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Applied and Environmental Microbiology, August 2005, p. 4784-4792, Vol. 71, No. 8
0099-2240/05/$08.00+0     doi:10.1128/AEM.71.8.4784-4792.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

Single-Nucleotide Polymorphism Phylotyping of Escherichia coli{dagger}

Florence Hommais,1,2* Sabrina Pereira,3 Cécile Acquaviva,3 Patricia Escobar-Páramo,1 and Erick Denamur1

INSERM U722 and Université Paris 7, Faculté de Médecine Xavier Bichat, 16 rue Henri Huchard, 75018 Paris, France,1 UMR 5122, Université Claude Bernard Lyon 1, 10 rue Dubois, 69622 Villeurbanne cedex, France,2 Service de Biochimie Génétique, Hôpital Robert Debré, 48 boulevard Sérurier, 75019 Paris, France3

Received 2 November 2004/ Accepted 22 February 2005

We describe a rapid and easily automated phylogenetic grouping technique based on analysis of bacterial genome single-nucleotide polymorphisms (SNPs). We selected 13 SNPs derived from a complete sequence analysis of 11 essential genes previously used for multilocus sequence typing (MLST) of 30 Escherichia coli strains representing the genetic diversity of the species. The 13 SNPs were localized in five genes, trpA, trpB, putP, icdA, and polB, and were selected to allow recovery of the main phylogenetic groups (groups A, B1, E, D, and B2) and subgroups of the species. In the first step, we validated the SNP approach in silico by extracting SNP data from the complete sequences of the five genes for a panel of 65 pathogenic strains belonging to different E. coli pathovars, which were previously analyzed by MLST. In the second step, we determined these SNPs by dideoxy single-base extension of unlabeled oligonucleotide primers for a collection of 183 commensal and extraintestinal clinical E. coli isolates and compared the SNP phylotyping method to previous well-established typing methods. This SNP phylotyping method proved to be consistent with the other methods for assigning phylogenetic groups to the different E. coli strains. In contrast to the other typing methods, such as multilocus enzyme electrophoresis, ribotyping, or PCR phylotyping using the presence/absence of three genomic DNA fragments, the SNP typing method described here is derived from a solid phylogenetic analysis, and the results obtained by this method are more meaningful. Our results indicate that similar approaches may be used for a wide variety of bacterial species.

* Corresponding author. Mailing address: UMR 5122, Université Claude Bernard Lyon 1, 10 rue Dubois, 69622 Villeurbanne cedex, France. Phone: 33 (0) 4 72 43 16 21. Fax: 33 (0) 4 72 43 26 86. E-mail: hommais{at}univ-lyon1.fr.

{dagger} Supplemental material for this article may be found at http://aem.asm.org/.

Applied and Environmental Microbiology, August 2005, p. 4784-4792, Vol. 71, No. 8
0099-2240/05/$08.00+0     doi:10.1128/AEM.71.8.4784-4792.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.



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