title: Comparative genomic analysis of a multiple antimicrobial resistant enterotoxigenic E. coli O157 lineage from Australian pigs.
abstract: BACKGROUND
  Enterotoxigenic Escherichia coli (ETEC) are a major economic threat to pig production globally, with serogroups O8, O9, O45, O101, O138, O139, O141, O149 and O157 implicated as the leading diarrhoeal pathogens affecting pigs below four weeks of age. A multiple antimicrobial resistant ETEC O157 (O157 SvETEC) representative of O157 isolates from a pig farm in New South Wales, Australia that experienced repeated bouts of pre- and post-weaning diarrhoea resulting in multiple fatalities was characterized here. Enterohaemorrhagic E. coli (EHEC) O157:H7 cause both sporadic and widespread outbreaks of foodborne disease, predominantly have a ruminant origin and belong to the ST11 clonal complex. Here, for the first time, we conducted comparative genomic analyses of two epidemiologically-unrelated porcine, disease-causing ETEC O157; E. coli O157 SvETEC and E. coli O157:K88 734/3, and examined their phylogenetic relationship with EHEC O157:H7.
  
  
  RESULTS
  O157 SvETEC and O157:K88 734/3 belong to a novel sequence type (ST4245) that comprises part of the ST23 complex and are genetically distinct from EHEC O157. Comparative phylogenetic analysis using PhyloSift shows that E. coli O157 SvETEC and E. coli O157:K88 734/3 group into a single clade and are most similar to the extraintestinal avian pathogenic Escherichia coli (APEC) isolate O78 that clusters within the ST23 complex. Genome content was highly similar between E. coli O157 SvETEC, O157:K88 734/3 and APEC O78, with variability predominantly limited to laterally acquired elements, including prophages, plasmids and antimicrobial resistance gene loci. Putative ETEC virulence factors, including the toxins STb and LT and the K88 (F4) adhesin, were conserved between O157 SvETEC and O157:K88 734/3. The O157 SvETEC isolate also encoded the heat stable enterotoxin STa and a second allele of STb, whilst a prophage within O157:K88 734/3 encoded the serum survival gene bor. Both isolates harbor a large repertoire of antibiotic resistance genes but their association with mobile elements remains undetermined.
  
  
  CONCLUSIONS
  We present an analysis of the first draft genome sequences of two epidemiologically-unrelated, pathogenic ETEC O157. E. coli O157 SvETEC and E. coli O157:K88 734/3 belong to the ST23 complex and are phylogenetically distinct to EHEC O157 lineages that reside within the ST11 complex.
authors.affiliation: The ithree institute, University of Technology Sydney, P.O. Box 123, Broadway, NSW, 2007, Australia. Ethan.Wyrsch@uts.edu.au.
authors.forename: Ethan
authors.initials: E
authors.lastname: Wyrsch
authors.affiliation: The ithree institute, University of Technology Sydney, P.O. Box 123, Broadway, NSW, 2007, Australia. Piklu.Bhattacharya@uts.edu.au.|NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Private Bag 4008, Narellan, NSW, 2567, Australia. Piklu.Bhattacharya@uts.edu.au.
authors.forename: Piklu
authors.initials: P
authors.lastname: Roy Chowdhury
authors.affiliation: NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Private Bag 4008, Narellan, NSW, 2567, Australia. sam.abraham@adelaide.edu.au.|School of Animal and Veterinary Sciences, University of Adelaide, Adelaide, South Australia, 5371, Australia. sam.abraham@adelaide.edu.au.
authors.forename: Sam
authors.initials: S
authors.lastname: Abraham
authors.affiliation: The ithree institute, University of Technology Sydney, P.O. Box 123, Broadway, NSW, 2007, Australia. Jerran.Santos@uts.edu.au.
authors.forename: Jerran
authors.initials: J
authors.lastname: Santos
authors.affiliation: The ithree institute, University of Technology Sydney, P.O. Box 123, Broadway, NSW, 2007, Australia. Aaron.Darling@uts.edu.au.
authors.forename: Aaron E
authors.initials: AE
authors.lastname: Darling
authors.affiliation: The ithree institute, University of Technology Sydney, P.O. Box 123, Broadway, NSW, 2007, Australia. Ian.Charles@uts.edu.au.
authors.forename: Ian G
authors.initials: IG
authors.lastname: Charles
authors.affiliation: NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Private Bag 4008, Narellan, NSW, 2567, Australia. toni.chapman@dpi.nsw.gov.au.
authors.forename: Toni A
authors.initials: TA
authors.lastname: Chapman
authors.affiliation: The ithree institute, University of Technology Sydney, P.O. Box 123, Broadway, NSW, 2007, Australia. Steven.Djordjevic@uts.edu.au.
authors.forename: Steven P
authors.initials: SP
authors.lastname: Djordjevic
mesh_terms: D000818:Animals; D024901:Drug Resistance, Multiple, Bacterial / Q000235:genetics; D019453:Escherichia coli O157 / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification / Q000472:pathogenicity; D016680:Genome, Bacterial; D023281:Genomics; D010802:Phylogeny; D013552:Swine / Q000382:microbiology; D037521:Virulence Factors / Q000235:genetics
chemical_list: D037521:Virulence Factors