skip to main content
10.1145/2665970.2665981acmconferencesArticle/Chapter ViewAbstractPublication PagescikmConference Proceedingsconference-collections
research-article

Identification of a Specific Base Sequence of Pathogenic E. Coli through a Genomic Analysis

Published: 07 November 2014 Publication History

Abstract

E. coli sequence type 131 (ST131) is one of pathogens that causes resistant infections. Comparative genome analyses allow interpretations of the virulence factors of pathogens. Thus, in this study, we analysis the genomic differences between the pathogenic E. coli ST131 and the non-pathogenic E. coli K-12. In this study, we identify the genomic differences between 96 E. coli ST131 strains and the E. coli K-12 in gene elements and their non-coding regulation elements. Using next-generation whole-genome sequencing data, we investigated genetic variations of protein-coding regions and their regulation regions. After the alignment of the sequence reads, large numbers of single nucleotide variants (SNVs) were observed in the regulation and protein-coding sequences. In the regulation regions, we found strong conserved regions, in this case, ribosome binding sites. In the gene regions, we found conserved start and stop codons with the specific position varying commonly in each codon. Except for these well-conserved regions, other variations were randomly distributed in regulation regions. Even a region having well-known conserved sequences such as -10 and -35 in the promoter had a similar level of variation. In this study, we found genomic variations between the pathogenic E. coli ST 131 strain and the non-pathogenic E. coli K-12. In addition, the numbers of sequence variations were determined in both the protein-coding regions and the regulation regions. However, we found that the effects of variations on the protein-coding regions are less significant than those on the regulation regions.

References

[1]
T.S. Avasthi, N. Kumar, R. Baddam, et al. Genome of multidrug-resistant uropathogenic Escherichia coli strain NA114 from India. J Bacteriol 193, 4272--4273, 2011.
[2]
T. Baba, T. Ara, M. Hasegawa, et al. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2, 2006 0008, 2006.
[3]
F.R. Blattner, G. Plunkett, 3rd, C.A. Bloch, et al. The complete genome sequence of Escherichia coli K-12. Science 277, 1453--1462, 1997.
[4]
G. Clark, K. Paszkiewicz, J. Hale, et al. Genomic analysis uncovers a phenotypically diverse but genetically homogeneous Escherichia coli ST131 clone circulating in unrelated urinary tract infections. J Antimicrob Chemother 67, 868--877, 2012.
[5]
F.H. Crick. Codon--anticodon pairing: the wobble hypothesis. J Mol Biol 19, 548--555, 1966.
[6]
M.A. DePristo, E. Banks, R. Poplin, et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43, 491--498, 2011.
[7]
J.R. Johnson, B. Johnston, C. Clabots, et al. Escherichia coli sequence type ST131 as the major cause of serious multidrug-resistant E. coli infections in the United States. Clin Infect Dis 51, 286--294, 2010.
[8]
J.R. Johnson, B. Johnston, C. Clabots, et al. Escherichia coli sequence type ST131 as an emerging fluoroquinolone-resistant uropathogen among renal transplant recipients. Antimicrob Agents Chemother 54, 546--550, 2010.
[9]
D. Kim, J.S. Hong, Y. Qiu, et al. Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling. PLoS Genet 8, 8, e1002867, 2012.
[10]
S.H. Lau, S. Reddy, J. Cheesbrough, et al. Major uropathogenic Escherichia coli strain isolated in the northwest of England identified by multilocus sequence typing. J Clin Microbiol 46, 1076--1080, 2008.
[11]
H. Li and R. Durbin. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754--1760, 2009.
[12]
H. Li, B. Handsaker, A. Wysoker, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078--2079, 2009.
[13]
M.L. Metzker. Sequencing technologies - the next generation. Nat Rev Genet 11, 31--46, 2010.
[14]
M.H. Nicolas-Chanoine, J. Blanco, V. Leflon-Guibout, et al. Intercontinental emergence of Escherichia coli clone O25:H4-ST131 producing CTX-M-15. J Antimicrob Chemother 61, 273--281, 2008.
[15]
N.K. Petty, N.L. Ben Zakour, M. Stanton-Cook, et al. Global dissemination of a multidrug resistant Escherichia coli clone. Proc Natl Acad Sci U S A 111, 5694--5699, 2014.
[16]
J.L. Platell, R.N. Cobbold, J.R. Johnson, et al. Commonality among fluoroquinolone-resistant sequence type ST131 extraintestinal Escherichia coli isolates from humans and companion animals in Australia. Antimicrob Agents Chemother 55, 3782--3787, 2011.
[17]
J. Shine and L. Dalgarno. The 3'-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites. Proc Natl Acad Sci U S A 71, 1342--1346, 1974.
[18]
H. Toh, K. Oshima, A. Toyoda, et al. Complete genome sequence of the wild-type commensal Escherichia coli strain SE15, belonging to phylogenetic group B2. J Bacteriol 192, 1165--1166, 2010.
[19]
M. Totsika, S.A. Beatson, S. Sarkar, et al. Insights into a multidrug resistant Escherichia coli pathogen of the globally disseminated ST131 lineage: genome analysis and virulence mechanisms. PLoS One 6, e26578, 2011.

Cited By

View all
  • (2014)DTMBIO 2014Proceedings of the 23rd ACM International Conference on Conference on Information and Knowledge Management10.1145/2661829.2663537(2090-2091)Online publication date: 3-Nov-2014

Recommendations

Comments

Information & Contributors

Information

Published In

cover image ACM Conferences
DTMBIO '14: Proceedings of the ACM 8th International Workshop on Data and Text Mining in Bioinformatics
November 2014
60 pages
ISBN:9781450312752
DOI:10.1145/2665970
Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

Sponsors

Publisher

Association for Computing Machinery

New York, NY, United States

Publication History

Published: 07 November 2014

Permissions

Request permissions for this article.

Check for updates

Author Tags

  1. comparative genomic
  2. essential genes
  3. pathogenic E. Coli
  4. sequence type 131

Qualifiers

  • Research-article

Funding Sources

Conference

CIKM '14
Sponsor:

Acceptance Rates

DTMBIO '14 Paper Acceptance Rate 22 of 211 submissions, 10%;
Overall Acceptance Rate 41 of 247 submissions, 17%

Upcoming Conference

CIKM '25

Contributors

Other Metrics

Bibliometrics & Citations

Bibliometrics

Article Metrics

  • Downloads (Last 12 months)1
  • Downloads (Last 6 weeks)0
Reflects downloads up to 27 Jan 2025

Other Metrics

Citations

Cited By

View all
  • (2014)DTMBIO 2014Proceedings of the 23rd ACM International Conference on Conference on Information and Knowledge Management10.1145/2661829.2663537(2090-2091)Online publication date: 3-Nov-2014

View Options

Login options

View options

PDF

View or Download as a PDF file.

PDF

eReader

View online with eReader.

eReader

Figures

Tables

Media

Share

Share

Share this Publication link

Share on social media