This Genetic Testing Tool Could Help Doctors Break The Chain During Superbug Outbreaks

Medical sleuths on the trail of drug-resistant bacteria could have a powerful new tool at their disposal.

When it comes to stopping the outbreak of a dangerous drug-resistant “superbug” bacteria, doctors often have to become detectives. They can treat each patient as they come in, but stopping the infection from spreading — that can be the key to saving even more lives.

Recently, a team at the University of Michigan and Rush University Medical Center used data from a real-world outbreak of a dangerous, drug-resistant superbug called CRKP to show that genetic testing can reveal how these superbugs are spreading, giving doctors a heads up on how to break the chain of infection and potentally stop an outbreak in its tracks.

A worker holding a petri dish full of E. coli bacteria, which are one of many different types of bacteria that may acquire antibiotic resistance. Photo by Christian Charisius/AFP/Getty Images.

The data from that CRKP outbreak provided researchers with the story of how the disease spread. In 2008, a man — who was incredibly sick and dying from a CRKP infection — was transferred to Rush University Medical Center in Chicago from a hospital in northern Indiana. Doctors there knew he wasn’t the first CRKP case in the Chicago area. Another case had cropped up just five months earlier.

Two cases of a dangerous superbug appearing in the same region had the doctors worried. A team headed by Mary Hayden, an infectious disease physician, began investigating. With a bit of legwork, they were able to find and map out the spread of the infection, watching how it hitched rides on dozens of different patients as they were transferred from hospital to hospital, nursing home to nursing home.

At the time, genetic analysis wasn’t sophisticated enough to really help Hayden track the chain of infection, but her team preserved samples from the patients anyway, hoping they could one day serve as time capsules for future investigations.

Now, they can.

The recent breakthrough involves whole genome sequencing. As bacteria grow and spread, they inevitably accumulate mutations in their genome, and by taking genetic samples from two different strains and comparing their unique mutations, scientists can tell if they’re related. It’s kind of like running a bacterial paternity test.

Hayden wanted to see if this kind of sequencing could have helped find the chain even faster during the 2008 outbreak.

To test her theory, she teamed up with Evan Snitkin’s genetics lab at the University of Michigan. Snitkin’s team tested each of Hayden’s samples in the order they were originally collected and without any prior information about each sample, essentially walking through the crisis beat-for-beat. As they did, they used the genome sequencing to build a kind of bacterial family tree.

When the two teams compared the new bacterial family tree with the results of Hayden’s 2008 investigation, they lined up nicely.

The technique won’t just duplicate conventional detective work, Hayden says. It could also help reveal nuances and insights into how a superbug is spreading, allowing doctors to move quickly to stop the chain of infection.

During the 2008 outbreak, for example, there were five patients, all at the same hospital, who had all caught CRKP. But doctors didn’t know how and when each patient picked up the bug. If one patient had carried it and spread it to all the others, for example, that’d mean the superbug was spreading within the hospital. On the other hand, if each patient had picked up the bug somewhere else and then came to the hospital, the source must be somewhere else.

Standard hygiene procedures are a cornerstone of a working hospital, but during an outbreak, further measures might need to be taken, such as isolating infected patients. Photo by Christopher Furlong/Getty Images.

Back then, the doctors had to work without knowing which scenario was true, but Hayden’s new genetic analysis showed that it had actually been a combination of both scenarios. Three of the patients contracted CRKP outside the hospital first, then two of them spread the bug to two other patients once they were hospitalized.

Had this technology been available at the time, doctors would have known as soon as they saw the test that they needed to do something to prevent transmission inside the hospital, such as isolating carriers and infected patients, as well as look for an outside source.

“The earlier we can intervene to contain an outbreak, the more likely it is that we can eradicate it," Hayden explained in a press release.

Drug-resistant bacteria like CRKP have become a major medical problem in the United States. At least 2 million Americans catch one of these infections each year and more than 20,000 die from one.

The team’s process will still need to be tested in other settings, like nursing homes and with other diseases, says Hayden, but it should work with nonbacterial infections, such as those caused by viruses and fungi, and could provide a powerful complement to standard epidemiological detective work. The team’s work appeared in the journal Science Translational Medicine.

The team isn’t the only lab that has this kind of equipment and capability, and as such, they’re hoping their results can serve as a proof of concept for doctors and public health agencies like the CDC.

When outbreaks happen, doctors have to become detectives. Thanks to tools like this, the medical Moriarty that is superbug outbreaks may soon be easier than ever to defeat.

Photo by Josh Couch on Unsplash

Christopher Columbus, Alexander Hamilton, William Shakespeare, and Sir Walter Scott are getting company. Statues of the famous men are scattered across Central Park in New York City, along with 19 others. But they'll finally be joined by a few women.

Susan B. Anthony, Elizabeth Cady Stanton, and Sojourner Truth are the subjects of a new statue that will be on display along The Mall, a walkway that runs through the park from 66th to 72nd street. It will be dedicated in August of next year, which is fittingly the 100-year anniversary of the 19th Amendment that granted women the right to vote.

Currently, just 3% of statues in New York City are dedicated to women. Out of 150 statues of historical figures across the city, only five statues are of historical women, including Joan of Arc, Golda Meir, Gertrude Stein, Eleanor Roosevelt, and Harriet Tubman.

Keep Reading Show less

It's easy to become calloused to everyday headlines with messages like, "the world is ending" and "everything is going extinct." They're so prevalent, in fact, that the severity of these statements has completely diminished to the point that no one pays them any attention. This environmental negativity (coined "eco-phobia") has led us to believe that all hope is lost for wildlife. But luckily, that isn't the case.

Historically, we have waited until something is near the complete point of collapse, then fought and clawed to bring the species numbers back up. But oftentimes we wait so long that it's too late. Creatures vanish from the Earth altogether. They go extinct. And even though I don't think for a single second that we should downplay the severity of extinction, if we can flip this on its head and show that every once in a while a species we have given up on is actually still out there, hanging on by a thread against all odds, that is a story that deserves to be told. A tragic story of loss becomes one about an animal that deserves a shot at preservation and a message of hope the world deserves to hear.

As a wildlife biologist and tracker who has dedicated his life to the pursuit of animals I believe have been wrongfully deemed extinct, I spend most of my time in super remote corners of the Earth, hoping to find some shred of evidence that these incredible creatures are still out there. And to be frank, I'm pretty damn good at it!

Keep Reading Show less
The Planet

For more than 20 years. Sen. Susan Collins (R-ME) has served the citizens of Maine in the U.S. Senate. For most of that time, she has enjoyed a hard-fought reputation as a moderate Republican who methodically builds bridges and consensus in an era of political polarization. To millions of political observers, she exemplified the best of post-partisan leadership, finding a "third way" through the static of ideological tribalism.

However, all of that has changed since the election of Donald Trump in 2016. Voters in Maine, particularly those who lean left, have run out of patience with Collins and her seeming refusal to stand up to Trump. That frustration peaked with the nomination of Brett Kavanaugh to the Supreme Court.

Keep Reading Show less
NHM Vienna/Hans Reschreiter

Wealth inequality has been a hot topic of discussion as of late, but it's something that's occurred all throughout history. Class structure is a complicated issue, especially when you consider that haves and have nots have been in existence for over 4,000 years.

A study published in Science took a look at over 100 late Neolithic and early Bronze Age skeletons found in a burial site in southern Germany. The study "shed light on the complexity of social status, inheritance rules, and mobility during the Bronze Age." Partly by looking at their teeth and the artifacts they were buried with, researchers were able to discover that wealth inequality existed almost 4,000 years ago. "Our results reveal that individual households lasting several generations consisted of a high-status core family and unrelated low-status individuals, a social organization accompanied by patrilocality and female exogamy, and the stability of this system over 700 years," the study said.

Keep Reading Show less
via / Flickr and Dimitri Rodriguez / Flickr

Bernie Sanders' presidential campaign looks to be getting a huge big shot in the arm after it's faced some difficulties over the past few weeks.

Alexandria Ocasio-Cortez, a leading voice in the Democratic parties progressive, Democratic Socialist wing, is expected to endorse Sanders' campaign at the "Bernie's Back" rally in Queens, New York this Saturday.

Fellow member of "the Squad," Ilhan Omar, endorsed him on Wednesday.

Keep Reading Show less