Plasmids shape the diverse accessory resistomes of Escherichia coli ST131

Abstract

The human gut microbiome includes beneficial, commensal and pathogenic bacteria that possess antimicrobial resistance (AMR) genes and 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 we examined this here using a preterm infant resistome. We found that 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.

Keywords: Escherichia coli; Genome; ST131; evolution; fimbrial; infection; plasmid.

Fig. 1.

The overlap of preterm infant AMR contigs across four ST131 subclade C2 assemblies (8289_1#3, 8289_1#24, 8289_1#27, 8289_1#34), two ST131 reference genomes (EC958 and SE15) and two HMP assemblies (83 972 and 3_2_53FAA). Top: The intersection sizes (y-axis) and the numbers of AMR contigs per set showed that most (210) AMR contigs were shared across all isolates. The non-unique AMR contigs indicated smaller numbers of unique AMR genes, so EC958’s 17 AMR contigs (red) corresponded to nine unique bla _CMY genes (Table S2); and 8289_1#24’s nine contigs (green) represented four aminoglycoside and tetracycline resistance genes (Table S3). All Clade C bar 8289_1#27 had 12 contigs (blue) denoting to five bla _TEM genes (Table S4). Bottom: The numbers of AMR contigs per sample with the corresponding sets (coloured circles).

Fig. 2.

Comparison of pEK499 (top, 117 536 bp) and pEK204 (bottom, 93 732 bp) with five ST131 C1 and C2 isolates, ST131 Clade A reference SE15 (navy) and two HMP assemblies (3_2_53FAA in dark green and 83 972 in cyan). Top: Normalised read coverage showed high copy numbers of IS1 (at 41 and 103 Kb of pEK499) and IS66 (at 75–77 Kb of pEK204, and at 113 Kb of pEK499). Bottom: blast alignments showed limited similarity for the HMP assemblies and SE15 relative to higher levels for Clade C for pEK499 : 8289_1#27 (C2, mauve), 8289_1#24 (C2, pink), 8289_1#35 (C1, grey), 8289_1#3 (C2, light green), 8289_1#34 (C2, beige). For pEK204, only 8289_1#27 had many regions of similarity. Genes encoding bla _TEM, bla _OXA-1 and bla _CTX-M-15 are at 40, 58 and 63 Kb on pEK499 (respectively). The bla _CTX-M gene was at 8 Kb, bla _TEM was at 13 Kb, followed by mixed conjugation and segregation genes at 36–70 Kb on pEK204. For pEK204, the bla _CTX-M-3 gene differs from bla _CTX-M-15 by a single R240G substitution, and so bla _CTX-M genes detected here were bla _CTX-M-15. The annotation was modified from [59]. Matches spanning >300 bp are shown.

Fig. 3.

The distributions of pEK204-like regions in ST131 Clade C genome assemblies with >1 Kb (left, n=3234) and >40 Kb (right, n=193) of matching segments. The regions of similarity were examined in (left) Subclades B0 (n=14 in black), C0 (n=51 in red), C1 (n=1119 in green) and C2 (n=2051 in blue), and (right) C0 (n=17 in red), C1 (n=82 in green) and C2 (n=94 in blue). The 8289_1#27 (c2) is highlighted in yellow. Similarity across pEK204 (93 732 bp) was based on blast alignment. The bla _CTX-M gene was at 8 Kb, bla _TEM was at 13 Kb, followed by a mix of conjugation and segregation genes at 36–70 Kb. This suggested independent integrations and rearrangements of pEK204-like plasmids across the subclades. The annotation was modified from [59].