Chemists Develop Color-Changing Test for Salmonella Detection in Less Than 4 Hours

Image created by Dr. Michael J. Miller

A group of chemists at the University at Albany have developed a new method for fast-acting salmonella detection. The test employs a paper strip that changes color in the presence of the bacterial genome, enabling quick screening for salmonella in food products.

Unlike other methods, which can take days to yield a result, this system can detect salmonella in under four hours. It is also able to identify and differentiate between two common salmonella strains, and costs less per test than current methods. The work was published in Advanced Healthcare Materials and was featured on the journal's September cover.

"Salmonella is one of the most common foodborne pathogens, making it a leading concern for food safety worldwide," said Mehmet Yigit, associate professor in UAlbany's Department of Chemistry and the RNA Institute, both part of the College of Arts & Sciences.

"Contamination occurs when food comes into contact with animal feces during production, processing or handling. Products like raw or undercooked meat, poultry, eggs, seafood and fresh produce are common sources. Even processed items like peanut butter or frozen meals have been linked to outbreaks.

"In this study, we demonstrate a new method for salmonella detection that uses a novel combination of molecular approaches to signal contamination in a food sample. Designed to be simple, fast and versatile, our method addresses a critical need for quicker, more accessible ways to identify foodborne pathogens.

"Being able to rapidly identify and isolate the source of a pathogen can reduce illness spread, minimize risks to vulnerable populations and reduce disruptions throughout the food supply chain."

Salmonellosis, the illness caused by ingesting salmonella, can trigger acute gastrointestinal issues and fever. While the illness can resolve without treatment, severe infections can require hospitalization, especially in young children, the elderly or those with weakened immune systems. According to the U.S. Centers for Disease Control and Prevention, about 1.35 million cases of salmonellosis and 420 related deaths occur in this country every year.

For food distributors and restaurants, monitoring for salmonella is both a health imperative and a business priority. Outbreaks are expensive; they can trigger costly product recalls, loss of consumer trust and even legal liabilities, disrupting operations with potential for long-term financial and reputational impacts.

Honing precise and affordable detection

The team's method uses CRISPR-Cas12a gene editing technology, combined with recombinase polymerase amplification (RPA) and a molecular tool called a "toehold switch" to trigger a visible color change on a paper test strip. In the presence of salmonella, the strip turns red, signaling contamination. If it turns yellow, the sample is clean.

This approach is not only quick and sensitive but also highly specific. The test can detect as few as 100 genome copies of salmonella bacteria and can distinguish between two common serotypes: S. Typhimurium and S. Enteritidis. Identifying the strain type can help track the origin of an outbreak and can dictate the optimal clinical approach to treat an infection.

"A strength of our system is its ability to minimize false-positive results," Yigit said. "Other approaches involving nanoparticle-based or instrumental techniques often can't differentiate between pathogens, which reduces practical efficacy in the field.

"Our method also offers cost savings. By using tiny paper disks as the medium for detection, rather than a vial of reaction solution, a much smaller amount of test solution is required to achieve a result. This makes our method about 20 times less expensive per test."

A portable, adaptable test kit

Unlike traditional methods, this test eliminates the need for extensive laboratory equipment or re-engineering for different bacterial strains, making it possible to implement in a variety of settings, including farms, food processing plants, distribution facilities or restaurants.

"With further development, we aim to transform this technology into a portable, user-friendly kit that can be used widely in the food supply chain," said lead author Mahera Kachwala, who worked on the project while completing her Ph.D. with Yigit at UAlbany.

"Anyone handling food will be able to easily integrate this test into daily on-site operations, making it possible to stop a salmonella outbreak before it spreads. It could also become a useful tool for restaurant workers and health inspectors, to help ensure that routine hygienic protocols are being employed effectively, and customers are receiving safe, high-quality food."

The system's design is also highly adaptable. By changing a single RNA element, it can be programmed to detect other pathogens responsible for food-borne illnesses. For example, the team is exploring ways to use their platform to test for additional types of salmonella, campylobacter and Shiga toxin-producing E. coli (STEC), which together account for millions of hospitalizations and billions in lost food production costs each year.

"Our method demonstrates the power of synthetic biology to create flexible tools for pathogen detection," Yigit said. "By collaborating with experts in nanotechnology and microbiology, we are excited to bring this innovative technology closer to portable, consumer-ready use."

Reference

Mahera J. Kachwala et al, Universal CRISPR‐Cas12a and Toehold RNA Cascade Reaction on Paper Substrate for Visual Salmonella Genome Detection, Advanced Healthcare Materials (2024). DOI: 10.1002/adhm.202400508

Abstract

Salmonella, the most prevalent food-borne pathogen, poses significant medical and economic threats. Swift and accurate on-site identification and serotyping of Salmonella is crucial to curb its spread and contamination. Here, a synthetic biology cascade reaction is presented on a paper substrate using CRISPR-Cas12a and recombinase polymerase amplification (RPA), enabling the programming of a standard toehold RNA switch for a genome of choice. This approach employs just one toehold RNA switch design to differentiate between two different Salmonella serotypes, i.e., S. Typhimurium and S. Enteritidis, without the need for reengineering the toehold RNA switch. The sensor exhibits high sensitivity, capable of visually detecting as few as 100 copies of the whole genome from a model Salmonella pathogen on a paper substrate. Furthermore, this robust assay is successfully applied to detect whole genomes in contaminated milk and lettuce samples, demonstrating its potential in real sample analysis. Due to its versatility and practical features, genomes from different organisms can be detected by merely changing a single RNA element in this universal cell-free cascade reaction.