NEW YORK (GenomeWeb News) – Scientists at Rice University will use a three-year grant from the Department of Defense to develop genomic knowledge for use in a rapid test to determine if a disease outbreak is caused by a natural pathogen or by a manmade, lab-grown agent.
Rice researchers have received roughly $900,000 grant from the Defense Threat Reduction Agency, the DoD's Combat Support Agency for countering weapons of mass destruction, for their research.
First, they will domesticate two common strains of wild bacteria, Enterococcus faecalis and Escherichia coli, in a lab. After the bacteria have evolved to acclimate to lab life, the researchers will study their genomes for changes that may provide 'telltale patterns' indicating that they were developed in and accustomed to living in biology labs.
"In a natural outbreak, there are classic rules of epidemiology that describe how particular types of diseases will spread," principal investigator Yousif Shamoo, associate professor of biochemistry and cell biology and director of Rice's Institute for Biosciences and Bioengineering, said in a statement.
"In a man-made outbreak, you may be faced with an actor who is continuously spreading the disease, or you might have a person who's engineered strains knowing public health strategy," he added.
Shamoo's lab studies evolution at the molecular level and how bacteria evolve to become drug resistant. He expects that the same forces that enable drug-resistant strains to out-compete their non-drug-resistant cousins also will allow researchers to distinguish pathogens that are natural from those developed in labs.
"The idea is to look for commonalities. Is there a common set of responses to domestication that you would likely see for any organism that's adapting from living in the wild to living in the laboratory?" he said.
The patterns Shamoo expects to find will be brought out by the environmental differences between lab life and the natural world.
"Living out in the wild is a pretty rough existence. By comparison, life in the laboratory is very posh. You live in very nice conditions on agar plates eating this very rich media," he said.
"Our expectation is that organisms will lose certain genes that allow them to get nutrition from the soil or the gut or wherever they came from, simply because they won't need them anymore."
These new bacteria should then be able to out-compete the wild type of bacteria in the lab setting, and they should have genetic differences to show for it, he explained. Shamoo also said he hopes that if genetic patterns linked to domestication can be located in these bacteria, they may be the useful in other bacteria as well.
Shamoo told GenomeWeb Daily News today that the research will involve sequencing the genomes of the bacteria at a beginning point, just as they are introduced to the new environment, and at an endpoint some generations later after they have adapted to the media-rich environment.
The US Army, Rice's partner in the project, will conduct the sequencing in its labs at the Edgewood Chemical Biological Center.
The researchers also plan to watch the mutation process in action by freezing samples along the way in order to "put together a record of the adaptation," Shamoo told GWDN. Once mutations are recorded and recognized, the Rice team will use mass spectroscopy to identify them in their samples as the study moves forward.
When Rice's research is over, the DoD will aim to develop a rapid test, such as a PCR-based, or even a sequencing-based assay, to identify lab-made from natural microbes.
The value to the US government, Shamoo said, is that being able to identify a man-made strain can let authorities know if a person is out there actively releasing the pathogen, enabling them to respond. Such a test also could tell authorities where the strain came from and provide other information about it, which could allow them to take other precautions and potentially to pursue the culprit.