Genome Projects: Modern Genetics and Genomic Technologies and Their Application in the Meat Industry – Red Meat, Animals, Poultry

Abstract

Food safety is a global concern, and consumers have the right to safe and nutritious food. Over the previous decades, food borne diseases become important cause of morbidity and mortality, and a significant issue affecting socio-economic development worldwide. The estimated annual burden of foodborne diseases at global level is 600 million foodborne illnesses and 420,000 deaths from 31 major food safety hazards. In the EU and US, five major food safety hazards (Campylobacter, Salmonella, Shiga toxin-producing E. coli/STEC, L. monocytogenes, norovirus) have been associated with majority of food borne outbreaks, together with related social and economic costs (hospitalization, loss of income, employment and market access). Food borne pathogens that were mostly associated with meat/meat products and/or mixed foods (e.g. meat in combination with vegetables) were Salmonella (in mixed foods, meat and meat products), Campylobacter (in meat and meat products) and Listeria monocytogenes (in fish and fishery products, meat and meat products). The implicated foods included mainly meat products with relatively long shelf life, e.g. cooked sausages, cooked sliced ham, jelly products, and, on some occasions, fermented salami. The most frequent scenario that led to foodborne outbreaks was related to the post-thermal treatment cross contamination of deli meat products during slicing and modified atmosphere packaging. The essential precondition for such cross contamination is the previous introduction of food borne pathogens (e.g. L. monocytogenes and Salmonella enteritidis) into the meat processing facility and subsequent colonization of production environment. Therefore, tracking the foodborne pathogens in food (meat) processing – distribution – retail – consumer continuum is of utmost importance for facilitation of outbreak investigation and rapid action in controlling/preventing foodborne outbreaks. Genomic technology, e.g. Whole Genome Sequencing (WGS) or next-generation sequencing (NGS) has recently emerged as a new tool and offers great potential in the way we investigate, assess and manage microbiological food safety issues and illnesses. The use of WGS can facilitate the understanding of contamination/colonization routes of foodborne pathogens within the meat production environment, and can also enable efficient tracking of pathogens` entering routes and their distribution along the meat chain. Implementation of WGS is likely to be beneficial for many countries in the foreseeable future, in support of food safety management systems and foodborne outbreak investigations. It allows the identification and characterization of microorganisms with a level of precision not previously possible, therefore potentially minimizing much of the uncertainty which impacts our ability to respond and manage microbiological food safety issues effectively and efficiently. For instance, meat/poultry establishments can use WGS technology on a cost-effective basis which may encompass in-house sequencing when sequencing equipment is used for multiple applications (WGS of pathogens, starter cultures and spoilage organisms).