Plasmids shape the diverse accessory resistomes of Escherichia coli ST131

Decano, A. G.; Tran, N.; Al-Foori, H.; Al-Awadi, B.; Leigh Campbell, L.; Ellison, K.; Mirabueno, L. P.; Nelson, M.; Power, S.; Smith, G.; Smyth, C.; Vance, Z.; Rahm, A.; Downing, T.

doi:10.1101/2020.05.07.081380

bioRxiv · 10.1101/2020.05.07.081380

Plasmids shape the diverse accessory resistomes of Escherichia coli ST131

Decano, A. G.·Tran, N.·Al-Foori, H.·Al-Awadi, B.·Leigh Campbell, L.·Ellison, K.·Mirabueno, L. P.·Nelson, M.·Power, S.·Smith, G.·Smyth, C.·Vance, Z.·Rahm, A.·Downing, T.

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Abstract

The human gut microbiome includes beneficial, commensal and pathogenic bacteria that possess antimicrobial resistance (AMR) genes that exchange these predominantly through conjugative plasmids. Escherichia coli is a significant component of the gastrointestinal microbiome and is typically non-pathogenic in this niche. In contrast, extra-intestinal pathogenic E. coli (ExPEC) including ST131 may occupy other environments like the urinary tract or bloodstream where they express genes enabling AMR and host cell adhesion like type 1 fimbriae. The extent to which commensal E. coli and uropathogenic ExPEC ST131 share AMR genes remains understudied at a genomic level, and here we examined this using a preterm infant resistome. Here, individual ST131 had small differences in AMR gene content relative to a larger shared resistome. Comparisons with a range of plasmids common in ST131 showed that AMR gene composition was driven by conjugation, recombination and mobile genetic elements. Plasmid pEK499 had extended regions in most ST131 Clade C isolates, and it had evidence of a co-evolutionary signal based on protein-level interactions with chromosomal gene products, as did pEK204 that had a type IV fimbrial pil operon. ST131 possessed extensive diversity of selective type 1, type IV, P and F17-like fimbriae genes that was highest in subclade C2. The structure and composition of AMR genes, plasmids and fimbriae vary widely in ST131 Clade C and this may mediate pathogenicity and infection outcomes. Data SummaryThe following files are available on the FigShare project "Plasmids_ST131_resistome_2020" : O_LI The set of 794 AMR genes derived from [74] are available (with their protein sequence translation) at FigShare at doi: dx.doi.org/10.6084/m9.figshare.11961402. C_LIO_LI The AMR gene profiles per sample determined by their BLAST sequence similarity results against CARD are available at FigShare at doi: dx.doi.org/10.6084/m9.figshare.11961612. This dataset includes the PlasmidFinder results. It also includes other AMR database comparisons (ARG-ANNOT, ResFinder, MegaRes, VFDB and VirulenceFinder). C_LIO_LI The BLAST sequence similarity results for the fim, pil, pap and ucl operons genes versus 4,071 E. coli ST131 assemblies from Decano & Downing (2019) are available at FigShare at doi: dx.doi.org/10.6084/m9.figshare.11961711. C_LIO_LI The genome sequences and annotation files for reference genomes NCTC13441, EC958 and SE15, along with the assembled contigs for 83972 and 3_2_53FAA are available at FigShare at doi: dx.doi.org/10.6084/m9.figshare.11961813. C_LIO_LI The 4,071 E. coli ST131 genome assemblies from Decano & Downing (2019) are available at FigShare at doi: 10.6084/m9.figshare.11962278 (the first 1,680 assemblies) and at doi: dx.doi.org/10.6084/m9.figshare.11962557 (the second 2,391 assemblies). C_LI

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Decano, A. G., Tran, N., Al-Foori, H., Al-Awadi, B., Leigh Campbell, L., Ellison, K., Mirabueno, L. P., Nelson, M., Power, S., Smith, G., Smyth, C., Vance, Z., Rahm, A., Downing, T.. 2020-05-08. Plasmids shape the diverse accessory resistomes of Escherichia coli ST131. https://doi.org/10.1101/2020.05.07.081380

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