Evolutionary Genetics of a New Pathogenic Escherichia Species: Escherichia albertii and Related Shigella boydii Strains

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Abstract
A bacterium originally described as Hafnia alvei induces diarrhea in rabbits and causes epithelial damage similar to the attachment and effacement associated with enteropathogenic Escherichia coli . Subsequent studies identified similar H. alvei -like strains that are positive for an intimin gene ( eae ) probe and, based on DNA relatedness, are classified as a distinct Escherichia species, Escherichia albertii . We determined sequences for multiple housekeeping genes in five E. albertii strains and compared these sequences to those of strains representing the major groups of pathogenic E. coli and Shigella . A comparison of 2,484 codon positions in 14 genes revealed that E. albertii strains differ, on average, at ∼7.4% of the nucleotide sites from pathogenic E. coli strains and at 15.7% from Salmonella enterica serotype Typhimurium. Interestingly, E. albertii strains were found to be closely related to strains of Shigella boydii serotype 13 ( Shigella B13), a distant relative of E. coli representing a divergent lineage in the genus Escherichia . Analysis of homologues of intimin ( eae ) revealed that the central conserved domains are similar in E. albertii and Shigella B13 and distinct from those of eae variants found in pathogenic E. coli . Sequence analysis of the cytolethal distending toxin gene cluster ( cdt ) also disclosed three allelic groups corresponding to E. albertii , Shigella B13, and a nontypeable isolate serologically related to S. boydii serotype 7. Based on the synonymous substitution rate, the E. albertii - Shigella B13 lineage is estimated to have split from an E. coli -like ancestor ∼28 million years ago and formed a distinct evolutionary branch of enteric pathogens that has radiated into groups with distinct virulence properties.