R-038. Recommendations for a Revised System of Nomenclature for Allelic Variants of Intimin (eae)

D. Lacher1, H. Steinsland2,3, T. Whittam2;
1US FDA, Laurel, MD, 2Michigan State Univ., East Lansing, MI, 3Univ. of Bergen, Bergen, NORWAY.

Intimin is a highly polymorphic protein encoded by the eae locus, and plays a crucial role in the attaching/effacing phenotype of diarrheagenic Escherichia coli. In recent years, a number of newly described eae alleles has resulted in a complex and confusing system of nomenclature for this gene. A prime example of this is multiple designations for the same allele (e.g., δ and κ). In an attempt to simplify this system, molecular evolutionary analyses were performed on eae sequences from 119 strains representing E. coli, Escherichia albertii, and Citrobacter rodentium. Phylogenetic compatibility analysis of 78 unique eae sequences revealed three distinct evolutionary histories encompassing different regions of the gene: 1) the periplasmic and transmembrane domains, 2) the D0 extracellular domain, and 3) the D1, D2, and D3 extracellular domains. Based on the compatibility findings, a revised system of nomenclature was developed. Sequences were assigned to one of seven allele families based on the pairwise proportion of differences (p distance) within the D1, D2, and D3 extracellular domains. Members of an allele family are <27% different than all other members of the same family, while between family differences range from 33 to 39% in this region of the gene. In keeping with the established Greek alphabet designations, the allele families were named α, β, γ, ε, ι, λ, and ρ after the first described allele within each family. After assignment to an allele family, specific allele designations (e.g., α1, α2, α3, etc.) were determined by pairwise comparison of the proportion of differences over the entire length of the gene. Sequences ≤1% different were given the same allele designation. This system of nomenclature was used to rename the 29 previously described eae alleles and to give designations to three newly discovered alleles from strains of E. albertii. In addition to being informative and straight-forward, the new system of nomenclature can easily classify new eae allelic sequences, as they become known.