2011 German Escherichia coli outbreak: Alignment-free whole-genome phylogeny by feature frequency profiles

Introduction: Accuracy of SNP-based whole-genome phylogeny reconstruction relies heavily on quality of sequence alignment which is particularly hindered by poorly assembled genomes. Alignment-free methods might provide additional insights. Here, we constructed a wholegenome phylogeny of 9 outbreak isolates against existing E. coli genomes using the alignment-free feature frequency profile (FFP) method (Sims et al. 2009). In addition, we looked for gene elements that distinguish the outbreak group from the other E. coli strains and possibly accounted for the emergence of the outbreak isolates using the distinguishing feature (DF) analysis.