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

Abstract

In total, 782 Escherichia coli 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. coli multilocus sequence typing (MLST) database. Allele-specific real-time PCR was used to screen 114 E. coli isolates from various fecal sources in Southeast Queensland (SEQ). The combined analysis of both the MLST database and SEQ E. coli 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. coli in environmental samples. However, a more diverse E. coli collection is required to determine animal-and environment-specific E. coli SNP profiles due to the abundance of human E. coli strains (56%) in the MLST database.

VIM‐1 carbapenemase‐producing Escherichia coli in gulls from southern France

“…Allele‐specific real‐time PCR was used to screen seven SNPs ( fadD234, clpX267, uidA138, clpX177, clpx234, lysP198, icdA177 ) on seven housekeeping genes (Sheludchenko, Huygens, & Hargreaves, 2010) using an Applied Biosystems 7300.…”

CRISPR Diversity in E. coli Isolates from Australian Animals, Humans and Environmental Waters

“…Recently, we reported development of a Single-Nucleotide Polymorphism Real-Time (SNP) genotyping method [ 24 ] for the purpose of determining host-specificity of E . coli isolated from water.…”

Single Nucleotide Polymorphisms (SNP)-specific Quantitative Real Time Polymerase Chain Reaction (PCR) Assay for Analyzing Competition and Emergence of the Military Hypersporulating Strains of Bacillus Atrophaeous var. Globigii

“…The (T:C) SNP corresponding to the H101R mutation is used as a marker for distinguishing between the two strains. SNP detection in mixed samples is commonly performed using either end-point detection methods (38)(39)(40) or real-time PCR (qPCR) (41)(42)(43)(44)(45)(46). Here SNP-specific qPCR assay based on the relative quantification method (47) is developed and used for calculation of the rate of change in frequency (48) in a hypothetical experiments of emergence of either Detrick-1 or Detrick-2.…”