Genomic Subtraction to Identify and Characterize Sequences of Shiga Toxin-producing Escherichia Coli O91:H21

Overview

Journal Appl Environ Microbiol

Specialties Environmental Health
Microbiology

Date 2002 Apr 27

PMID 11976103

Citations 9

Authors

Nathalie Pradel

Sabine Leroy-Setrin

Bernard Joly

Valerie Livrelli

Affiliations

Soon will be listed here.

Abstract

To identify Shiga toxin-producing Escherichia coli genes associated with severe human disease, a genomic subtraction technique was used with hemolytic-uremic syndrome-associated O91:H21 strain CH014 and O6:H10 bovine strains. The method was adapted to the Shiga toxin-producing E. coli genome: three rounds of subtraction were used to isolate DNA fragments specific to strain CH014. The fragments were characterized by genetic support analysis, sequencing, and hybridization to the genome of a collection of Shiga toxin-producing E. coli strains. A total of 42 fragments were found, 19 of which correspond to previously identified unique DNA sequences in the enterohemorrhagic E. coli EDL933 reference strain, including 7 fragments corresponding to prophage sequences and others encoding candidate virulence factors, such a SepA homolog protein and a fimbrial usher protein. In addition, the subtraction procedure yielded plasmid-related sequences from Shigella flexneri and enteropathogenic and Shiga toxin-producing E. coli virulence plasmids. We found that lateral gene transfer is extensive in strain CH014, and we discuss the role of genomic mobile elements, especially bacteriophages, in the evolution and possible transfer of virulence determinants.

Citing Articles

Enterohemorrhagic Escherichia coli pathogenesis: role of Long polar fimbriae in Peyer's patches interactions.

Cordonnier C, Etienne-Mesmin L, Thevenot J, Rougeron A, Renier S, Chassaing B Sci Rep. 2017; 7:44655.

PMID: 28317910 PMC: 5357955. DOI: 10.1038/srep44655.

In vitro adhesion properties of Shiga toxin-producing Escherichia coli isolated from cattle, food, and humans.

Pradel N, Etienne-Mesmin L, Thevenot J, Cordonnier C, Blanquet-Diot S, Livrelli V Front Microbiol. 2015; 6:156.

PMID: 25774152 PMC: 4343011. DOI: 10.3389/fmicb.2015.00156.

Interactions with M cells and macrophages as key steps in the pathogenesis of enterohemorrhagic Escherichia coli infections.

Etienne-Mesmin L, Chassaing B, Sauvanet P, Denizot J, Blanquet-Diot S, Darfeuille-Michaud A PLoS One. 2011; 6(8):e23594.

PMID: 21858177 PMC: 3157389. DOI: 10.1371/journal.pone.0023594.

Effect of probe characteristics on the subtractive hybridization efficiency of human genomic DNA.

Archer M, Long N, Lin B BMC Res Notes. 2010; 3:109.

PMID: 20406484 PMC: 2862039. DOI: 10.1186/1756-0500-3-109.

Next-generation sequencing and metagenomic analysis: a universal diagnostic tool in plant virology.

Adams I, Glover R, Monger W, Mumford R, Jackeviciene E, Navalinskiene M Mol Plant Pathol. 2009; 10(4):537-45.

PMID: 19523106 PMC: 6640393. DOI: 10.1111/j.1364-3703.2009.00545.x.

References

Perna N, Plunkett 3rd G, Burland V, Mau B, Glasner J, Rose D . Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature. 2001; 409(6819):529-33. DOI: 10.1038/35054089. View

Unkmeir A, Schmidt H . Structural analysis of phage-borne stx genes and their flanking sequences in shiga toxin-producing Escherichia coli and Shigella dysenteriae type 1 strains. Infect Immun. 2000; 68(9):4856-64. PMC: 101682. DOI: 10.1128/IAI.68.9.4856-4864.2000. View

Brunder W, Schmidt H, Frosch M, Karch H . The large plasmids of Shiga-toxin-producing Escherichia coli (STEC) are highly variable genetic elements. Microbiology (Reading). 1999; 145 ( Pt 5):1005-1014. DOI: 10.1099/13500872-145-5-1005. View

Feng P, Lampel K, Karch H, Whittam T . Genotypic and phenotypic changes in the emergence of Escherichia coli O157:H7. J Infect Dis. 1998; 177(6):1750-3. DOI: 10.1086/517438. View

Brown P, Curtiss 3rd R . Unique chromosomal regions associated with virulence of an avian pathogenic Escherichia coli strain. Proc Natl Acad Sci U S A. 1996; 93(20):11149-54. PMC: 38299. DOI: 10.1073/pnas.93.20.11149. View

Wells J, Shipman L, Greene K, Sowers E, Green J, Cameron D . Isolation of Escherichia coli serotype O157:H7 and other Shiga-like-toxin-producing E. coli from dairy cattle. J Clin Microbiol. 1991; 29(5):985-9. PMC: 269920. DOI: 10.1128/jcm.29.5.985-989.1991. View

Reid S, Herbelin C, Bumbaugh A, Selander R, Whittam T . Parallel evolution of virulence in pathogenic Escherichia coli. Nature. 2000; 406(6791):64-7. DOI: 10.1038/35017546. View

Brunder W, Schmidt H, Karch H . EspP, a novel extracellular serine protease of enterohaemorrhagic Escherichia coli O157:H7 cleaves human coagulation factor V. Mol Microbiol. 1997; 24(4):767-78. DOI: 10.1046/j.1365-2958.1997.3871751.x. View

Wieler L, McDaniel T, Whittam T, Kaper J . Insertion site of the locus of enterocyte effacement in enteropathogenic and enterohemorrhagic Escherichia coli differs in relation to the clonal phylogeny of the strains. FEMS Microbiol Lett. 1997; 156(1):49-53. DOI: 10.1111/j.1574-6968.1997.tb12704.x. View

10.

Baumler A, Heffron F . Identification and sequence analysis of lpfABCDE, a putative fimbrial operon of Salmonella typhimurium. J Bacteriol. 1995; 177(8):2087-97. PMC: 176853. DOI: 10.1128/jb.177.8.2087-2097.1995. View

11.

Ouagued M, Picard B, GOULLET P, Krishnamoorthy R . A simple, sensitive method of analyzing bacterial ribosomal DNA polymorphism. Electrophoresis. 1989; 10(3):186-9. DOI: 10.1002/elps.1150100306. View

12.

Sansonetti P, Parsot C . SepA, the major extracellular protein of Shigella flexneri: autonomous secretion and involvement in tissue invasion. Mol Microbiol. 1995; 17(1):123-35. DOI: 10.1111/j.1365-2958.1995.mmi_17010123.x. View

13.

Blanco M, Blanco J, Blanco J, Mora A, Prado C, Alonso M . Distribution and characterization of faecal verotoxin-producing Escherichia coli (VTEC) isolated from healthy cattle. Vet Microbiol. 1997; 54(3-4):309-19. DOI: 10.1016/s0378-1135(96)01292-8. View

14.

Dower W, Miller J, Ragsdale C . High efficiency transformation of E. coli by high voltage electroporation. Nucleic Acids Res. 1988; 16(13):6127-45. PMC: 336852. DOI: 10.1093/nar/16.13.6127. View

15.

Datz M, Franke S, Gunzer F, Schmidt H, Karch H . Analysis of the enterohemorrhagic Escherichia coli O157 DNA region containing lambdoid phage gene p and Shiga-like toxin structural genes. Appl Environ Microbiol. 1996; 62(3):791-7. PMC: 167845. DOI: 10.1128/aem.62.3.791-797.1996. View

16.

LeClerc J, Li B, Payne W, Cebula T . Promiscuous origin of a chimeric sequence in the Escherichia coli O157:H7 genome. J Bacteriol. 1999; 181(24):7614-7. PMC: 94221. DOI: 10.1128/JB.181.24.7614-7617.1999. View

17.

Straus D, Ausubel F . Genomic subtraction for cloning DNA corresponding to deletion mutations. Proc Natl Acad Sci U S A. 1990; 87(5):1889-93. PMC: 53589. DOI: 10.1073/pnas.87.5.1889. View

18.

Wagner P, Acheson D, Waldor M . Isogenic lysogens of diverse shiga toxin 2-encoding bacteriophages produce markedly different amounts of shiga toxin. Infect Immun. 1999; 67(12):6710-4. PMC: 97090. DOI: 10.1128/IAI.67.12.6710-6714.1999. View

19.

Karmali M, Petric M, Lim C, Fleming P, Arbus G, Lior H . The association between idiopathic hemolytic uremic syndrome and infection by verotoxin-producing Escherichia coli. J Infect Dis. 1985; 151(5):775-82. DOI: 10.1093/infdis/151.5.775. View

20.

Burland V, Shao Y, Perna N, Plunkett G, Sofia H, Blattner F . The complete DNA sequence and analysis of the large virulence plasmid of Escherichia coli O157:H7. Nucleic Acids Res. 1998; 26(18):4196-204. PMC: 147824. DOI: 10.1093/nar/26.18.4196. View