Highly Discriminatory Single-Nucleotide Polymorphism Interrogation of Escherichia coli by Use of Allele-Specific Real-Time PCR and eBURST Analysis.

In total, 782 Escherichia coil strains originating from various host sources have been analyzed in this study by using a highly discriminatory single-nucleotide polymorphism (SNP) approach. A set of eight SNPs, with a discrimination value (Simpson's index of diversity [D]) of 0.96, was determined using the Minimum SNPs software, based on sequences of housekeeping genes from the E. coil multilocus sequence typing (MLST) database. Allele-specific real-time PUR was used to screen 114 E. coil isolates from various fecal sources in Southeast Queensland (SEQ). The combined analysis of both the MLST database and SEQ E. coil isolates using eight high-D SNPs resolved the isolates into 74 SNP profiles. The data obtained suggest that SNP typing is a promising approach for the discrimination of host-specific groups and allows for the identification of human-specific E. coil in environmental samples. However, a more diverse E. coil collection is required to determine aninial- and environment-specific E. coil SNP profiles due to the abundance of human E. coil strains (56%) in the MLST database. [ABSTRACT FROM AUTHOR]