The Escherichia coli F plasmidome: an Australian perspective

ColV/ColBM and ColIa/senB F virulence plasmids feature prominently in Escherichia coli associated with urinary tract and bloodstream infections globally. Australian-sourced E. coli that carry these plasmids were examined among 5,471 isolates (3,316 sequenced by the APG and AusGEM programmes; 2,155 from public databases) spanning years 1986-2020 from humans (n=2,996/5,471; 54.8%), wild animals (n=870/5,471; 15.9%), livestock (n=649/5,471; 11.9%), companion animals (n=375/5,471; 6.9%), environmental sources (n=292/5,471; 5.3%) and food (n=289/5,471; 5.3%). Putative plasmid reconstruction, assisted by a plasmid database comprising 23,700 complete plasmid sequences, identified 22,534 putative plasmids of which 21,814 (96.8%) represented 547 known plasmid clusters. E. coli harbouring ColV-associated putative plasmids, particularly plasmid cluster AA176 [F replicon sequence type (RST): F18:A-:B1 (repFII-18:repFIA-null:repFIB-1)] was identified among phylogenetically diverse strains from humans, livestock, particularly poultry, and food. Closely related isolates, defined as ≤10 core-genome multilocus sequence type allelic distance, that carried either ColV or ColIa/senB-associated putative (F) plasmids were identified across multiple sources and diverse phylogenetic backgrounds. ColIa/senB-associated putative (F) plasmid clusters AA337 (RST: F29:A-:B10) and AA171 (RST: F2:A1:B20) were associated with phylogenetically closely related isolates from humans, wild animals and companion animals, but their absence in E. coli sourced from food and livestock was notable. E. coli carrying ColV and ColIa/senB plasmids frequently exhibit genotypic multidrug resistance, many with critically important antimicrobial resistance genes, highlighting their role in the evolution of clinically problematic lineages. Our study has important epidemiological considerations for understanding the spread of extraintestinal pathogenic and hybrid E. coli lineages across the One Health spectrum.