Whole Genome Sequencing as a Public Health Tool

July 12, 2016
Whole Genome Sequencing as a Public Health Tool
Source: CDC

Researchers from The University of Texas at San Antonio (UTSA) have harnessed the power of next-generation sequencing to develop innovative strategies for tracking disease-causing pathogens like E. coli. The investigators hope their new study—“Whole Genome Sequencing for Genomics-Guided Investigations of Escherichia coli O157: H7 Outbreaks”—published recently in Frontiers in Microbiology, will aid in halting and preventing large-scale microbial outbreaks.

“When there's an outbreak of human pathogenic E. coli, a timely response is very important," explained senior study author Mark Eppinger, Ph.D., assistant professor in the department of biology at UTSA and a member of the UTSA South Texas Center for Emerging Infectious Diseases. "Usually, at first, no information is available about where the disease originated."

Dr. Eppinger has modified a form of whole genome sequencing to classify outbreak strains by looking for unique characteristics and subtle traits that make them distinguishable from one another. He likened the investigation to looking at a parking lot full of the same blue car. They all look very similar, but Dr. Eppinger and his team are looking for the tiniest differences such as a dent, a scratch, or a broken tail light.

"No detail is too small," Dr. Eppinger noted. "We can use these differences to trace the outbreak back to its contaminated source by looking to see if these traits existed in other reported outbreaks of the same pathogen."

Searching for similarities between outbreaks allows for pathogens to be traced back to an individual country or region, or even to a singular location. The more quickly investigators can find the source of an outbreak, the faster they can contain the epidemic. The UTSA team’s strategies may also aid in identifying how lethal the pathogen can be. For instance, in the current study, the authors focused on outbreaks of E. coli, which recently affected restaurants like Chipotle and companies like Totino's, who sell frozen pizza products.

"Some outbreaks can be more severe than others," Dr. Eppinger remarked. "As a result of the 2006 outbreak, which spread through spinach, nearly half the people affected were hospitalized, and a large portion had permanent kidney damage."

By studying strains from different past E. coli outbreaks with this new set of techniques, the researchers are able to measure the amount of toxin produced in each strain, which is a direct mediator of disease and shows how severe the resulting illness could be. Moreover, the scientists were able to characterize differences in the phage inventory of the microbes, allowing them to identify plasticity among outbreak strains that are not typically detectable at the core genome level.

"In terms of outbreak investigation, you can ask a person where they've eaten, where they work and if they've traveled recently," Dr. Eppinger stated. "If we get an outbreak strain, we can map it directly to other outbreak strains and pinpoint the origin. The answer is there in these tiny details."

The authors concluded their study by stating that “while we eagerly anticipate the introduction of sequence-based pathogen typing as a public health and disease prevention tool, we share the concerns of previous research, that stresses this powerful technology be employed as an adjunct to, and not a replacement for, case interviewing (descriptive epidemiology) and environmental investigations.”

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