- IV — Inventaire, Caractérisation et Suivi de la Diversité Microbienne / Inventory, Characterization and Monitoring of Microbial Diversity
- Open access
- Published:
Experimental and theoretical evaluation of typing methods based upon random amplification of genomic restriction fragments (AFLP) for bacterial population genetics
Évaluation expérimentale et théorique des methodes de typages basées sur l’amplification aléatoire de fragments de restriction pour l’étude des populations bactériennes
Genetics Selection Evolution volume 33, Article number: S319 (2001)
Abstract
The reliability and the level of taxonomie 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 to be 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 be-longing 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 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 respec-tive 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.
Résumé
La reproductibilité et Ie niveau de resolution taxo-nomique de ramplification aléatoire de fragments de restriction (AFLP) ont été éval-ués avec divers modèles pathogènes de l’homme, des animaux et des plantes. La methode est tres adaptable et peut être modifiée en fonction des particularités génomiques de chaque espèce. La différence nucléotidique moyenne réelle entre les genomes est une mesure de la distance génomique entre bactéries qui peut être estimée a partir de l’AFLP. Cette mesure permet la comparaison de données AFLP obtenues de fagons différentes. Avec la plupart des modèles, Ie seuil discriminant les distances interdes distances infra-spécifiques correspond a des differences nucléotidiques de l’ordre de 14% (d — 0,14). L’AFLP s’est montrée plus résolutive que la sérologie, la lyso-typie, l’électrophorèse en champs pulsés, et la PCR-RFLP de l’intergène ribosomique. L’analyse montre ainsi que la PCR-RFLP de l’intergène ribosomique permet de dis-tinguer des bactéries présentant au moins 3,4% (d = 0,034) de differences entre leurs genomes respectifs. Une procédure Standard d’aquisition et de traitement numérique des données incluant des logiciels adaptés est également proposée.
References
Arnold C., Metherell L., Clewley P., Stanley J., Predictive modelling of fluo-rescent AFLP: a new approach to the molecular epidemiology of E. coli, Res. Microbiol. 150 (1999) 33–44.
Asai T., Zaporojets D., Squires C, Squires C.L., An Escherichia coli strain with all chromosomal rRNA operons inactivated: complete exchange of rRNA genes between bacteria, Proc. Natl. Acad. Sci. USA 96 (1999) 1971–1976.
Ausubel F.M., Brent R., Kingston R.E., Moore D.D., Smith J.A., Seidman J.G., Struhl K., Current protocols in molecular biology, Greene Publishing Associates, Wiley Interscience, New-York, 1992.
Boumedine K.S., Rodolakis A., AFLP allows the identification of genomic markers of ruminant Chlamydia psittaci strains useful for typing and epidemiological studies, Res. Microbiol. 149 (1998) 735–744.
Campbell A., Mrazek J., Karlin S., Genome signature comparisons among prokaryote, plasmid, and mitochondrial DNA, Proc. Natl. Acad. Sci. USA 96 (1999) 9184–9189.
Clerc A., Manceau C., Nesme X., Comparison of Random Amplified Polymor-phism DNA (RAPD) with Amplified Fragment Lenght Polymorphism (AFLP) to assess the genetic diversity and genetic relatednesses within the genospecies III of Pseudomonas syringae, Appl. Environ. Microbiol. 64 (1998) 1180–1187.
Coenye T., Schouls L.M., Govan J.R.W., Kersters K., Vandamme P., Identification of Burkholderia species and genomovars from cystic fibrosis patients by AFLP fingerprinting, Int. J. Syst. Bacteriol. 49 (1999) 1657–1666.
Felsenstein J., PHYLIP (Phylogeny Inference Package) version 3.5c, Distributed by the author, Department of genetics, University of Whashington, Seattle, USA, 1993.
Gardan L., Shafik H., Belouin S., Broch R., Grimont F., Grimont P.A., DNA relatedness among the pathovars of Pseudomonas syringae and description of Pseudomonas tremae sp. nov. and Pseudomonas cannabina sp. nov. (ex Sutic and Dowson 1959), Int. J. Syst. Bacteriol. 49 (1999) 469–478.
Hauben L., Vauterin L., Moore E.R., Hoste B., Swings J., Genomic diversity of the genus Stenotrophomonas, Int. J. Syst. Bacteriol. 49 (1999) 1749–1760.
Huys G., Coopman R., Janssen P., Kersters K., High-resolution genotypic anal-ysis of the genus Aeromonas by AFLP fingerprinting, Int. J. Syst. Bacteriol. 46 (1996) 572–580.
Jarraud S., Lyon G.J., Figueiredo A.M., Lina G., Vandenesch F., Etienne J., Muir TW, Novick RP.Exfoliatin-producing strains define a fourth agr specificity group in Staphylococcus aureus. J. Bacteriol. 22 (2000) 6517–6522.
Lina G., Vandenesch F., Etienne J., Kreiswirth B., Fleurette J., Comparison of coagulase-negative staphylococci by pulsed-field gel electrophoresis, FEMS Microbiol. Lett. 92 (1992) 133–138.
Maidak B.L., Cole J.R., Parker C.T.Jr., Garrity G.M., Larsen N., Li B., Lil-burn T.G., McCaughey M.J., Olsen G.J., Overbeek R., Pramanik S., Schmidt T.M., Tiedje J.M., Woese CR., A new version of the RDP (Ribosomal Database Project), Nucleic Acids Res. 27 (1999) 171–173.
Maynard-Smith J., Smith N.H., O’Rourke M., Spratt B.G., How clonal are bacteria?, Proc. Natl. Acad. Sci. USA 90 (1993) 4384–4388.
Mazurek G., Reddy V., Marston B.J., Haas W.H., Crawford J.T., DNA fingerprinting by infrequent-restriction-site amplification, 1996. J. Clin. Microbiol. 34 (1996) 2386–2390.
Navarro E., Rouvier C, Normand P., Domenach A.M., Simonet P., Prin Y., Evolution of Frankia-Casuarinaceae interactions, Genet. Select. Evol. 30 (Suppl. 1) (1998) S357–S372.
Nei M., Li. W.H., Mathematical model for studying genetic variation in terms of restriction endonucleases, Proc. Natl. Acad. Sci. USA 76 (1979) 5269–5273.
Nesme X., Steenackers M., Steenackers V., Picard C., Ménard M., Ridé S., Ridé M., Differential host-pathogen interactions among clones of poplar and strains of Xanthomonas populi pv. populi, Phytopathology 84 (1994) 101–107.
Nesme X., Vaneechoutte M., Orso S., Hoste B., Swings J., Diversity and genetic relatedness within genera Xanthomonas and Stenotrophomonas using restriction endonuclease site differences of PCR-amplified 16SrRNA gene, System. Appl. Microbiol. 18 (1995) 127–135.
Oger P., Dessaux Y., Petit A., Gardan L., Manceau C., Chomel C., Nesme X., Validity sensitivity, and resolution limit of PCR-RFLP analysis of the rrs (16S rRNA gene) as a tooi to identify soil-borne and plant-associated bacterial populations, Genet. Select. Evol. 30 (Suppl. 1) (1998) S311-S332.
Ponsonnet C., Nesme X., Identification of Agrobacterium strains by PCR-RFLP analysis of pTi and chromosomal regions, Arch. Microbiol. 161 (1994) 300–309.
Popoff M.Y., Kersters K., Kiredjian M., Miras L., Coynault C., Position taxonomique des souches de Agrobacterium d’origine hospitalière, Ann. Microbiol. (Inst. Pasteur) 135A (1984) 427–442.
Rademaker J.L., Hoste B., Louws F.J., Kersters K., Swings J., Vauterin L., Vauterin P., de Bruijn F.J., Comparison of AFLP and rep-PCR genomic fingerprinting with DNA-DNA homology studies: Xanthomonas as a model system, Int. J. Syst. Evol. Microbiol. 2 (2000) 665–677.
Riffard S., Lo Prest i F., Vandenesch F., Forey F., Reyrolle M., Etienne J., Comparative analysis of infrequent-restriction-site PCR and pulsed-field gel electrophoresis for epidemiological typing of Legionella pneumophila serogroup 1 strains, J. Clin. Microbiol. 36 (1998) 161–167.
Sambrook J.E., Fristsch F., Maniatis T., Molecular cloning: a laboratory manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1989.
Sokal R.R., Sneath P.H.A., The construction of a taxonomie system, in: Principles of numerical taxonomy, chap. 7, Freeman, San Fransisco, USA, 1989, pp. 169–210.
Stackebrandt E., Goebel B.M., Taxonomie note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology, Int. J. Syst. Bacteriol. 44 (1994) 846–849.
Teyssier-Cuveile S., Mougel C, Nesme X., Direct conjugal transfers of Ti plasmid to soil microflora. Mol. Ecol. 8 (1999) 1273–1284.
Thioulouse J., Chessel D., Dolédec S., Olivier J.M. ADE-4: a multivariate analysis and graphical display software. Stat. Comput. 7 (1997) 75–83.
Vos P.R., Hogers R., Bleeker M., Reijans M., van der Lee T., Hornes M., Fridjers A., Pot J., Peleman J., Kuiper M., Zabeau M., AFLP: a new technique for DNA fingerprinting, Nucleic Acids Res. 23 (1995) 4407–4414.
Wayne L.G., Brenner D.J., Colwell R.R., Grimont P.A.D., Kandler O., Krichevsky M.I., Moore L.H., Moore W.E.C., R.G.E., Stackebrandt E., Starr M.P., Trüper H.G., Report of the ad hoc comittee on reconciliation of approaches to bacterial systematics, Int. J. Syst. Bacteriol. 37 (1987) 463–464.
Willems A.F., Doignon-Bourcier F., Coopman R., Hoste B., de Lajudie P., Gillis M., AFLP fmgerprint analysis of Bradyrhizobium strams isolated from Faidherbia albida and Aeschynomenes species, Syst. Appl. Microbiol. 23 (2000) 137–147.
Yap W.H., Zhang Z., Wang Y., Distinct types of rRNA operons exist in the genome of the actinomycete Therrnomonospora chromogena and evidence for horizontal transfer of an entire rRNA operon, J. Bacteriol. 181 (1999) 5201–5209.
Zabeau M., Vos P., Selective restriction fragment ampliflcation: a general method for DNA fingerprinting, Publication 0 534 858 Al, European Patent Office, Münich, 1993.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
About this article
Cite this article
Mougel, C., Teyssier, S., d’Angelo, C. et al. Experimental and theoretical evaluation of typing methods based upon random amplification of genomic restriction fragments (AFLP) for bacterial population genetics. Genet Sel Evol 33 (Suppl 1), S319 (2001). https://doi.org/10.1186/BF03500887
Published:
DOI: https://doi.org/10.1186/BF03500887