Comparison of dkgB-linked intergenic sequence ribotyping to DNA microarray hydridization for assigning serotype to Salmonella enterica.

Authors: Guard, Jean; Sanchez-Ingunza, Roxana; Morales, Cesar; Stewart, Tod; LILJEBJELKE, KAREN - University Of Calgary; Van Kessel, Jo Ann; Ingram, Kimberly; Jones, Deana; Jackson, Charlene; Cray, Paula; Frye, Jonathan; Gast, Richard; Hinton Jr, Arthur

Submitted to: FEMS Microbiology Letters
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/5/2012
Publication Date: 12/3/2012
Citation: Guard, J.Y., Sanchez-Ingunza, R., Morales, C., Stewart, T.E., Liljebjelke, K., Van Kessel, J.S., Ingram, K.D., Jones, D.R., Jackson, C.R., Cray, P.J., Frye, J.G., Gast, R.K., Hinton Jr, A. 2012. Comparison of dkgB-linked intergenic sequence ribotyping to DNA microarray hydridization for assigning serotype to Salmonella enterica. FEMS Microbiology Letters. 337:61-72.

Interpretive Summary: The Kauffman-White scheme has been used for decades to serotype Salmonella enterica, which is a pervasive and persistent cause of food-borne illness. Analysis of whole genomes of the bacterium has revealed that it is unlikely that the Kauffman-White scheme provides the level of discrimination required to make progress in understanding the epidemiology of Salmonella enterica. USDA in Athens, GA has developed a new method to serotype Salmonella enterica. It called dkgB-linked Intergenic Sequence Ribotyping (ISR). It uses sequence from one site in the genome that is 257 to 530 base pairs to assign serotype. It was compared to another commercially available method that is called a DNA microarray. The USDA ISR method cost 60 to 75% less to perform than the Kauffman-White method and the DNA microarray, respectively. Equipment and reagent costs to conduct ISR are much less than for the other two methods. The relative costs of the three methods per sample are $10 (ISR), $35 - $185 (Kauffman-White) and $50 (DNA microarray). ISR also detects mixtures of serotypes in culture. Routine screening for Salmonella enterica in clinics and from foods may increase if a simple and inexpensive approach to serotyping such as ISR is available. By coordinating use of ISR with more complex methods that evaluate multiple areas in the genome, costs of epidemiological investigations and clinical analysis for serotyping may be reduced. Detection of mixtures of serotypes within cultures aids better characterization of outbreaks.

Technical Abstract: The Kauffman-White scheme has been used for decades to serotype Salmonella enterica, which is a pervasive and persistent cause of food-borne illness. Analysis of whole genomes of the bacterium has revealed that it is unlikely that the Kauffman-White scheme provides the level of discrimination required to make progress in understanding the epidemiology of Salmonella enterica. USDA in Athens, GA has developed a new method to serotype Salmonella enterica. It called dkgB-linked Intergenic Sequence Ribotyping (ISR). It uses sequence from one site in the genome that is 257 to 530 base pairs to assign serotype. It was compared to another commercially available method that is called a DNA microarray. The USDA ISR method cost 60 to 75% less to perform than the Kauffman-White method and the DNA microarray, respectively. Equipment and reagent costs to conduct ISR are much less than for the other two methods. The relative costs of the three methods per sample are $10 (ISR), $35 - $185 (Kauffman-White) and $50 (DNA microarray). ISR also detects mixtures of serotypes in culture. Routine screening for Salmonella enterica in clinics and from foods may increase if a simple and inexpensive approach to serotyping such as ISR is available. By coordinating use of ISR with more complex methods that evaluate multiple areas in the genome, costs of epidemiological investigations and clinical analysis for serotyping may be reduced. Detection of mixtures of serotypes within cultures aids better characterization of outbreaks.