Validation of ExPEC Virulence Markers

The initial proof of concept analysis used nine strains—hereafter termed control strains—that had previously been classified by multiplex PCR as representing ExPEC_JJ. They were included for validation of 18 singleton genes and genes representing two operons (foc-sfa and afa-dra-daa) in the VirulenceFinder ExPEC database (6 (link)). Of the nine control strains, five (BioProject accession numbers PRJNA169903, PRJNA475142, PRJNA479435, PRJNA475142, PRJNA16235) had publicly available genomes that, for this study, were collected from NCBI, whereas two (11A and 31A) underwent WGS within this study. One of the nine control strains (L31) ultimately was excluded for reasons described in Text S1 in the supplemental material. Additionally, strain JJ055 (positive for fimH and ompT) was replaced by K-12 strain MG1655 (GenBank accession number U00096.3) as a non-ExPEC negative control.

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Malberg Tetzschner A.M., Johnson J.R., Johnston B.D., Lund O, & Scheutz F. (2020). In Silico Genotyping of Escherichia coli Isolates for Extraintestinal Virulence Genes by Use of Whole-Genome Sequencing Data. Journal of Clinical Microbiology, 58(10), e01269-20.

Publication 2020

Expec Genes Genomes Multiplex pcr Operons Strain

Corresponding Organization :

Other organizations : Technical University of Denmark, Minneapolis VA Health Care System, University of Minnesota, Statens Serum Institut

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Variable analysis

independent variables

Strains used for validation of 18 singleton genes and genes representing two operons (foc-sfa and afa-dra-daa) in the VirulenceFinder ExPEC database

dependent variables

Validation of 18 singleton genes and genes representing two operons (foc-sfa and afa-dra-daa) in the VirulenceFinder ExPEC database

control variables

Nine control strains previously classified by multiplex PCR as representing ExPECJJ
Five control strains with publicly available genomes collected from NCBI
Two control strains that underwent WGS within this study
One control strain (L31) that was ultimately excluded
Strain JJ055 (positive for fimH and ompT) that was replaced by K-12 strain MG1655 as a non-ExPEC negative control

positive controls

Nine control strains previously classified by multiplex PCR as representing ExPECJJ

negative controls

K-12 strain MG1655 as a non-ExPEC negative control

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