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Chapter 2 : Understanding the Model and the Menace: a Postgenomic View of Escherichia coli
Category: Genomics and Bioinformatics; Bacterial Pathogenesis
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This chapter discusses the insights into pathogenicity and the wider processes of Escherichia coli genome evolution that have resulted from the sequencing of the E. coli K-12 genome, and, more recently, those from a number of pathogenic E. coli strains, including several from the related “genus” Shigella. It also discusses the available resources for E. coli genomics and the progress that has been made in recent years toward a complete understanding of E. coli biology. Genes that are acquired by horizontal transfer subsequently undergo a process of amelioration as their base composition becomes acclimatized to the new host. Programs such as BLAST can be used to identify unexpected similarities between genes in phylogenetically distinct species, although it should be noted that BLAST results do not necessarily correspond to those from more robust phylogenetic analyses. Interestingly, strains classified as group B2 are rarely found as human commensals, and the group includes many strains with extraintestinal pathogenic E. coli (ExPEC) virulence determinants. As with enterohemorrhagic E. coli (EHEC) O157:H7, Shigella flexneri serotype 2a was an obvious target for whole-genome sequencing because of its importance as a pathogen. The processes of E. coli genome evolution are clear from the genome sequences already available.
Phylogenetic relationships between the strains in the ECOR collection, as assessed by MLEE ( 123 ). Data were obtained from http://foodsafe.msu.edu/whittam, and a neighbor-joining tree was generated by neighbor, part of the PHYLIP package. The tree was rooted using group B2 as an outgroup ( 70 ).
E. coli genome projects completed and underway as of April 2006 a
Selected online resources for E. coli genomics a