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Chapter 1 : Insights from Genomic Studies of the Foodborne and Waterborne Pathogen Escherichia coli O157:H7
Category: Applied and Industrial Microbiology; Food Microbiology
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In this chapter, the knowledge of the genome of E. coli O157:H7 may be used in the control of serious foodborne pathogen, E. coli strains are associated with gastrointestinal and extraintestinal illness. The E. coli O157:H7 genome provides us with information about the evolution and emergence of pathogen and the diversity that exists within populations of E. coli O157:H7. Most of E. coli prophage are defective and cannot form infectious phage. This chapter provides a brief review of subtyping methods used to characterize E. coli O157:H7 strains. Differences in biochemical utilization can be used to distinguish large categories of E. coli strain. Following the generation of cDNA from the bacteria’s mRNA using the enzyme reverse transcriptase, the level of gene expression is inferred from the intensity of the label signal from gene-specific microarray spots following hybridization. This procedure is the foundation of the new science of transcriptomics. Typically, quantitative PCR assays are also carried out on selected genes to measure mRNA levels to verify the significant changes in expression of genes observed in microarray-based transcriptomics studies. It is also evident that our understanding of E. coli O157:H7 gene regulatory systems will be enhanced through genomic sciences. E. coli O157:H7 and other bacterial pathogens have evolved through the acquisition of gene clusters borne on plasmids, bacteriophages, and genomic islands. Finally, with the arrival of the genomics revolution researchers are able to examine the "pan-genome" of the species and specific groups within species such as enterohemorrhagic E. coli(EHEC) and E. coli O157:H7.
The supernetwork created from the combination of data from the following six typing methods: Stx-phage insertion site typing, MLVA, CGF, SNP genotyping, mCGH, and genomic in silico subtractive hybridization based novel region distribution. Both mCGH and CGF datasets included experimental data as well as in silico data. Maximum parsimony trees from each method were created using PAUP* 4.0 ( 151 ) and then combined in SplitsTree v4.1 ( 59 ) using the unweighted mean distance and Z-closure with 1,000 iterations; the resulting supernetwork was displayed using the equal angle method.
Major outbreaks of E. coli O157 infections since 1982
Bacteriophages present in E. coli O157:H7 lineage I strain Sakai a
Selected O islands (OI) of E. coli O157:H7 strain EDL933 and their corresponding S-loops of E. coli O157:H7 strain Sakai, the location of each within the genome, and their function