Escherichia coli ST8196 is a novel, locally evolved, and extensively drug resistant pathogenic lineage within the ST131 clonal complex

Abstract

The H30Rx subclade of Escherichia coli ST131 is a clinically important, globally dispersed extra-pathogenic lineage that typically displays resistance to fluoroquinolones and extended spectrum ß-lactams. Here we describe isolates EC233 and EC234, both variants of ST131-H30Rx with a novel sequence type (ST) 8196, from unrelated patients presenting with bacteraemia at Concord Repatriation Hospital in Sydney in 2014. EC233 and EC234 are phylogroup B2, serotype O25:H4A, resistant to ampicillin, amoxicillin, cefoxitin, ceftazidime, ceftriaxone, ciprofloxacin, norfloxacin and gentamicin and are likely clonal. Both isolates carry an IncFII_2 plasmid similar to pSPRC_Ec234-FII (85,199 bp characterised in EC234), two small plasmids and a novel IncI1 plasmid similar to pSPRC_Ec234-I (92,955 bp characterised in EC234). Apart from a chromosomally located bla CTX-M-15 module, the resistance genes are flanked by IS26 and form a complex resistance locus (CRL) on pSPRC_Ec234-FII. SNP-based phylogenetic analysis of the core genome of all ST representatives within the ST131 clonal complex places both isolates in a small subclade with 3 other clinical Australian ST131-H30Rx clade C isolates. MrBayes phylogeny analysis of ST8196 using a global collection of ST131 genomes indicated EC233 and EC234 share a most recent common ancestor with EC70, a MDR ST131-H30Rx clone, isolated from the same Sydney hospital in 2013. Our study identified genomic hallmarks that define the ST131-H30Rx subclade in both the ST8196 isolates and highlights the requirement for unbiased genomic surveillance approaches to identify and track novel high-risk MDR E. coli pathogens that impact healthcare facilities.