A Pathogen Is Persisting in Infant Formula. UMD Researchers Found Genetic Clues to Explain Why

University of Maryland researchers are shedding new light on how a dangerous foodborne pathogen may have adapted to thrive in dried and powdered foods across the global supply chain. Their study, recently published online in the International Journal of Food Microbiology, could transform how we monitor and prevent contamination in critical food products like powdered infant formula.

Cronobacter sakazakii has made international headlines in recent years following recalls of powdered infant formula and has been linked to life-threatening infections in premature infants, the elderly and other vulnerable populations. Although infections are rare, the consequences can be devastating—ranging from meningitis to long-term developmental issues.

To better understand the pathogen’s persistence and transmission, the researchers conducted the first genomic meta-analysis of C. sakazakii bacteria strains from all over the world. Using an AI large language model (LLM) to standardize data from massive and inconsistent collections, and machine learning to identify potentially significant genes.

"We’re seeing how certain accessory genes—those not essential to survival but beneficial under specific environmental conditions—could confer advantages that help Cronobacter sakazakii persist in food systems and possibly even resist sanitation protocols,” said Ryan Blaustein, an assistant professor in the Department of Food and Nutrition Science, and the senior author of the study. Other team members were two department colleagues, Professor Abani Pradhan and Postdoctoral Associate Maurui Gao. Their work was supported in part through a grant from the U.S. Department of Agriculture National Institute of Food and Agriculture.

Individuals of a species carry a core set of genes that are shared across the species. But different strains or variants from different regions contain additional accessory genes unique to that strain. Blaustein and his colleagues analyzed 748 whole genome sequences collected from food, clinical and environmental sources across North America, Europe and Asia to identify the most complete set of C. sakazakii genes—also known as a pangenome—to date.

The LLM standardized inconsistent metadata about the origins and sources of each sample, among other things, making large-scale comparison possible.

“Everyone enters things differently, from the date and time to things like ‘powdered infant formula” using a capital “P” or lowercase “p” or just powdered formula or even PFI,” Blaustein said. “We used the language model to recategorize everything that was already in the public database and assign it with a very high accuracy. That hadn’t been done in this setting before.”

Once the team had standardized the data, it used machine learning models to identify core genes and paint a clearer picture of how the accessory genes varied among samples from different locations, environments and conditions. This helped them identify genetic signatures associated with where and how the sample was taken.

They found that samples from powdered foods (including infant formula and powdered milk) relative to other types had larger genomes, and a higher frequency of genes involved in DNA recombination, repair and desiccation resistance, all of which could contribute to the bacterium’s survival in dry conditions. In addition, there was a greater prevalence of genes associated with higher virulence in strains that were likely to persist in the food chain and cause illness.

The team also found correlations between geographic regions and genes associated with formation of biofilms and resistance to heavy metals like copper that show up in some food systems as a component of pesticides or as an essential nutrient, but can also act as an antimicrobial at high levels.

The presence of so many accessory genes with potentially adaptive traits may be what enables C. sakazakii to persist across a variety of ecological niches, including hospitals, food facilities and dried food products. Understanding which genes support C. sakazakii's survival in a variety of environments could help target sanitation measures and guide the development of safer processing protocols and technologies. The findings also raise important considerations for the food industry, especially manufacturers of powdered foods.

Importantly, this study provides a pathway to identify genes with key traits of interest for a variety of pathogens. The integration of AI models to clean, standardize and interpret genomic and epidemiological data could help create faster, more accurate molecular surveillance systems for emerging pathogens.

This research underscores the need for international cooperation in understanding how foodborne pathogens evolve and move through the food system, the researchers say. With food products routinely crossing borders and oceans, tracking genetic markers of virulence and resistance has never been more critical.