A comparative phylotyping analysis of E. coli originating from avian colibacillosis based on the Clermont triplex scheme and gyrA gene sequencing

Abstract

Avian colibacillosis (AC) is frequently reported from poultry farms in the west of Iran. The aim of the present survey wasto evaluate the phylogeny of Escherichia coli isolated from AC through the Clermont triplex protocol and gyrA gene sequencing. Onehundred and fifty fresh carcasses suspected of having died from colibacillosis were sampled. The specimens were examined for E. coliisolation and identification. The extracted DNA repertoire of the isolates was subjected to phylogenetic analysis using Clermont triplexPCR. A DNA fragment of 1.8 kbp of the gyrA gene was amplified from a representative of each phylogroup or subgroup and the finalproduct was sequenced to depict a phylogenetic tree. In general, among 119 E. coli isolates, 31.93%, 6.72%, 34.45%, and 23.52% wereclustered in phylogroups A, B1, B2, and D, respectively. The phylogenetic assignment of the isolates based on the phylogenetic tree wascompletely uniform with the results of the triplex method. The outcome represents the segregation of avian pathogenic E. coli isolates tovarious phylogroups in the region. Moreover, the precise cluster analysis of E. coli based on gyrA sequencing confirms this method as arobust candidate for phylotyping of the bacterium.