After being handed a cool $23.6 million from investors, OpGen has decided to turn its sails toward the clinic — clinical microbiology, that is. At the advice of investors, which include CHL Medical Partners, Highland Capital Partners, and Versant Ventures, the Madison, Wis.-based company has switched focus to developing its optical mapping tool for identifying strains of bacteria in clinical microbiology labs. Founded off technology created by scientists at New York University, the company previously provided optical mapping as a service to the research community, focusing on DNA sequence assembly and comparative genomics.
“Although the technology is extremely versatile, there is a critical need in clinical microbiology for improved methods for microbial identification,” says Colin Dykes, chief scientific officer. “Now what we’re going to be doing is focusing on using optical mapping to identify organisms in clinical samples, based on direct analysis of the DNA taken right out of the organism.”
Optical mapping slices up DNA along restriction sites, and then uses these overlapping fragments as a map to assemble DNA sequences. These restriction maps can be used to resolve both large and small genomes. “The pattern of restriction sites in any organism is highly characteristic of the species and, in fact, of a sub-strain or even of an individual isolate,” Dykes says, adding that optical mapping “can pick up very, very subtle difference between strains.”
Finding a particular strain of bacteria is especially useful to clinical microbiology labs that still rely on culturing microorganisms in media, a process that takes days. OpGen’s optical mapping technique can produce the identity of the bacterial strain “in a matter of hours,” Dykes says, enabling physicians to diagnose and then prescribe antibiotics faster.
Another major application is in the area of microbial forensics. Controlling mutant bacterial strains in hospitals, tracking the cause of infectious diseases, and tracing the source of microbial contamination are all areas that could benefit from this type of technology. The FDA used OpGen’s technology to determine the strain of bacteria that led to the outbreak of contaminated spinach in the US last year, which gave many Californians food poisoning.
Dykes is optimistic about both being able to get FDA approval to use the technology in clinical labs, as well as its utility there. “Automation, speed, and accuracy are the three big differentiators,” he says of optical mapping over the “19th century” technique of growing bacteria up in culture. As with all new technologies, uptake might simply depend on whether current labs are willing to adopt newer, high-throughput technologies in a field that has only recently entered the large-scale bio realm. “Some labs embrace new technologies vigorously and others tend to be resistant to new technologies,” Dykes says. “We’re going to encounter both of those phenomena.”