When a patient is admitted to the hospital with signs of a dangerous systemic bacterial infection, or when a post-office worker finds white powder in a suspicious-looking envelope, the ability to quickly identify potential pathogens is important. To accomplish that, a team of Massachusetts researchers is developing a microfluidic chip that performs fast DNA sequencing to rapidly identify bacteria. The goal is a device simple enough to use in airport and other security screening.
In order to identify the bacteria in a blood sample or in a building’s ventilation system, researchers or clinicians usually must start by coaxing it to grow in culture in the lab. This takes about 14 to 48 hours. In the meantime, a patient with a drug-resistant infection may be given the wrong antibiotic, or emergency medical workers may miss the signs of a potential bioterror attack.
Researchers at U.S. Genomics, in Woburn, MA, and Draper Laboratory, in Cambridge, MA, are working together to improve technology that allows for the sequencing and identification of bacteria and other pathogens without culturing. The researchers don’t read every single base on a strand of DNA, but they look for distinctive patterns of repetition of a single, very short sequence. There are only four elements to the genetic code, so six to eight base lengths like GTAGCC occur many times within all genomes. But in each species, such a sequence will occur in a unique pattern. Even different strains of the same kind of bacteria will have unique identifying patterns of a given short sequence.
U.S. Genomics has built a database of these patterns, which it calls bar codes, for many bacterial species and strains. Because the work is being funded by the U.S. Department of Homeland Security, the company will not disclose how many pathogens are in its database or what they are. Staff scientist Jeff Krogmeier does say that the government agency is interested in an instrument “that would sit in an airport, mall, or other public area and continuously monitor the air.” Its compact analysis chip is a step in this direction in that it can identify bacteria based on analysis of long strands of DNA that don’t need to be extensively treated. “We just need a few molecules [of DNA],” says Krogmeier.
First, DNA must be extracted from the sample and labeled with a fluorescent tag that attaches only to places along the strand where the short sequence of interest occurs. (U.S. Genomics is working to simplify this step, which currently must be done in the lab.) Single long molecules of DNA are then fed into a microfluidic chip, where hydrostatic pressure pulls them at a constant speed through a narrow channel. As the labeled DNA flows through the channel, it passes over a very narrowly focused beam of light. When the DNA pass over the beam, the labels fluoresce. Flashes of light from the labels are recorded like a bar code and compared with the U.S. Genomics database to identify the organism that the DNA came from.