioWeatherMap, which asks volunteers to swab commonly used public surfaces, such as door knobs or crosswalk buttons, to track pending microbial storm fronts.