ArticleJournal of clinical microbiology2017
Identification of Escherichia coli and Shigella Species from Whole-Genome Sequences.
Article in Journal of clinical microbiology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 82 papers.
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Who cites it
82 citing papers in PubMed, 135 citations in OpenAlex.
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- Genomic insights into Shigella species isolated from small ruminants and manure in the North West Province, South Africa.Applied microbiology and biotechnology · 2025Article
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- High pathogenic potential of Shigella flexneri strains descending from a common ancestor isolated over 34 years in Brazil.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2025Article
- Phenotypic and genotypic relationships between Shigella species and Escherichia coli O37:H10 isolates in Addis Ababa, Ethiopia.BMC research notes · 2025Article
- Temporal establishment of the colon microbiota in Angus calves from birth to post-weaning.PloS one · 2025Article
- Molecular identification and antimicrobial resistance patterns of enterobacterales in community urinary tract infections among indigenous women in Ecuador: addressing microbiological misidentification.BMC infectious diseases · 2024Article
- Trends in shigellosis notifications in England, January 2016 to March 2023.Epidemiology and infection · 2024Article
- The clinical application value of multi-site mNGS detection of patients with sepsis in intensive care units.BMC infectious diseases · 2024Article
- Enhancing insights into diseases through horizontal gene transfer event detection from gut microbiome.Nucleic acids research · 2024Article
22 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Escherichia coli and Shigella species are closely related and genetically constitute the same species. Differentiating between these two pathogens and accurately identifying the four species of Shigella are therefore challenging. The organism-specific bioinformatics whole-genome sequencing (WGS) typing pipelines at Public Health England are dependent on the initial identification of the bacterial species by use of a kmer-based approach. Of the 1,982 Escherichia coli and Shigella sp. isolates analyzed in this study, 1,957 (98.4%) had concordant results by both traditional biochemistry and serology (TB&S) and the kmer identification (ID) derived from the WGS data. Of the 25 mismatches identified, 10 were enteroinvasive E. coli isolates that were misidentified as Shigella flexneri or S. boydii by the kmer ID, and 8 were S. flexneri isolates misidentified by TB&S as S. boydii due to nonfunctional S. flexneri O antigen biosynthesis genes. Analysis of the population structure based on multilocus sequence typing (MLST) data derived from the WGS data showed that the remaining discrepant results belonged to clonal complex 288 (CC288), comprising both S. boydii and S. dysenteriae strains. Mismatches between the TB&S and kmer ID results were explained by the close phylogenetic relationship between the two species and were resolved with reference to the MLST data. Shigella can be differentiated from E. coli and accurately identified to the species level by use of kmer comparisons and MLST. Analysis of the WGS data provided explanations for the discordant results between TB&S and WGS data, revealed the true phylogenetic relationships between different species of Shigella, and identified emerging pathoadapted lineages.
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