Evolutionary History of the Global Emergence of the Escherichia coli Epidemic Clone ST131

Abstract

Escherichia colisequence type 131 (ST131) has emerged globally as the most predominant extraintestinal pathogenic lineage within this clinically important species, and its association with fluoroquinolone and extended-spectrum cephalosporin resistance impacts significantly on treatment. The evolutionary histories of this lineage, and of important antimicrobial resistance elements within it, remain unclearly defined. This study of the largest worldwide collection (n= 215) of sequenced ST131E. coliisolates to date demonstrates that the clonal expansion of two previously recognized antimicrobial-resistant clades, C1/H30R and C2/H30Rx, started around 25 years ago, consistent with the widespread introduction of fluoroquinolones and extended-spectrum cephalosporins in clinical medicine. These two clades appear to have emerged in the United States, with the expansion of the C2/H30Rx clade driven by the acquisition of ablaCTX-M-15-containing IncFII-like plasmid that has subsequently undergone extensive rearrangement. Several other evolutionary processes influencing the trajectory of this drug-resistant lineage are described, including sporadic acquisitions of CTX-M resistance plasmids and chromosomal integration ofblaCTX-Mwithin subclusters followed by vertical evolution. These processes are also occurring for another family of CTX-M gene variants more recently observed among ST131, theblaCTX-M-14/14-likegroup. The complexity of the evolutionary history of ST131 has important implications for antimicrobial resistance surveillance, epidemiological analysis, and control of emerging clinical lineages ofE. coli These data also highlight the global imperative to reduce specific antibiotic selection pressures and demonstrate the important and varied roles played by plasmids and other mobile genetic elements in the perpetuation of antimicrobial resistance within lineages.

Importance: Escherichia coli, perennially a major bacterial pathogen, is becoming increasingly difficult to manage due to emerging resistance to all preferred antimicrobials. Resistance is concentrated within specificE. colilineages, such as sequence type 131 (ST131). Clarification of the genetic basis for clonally associated resistance is key to devising intervention strategies. We used high-resolution genomic analysis of a large global collection of ST131 isolates to define the evolutionary history of extended-spectrum beta-lactamase production in ST131. We documented diverse contributory genetic processes, including stable chromosomal integrations of resistance genes, persistence and evolution of mobile resistance elements within sublineages, and sporadic acquisition of different resistance elements. Both global distribution and regional segregation were evident. The diversity of resistance element acquisition and propagation within ST131 indicates a need for control and surveillance strategies that target both bacterial strains and mobile genetic elements.

FIG 1

Time-scaled phylogeny of ST131 E. coli (n = 215), with associated bla_CTX-M/fimH variants, and quinolone resistance-determining region (QRDR) mutations in gyrA (WT, wild-type QRDR). Curly brackets represent ST131 clades as described in the text. Tips are colored by geographic region, per the key. T, bla_CTX-M plasmid transformant generated for strain; *, cases with putative deletions in the assembled bla_CTX-M-15 gene.

FIG 2

Chromosomal location of ISEcp1-mediated bla_CTX-M-15 insertion events and evidence of acquisition and evolution by descent (inset phylogeny) over approximately 8 years across two geographic regions (Oxford, United Kingdom; Mae Sot, Thailand-Myanmar border). Coloring of isolate names represents geographic location (red, Europe; green, Southeast Asia; blue, North America).

FIG 3

Genetic flanking context of bla_CTX-M-15 region for clade C2/H30Rx isolates. (Top) Putative source element. (Left) C2/H30Rx phylogeny. Many contexts are limited by the extent of the assembled region around the bla_CTX-M-15 gene (marked with “X”). For all similarly colored, vertically aligned regions below the “Putative source element,” sequence identity is 100%. Curly brackets cluster those isolates with identical flanking sequences. Flanking contexts are not shown and tip labels are omitted for isolates with known chromosomal integration of bla_CTX-M, for bla_CTX-M-negative isolates in the clade, or for isolates where the flanking sequence was not evaluable (see Results).

FIG 4

Mean pairwise percent difference between all transformed plasmid sequence pairs plotted against time to most recent common ancestor (TMRCA) for the two strains hosting the respective transformant plasmids. Red circles indicate pairs where both strains are in C2; blue triangles indicate pairs where one or both strains are outside C2. The lower panel represents the same data but limited to strains with a TMRCA of less than 30 years.

FIG 5

(Top) BLASTn-based comparison across the ST131 data set, using the bla_CTX-M-15-containing 11B00320_T as a reference. Color represents degree of presence/absence of identity to the 11B00320_T sequence on an isolate-by-isolate basis per row. Rows/isolates are arranged as in the Fig. 1 phylogeny. (Bottom) ProgressiveMauve alignment of 11B00320_T and the CTX-M-15-containing contigs for two other isolates in clade A. Alignments with substantial homology are represented as similarly colored blocks (“locally collinear blocks”); white regions within these blocks represent low homology. Vertical red lines represent contig breaks.

FIG 6

ProgressiveMauve alignment of assembled contigs, ordered with respect to pP46212, for 17 bla_CTX-M-15 FII plasmids derived from sequenced transformants, all in clade C2/H30Rx. Plasmids are ordered with respect to the position of their host strains in the main phylogeny (except pP46212 [Fig. 1]). Alignments with substantial homology are represented as colored blocks (“locally collinear blocks”) and are linked with colored lines; white regions within these blocks represent low homology.

FIG 7

(Top) BLASTn-based comparisons across the ST131 data set, using the bla_CTX-M-14-containing uk_8A9B_T as a reference. Color represents degree of presence/absence of identity to the uk_8A9B_T sequence on an isolate-by-isolate basis per row. Rows/isolates are arranged as in the Fig. 1 phylogeny. (Bottom) ProgressiveMauve alignment of uk_8A9B_T, cam1071_T, la_5108_T, and 11B01979_T, with the last three ordered using uk_8A9B_T as a reference and contig boundaries represented as vertical red lines. Alignments with substantial homology are represented as colored blocks (“locally collinear blocks”); white regions within these blocks represent low homology. Vertical red lines represent contig breaks.