Zoonotic Transfer of Clostridium difficile Harboring Antimicrobial Resistance between Farm Animals and Humans

Abstract

The emergence of Clostridium difficile as a significant human diarrheal pathogen is associated with the production of highly transmissible spores and the acquisition of antimicrobial resistance genes (ARGs) and virulence factors. Unlike the hospital-associated C. difficile RT027 lineage, the community-associated C. difficile RT078 lineage is isolated from both humans and farm animals; however, the geographical population structure and transmission networks remain unknown. Here, we applied whole-genome phylogenetic analysis of 248 C. difficile RT078 strains from 22 countries. Our results demonstrate limited geographical clustering for C. difficile RT078 and extensive coclustering of human and animal strains, thereby revealing a highly linked intercontinental transmission network between humans and animals. Comparative whole-genome analysis reveals indistinguishable accessory genomes between human and animal strains and a variety of antimicrobial resistance genes in the pangenome of C. difficile RT078. Thus, bidirectional spread of C. difficile RT078 between farm animals and humans may represent an unappreciated route disseminating antimicrobial resistance genes between humans and animals. These results highlight the importance of the "One Health" concept to monitor infectious disease emergence and the dissemination of antimicrobial resistance genes.

Keywords: Clostridium difficile; One Health concept; RT078; accessory genome; antibiotic resistance; intercontinental transmission; interhost transmission.

FIG 1

Phylogeography of human and animal Clostridium difficile RT078 strains. Maximum likelihood, midpoint-rooted phylogenetic tree of 248 genomes represents strains isolated from human (dark blue), animal (red), food (orange), and environmental (light blue) sources and collected from Europe (dark green), North America (purple), Asia (pink), and Australia (light green). Branches with bootstrap confidence values above 0.7 are shown as solid lines. The phylogeny demonstrates clear mixing of European and North American strains, indicating multiple transmission events between continents, and mixing of human and animal strains, indicating multiple transmissions events between these hosts. Closely related clusters (see Table 1) containing both human and animal isolates are labeled 1 through 6 and highlighted in yellow.

FIG 2

Indistinguishable accessory genome of C. difficile RT078 harbors a variety of antimicrobial resistance genes. (A) The accessory genes (n = 2,859) categorized according to host origin. The number of accessory genes (x axis) only found in human genomes (dark blue), only found in animal genomes (red), or found in both human and animal genomes (green) is plotted against the number of genomes in which these genes are present (y axis). (B) The frequency of predicted antimicrobial resistance genes (ARGs) within the 243 C. difficile RT078 strains. Human (dark blue) and animal (red) isolation sources are shown by color.