Phylogenetix Laboratories, Inc., a company based in the Kansas City area, is riding the crest of a wave of developments in the field of molecular identification. Founded in 1995 by Peter Rogan, associate professor of medical genetics and molecular medicine at the UMKC School of Medicine and by its treasurer Robert Levy, the company grew out of a need to improve testing technology used to identify infectious agents. These traditional testing methods required significant time for the culturing of samples, had difficulty identifying new or unusual strains of an infectious agent, and couldn’t quickly identify the type of infection in high-risk, immunosuppressed patients. These technologies could identify only a collection of organisms or species, not the specific infectious agent.

Phylogenetix’s patented technology, OmniAmp®, addressed all of these problems. It joined the ranks of the new technologies called bioinformatics–ones that use computers, software, and databases to track, process, store, retrieve and analyze data generated by geno-mic research. OmniAmp® can directly and rapidly identify a wide variety of bacterial or fungal infectious agents. Also, it eliminates the need for culturing a sample by making use of a retrospective clinical trial. In just hours, OmniAmp® is capable of identifying an unlimited number of species of infectious organisms by pinpointing subtle variations in the DNA sequence that may be shared among many different organisms. OmniAmp® then determines a sequence of that amplified DNA, and compares it with a database of related sequences.

"The result," says Rogan, "is that we can single out a specific infectious agent from among a database of over 11,000 sequences. We don’t have to have identified a suspect organism causing the infectious disease prior to running a test."

Revolutionizing immunization
Using OmniAmp®, Phylogenetix is currently conducting feasibility studies for a technology that could revolutionize the immunization of children in developing countries. (See related article page 3) The inoculation device, called a repeating injector, under development by Felton Medical of Overland Park, Kansas, could be used to give numerous repeated inoculations against diseases such as measles and hepatitis B in a timely and cost-effective manner. Previously, repeatable injectors have been pulled from the market when it was proven that they allowed backflow of infection into the mechanism. What makes Felton Medical’s device different is a cap that prevents this backflow after each inoculation.

"We’re hoping to help Felton Medical determine the levels of cross-contamination, if any, from Hepatitis B virus carry-over from consecutive injections using defined quantities of recombinant hepatitis B genomic DNA," Rogan said. "When our study is complete, Felton intends to use the data as part of an application to the Food and Drug Administration for approval. Felton is optimistic that this approach will gain acceptance and will be adopted by the World Health Organization and the Centers for Disease Control."

This figure shows DNA sequences from four different pathogenic bacterial species. Each sequence is composed of four lanes, corresponding to the different components of the DNA sequence (G, A, T, C). Note the differences between the patterns, which represent unique sequences in a particular species. The sequences were determined from DNA fragments generated with the OmniAmp ® process.

Detecting pathogens
Recently, Phylogenetix responded to the rise in concern over food-borne pathogens. Working in partnership with the Johnson County Enterprise Center, the company is developing the capability of OmniAmp® to determine that food is safe for consumption. Not only will OmniAmp® be able to detect pathogens in raw meat, it will also prevent contamination of meat in processing plants by performing rapid assays to detect bacterial contamination of equipment with pathogens such as Listeria, Salmonella and E. coli.

Nutraceuticals
Phylogenetix is applying its combined capabilities in laboratory molecular biology and bioinformatics to a broad range of applications. For example, the company recently entered the burgeoning field of nutraceuticals. Though U.S. regulations have allowed the use of nutraceutical ingredients in a wide range of consumer products without premarket clinical testing, consumer and medical groups are seeking more stringent regulations. Also, larger pharmaceutical firms are seeking higher production standards to ensure quality of nutraceuticals.

Awarded a grant by the Kansas Technology Enterprise Corporation to perform genomic analysis of plant species. Phylogenetix recently signed a letter of intent for the licensing agreement for a specific test that allows OmniAmp® to distinguish the popular nutraceutical Echinacea from plant contaminants. Echinacea is often used by naturopathic physicians to boost the immune system’s ability to fight the common cold.

Using OmniAmp® to pinpoint the specific DNA sequence of a plant such as Echinacea ensures that it hasn’t been adulterated with other chemical compounds. Essentially, the DNA sequence doesn’t lie.

Rogan said, "What has resulted is a collaboration between scientists at the University of Kansas and the Kansas Biological Survey, who have used OmniAmp® to develop a test that could distinguish medicinal plants from contaminants in those plants. We’ve determined sequences of about three different genes multiplied by about 120 specimens collected from all across the plains, from Montana to Arkansas. We have a digital assay now. Though it’s a simple test, it’s a pretty robust one because it’s based on a large number of plant specimens collected over a broad geographic region."

OmniAmp® will create a new standard for certifying many such nutra-ceuticals, assisting everyone from farmers and wildcrafters to manufacturers and retailers in validating the purity of material being sold and packaged.

With increase in population size, the world has growing needs for molecular identification. Phylogenetix is poised to put themselves and Kansas on the map as leaders in the field. At this point, OmniAmp® and the company’s molecular identification expertise can be applied to a limitless number of situations.