Contamination recalls cost money

Preventing recalls or limiting their scope reduces costs for food businesses and helps protect consumers. In the food industry, product recalls due to contamination or safety concerns can lead to significant financial losses, damaged reputations and disrupted supply chains.

Traditional microbiological testing, while an essential component of a food safety regime, often lacks the speed and precision needed to identify potential hazards before they reach the consumer. High-throughput and whole genome sequencing (WGS) technologies offer a transformative solution to this problem. These advanced techniques provide more detailed insights into pathogens, enabling food businesses to detect issues early and accurately. By enhancing traceability and reducing false positives, they may help minimise recall costs and protect brand reputation more effectively than conventional microbiological testing.

High-throughput sequencing

Genomic technologies allow the unravelling of organisms’ genetic codes, identifying the sequences of DNA letters, or bases (A, T, C and G), which make up their genomes; hence the term, DNA sequencing. In the food industry this has two main applications:  whole-genome sequencing and identification of strains in a mixed community.

Whole-genome sequencing

Whole-genome sequencing (WGS) identifies the entire genetic sequence (genome) of an individual organism. From a food microbiology point of view, this typically refers to a single bacterial isolate. The general workflow involves obtaining a pure isolate using conventional microbiological techniques, followed by DNA extraction, sequencing the resulting DNA and then bioinformatic analysis to interpret the sequences obtained. The amount of genetic information contained in the genome depends on the organism involved – for example, Listeria monocytogenes has a comparatively short genome, around 2.9 million bases long, whereas Salmonella enterica has a much larger genome, typically around five million bases. WGS analysis sequences all of these bases and identifies their order along the bacterial chromosome, as well as any other DNA elements such as plasmids.

This process has several applications – for example, identifying virulence genes such as shiga toxin genes in STEC strains, or genes involved in resistance to antibiotics or biocides. These findings might inform appropriate treatment or cleaning regimes. However, the most straightforward application of WGS is in traceback or root cause analysis. The similarity or difference between the genomes of two bacterial strains is roughly proportionate to how recently they diverged from a common ancestor, allowing inferences about contamination sources. For example, two strains from different parts of a factory with identical or nearly identical genomes probably share a source. Contamination may have spread from one site to another or to both locations from a third site (known or unknown), and unravelling this story requires additional information about dates of isolation, sample types and movement patterns in the factory.

This can be taken further by comparing sequences to previously sequenced genomes, either from the same facility or publicly available reference databases. This comparison is useful for identifying persistent contamination within a facility or linking contamination to particular commodities.

Identification of microbial communities

This same technology applied to a single bacterial isolate for WGS can also be applied to mixed samples to perform other techniques, including microbial community analysis. There are various approaches to this, but they generally fall under the umbrella term of metagenomics, wherein it is possible to identify the microbes present in a mixed sample, negating the requirement to obtain pure cultures first. This can be applied to a range of different sample types, including food and feed, water, biofilms and swab samples from surfaces.

However, the limitations of  mixed culture analysis mean that less sequence data is obtained from each constituent member, so it is highly unlikely that whole genome sequences of all present microbes will be obtained. In fact, with the most widely used metagenomic approach, metabarcoding, this is not even technically feasible. Nevertheless, the taxonomic identity of many microbes – including families, genera, and sometimes species present – can be determined.

This approach offers two main advantages over traditional culture-based methods. Firstly, traditional culture normally involves the use of selective agars to search for a specific bacterial species or group. Metagenomic approaches do not require this and can detect bacteria that are present without prior knowledge. Secondly, some bacteria can enter a viable but non-culturable (VBNC) state. These VBNC bacteria will not grow in culture but can be identified through their DNA. However, several drawbacks to metagenomics exist, including cost, turnaround time, the inability to distinguish live bacteria from dead and the taxonomic resolution with which microbes can be identified.

On-site diagnostics

Another group of technologies that may be relevant to enhanced food safety are on-site diagnostics. This broad term refers to various underlying technologies that can  be performed outside of a traditional laboratory environment, such as in the field or factory. There are many different technologies, such as ATP tests, antibody-based lateral flow tests, rapid culture approaches, and DNA-based technologies such as rapid polymerase chain reaction(PCR) and loop-mediated isothermal amplification (LAMP) assays. The potential benefits of these approaches include a rapid time to result, allowing real-time hygiene decisions based on the test results.

However, these technologies vary greatly in aspects such as sensitivity (the amount of target required for detection), specificity (how well the test distinguishes target from non-target), time to result, cost (both per test and for equipment), and the amount of training needed to operate. While some tests such as ATP tests are currently used in hygiene monitoring, further development of other approaches is required to meet food industry testing standards.

Other tools available include collaborative software and data platforms that support supply chain management by helping industry stay ahead of emerging food safety challenges. These tools identify issues days earlier than other sources.

One such platform is HorizonScan, a technology-led solution for managing complex supply chains, providing food retailers, foodservice operators and manufacturers with unprecedented insight into their direct and indirect supply chain. It keeps businesses posted on hazard and risk assessments across all food sectors worldwide and specific issues of concern such as microbial contaminants as well as fraud, authenticity and many more. Delivering the requisite tools that enable food companies to uphold the highest standards of food safety, safeguarding both the business and its customers, helps build vital brand trust.

High-throughput WGS microbial community identification, coupled with on-site diagnostics and HorizonScan, offers significant advantages over traditional microbiological testing in terms of reducing recall costs for food businesses. High-throughput sequencing allows detailed characterisation of individual bacteria and provides comprehensive analysis of the entire microbial population in food samples. This enables more accurate detection and identification of potential pathogens or spoilage organisms. On-site diagnostics permit real-time monitoring and faster decision making, reducing the time between contamination detection and action.

Both WGS and on-site diagnostic approaches are being developed through collaborative programmes, such as the cross-government PATH-SAFE programme and the industry-focused Food Safety Research Network. HorizonScan, a global food safety risk assessment tool, helps predict emerging threats by tracking contamination patterns and trends. Together, these advanced technologies enhance food safety, minimise costly recalls, and improve supply chain management by providing faster, more precise and predictive solutions compared to conventional microbiological testing.