Emergence and global spread of epidemic healthcare-associated Clostridium difficile

Abstract

Epidemic C. difficile (027/BI/NAP1) has rapidly emerged in the past decade as the leading cause of antibiotic-associated diarrhea worldwide. However, the key events in evolutionary history leading to its emergence and the subsequent patterns of global spread remain unknown. Here, we define the global population structure of C. difficile 027/BI/NAP1 using whole-genome sequencing and phylogenetic analysis. We show that two distinct epidemic lineages, FQR1 and FQR2, not one as previously thought, emerged in North America within a relatively short period after acquiring the same fluoroquinolone resistance-conferring mutation and a highly related conjugative transposon. The two epidemic lineages showed distinct patterns of global spread, and the FQR2 lineage spread more widely, leading to healthcare-associated outbreaks in the UK, continental Europe and Australia. Our analysis identifies key genetic changes linked to the rapid transcontinental dissemination of epidemic C. difficile 027/BI/NAP1 and highlights the routes by which it spreads through the global healthcare system.

Figure 1

Phylogeny of C. difficile 027/BI/NAP1 based on core genome SNPs. a, Global phylogeny (n=151 isolates). Colored nodes indicate the geographical source of the isolates. The position of the inferred root is indicated by a dashed line. b, Phylogeny of UK isolates (n=188) colored according to geographical source of isolates (gray - non-UK isolates). Dashed-line circled areas indicate the isolates with Thr82Ile substitution in gyrA associated with fluoroquinolone resistance. Black arrows show insertion of selected mobile elements.

Figure 2

Transmission events inferred for epidemic C. difficile 027/BI/NAP1. a, Global spread of lineages FQR1 (red arrows) and FQR2 (blue arrows) inferred from phylogeographic analysis (Supplementary Fig. 5). Global map demonstrating the countries where fluoroquinolone-resistant (pink) and fluoroquinolone-sensitive (yellow) C. difficile 027/BI/NAP1 has been reported. Width of the arrow is approximately proportional to the number of descendents from each sub-lineage. b, Inferred arrivals (blue dashed arrows) and transmissions (red arrows) of FQR2 into and within the UK based on phylogeographic analysis (Supplementary Fig. 5) and maximum likelihood phylogeny (Fig. 1b).