An Innovative Strategy for the Effective Reduction of MDR Pathogens from the Nosocomial Environment

Profiling the resistome and virulome of Bacillus strains used for probiotic-based sanitation: a multicenter WGS analysis

BACKGROUND

Healthcare-associated infections (HAIs) caused by microbes that acquire antimicrobial resistance (AMR) represent an increasing threat to human health worldwide. The high use of chemical disinfectants aimed at reducing the presence of pathogens in the hospital environment can simultaneously favor the selection of resistant strains, potentially worsening AMR concerns. In the search for sustainable ways to control bioburden without affecting this aspect, probiotic-based sanitation (PBS) using Bacillus spp. was proposed to achieve stable reduction of pathogens, AMR, and associated HAIs. Although Bacillus probiotics are classified as nonpathogenic, comprehensive data about the potential genetic alterations of these probiotics following prolonged contact with surrounding pathogens are not yet available. This study aimed to assess in depth the genetic content of PBS-Bacillus isolates to evaluate any eventual variations that occurred during their usage.

RESULTS

WGS analysis was used for the precise identification of PBS-Bacillus species and detailed profiling of their SNPs, resistome, virulome, and mobilome. Analyses were conducted on both the original PBS detergent and 172 environmental isolates from eight hospitals sanitized with PBS over a 30-month period. The two species B. subtilis and B. velezensis were identified in both the original product and the hospital environment, and SNP analysis revealed the presence of two clusters in each species. No virulence/resistance genes or mobile conjugative plasmids were detected in either the original PBS-Bacillus strain or any of the analyzed environmental isolates, confirming their high genetic stability and their low/no tendency to be involved in horizontal gene transfer events.

CONCLUSIONS

The data obtained by metagenomic analysis revealed the absence of genetic sequences associated with PBS-Bacillus and the lack of alterations in all the environmental isolates analyzed, despite their continuous contact with surrounding pathogens. These results support the safety of the Bacillus species analyzed. Further metagenomic studies aimed at profiling the whole genomes of these and other species of Bacillus, possibly during longer periods and under stress conditions, would be of interest since they may provide further confirmation of their stability and safety.

A Sustainable Combined Approach to Control the Microbial Bioburden in the School Environment

The indoor microbiome is a dynamic ecosystem including pathogens that can impact human health. In this regard, the school environment represents the main living space of humans for many years, and an unhealthy environment can significantly condition students' health. School rooms can suffer from insufficient ventilation and the use of building materials that may favor pathogen contamination, mostly sanitized by conventional chemical-based methods, which can impact pollution, have temporary effects, and induce the selection of antimicrobial resistance (AMR) in persistent microbes. In the search for sustainable and effective methods to improve the healthiness of the classroom environment, a pre-post case-control study was performed in an Italian high school. Over a year, different interventions were sequentially placed and evaluated for their impact on bioburden and air quality, including the introduction of plants, a mechanical ventilation system, and probiotic-based sanitation (PBS) in substitution for chemical sanitation. Through continuous microbial monitoring of the enrolled school rooms, via culture-dependent and -independent methods, a remarkable bioburden level was detected at baseline (around 12,000 and 20,000 CFU/m2, before and after classes, respectively), composed mostly of Staphylococcus spp. and fungi. Some decrease in fungal contamination was observed following the introduction of plants. Still, the most significant decrease in pathogens and associated AMR was detected following the introduction of ventilation and PBS, which decreased pathogen level by >80% (p < 0.001) and AMR by up to 3 Log10 (p < 0.001) compared to controls. Collected data support the use of combined strategies to improve indoor microbial quality and confirm that PBS can effectively control bioburden and AMR spread not only in sanitary environments.

Can probiotics trigger a paradigm shift for cleaning healthcare environments? A narrative review

BACKGROUND

The environment of healthcare institutions plays a major role in the transmission of multidrug resistant organisms (MDRO) and likely in subsequent healthcare-associated infections (HAIs). Probiotic cleaning products are a novel option for environmental cleaning. They represent a sustainable and biodegradable alternative to conventional chemical disinfectants for controlling microbial bioburden, and preventing pathogen transmission in hospital environments. High-quality studies including randomized clinical trials (RCT) triggered a summary with expert recommendations until further studies allow a critical review and meta-analysis of the data.

METHODS

Infection control experts from five European countries summarized available data as of June 2023. Authors presented their published RCTs, reviewed the existing literature on probiotic cleaning, summarized the results and identified knowledge gaps and subsequent research needs.

RESULTS

Probiotic cleaning was similarly effective for reducing HAI-related pathogens, enveloped viruses such as SARS-CoV-2 and MDRO in environmental samples compared to conventional chemical disinfectants. More importantly, probiotic cleaning was non-inferior to disinfectants in terms of preventing HAI in a large RCT. In addition, probiotic cleaning has also been shown to reduce antimicrobial resistance genes (ARG), costs and antimicrobial consumption in other hospital trials. They are biodegradable, do not require any protection for chemical hazards, and are compliant with occupational health. A paradigm shift, however, requires a very strong evidence to justify for such a change. In the past, this evidence was limited by the heterogeneity of study design, products, protocols, and few studies on clinical outcomes used in the trials. Furthermore, the regulatory, safety, and quality aspects of probiotic cleaning products are not, yet, completely defined and require clearing by authorities.

CONCLUSION

To date, probiotic cleaning is a breakthrough technology and a biological alternative for chemical disinfectant when treating hospital environment. It may also have a positive effect on MDRO transmission. However, the different compositions of probiotic products will require standardization, and more robust data should be generated to support these promising results on different compositions. This may trigger a paradigm shift in cleaning of healthcare institutions from chemical to biological control of the hospital environment.

Tackling transmission of infectious diseases: A probiotic-based system as a remedy for the spread of pathogenic and resistant microbes

Built environments (BEs) currently represent the areas in which human beings spend most of their life. Consistently, microbes populating BEs mostly derive from human occupants and can be easily transferred from BE to occupants. The hospital microbiome is a paradigmatic example, representing a reservoir for harmful pathogens that can be transmitted to susceptible patients, causing the healthcare-associated infections (HAIs). Environmental cleaning is a crucial pillar in controlling BE pathogens and preventing related infections, and chemical disinfectants have been largely used so far towards this aim. However, despite their immediate effect, chemical-based disinfection is unable to prevent recontamination, has a high environmental impact, and can select/increase antimicrobial resistance (AMR) in treated microbes. To overcome these limitations, probiotic-based sanitation (PBS) strategies were recently proposed, built on the use of detergents added with selected probiotics able to displace surrounding pathogens by competitive exclusion. PBS was reported as an effective and low-impact alternative to chemical disinfection, providing stable rebalance of the BE microbiome and significantly reducing pathogens and HAIs compared to disinfectants, without exacerbating AMR and pollution concerns. This minireview summarizes the most significant results obtained by applying PBS in sanitary and non-sanitary settings, which overall suggest that PBS may effectively tackle the infectious risk meanwhile preventing the further spread of pathogenic and resistant microbes.

Biocontrol in built environments to reduce pathogen exposure and infection risk

The microbiome of the built environment comprises bacterial, archaeal, fungal, and viral communities associated with human-made structures. Even though most of these microbes are benign, antibiotic-resistant pathogens can colonize and emerge indoors, creating infection risk through surface transmission or inhalation. Several studies have catalogued the microbial composition and ecology in different built environment types. These have informed in vitro studies that seek to replicate the physicochemical features that promote pathogenic survival and transmission, ultimately facilitating the development and validation of intervention techniques used to reduce pathogen accumulation. Such interventions include using Bacillus-based cleaning products on surfaces or integrating bacilli into printable materials. Though this work is in its infancy, early research suggests the potential to use microbial biocontrol to reduce hospital- and home-acquired multidrug-resistant infections. Although these techniques hold promise, there is an urgent need to better understand the microbial ecology of built environments and to determine how these biocontrol solutions alter species interactions. This review covers our current understanding of microbial ecology of the built environment and proposes strategies to translate that knowledge into effective biocontrol of antibiotic-resistant pathogens.

Characterization of the Pathogenic Potential of the Beach Sand Microbiome and Assessment of Quicklime as a Remediation Tool

Beach sand may act as a reservoir for potential human pathogens, posing a public health risk. Despite this, the microbiological monitoring of sand microbiome is rarely performed to determine beach quality. In this study, the sand microbial population of a Northern Adriatic Sea beach sand was profiled by microbiological (CFU counts) and molecular methods (WGS, microarray), showing significant presence of potential human pathogens including drug-resistant strains. Consistent with these results, the potential of quicklime as a restoring method was tested in vitro and on-field. Collected data showed that adding 1-3% quicklime (w/w) to sand provided an up to -99% of bacteria, fungi, and viruses, in a dose- and time-dependent manner, till 45 days post-treatment. In conclusion, data suggest that accurate monitoring of sand microbiome may be essential, besides water, to assess beach quality and safety. Moreover, first evidences of quicklime potential for sand decontamination are provided, suggesting its usage as a possible way to restore the microbiological quality of sand in highly contaminated areas.

Bacteriophages in Infectious Diseases and Beyond-A Narrative Review

The discovery of antibiotics has revolutionized medicine and has changed medical practice, enabling successful fighting of infection. However, quickly after the start of the antibiotic era, therapeutics for infectious diseases started having limitations due to the development of antimicrobial resistance. Since the antibiotic pipeline has largely slowed down, with few new compounds being produced in the last decades and with most of them belonging to already-existing classes, the discovery of new ways to treat pathogens that are resistant to antibiotics is becoming an urgent need. To that end, bacteriophages (phages), which are already used in some countries in agriculture, aquaculture, food safety, and wastewater plant treatments, could be also used in clinical practice against bacterial pathogens. Their discovery one century ago was followed by some clinical studies that showed optimistic results that were limited, however, by some notable obstacles. However, the rise of antibiotics during the next decades left phage research in an inactive status. In the last decades, new studies on phages have shown encouraging results in animals. Hence, further studies in humans are needed to confirm their potential for effective and safe treatment in cases where there are few or no other viable therapeutic options. This study reviews the biology and applications of phages for medical and non-medical uses in a narrative manner.

ESKAPEE Pathogen Biofilm Control on Surfaces with Probiotic Lactobacillaceae and Bacillus species

Combatting the rapidly growing threat of antimicrobial resistance and reducing prevalence and transmission of ESKAPEE pathogens in healthcare settings requires innovative strategies, one of which is displacing these pathogens using beneficial microorganisms. Our review comprehensively examines the evidence of probiotic bacteria displacing ESKAPEE pathogens, with a focus on inanimate surfaces. A systematic search was conducted using the PubMed and Web of Science databases on 21 December 2021, and 143 studies were identified examining the effects of Lactobacillaceae and Bacillus spp. cells and products on the growth, colonization, and survival of ESKAPEE pathogens. While the diversity of study methods limits evidence analysis, results presented by narrative synthesis demonstrate that several species have the potential as cells or their products or supernatants to displace nosocomial infection-causing organisms in a variety of in vitro and in vivo settings. Our review aims to aid the development of new promising approaches to control pathogen biofilms in medical settings by informing researchers and policymakers about the potential of probiotics to combat nosocomial infections. More targeted studies are needed to assess safety and efficacy of different probiotic formulations, followed by large-scale studies to assess utility in infection control and medical practice.

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

Microbial contamination in the hospital environment is a major concern for public health, since it significantly contributes to the onset of healthcare-associated infections (HAIs), which are further complicated by the alarming level of antimicrobial resistance (AMR) of HAI-associated pathogens. Chemical disinfection to control bioburden has a temporary effect and can favor the selection of resistant pathogens, as observed during the COVID-19 pandemic. Instead, probiotic-based sanitation (probiotic cleaning hygiene system, PCHS) was reported to stably abate pathogens, AMR, and HAIs. PCHS action is not rapid nor specific, being based on competitive exclusion, but the addition of lytic bacteriophages that quickly and specifically kill selected bacteria was shown to improve PCHS effectiveness. This study aimed to investigate the effect of such combined probiotic–phage sanitation (PCHSφ) in two Italian hospitals, targeting staphylococcal contamination. The results showed that PCHSφ could provide a significantly higher removal of staphylococci, including resistant strains, compared with disinfectants (−76%, p < 0.05) and PCHS alone (−50%, p < 0.05). Extraordinary sporadic chlorine disinfection appeared compatible with PCHSφ, while frequent routine chlorine usage inactivated the probiotic/phage components, preventing PCHSφ action. The collected data highlight the potential of a biological sanitation for better control of the infectious risk in healthcare facilities, without worsening pollution and AMR concerns.

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

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. Video Abstract.

Next-generation sequencing and PCR technologies in monitoring the hospital microbiome and its drug resistance

The hospital environment significantly contributes to the onset of healthcare-associated infections (HAIs), which represent one of the most frequent complications occurring in healthcare facilities worldwide. Moreover, the increased antimicrobial resistance (AMR) characterizing HAI-associated microbes is one of the human health’s main concerns, requiring the characterization of the contaminating microbial population in the hospital environment. The monitoring of surface microbiota in hospitals is generally addressed by microbial cultural isolation. However, this has some important limitations mainly relating to the inability to define the whole drug-resistance profile of the contaminating microbiota and to the long time period required to obtain the results. Hence, there is an urgent need to implement environmental surveillance systems using more effective methods. Molecular approaches, including next-generation sequencing and PCR assays, may be useful and effective tools to monitor microbial contamination, especially the growing AMR of HAI-associated pathogens. Herein, we summarize the results of our recent studies using culture-based and molecular analyses in 12 hospitals for adults and children over a 5-year period, highlighting the advantages and disadvantages of the techniques used.

Introduction of Probiotic-Based Sanitation in the Emergency Ward of a Children’s Hospital During the COVID-19 Pandemic

Background

Antimicrobial resistance (AMR) represents a major threat to public health, especially in the hospital environment, and the massive use of disinfectants to prevent COVID-19 transmission might intensify this risk, possibly leading to future AMR pandemics. However, the control of microbial contamination is crucial in hospitals, since hospital microbiomes can cause healthcare-associated infections (HAIs), which are particularly frequent and severe in pediatric wards due to children having high susceptibility.

Aim

We have previously reported that probiotic-based sanitation (PCHS) could stably decrease pathogens and their AMR in the hospital environment, reduce associated HAIs in adult hospitals, and inactivate enveloped viruses. Here, we aimed to test the effect of PCHS in the emergency room (ER) of a children’s hospital during the COVID-19 pandemic.

Methods

Conventional chemical disinfection was replaced by PCHS for 2 months during routine ER sanitation; the level of environmental bioburden was characterized before and at 2, 4, and 9 weeks after the introduction of PCHS. Microbial contamination was monitored simultaneously by conventional culture-based CFU count and molecular assays, including 16S rRNA NGS for bacteriome characterization and microarrays for the assessment of the resistome of the contaminating population. The presence of SARS-CoV-2 was also monitored by PCR.

Results and conclusions

PCHS usage was associated with a stable 80% decrease in surface pathogens compared to levels detected for chemical disinfection (P < 0.01), accompanied by an up to 2 log decrease in resistance genes (Pc < 0.01). The effects were reversed when reintroducing chemical disinfection, which counteracted the action of the PCHS. SARS-CoV-2 was not detectable in both the pre-PCHS and PCHS periods. As the control of microbial contamination is a major issue, especially during pandemic emergencies, collected data suggest that PCHS may be successfully used to control virus spread without simultaneous worsening of the AMR concern.

Pathogen Control in the Built Environment: A Probiotic-Based System as a Remedy for the Spread of Antibiotic Resistance

The high and sometimes inappropriate use of disinfectants and antibiotics has led to alarming levels of Antimicrobial Resistance (AMR) and to high water and hearth pollution, which today represent major threats for public health. Furthermore, the current SARS-CoV-2 pandemic has deeply influenced our sanitization habits, imposing the massive use of chemical disinfectants potentially exacerbating both concerns. Moreover, super-sanitation can profoundly influence the environmental microbiome, potentially resulting counterproductive when trying to stably eliminate pathogens. Instead, environmentally friendly procedures based on microbiome balance principles, similar to what applied to living organisms, may be more effective, and probiotic-based eco-friendly sanitation has been consistently reported to provide stable reduction of both pathogens and AMR in treated-environments, compared to chemical disinfectants. Here, we summarize the results of the studies performed in healthcare settings, suggesting that such an approach may be applied successfully also to non-healthcare environments, including the domestic ones, based on its effectiveness, safety, and negligible environmental impact.

Potential of an Eco-Sustainable Probiotic-Cleaning Formulation in Reducing Infectivity of Enveloped Viruses

The COVID-19 pandemic has deeply influenced sanitization procedures, and high-level disinfection has been massively used to prevent SARS-CoV-2 spread, with potential negative impact on the environment and on the threat of antimicrobial resistance (AMR). Aiming to overcome these concerns, yet preserving the effectiveness of sanitization against enveloped viruses, we assessed the antiviral properties of the Probiotic Cleaning Hygiene System (PCHS), an eco-sustainable probiotic-based detergent previously proven to stably abate pathogen contamination and AMR. PCHS (diluted 1:10, 1:50 and 1:100) was tested in comparison to common disinfectants (70% ethanol and 0.5% sodium hypochlorite), in suspension and carrier tests, according with the European UNI EN 14476:2019 and UNI EN 16777:2019 standards. Human alpha- and beta-coronaviruses hCoV-229E and SARS-CoV-2, human herpesvirus type 1, human and animal influenza viruses, and vaccinia virus were included in the study. The results showed that PCHS was able to inactivate 99.99% of all tested viruses within 1-2 h of contact, both in suspension and on surface. Notably, while control disinfectants became inactive within 2 h after application, the PCHS antiviral action persisted up to 24 h post-application, suggesting that its use may effectively allow a continuous prevention of virus spread via contaminated environment, without worsening environmental pollution and AMR concern.

Targeted Molecular Detection of Nosocomial Carbapenemase-Producing Gram-Negative Bacteria-On Near- and Distant-Patient Surfaces

Background: Here, we describe an integrative method to detect carbapenemase-producing Gram-negative bacteria (gn-Cp) on surfaces/fomites in the patient environment. We examined environmental samples from 28 patient rooms occupied with patients who were proven to be colonised with gn-Cp by rectal screening. Methods: We took samples after 24 h, 72 h and one week. For sampling, we divided the patient environment into four parts and took samples from near- and extended patient areas. To obtain a representative bacterial swab from a larger surface, such as the patient cabinet, we used Polywipes. Bacterial DNA was isolated. Carbapenemase was detected with specific qPCR primers. Results: With this culture- and molecular-based approach, we could control the effectiveness of cleaning and disinfection in everyday clinical practice. Therefore, we could track the spread of gn-Cp within the patient room. The number of positive detections fluctuated between 30.5% (mean value positive results after 72 h) and 35.2% (after 24 h and one week). Conclusion: The method used to detect multidrug-resistant bacteria in the environment of patients by using Polywipes^TM is reliable and can therefore be used as an effective, new tool in hygiene and infection control.

Bacterial survival on inanimate surfaces: a field study

OBJECTIVE

Environmental surfaces may serve as potential reservoirs for nosocomial pathogens and facilitate transmissions via contact depending on its tenacity. This study provides data on survival kinetics of the most important nosocomial bacteria on a panel of commonly used surfaces. Type strains of S. aureus, K. pneumoniae, P. aeruginosa, A. baumannii, S. marcescens, E. faecium, E. coli, and E. cloacae were suspended in 0.9% NaCl solution at a McFarland of 1 and got then plated via cotton swabs either on glass, polyvinyl chloride, stainless steel, or aluminum. Surfaces were stored at regular ambient temperature and humidity to simulate routine daycare conditions. Sampling was performed by contact plates for a time period of four weeks.

RESULTS

The longest survival was observed for A. baumannii and E. faecium on all materials (at least four weeks). S. aureus remained viable for at least one week. Gram negative species other than A. baumannii were usually inactivated in less than two days. Nosocomial transmission of the above mentioned bacteria may easily occur if no appropriate infection control measures are applied on a regular daily basis. This might be of particular importance when dealing with outbreaks of A. baumannii and E. faecium.

Bacteriophages as a Potential 360-Degree Pathogen Control Strategy

Bacteriophages are viruses that exclusively kill bacteria and are the most ubiquitous organisms on the planet. Since their discovery, bacteriophages have been considered an important weapon to fight human and animal infections of bacterial origin due to their specific ability to attack the associated target bacteria. With the discovery of antibiotics, phage treatment was progressively abandoned in Western countries. However, due to the recent emergence of growing antimicrobial resistance (AMR) to antibiotics, interest in phage use in human therapy has once again grown. Similarly, at the environmental level, the extensive use of disinfectants based on chemicals, including biocides in agriculture, has been associated with the emergence of resistance against disinfectants themselves, besides having a high environmental impact. Due to these issues, the applications of phages with biocontrol purposes have become an interesting option in several fields, including farms, food industry, agriculture, aquaculture and wastewater plants. Notably, phage action is maintained even when the target bacteria are multidrug resistant (MDR), rendering this option extremely interesting in counteracting AMR emergence both for therapeutical and decontamination purposes. Based on this, bacteriophages have been interestingly proposed as environmental routine sanitizers in hospitals, to counteract the spread of the pathogenic MDR bacteria that persistently contaminate hard surfaces. This review summarizes the studies aimed at evaluating the potential use of phages as decontaminants, with a special focus on hospital sanitation.