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Updated: Dec 27, 2025

Characterization of a Pathogenic Escherichia coli Strain Derived from Oreochromis spp. Farms Using Whole-Genome Sequencing
Published on: December 23, 2022
Complete genome sequences of two Enterococcus faecium strains and comparative genomic analysis
Yong-Qi Gan1, Tao Zhang1, Yong-Qiang Gan1
1Guangxi Institute for Food and Drug Control, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China.
Two clinically used Enterococcus strains, National Institute for Food and Drug Control (140623) and Shin Biofermin S (SBS-1), were identified as Enterococcus faecium. Genomic and biochemical analyses confirmed their classification, revealing insights into their potential clinical applications.
Area of Science:
- Microbiology
- Genomics
- Bioinformatics
Background:
- Enterococci, including Enterococcus faecalis and Enterococcus faecium, offer intestinal health benefits.
- Similar morphologies of E. faecalis and E. faecium can cause identification confusion.
- Strain 140623 (National Institute for Food and Drug Control) and strain SBS-1 (Shin Biofermin S) are clinically significant Enterococcus strains.
Purpose of the Study:
- To accurately identify and characterize two clinically used Enterococcus strains, 140623 and SBS-1.
- To compare the genomic and biochemical profiles of these strains with E. faecalis and E. faecium.
- To assess the potential clinical and food safety implications of these strains.
Main Methods:
- Whole-genome sequencing using Illumina HiSeq 2000.
- Biochemical characterization.
- Gas chromatography and mass spectrometry (GC-MS).
- Phylogenetic analysis.
- Functional annotation using Gene Ontology, KEGG, and COG classifications.
Main Results:
- Biochemical and GC-MS analyses indicated that strains 140623 and SBS-1 are more closely related to E. faecium than E. faecalis.
- Genomic sequencing revealed genome sizes of 2,812,926 bp for 140623 and 2,797,745 bp for SBS-1.
- Phylogenetic analysis confirmed that both strains belong to the E. faecium phylogenetic group.
- Functional annotation showed high conservation with reference E. faecium strains.
- Identified 6 virulence-associated genes, 15 antibiotic resistance genes, and 31 bacterial toxin genes.
Conclusions:
- Strains 140623 and SBS-1 were definitively identified as Enterococcus faecium.
- The identified genes provide insights into their resistance mechanisms and potential for safe clinical and food applications.
- Genomic data supports the clinical utility of these E. faecium strains in food and drug safety contexts.
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