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This study evaluates the clonal heterogeneity and efficacy of BOX-PCR and (GTG)5-PCR for DNA-based typing of Escherichia coli strains isolated from feces of chickens in IRI. Fecal samples were collected from chicken husbandry followed by E. coli isolation through biochemical tests. Isolates were finger printed by BOX-A1 and (GTG)5 primers. Dendrograms were generated based on 80% similarity and Shannon-Weaver index was calculated. One hundred and six E. coli isolates were obtained from chicken"s fecal sample. By (GTG)5 primer, of 106 isolates, two isolates were untypeable, while 104 isolates generated 100 unique, and 2 duplicate profiles. The dendrogram generated six clusters (G1-G6). With BOX-PCR, 106 E. coli isolates revealed 50 unique BOX profiles, in addition to 22 repetitive profiles, while 12 isolates were untypeable. Based on the bands and dendrogram, the 106 strains were grouped into six clusters (B1-B6). Shannon-Weaver index was 4.665 for (GTG)5- PCR and 0.281 for BOX-PCR. (GTG)5-PCR revealed complex clonal heterogeneity, more discriminatory power, less untypeable isolates, higher Shannon-Weaver index, and less isolates with the same profile in comparison to BOX-PCR. Although (GTG)5-PCR proved to be a powerful typing method, it is recommended to combine two or more different typing methods for higher discriminatory power.

Background: The human and animal intestinal tract harbors a complex community of microbes which enables bacteria to inherit antibiotic resistance genes. The aims of this study were to investigate clonality, antimicrobial resistance, prevalence and gene cassette arrays of class I and II integrons among commensal Escherichia coli from human and animals., Methods: A total of 200 E. coli isolates from human, chicken, cattle, and sheep were isolated followed by phenotypic antibiotic susceptibility testing and detection of class I and II integrons gene cassettes arrays. The clonal relationship of the isolates were analyzed by (GTG)5-PCR., Results: Of 200 isolates, 136 isolates were multi drug resistance (MDR) including 47, 40, 31 and 18 isolates from chicken, human, cattle and sheep, respectively. Class I integron was detected in 50, 38, 6 and 16 %, while class II was detected in 26, 8, 0 and 4 % of chicken, human, cattle and sheep isolates, respectively. Variable regions were amplified and sequenced. Cassette arrays in class I integrons were: dfrA1, dfrA5, dfrA7, dfrA12, aadA1, dfrA17 aadA1, aadA22, aadB-aadA2 and dfrA12-orfF-aadA2, and for class II, dfrA1-sat-aadA1, and sat-sat1-aadA1 were detected. Six class I and three class II positive strains did not produce any amplicons for variable region. Integron-positive isolates showed higher rate of resistance to streptomycin and trimethoprim-sulphamethoxazole, especially in chicken isolates which were fed antibiotics. Low similarity and great genetic diversity of class I and II integrons carrying isolates indicated no clonal relation., Conclusions: Integrons encoding for antibiotic resistance are significantly present among non-pathogenic commensal E. coli, especially from the hosts medicated by antibiotics. Uncontrolled use of antibiotics will increase the numbers of multiple drug resistant isolates and integrons prevalence.