Extensive Genetic Commonality among Wildlife, Wastewater, Community, and Nosocomial Isolates of Escherichia coli Sequence Type 131 (H 30R1 and H 30Rx Subclones) That Carry blaCTX-M-27 or blaCTX-M-15

Abstract

Escherichia coli sequence type 131 (ST131) is currently one of the leading causes of multidrug-resistant extraintestinal infections globally. Here, we analyzed the phenotypic and genotypic characteristics of 169 ST131 isolates from various sources (wildlife, wastewater, companion animals, community, and hospitals) to determine whether wildlife and the environment share similar strains with humans, supporting transmission of ST131 between different ecological niches. Susceptibility to 32 antimicrobials was tested by disc diffusion and broth microdilution. Antibiotic resistance genes, integrons, plasmid replicons, 52 virulence genes, and fimH-based subtypes were detected by PCR and DNA sequencing. Genomic relatedness was determined by pulsed-field gel electrophoresis (PFGE). The genetic context and plasmid versus chromosomal location of extended-spectrum beta-lactamase and AmpC beta-lactamase genes was determined by PCR and probe hybridization, respectively. The 169 ST131 study isolates segregated predominantly into bla_CTX-M-15H30Rx (60%) and bla_CTX-M-27H30R1 (25%) subclones. Within each subclone, isolates from different source groups were categorized into distinct PFGE clusters; genotypic characteristics were fairly well conserved within each major PFGE cluster. Irrespective of source, the bla_CTX-M-15H30Rx isolates typically exhibited virotype A (89%), an F2:A1:B- replicon (84%), and a 1.7-kb class 1 integron (92%) and had diverse structures upstream of the bla_CTX-M region. In contrast, the bla_CTX-M-27H30R1 isolates typically exhibited virotype C (86%), an F1:A2:B20 replicon (76%), and a conserved IS26-ΔISEcp1-bla_CTX-M-like structure. Despite considerable overall genetic diversity, our data demonstrate significant commonality between E. coli ST131 isolates from diverse environments, supporting transmission between different sources, including humans, environment, and wildlife.

Keywords: ESBL; Escherichia coli ST131; environment; nosocomial and community-acquired infections; virulence; wildlife.

FIG 1

The clonality and common characteristics of representatives of 169 Escherichia coli ST131 from various sources. The superscript notations in the figure are defined as follows. ^aNT, not typeable using reference pulsotypes 788, 797, 800, 805, 806, 812, 837, 842, 903, 905, 906, 943, 945, 968, 987, 1067, 1140, 1676, 1733, 1734, 1735, 1737, 1738, and 1739. ^bHuman clinical isolates: hospital 1, St. Anne's Faculty Hospital, Brno, Czech Republic (CZ); hospital 2, Children's Medical Center, Brno, CZ; hospital 3, University Hospital Motol, Prague, CZ; Community: human community isolate, Karvina, CZ. ^cWWTP, wastewater treatment plant. ^d,g,iAn empty box indicates that no corresponding gene was detected. ^eFQ, fluoroquinolones (an empty box indicates that the isolate was not resistant to fluoroquinolone antibiotics). ^f,hAn empty box indicates that the isolate could not be assigned to particular subclone or virotype. ^gThe structure of bla_CTX-M and bla_CMY genetic environment is displayed in Fig. 2; ND, not determined.

FIG 1

The clonality and common characteristics of representatives of 169 Escherichia coli ST131 from various sources. The superscript notations in the figure are defined as follows. ^aNT, not typeable using reference pulsotypes 788, 797, 800, 805, 806, 812, 837, 842, 903, 905, 906, 943, 945, 968, 987, 1067, 1140, 1676, 1733, 1734, 1735, 1737, 1738, and 1739. ^bHuman clinical isolates: hospital 1, St. Anne's Faculty Hospital, Brno, Czech Republic (CZ); hospital 2, Children's Medical Center, Brno, CZ; hospital 3, University Hospital Motol, Prague, CZ; Community: human community isolate, Karvina, CZ. ^cWWTP, wastewater treatment plant. ^d,g,iAn empty box indicates that no corresponding gene was detected. ^eFQ, fluoroquinolones (an empty box indicates that the isolate was not resistant to fluoroquinolone antibiotics). ^f,hAn empty box indicates that the isolate could not be assigned to particular subclone or virotype. ^gThe structure of bla_CTX-M and bla_CMY genetic environment is displayed in Fig. 2; ND, not determined.

FIG 2

Genetic environment of bla_CTX-M and bla_CMY-2 groups among E. coli ST131 isolates. A dotted line in a gene box indicates truncation. IRR, right-hand inverted repeat; IRL, left-hand inverted repeat; DR, direct repeat of partial ISEcp1 inverted repeat; *, shortened spacer (32 bp) in variant 1c3; white triangle, IS26 inverted repeat; black triangle, ISEcp1 inverted repeat. ^aNovel genetic environment structure found in this study (no identical sequence was deposited in GenBank).

FIG 3

Principal-coordinate analysis (PCoA) of virulence genes, O-type, and H30 subclone designation among 169 E. coli ST131 isolates. The PCoA was based on results of all 52 virulence genes, O25b, and H30R1 and H30Rx status. Each isolate is plotted according to its value for PCoA coordinates 1 (horizontal axis) and 2 (vertical axis), where coordinates 1 and 2 capture 55.6% and 18.1% of the total variation, respectively. Based on PCoA, the genotypes and phylogeny structure of ST131 overlap extensively across the source groups.