Candida auris and the great ESKAPE: the skin as a reservoir for multi-drug resistance and transmission

Background: Candida auris is an emerging fungal pathogen of urgent concern due to its ability to cause healthcare-associated infections and outbreaks, its resistance to antimicrobials and disinfectants and its persistence on human skin and in the environment. Early genome sequencing of surveillance isolates indicates that C. auris exhibits limited genomic diversity within an outbreak.

Methods: We sought to identify transmission patterns of C. auris in a skilled nursing facility with high prevalence of C. auris asymptomatic colonization. Our clinical study leveraged patient trace data, medication history and clinical microbiology findings for 36 residents who underwent serial sample collection monthly over 3 months. To quantify the genomic diversity of C. auris colonizing a patient, we integrated sequencing of 75 isolates (175 Gb total) with plate metagenomics of original culture plates (N=28; 6.4Gb), permitting the analysis of tens to thousands of C. auris isolates per patient. Complementing isolate analyses, shotgun metagenomic sequencing of 210 skin, nasal, and perianal samples (3.2 Tb total) was used for metagenome assembled genome (MAG) and read-based analyses to assess strain sharing of C. auris and ESKAPE (Escherichia coli, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp.) pathogens in this facility. To assess the generalizability of our findings, we then analyzed over 1,300 publicly available shotgun metagenomic sequencing samples (stool, skin) collected from patients in 7 other facilities.

Results: Fewer than 300 single nucleotide polymorphisms (SNPs) separated C. auris isolates from this facility and the first isolate identified in the Chicago region, which was collected 3 years earlier. On average, 5 SNPs separated C. auris isolates collected from the same individual with 7-28 SNPs private to each subject, suggesting limited personalized diversification of clones. Strikingly, from these 210 shotgun metagenomic samples, we recovered >5X coverage of the C. auris genome from 22 samples, enabling independent estimates of genomic diversity. In addition, we recovered metagenome-assembled-genomes (MAGs) for all ESKAPE pathogens (16 E.coli, 1 S. aureus, 21 A. baumannii, 39 K. pneumoniae, 37 P. aeruginosa, 2 E. faecalis MAGs), and species previously shown to correlate with C. auris relative abundance, including Staphylococcus pettenkoferi (N=42), Providencia stuartti (N=62), and Proteus mirabilis (N=60). Importantly, MAGs for these species had depth > 5X and fraction aligned > 75% (median 86.22%), suggesting strain tracking could be deployed. Incorporating Refseq genomes into phylogenetic trees of MAG single copy marker genes (N=169) and subsequent sequence typing (ST) suggested clonal separation of each pathogen within the facility. Moreover, SNP-based analyses implicated either undetected transmission of ESKAPE pathogens within the facility or very recent acquisition prior to facility admission. For example, only 0-46 SNPs separated the 39 K. pneumoniae MAGs (mean=8.4) with 2 clusters each reaching >99.9% average nucleotide identity (ANI). Intriguingly, even the commensal S. pettenkoferi MAGs (N=42) clustered together in one group at >99.9% ANI, separated by just 0-32 SNPs. Analysis of publicly available metagenomes revealed clonal spread on skin of S. pettenkoferi in 4 other facilities and widespread sharing of E. coli ST131 across virtually all nursing homes. Taken together, our data suggest the skin is a reservoir for ESKAPE pathogens and that it may potentially serve as a reservoir for their transmission.