Experimental and theoretical evaluation of typing methods based upon random amplification of genomic restriction fragments (AFLP) for bacterial population genetics

Mougel, C.; Teyssier, S.; D' Angelo, C.; Groud, K.; Neyra, M.; Sidi Boumedine, K.; Cloeckaert, A.; Peloille, M.; Baucheron, S.; Chaslus Dancla, E.; Jarraud, S.; Meugnier, H.; Forey, F.; Vandenesch, F.; Lina, G.; Etienne, J.; Thioulouse, J.; Manceau, C.; Robbe, P.; Nalin, R.; Briolay, J.; Nesme, X.

Genetics, Selection, Evolution 33(Suppl 1): S319-S338


ISSN/ISBN: 0999-193X
Accession: 003763945

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The reliability and the level of taxonomic resolution of the amplified fragment length polymorphism (AFLP) method were evaluated with species of pathogenic bacteria involved in human, animal and plant diseases (Agrobacterium, Pseudomonas syringae, Xanthomonas populi, Salmonella enterica, Staphylococcus aureus, Xylophylus ampelinus, Legionella pneumophila and Frankia). The method was 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 dissimilarity 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 infraspecific distances indicates a critical overall genome diversity of about 14% (d=0.14). AFLP had more resolution 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 to standardize the capture of reliable data and their numeric treatment for the future development of AFLP data bases.