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Phylogeny of the Enterobacteriaceae based on genes encoding elongation factor Tu and F-ATPase -subunit

¹ Centre de recherche en infectiologie de l'Université Laval, Centre hospitalier universitaire de Québec (pavillon CHUL), Sainte-Foy, Québec, Canada G1V 4G2
² Division de microbiologie, faculté de Médecine, Université Laval, Sainte-Foy, Québec, Canada G1K 7P4
³ département de biochimie et microbiologie, faculté des Sciences et Génie, Université Laval, Sainte-Foy, Québec, Canada G1K 7P4
⁴ Infectio Diagnostic (I.D.I.) Inc., Sainte-Foy, Québec, Canada G1V 2K8

Correspondence
Michel G. Bergeron
Michel.G.Bergeron{at}crchul.ulaval.ca

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 -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.

The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA, tuf and atpD gene sequences obtained in this study are listed in Table 1.

Further trees based on tuf, atpD and 16S rRNA gene sequences, and scatterplots comparing pairwise distance between taxa, are available as supplementary figures in IJSEM Online.

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