Multiple evolutionary trajectories for non-O157 Shiga toxigenic Escherichia coli

Alikhan, N-F; Bachmann, NL; Zakour, NLB; Petty, NK; Stanton-Cook, M; Gawthorne, JA; Easton, DM; Mahony, TJ; Cobbold, R; Schembri, MA; Beatson, SA

Multiple evolutionary trajectories for non-O157 Shiga toxigenic Escherichia coli

Alikhan, N-F

Bachmann, NL Zakour, NLB

Petty, NK

Stanton-Cook, M Gawthorne, JA Easton, DM Mahony, TJ Cobbold, R Schembri, MA

Beatson, SA

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Publisher:: Cold Spring Harbor Laboratory
Publication Type:: Journal Article

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Field	Value	Language
dc.contributor.author	Alikhan, N-F https://orcid.org/0000-0002-1243-0767	en_US
dc.contributor.author	Bachmann, NL	en_US
dc.contributor.author	Zakour, NLB https://orcid.org/0000-0002-6949-1755	en_US
dc.contributor.author	Petty, NK https://orcid.org/0000-0001-6528-9886	en_US
dc.contributor.author	Stanton-Cook, M	en_US
dc.contributor.author	Gawthorne, JA	en_US
dc.contributor.author	Easton, DM	en_US
dc.contributor.author	Mahony, TJ	en_US
dc.contributor.author	Cobbold, R	en_US
dc.contributor.author	Schembri, MA https://orcid.org/0000-0003-4863-9260	en_US
dc.contributor.author	Beatson, SA https://orcid.org/0000-0002-1806-3283	en_US
dc.identifier.uri	http://hdl.handle.net/10453/138398
dc.description.abstract	<jats:title>Abstract</jats:title><jats:sec><jats:title>Background</jats:title><jats:p>Shiga toxigenic <jats:italic>Escherichia coli</jats:italic> (STEC) is an emerging global pathogen and remains a major cause of food-borne illness with more severe symptoms including hemorrhagic colitis and hemolytic-uremic syndrome. Since the characterization of the archetypal STEC serotype, <jats:italic>E. coli</jats:italic> O157:H7, more than 250 STEC serotypes have been defined. Many of these non-O157 STEC are associated with clinical cases of equal severity as O157. In this study, we utilize whole genome sequencing of 44 STEC strains from eight serogroups associated with human infection to establish their evolutionary relationships and contrast this with their virulence gene profiles and established typing methods.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>Our phylogenomic analysis delineated these STEC strains into seven distinct lineages, each with a characteristic repertoire of virulence factors. Some lineages included commensal or other <jats:italic>E. coli</jats:italic> pathotypes. Multiple independent acquisitions of the Locus for Enterocyte Effacement were identified, each associated with a distinct repertoire of effector genes. Lineages were inconsistent with O-antigen typing in several instances, consistent with lateral gene transfer within the O-antigen locus. STEC lineages could be defined by the conservation of clustered regularly interspaced short palindromic repeats (CRISPRs), however, no CRISPR profile could differentiate STEC from other <jats:italic>E. coli</jats:italic> strains. Six genomic regions (ranging from 500 bp - 10 kbp) were found to be conserved across all STEC in this dataset and may dictate interactions with Stx phage lysogeny.</jats:p></jats:sec><jats:sec><jats:title>Conclusions</jats:title><jats:p>The genomic analyses reported here present non-O157 STEC as a diverse group of pathogenic <jats:italic>E. coli</jats:italic> emerging from multiple lineages that independently acquired mobile genetic elements that promote pathogenesis.</jats:p></jats:sec>	en_US
dc.publisher	Cold Spring Harbor Laboratory	en_US
dc.relation.isbasedon	10.1101/549998	en_US
dc.title	Multiple evolutionary trajectories for non-O157 Shiga toxigenic Escherichia coli	en_US
dc.type	Journal Article
pubs.embargo.period	Not known	en_US
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Science
pubs.organisational-group	/University of Technology Sydney/Strength - ithree - Institute of Infection, Immunity and Innovation
utslib.copyright.status	open_access

Abstract:

AbstractBackgroundShiga toxigenic Escherichia coli (STEC) is an emerging global pathogen and remains a major cause of food-borne illness with more severe symptoms including hemorrhagic colitis and hemolytic-uremic syndrome. Since the characterization of the archetypal STEC serotype, E. coli O157:H7, more than 250 STEC serotypes have been defined. Many of these non-O157 STEC are associated with clinical cases of equal severity as O157. In this study, we utilize whole genome sequencing of 44 STEC strains from eight serogroups associated with human infection to establish their evolutionary relationships and contrast this with their virulence gene profiles and established typing methods.ResultsOur phylogenomic analysis delineated these STEC strains into seven distinct lineages, each with a characteristic repertoire of virulence factors. Some lineages included commensal or other E. coli pathotypes. Multiple independent acquisitions of the Locus for Enterocyte Effacement were identified, each associated with a distinct repertoire of effector genes. Lineages were inconsistent with O-antigen typing in several instances, consistent with lateral gene transfer within the O-antigen locus. STEC lineages could be defined by the conservation of clustered regularly interspaced short palindromic repeats (CRISPRs), however, no CRISPR profile could differentiate STEC from other E. coli strains. Six genomic regions (ranging from 500 bp - 10 kbp) were found to be conserved across all STEC in this dataset and may dictate interactions with Stx phage lysogeny.ConclusionsThe genomic analyses reported here present non-O157 STEC as a diverse group of pathogenic E. coli emerging from multiple lineages that independently acquired mobile genetic elements that promote pathogenesis.

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http://hdl.handle.net/10453/138398