Picture of Chronobacter made with a scanning electron micrograph, showing the rod-shape of these bacteria.

The microbe behind the baby formula recall can be benign—or deadly

Cronobacter sakazakii, a little-known microbe, has evolved traits that make it difficult to destroy, posing a threat to our food safety.

Colored scanning electron micrograph of Cronobacter sakazakii bacteria. C. sakazakii is found in many environments, from soil to the human gut, and has been linked to infant meningitis and necrotizing enterocolitis, most likely via contamination of milk-based infant formula. It can also cause bloodstream and central nervous system infections with associated seizures, brain abscesses, and hydrocephalus. 
Photograph by Dennis Kunkel Microscopy, Science Source

The bacterium behind the baby formula recall, Cronobacter sakazakii, is less well-known than other food-borne pathogens like E. coli or Salmonella, but it can wreak havoc in vulnerable populations like newborns or people with compromised immune systems.

When two infants died earlier this year after drinking bacteria-contaminated baby formula produced by Abbot Nutrition, the tragedy sparked a sweeping recall, eventually shutting down the company’s Michigan-based plant. Parents and caregivers—already squeezed by pandemic-related supply chain hiccups—scrambled to feed their babies. The deaths, and the shortage that followed, exposed weaknesses in the food safety system in the United States when pitted against C. sakazakii.

Fortunately, infection with this “nasty little bug”—which kills between 50 and 80 percent of infected newborns—is relatively rare with just a handful of cases in the U.S. identified per year, says Amy Edwards, a pediatrician and associate medical director for infection control at UH Rainbow Babies & Children’s Hospital in Ohio. In the 12 years Edwards has worked in neonatal intensive care, she’s encountered it five to 10 times. “But if you call me and tell me you’ve got a two-month-old whose culture is growing Cronobacter sakazakii, I’ll freak out a little bit,” she says. “It scares me more than E. coli does.”

Named after Cronos—the Titan god from Greek mythology who consumed his children, as well as Japanese microbiologist Riichi Sakazaki who characterized the species—the wily bug has evolved a few tricks to help it thrive under conditions most of its brethren would find impossible to survive.

That makes C. sakazakii a bacterium to watch, according to Benjamin Chapman, a microbiologist and food safety specialist at North Carolina State University.

What is Cronobacter sakazakii?

Despite its comparatively low profile and infection rates, C. sakazakii is common. “It’s in soil and in the environment,” Chapman says. The bacterium has also been detected in homes—including on countertops, air filters, and other surfaces. And although it’s infamously linked to powdered baby formula, now and in the past, the microbe has popped up in everything from fresh produce and herbal teas to sewer water.

C. sakazakii “are also part of normal human flora that reside in the gut in small amounts, where they’re kept under control by other bacteria,” Edwards says. Dubbed the gut microbiome, this community of (mostly) beneficial microbes in the intestines, ensures the body is functioning optimally. For healthy children or adults, therefore, small quantities of pathogenic bacteria “don’t really cause problems.”

Erika Claud—a neonatologist at the University of Chicago, who studies the effects of a disease of the intestines often caused by C. sakazakii—agrees. “Think of your microbiome like an ecosystem such as a forest or a pond: All of the elements keep everything else in check.” When such a system is in balance, good bacteria can block harmful ones from adhering to human cells. They also compete for available nutrients, preventing bad bugs from flourishing.

When Cronobacter sakazakii is harmful

But newborns, with their still-developing immune systems and immature gut microbiomes, can be quickly overwhelmed by pathogens like C. sakazakii, which are primarily introduced through powdered formula or via the birth canal during delivery.

A typical route of attack for the bacteria, says John Swartzberg, a professor emeritus of infectious diseases at the University of California, Berkeley, is through the gastrointestinal tract. Normally, pathogens are trapped by the mucus layer separating what’s inside the intestines from the rest of the body. But in newborns or immunocompromised adults, he says, “Cronobacter sakazakii can penetrate the mucosal wall, get into the bloodstream, and travel to the rest of the body.”

The bacteria can then “cause sepsis, which is where the blood vessels become leaky because you’re inflamed, and multiple organs, like the heart and kidneys, begin to fail,” Edwards says.

Another target C. sakazakii favors is the brain. “It has a predilection for the lining of the brain, or the meninges, causing bacterial meningitis,” Swartzberg explains. And if the child survives the infection, the consequences are often dire—including seizures, cognitive impairment, and developmental delays.

Science of Cronobacter sakazakii

Part of the Enterobacteriaceae family, these bacteria are rod-shaped organisms with whiplike appendages that help them move towards nutrients and other targets.

Not only is this bacterium mobile, C. sakazakii is also exceptionally hardy; viable bacteria have been discovered in powdered formula left on the shelf for up to two years. “The fact that it survives in arid environments for a long time is really special,” Chapman says. This trait renders traditional food safety strategies like drying food to inhibit bacterial growth useless against C. sakazakii.

The bacterium’s secret lies in its genome, according to Roy Sleater, a molecular biologist at Munster Technological University in Ireland. Sleater and his team found that C. sakazakii contains seven copies of an osmotolerane gene—which encodes a protein that helps protect the bacteria in low moisture environments—while other bacteria have just one. This enables C. sakazakii to produce much more of this protective protein compared to their less desiccation-resistant peers. And “this protection extends to other forms of stress such as high temperatures and high pressure,” Sleater says, referring to previous research that found bacteria that can survive low moisture also become more resistant to heat.

C. sakazakii is also capable of forming a biofilm, a community of bacteria that live together in a sugary matrix its members produce, Claud says. This biofilm can adhere to surfaces like countertops or hospital equipment as well as organic matter like a baby’s intestinal cells. And in a case of “together we stand and divided we fall,” a biofilm is much more than the sum of its parts—the bacteria within it communicate with one another and adapt to changes in the environment. This flexibility makes biofilms especially tough to destroy.

Chapman hopes that the events of the past few months will lead to C. sakazakii’s moment in the sun. So far, “it hasn’t made it to the list of things that we’re tracking—like E. coli or Salmonella,” he says. But the impact on infants who rely on powdered formula as their sole source of nutrition can be huge. “I’d like to see Cronobacter sakazakii elevated to something that we track and becomes a notifiable disease.”

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