Analysis of the resistome of the microbiota contaminating hospital surfaces: modulation by a sanitizing probiotic-based intervention

Introduction The growing drug resistance (R) of pathogens is a global concern, thus it is important to set up methods able to detect R onset in a sensitive and fast way. Recently, we were involved in the study of a new approach for sanitization, based on cleansers containing spores of some probiotic Bacillus strains, which is now used by several hospitals in Italy and Europe, as it was shown able to induce a drop of several pathogens on hospital surfaces [1]. Here, we wanted to analyze the R features of the microbial population persistently contaminating hospital surfaces, in order to evidence any variation in its resistome upon use of probiotic cleansers. In parallel, we evaluated the genetic stability of the probiotic Bacilli contained in the cleansers, and their eventual potential to infect hospitalized patients. Materials and Methods Both surface microbial population and cleanser Bacilli were analyzed by a real-time PCR microarray, capable of evidencing and quantifying simultaneously 84 different R genes (sensitivity ~ 10 copies/reaction). Each molecularly evidenced R was confirmed by conventional antibiograms. In parallel, all the clinical samples derived from the patients admitted to the hospitals enrolled in the study were analyzed for the presence of Bacillus strains, by conventional microbiology or by specific real time PCR. Results Results showed that: 1) microarray analyses allow to detect small traces of R genes in a contaminating population, otherwise not detectable; 2) detected R genes correspond to actual drug R when tested by antibiograms; 3) Bacilli-based cleansers did not select R species, but conversely induced a strong decrease of R genes in the resistome of the original contaminating population; 4) probiotic-Bacilli did not acquire/transfer R genes to surface pathogens, even after prolonged continuous contact on treated surfaces. Furthermore, probiotic Bacilli were never detected in biological fluids of patients hosted in the treated areas, and no HAIs attributable to Bacilli were detected in 4 years of continuous use of probiotic cleansers. Conclusions The results suggest that molecular assays can represent a very fast, precise and reliable tool to monitor the drug R features of a microbial population. By this method, we were able to evidence that probiotic-based sanitation can modulate the resistome of the contaminating population, decreasing the original drug R, without acquiring or transferring new R genes. Also, both molecular and microbiological analyses performed on clinical samples suggest that probiotic Bacilli rarely or at all can cause infections, even following continuous contact with subjects at higher risk for adverse events, such as hospitalized patients.