Faster detection of Salmonella strains on the horizon?

A new technique looking at DNA sequences uses a half of the time to identify Salmonella

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.

Salmonella Newport is the third most common serological variant of Salmonella and its incidence increased by 46% between 1999 and 2009. In 2009, Salmonella Newport accounted for 9.3% of total salmonellosis cases, according to study lead author Nikki Shariat, postdoctoral researcher in molecular microbiology in the Penn State Department of Food Sciences.

Detection time: Scientists said the method often takes just one day to identify the strain of the pathogen.  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. This method allows speeds up the epidemiological investigators to identify the strains that make people sick and to quickly find and eliminate the source of the disease.

DNA method:  This method is different because it looks at the DNA sequence, whereas PFGE 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 other that cause foodborne illness, such as Campylobacter jejuni and E. coli.

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 20 isolates, 10 from the outbreak and 10 not from the outbreak and the analysis the analysis were conducted not knowing which ones were which. At the end the outbreak strains were identified exactly from those not involved.

Source: Journal of Clinical Microbiology, http://jcm.asm.org/content/early/2013/05/10/JCM.00608-13.full.pdf+html