Shaping the subway microbiome through probiotic-based sanitation during the COVID-19 emergency: a pre–post case–control study

Abstract

Background The COVID-19 pandemic has highlighted the extent to which the public transportation environment, such as in subways, may be important for the transmission of potential pathogenic microbes among humans, with the possibility of rapidly impacting large numbers of people. For these reasons, sanitation procedures, including massive use of chemical disinfection, were mandatorily introduced during the emergency and remain in place. However, most chemical disinfectants have temporary action and a high environmental impact, potentially enhancing antimicrobial resistance (AMR) of the treated microbes. By contrast, a biological and eco-sustainable probiotic-based sanitation (PBS) procedure was recently shown to stably shape the microbiome of treated environments, providing effective and long-term control of pathogens and AMR spread in addition to activity against SARS-CoV-2, the causative agent of COVID-19. Our study aims to assess the applicability and impact of PBS compared with chemical disinfectants based on their effects on the surface microbiome of a subway environment. Results The train microbiome was characterized by both culture-based and culture-independent molecular methods, including 16S rRNA NGS and real-time qPCR microarray, for profiling the train bacteriome and its resistome and to identify and quantify specific human pathogens. SARS-CoV-2 presence was also assessed in parallel using digital droplet PCR. The results showed a clear and significant decrease in bacterial and fungal pathogens (p < 0.001) as well as of SARS-CoV-2 presence (p < 0.01), in the PBS-treated train compared with the chemically disinfected control train. In addition, NGS profiling evidenced diverse clusters in the population of air vs. surface while demonstrating the specific action of PBS against pathogens rather than the entire train bacteriome. Conclusions The data presented here provide the first direct assessment of the impact of different sanitation procedures on the subway microbiome, allowing a better understanding of its composition and dynamics and showing that a biological sanitation approach may be highly effective in counteracting pathogens and AMR spread in our increasingly urbanized and interconnected environment.

Probiotic-Based Sanitation in the Built Environment—An Alternative to Chemical Disinfectants

“…PBS application led to a nearly 60% reduction in the surface and air pathogen burden within 2 weeks, and to a complete abatement of pathogens by the end of the 12-week study. In contrast, the application of chemical disinfectants was not associated with a reduction in pathogen numbers at any time point during the study [75]. Similarly to PBS use in hospital environments, the reduction in the pathogen burden was associated with a concomitant decrease in the detection of AMR genes.…”

“…Notably, while COVID-positive adult and pediatric patients were admitted throughout the study, no positive SARS-CoV-2 surface samples were detected with chemical disinfectant use or PBS use [77]. Despite these overwhelmingly positive results in the hospital environment, the first, and to our knowledge, the only study to-date assessing the impact of Bacillus-based PBS in non-healthcare public BEs was recently conducted in an Italian subway system [75]. PBS application led to a nearly 60% reduction in the surface and air pathogen burden within 2 weeks, and to a complete abatement of pathogens by the end of the 12-week study.…”

“…Similarly to PBS use in hospital environments, the reduction in the pathogen burden was associated with a concomitant decrease in the detection of AMR genes. Importantly, a significant decrease in SARS-CoV-2 positive samples were detected in the PBS-treated train, as compared to the train treated with chemical disinfectants [75]. While the size and scope of these studies are limited, taken together the data suggests that PBS is effective in limiting the spread of SARS-CoV-2, and recognizes PBS as a promising, safe, highly effective and eco-sustainable alternative to chemical disinfectants.…”

“…Yet, in the past decade, there have been fewer than twenty published peer-reviewed studies investigating the efficacy of PBS in practice (Table 1). Many of these in situ studies were conducted in European hospitals and healthcare settings and used the patented Bacillus-based probiotic cleaning and hygiene system developed by Copma (Ferrara, Italy) [8,69,[71][72][73][74][75][76][77]. All studies identified in Table 1 compared the effectiveness of PBS to conventional chemical disinfectants.…”

Potential Use of a Combined Bacteriophage–Probiotic Sanitation System to Control Microbial Contamination and AMR in Healthcare Settings: A Pre-Post Intervention Study

“…In fact, when examining the number of extraordinary 3% NaClO disinfections performed in the study period, a clear-cut difference emerges in the frequency of such disinfections, with the HS-2 setting showing a very frequent usage of this procedure compared with the sporadic use of emergency disinfection in HS-1. This is crucial, since while PCHS is compatible with some disinfectants (including ethanol) [ 48 ], we already observed in previous studies that the effect of PCHS was reversed by the simultaneous daily use of bactericidal/sporicidal chemical disinfection [ 49 ]. This is related to the mechanism of PCHS action, which is exerted by the vegetative forms of the Bacillus spores contained in the PCHS product that germinate on treated surfaces [ 20 , 22 , 23 ].…”