2011 German Escherichia coli O104:H4 outbreak: whole-genome phylogeny without alignment.

ABSTRACT:

Background

A large-scale Escherichia coli O104:H4 outbreak occurred in Germany from May to July 2011, causing numerous cases of hemolytic-uremic syndrome (HUS) and deaths. Genomes of ten outbreak isolates and a historical O104:H4 strain isolated in 2001 were sequenced using different new generation sequencing platforms. Phylogenetic analyses were performed using various approaches which either are not genome-wide or may be subject to errors due to poor sequence alignment. Also, detailed pathogenicity analyses on the 2001 strain were not available.

Findings

We reconstructed the phylogeny of E. coli using the genome-wide and alignment-free feature frequency profile method and revealed the 2001 strain to be the closest relative to the 2011 outbreak strain among all available E.

SUBMITTER: Cheung MK 

PROVIDER: S-EPMC3280199 | biostudies-literature | 2011 Dec

REPOSITORIES: biostudies-literature