Evaluation of a Culture-Dependent Algorithm and a Molecular Algorithm for Identification of Shigella spp., Escherichia coli, and Enteroinvasive E. coli

Maaike J. C. van den Beld*, Richard F. de Boer, Frans A. G. Reubsaet, John W. A. Rossen, Kai Zhou, Sjoerd Kuiling, Alexander W. Friedrich, Mirjam A. M. D. Kooistra-Smidb

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

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Identification of Shigella spp., Escherichia coli, and enteroinvasive E. coli (EIEC) is challenging because of their close relatedness. Distinction is vital, as infections with Shigella spp. are under surveillance of health authorities, in contrast to EIEC infections. In this study, a culture-dependent identification algorithm and a molecular identification algorithm were evaluated. Discrepancies between the two algorithms and original identification were assessed using whole-genome sequencing (WGS). After discrepancy analysis with the molecular algorithm, 100% of the evaluated isolates were identified in concordance with the original identification. However, the resolution for certain serotypes was lower than that of previously described methods and lower than that of the culture-dependent algorithm. Although the resolution of the culture-dependent algorithm is high, 100% of noninvasive E. coli, Shigella sonnei, and Shigella dysenteriae, 93% of Shigella boydii and EIEC, and 85% of Shigella flexneri isolates were identified in concordance with the original identification. Discrepancy analysis using WGS was able to confirm one of the used algorithms in four discrepant results. However, it failed to clarify three other discrepant results, as it added yet another identification. Both proposed algorithms performed well for the identification of Shigella spp. and EIEC isolates and are applicable in low-resource settings, in contrast to previously described methods that require WGS for daily diagnostics. Evaluation of the algorithms showed that both algorithms are capable of identifying Shigella species and EIEC isolates. The molecular algorithm is more applicable in clinical diagnostics for fast and accurate screening, while the culture-dependent algorithm is more suitable for reference laboratories to identify Shigella spp. and EIEC up to the serotype level.

Original languageEnglish
Article numbere00510-18
Number of pages13
JournalJournal of Clinical Microbiology
Issue number10
Early online date18-Jul-2018
Publication statusPublished - Oct-2018


  • EIEC
  • Escherichia coli
  • Shigella
  • whole-genome sequencing
  • enteroinvasive E. coli
  • identification
  • molecular methods
  • phenotypic methods

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