For years, researchers have been tracking a particularly nasty family of superbugs called CREs, or carbapenem-resistant Enterobacteriaceae, which can thwart antibiotics in our last lines of defense. Researchers have watched in horror as clinical isolates gathered new molecular weaponry, spread through medical facilities across the globe, and started causing more and more life-threatening infections.

But a new study suggests we’re still only seeing a glimpse of what they’re up to.

In a genetic analysis of 122 CREs that popped up in four US hospitals, researchers discovered that isolates are far more diverse than expected, and some of them could disarm our toughest drugs using methods researchers had never even seen before. The hospitals—three in Boston and one in Irvine, California—had little overlap in their CRE collections. Within each hospital, there was a variety of CRE types, spanning several species, with a medley of genetic backgrounds and resistance genes.

The revelation, published Monday in PNAS, suggests that CREs are nimble adapters. And the variety with which they’re showing up in the sick could be explained by silent transmission among the healthy, the study authors speculate.

If true—and more surveillance of CREs among healthy and sick people are needed to prove it—we would need to rethink our strategy of fighting these dastardly microbes, lead study author William Hanage, an epidemiologist at Harvard, told Ars.

“If you want to understand a population of something, you want to take a representative sample of it,” Hanage says. But so far, doctors have tended to focus on interesting clinical cases and the most severe infections. “They have not gone out and tried to identify asymptomatic carriage,” he notes, “even though that could be the majority of transmission.”

If that’s the case, he says, “We are playing catch-up and it’s a bit of a shame.”

According to the Centers for Disease Control and Prevention, CREs cause about 9,300 infections in healthcare settings each year in the US, and the two most common CREs cause around 600 deaths each year. In infected patients, CREs show up most often in the urine, but also in respiratory tracts, wounds, and blood. Among patients that get CRE bloodstream infections, up to 50 percent die.

Superbug dark matter

Enterobacteriaceae—the ‘E’ in CRE—is a huge family of Gram-negative bacteria that includes a cast of dangerous and harmless characters, from E. coli to Klebsiella, Shigella, Salmonella, Enterobacter, and Yersinia pestis (the cause of the black plague). The group gets its name from the more casual term “enteric bacteria,” because many of them—but not all—live in intestines.

Members of this big family morph into deadly CREs when they develop or acquire genes that code for resistance to carbapenems—a group of antibiotics used to treat severe infections that are often already resistant to several other antibiotics. These carbapenem resistance genes come in several types and are often on mobile pieces of DNA or on shareable loops of DNA called plasmids. In other words, there’s a bunch of them and they can spread around frighteningly easily. Bacteria can share resistance with their comrades or even to distant relatives; E. coli can spread resistance genes to neighboring Klebsiella, for instance. (In the US, those two are the most common CREs.)

With the spread-ability of resistance and the seemingly endless varieties of CREs that it could create, researchers didn’t have a good handle on the makeup of CRE populations. So Hanage and his colleagues dug into isolates from the four hospitals, all collected in a 16-month window spanning 2012 to 2013. The three hospitals in Boston were close to each other, so you might expect them to see similar CREs that would spread within each hospital. The California hospital’s isolates were included to get a glimpse of nationwide spread.

Unexpectedly, the researchers found a wide variety even within and among the three neighboring hospitals. Overall, there were three common CRE species: Klebsiella pneumoniae, E. coli, and Enterobacter cloacae. But commonality broke down after that. Isolates among those three species broke into 17 genetic lineages. Most of those lineages were only found in one hospital. Many were only found in one patient. Just five of the 17 lineages were found in more than one hospital. Only two of the lineages were found on both coasts.

Within each of the 17 lineages, there were often several types of resistance genes. But different lineages often shared the same resistance genes. Two isolates had resistance genes that the researchers had never seen before, which Hanage described as “a sort of dark matter of antibiotic resistance genes.”

The researchers tried to use detailed genetic information to see if they could retrace how the different but related germs might have spread among the patients. But they couldn’t. They just didn’t have enough isolates to connect all the far-flung dots (if there were dots to connect).

“This result may suggest multiple unsampled transmission chains throughout the continuum of care, consistent with recent reports of asymptomatic carriage, which we know can continue for months after discharge,” Hanage and his co-authors wrote.

When talking with Ars, Hanage explained that these bacteria “can be deadly, but they’re not always deadly.” That’s why looking only within hospitals isn’t enough to understand, spot, and stop transmission. Instead, we need to start surveying outside of hospital settings and identifying those asymptomatic cases, he argues.

In other words, Hanage continues: “We need to change from playing this defensive game to actually taking control and being able to identify these tracks as they emerge rather than just coming along afterwards and saying ‘oh look, there are people dying.'"

PNAS, 2017. DOI: 10.1073/pnas.1616248114 (About DOIs).