Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Case Reports
. 2017 Feb 6:9:7.
doi: 10.1186/s13099-017-0156-2. eCollection 2017.

Comparative genomic analysis of Shiga toxin-producing and non-Shiga toxin-producing Escherichia coli O157 isolated from outbreaks in Korea

Taesoo Kwon  1   2 , Won Kim #  1 , Seung-Hak Cho #  3
Affiliations
Case Reports

Comparative genomic analysis of Shiga toxin-producing and non-Shiga toxin-producing Escherichia coli O157 isolated from outbreaks in Korea

Taesoo Kwon et al. Gut Pathog. .

Abstract

Background: The Shiga toxin-producing Escherichia coli (STEC) O157 strain NCCP15739 and non-STEC O157 strain NCCP15738 were isolated from outbreaks in Korea. We characterized NCCP15739 and NCCP15738 by genome sequencing and a comparative genomic analysis using two additional strains, E. coli K-12 substr. MG1655 and O157:H7 EDL933.

Results: Using the Illumina HiSeq 2000 platform and the RAST server, the whole genomes of NCCP15739 and NCCP15738 were obtained and annotated. NCCP15739 and NCCP15738 clustered with different E. coli strains based on a whole-genome phylogeny and multi-locus sequence typing analysis. Functional annotation clustering indicated enrichment for virulence plasmid and hemolysis-related genes in NCCP15739 and conjugation- and flagellum-related genes in NCCP15738. Defense mechanism- and pathogenicity-related pathways were enriched in NCCP15739 and pathways related to the assimilation of energy sources were enriched in NCCP15738. We identified 66 and 18 virulence factors from the NCCP15739 and NCCP15738 genome, respectively. Five and eight antibiotic resistance genes were identified in the NCCP15739 and NCCP15738 genomes, respectively. Based on a comparative analysis of phage-associated regions, NCCP15739 and NCCP15738 had specific prophages. The prophages in NCCP15739 carried virulence factors, but those in NCCP15738 did not, and no antibiotic resistance genes were found in the phage-associated regions.

Conclusions: Our whole-genome sequencing and comparative genomic analysis revealed that NCCP15739 and NCCP15738 have specific genes and pathways. NCCP15739 had more genes (410), virulence factors (48), and phage-related regions (11) than NCCP15738. However, NCCP15738 had three more antibiotic resistance genes than NCCP15739. These differences may explain differences in pathogenicity and biological characteristics.

Keywords: Alpha-hemolysin; Comparative genomics; Draft genome; Non-Shiga-like toxin-producing Escherichia coli O157; Shiga-like toxin-producing Escherichia coli O157.

PubMed Disclaimer

Figures

Fig. 1
Fig. 1
Circular map of the NCCP15739 and NCCP15738 draft genomes. Circular map of genes and genome statistics were visualized for NCCP15739 and NCCP15738 using Circos (version 0.64). All CDSs are syntenic regions of NCCP15739 that were determined using BLAST searches
Fig. 2
Fig. 2
Phylogenetic tree of NCCP15739 and NCCP15738. a Whole-genome phylogeny, b multi-locus sequence typing phylogeny. Evolutionary time was scaled by 100; lower values imply a relatively recent branching event. The scale indicates the number of substitutions per site. NCCP15739, NCCP15738, and the reference strains are highlighted in different colors: NCCP15739 (red), NCCP15738 (orange), Escherichia coli K-12 substr. MG1655 (blue), and E. coli O157:H7 str. EDL933 (green)
See this image and copyright information in PMC

References

    1. Karmali MA, Steele BT, Petric M, Lim C. Sporadic cases of haemolytic-uraemic syndrome associated with faecal cytotoxin and cytotoxin-producing Escherichia coli in stools. Lancet. 1983;1(8325):619–620. doi: 10.1016/S0140-6736(83)91795-6. - DOI - PubMed
    1. Riley LW, Remis RS, Helgerson SD, McGee HB, Wells JG, Davis BR, Hebert RJ, Olcott ES, Johnson LM, Hargrett NT, et al. Hemorrhagic colitis associated with a rare Escherichia coli serotype. N Engl J Med. 1983;308(12):681–685. doi: 10.1056/NEJM198303243081203. - DOI - PubMed
    1. Wells JG, Davis BR, Wachsmuth IK, Riley LW, Remis RS, Sokolow R, Morris GK. Laboratory investigation of hemorrhagic colitis outbreaks associated with a rare Escherichia coli serotype. J Clin Microbiol. 1983;18(3):512–520. - PMC - PubMed
    1. Nataro JP, Kaper JB. Diarrheagenic Escherichia coli. Clin Microbiol Rev. 1998;11(1):142–201. - PMC - PubMed
    1. Caprioli A, Morabito S, Brugere H, Oswald E. Enterohaemorrhagic Escherichia coli: emerging issues on virulence and modes of transmission. Vet Res. 2005;36(3):289–311. doi: 10.1051/vetres:2005002. - DOI - PubMed

Publication types

LinkOut - more resources