The phylogeny of enterobacterial species commonly found in clinical samples was analysed by comparing partial sequences of their elongation factor Tu gene (tuf ) and of their F-ATPase b-subunit gene (atpD). An 884 bp fragment for tuf and an 884 or 871 bp fragment for atpD were sequenced for 96 strains representing 78 species from 31 enterobacterial genera. The atpD sequence analysis exhibited an indel specific to Pantoea and Tatumella species, showing, for the first time, a tight phylogenetic affiliation between these two genera. Comprehensive tuf and atpD phylogenetic trees were constructed and are in agreement with each other. Monophyletic genera are Cedecea, Edwardsiella, Proteus, Providencia, Salmonella, Serratia, Raoultella and Yersinia. Analogous trees based on 16S rRNA gene sequences available from databases were also reconstructed. The tuf and atpD phylogenies are in agreement with the 16S rRNA gene sequence analysis, and distance comparisons revealed that the tuf and atpD genes provide better discrimination for pairs of species belonging to the family Enterobacteriaceae. In conclusion, phylogeny based on tuf and atpD conserved genes allows discrimination between species of the Enterobacteriaceae. INTRODUCTIONMembers of the family Enterobacteriaceae are facultatively anaerobic, Gram-negative rods that are catalase-positive and oxidase-negative (Brenner, 1984). They are found in soil, water and plants, and also in animals ranging from insects to humans. Many enterobacteria are opportunistic pathogens. In fact, members of this family are responsible for about 50 % of nosocomial infections in the US (Brenner, 1984). Therefore, this family is of considerable clinical importance.The major classification studies on the family Enterobacteriaceae were based on phenotypic traits (Brenner et al., , 1999Dickey & Zumoff, 1988;Farmer et al., 1980Farmer et al., , 1985a such as biochemical reactions and physiological characteristics. However, phenotypically distinct strains may be closely related by genotypic criteria and may belong to the same genospecies (Bercovier et al., 1980;Hartl & Dykhuizen, 1984). Also, phenotypically close strains (biogroups) may belong to different genospecies, like Klebsiella pneumoniae and Enterobacter aerogenes (Brenner, 1984), for example. Consequently, identification and classification of certain species may be ambiguous with techniques based on phenotypic tests (Janda et al., 1999;Kitch et al., 1994;Sharma et al., 1990).More advances in the classification of members of the family Enterobacteriaceae have come from DNA-DNA hybridization studies (Brenner et al., , 1986(Brenner et al., , 1993Farmer et al., 1980Farmer et al., , 1985aIzard et al., 1981;Steigerwalt et al., 1976). The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA, tuf and atpD gene sequences obtained in this study are listed in Furthermore, the phylogenetic significance of bacterial classification based on 16S rRNA gene sequences has been recognized by many workers Wayne et al., 1987). However, members of the family En...

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