Poster Presentation Australian Society for Microbiology Annual Scientific Meeting 2022

The complete genome sequence of five Escherichia coli sequence type (ST)1193 strains provides detailed insight into a contemporary pathogen (#170)

Rhys T White 1 2 , Melinda M Ashcroft 1 2 , Leah W Roberts 1 2 3 , Minh Duy Phan 2 , Kate M Peters 2 , Laura Álvarez-Fraga 2 4 , Michelle J Bauer 5 , Dominika Butkiewicz 5 , Darren J Trott 6 , Justine S Gibson 7 , Joanne L Mollinger 8 , Ben A Rogers 9 , Amanda K Kidsley 6 , Jan Bell 6 , John Turnidge 7 , Mark A Schembri 2 , Brian M Forde 10 , Scott A Beatson 1 2
  1. Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Queensland, Australia
  2. School of Chemistry and Molecular Biosciences, Australian Infectious Disease Research Centre, The University of Queensland, Brisbane, Queensland, Australia
  3. European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom
  4. University Hospital Complex of A Coruña (CHUAC), Biomedical Research Institute of A Coruña (INIBIC), A Coruña, Spain
  5. UQ Centre for Clinical Research (UQCCR), The University of Queensland, Brisbane, Queensland, Australia
  6. Australian Centre for Antimicrobial Resistance Ecology, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, South Australia, Australia
  7. School of Veterinary Science, The University of Queensland, Gatton, Queensland, Australia
  8. Department of Agriculture and Fisheries, Biosecurity Sciences Laboratory, Brisbane, Queensland, Australia
  9. School of Clinical Sciences, Monash University, Clayton, Victoria, Australia
  10. UQ Centre for Clinical Research (UQCCR), Australian Infectious Disease Research Centre, The University of Queensland, Brisbane, Queensland, Australia

Fluoroquinolone-resistant Escherichia coli sequence type (ST)1193 is a profound, emerging lineage associated with systemic, urinary tract, and neonatal infections. Humans, companion animals, and the environment are reservoirs for ST1193, which has disseminated globally. Following its detection in 2007, ST1193 has been identified repeatedly amongst fluoroquinolone-resistant clones in Australia. However, despite the growing importance of ST1193, only three complete genomes are publicly available. Here we expand on the available ST1193 resources with the complete genomes of five ST1193 strains. Additionally, we curate mobile genetic elements and define the complement and genomic context of virulence and antibiotic resistance genes. The five ST1193 strains underwent Nanopore and Illumina sequencing. Published complete genomes of three ST1193 strains were used for context and to investigate recombination. Antibiotic resistance, virulence genes, and mobile genetic elements were determined using in silico genotyping. Antibiotic susceptibility testing confirmed resistance profiles. The five ST1193 strains sequenced here provide a broader representation of the major ST1193 clades. Our reference genome was strain MS10858, a clinical isolate obtained early during the ST1193 expansion and falls within the predominant clade associated with the K1 capsular antigen. Uropathogenicity factors, including three separate siderophore-encoding loci, were conserved in chromosomal and plasmid regions. Using all complete genomes, we further elucidated the recombination events surrounding the previously described K5/K1 capsular loci switch. All ST1193 strains were multi-drug resistant, including resistance to fluoroquinolones and cephalosporins, and most antibiotic susceptibility testing phenotypes correlated with their genotypes. The exception was MS8320, which had additional in vitro resistance to piperacillin/tazobactam, ampicillin/sulbactam, cefazolin and doripenem (carbapenem). Further investigation identified seven additional copies of an IS26 transposable unit carrying a blaTEM-1B beta-lactamase gene, suggesting this tandem amplification is associated with extended resistance phenotypes. This study provides five new reference ST1193 genomes, including the first complete K5-capsule ST1193 genomes. These findings lay the foundations for further genomic and molecular analyses that may help understand the underlying reasons for the rapid global expansion of ST1193.