Background. Uropathogenic Escherichia coli (UPEC) are the primary cause of urinary tract infections (UTIs), with >360.8 million global cases in 20161. UTIs have become increasingly difficult to treat due to rising antibiotic resistance. Sequence type (ST)1193 is an emerging fluoroquinolone-resistant UPEC lineage increasingly associated with UTIs. Despite its clinical significance, all previous investigations of ST1193 have lacked high-resolution genomic analyses obtainable through whole-genome sequencing (WGS).
Methods. Here, through WGS and temporal phylogenomic analysis of 55 Australian ST1193 isolates spanning 2007–2013, combined with high-quality draft genomes of 50 publicly available ST1193 assemblies, we provide the most comprehensive phylogenomic characterisation of the ST1193 lineage to date. Furthermore, by generating a complete genome we have been able to characterise mobile genetic elements (MGE), allowing analysis of virulence and resistance profiles across the lineage.
Results. Our data report the earliest association of ST1193 with UTIs. Phylogenomic characterisation clusters global ST1193 isolates into two distinct clades , where clade 1 is geographically isolated to Australia. We show that ST1193 isolates from Australia are highly similar at the genomic level, however key inter-clade differences include a switch from K5 to K1 capsular antigen. The K1 capsule is associated with increased serum resistance and may be associated with the global expansion of clade 2. The majority (92.7%) of ST1193 in this study are multidrug-resistant, with eight isolates being resistant to third-generation cephalosporins following acquisition of an IncI1 plasmid carrying the β-lactamase genes blaCTX-M-14 (n=1), blaCTX-M-15 (n=4), and blaCTX-M-55 (n=3).
Conclusion. This work represents the first comprehensive genomic characterisation of ST1193, a recently emerged fluoroquinolone-resistant UPEC clonal lineage. Our work highlights an important difference in the capsule locus within a single UPEC clone, likely due to recombination.