COMPARATIVE AND LIBRARY EPIDEMIOLOGIC TYPING SYSTEMS - OUTBREAK INVESTIGATIONS VERSUS SURVEILLANCE SYSTEMS

A number of high-resolution molecular typing systems have been develop ed in recent years. Their availability raises the new issues of select ing the method(s) best suited for a particular purpose and interpretin g and communicating typing results. Most of the currently available me thods are comparative only: they allow testing of a sample of isolates for delineation of those closely related from those markedly differen t in genomic backgrounds. This approach is adequate for outbreak inves tigation, allowing determination of clonal spread in a microenvironmen t and identification of the source of infection. Comparative methods w ith sufficient resolution for most pathogens include restriction fragm ent-length polymorphism (RFLP), pulsed-field gel electrophoresis (PFGE ), and arbitrarily primed and randomly amplified polymorphic DNA-polym erase chain reaction (PCR) analysis. For surveillance systems, monitor ing clonal spread and prevalence in populations over extended periods of time requires library typing systems. These must be standardized, m ust have a high throughput, and must use a uniform nomenclature. Promi sing or validated methods include serotyping, insertion sequence finge rprinting, ribotyping, PFGE, amplified fragment-length polymorphism (A FLP), infrequent-restriction-site amplification PCR, interrepetitive e lement PCR typing (rep-PCR) and PCR-RFLP of polymorphic loci. PCR meth ods generating arrays of size-specific amplicons (AFLP, rep-PCR) can b e more reproducibly analyzed by using denaturing polyacrylamide gel or capillary electrophoresis with automated laser detection. Binary prob e typing systems appear optimal and should be enhanced further through use of DNA chip technology. In these systems, amplification of polymo rphic regions is followed by solid-phase hybridization with a referenc e panel of sequence-variant specific probes. The resulting binary type results allow determination of reproducible, numeric profiles. Howeve r, interpretation and nomenclature of typing results for large-scale s urveillance purposes still require a better understanding of populatio n structure and microevolution of most microbial pathogens.