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

Priyanka Hastak; Mathieu Fourment; Aaron E Darling; Thomas Gottlieb; Elaine Cheong; John Merlino; Garry S A Myers; Steven P Djordjevic; Piklu Roy Chowdhury

doi:10.1080/22221751.2020.1797541

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

Emerg Microbes Infect. 2020 Dec;9(1):1780-1792. doi: 10.1080/22221751.2020.1797541.

Authors

Priyanka Hastak¹, Mathieu Fourment¹, Aaron E Darling¹, Thomas Gottlieb^{2

3}, Elaine Cheong^{2

3}, John Merlino^{2

3}, Garry S A Myers¹, Steven P Djordjevic^{1

4}, Piklu Roy Chowdhury^{1

4}

Affiliations

¹ The ithree institute, University of Technology Sydney, Ultimo, Australia.
² Department of Microbiology and Infectious Diseases, Concord Hospital, Concord, Australia.
³ Faculty of Medicine, University of Sydney, Sydney, Australia.
⁴ Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Broadway, Australia.

Abstract

The H30Rx subclade of Escherichia coli ST131 is a clinically important, globally dispersed pathogenic lineage that typically displays resistance to fluoroquinolones and extended spectrum β-lactams. Isolates EC233 and EC234, variants of ST131-H30Rx with a novel sequence type (ST) 8196, isolated from unrelated patients presenting with bacteraemia at a Sydney Hospital in 2014 are characterised here. EC233 and EC234 are phylogroup B2, serotype O25:H4A, and resistant to ampicillin, amoxicillin, cefoxitin, ceftazidime, ceftriaxone, ciprofloxacin, norfloxacin and gentamicin and are likely clonal. Both harbour an IncFII_2 plasmid (pSPRC_Ec234-FII) that carries most of the resistance genes on an IS26 associated translocatable unit, two small plasmids and a novel IncI1 plasmid (pSPRC_Ec234-I). SNP-based phylogenetic analysis of the core genome of representatives within the ST131 clonal complex places both isolates in a subclade with three clinical Australian ST131-H30Rx clade-C isolates. A MrBayes phylogeny analysis of EC233 and EC234 indicates ST8196 share a most recent common ancestor with ST131-H30Rx strain EC70 isolated from the same hospital in 2013. Our study identified genomic hallmarks that define the ST131-H30Rx subclade in the ST8196 isolates and highlights a need for unbiased genomic surveillance approaches to identify novel high-risk MDR E. coli pathogens that impact healthcare facilities.

Keywords: E. coli ST131 clonal complex; Escherichia coli ST8196; bla CTX-M-15; qnrB4; ST131- H30Rx.

MeSH terms

Anti-Bacterial Agents / pharmacology*
Australia / epidemiology
Bacteremia / drug therapy
Bacteremia / microbiology
Drug Resistance, Multiple, Bacterial / genetics*
Escherichia coli / classification
Escherichia coli / drug effects
Escherichia coli / genetics*
Escherichia coli / isolation & purification
Escherichia coli Infections / drug therapy
Escherichia coli Infections / epidemiology*
Escherichia coli Infections / microbiology
Fluoroquinolones / pharmacology
Genome, Bacterial / genetics
Humans
Microbial Sensitivity Tests
Phylogeny
Plasmids / genetics
beta-Lactamases / genetics*
beta-Lactams / pharmacology

Substances

Anti-Bacterial Agents
Fluoroquinolones
beta-Lactams
beta-lactamase CTX-M-15
beta-Lactamases

Grants and funding

This project was funded by the Australian Centre for Genomic Epidemiological Microbiology (AusGEM), a strategic partnership between the NSW-Department of Primary Industries and the University of Technology Sydney. The results presented in this manuscript are helping to inform the OUTBREAK decision support system funded by the Medical Research Future Fund Frontier Health and Medical Research Program (grant number MRFF75873).