Genetic and phylogenetic analysis of avian extraintestinal and intestinal Escherichia coli.

Extraintestinal pathogenic Escherichia coli (ExPEC) isolates of animals and man are known to carry specific virulence associated genes. The intestinal tract, it is primarily colonized by various strains of commensal E. coli but it may include ExPEC as well. Here we aimed to assess possible genetic and evolutionary linkages between extraintestinal pathogenic and intestinal (commensal) E. coli of poultry. For that purpose we analysed 71 ExPEC isolates, and 40 intestinal isolates assumed to be commensal E. coli (IntEC), from dead chickens and turkey poults for 26 virulence related genes. Although the two groups shared several virulence determinants the genes pic, papC, and cdtIV were exclusively present in ExPEC and further five genes (colV, iss, kpsM, tsh and iutA), were significantly more frequent among ExPEC. Phylogenetic backgrounds of ExPEC and of IntEC isolates indicated significant differences. A 40% of ExPEC belonged to phylogroup A primarily containing strains of serogroup O78. Phylogroup D contained ExPEC strains of serogroups O53 (2 strains) and O115 (5 strains) characterized by the cdt-IV genes, suggesting the existence of new clones of avian ExPEC in phylogenetic group D. On the other hand, a 42.5% of IntEC belonged to phylogroup B1 with diverse serogroups. Our data provide insight into the clonal evolution of avian ExPEC especially in phylogenetic groups A and D, resulting avian ExPEC with similarities to human ExPEC.