Whole-genome sequence analysis of environmental Escherichia coli from the faeces of straw-necked ibis (Threskiornis spinicollis) nesting on inland wetlands

Abstract

<jats:p>Wildlife, and birds in particular, play an increasingly recognized role in the evolution and transmission of <jats:italic> <jats:named-content content-type="species"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.3093" xlink:type="simple">Escherichia coli</jats:ext-link> </jats:named-content> </jats:italic> that pose a threat to humans. To characterize these lineages and their potential threat from an evolutionary perspective, we isolated and performed whole-genome sequencing on 11 sequence types (STs) of <jats:italic> <jats:named-content content-type="species"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.3093" xlink:type="simple">E. coli</jats:ext-link> </jats:named-content> </jats:italic> recovered from the desiccated faeces of straw-necked ibis (<jats:italic>Threskiornis spinicollis</jats:italic>) nesting on inland wetlands located in geographically different regions of New South Wales, Australia. Carriage of virulence-associated genes was limited, and no antimicrobial resistance genes were detected, but novel variants of an insertion element that plays an important role in capturing and mobilizing antibiotic resistance genes, IS<jats:italic>26</jats:italic>, were identified and characterized. The isolates belonged to phylogroups B1 and D, including types known to cause disease in humans and animals. Specifically, we found <jats:italic> <jats:named-content content-type="species"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.3093" xlink:type="simple">E. coli</jats:ext-link> </jats:named-content> </jats:italic> ST58, ST69, ST162, ST212, ST446, ST906, ST2520, ST6096 and ST6241, and a novel phylogroup D strain, ST10208. Notably, the ST58 strain hosted significant virulence gene carriage. The sequences of two plasmids hosting putative virulence-associated factors with incompatibility groups I1 and Y, an extrachromosomal integrative/conjugative element, and a variant of a large <jats:italic> <jats:named-content content-type="genus"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.3092" xlink:type="simple">Escherichia</jats:ext-link> </jats:named-content> </jats:italic> phage of the family <jats:italic>Myoviridae</jats:italic>, were additionally characterized. We identified multiple epidemiologically relevant gene signatures that link the ibis isolates to sequences from international sources, plus novel variants of IS<jats:italic>26</jats:italic> across different sequence types and in different contexts.</jats:p>

Duplication and diversification of a unique chromosomal virulence island hosting the subtilase cytotoxin in Escherichia coli ST58

“…The long-read assembly of E. coli strain IBS28 resolved two contigs, a 4 934 027 bp chromosome, plus the ICE pIBS28_1, as described previously [ 43 ]. Automated annotation identified 4877 open reading frames (ORFs) and 112 RNA coding sequences in the chromosome.…”

“…Here we characterized an environmentally associated E. coli ST58 (ISB28) from the straw-necked ibis. Our initial analysis utilizing short-read whole-genome data indicated that IBS28 was closely related to a series of strains from North America dating back to 1988, and we detected several virulence genes plus an unusual chromosomal IS 6 family element [ 43 ]. Members of the IS 6 family are frequently involved in the dissemination of antimicrobial resistance genes [ 53 ], although none were detected within the strain.…”

“…The isolation and initial analysis of strain E. coli IBS28 has been reported previously [ 43 ]. The strain was derived from a desiccated faecal sample initially taken from an ibis nest at an inland wetland during 2012, in New South Wales, Australia.…”

“… E. coli ST58 belongs to a phylogroup B1 commensal lineage that has been isolated from diverse animal, environmental and human hosts [ 40–42 ], demonstrating links with human urinary tract infections and urosepsis, and it can carry a colV-like virulence resistance plasmid [ 40 ]. Recently we characterized an environmental ST58 isolate recovered from the faeces of a straw-necked ibis nest in inland wetlands, New South Wales, Australia [ 43 ].…”

“…The short-read assembly analysis of this ST58:ONT:H25 isolate (IBS28) indicated that it was closely related to 4 North American strains from a collection of 69 diverse ST58 genomes [ 43 ]. Strain ISB28 was distinct from known Australian human ST58 pathogen E. coli 2009–52 [ 40 ] and avian pathogen E. coli A193 [ 44 ], which have been described recently.…”