Penn State Researchers Developing Genomic Resources to Identify Novel Pathogens

The research team (from left): Grant Harm, undergraduate research assistant; Xiaoyuan Wei, postdoctoral scholar; Taejung Chung, doctoral student; and Jasna Kovac, assistant professor of food science and Lester Earl and Veronica Casida Career Development Professor of Food Safety. IMAGE

To enhance the early detection of novel infectious bacteria that could cause outbreaks of infectious disease and public health emergencies, a team of researchers in Penn State’s College of Agricultural Sciences will sequence the genomes of 700 Bacilli bacteria — near relatives of the biothreat pathogen that causes anthrax.

Funded by a $1.2 million grant from the U.S. Centers for Disease Control and Prevention, the research will support the development of genomic resources and DNA sequence databases for the federal agency to increase its capacity for rapidly detecting novel pathogens, according to team leader Jasna Kovac, assistant professor of food science and Lester Earl and Veronica Casida Career Development Professor of Food Safety.

A nanopore sequencer like this one will be used in the study to sequence the genomes of 700 Bacilli bacteria — near relatives of the biothreat pathogen Bacillus anthracis.

“You may have heard of the 2001 bioterrorist attacks in which spores of the bacteria Bacillus anthracis that cause anthrax were circulated in the mail,” she said. “People who inhale these spores can get sick with anthrax, which is often fatal.”

From a biodefense standpoint, it is important to understand the diversity of environmental Bacilli that could become novel biothreats such as anthrax, added Kovac, who has extensive experience with the genomics of Bacilli.

“There are known examples among Bacillus cereus group bacteria where ‘benign’ environmental strains have acquired anthrax-causing capabilities,” she said. “We are interested in detecting and characterizing similar strains of Bacilli that have both the characteristics of known biothreats and harmless environmental microorganisms.”

An electron micrograph image of a Bacillus strain.

If emerging pathogens or biothreats are detected early on, they are more likely to be contained effectively to prevent a public health emergency, Kovac noted. “We are partnering with the CDC to create a large database of Bacilli to support its development of rapid laboratory methods for the detection of novel, naturally occurring or engineered pathogens and potential emerging biothreats,” she said.

The databases will enhance and strengthen existing genomics approaches and bioinformatics pipelines developed by the CDC’s Division of Preparedness and Emerging Infections group. This will allow for the rapid detection of genomic markers associated with increased biothreat risk, Kovac pointed out.

“We are uniquely positioned to complete the proposed work and support CDC’s expansion of reference databases for the detection of novel, emerging infectious diseases,” she said. “Here in Penn State’s Department of Food Science, we have microbiology and genomic expertise and access to a large number of unique, environmental and food Bacilli, deposited in the Food Microbe Tracker culture collection and database curated by our collaborators at Cornell University.”

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