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

Journal of Clinical Microbiology
M J C van den BeldMirjam A M D Kooistra-Smid

Abstract

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...Continue Reading

References

Jun 1, 1991·Microbiological Reviews·T L Hale
Jun 1, 1989·Journal of Clinical Microbiology·N I CarlinA A Lindberg
Jul 1, 1972·Applied Microbiology·P A GuinéeW H Jansen
May 2, 1974·The New England Journal of Medicine·R L KaganJ D MacLowry
May 1, 1980·Journal of Clinical Microbiology·R M SilvaL R Trabulsi
Aug 24, 2000·Proceedings of the National Academy of Sciences of the United States of America·G M PupoP R Reeves
Aug 24, 2004·Infection and Immunity·Ruiting LanPeter R Reeves
Apr 22, 2008·FEMS Microbiology Reviews·Bin LiuLei Wang
Dec 17, 2008·Journal of Medical Microbiology·Yayue LiLei Wang
Sep 1, 2009·Journal of Bacteriology·Robert M StaggNaresh K Verma
Sep 24, 2010·Journal of Clinical Microbiology·Richard F de BoerAnna M D Kooistra-Smid
Feb 22, 2011·Journal of Applied Microbiology·M PavlovicI Huber
Sep 9, 2011·European Journal of Clinical Microbiology & Infectious Diseases : Official Publication of the European Society of Clinical Microbiology·M J C van den Beld, F A G Reubsaet
Jun 5, 2012·Nucleic Acids Research·Panu ArtimoHeinz Stockinger
Dec 11, 2013·The Journal of Biological Chemistry·Tomasz K GozdziewiczJolanta Lukasiewicz
Jan 16, 2015·Journal of Clinical Microbiology·Jason W SahlDavid A Rasko
Apr 25, 2016·Diagnostic Microbiology and Infectious Disease·P Van LintJ Van Schaeren
Oct 26, 2016·Journal of Microbiological Methods·Maaike J C van den BeldUNKNOWN participating Medical Microbiological Laboratories
Oct 22, 2016·European Journal of Microbiology & Immunology·I LøbersliL T Brandal
Dec 16, 2016·Journal of Clinical Microbiology·Marie A ChattawayClaire Jenkins
Jan 11, 2018·EcoSal Plus·Keith A LampelAnthony T Maurelli

❮ Previous
Next ❯

Citations

Sep 16, 2021·Brazilian Journal of Microbiology : [publication of the Brazilian Society for Microbiology]·Fatima Bachir HalimehMonzer Hamze

❮ Previous
Next ❯

Datasets Mentioned

BETA
ERR2287281
ERR2287282
ERR2287283
ERR2300644
ERR2300645
ERR2300646
ERR2300647

Methods Mentioned

BETA
PCR
genotyping

Software Mentioned

BLAST
CLC Genomics Workbench
BLASTp
BioNumerics
ExPASy
SerotypeFinder
cgMLST
SeqSphere

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.