Highly discriminatory single-nucleotide polymorphism interrogation of Escherichia coli by use of allele-specific real-time PCR and eBURST analysis.
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.
Sheludchenko
Maxim S
MS
Cell and Molecular Biosciences, Faculty of Science and Technology, Queensland University of Technology (QUT), 4 George Street, Brisbane, Queensland 4000, Australia.
Huygens
Flavia
F
Hargreaves
Megan H
MH
D000483:Alleles; D000818:Animals; D015373:Bacterial Typing Techniques / Q000379:methods*; D001483:Base Sequence; D002417:Cattle; D004269:DNA, Bacterial / Q000032:analysis / Q000235:genetics; D030561:Databases, Nucleic Acid; D004285:Dogs; D004784:Environmental Monitoring / Q000379:methods; D004926:Escherichia coli / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D005243:Feces / Q000382:microbiology; D005838:Genotype; D006801:Humans; D016133:Polymerase Chain Reaction / Q000379:methods*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D011793:Queensland; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D012984:Software; D013045:Species Specificity; D014876:Water Pollution / Q000032:analysis
D004269:DNA, Bacterial
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