Siderophore-Mediated Iron Acquisition in Clostridioides difficile: A Genomic Survey of Prevalence, Phylogenetic Distribution, and Association with Clinical Hypervirulence

Abstract

Clostridioides difficile infections represent a major challenge to healthcare systems, and the acquisition of iron appears to be important for the virulence of enteric pathogens. Despite the presence of a siderophore biosynthesis gene cluster encoded by nonribosomal peptide synthetases in some C. difficile strains, little is known about the frequency of this gene cluster and whether it affects clinical outcomes. We assessed the presence of this gene cluster in 4,689 publicly available assemblies of C. difficile genomes via a BLAST pipeline and examined the relationship of the gene cluster to C. difficile phylogeny, binary toxin carriage, and clinical outcome. The siderophore gene cluster was found in 141 genomes (3.01%, 95% confidence interval 2.54–3.54%). The prevalence of this gene cluster varies between clades, with Clade 3 having the highest prevalence (36.0%) while no positive genomes were present in Clades 4 and 5, the most prevalent lineages. The siderophore biosynthesis gene cluster had no correlation with binary toxin presence (Fisher's exact p = 0.54). In a subset of 455 genomes with clinical outcome annotations, multivariable logistic regression confirmed that binary toxin carriage is the best indicator of virulence (odds ratio = 4.03, 95% confidence interval 2.56–6.33, p < 0.001) while siderophore gene cluster is not an independent predictor of hypervirulence (odds ratio = 0.132, 95% confidence interval 0.016–1.082, p = 0.059).