Cultivated anaerobic Klebsiella pneumoniae bacteria. Image: CDC

When an outbreak occurs, in order to effectively figure out how to stop it, researchers typically try to figure out how it started. The answer to that question, though, can be elusive. And as so-called superbug infections have spread across the country’s hospitals, scientists and public health officials have subsequently struggled to understand how these pathogens spread.

Genetics, though, may provide a pretty good clue. A paper published Wednesday in Science Translational Medicine details how the antibiotic-resistant Klebsiella bacteria spread through 26 healthcare facilities and sickened 40 people in 2008. To track the spread, they relied on a combination of genomic sequencing and information about patient movement.

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“My research group and many others in recent years have been using these technologies to study how bacteria moves through one institution,” Evan Snitkin, a University of Michigan microbiologist and lead study author, told Gizmodo. “But these organisms permeate healthcare institutions across regions. We wanted to see if you could also track them as they spread across facilities.”

Typically, outbreak investigations rely on information about patient movement, but that data simply isn’t detailed enough to provide solid evidence of how an outbreak starts and spreads. By sequencing the genome of the bacteria in question as it mutated between hospitals, they were able to trace the origins of the 2008 outbreak to a single strain introduced into the Chicago area in late 2007. From there, they were able to paint a picture of how events at one particular hospital contributed to the spread of the infection. Their analysis found that one nursing home was an important transmission hub, with patients from that facility spreading the infection far and wide.

“This was a proof of principle,” said Snitkin. “It could really transform how we do infection control across regions. We could use it to really get a better handle on outbreaks.”

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Snitkin said that real-time tracking in a future outbreak could help determine, say, if a hospital needs to crack down on things like hand washing to stop the spread of an outbreak from within or whether the problem is that it needs to better monitor incoming patients.

“You can start to connect the dots,” he said. “In this case, the center of transmission was a single facility and we expect that won’t be uncommon.”

Superbugs that have evolved resistance to multiple antibiotics have become a major problem in the US, with some bacteria evolving resistance to so many drugs there is no longer a readily available way to kill them. According to the CDC, each year at least two million people become infected with bacteria that are resistant to antibiotics in the US and at least 23,000 people die as a direct result of these infections. Klebsiella is a member of a class of superbugs known as carbapenem-resistant bacteria. The CDC first detected this type of antibiotic-resistant bacteria in 2000 and since then it has spread across the country to most states.

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Snitkin said that the next question is whether the same technique can also be used once a superbug has become endemic to an area, as Klebsiella now is in the Chicago area.

“The big question,” he said, “is what will be the lessons we can use to get a hold on antibiotic-resistance which has become a major public threat?”