Whole-genome analysis of extraintestinal Escherichia coli sequence type 73 from a single hospital over a 2 year period identified different circulating clonal groups

Microbial Genomics
Daniel BogemaS P Djordjevic

Abstract

Sequence type (ST)73 has emerged as one of the most frequently isolated extraintestinal pathogenic Escherichia coli. To examine the localized diversity of ST73 clonal groups, including their mobile genetic element profile, we sequenced the genomes of 16 multiple-drug resistant ST73 isolates from patients with urinary tract infection from a single hospital in Sydney, Australia, between 2009 and 2011. Genome sequences were used to generate a SNP-based phylogenetic tree to determine the relationship of these isolates in a global context with ST73 sequences (n=210) from public databases. There was no evidence of a dominant outbreak strain of ST73 in patients from this hospital, rather we identified at least eight separate groups, several of which reoccurred, over a 2 year period. The inferred phylogeny of all ST73 strains (n=226) including the ST73 clone D i2 reference genome shows high bootstrap support and clusters into four major groups that correlate with serotype. The Sydney ST73 strains carry a wide variety of virulence-associated genes, but the presence of iss, pic and several iron-acquisition operons was notable.

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Datasets Mentioned

BETA
SRR3466142
SRR4098824
PRJEB9931-U24
SRR786046
SRR958613
SRR786213
SRR786247
SRR958664
SRR786270
SRR786300

Methods Mentioned

BETA
PCR
Illumina sequencing

Software Mentioned

srst2
arg
freebayes
blastn
annot
Gubbins
EcOH
bwa mem
SPAdes
vcftools

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