ST131 is a leading extraintestinal pathogenic E. Supplementary material can be found in Figshare. The genome sequences of all other isolates have been deposited in Genbank under BioProject PRJNA721525 with SRA accession numbers from SRR14229529 to SRR14229538.Īssemblies and annotated genomes for all Australian ST131 genomes used in this study are available with the online version of this article. The genome sequences of South Australia Environment (SAE) isolates are available at GenBank under BioProject PRJNA706036, SRA accession numbers SRR14763817 to SRR14763821.įor Sydney Adventist Hospital (SAH) isolates the genome sequenc of isolate SAH2009_36 has been published previously under SRA accession number SRX5100115. The genome sequences of Australian silver gull isolates (with ‘CE’ prefix and a single 1716 h isolate) have been deposited in GenBank under BioProject PRJNA630096 with SRA accession numbers SRR13834344 to SRR13834353.
#Solid v dotted line in map snapgene viewer archive
The genome sequences of Orange Base Hospital (OBH) isolates (HOS77–HOS99) have been deposited in GenBank under BioProject PRJNA705804 with Sequence Read Archive (SRA) accession numbers SRR13843903 to SRR13843925. The results of this study indicate that the the ST131 population in Australia carries diverse antimicrobial resistance genes and plasmid replicons and indicate cross-species movement of ST131 strains across diverse reservoirs. Notably, dual parC-1aAB and gyrA-1AB fluoroquinolone resistant mutations, a unique feature of clade C ST131 isolates, were identified in some clade A isolates. Most (73 %) Australian ST131 isolates carry at least one extended spectrum β-lactamase gene, typically bla CTX-M-15 and bla CTX-M-27. The module intI1–dfrA17–aadA5–qacEΔ1–sul1–ORF –chrA–padR–IS 1600–mphR–mrx–mphA, conferring resistance to trimethoprim, aminoglycosides, quaternary ammonium compounds, sulphonamides, chromate and macrolides, was the most common structure. Many ST131 carried resistance genes to multiple antibiotic classes and while 41 (14 %) contained the complete class one integron–integrase intI1, 128 (45 %) isolates harboured a truncated intI1 (462–1014 bp), highlighting the ongoing evolution of this element. Within this cluster, human sourced isolates differed by approximately 37 SNPs from isolates sourced from canines, approximately 50 SNPs from isolates from wild birds, and approximately 52 SNPs from isolates from wastewater. Forty-five isolates from clade C1 from four sources formed a cluster with an average of 46 SNPs. Thirty-five isolates (29 of human and six of wild bird origin) from clade A (32 fimH41, 2 fimH89, 1 fimH141) were observed to differ by an average of 76 SNPs. Indeed, interspecies relatedness was a feature of this study. Our phylogeny and the results of single nucleotide polymorphism (SNP) analysis show the typical ST131 clade distribution with clades A, B and C clearly displayed, but no niche associations were observed. coli isolates from diverse sources, including clinical, food and companion animals, wildlife and the environment. Here we describe a detailed phylogenetic analysis of the whole genome sequences of 284 Australian ST131 E. coli lineage contributing significantly to hospital and community acquired urinary tract and bloodstream infections. Escherichia coli ST131 is a globally dispersed extraintestinal pathogenic E.
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