Abrupt emergence of a single dominant multidrug-resistant strain of Escherichia coli

Abstract

Background: Fluoroquinolone-resistant Escherichia coli are increasingly prevalent. Their clonal origins--potentially critical for control efforts--remain undefined.

Methods: Antimicrobial resistance profiles and fine clonal structure were determined for 236 diverse-source historical (1967-2009) E. coli isolates representing sequence type ST131 and 853 recent (2010-2011) consecutive E. coli isolates from 5 clinical laboratories in Seattle, Washington, and Minneapolis, Minnesota. Clonal structure was resolved based on fimH sequence (fimbrial adhesin gene: H subclone assignments), multilocus sequence typing, gyrA and parC sequence (fluoroquinolone resistance-determining loci), and pulsed-field gel electrophoresis.

Results: Of the recent fluoroquinolone-resistant clinical isolates, 52% represented a single ST131 subclonal lineage, H30, which expanded abruptly after 2000. This subclone had a unique and conserved gyrA/parC allele combination, supporting its tight clonality. Unlike other ST131 subclones, H30 was significantly associated with fluoroquinolone resistance and was the most prevalent subclone among current E. coli clinical isolates, overall (10.4%) and within every resistance category (11%-52%).

Conclusions: Most current fluoroquinolone-resistant E. coli clinical isolates, and the largest share of multidrug-resistant isolates, represent a highly clonal subgroup that likely originated from a single rapidly expanded and disseminated ST131 strain. Focused attention to this strain will be required to control the fluoroquinolone and multidrug-resistant E. coli epidemic.

Figure 1.

XbaI pulsed-field gel electrophoresis-based dendrogram for 85 sequence type ST131 Escherichia coli isolates (1967–2011). FQ, fluoroquinolone phenotype (R, resistant; S, susceptible); fimH, allele of fimH (type 1 fimbrial adhesin); PFGE, pulsotype; Year, year of isolation or submission to reference laboratory. Bullets (to right) mark isolates with the fimH30 allele. Horizontal line separates isolates with ≥75% overall profile similarity (top, n = 50) from less-similar isolates (bottom, n = 35).

Figure 2.

Distribution of fluoroquinolone-susceptible (FQ-S) and resistant (FQ-R) isolates among the 7 fimH-based (H) ST131 subclones. Area of circle is proportional to the relative abundance of the particular H subclone within the particular time period. Percentage values are shown relative to the total no. of isolates within the time period. (A) Clonal distribution by time period. (B) Overall clonal distribution. The gyrA and parC allele combinations observed among FQ-S (in green) and FQ-R (in red) isolates are labeled according to the nomenclature shown in Figure 3. Asterisks identify the ST131 isolates’ principal gyrA/parC allele combination (ie, gyrA1AB/parC1aAB).

Figure 3.

ST131-associated gyrA and parC alleles: gene phylogeny and combinations. Green, alleles (or combinations) associated with fluoroquinolone-susceptible isolates. Red, alleles (or combinations) associated with fluoroquinolone-resistant isolates. Single letter amino acid code: G (Gly), D (Asp), E (Glu), I (Ile), L (Lys), N (Asn), P (Pro), R (Arg), S (Ser), V (Val), and Y (Tyr). (A and B) Phylogeny of the ST131-associated gyrA and parC alleles. Labels inside circles: allele designations. In parentheses: earliest known year of isolation for the allele. Along the branches: lower-case numbers are nucleotide positions with silent mutations, upper-case numbers are amino acid positions with amino acid replacement mutations. Arrows: putative evolutionary order of mutations (double arrow between allele 1 and 1′ indicates uncertainty of the order). Gray boxes: phylogenetic clades within which nearest alleles differ by no more than one silent nucleotide change. (C) gyrA and parC allele combinations. Numbers inside cells: number of ST131 isolates with the corresponding allele combination. The predominant allele combination among FQ-R isolates is shown in boldface.

Figure 4.

gyrA and parC phylogenetic trees for ST131 isolates and diverse fluoroquinolone (FQ)-resistant non-ST131 Escherichia coli isolates. Trees were built based on silent variation only (green branches); FQ-resistance-determining amino acid replacement changes were then added manually (red branches and labels). STc: ST complexes (groups of closely related STs) within which the indicated alleles are found. Diagonal lines indicate gyrA/parC combinations (dashed green, in FQ-susceptible ST131 isolates; dashed red, in FQ-R ST131 isolates; solid black, in FQ-R non-ST131 isolates). Blue/boldface labels: the 17 alleles found in ST131, named according to the nomenclature used in Figure 3. “ST131 (historic)” marks ST131-associated alleles found only in historic ST131 isolates.

Figure 5.

Prevalence of the H30 ST131 subclone among 853 recent clinical Escherichia coli isolates. Orange, H30 ST131 subclone. Gray, 11 most prevalent non-ST131 H subclones. Each H subclone is labeled along the Z-axis (right side of chart) with its fimH allele and ST number. “Total isolates” columns (at left) are darker than the rest. Antimicrobials are listed along the X-axis (front of chart) in descending order of resistance prevalence (shown in parentheses). Y-axis (vertical) gives number of total or resistant isolates. Percentage numbers above the pink H30 columns indicate the H30 subclone's relative prevalence within each category (total, or specific resistance phenotypes). Abbreviations: AMP, ampicillin; A/S, ampicillin/sulbactam; CIP, ciprofloxacin; CZ, cefazolin; GM, gentamicin; NIT, nitrofurantoin; PTZ, piperacillin/tazobactam; TET, tetracycline; T/S, trimethoprim/sulfamethoxazole. No imipenem resistance was detected. MDR, multidrug resistant (ie, to ≥3 or ≥5 classes, with penicillins and cephalosporins counted separately).