The method focuses on two virulence genes and two novel regions of Salmonella DNA called clustered regularly interspaced short palindromic repeats (CRISPRs).
Researchers from Penn State's College of Agricultural Sciences devised a method of multi-virulence-locus sequence typing (MVLST) that can detect strain-specific differences in the DNA at these four locations.
The method was designated as CRISPR-MVLST and was developed to identify strains of the Salmonella serotype Newport.
Newport is the third most common serological variant of Salmonella and its incidence increased by 46% between 1999 and 2009.
In 2009, Newport accounted for 9.3% of total salmonellosis cases, according to study lead author Nikki Shariat, postdoctoral researcher in molecular microbiology in the Department of Food Science.
Detection time
Scientists said the method often takes just one day to designate the strain of the pathogen.
Currently, public-health laboratories use a technique called pulse field gel electrophoresis (PFGE) to subtype Salmonella strains, and it can take one to three days to identify a specific strain, said the researchers.
The findings aim to speed up the response to outbreaks of foodborne illness, allowing epidemiological investigators to identify the strains that make people sick and to quickly find and eliminate the source of the disease.
Shariat said: "The significance of that is you need to trace the source of an outbreak as quickly as you can before you start insisting on restaurant and farm closures. It is important to pinpoint the source of the bacteria -- the quicker you do that the quicker you can respond to the disease outbreak."
DNA method
She explained that the method is different because it looks at the DNA sequence, whereas the other method cuts the DNA into small pieces with no actual sequence information.
"Fifty per cent of bacteria have CRISPR regions, and using these for identification has been done with quite a few bacteria, such as Mycobacterium tuberculosis, as well as with some that cause foodborne illness, such as Campylobacter and E coli.”
Working with Carol Sandt, a scientist with the Bureau of Laboratories, Division of Clinical Microbiology in the Pennsylvania Department of Health and Eija Trees, a microbiologist at the CDC, Shariat used Salmonella samples supplied by the state health department.
Toward the end of the research project, which was funded by the US Army Research Office, they applied their analysis to a Salmonella outbreak, associated with tomatoes in Pennsylvania in 2012 in which 37 people got sick.
"The Pennsylvania Department of Health sent us 20 isolates, 10 from the outbreak and 10 not from the outbreak, and we did the analysis not knowing which ones were which," Shariat explained.
"We were able to identify exactly those that were associated with the outbreak."
Source: Journal of Clinical Microbiology
Online ahead of print DOI: 10.1128/JCM.00608-13
“CRISPR-MVLST Subtyping of Salmonella serovar Newport Outbreak Isolates and Determination of the Relationship Between CRISPR-MVLST and PFGE”
Authors: Nikki Shariat, Margaret K. Kirchner, Carol H. Sandt, Eija Trees, Rodolphe Barrangou, and Edward G. Dudley