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Series GSE17036 Query DataSets for GSE17036
Status Public on Jul 11, 2009
Title Variation in the Genomic islands of porcine enteropathogenic E. coli strains of serogroup O45 revealed by CGH and PCR.
Platform organism Escherichia coli
Sample organisms Escherichia coli; Escherichia coli O157:H7; Escherichia coli O157:H7 str. EDL933; Escherichia coli O157:H7 str. Sakai; Escherichia coli str. K-12 substr. MG1655
Experiment type Genome variation profiling by array
Summary Background: Members of E. coli serogroup O45 are porcine enteropathogenic E. coli (PEPEC) strains which cause post-weaning diarrhea and produce characteristic attaching and effacing (A/E) lesions. Most of O45 PEPEC strains possess the locus of enterocyte effacement (LEE), encoding the virulence factors for A/E lesions, and often possess the paa gene, which is thought to contribute to the early stages of PEPEC virulence.
Methodology: Nine O45 PEPEC strains and a rabbit enteropathogenic (REPEC) strain, known to produce A/E lesions, were characterized using an E. coli O157-E. coli K12 whole genome microarray and a virulence gene-specific microarray, and by PCR experiments.
Results: Based on their virulence genes profiles, the 10 strains were characterized as atypical EPEC. The differences in their genomes pointed to two distinct evolutionary groups of O45 PEPEC, Group I and Group II, and to the contribution these genetic differences have on virulence in pigs. Group I contained the REPEC strain and four O45 PEPEC strains known to induce severe A/E lesions in challenged pigs whereas Group II was composed of five other O45 PEPEC strains which induced less severe or no A/E lesions in challenged pigs. Significant differences between Groups I and II were found in the presence or absence of 50 O-Islands (OIs) or S-loops and 13 K-islands (KIs) or K-loops, including the virulence-associated islands OI#1 (S-loop#1), OI#47 (S-loop#71), OI#57 (S-loop#85), OI#71 (S-loop#108), OI#115, OI#122, and OI#154 (S-loop#253).
Overall design 10 samples, with two microarrays per sample. Each microarray includes duplicates of every spot.
Contributor(s) Bruant G, Zhang Y, Garneau P, Wong J, Laing C, Fairbrother JM, Gannon VP, Harel J
Citation(s) 19709428
Submission date Jul 10, 2009
Last update date Mar 21, 2012
Contact name Chad R Laing
Organization name Public Health Agency of Canada
Department Laboratory for Foodborne Zoonoses
Street address Twp Rd 9-1
City Lethbridge
State/province Alberta
ZIP/Postal code T1J3Z4
Country Canada
Platforms (1)
GPL533 MWG E. coli O157
Samples (12)
GSM426428 86-1390
GSM426429 86-4220
GSM426430 81-4420
BioProject PRJNA117835

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE17036_RAW.tar 26.6 Mb (http)(custom) TAR (of GPR)
Processed data included within Sample table

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