Quicker method to track outbreaks from poo in the pool

Whole genome sequencing technology may give scientists and health care workers a powerful weapon in tracking—and possibly controlling—outbreaks of serious diseases, researchers say.

In a new study, researchers discovered that both international and domestic sources of Shigella sonnei—the fourth most common cause of bacterial foodborne illnesses in the US, came from a related group of the bacteria, called Lineage II.

Experts had originally proposed that the international and domestic strains of Shigella likely came from different sources, according to the paper in Microbial Genomics.

“One of the questions we asked was, genetically, are the domestic Shigella distinct from those that are coming internationally and, in the end, the answer was, no, they are not distinct—there doesn’t appear to be any stratification based on genetic relatedness,” says Edward Dudley, professor of food science at Penn State and associate of the Institute for CyberScience, which provides Penn State researchers access to supercomputing resources.

Because different strains of Shigella may require certain treatments, identifying the correct type of in a timely fashion could give public health officials a critical head start on both notifying the public about an outbreak and alerting medical staff on best treatment options.

What’s in the pool?

Shigella, which causes severe diarrhea and stomach discomfort, is typically passed through stool. Because infected swimmers at public pools and swimming areas are often a common source of Shigella outbreaks, the quicker officials who run those facilities are alerted about a possible outbreak, the quicker they can take preventative action and issue warnings.

Comparing Shigella samples during an outbreak could also give health officials the ability to identify possible sources of the disease, help them monitor its progress, and warn officials in locations that might lie in the outbreak’s path.

“In this study, with this particular species of Shigella, there were known to be five different lineages and we identified signatures in the genomes of these organisms that allow us to very rapidly say which of these five it segregates into,” Dudley says.

“This helps the department of health to not only show how they can use whole genome technology for research, but maybe even how they can even use it to develop a new diagnostic tool.”

Whole genome sequencing can determine an organism’s complete genome, including the organism’s chromosomal DNA and mitochondrial DNA. Whole genome sequencing is faster and more accurate than pulsed-field gel electrophoresis, or PFGE, the previous standard test that only offered a basic genetic fingerprint of bacteria, Dudley says.

“DNA sequencing data is a lot clearer to look at—PFGE is more pattern based—and it’s a lot more specific,” Dudley says. “If you sequence the genome of the bacteria, you now have 5.5 million data points. If there’s a perfect match between the food and the patient, then it’s inarguable that there’s a relationship between the two of them.”

Whole genome analysis delivers results in a little over a day, which is much faster than PFGE. As computer technology advances, Dudley expects the speed of sequencing to increase, perhaps delivering results in a matter of hours.

Salmonella, too

In an earlier study, Dudley’s laboratory at Penn State also used whole genome analysis to study Salmonella, a leading cause of foodborne illnesses in the US that causes about 450 deaths annually and often links with contaminated retail meats.

In a paper published in Microbiology, the researchers say that Salmonella collected from people was genetically distinct from the types collected from the meats, such as ground turkey, pork chops, and chicken breasts.

“By using the PFGE method, the Pennsylvania Department of Health concluded that human isolates and the meat isolates were identical,” Dudley says.

“However, we could show them by using whole genome sequencing that—not so fast—you can actually distinguish them with this new method. So, from this, we could bolster the argument that these people were not getting sick from meats that were contaminated with those particular strains.”

For Shigella, the researchers sequenced a total of 22 isolated samples of the bacteria, also known as isolates—11 from domestic sources and 11 international ones. Both sample sets were resistant to at least three classes of antibiotics. In the Salmonella study, the team sequenced a total of 50 isolates of the bacteria.

The collected data is stored on the FDA’s GenomeTrakr, a distributed network that allows researchers and public health officials to conduct real-time comparison and analysis to speed up foodborne illness outbreak investigations and reduce foodborne illnesses and deaths.

Additional coauthors are from Penn State, the Pennsylvania Department of Health, the Maryland Department of Health, and the US Food and Drug Administration. The Centers for Disease Control and Prevention, the US Department of Agriculture, and the US Food and Drug Administration supported this work.

Source: Penn State

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