Dr. Michael Hansen, Senior Scientist at Consumer Reports contributed to this article.
The 2022 infant formula crisis focused renewed attention on the dangers posed by Cronobacter infections to newborns, but recent research has made clear that reducing these risks may be significantly more complex than many of us anticipated.
This conclusion is based on a better understanding of the ecology of the pathogen and, in particular, the results of a recent study released by IEH Laboratories, which provides a further understanding of the bacterial pathogen itself by finding it in the home environment and other foods. It’s become evident that the link between Cronobacter sakazakii and powdered infant formula (PIF) might not be as straightforward as we originally thought. While the conventional narrative has pointed to the production environment as the source of the pathogen, this new research suggests that the home environment and foods also may play a role.
Our understanding of the pathogen involved in sickening infants has evolved over time. The first attention given to this pathogen was in 1961, where there was an outbreak of Cronobacter infections in infants (neonates) in the United Kingdom. A number of cases were also reported among newborns in Macon, Georgia in 1979.
At the time, the pathogen responsible for these cases was identified as Enterobacter sakazakii, a kind of bacteria known to colonize the guts of animals and humans. In 2001, there was an outbreak of E. sakazakii in a neonatal intensive care unit (NICU) in Tennessee that involved 9 infants who were fed a certain PIF brand. Testing found E. sakazakii in both opened PIF fed to NICU patients, and unopened PIF with the same batch number. They appeared to be identical based on the Pulsed-field gel electrophoresis (PFGE) pattern – which was the standard detection method used at the time – clearly implying that the PIF was the source of the pathogen. This led to a recall by the manufacturer.
Historically, only approximately 30 percent of Cronobacter sakazakii cases involving invasive illness in infants in the US have been linked to contaminated powdered infant formula. Yet, in those cases, the exact strain of C. sakazakii that sickened those infants was never found in unopened PIF, except in the 2001 Tennessee NICU outbreak. This raises the question of whether other sources of C. sakazakii could be the cause of the contamination, especially given that previous studies found the same strain of C. sakazakii that sickened infants in the home environment, particularly the kitchen of those sickened infants.
Other new scientific findings have changed how we look at the pathogen. By 2008, scientists had realized that E. sakazakii was not just a single species, but was, in fact, 7 different species in the Cronobacter genus. The Cronobacter spp that was linked to most of the neonatal meningitis cases was dubbed C. sakazakii, although the other species have been linked to human illness as well. Further genetic work suggested that the original environment in which Cronobacter evolved was not in the gut of animals but rather was associated with the roots of plants. This finding suggests that Cronobacter might be more prevalent in the environment and perhaps even in plant-based foods.
This recent IEH study provided additional evidence, having found that Cronobacter spp. and C.sakazakii, were prevalent in both the home environment and in various foods. This broad study sampled 263 homes and over 4,000 retail food items, and the results were stunning.
Approximately one-quarter of the homes contained C. sakazakii, with the highest incidence being found on floors, particularly the entryway (21 percent), and in the kitchen.
Of the 4,009 retail foods that were sampled, five percent tested positive for C. sakazakii, while the incidence was higher for specific food categories; it was most prevalent in grains/baked goods/flours (25.8 percent), nuts/nut butters (10.1 percent), and seeds/sprouts/beans (9.9 percent). The results from this study provide a good follow-up to a more limited test of food items by FDA scientists in 2022, which found the presence of pathogenic C. sakazakii in foods and recommended more study. As FDA concluded, “Finding virulent plant-origin C.sakazakii possessing significant genomic features of clinically relevant STs [sequence types] suggests that these foods can serve as potential transmission vehicles and supports widening the scope of continued surveillance for this important foodborne pathogen.”
Furthermore, as part of the IEH study, the testing of 386 high-quality genetic sequences of Cronobacter spp. and C.sakazakii isolates collected from homes and food revealed significant genetic diversity in the samples, indicating that the results are not due to contamination. In other words, if there had been contamination of the samples,there would have been more exact genetic sequences in multiple samples.
Also, the use of whole genome sequencing (WGS) revealed that some of the isolates collected from homes showed striking genetic similarity to known C.sakazakii pathovars (e.g., strains of C.sakazakii found in sickened infants). One of the most common strains found was ST4, which has been linked with neonatal meningitis. Indeed, ST4 was the most common C.sakazakii found on kitchen surfaces and floors and also some food items – pet foods and tree nuts and peanuts.
Finally, genes associated with resistance to multiple classes of antibiotics were found in most or all of the genomes. Genes associated with infectivity and host resistance (e.g., virulence) were also found in the majority of the genomes. More importantly, most of these genes were found on mobile genetic elements which means that they can be transferred much more easily between Cronbacter species.
On July 20, 2024, the Canadian Food Inspection Agency issued a recall on Baby Gourmet Organic brand Banana raisin oatmeal cereal due to the presence of Cronobacter spp, which demonstrates that Canada considers it an adulterant in foods beyond powdered infant formula.
Given the findings of the IEH and FDA studies, it would seem that all Cronobacter species – or at the very least C. sakazakii – should be declared an adulterant for some foods, such as grains, baked goods, flours or foods made from them, nuts, and pet foods. Protecting babies from the risks posed by this potentially deadly bacteria will therefore require action beyond stepping up efforts to ensure infant formula is free of contamination.
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