Molecular genotyping methods and computerized analysis for the study of Salmonella enterica

Salmonella enterica is widely recognized as a major cause of foodborne diseases in humans and animals and has been isolated from environmental sources in increasing numbers worldwide. Conventional typing methods such as serotyping and phage typing have been and still are the mainstay in descriptive epidemiology of this microorganism. Nevertheless, limitations on the availability of phage reagents circumscribes the performance of such technique in reference laboratories. The resolving power of epidemiological typing has been expanded during recent years through the molecular analysis of microbial DNA. The broader availability of the reagents and equipment is accelerating their generalized use in clinical and public health laboratories. Important differences in the performance criteria of the genotyping techniques (typability, reproducibility, stability, and discriminatory power) and the convenience criteria (flexibility, accessibility, and ease of use) exist between them, and there is no ideal typing system for universal use. Most of these powerful strain-discriminative techniques are based on comparison of electrophoretic patterns or fingerprints, for which computer-assisted strategies and software packages have been developed to help in construction and analysis of microbial databases. Several initiatives, such as PulseNet (http://www.cdc.gov/pulsenet) or Harmony (http://www.phls.org.uk/inter/harmony), have arisen during recent years for international construction of such fingerprinting databases, which will allow the rapid detection of new strains and the spread of pathogenic clones of bacteria through different regions or countries. Nevertheless, complete consensus has not yet been achieved on the techniques to use or the criteria for interpretation of the results, but these goals may be reached soon.