The reliability and the level of taxonomic resolution of the amplified
fragment length polymorphism (AFLP) method were evaluated with species of patho-
genic bacteria involved in human, animal and plant diseases. The method was found
very versatile as it can be adapted to the individual genome constraints of all tested
species. The calculation of a genetic distance d corresponding to the average dissim-
ilarity between actual overall genome sequences was proposed for comparing AFLP
data. Bacterial models showed clearly different patterns between strains belonging to
different genomic species, while patterns were clearly similar within a given species.
The threshold which distinguishes between inter and infra-specific distances indicates
a critical overall genome diversity of about 14% (d = 0.14). AFLP had more resolu-
tion power than serology, phage typing, PFGE and restriction analysis of ribosomal
intergenic spacers. In the latter case, regression analysis showed that PCR-RFLP
of ribosomal intergenic spacers can only be used to differentiate bacteria which have
at least 3.4% (d = 0.034) nucleotide differences between their respective genomes.
Finally, an improved procedure using newly developed software was also proposed in
order to standardize the capture of reliable data and their numeric treatment for the
future development of AFLP data bases.