Clonal Heterogeneity and Efficacy of BOX and (GTG)5 Fingerprinting Methods for Molecular Typing of Escherichia coli Isolated from Chickens in IRI

Bu çalışma ile İran'da tavuk dışkılarından izole edilen Escherichia coli suşlarının DNA temelli tiplendirmesinde BOX-PCR ve (GTG)5-PCR metotlarının klonal heterojenitesi ve yeterliliği araştırılmıştır. Biyokimyasal test ile E. coli tespit edilen kümeslerden dışkı örnekleri toplandı. İzolatların parmakizi BOX-A1 ve (GTG)5 primerler kullanılarak alındı. Dendrogramlar %80 benzerlik baz alınarak üretildi ve ShannonWeaver endeksi hesaplandı. Yüzsekiz E. coli izolatı tavuk dışkı örneklerinden elde edildi. (GTG)5 primer ile yapılan analizde 106 izolatın 2'si tiplendirilemezken 104 izolattan 100 özgün ve 2 duplike profil üretildi. Dendrogram altı küme (G1-G6) oluşturdu. BOX-PCR ile 106 E. coli izolatından 22 tekrarlayan profile ile birlikte 50 özgün BOX profili oluşurken 12 izolat tiplendirilemedi. Oluşan bantlar ve dendrograma göre 106 suş 6 küme (G1-G6) içerisinde gruplandırıldı. Shannon-Weaver endeksi (GTG)5-PCR için 4.665, BOX-PCR için ise 0.281 olarak belirlendi. (GTG)5-PCR; BOX-PCR ile karşılaştırıldığında kompleks klonal heterojenite, daha fazla ayırt edici güç, daha az tiplendirilemeyen izolat, daha yüksek Shannon-Weaver endeksi ve daha az aynı profilli izolat elde edilmesini sağladı. (GTG)5-PCR daha güçlü tiplendirme metodu olmasına rağmen iki veya daha fazla tiplendirme metodunun birlikte kullanılması daha yüksek ayırıcı güç için önerilmektedir

BOX ve (GTG)5 Parmak izi Metotlarının İran’da Tavuklardan İzole Edilen Escherichia coli’nin Moleküler Tiplendirilmesinde Klonal Heterojenite ve Yeterliliği

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)5PCR 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

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