ORIGINAL ARTICLE Phylogenetic typing and virulence gene profile of pathogenic and commensal avian Escherichia coli in Iran: a notable finding N. Zakariazadeh 1 & J. Shayegh 2 & A. Ghorbani 1 Received: 20 October 2018 /Accepted: 30 January 2019 # Springer-Verlag London Ltd., part of Springer Nature 2019 Abstract The aim of this study was to compare phylogenic groups and virulence genes profiles of Escherichia coli isolated from poultry suffering from Colibacillosis with E.coli in the intestinal flora of healthy poultry. For this purpose, var, tsh, iucd, papc, irp2, and iss virulence genes of E. coli were investigated by multiplex PCR in 70 isolates (35 obtained from healthy samples and the other 35 isolated were attained form those with Colibacillosis) in Ardabil province, northwest of Iran. The phylogenic groups were also determined through use of PCR multiplex. Among them, 32 isolates (91%) of samples taken from poultry with Colibacillosis and 27 isolates (77%) from healthy samples contained papc gene. The results for iucd, var, and irp2 genes were 17 healthy and 20 diseased isolates, 23 healthy and 28 diseased isolates, and 32 healthy and 29 diseased isolates, respectively. In the case of tsh gene, only one isolate from healthy samples included the mentioned gene; while iss gene was observed in none of the isolates. In terms of phylogeny groups, except one, all the isolates belonged to the phylogenic group D. Results of present research revealed that the frequency of virulence genes and the diversity of phylogeny groups in isolates from healthy and diseased samples are not significantly different in the studied area. Keywords Escherichia coli . Colibacillosis . PCR multiplex Introduction One century has passed from the recognition of Escherichia coli as a pathogenic bacterium in poultry. Since then, its asso- ciation with many poultry diseases has been proven. Colibacillosis is the most important E. coli-induced disease in poultry in which the mentioned bacterium is involved as first and secondary pathogens. This disease has been reported from all around the world and has caused huge loss in poultry industry (Dziva and Stevens 2008). The significant way of disease induction is feces and oral transmittance. Therefore, E. coli can be excreted as the natural intestinal flora; but under stressful conditions, this natural flora may be as pathogen. Although stress has been identified as the major underlying causes of E. coli disease in poultry especially Colibacillosis, however, the pathogenicity of the pathogen still plays an im- portant role. Molecular studies based on techniques such as Rep-PCR, ERIC-PCR, RFLP, and PFGE along with phyloge- netic studies have indicated that among natural flora popula- tions, some specific clones are more associated with the path- ogenicity of this bacterium (Gordon 2010). These colons are sometimes composed of 10–15% of E. coli population of in- testine and are responsible for about 83% of poultry diseases. These strains are called Avian pathogenic E. coli (APEC) (Dziva and Stevens 2008). MLEE- and MLST-based phylogenetic determination of groups in E. coli is crucial in identifying E. coli pathogenic colons. In this regard, E. coli bacteria are divided into four phylogenetic groups: A, B1, B2, D. Strains of group B2 and D are predominantly extracellular pathogenic strains, while commensal E. coli strains mainly belong to group A (Johnson and Stell 2000; Picard et al. 1999). * J. Shayegh jalalshayegh@gmail.com N. Zakariazadeh zakariya.nad@gmail.com A. Ghorbani abolfazlgorbani@gmail.com 1 Department of Animal Science, Islamic Azad University, Shabestar Branch, Shabestar, Iran 2 Department of Veterinary Medicine, Islamic Azad University, Shabestar Branch, Shabestar, Iran Comparative Clinical Pathology https://doi.org/10.1007/s00580-019-02921-2