Most strains of Escherichia coli, or E. coli, are harmless. Shiga-toxigenic E. coli, or STEC, is not one of those strains.

In 2016, South Dakota had the highest per capita rate of illness due to STEC in America. But a recent study out of the South Dakota School of Mines & Technology that identified genes related to harmful E. coli strains may help public health officials monitor, predict and prevent future outbreaks.

Currently, health officials measure the concentration of E. coli in waterways. If it exceeds a certain level, the water may pose a potential safety risk and is thus deemed “impaired” by the South Dakota Department of Environment and Natural Resources.

The recent study by Ph.D. student Kelsey Murray, under the direction of Linda DeVeaux, Ph.D. and Lisa Kunza, Ph.D., may soon replace that testing methodology, though.

“We just look at the bacterial DNA, basically,” Murray said from a room in the Mines’ Chemical and Biological Engineering/Chemistry building on Wednesday morning. “We look at their genes to see whether or not they carry particular genes that are associated with certain pathogens.”

Again, not all forms of E. coli are harmful. Murray’s testing methodology searches for the particular genes that can create the harmful strains.

“Our method more clearly defines the risk,” she said.

DeVeaux explained the difference between the current form of E. coli testing and this new methodology a bit further.

“What they’re (EPA) doing is a much broader and general,” DeVeaux said. “They just correlate overall that in the past, if there was this level of E. coli, they saw X number of infections from it.”

But E. coli levels are only part of the story, DeVeaux said.

“They give some indication generally about the risk, but we can pinpoint it probably better using something like this,” she said of the new methodology, which included taking water samples from different locations along Rapid Creek and Big Sioux River and then screening for 33 different types of genes which, in various combinations, can create the harmful E. coli strains.

Though the study didn’t quantify the number of genes, it’s known that as the number of genetic combinations rise, so too does the potential for a harmful strain to develop.

In Rapid Creek, the genetic density and proximity was highest in water samples taken shortly after leaving the city’s wastewater treatment facility. But nothing in this area compared to the Big Sioux River.

“We definitely found the genes in the Big Sioux and their total bacterial load is significantly higher than this side of the state,” Murray said. “So while we didn’t quantitate the genes, we can say there’s just more of a chance of them exchanging among the bacterial population just by the density and proximity of the bacteria.”

In South Dakota in 2016, there were 80 cases of people becoming sick from contact with STEC, a rate of 9.3 cases per 100,000 people. Though seven of the 80 cases in 2016 came from the Rapid City metropolitan area, the greatest concentration came in the northeast and southeast part of the state, near where the Big Sioux River traces its winding path before emptying into the Missouri River in Sioux City, Iowa. The northeast section of the state experienced 23 cases (13.3 per 100,000 people), while the southeast section saw 17 cases (15.1 per 100,000 people).

Though the groundbreaking study presents a new way forward for E. coli and water testing, the next test comes in trying to find a correlation between the strains found in waterways and those found in patients coming to the hospital with E. coli related illnesses.

“The thing that we really need to do is correlate what we’re finding in the water with what’s showing up in the clinic,” DeVeaux said. “Is the water the source of the people who are ending up in hospitals? Are they the same combinations that we’re finding in the water?”

Improved and consistent monitoring is also paramount, Deveaux added.

“We don’t even know what these bacteria can evolve to do, so that’s why continuing to monitor all of them, rather than just the ones that we know come together in organisms that we’ve seen causing disease, is necessary,” she said.

To Kunza, the next step for environment and health officials is just as clear.

“If the EPA were to adopt a method similar to this instead of E. coli as their general characteristics ... that would allow people to have a much better idea of the health risk associated with using waterways, certainly,” Kunza said.

But as Murray, Kunza and Mines spokesman Charles Michael Ray made clear, the implementation will, perhaps regrettably, be left to others.

“This research just lies out, here’s the science,” Ray said. “Here’s what we should be concerned about."

Contact Samuel Blackstone at and follow him on Twitter or Facebook @SDBlackstone.