Pandemic fluoroquinolone resistant Escherichia coli clone ST1193 emerged via simultaneous homologous recombinations in 11 gene loci

Abstract

Global growth in antibiotic resistance is a major social problem. A high level of resistance to fluoroquinolones requires the concurrent presence of at least 3 mutations in the target proteins-2 in DNA gyrase (GyrA) and 1 in topoisomerase IV (ParC), which occur in a stepwise manner. In the Escherichia coli chromosome, the gyrA and parC loci are positioned about 1 Mb away from each other. Here we show that the 3 fluoroquinolone resistance mutations are tightly associated genetically in naturally occurring strains. In the latest pandemic uropathogenic and multidrug-resistant E. coli clonal group ST1193, the mutant variants of gyrA and parC were acquired not by a typical gradual, stepwise evolution but all at once. This happened as part of 11 simultaneous homologous recombination events involving 2 phylogenetically distant strains of E. coli, from an uropathogenic clonal complex ST14 and fluoroquinolone-resistant ST10. The gene exchanges swapped regions between 0.5 and 139 Kb in length (183 Kb total) spread along 976 Kb of chromosomal DNA around and between gyrA and parC loci. As a result, all 3 fluoroquinolone resistance mutations in GyrA and ParC have simultaneously appeared in ST1193. Based on molecular clock estimates, this potentially happened as recently as <12 y ago. Thus, naturally occurring homologous recombination events between 2 strains can involve numerous chromosomal gene locations simultaneously, resulting in the transfer of distant but tightly associated genetic mutations and emergence of a both highly pathogenic and antibiotic-resistant strain with a rapid global spread capability.

Keywords: Escherichia coli ST1193; QRDR mutations; homologous recombination; resistance to fluoroquinolones; urinary tract infections.

Fig. 1.

E. coli phylogenetic trees. (A) Tree built using concatenated alleles of 7 MLST loci of top 25 extraintestinal STs (>0.5% E. coli subpopulation); ST14 clonal complex is circled with ST1193 in bold. Major phylogroups are indicated on the right. (B) Tree built using concatenated core genes for isolates belonging to closely related STs within the ST14 clonal complex, with ST names indicated on the right side. Isolates harboring 1 QRDR mutation are marked with solid circles for the GyrA-S83L mutation, diamond for GyrA-D87N, and triangle for GyrA-D87Y; ST1193 isolates harboring 3 QRDR mutations are marked with thick black branches.

Fig. 2.

Recombination in gyrA and parC regions in ST1193. (A and B) Polymorphic positions in gyrA and parC alleles identified in isolates belonging to closely related ST14cc. The most common non-ST1193 allele of either gene is assigned as an ST14cc consensus ancestor. Positions with nonsynonymous changes are marked with asterisks (*); QRDR positions are marked with squares (□). Inferred susceptibility (S); intermediate (I) or high (R) resistance to FQs. (C and D) Nucleotide diversity of ST1193 vs. ST14cc consensus ancestor plotted for ordered core genes in the chromosomal regions flanking (C) gyrA and (D) parC (indicated with pointed rectangle). (E and F) Same as C and D with diversity of consensus ST1193 vs. consensus ST10-H54 ancestor (blue).

Fig. 3.

Recombination regions in ST1193. (A) Nucleotide diversity of consensus ST1193 vs. consensus ST14cc ancestor plotted on MCJCHV-1 chromosome. (B) Close-ups for each recombinant region with diversity vs. consensus ST10-H54 donor added in blue.

Fig. 4.

Phylogenetic tree built for core genomes of a subset of ST10-H54 isolates from Enterobase database. Green, isolates without QRDR mutations in gyrA and parC (presumably, FQ-S); yellow, isolates with 1 QRDR mutation (FQ-I); red, isolates with ≥3 QRDR mutations (FQ-R).

Fig. 5.

Prevalence of E. coli clones among extraintestinal isolates. (A) FQ-R E. coli collected in 2010 to 2011 (n = 251). (B) FQ-R E. coli collected in 2016 to 2017 (n = 1,443). (C) All E. coli collected from 2013 to 2017 (n = 8,637), including FQ-R E. coli from A and B. Red, ST131-H30; orange, ST1193; green, ST14cc; blue, ST10-H54.