Characterization of pathogenic microbiome on removable prostheses with different levels of cleanliness using 2bRAD-M metagenomic sequencing.

Background: The microbiomes on the surface of unclean removable prostheses are complex and yet largely underexplored using metagenomic sequencing technology. Objectives: To characterize the microbiome of removable prostheses with different levels of cleanliness using Type IIB Restriction-site Associated DNA for Microbiome (2bRAD-M) sequencing and compare the Microbial Index of Pathogenic Bacteria (MIP) between clean and unclean prostheses. Materials and Methods: Ninety-seven removable prostheses were classified into 'clean' and 'unclean' groups. All prosthesis plaque samples underwent 2bRAD metagenomic sequencing to characterize the species-resolved microbial composition. MIPs for clean and unclean prostheses were calculated based on the sum of the relative abundance of pathogenic bacteria in a microbiome using a reference database that contains opportunistic pathogenic bacteria and disease-associated information. Results: Beta diversity analyses based on Jaccard qualitative and Bray-Curtis quantitative distance matrices identified significant differences between the two groups (p < 0.05). There was a significant enrichment of many pathogenic bacteria in the unclean prosthesis group. The MIP for unclean prostheses (0.47 ± 0.25) was significantly higher than for clean prostheses (0.37 ± 0.29), p = 0.029. Conclusions: The microbial community of plaque samples from 'unclean' prostheses demonstrated compositional differences compared with 'clean' prostheses. In addition, the pathogenic microbiome in the 'unclean' versus 'clean' group differed. KEY MESSAGES: The pathogenic microbiome in the unclean removable prosthesis group tends to be more abundant than that of the clean counterpart among participants with the majority being elders attending a teaching hospital. This finding is worrying because a general decline in systemic health among community-dwelling elders may predispose them to life-threatening diseases. By understanding the characteristics of the microbiome of removable prostheses with different levels of cleanliness and the related microbial-infection risks after a comprehensive whole metagenomic sequencing, appropriate prosthesis hygiene care should be emphasized. This study introduced a comprehensive and novel method of microbiological investigation of plaque using 2bRAD-M. The taxonomic profile of the microbiome of whole genomes was demonstrated and resolved at the species-level taxonomy for prosthesis biofilms. The biggest advantage of this method included overcoming the DNA sample problems particularly the low-biomass nature of 'clean' prosthesis plaque samples. The findings will add to our understanding of the microbiological aspect of removable prosthesis plaque. [ABSTRACT FROM AUTHOR]