Currently, eight types of botulinum toxins are known - A, B, C, D, E, F and G, as well as botulinum X, identified in 2017. In 2018, researchers reported a new botulinum neurotoxin gene cluster in Enterococcus faecium strains identified from cow feces in South Carolina. The significance of the case is that the botulinum toxin gene cluster was not found in a genome of Clostridium origin. E. faecium is widespread in most terrestrial animals and is a core commensal member in the human gut, potentially indicating the possibility of in vivo toxin release from strains that have acquired the BoNT gene cluster.

Among the Enterococci, some species are used as probiotics (E. faecalis) in healthy people and some species as starter cultures. However, they are also capable of causing disease (E. faecium - neonatal meningitis), the exact mechanism of which is not known, and therefore Enterococci have not been granted QPS (Qualified Presumption of Safety) status by the European Food Safety Authority (EFSA).

The above study points to several serious knowledge gaps that will certainly need to be addressed by professionals in the future. These are:

• How did Enterococcus get the gene cluster (if not from Clostridium)?
• If Enterococcus sp. can take over gene clusters, can it pass them on? A similarly important question is that of antibiotic resistance. Is it able to take over and pass on AMR gene clusters? Vancomycin resistance is currently known in Enterococci.
• What is the ecological advantage to Enterococcus faecium of acquiring this gene?
• Does this new toxin cause botulism?
• Can the gene be expressed in E. faecium?
• Is it possible that some botulism cases not attributed to C. botulinum were caused by Enterococci or other non-clostridial bacteria?
• Does Enterococci expressing botulinum toxin pose a greater risk of botulism in infants?
• Are there new foods with higher risks that can be identified?
• Could the combination of BoNT expression with commensal, pathogenic or antibiotic-resistant phenotypes represent an emerging risk?

The questions highlight that, although we have a broad knowledge of food-associated microbes, much more information is not available. We know a lot about individual micro-organisms, but much less about how microbes interact with each other.

This case also highlights the issue of AMR. To take preventive measures to reduce the use of drugs, it is not enough to know about resistance in microbes. How the different microbes can transmit this property is also an important area of research.