E. coli MLST Identification Protocol

The initial analysis and identification of the strains were performed using an in silico E. coli MLST approach, based on the information available at the E. coli MLST website (http://mlst.warwick.ac.uk/mlst/dbs/Ecoli) and using Ridom SeqSphere+ software v2.4.0 (Ridom; Münster, Germany) (http://www.ridom.com/seqsphere). Seven housekeeping genes (dnaE, gyrB, recA, dtdS, pntA, pyrC, and tnaA), described previously for E. coli [36 (link)], were used for MLST analysis. The same E. coli MLST database was also used to assign numbers for alleles and STs.

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González-Escalona N, & Kase J.A. (2019). Virulence gene profiles and phylogeny of Shiga toxin-positive Escherichia coli strains isolated from FDA regulated foods during 2010-2017. PLoS ONE, 14(4), e0214620.

Publication 2019

SeqSphere+ software v2.4.0

Alleles Dtds E coli Housekeeping genes Strains

Corresponding Organization : Center for Food Safety and Applied Nutrition

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Variable analysis

independent variables

In silico E. coli MLST approach
Ridom SeqSphere+ software v2.4.0

dependent variables

Identification of strains

control variables

Seven housekeeping genes (dnaE, gyrB, recA, dtdS, pntA, pyrC, and tnaA) described previously for E. coli
E. coli MLST database used to assign numbers for alleles and STs

controls

Positive control: None mentioned
Negative control: None mentioned

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