Sequential acquisition of virulence and fluoroquinolone resistance has shaped the evolution of Escherichia coli ST131

Abstract

Escherichia coli ST131 is the most frequently isolated fluoroquinolone resistant (FQR) E. coli clone worldwide and a major cause of urinary tract and bloodstream infections. Although originally identified through its association with the CTX-M-15 extended-spectrum β-lactamase resistance gene, global genomic epidemiology studies have failed to resolve the geographical and temporal origin of the ST131 ancestor. Here, we developed a framework for the reanalysis of publicly available genomes from different sources and used this dataset to reconstruct the evolutionary steps that led to the emergence of FQR ST131. Using Bayesian estimation, we show that point mutations in chromosomal genes that confer FQR coincide with the first clinical use of fluoroquinolone in 1986, and illustrate the impact of this pivotal event in the rapid population expansion of ST131 worldwide from an apparent origin in North America. Furthermore, we identify key virulence factor acquisition events that predate the development of FQR, suggesting that the gain of virulence-associated genes followed by the tandem development of antibiotic resistance primed the successful global dissemination of ST131.