Comparative typing of Pseudomonas aeruginosa by random amplification of polymorphic DNA or pulsed-field gel electrophoresis of DNA macrorestriction fragments

Abstract

Eighty-seven strains of Pseudomonas aeruginosa were typed by random amplification of polymorphic DNA (RAPD) and pulsed-field gel electrophoresis (PFGE) of macrorestriction fragments. Strains were clustered on the basis of interpretative criteria as presented previously for the PFGE analysis. Clusters of strains were also defined on the basis of epidemiological data and subsequently reanalyzed by RAPD. It was found that in an RAPD assay employing the enterobacterial repetitive intergenic consensus sequence ERIC2 as a primer, single band differences can be ignored; in this case, clonally related strains could be grouped as effectively and reliably as with PFGE. These data could be corroborated by the use of other primer species. However, some primers either showed reduced resolution or, in contrast, identified DNA polymorphisms beyond epidemiologically and PFGE-defined limits. Apparently, different primers define different windows of genetic variation. It is suggested that criteria for interpretation of the ERIC2 PCR fingerprints can be simple and straightforward: when single band differences are ignored, RAPD-determined grouping of P. aeruginosa is congruent with that obtained by PFGE. Consequently, this implies that RAPD can be used with trust as a first screen in epidemiological characterization of P. aeruginosa. The ability to measure the rate of molecular evolution of the P. aeruginosa genome clearly depends on the choice of restriction enzyme or primer when RAPD or PFGE, respectively, is applied for the detection of DNA polymorphisms.

Random amplification of polymorphic DNA versus pulsed field gel electrophoresis of SmaI DNA macrorestriction fragments for typing strains of vancomycin-resistant enterococci

“…RAPD analysis of these VRE strains showed no relationship with VRE strains that clustered with PFGE. These phenomena have been described before for VRE and other organisms [7,10,15].…”

“…In addition, the two multicentre studies performed to date on Staphylococcus aureus strains show a disappointing degree of reproducibility between centres (see [9] and references therein). Because of these inconsistencies, we became interested in the establishment of interstrain relatedness of vancomycin-resistant enterococci (VRE) by multiple DNA-mediated technologies in order to verify the guidelines brought forward for PFGE [8] while at the same time trying to establish similar frameworks for RAPD typing data [10]. One hundred VRE strains from the UK and The Netherlands were combined in a single collection and for all strains both RAPD and PFGE were performed.…”

Comparative typing of Pseudomonas species isolated from the aquatic environment in Greece by SDS-PAGE and RAPD analysis

“…Molecular typing techniques search the bacterial identities in more depth since the genome of any organism reflects its uniqueness. It has been reported that genetic analysis at the species level gives insight into the variability within a bacterial population and generates evidence on bacterial adaptation to various environmental conditions (Renders et al 1996).…”

“…Randomly amplified polymorphic DNA (RAPD) techniques have been successfully applied to genetic population analysis of a broad range of microorganisms (Olive and Bean 1999) and specifically of Pseudomonas species (Bukanov et al 1994;Elaichouni et al 1994;Haase et al 1995a,b;Renders et al 1996;Hernández et al 1997). It has been demonstrated that RAPD is a universally applicable, rapid and highly discriminating typing method (Elaichouni et al 1994).…”

Phenotypic properties, drug susceptibility and genetic relatedness of Stenotrophomonas maltophilia clinical strains from seven hospitals in Rio de Janeiro, Brazil

“…Although PFGE is regarded as the most discriminatory method for epidemiological purpose, the results obtained with RAPD-PCR typing have demonstrated good correlation with PFGE (Renders et al 1996). However, preliminary trials of RAPD analysis with several different oligonucleotides primers are necessary to determine the optimal primers and reaction conditions for generation of suitable numbers of DNA bands.…”