Clonal ST131- H 22 Escherichia coli strains from a healthy pig and a human urinary tract infection carry highly similar resistance and virulence plasmids

Abstract

The interplay between food production animals, humans and the environment with respect to the transmission of drug-resistant pathogens is widely debated and poorly understood. Pandemic uropathogenic Escherichia coli ST131-H30Rx, with conserved fluoroquinolone and cephalosporin resistance, are not frequently identified in animals. However, the phylogenetic precursor lineage ST131-H22 in animals and associated meat products is being reported with increasing frequency. Here we characterized two highly related ST131-H22 strains, one from a healthy pig and the other from a human infection (in 2007 and 2009, respectively). We used both long and short genome sequencing and compared them to ST131-H22 genome sequences available in public repositories. Even within the context of H22 strains, the two strains in question were highly related, separated by only 20 core SNPs. Furthermore, they were closely related to a faecal strain isolated in 2010 from a geographically distinct, healthy human in New South Wales, Australia. The porcine and hospital strains carried highly similar HI2-ST3 multidrug resistant plasmids with differences in the hospital strain arising due to IS-mediated insertions and rearrangements. Near identical ColV plasmids were also present in both strains, further supporting their shared evolutionary history. This work highlights the importance of adopting a One Health approach to genomic surveillance to gain insights into pathogen evolution and spread.

Keywords: ColV; ExPEC; H22; HI2; ST131; fimH22; porcine commensal E. coli.

Fig. 1.

Maximum-likelihood tree of 282 ST131-H22 sequences derived from a core genome alignment of 3720 variable sites against reference genome JJ1897. Coloured bars and black dots show metadata associated with each strain.

Fig. 2.

Mauve comparison of pF2_14D_HI2 and p2009_36_HI2. Grey colouring between plasmids indicates sequence inversion. Coloured arrows represent genes and their functions.

Fig. 3.

Schematic map of pF2_14D_HI2 (outer ring) and BRIG compared to p2009_36_HI2 and 41 HI2-ST3 complete plasmids. Coloured arrows represent genes and their functions. Coloured rings indicate regions of sequence homology to pF2_14D_HI2 and white space indicates an absence of homologous sequence. Host species abbreviations are as follows: Ec, Escherichia coli ; Se, Salmonella enterica ; Ro, Raoultella ornitholytica; Sf, Shigella flexneri ; Kp, Klebsiella pneumoniae.

Fig. 4.

Mauve comparison of pF2_14D_F, p2009_36_F and pCERC5. Coloured blocks indicate regions of sequence homology, and white space indicates absence of homology. Grey colouring between plasmids shows deletion in F2_14D_F. Coloured arrows represent genes and their functions.

Fig. 5.

Schematic map of pF2_14D_F (outer ring) and BRIG compared to p2009_36_F and 13 F2:B1 complete plasmids. Coloured arrows represent genes and their functions. Coloured rings indicate regions of sequence homology to pF2_14D_F and white space indicates absence of homologous sequence. Host species abbreviations are as follows: Ec, Escherichia coli; Se, Salmonella enterica.