Recent genomic sequencing research has revealed that individual strains of life-threatening, antibiotic-resistant bacteria and Candida auris fungi may persistently colonize human skin and spread between nursing home residents, creating a significant reservoir for transmission throughout health care systems.
In a study published in Nature, researchers, led by Diana Proctor, utilized strain-resolved metagenomics to identify the sharing of multiple pathogenic strains among nursing home residents, including multidrug-resistant bacterial pathogens and C auris. They examined skin colonization across five body sites in 42 individuals over a 3-month period, finding notable variations in colonization patterns: C auris was detected in 21% of toe webs, 19% of fingertips, 18% of nasal passages, 10% of inguinal creases, and 3% of perianal sites.
"This study presents an alarming picture in which nursing homes are a reservoir for antimicrobial resistance to first-line therapeutics, and strain sharing of these dangerous microorganisms is widespread," reported Teresa R. O'Meara, PhD, in a companion Nature News and Views article analyzing the study's implications.
The researchers found C auris colonization and at least one ESKAPE pathogen (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) on the skin of most individuals sampled. Among the ESKAPE pathogens, colonization rates were highest in the perianal region (71%) and inguinal crease (63%), with lower rates in nasal passages (58%), fingertips (26%), and toe webs (15%). This colonization persisted throughout the 3-month sampling period, indicating either persistent colonization or repeated recolonization.
The comprehensive genomic approach enabled the researchers to identify strain replacement or infection with multiple different strains of the same pathogen in some residents, whereas in other cases, there was "clear domination by a single strain shared between residents," the study authors noted. One particularly concerning finding was the spread of a single clonal genetic lineage of C auris across multiple facilities in the Chicago metropolitan area and through organ donation to a recipient in Massachusetts.
Interestingly, the study revealed specific microbial associations, with C auris frequently found alongside Staphylococcus pettenkoferi but not with P aeruginosa or species of the fungal genus Malassezia. Distinct colonization patterns emerged across body sites: bacteria that didn't require oxygen (anaerobes) were more commonly found in perianal regions and the nearby inguinal crease, while microbes able to thrive in both low and high oxygen environments (facultative anaerobes), including ESKAPE pathogens, were more prevalent on fingertips, toe webs, and nasal passages.
Genes conferring resistance to carbapenem antibiotics were detected on the skin "even months after clinical testing initially detected signs of microbes that have this sort of drug resistance," the study authors stressed, indicating persistent or repeated colonization by drug-resistant pathogens. This genetic signature was present across body sites, not just in perianal regions.
The researchers noted that despite sequence similarity between clonal strains, their clinical characteristics might still vary significantly. Many drug-resistant C auris strains arise from single nucleotide changes in genes needed to produce ergosterol, a component of the fungal cell membrane, highlighting how minor genetic variations can have major clinical implications.
"Future work on these transmission dynamics will be crucial for developing targeted efforts to prevent infection to avoid spreading these drug-resistant pathogens throughout health care systems," Dr. O'Meara noted.
The findings suggested that nursing homes, particularly those providing short-term intensive care rather than long-term care, may serve as important reservoirs for antimicrobial resistance and pathogen transmission within health care networks.
The author declared no competing interests.