Complete assembly of Escherichia coli ST131 genomes using long reads demonstrates antibiotic resistance gene variation within diverse plasmid and chromosomal contexts

The incidence of infections caused by extraintestinal Escherichia coli (ExPEC) is rising globally, which is a major public health concern. ExPEC strains that are resistant to antimicrobials have been associated with excess mortality, prolonged hospital stays and higher healthcare costs. E. coli ST131 is a major ExPEC clonal group worldwide with variable plasmid composition, and has an array of genes enabling antimicrobial resistance (AMR). ST131 isolates frequently encode the AMR genes bla_{CTX-M-14/15/27}, which are often rearranged, amplified and translocated by mobile genetic elements (MGEs). Short DNA reads do not fully resolve the architecture of repetitive elements on plasmids to allow MGE structures encoding bla_CTX-M genes to be fully determined. Here, we performed long read sequencing to decipher the genome structures of six E. coli ST131 isolated from six patients. Most long read assemblies generated entire chromosomes and plasmids as single contigs, contrasting with more fragmented assemblies created with short reads alone. The long read assemblies highlighted diverse accessory genomes with bla_CTX-M-15, bla_CTX-M-14 and bla_CTX-M-27 genes identified in three, one and one isolates, respectively. One sample had no bla_CTX-M gene. Two samples had chromosomal bla_CTX-M-14 and bla_CTX-M-15 genes, and the latter was at three distinct locations, likely transposed by the adjacent MGEs: ISEcp1, IS903B and Tn2. This study showed that AMR genes exist in multiple different chromosomal and plasmid contexts even between closely-related isolates within a clonal group such as E. coli ST131.