The ERIC-PCR technique uses higher annealing temperatures (approximately 50–58°C) and longer primers (20 nucleotides) than the RAPD method. These primers are specific for SN-38 areas of the genome that are highly conserved and include an inverted repeat. The RAPD assay uses low stringency conditions of approximately 30–36°C annealing temperatures and short (10 nucleotide) primers. One or more of these arbitrarily chosen RAPD primers can anneal at multiple locations throughout the genome and amplify many products of the template DNA. In addition to genomic-based methods, protein-based methods offer a different and complementary approach.
Whole cell protein (WCP; [29–32] profiles or outer membrane protein profiles  of H. parasuis, which use a sodium dodecyl sulfate polyacrylamide gel electrophoresis
(SDS-PAGE) technique have been described. These studies suggested that isolates from systemic sites had unique protein profiles. Isolates from respiratory sites had different selleck kinase inhibitor protein profiles than the systemic isolates had. The 36–38.5 kDa proteins were described as virulence markers based on the isolation site of the strain . This work analyzed the DNA and protein profiles of 46 H. parasuis reference and field isolates. Random amplified polymorphic DNA is a molecular typing technique that is often used to differentiate closely related strains. It is especially sensitive to strain variation when three optimized primers are employed [34–36]. Random amplified polymorphic
DNA 3-mercaptopyruvate sulfurtransferase may detect single base changes in genomic DNA and genetic maps consisting of RAPD markers can be generated more efficiently than by using RFLP targeted PCR-based methods . Intra-specific variation in the RAPD patterns can be observed for each primer and the sequence SAHA HDAC concentration complexity of small plasmids is unlikely to contribute to the patterns . However, bacteriophage and larger plasmids with transposons could possibly mediate horizontal gene transfer between strains and increase RAPD heterogeneity . By using the relatively simple and economical RAPD technique, known primer sequences can be utilized by different laboratories, making it a standardized technique and amenable to epidemiological studies. However, interpretation of gel electrophoresis results could introduce some variability between laboratories. The objectives of this study were to compare the relatedness of the reference strains and field isolates based on the RAPD and WCP lysate profiles and to determine if clustering that occurred was related to the site of isolation or to the pathogenicity of the strain. Results Comparison of RAPD profiles and pattern analysis Of the three primers used for genotyping, primer 2 had an intermediate number of bands; primer 7 had the most polymorphic DNA bands; and primer 12 had the least number of polymorphic DNA bands (Figure 1).