Use of Metagenomic Shotgun Sequencing Technology To Detect Foodborne Pathogens within the Microbiome of the Beef Production Chain

Abstract

Foodborne illnesses associated with pathogenic bacteria are a global public health and economic challenge. The diversity of microorganisms (pathogenic and nonpathogenic) that exists within the food and meat industries complicates efforts to understand pathogen ecology. Further, little is known about the interaction of pathogens within the microbiome throughout the meat production chain. Here, a metagenomic approach and shotgun sequencing technology were used as tools to detect pathogenic bacteria in environmental samples collected from the same groups of cattle at different longitudinal processing steps of the beef production chain: cattle entry to feedlot, exit from feedlot, cattle transport trucks, abattoir holding pens, and the end of the fabrication system. The log read counts classified as pathogens per million reads for Salmonella enterica, Listeria monocytogenes, Escherichia coli, Staphylococcus aureus, Clostridium spp. (C. botulinum and C. perfringens), and Campylobacter spp. (C. jejuni, C. coli, and C. fetus) decreased over subsequential processing steps. Furthermore, the normalized read counts for S. enterica, E. coli, and C. botulinum were greater in the final product than at the feedlots, indicating that the proportion of these bacteria increased (the effect on absolute numbers was unknown) within the remaining microbiome. From an ecological perspective, data indicated that shotgun metagenomics can be used to evaluate not only the microbiome but also shifts in pathogen populations during beef production. Nonetheless, there were several challenges in this analysis approach, one of the main ones being the identification of the specific pathogen from which the sequence reads originated, which makes this approach impractical for use in pathogen identification for regulatory and confirmation purposes.

Metagenome‐based surveillance and diagnostic approaches to studying the microbial ecology of food production and processing environments

“…The advantages of this approach over compositional metagenomics has been outlined in even greater depth recently (Bokulich et al, 2016). To date, this type of approach has only been applied to the beef production chain (Yang et al, 2016), and has yet to be applied to the food processing environment but has been used to characterize the microbial communities present in fermented foods (Wolfe et al, 2014;Walsh et al, 2016) and in cleanrooms (Bashir et al, 2016). In the analysis of the beef production chain (Yang et al, 2016), shotgun metagenomics facilitated the detection of pathogens at the species level throughout the production chain.…”

Potential application of Brassica rapa subsp. pekinensis extract on fresh beef meat during refrigeration storage

“…Fresh meat is an easy target for microbial spoilage due to its perishable nature (high moisture content) and accessibility of important nutrients and causes lipid oxidation, biochemical, and enzymatic deterioration (Raeisi, Tabaraei, Hashemi, & Behnampour, ). The outcome of microbial contamination occurs not only by the depletion of product's shelf life and food deterioration (in terms of color variation, putrid flavor, and depletion of nutrients, all of which are pivotal features of meat quality) but also leads to illness and economic deprivation (Yang et al, ). In addition, improper slaughtering, manipulation, and storage can lead to meat contamination with pathogens, including Salmonella spp., Listeria monocytogenes , Escherichia coli , and Staphylococcus aureus (Mangal, Bansal, Sharma, & Gupta, ; Valderrama, Dudley, Doores, & Cutter, ; Yang et al, ) and food spoilage organism such as Pseudomonas (Kumar, Franzetti, Kaushal, & Kumar, ).…”

“…The outcome of microbial contamination occurs not only by the depletion of product's shelf life and food deterioration (in terms of color variation, putrid flavor, and depletion of nutrients, all of which are pivotal features of meat quality) but also leads to illness and economic deprivation (Yang et al, ). In addition, improper slaughtering, manipulation, and storage can lead to meat contamination with pathogens, including Salmonella spp., Listeria monocytogenes , Escherichia coli , and Staphylococcus aureus (Mangal, Bansal, Sharma, & Gupta, ; Valderrama, Dudley, Doores, & Cutter, ; Yang et al, ) and food spoilage organism such as Pseudomonas (Kumar, Franzetti, Kaushal, & Kumar, ). Moreover, the opening of markets via the free trade consents makes the increased import of meat and ensuring the safety of meat at each stage of distribution is an international issue (Kim et al, ).…”

“…). In addition, improper slaughtering, manipulation, and storage can lead to meat contamination with pathogens, including Salmonella spp., Listeria monocytogenes, Escherichia coli, and Staphylococcus aureus (Mangal, Bansal, Sharma, & Gupta, 2016;Valderrama, Dudley, Doores, & Cutter, 2016;Yang et al, 2016) and food spoilage organism such as Pseudomonas (Kumar, Franzetti, Kaushal, & Kumar, 2019).…”

High-Throughput Sequencing Technologies and new Approaches in Food Microbiology

“…A relevant application based this metagenomic approach concerns the detection of foodborne pathogens [41,42]. Other metagenomics applications in food safety include the identification of novel and nonculturable agents that cause disease [43].…”