Quantitative microbial risk assessment for Salmonella: Inclusion of whole genome sequencing and genomic epidemiological studies, and advances in the bioinformatics pipeline

Despite the implementation of extensive measures to control food-borne illness caused by Salmonella since the beginning of the 20th century, it remains one of the most important and widespread food-borne pathogens. Quantitative microbial risk assessment (QMRA) has become essential to evaluating and mitigating the public health risk of Salmonella. However, current QMRA models do not incorporate the minute changes in microbial behavior arising from differences in the microbial genome. Genomic analysis, particularly whole genome sequencing (WGS), has undergone significant progress over the past two decades, facilitating rapid data accumulation. This presents an unprecedented opportunity to incorporate genomic data into a QMRA for Salmonella. This review aims to explore the applicability of WGS and other genomic technologies in Salmonella QMRA, and to outline the added value and current limitations and promise of genomics, particularly bacterial WGS, in supporting the integration of this data in a framework to assess the risk of Salmonella. Our review indicated that although comparative genomic studies for Salmonella using WGS has seen a considerable amount of interest over the past decade, the incorporation of genomic data into QMRA remains a difficult and arduous prospect. However, with the progress in bioinformatics and genomic epidemiology, genomic data could certainly be utilized in QMRA to improve and update risk assessment models and risk management strategies for Salmonella, as well as other foodborne pathogens of interest.