Discovering Biology in a Digital World

It looked like just any other rainy Saturday morning in the Pacific Northwest, but no, this Saturday was a day for microbiology. Reluctantly, I crawled out of my warm bed and headed over to the University of Washington to attend a meeting of the Pacific NW branch of the American Society for Microbiology (ASM).

My goals for this venture were diverse. Of course, I wanted to go hear some good science and see some old friends. But I also wanted to learn more about what microbiologists are actually doing these days, out there in the wild.

In my world, since all we hear about are nucleic acid based technologies, we sometimes get a bit of tunnel vision. To me it seems reasonable that all microbes might be detected by PCR or some kind of chip assay, but deep down, I knew that it couldn't be true.

Mostly, I was surprised to learn, that today's clinical lab hasn't changed too much in the 18 years since I finished grad school. It isn't just the techniques either. Even many of the people speaking and attending the talks were the same people I remember from graduate school.

Phil Tarr must have felt the same way. He distilled all of these thoughts by showing one power point slide with agar plates and brightly colored test tubes full of brightly-colored liquids and mentioning that Louis Pasteur would feel at home if he were to rise from the grave and walk into a clinical micro lab.

Talk #1 Life in a clinical reference lab
And in fact, the first talk that I attended was from a speaker in a clinical lab who discussed how they trained the lab staff to give consistent interpretations of gram stains. At first, I was a bit surprised. Then I thought back to when I was teaching students how to do gram stains and what could happen with slides that were decolorized just a bit too long. Okay, I got it that part, but I was still a little surprised at the role that gram stains play in their decision process. All of the steps carried out in their lab are guided by the results of those stains. It was also interesting to learn from her (and a later speaker) about the problems they have with getting physicians and nurses to collect useful ("clinically relevant") samples and the kinds of instructional messages that her lab sends to physicians to help them use the information from microbiological test results.

Talk #2 Phillip Tarr and E. coli O157:H7
The next talk was from Phil Tarr who gave an enthusiastic presentation about E. coli O157:H7. He stressed that a physician might only see a case of O157:H7 once in 5 years and so it's really important for a clinical lab to help with identifying the bacteria and getting information to a physician as soon as possible. He also explained the reason why immediate action is critical and described what happens when children are infected with this strain of E. coli. In about 15% of infected kids, these bacteria produce a toxin (Shiga toxin) that activates thrombin (a clotting enzyme) and thrombin starts clotting blood throughout their bodies. According to Tarr, it's important to get kids on IV bags with saline ASAP. If kids develop hemolytic uremic syndrome and they don't get treated within a short period of time, they're likely to die. Research studies have found that the most important factor in preventing death was an early diagnosis.

How do you diagnose E. coli O157:H7?
Apparently you need to start out by getting a stool sample (If you didn't already know this, stool = poop). Not all hospitals do this routinely and not all labs are real keen on these samples, but if you don't do it when you should, well....

What do labs do next?
Some labs plate material on MacConkey agar with sorbitol and look for lactose fermenters. Some labs use an enzyme immunoassay to test for Shiga toxin. Interestingly, Tarr quoted a research study by Voetsch et. al. (1) that found that even though doctors think that clinical labs are testing for E. coli O157:H7, only 57% of the labs actually do test for this strain of bacteria. Unfortunately, with E. coli O157:H7, time is of the essence and bacteria take time to grow.

Behold the future: it's the "Lab-on-a-chip"
At the end of the talk, Tarr showed us an interesting glimpse into the future of clinical microbiology with the "lab on a chip." This is a technology that is being developed by Micronics, Inc. in conjunction with PATH. It works with diffusion and microfluidics. You add a small amount of solution to the chamber with a pipette. The liquid diffuses into the chamber and mixes with other liquids, chemicals and enzyme solutions. This is really nice because all the materials are measured out and already present in the reaction chamber. The chambers are small by the way, I think about the size of a credit card or even smaller.

At some point, although I'm not sure when, nucleic acids from the sample get immobilized onto a filter. Then a technician can put the chamber into an incubator where the sample goes through several cycles of PCR. After that, the PCR products are detected on the filter.

There are many practical things about this technology. The assays are quick - they can be completed in lless than an hour. You don't need a clean room. You're not asking for as much in terms of having a trained person evaluate the results or perform the assay. You're detecting the toxin gene itself, not a labile or low-concentration toxin. Last, this is a technology that looks like it's really easy to use. You won't have to ask people to mix several reagents together and follow several complicated steps. Everything is ready to go inside the chamber. I was pretty impressed last year when I heard Karen Hedine talk about Micronics at the LEAP summit, but after hearing this talk, I'm really convinced that "lab-on-a-chip" technology is going to revolutionize clinical microbiology in the years to come.

Reference:
1. Voetsch AC, Angulo FJ, Rabatsky-Ehr T, Shallow S, Cassidy M, Thomas SM,Swanson E, Zansky SM, Hawkins MA, Jones TF, Shillam PJ, Van Gilder TJ, Wells JG, Griffin PM; Emerging Infections Program FoodNet Working Group.
Laboratory practices for stool-specimen culture for bacterial pathogens,including Escherichia coli O157:H7, in the FoodNet sites, 1995-2000. Clin Infect Dis. 2004 Apr 15;38 Suppl 3:S190-7.