Journal Article

Comparative Evaluation of Genomic and Laboratory Approaches for Determination of Shiga Toxin Subtypes in Escherichia coli

Carrillo, Catherine D., Amoako, Kingsley, Huszczynski, George, Koziol, Adam G., Gauthier, Martine, Goji, Noriko, Lambert, Dominic, Mathews, Amit, Blais, Burton W.

2016

Overview

The determination of Shiga toxin (ST) subtypes can be an important element in the risk characterization of foodborne ST-producing Escherichia coli (STEC) isolates for making risk management decisions. ST subtyping methods include PCR techniques based on electrophoretic or pyrosequencing analysis of amplicons and in silico techniques based on whole genome sequence analysis using algorithms that can be readily incorporated into bioinformatics analysis pipelines for characterization of isolates by their genetic composition. The choice of technique will depend on the performance characteristics of the method and an individual laboratory's access to specialized equipment or personnel. We developed two whole genome sequence-based ST subtyping tools: (i) an in silico PCR algorithm requiring genome assembly to replicate a reference PCR-based method developed by the Statens Serum Institut (SSI) and (ii) an assembly-independent routine in which raw sequencing results are mapped to a database of known ST subtype sequence variants (V-Typer). These tools were evaluated alongside the SSI reference PCR method and a recently described PCR-based pyrosequencing technique. The V-Typer method results corresponded closely with the reference method in the analysis of 67 STEC cultures obtained from a World Health Organization National Reference Laboratory. In contrast, the in silico PCR method failed to detect ST subtypes in several cases, a result which we attribute to assembly-induced errors typically encountered with repetitive gene sequences. The V-Typer can be readily integrated into bioinformatics protocols used in the identification and characterization of foodborne STEC isolates.

• Publisher: Elsevier Limited
• Subject: Algorithms / Bioinformatics / blood serum / E coli / electrophoresis / Epidemiology / Escherichia coli Infections - diagnosis / Escherichia coli Proteins - genetics / Food safety / Genes / Genetic testing / genome / genome assembly / Genomes / Genomics / human resources / Humans / Management decisions / Methods / nucleotide sequences / Pathogens / polymerase chain reaction / risk characterization / Risk management / Serology / Shiga toxin / Shiga Toxin - genetics / Shiga Toxin 1 - genetics / Shiga Toxin 2 - genetics / Shiga toxin-producing Escherichia coli / Shiga-Toxigenic Escherichia coli - isolation & purification / Software / Studies / Testing laboratories / Toxins / Virulence / Whole genome sequencing / World Health Organization