Whole Genome Sequencing Could Transform Salmonella Detection

Salmonella is one of the most common organisms responsible for symptomatic and severe food poisoning. Methods for detecting it have evolved from gross microscopic identification to serotype detection.

Scientists from Cornell University and the Beijing Global Food Safety Center (GFSC) said they could use high-resolution genome-wide sequencing technology to safely and consistently identify harmful variants. of this bacteria.

"Salmonella is the foodborne pathogen that has the greatest impact on public health and the economy in the world. This is one of the leading causes of diarrhea in the world, "said Martin Wiedmann. "Salmonella can be benign or cause death because its severity depends on Salmonella serotypes. [distinct variations] – and that's what we are trying to discover. "

Salmonella generally contaminates relatively dry, ready-to-eat foods, such as raw almonds or peanut butter. The occurrence of many such cases makes it important to track salmonella in the food supply chain to control this contamination. At present, there are more than 2,500 serotypes or serotypes of salmonella, but fewer than a hundred are generally responsible for human diseases.

Salmonella in the shape of a green stem. Image Credit: Studiovin / Shutterstock

Microbiologists around the world have used traditional subtyping techniques to characterize salmonella strains identified during various outbreaks of food poisoning. In fact, some of them date back to the first decades of this century, when technology was limited. It usually takes more than 3 days to find the serotype of an organism from the moment of its isolation, and sometimes more than 12 days. In addition to being a lengthy process, it requires a lot of manpower, skills and often inaccurate. False positives are common.

However, with the advent of modern molecular methods, such as methods based on nucleotide band models and sequence-based methods, scientists can now identify these variants with much more precision, as well as follow the path of the epidemic and its origin.

The present study focuses on whole genome sequencing, which reveals the complete genetic makeup of an organism at the same time, instead of being fragmented. This can be applied consistently to identify variations that will help clbadify pathogens such as salmonella based on their differences in serotypes. This will help researchers determine whether a strain is pathogenic or not and track the source in a contaminated food supply chain.

An illustration was produced in July 2019, when 45 cases of salmonellosis broke out in 13 states and required 12 hospitalizations. This culminated in a collaborative exercise between the US Food and Drug Administration (FDA) and the Centers for Disease Control and Prevention (CDC), using whole genome sequencing to link people handling a certain type of disease. dog treats called treats the contaminating bacteria.

By using less sensitive methods, source tracking could be difficult. The complex supply chains in use currently offer a number of loopholes in which food safety could be threatened by the introduction of a harmful bacterial strain. The occurrence of this outbreak underscores the usefulness of this technique for enhancing surveillance of salmonella in the food industry, as it is very useful for quickly and accurately detecting the source of these contaminating microbes. The key lies in the availability of subtyping tools with sequencing of the entire genome, making it "the method of choice for subtyping salmonella," according to lead author Silin Tang.

In fact, Tang is considering a broader application for this technology. This could promote the emergence of a group of trained food industry professionals using software, able to handle biological information such as the salmonella genome and differences between various serotypes. This would help unlock more applications of this highly versatile and powerful technology, such as ingredient monitoring, persistent microbial detection in food processing environments and the prediction of the onset of disease. drug resistance. This will help improve hygiene during food processing, control contamination and badess microbiological risk.

Another advantage is that a purely academic tool has become a practical technique of the industry. For example, sequenced genomes can be placed in the public domain on the National Biotechnology Information Center Web site, thus allowing the badysis of online or offline data of whole genomes.

The cost of this tool is potentially a deterrent, especially for the sequencing of organisms in small quantities. Regulatory mechanisms, standardized badytical tools and reporting, as well as data interpretation, are other areas to develop before becoming the absolute standard in this area. Wiedmann says: "This will help the sector to implement better ways of proactively addressing the complications and complexity of salmonella."

The paper was published in the newspaper Frontiers in Microbiology July 12, 2019.