16S Rrna-Based Metagenomic Profiling of Microbes on Contact Surfaces Within Shared Sanitation Facilities

Contact surfaces within shared sanitation facilities could lead to disease transmission due to contamination. In this study, we applied metagenomics, by targeting the 16S rRNA gene region using illumina sequencing to determine the common bacterial communities on key contact surfaces in shared sanitation facilities within a metropolitan area. The common bacterial phyla identified on these surfaces were Actinobacteria, Firmicutes, Proteobacteria and Bacteroidetes, with average counts up to 12 Log10 and a prevalence of 100% for each of these phyla. Known diarrhoeal pathogens like, Salmonella enterica, Bacillus cereus, Campylobacter jejuni, Campylobacter coli, Yersinia pestis, Yersinia pseudotuberculosis, Vibrio cholerae, Vibrio parahaemolyticus and Vibrio vulnificus were detected on almost all surfaces. Cistern handles, tap handles and toilet seats had the highest number of potentially pathogenic bacteria, such as S. enterica. Additionally, uncommon and very rarely pathogenic bacteria such as Cedecea neteri, Enterobacter hormaechei, Klebsiella michiganensis, Pluralibacter gergoviae, Kosakonia cowanii and Raoultella ornithinolytica were also detected. Many of these can be considered as environmental commensals. These results show that contact surfaces within shared sanitation facilities could have been contaminated with faecal matter as well as soil. In conclusion, being the first study to apply metagenomics in profiling bacterial communities on contact surfaces in shared sanitation facilities in South Africa, it shows the potential of disease transmission via the use of these shared facilities. Additionally, the results also show the application of 16S rRNA-based metagenomics in determining the potential role of shared sanitation in disease transmission.