High Risk Clone: A Proposal of Criteria Adapted to the One Health Context with Application to Enterotoxigenic Escherichia coli in the Pig Population

Abstract

The definition of a high risk clone for antibiotic resistance dissemination was initially established for human medicine. We propose a revised definition of a high risk clone adapted to the One Health context. Then, we applied our criteria to a cluster of enrofloxacin non susceptible ETEC:F4 isolates which emerged in 2013 in diseased pigs in Quebec. The whole genomes of 183 ETEC:F4 strains isolated in Quebec from 1990 to 2018 were sequenced. The presence of virulence and resistance genes and replicons was examined in 173 isolates. Maximum likelihood phylogenetic trees were constructed based on SNP data and clones were identified using a set of predefined criteria. The strains belonging to the clonal lineage ST100/O149:H10 isolated in Quebec in 2013 or later were compared to ETEC:F4 whole genome sequences available in GenBank. Prior to 2000, ETEC:F4 isolates from pigs in Quebec were mostly ST90 and belonged to several serotypes. After 2000, the isolates were mostly ST100/O149:H10. In this article, we demonstrated the presence of a ETEC:F4 high risk clone. This clone (1) emerged in 2013, (2) is multidrug resistant, (3) has a widespread distribution over North America and was able to persist several months on farms, and (4) possesses specific virulence genes. It is crucial to detect and characterize high risk clones in animal populations to increase our understanding of their emergence and their dissemination.

Keywords: ETEC:F4; Escherichia coli; North America; antimicrobial resistance; fluoroquinolones non-susceptibility; genomics; multidrug resistance; pigs.

Figure 1

(A) Global phylogeny: Circular Tree based on SNP phylogeny. The length of the branches is not proportionate to the phylogenetic distance. Gubbins was used to eliminate the recombination signal. The total SNP number was 19,299. Each branch with a bootstrap value under 1 was collapsed. The capital letters designate each clonal lineage. Filled triangles indicate the presence of the corresponding mutation, empty triangles indicate the absence of the corresponding mutation. (B) Clonal lineage A (same phylogeny is used): The number associated with the letter A designates each clone. The identification name for each isolate belonging to a clone is highlighted in a specific color. Circles represent the proportion of the age of the pigs within each corresponding branch. Columns entitled Tet, Amp, Cef, Enro, represent respectively the susceptibility to tetracycline, ampicillin, ceftiofur and enrofloxacin (code for the corresponding color is available on the figure).

Figure 2

Circular Tree based on SNP phylogeny. The length of the branches is not proportionate to the phylogenetic distance. All isolates belong to the clonal lineage A (ST100-O149H10-phylogroupA-no fimH gene) and originated from 2013 or after. Each branch with a bootstrap value under 1 was collapsed. QC = Quebec, SW = Switzerland, MN (in grey) = Manitoba, ON = Ontario, MI = Michigan, MN (in blue) = Minnesota. MO = Missouri, NC = North Carolina, TX = Texas, IA = Iowa, KS = Kansas, WI = Wisconsin, IN = Indiana, IL = Illinois, OK = Oklahoma, NE = Nebraska, SD = South Dakota, VA = Virginia. A-I and A-II designate each clone and A-I-sub designates the subclone within the clone A-I. The 3 isolates colored in black are the three outsiders (more than 70 SNPs of differences in the pairwise distance comparison). The identification name for each isolate belonging to a clone is highlighted in a specific color.