Clonal heterogeneity and efficacy of box and (gtg)5 fingerprinting methods for molecular typing of escherichia coli isolated from chickens in iri

Abstract

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.

Keywords

• box-pcr
• chicken
• clonal heterogeneity
• escherichia coli
• (gtg)5-pcr
• molecular typing