Microbial communities in the food chain: application of whole genome sequencing and metagenomics to investigate interactions between pathogens, commen

Foodborne illness remains a national and global health concern. According to the Food Standards Agency (2011), it is estimated that around 1 million people suffer a foodborne illness every year, with approximately 20,000 requiring hospital treatment and 500 deaths resulting from foodborne illness. The costs associated with foodborne disease in the UK are estimated to be £1.5 billion. Considering the public health impact and economic impact of foodborne illness, it is important to better understand the distribution of foodborne pathogens in food production chains and to develop reliable and rapid methods for foodborne pathogen detection and tracking, particularly pathogenic bacteria that cause a large-numbers of cases of foodborne disease. It is well known that surrounding environments cause stresses on bacterial populations and lead to reorganisation of microbial communities and these have the potential to influence the persistence of pathogenic bacteria in the food production chain. A number of outbreaks including the recent salmonellosis outbreak in France linked to infant formula in 2018 serve to demonstrate the importance of understanding persistence and the factors that influence this, in order to develop strategies to prevent this occurring. The advent of omics technologies enables advances in relation to characterization of microbial communities and their influence on the presence of pathogens. For example, metagenomics has recently been used for the detection, identification and characterisation of pathogens in food and in the food chain environment. It provides an opportunity to look at the diversity and the dynamic abundance of pathogens within a sample in an unbiased manner and is being used to improve culture-based enrichment methods. Shotgun metagenomics can provide a valuable, rapid view of the presence of genetic markers specifying species, serotype, virulence and antimicrobial resistance genes etc. although, at present, these markers cannot be assigned to specific bacterial genomes due to the complexity of the metagenomic data. Future metagenomic and metabarcoding bioinformatic developments are likely to make this and the ability to investigate phylogeny possible, and perhaps allow links to be drawn between presence of pathogens, such as Salmonella, and wider sub-groups, such as the Enterobacteriaceae. Culture-based methods followed by whole-genome sequencing may be used as a complementary approach to allow pathogen confirmation and tracking.

Mondelez would like to explore application of these new techniques to better understand persistence of pathogens in food manufacturing settings with the aim of developing approaches to prevent occurrence and to identify strategies to remove persisting unwanted microorganisms. To that effect, Mondelez is interested in the fundamental understanding of pathogen persistence and the interactions between the wider bacterial communities to identify technological approaches to identify markers for pathogen presence and for tracking pathogens through the food chain.

To characterise and describe the genetic relationships between a collection of Salmonella species recovered from a designated food production environment; and elucidate the dynamic colonisation patterns based on culture-independent methods to discover novel naturally-acting biocontrol strategies