Comparison of AFLP and rep-PCR genomic fingerprinting with DNA-DNA homology studies: Xanthomonas as a model system

The genus Xanthomonas contains a large number of strains, which have been c haracterized by a variety of phenotypic and genotypic classification method s. The Xanthomonas collection constitutes one of the largest groups of bact eria that have been characterized phylogenetically by DNA-DNA homology stud ies and genomic fingerprinting. Presently, a total genomic DNA-DNA homology value of 70% represents an internationally accepted criterion to define ba cterial species levels. However, the complexity of DNA-DNA reassociation ki netics methods precludes the rapid analysis of large numbers of bacterial i solates, which is imperative for molecular microbial diversity studies. The refore, the aim of this study was to compare more facile PCR-based genomic fingerprinting techniques, such as repetitive-sequence-based (rep)PCR and A FLP genomic fingerprinting, to DNA-DNA hybridization studies. Using three d ifferent primer sets, rep-PCR genomic fingerprint patterns were generated f or 178 Xanthomonas strains, belonging to all 20 previously defined DNA-DNA homology groups, and one Stenotrophomonas maltophilia strain. In addition, AFLP genomic fingerprints were produced for a subset of 80 Xanthomonas stra ins belonging to the 20 DNA-DNA homology groups and for the S. maltophilia strain. Similarity values derived from rep-PCR- and AFLP-generated fingerpr inting analyses were calculated and used to determine the correlation betwe en rep-PCR- or AFLP-derived relationships and DNA-DNA homology values. A hi gh correlation was observed, suggesting that genomic fingerprinting techniq ues truly reveal genotypic and phylogenetic relationships of organisms. On the basis of these studies, we propose that genomic fingerprinting techniqu es such as rep-PCR and AFLP can be used as rapid, highly discriminatory scr eening techniques to determine the taxonomic diversity and phylogenetic str ucture of bacterial populations.