Genomic differentiation of Escherichia coli isolates from chicken and multiple aquatic sources using Enterobacterial Repetitive inter-genic Consensus PCR

Suryakant Mishra 1, S.S. Mishra 2, R.P. Sharma 1,
A. Dharani Kumar 3 and B.J.R. Sharma 3

1. Project Directorate on Poultry, Rajendranagar, Hyderabad- 500 030,
2. Central inland fisheries research institute, Barrakpore, Kolkata- 700 120 and
3. Department of Microbiology, ANGRAU, Hyderabad-500 030

Genomic differentiation of E.coli strains isolated from affected chickens, in and around Hyderabad region versus E.coli strains sampled from multiple aquatic sources, was attempted, using Enterobacterial Repetitive Intergenic Consensus (ERIC) PCR. ERIC sequences are novel interspersed repetitive DNA sequences, which are native to Enterobacterial species, which are present in transcribed region of the E.coli genome (either in the inter-genic regions or in the UTR regions close to major ORFs). With such significance, 47 E.coli isolates sourced from chicken carcasses, pre-typed by surface-antigen characteristics (“O” antigens belonging to 14 distinct serotypes were compared to 19 E.coli samples, from multiple aquatic sources by ERIC PCR, under standard protocols. The aquatic sources included E.coli harvested from fresh-water fish carcasses, Gut contents from fresh-water fishes, Prawn (Monodon) carcasses and from the water samples that represented the aquatic-environment harbored by these species. The fingerprints raised from UV-illuminated electrophoresed PCR products, from recommended agarose gel conditions, were analyzed separately, for these samples. Inter-sample genomic diversity analysis via standard softwares, through dice coefficients, revealed highly-heterogeneous clustering patterns among samples of aquatic-sources with an average similarity coefficient: 39.9% where as, the average coefficient for chicken-origin sample was 49.2%. Co-clustering of samples was evidenced for almost all the aquatic origin E.coli groups, while the chicken origin samples could be clustered into 3 major groups. When probed further into patterns generated from chicken-E.coli sources, it was seen that bulks of the isolates harvested from air-sac (56.7%), heart (55.6%) and liver (71.4%) could be grouped into respective major clusters enunciated by DICE-UPGMA phylogenetic tree. It was also observed that ERIC PCR could accurately differentiate chicken source E.coli samples from each other even when they belonged to the same serotypes. The profiles for samples of aquatic sources yielded many additionally-scored fingerprint alleles than chicken-origin samples (average: 19 versus 10 for chicken) per profile, while indicating source-specific fingerprints for the ones harvested from fish, prawn and water-samples respectively. The study concluded that ERIC-PCR was a robust fingerprinting methodology for diversity analysis of E.coli samples and was able to genomically delineate both antigenically-differentiated and unclassified strains sourced from wide variety of hosts ranging from chickens to fish and prawn samples.

Source : IPSACON-2005

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