Scientists at the USDA’s Agriculture Research Service have demonstrated the potential of a form of whole genome sequencing for the early detection of Salmonella on food contact surfaces.

The research into long-read whole genome sequencing (WGS) could give food processors more time to initiate sanitation of surfaces before biofilms are formed. Biofilms form on surfaces, are very difficult to remove and can harbor pathogens. In addition to faster detection, long-read WGS can test up to 96 samples at a time.

Early and accurate detection of Salmonella in production environments has previously been difficult, hindering the application of sanitization intervention before biofilms form and pathogens contaminate food. The longer a biofilm is allowed to grow the stronger the intervention is required. This can cause problems in food environments because chemical sanitizers can generate toxic byproducts and contribute to antibiotic-resistant bacteria.

New technology involving long-read WGS offers more rapid and sensitive alternatives to commonly used detection methods. However, long-read WGS has not yet been used to detect foodborne pathogens on surfaces, so scientists designed the study to compare culture-based detection methods with other sequencing methods to identify Salmonella during the early stages of biofilm development on food-contact surfaces.

To conduct their experiment, the researchers used a strain of Salmonella Typhrimurim that was seen in earlier studies to quickly form strong biofilms, sometimes as fast as 24 hours. Materials commonly used in food contact surfaces in the egg industry — stainless steel, silicone and nylon — were used in the testing. 

Findings show that long-read WGS can be a more sensitive method for detecting the early formation of Salmonella on surfaces than culturing methods. Sequencing can also provide information on Salmonella serotypes, their antibiotic resistance and virulence.

Authors on the study include Daniela Bermudez-Aguirre, Ph.D.; Shannon Tilman; Brendan A. Niemira, Ph.D.; and Katrina L. Counihan, Ph.D.; all with USDA’s Agricultural Research Service.