AN EVALUATION OF DNA-BASED METHODOLOGIES FOR SUBTYPING SALMONELLA

Bacteria of the genus Salmonella are major human and animal pathogens worldwide, with over 2000 serotypes. Although most authorities agree t hat there are only one or two true species of Salmonella, serotypes ar e accepted as pseudo-species. In addition, although serotype identific ation is important, without additional subtyping, serotyping has limit ed usefulness for epidemiology as three serotypes (S. typhimurium, S. enteriditis, and S. heidelberg) account for 50% of human infections wo rldwide. The purpose of this review is to evaluate different methods o f DNA typing and fingerprinting of Salmonella strains and to report th e most important epidemiological and phylogenetic discoveries that hav e been made using these methods. These include plasmid analysis (plasm id profiles and plasmid fingerprints, restriction fragment length poly morphism (RFLP) analysis, and polymerase chain reaction (PCR) fingerpr inting). Plasmids are common but not universal in Salmonella isolates and can be used to discriminate isolates through plasmid profiles or r estriction digests of plasmid DNA. They have been used with some succe ss to subtype some serotypes. The correlation, however, is not always perfect. RFLP fingerprinting has also been used to subtype serotypes. Specifically, the IS200 insertion sequence has been used to probe rest riction digests of chromosomal DNA. Probes derived from 16S sequences have been used similarly in 'ribotyping' studies but with less success . RFLP fingerprinting has been used in both phylogenetic and epidemiol ogy studies of Salmonella and is considered to be a more stable and re liable method than plasmid analysis. PCR fingerprinting techniques, in cluding arbitrarily primed PCR (AP PCR), repetitive sequence (REP) PCR and restriction digests of PCR-amplified 16S rDNA sequences have also been used to discriminate between Salmonella serotypes. The success o f PCR methods is variable and depends on specific primers utilized. Ov erall, many fingerprinting techniques can discriminate between isolate s but are often not successful in subtyping serotypes.