Over the last five years, Escherichia coli of serotype O25b:H4 and sequence type 131 (E. coli ST131) have emerged worldwide as a major multidrug (MDR) resistant clone responsible for a high proportion of urinary tract and bloodstream infections. To investigate the molecular epidemiology of this successful clone, we use Illumina HiSeq 2000 sequencing technology to sequence a global collection of 95 ST131 strains from Australia, Europe, India and North America and spanning 2000 to 2011. Comparative genomics and phylogenetic analysis were performed using a combination of in-house and publically available software to examine the evolutionary relationships of E. coli ST131 strains.
Our analyses showed that ST131 strains clustered within three discrete sub-lineages that are each characterised by differences in mobile genetic elements (MGE), virulence gene repertoire and antibiotic resistance gene profiles but are not associated with a particular geographical region. We also found that up to 20% of the genome of some ST131 strains was predicted to have undergone distinct recombination events, thus allowing for the acquisition of novel variants of virulence factors. We also found >75% of single-nucleotide variants defining the fluoroquinoline resistant fimH30 clade of the ST131 lineage could be accounted for by recombination. In contrast to previous work, we demonstrated that recombination also has played a major role in shaping the evolution of E. coli ST131 and undoubtedly contributed to its successful global spread.