Global dissemination of a multidrug resistant Escherichia coli clone

Abstract

Escherichia coli sequence type 131 (ST131) is a globally disseminated, multidrug resistant (MDR) clone responsible for a high proportion of urinary tract and bloodstream infections. The rapid emergence and successful spread of E. coli ST131 is strongly associated with several factors, including resistance to fluoroquinolones, high virulence gene content, the possession of the type 1 fimbriae FimH30 allele, and the production of the CTX-M-15 extended spectrum β-lactamase (ESBL). Here, we used genome sequencing to examine the molecular epidemiology of a collection of E. coli ST131 strains isolated from six distinct geographical locations across the world spanning 2000-2011. The global phylogeny of E. coli ST131, determined from whole-genome sequence data, revealed a single lineage of E. coli ST131 distinct from other extraintestinal E. coli strains within the B2 phylogroup. Three closely related E. coli ST131 sublineages were identified, with little association to geographic origin. The majority of single-nucleotide variants associated with each of the sublineages were due to recombination in regions adjacent to mobile genetic elements (MGEs). The most prevalent sublineage of ST131 strains was characterized by fluoroquinolone resistance, and a distinct virulence factor and MGE profile. Four different variants of the CTX-M ESBL-resistance gene were identified in our ST131 strains, with acquisition of CTX-M-15 representing a defining feature of a discrete but geographically dispersed ST131 sublineage. This study confirms the global dispersal of a single E. coli ST131 clone and demonstrates the role of MGEs and recombination in the evolution of this important MDR pathogen.

Keywords: bacterial evolution; genomic epidemiology; genomics; phylogeography.

Fig. 1.

Phylogenetic relationship of ST131 strains. (A) ML phylogram with triangles indicating bootstrap support of >90% from 1,000 replicates. The tree is rooted by using the outgroup phylogroup D strain UMN026; branch lengths correspond to the number of SNPs difference (scale bar bottom left). The phylogram was built from 119,514 substitution-only SNPs determined by read-mapping using E. coli SE15 as reference excluding recombinant regions, as defined by BRATNextGen analysis (34). The taxa labels for sequenced ST131 strains are colored red (clade A), orange (clade B) and green (clade C). Previously sequenced reference strains are colored black. Colored circles next to each strain correspond to country and year of isolation (see key). Squares indicate allelic profiling for fimH, parC, gyrA, and CTX-M (see key). A missing square indicates the gene is absent. (B) Several well-supported subclades are evident in the ST131 phylogeny, with the CTX-M-15 gene confined to the second subclade of clade C. The topology-only cladogram (not to scale) corresponding to the phylogram in A is shown in gray, with node support of >90% depicted as gray diamonds. The number of SNPs that define clade C and sublineages C1 (Upper) and C2 (Lower) are shown below relevant branches (nonsynonymous, synonymous, intergenic); refer to Dataset S2 for full list of SNPs and consequences.

Fig. 2.

Distribution of ST131-only core SNPs in recombinant versus nonrecombinant regions. (A) Comparison of the linear genome arrangement of the clade C strain EC958 (Upper) and the clade A strain SE15 (Lower). Solid dark-blue lines between EC958 and SE15 indicate BLAST match of ≥99% nucleotide identity between the two genomes. Genomic features of interest are highlighted for both strains as follows: prophages (pink); ST131 characteristic ROD1, ROD2, and ROD3 (yellow); previously characterized genomic islands (blue); and other regions of interest (turquoise). Labels refer to the ST131-characteristic regions defined in the genome of EC958 (15). (B) Heatmap showing the density of 16,424 ST131-only core SNPs along the SE15 chromosome: Syn_NR (synonymous, nonrecombinant); NSyn_NR (nonsynonymous, nonrecombinant); Syn_R (synonymous, recombinant); and NSyn_R (nonsynonymous, recombinant). ST131-only core SNPs were defined as bases called from the mapping data in all strains of the dataset with polymorphisms specific to the ST131 lineage. Recombinant region coordinates were delineated by using BratNextGen. The SNP density heatmap with (number of SNPs per 1 kbp nonoverlapping bin) is indicated by the color key. The x axis at the bottom of the figure represents the SE15 reference chromosome coordinates.

Fig. 3.

Selected regions of interest in ST131 strains. ST131-characteristic regions previously defined in the genome of EC958 (15) are shown along the x axis with strain identifiers listed on the y axis according to the phylogenetic tree order displayed in Fig. 1A. Regions A–M are shown to scale in order of their location relative to the SE15 chromosome (Fig. 2) and correspond to: A, flag2 flagellar region (38.1 kb); B, GI-ThrW genomic island; C, ROD1; D, Phi1 prophage; E, Phi2 prophage; F, Phi3 prophage; G, ROD2; H, Phi4 prophage; I, Phi5 prophage; J, Phi6 prophage; K, High-Pathogenicity Island; L, cryptic prophage; M, O-antigen 1 region (wbbJ-rfbE); N, Phi7 prophage; O, RatA-like region; P, T6SS region; Q, GI-PheV genomic island; R, capsule region; S, O-antigen2 region; T, GI-SelC genomic island; U, ROD3; V, GI-LeuX. Black shading indicates a match of ≥95% nucleotide identity in a minimum window of 200 bp calculated by comparing the query sequence to the assembled contigs or the consensus from mapped reads for each strain, as implemented in seqfindr (http://github.com/mscook/seqfindr).