Comprehensive compositional analysis of the slit lamp bacteriota. Slit lamp bacteriota at two clinical sites in Germany

Regularly touched surfaces usually represent fomites, particularly if used by different persons. In eye clinics, slit lamps are routinely used to examine large numbers of patients every day. Previous, cultivation-based results suggested slit lamps to be contaminated with bacteria, mostly coagulase-negative staphylococci, followed by micrococci, bacilli, but also Staphylococcus aureus. To obtain a comprehensive, cultivation-independent view of the community profile and its hygienic relevance, we performed extensive 16S rRNA gene sequencing of the slit lamp bacteriota. We analysed 46 slit lamps from two different German university hospitals (Freiburg, Tuebingen) at two sampling sites, respectively. 82 samples yielded enough sequences for downstream analyses and revealed contamination with bacteria of mostly human skin, mucosa and probably eye origin, predominantly cutibacteria, staphylococci and corynebacteria. The taxonomic assignment of 3369 ASVs (amplicon sequence variants) revealed 19 bacterial phyla and 468 genera across all samples. As antibiotic resistances are of major concern, we screened all samples for Methicillin-resistant Staphylococcus aureus (MRSA) using qPCR, however, no signals above the detection limit were detected. Our study provides first comprehensive insight into the slit lamp microbiota. It underlines that slit lamps carry a highly diverse, skin-like bacterial microbiota and that thorough cleaning and disinfection after use is highly recommendable to prevent eye and skin infections.