Microbial biogeography of public restroom surfaces

A case study showing highly traceable sources of bacteria on surfaces of university buildings

University students predominantly spend their time indoors, where prolonged exposure raises the risk of contact with microorganisms of concern. However, our knowledge about the microbial community characteristics on university campus and their underpinnings is limited. To address it, we characterized bacterial communities from the surfaces of various built environments typical of a university campus, including cafeterias, classrooms, dormitories, offices, meeting rooms, and restrooms, in addition to human skin. The classrooms harbored the highest α-diversity, while the cafeterias had the lowest α-diversity. The bacterial community composition varied significantly across different building types. Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, and Cyanobacteria were common phyla in university buildings, accounting for more than 90 % of total abundance. Staphylococcus aureus was the most abundant potential pathogen in classrooms, dormitories, offices, restrooms, and on human skin, indicating a potential risk for skin disease infections in these buildings. We further developed a new quantitative pathogenic risk assessment method according to the threat of pathogens to humans and found that classrooms exhibited the highest potential risk. The fast expectation-maximization algorithm identified 59 %-86 % of bacterial sources in buildings, with the human skin as the largest bacterial source for most buildings. As the sources of bacteria were highly traceable, we showed that homogeneous selection, dispersal limitation, and ecological drift were major ecological forces that drove community assembly. Our findings have important implications for predicting the distribution and sources of indoor dust bacterial communities on university campus.

Forensic Microbiology: When, Where and How

Forensic microbiology is a relatively new discipline, born in part thanks to the development of advanced methodologies for the detection, identification and characterization of microorganisms, and also in relation to the growing impact of infectious diseases of iatrogenic origin. Indeed, the increased application of medical practices, such as transplants, which require immunosuppressive treatments, and the growing demand for prosthetic installations, associated with an increasing threat of antimicrobial resistance, have led to a rise in the number of infections of iatrogenic origin, which entails important medico-legal issues. On the other hand, the possibility of detecting minimal amounts of microorganisms, even in the form of residual traces (e.g., their nucleic acids), and of obtaining gene and genomic sequences at contained costs, has made it possible to ask new questions of whether cases of death or illness might have a microbiological origin, with the possibility of also tracing the origin of the microorganisms involved and reconstructing the chain of contagion. In addition to the more obvious applications, such as those mentioned above related to the origin of iatrogenic infections, or to possible cases of infections not properly diagnosed and treated, a less obvious application of forensic microbiology concerns its use in cases of violence or violent death, where the characterization of the microorganisms can contribute to the reconstruction of the case. Finally, paleomicrobiology, e.g., the reconstruction and characterization of microorganisms in historical or even archaeological remnants, can be considered as a sister discipline of forensic microbiology. In this article, we will review these different aspects and applications of forensic microbiology.

Surveillance of Bacterial Load and Multidrug-Resistant Bacteria on Surfaces of Public Restrooms

Public restrooms are often a hub of microbial contamination and the examination of bacterial contamination in these facilities can serve as an important indicator of the transmission of infectious diseases. This study was conducted to determine the prevalence of bacterial contamination in public restrooms based on the economic class of the building. Samples were collected from various spots in 32 restrooms found in 10 shopping malls, classifying them into two categories: upper-end restrooms and lower-end restrooms. The findings showed that the level of contamination was higher in the lower-end restrooms, with the seat being the most contaminated area. The most dominant Gram-positive bacteria were of the coagulase-negative staphylococci species, making up 86% of the identified Gram-positive isolates. The most dominant Gram-negative bacteria identified were Klebsiella pneumoniae (K. pneumoniae) and Pseudomonas aeruginosa (P. aeruginosa). The antibiotic sensitivity test results revealed the presence of multidrug-resistant bacteria among the Gram-positive and negative isolates, including Staphylococcus haemolyticus (S. haemolyticus), Staphylococcus kloosii (S. kloosii), Acinetobacter baumanii (A. baumanii), and P. aeruginosa. In conclusion, the study underscores the significance of monitoring bacterial contamination in public restrooms and the need for measures to reduce the spread of infectious diseases. Further research is crucial to gain a complete understanding of the bacterial contamination in public restrooms and their resistance patterns, to ensure the safety and health of the public. The implementation of improved cleaning practices and hands-free designs in addition to the installation of antimicrobial surfaces in restrooms can help reduce the risk of cross-contamination and prevent the spread of diseases.

New generation sequencing: molecular approaches for the detection and monitoring of bioaerosols in an indoor environment: a systematic review

INTRODUCTION

The exposure of occupants to indoor air pollutants has increased in recent decades. The aim of this review is to discuss an overview of new approaches that are used to study fungal aerosols. Thus, this motivation was to compensate the gaps caused by the use of only traditional approaches in the study of fungal exposure.

CONTENT

The search involved various databases such as; Science Direct, PubMed, SAGE, Springer Link, EBCOHOST, MEDLINE, CINAHL, Cochrane library, Web of Science and Wiley Online Library. It was limited to full text research articles that reported the use of non-viable method in assessing bioaerosol, written in English Language, full text publications and published from year 2015-2022.

SUMMARY AND OUTLOOK

A total of 15 articles met the inclusion criteria and was included in this review. The use of next-generation sequencing, which is more commonly referred to as high-throughput sequencing (HTS) or molecular methods in microbial studies is based on the detection of genetic material of organisms present in a given sample. Applying these methods to different environments permitted the identification of the microorganisms present, and a better comprehension of the environmental impacts and ecological roles of microbial communities. Based on the reviewed articles, there is evidence that dust samples harbour a high diversity of human-associated bacteria and fungi. Molecular methods such as next generation sequencing are reliable tools for identifying and tracking the bacterial and fungal diversity in dust samples using 18S metagenomics approach.

Detection of clinically relevant antibiotic-resistant bacteria in shared fomites, waste water and municipal solid wastes disposed near residential areas of a Nigerian city

Studies investigating environmental hotspots of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in Nigeria are limited. This study was designed to assess various environmental sources and commonly touched surfaces as potential carriers of ARB and ARGs with implications for public health. A total of 392 samples, including sewage (36), sludge (36), diapers (20), plastics (20), water sachet polythene bags (20), food wastes (20), soil beneath dump sites (20), and frequently touched surfaces such as restroom floors (80), corridors (24), door handles (56), and room floors and walls (60), were collected and screened for the presence of resistant bacteria carrying genes such as bla KPC, bla NDM-1, bla CMY-2, bla IMP, bla OXA66 and MecA. Additionally, we employed standard techniques to detect methicillin-resistant Staphylococcus aureus (MRSA) and extended-spectrum β-lactamase (ESBL)-producing Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa and Acinetobacter baumannii . We also evaluated the effectiveness of routine disinfection procedures in eliminating ARB from restroom floors. Our findings revealed that sewage, sludge, diapers, food wastes and restroom floors are frequently contaminated with highly and moderately resistant strains of E. coli, K. pneumoniae, P. aeruginosa and MRSA. Notably, we identified two variants of the bla OXA51-like gene (bla OXA-66 and bla OXA-180) in A. baumannii isolated from these environmental sources. Furthermore, we detected seven ESBL- K. pneumoniae , five ESBL- A. baumannii , two ESBL- E. coli and one ESBL- P. aeruginosa , all carrying one or more ARGs (bla KPC, bla NDM-1, bla CMY-2), in isolates recovered from sewage, sludge, restroom floors and plastics. It is of note that ARB persisted on restroom floors even after disinfection procedures. In conclusion, this study highlights that environmental wastes indiscriminately discarded in residential areas and shared surfaces among individuals are heavily colonized by ARB carrying ARGs of significant public health importance.

Bacterial composition of refrigerators in households and inactivation of airborne Staphylococcus aureus using a TiO2-UVLED module in a 512 L aerobiology chamber

This study aimed to investigate the microbiota in the air and on the surface of a refrigerator and to inactivate aerosolized Staphylococcus aureus using a TiO₂-UVLED module. A total of 100 L of the air and 5000 cm² surfaces in seven household refrigerators were collected using an air sampler and a swab, respectively. Samples were subjected to microbiota analysis as well as quantitative analyses of aerobic or anaerobic bacteria. The level of airborne aerobic bacteria was 4.26 log CFU/vol (100 L), while that of surface aerobic bacteria was 5.27 log CFU/surface (5000 cm²). PCoA based on the Bray-Curtis metric revealed that the bacterial composition differed between samples collected from refrigerators with and without a vegetable drawer. Moreover, pathogenic bacteria containing genera and order from each sample were found, such as Enterobacaterales, Pseudomonas, Staphylococcus, Listeria, and Bacillus. Among them, Staphylococcus aureus was determined to be a core hazardous pathogen in air. Therefore, three S. aureus strains isolated from the air in refrigerators, as well as a reference strain of S. aureus (ATCC 6538P), were inactivated by a TiO₂-UVLED module in a 512 L aerobiology chamber. All aerosolized S. aureus were reduced over 1.6 log CFU/vol after treatment with TiO₂ under UVA (365 nm) light at 40 J/cm². These findings suggest that TiO₂-UVLED modules have the potential to be used to control airborne bacteria in household refrigerators.

A review of latrine front-end characteristics associated with microbial infection risk; reveals a lack of pathogen density data

Unsafe sanitation accounts for an estimated 898,000 global deaths annually. The faecal pathogen transmission pathway is complex with several possible routes. Latrine front-end characteristics and usage behaviours are one key transmission pathway for microbial pathogens, however, there has not yet been a synthesis of the available research. This review aims to compare the microbial infection risks with latrine front-end components including any quantified microbial densities within the household latrines. This review was conducted with no restriction on the geographical location of the research. Of 118 studies reviewed, only ten (8%) have quantified the microbial density inside the household latrines compared to 109 (92%) measuring the infection risks. The reported risks were most frequent for specific bacterial (n = 34), and helminths infections (n = 32) compared to diarrhoea (n = 23), combined (n = 15), protozoan (n = 4), and viral (n = 4) infections. The infections risk decreased for using latrines lying at a higher position on the sanitation ladder (for example flush latrines) compared to those lying lower (for example pit latrines). The trend was similar for using floor materials that were easier to clean and less favourable for pathogen survival inside the latrines (for example, concrete as opposed to earth). Faecal coliforms were reported highest on the surface of the squat pan (743 CFU/cm2) of pour-flush latrines and helminths on earth floors of pit latrines (1.5 eggs and larvae per gram of soil). Irrespective of latrine type and its position on the sanitation ladder, a dirty latrine, evidenced by a visible lack of cleanliness, significantly increased the risk for all infections. This study recommends that effective microbial infection risk reduction in latrines can be gained efficiently by ensuring washable surfaces and consistent cleaning practices. Future studies should include more rigorous measurements of microbial densities in various latrine types incorporating the different front-end components and usage behaviours.

Microbiota Profiling on Veterinary Faculty Restroom Surfaces and Source Tracking

In this study, we aimed to develop a comprehensive microbial source amplicon database tailored for source tracking in veterinary settings. We rigorously tested our locally curated source tracking database by selecting a frequently accessed environment by veterinary students and veterinarians. By exploring the composition of resident microbiota and identifying potential sources of contamination, including animals, the environment, and human beings, we aimed to provide valuable insights into the dynamics of microbial transmission within veterinary facilities. The 16S rDNA amplicon sequencing was used to determine the bacterial taxonomic profiles of restroom surfaces. Bacterial sources were identified by linking our metadata-enriched local database to the microbiota profiling analysis using high-quality sequences. Microbiota profiling shows the dominance of four phyla: Actinobacteria, Bacteroidetes, Proteobacteria, and Firmicutes. If the restroom cleaning process did not appear to impact microbiota composition, significant differences regarding bacterial distribution were observed between male and female users in different sampling campaigns. Combining 16S rDNA profiling to our specific sources labeling pipeline, we found aquatic and human sources were the primary environment keywords in our campaigns. The probable presence of known animal sources (bovids, insects, equids, suids…) associated with bacterial genera such as Chryseobacterium, Bergeyella, Fibrobacter, and Syntrophococcus was also involved in restroom surfaces, emphasizing the proximity between these restrooms and the exchange of bacteria between people involved in animals handling. To summarize, we have demonstrated that DNA sequence-based source tracking may be integrated with high-throughput bacterial community analysis to enrich microbial investigation of potential bacterial contamination sources, especially for little known or poorly identified taxa. However, more research is needed to determine the tool's utility in other applications.

Indoor particle dispersion due to hand dryer in public washroom: an in silico study

Hand dryer in public washroom has been reported likely to be a reservoir of drug-resistant bacteria. When a hand dryer being used, the high-velocity air jet from the dryer outlet can carry aerosol particles to hand surfaces, the user, and indoor space. This in silico study considered the effect of different airflow speed of hand dryers on the dispersion of particles in different diameters with and without the user. The aim of this study was to apply the computational fluid dynamics (CFD) method based on the discrete phase model to investigate the trajectory of indoor particles from the hand dryer in public washroom. The CFD results showed that, when the user was using the hand dryer, 42.3% of the particles were distributed on the wall against the user, and 31.6% were distributed on the user's body, including their hands. When no one was standing in front of the hand dryer, 87.6% of the particles fell on the ground. The blocking of user's hand dispersed the particles to a wide range, particularly for the larger diameter particles which were scattered on the user's body or on the ground. In addition, the dispersion proportion of particles did not vary with the speed of airflow, but the area of particles distribution became larger as the speed increased. Our findings suggest that the contamination of the indoor environment caused by the hand dryer could not be ignored, incorporating filters into hand dryers is essential. Furthermore, our work offers valuable insights for optimizing the design of hand dryers.

SNV-FEAST: microbial source tracking with single nucleotide variants

Elucidating the sources of a microbiome can provide insight into the ecological dynamics responsible for the formation of these communities. Source tracking approaches to date leverage species abundance information; however, single nucleotide variants (SNVs) may be more informative because of their high specificity to certain sources. To overcome the computational burden of utilizing all SNVs for a given sample, we introduce a novel method to identify signature SNVs for source tracking. Signature SNVs used as input into a previously designed source tracking algorithm, FEAST, can more accurately estimate contributions than species and provide novel insights, demonstrated in three case studies.

Characterization of SARS-CoV-2 Distribution and Microbial Succession in a Clinical Microbiology Testing Facility during the SARS-CoV-2 Pandemic

The exchange of microbes between humans and the built environment is a dynamic process that has significant impact on health. Most studies exploring the microbiome of the built environment have been predicated on improving our understanding of pathogen emergence, persistence, and transmission. Previous studies have demonstrated that SARS-CoV-2 presence significantly correlates with the proportional abundance of specific bacteria on surfaces in the built environment. However, in these studies, SARS-CoV-2 originated from infected patients. Here, we perform a similar assessment for a clinical microbiology lab while staff were handling SARS-CoV-2 infected samples. The goal of this study was to understand the distribution and dynamics of microbial population on various surfaces within different sections of a clinical microbiology lab during a short period of 2020 Coronavirus disease (COVID-19) pandemic. We sampled floors, benches, and sinks in 3 sections (bacteriology, molecular microbiology, and COVID) of an active clinical microbiology lab over a 3-month period. Although floor samples harbored SARS-CoV-2, it was rarely identified on other surfaces, and bacterial diversity was significantly greater on floors than sinks and benches. The floors were primarily colonized by bacteria common to natural environments (e.g., soils), and benchtops harbored a greater proportion of human-associated microbes, including Staphylococcus and Streptococcus. Finally, we show that the microbial composition of these surfaces did not change over time and remained stable. Despite finding viruses on the floors, no lab-acquired infections were reported during the study period, which suggests that lab safety protocols and sanitation practices were sufficient to prevent pathogen exposures. IMPORTANCE For decades, diagnostic clinical laboratories have been an integral part of the health care systems that perform diagnostic tests on patient's specimens in bulk on a regular basis. Understanding their microbiota should assist in designing and implementing disinfection, and cleaning regime in more effective way. To our knowledge, there is a lack of information on the composition and dynamics of microbiota in the clinical laboratory environments, and, through this study, we have tried to fill that gap. This study has wider implications as understanding the makeup of microbes on various surfaces within clinical laboratories could help identify any pathogenic bacterial taxa that could have colonized these surfaces, and might act as a potential source of laboratory-acquired infections. Mapping the microbial community within these built environments may also be critical in assessing the reliability of laboratory safety and sanitation practices to lower any potential risk of exposures to health care workers.

Toilet plume bioaerosols in health care and hospitality settings: A systematic review

BACKGROUND

The spread of some respiratory and gastro-intestinal infections has been linked to the exposure to infectious bioaerosols released after toilet flushing. This represents a health hazard and infection risk for immunocompromised patients, health workers and the public, particularly within the health care and hospitality settings. This systematic review provides current knowledge and identifies gaps in the evidence regarding toilet plume bioaerosols and the potential contributory role in spreading infections in health care and hospitality settings.

METHODS

The PRISMA guidelines were used. Searches were run in PubMed, Scopus, and Google Scholar from 1950 to 30th June 2021. Searches of global and regional reports and updates from relevant international and governmental organizations were also conducted.

RESULTS AND CONCLUSION

The search yielded 712 results, and 37 studies were finally selected for this review. There is a lack of national and international bioaerosol sampling and exposure standards for health care and hospitality settings. Toilet plume bioaerosols are complex in nature, thus, measured bioaerosol concentrations in these settings depend on many variables and may differ for every pathogen responsible for a particular infectious disease. The contact and airborne transmission risks posed by toilet plume bioaerosols also remain unquantified. They are an important pathway that can increase the exposure to enteric and airborne pathogens. Hence, quantitative risk assessment and related research are needed to investigate these transmission risks.

Assessment of a novel continuous cleaning device using metatranscriptomics in diverse hospital environments

Introduction

Despite routine implementation of cleaning and disinfection practices in clinical healthcare settings, high-touch environmental surfaces and contaminated equipment often serve as reservoirs for the transmission of pathogens associated with healthcare-associated infections (HAIs).

Methods

The current study involved the analysis of high-touch surface swabs using a metatranscriptomic sequencing workflow (CSI-Dx™) to assess the efficacy of cleanSURFACES® technology in decreasing microbial burden by limiting re-contamination. This is a non-human single center study conducted in the Emergency Department (ED) and on an inpatient Oncology Ward of Walter Reed National Military Medical Center that have followed hygienic practices during the COVID-19 pandemic environment.

Results

Although there was no difference in observed microbial richness (two-tailed Wilcoxon test with Holm correction, P > 0.05), beta diversity findings identified shifts in microbial community structure between surfaces from baseline and post-intervention timepoints (Day 1, Day 7, Day 14, and Day 28). Biomarker and regression analyses identified significant reductions in annotated transcripts for various clinically relevant microorganisms' post-intervention, coagulase-negative staphylococci and Malassezia restricta, at ED and Oncology ward, respectively. Additionally, post-intervention samples predominantly consisted of Proteobacteria and to a lesser extent skin commensals and endogenous environmental microorganisms in both departments.

Discussion

Findings support the value of cleanSURFACES®, when coupled with routine disinfection practices, to effectively impact on the composition of active microbial communities found on high-touch surfaces in two different patient care areas of the hospital (one outpatient and one inpatient) with unique demands and patient-centered practices.

Adolescent Women's Perspectives on Barriers and Facilitators to High School Bathroom Use

Bathroom access and use in conjunction with biological urge to void is an important part of optimal bladder health. School settings are uniquely positioned to influence the development of bladder habits. The aim of this study was to identify barriers and facilitators to high school bathroom use for adolescent women. A qualitative study design was used to conduct semi-structured interviews focused on experiences with bathroom use while at school. Thirty adolescent women were interviewed, and transcripts were analyzed using thematic analysis methods. Barriers included unpleasant bathroom environments, lack of privacy, and school/teacher policies. Facilitators included clean, private bathrooms and menstruation. Improving bathroom cleanliness, privacy, and eliminating policies aimed at controlling bathroom access may reduce barriers to bathroom use. School nurses have a unique role in educating teachers, administrators, and students about the importance of clean bathrooms and policies that support bathroom use in conjunction with biological urge.

Sampling from four geographically divergent young female populations demonstrates forensic geolocation potential in microbiomes

Studies of human microbiomes using new sequencing techniques have increasingly demonstrated that their ecologies are partly determined by the lifestyle and habits of individuals. As such, significant forensic information could be obtained from high throughput sequencing of the human microbiome. This approach, combined with multiple analytical techniques demonstrates that bacterial DNA can be used to uniquely identify an individual and to provide information about their life and behavioral patterns. However, the transformation of these findings into actionable forensic information, including the geolocation of the samples, remains limited by incomplete understanding of the effects of confounding factors and the paucity of diverse sequences. We obtained 16S rRNA sequences of stool and oral microbiomes collected from 206 young and healthy females from four globally diverse populations, in addition to supporting metadata, including dietary and medical information. Analysis of these microbiomes revealed detectable geolocation signals between the populations, even for populations living within the same city. Accounting for other lifestyle variables, such as diet and smoking, lessened but does not remove the geolocation signal.

Determinants of diarrhoeal infections among users of shared sanitation in informal settlements in Durban, South Africa

Diarrhoeal disease continues to be a major health problem in many parts of the world, especially in developing countries, mainly due to the lack of access to sanitation, water, and hygienic living conditions. Identifying the determinants of diarrhoeal infections continues to be a challenge in developing countries. In this study, we ascertained the factors behind diarrhoea among inhabitants of informal settlements in the city of Durban, South Africa. Prevalence of diarrhoea in the study area varied between 7-year historical clinical records and data collected during the current study (primary data), with the primary data giving the highest monthly prevalence odds ratio (POR) up to 18.1 (±1.6)%. The main factors associated with diarrhoeal infections were open defaecation (POR = 1.8; 95% confidence interval (CI): 0.9-3.12), use of shared sanitation (POR = 1.7; 95%; CI: 1.05-2.26), and exposure to faecal matter around the homes (POR = 1.69; 95% CI: 1.25-3.10). Several other factors were also determined to be associated with diarrhoeal infections, such as hygiene practices in the communities, the non-treatment of water before use, and the presence of solid waste and faecal materials around the households. This study shows that diarrhoeal disease infections in informal settlements could be multifactorial; therefore, a multifactorial approach is needed to reduce these infections. These could include improving education on hygiene practices within the home setting as well as in public places, such as the community ablution blocks.

Changes in residents' hygiene awareness and behaviors in public toilets before and during the COVID-19 pandemic in Hangzhou, China: a two-round cross-sectional study

Background

Hygiene behaviors in public toilets are important to prevent the transmission of infectious diseases, especially during the pandemic. All through the novel coronavirus (COVID-19) pandemic, governments in many countries published guidance on personal hygiene for the general population to prevent disease transmission. This study aimed to investigate improvements in residents’ hygiene awareness and behaviors in public toilets before and during the pandemic.

Methods

We recruited 316 residents between November and December 2018 before the pandemic, and 314 residents between December 2020 and January 2021 during the pandemic in the same study sites in Hangzhou, a well-developed city in China. Residents’ hygiene behaviors in public toilets, hygiene awareness, risk perception, and sociodemographic factors were collected. Bivariate analysis and multivariable logistic regressions were used to test the differences between the two rounds. We conducted an observational study to record the provision of hygiene amenities at toilets during the pandemic.

Results

After controlling for sociodemographic factors (gender, marital status, age, education level, and monthly household income), compared with respondents recruited before the pandemic, respondents recruited during the pandemic were more likely to perceive the risks of infection when using public toilets (aOR = 1.77, 95%CI [1.20, 2.60]), and were more likely to be aware of the risks of touching contaminated toilet facilities (aOR = 1.72, 95%CI [1.17, 2.54]) and the risks of not using soap to wash one’s hands after using the toilet (aOR = 1.93, 95%CI [1.38, 2.72]). They were more likely to always clean their toilet seat with alcohol (aOR = 1.88, 95%CI [1.01, 3.51]), wash hands with soap (aOR = 1.52, 95%CI [1.09, 2.10]) and dry their hands with a dryer (aOR = 1.78, 95%CI [1.16, 2.71]), but they were less likely to always wash their hands after using the toilets (aOR = 0.57, 95%CI [0.32, 1.00]). Among 70 public toilets observed, 9 provided alcohol for toilet seat disinfection, 52 provided soap, 33 provided paper towels, and 41 had working hand dryers.

Conclusions

Despite the overall improvement, residents’ hygiene behaviors in public toilets and the supply of hygiene amenities were still suboptimal during the pandemic. Further hygiene education and an adequate supply of hygiene amenities in public toilets are needed to promote residents’ hygiene behaviors.

Airborne microbial community structure and potential pathogen identification across the PM size fractions and seasons in the urban atmosphere

As a vital component of airborne bioaerosols, bacteria and fungi seriously endanger human health as pathogens and allergens. However, comprehensive effects of environmental variables on airborne microbial community structures remain poorly understood across the PM sizes and seasons. We collected atmospheric PM_1.0, PM_2.5, and PM₁₀ samples in Hefei, a typical rapidly-developing city in East China, across three seasons, and performed a comprehensive analysis of airborne microbial community structures using qPCR and high-throughput sequencing. Overall the bacterial and fungal abundances in PM_1.0 were one to two orders of magnitude higher than those in PM_2.5 and PM₁₀ across seasons, but their α-diversity tended to increase from PM_1.0 to PM₁₀. The bacterial gene abundances showed a strong positive correlation (P < 0.05) with atmospheric SO₂ and NO₂ concentrations and air quality index. The bacterial gene abundances were significantly higher (P = 0.001) than fungi, and the bacterial diversity showed stronger seasonality. The PM sizes influenced distribution patterns for airborne microbial communities within the same season. Source-tracking analysis indicated that soils, plants, human and animal feces represented important sources of airborne bacteria with a total relative abundance of more than 60% in summer, but total abundance from the unidentified sources surpassed in fall and winter. Total 10 potential bacterial and 12 potential fungal pathogens were identified at the species level with the highest relative abundances in summer, and their abundances increased with the PM sizes. Together, our results indicated that a complex set of environmental factors, including water-soluble ions in PM, changes in air pollutant levels and meteorological conditions, and shifts in the relative importance of available microbial sources, acted to control the seasonal compositions of microbial communities in the urban atmosphere.

The sanitary indoor environment-a potential source for intact human-associated anaerobes

A healthy human microbiome relies on the interaction with and exchange of microbes that takes place between the human body and its environment. People in high-income countries spend most of their time indoors and for this reason, the built environment (BE) might represent a potent source of commensal microbes. Anaerobic microbes are of particular interest, as researchers have not yet sufficiently clarified how the human microbiome acquires oxygen-sensitive microbes. We sampled the bathrooms in ten households and used propidium monoazide (PMA) to assess the viability of the collected prokaryotes. We compared the microbiome profiles based on 16S rRNA gene sequencing and confirmed our results by genetic and cultivation-based analyses. Quantitative and qualitative analysis revealed that most of the microbial taxa in the BE samples are human-associated. Less than 25% of the prokaryotic signatures originate from intact cells, indicating that aerobic and stress resistant taxa display an apparent survival advantage. However, we also confirmed the presence of intact, strictly anaerobic taxa on bathroom floors, including methanogenic archaea. As methanogens are regarded as highly sensitive to aerobic conditions, oxygen-tolerance experiments were performed with human-associated isolates to validate their survival. These results show that human-associated methanogens can survive oxic conditions for at least 6 h. We collected strong evidence that supports the hypothesis that obligate anaerobic taxa can survive in the BE for a limited amount of time. This suggests that the BE serves as a potential source of anaerobic human commensals.

Manual emptying of ventilated improved pit latrines and hygiene challenges - a baseline survey in a peri-urban community in KwaZulu-Natal, South Africa

The presence of Escherichia coli and Staphylococcus spp. was determined on the skin, personal protective equipment, the municipal vehicle, and various surfaces at ten households in a peri-urban community (KwaZulu-Natal, South Africa) before and after manual emptying of ventilated improved pit latrines. Surface samples (n = 14) were collected using sterile wet wipes, and target bacteria were detected using standard procedures. Additionally, E. coli was enumerated in soil samples from an area of open defecation (log₁₀ 3.7 MPN/g) and areas where geophagia occurred (log₁₀ 2.7 - log₁₀ 3.3 MPN/g), using a most probable number (MPN) method. The detection frequency for the target bacteria on household surfaces (e.g., the walkway between the pit latrine and the municipal vehicle) and on municipal workers' hands (which were frequently contaminated before pit emptying), occasionally increased after the pits were emptied, indicating that manual pit emptying might pose a potential health risk to workers and community members.

Where environmental microbiome meets its host: subway and passenger microbiome relationships

Subways are urban transport systems with high capacity. Every day around the world, there are more than 150 million subway passengers. Since 2013, thousands of microbiome samples from various subways worldwide have been sequenced. Skin bacteria and environmental organisms dominate the subway microbiomes. The literature has revealed common bacterial groups in subway systems; even so, it is possible to identify cities by their microbiome. Low-frequency bacteria are responsible for specific bacterial fingerprints of each subway system. Furthermore, daily subway commuters leave their microbial clouds and interact with other passengers. Microbial exchange is quite fast; the hand microbiome changes within minutes, and after cleaning the handrails, the bacteria are re-established within minutes. To investigate new taxa and metabolic pathways of subway microbial communities, several high-quality metagenomic-assembled genomes (MAG) have been described. Subways are harsh environments unfavorable for microorganism growth. However, recent studies have observed a wide diversity of viable and metabolically active bacteria. Understanding which bacteria are living, dormant, or dead allows us to propose realistic ecological interactions. Questions regarding the relationship between humans and the subway microbiome, particularly the microbiome effects on personal and public health, remain unanswered. This review summarizes our knowledge of subway microbiomes and their relationship with passenger microbiomes.

The bacterial community of childcare centers: potential implications for microbial dispersal and child exposure

BACKGROUND

Bacterial communities within built environments reflect differences in sources of bacteria, building design, and environmental contexts. These communities impact the health of their occupants in many ways. Children interact with the built environment differently than do adults as a result of their unique behaviors, size, and developmental status. Consequently, understanding the broader bacterial community to which children are exposed will help inform public health efforts and contribute to our growing understanding of the bacterial community associated with childcare centers.

METHODS

We sampled childcare centers to survey the variation in bacterial community composition across five surfaces found inside and outside twelve classrooms and six centers using 16S rRNA marker gene amplicon sequencing. We then correlated these bacterial community analyses of surfaces with environmental and demographic measures of illumination and classroom occupant density.

RESULTS

The childcare environment was dominated by human-associated bacteria with modest input from outdoor sources. Though the bacterial communities of individual childcare centers differed, there was a greater difference in the bacterial community within a classroom than among centers. Surface habitats-fomites-within the classroom, did not differ in community composition despite differing proximity to likely sources of bacteria, and possible environmental filters, such as light. Bacterial communities did correlate with occupant density and differed significantly between high and low usage surfaces.

CONCLUSIONS

Our results suggest built environments inhabited by young children are similar to functionally equivalent built environments inhabited by adults, despite the different way young children engage with their environment. Ultimately, these results will be useful when further interrogating microbial dispersal and human exposure to microorganisms in built environments that specifically cater to young children.

An assessment of the health risks associated with shared sanitation: a case study of the community ablution blocks in Durban, South Africa

Shared sanitation facilities have been hailed as an innovative approach to solve the challenge with sanitation access. However, these facilities may act as hotspots for disease transmission due to unhygienic conditions. In this study we used quantitative (based on Escherichia coli contamination) techniques to assess the health risks associated with the use of community ablution blocks (CABs). The most contaminated surfaces were the cistern handle (5.7 Log₁₀ cfu/cm²) and internal pull latch (5.8 Log₁₀ cfu/cm²). Based on the E. coli contamination, at least two people out of 100 CAB users might be potentially infected when they touch "hot" surfaces. These risks were modelled assuming transfer of potentially pathogenic E. coli from these surfaces to the mouth. The incorporation of risk-reduction measures, such as wiping of these surfaces or washing of hands, could potentially result in significant reduction of infection risks. The most significant risk-reduction intervention was determined to be wiping of the contact surfaces, especially twice prior to contact. A combination of risk-reduction interventions could further reduce the risks. This study shows that contamination of contact surfaces within shared CABs could lead to increased risks of infections, requiring measures aimed at reducing the associated risks. The risk assessment framework used in this study could therefore be applied in similar settings to estimate associated health risks with the use of such facilities.

A biogeographic 16S rRNA survey of bacterial communities of ureolytic biomineralization from California public restrooms

In this study, we examined the total bacterial community associated with ureolytic biomineralization from urine drainage systems. Biomineral samples were obtained from 11 California Department of Transportation public restrooms fitted with waterless, low-flow, or conventional urinals in 2019. Following high throughput 16S rRNA Illumina sequences processed using the DADA2 pipeline, the microbial diversity assessment of 169 biomineral and urine samples resulted in 3,869 reference sequences aggregated as 598 operational taxonomic units (OTUs). Using PERMANOVA testing, we found strong, significant differences between biomineral samples grouped by intrasystem sampling location and urinal type. Biomineral microbial community profiles and alpha diversities differed significantly when controlling for sampling season. Observational statistics revealed that biomineral samples obtained from waterless urinals contained the largest ureC/16S gene copy ratios and were the least diverse urinal type in terms of Shannon indices. Waterless urinal biomineral samples were largely dominated by the Bacilli class (86.1%) compared to low-flow (41.3%) and conventional samples (20.5%), and had the fewest genera that account for less than 2.5% relative abundance per OTU. Our findings are useful for future microbial ecology studies of urine source-separation technologies, as we have established a comparative basis using a large sample size and study area.

Transmission of COVID-19 and other infectious diseases in public washrooms: A systematic review

BACKGROUND

The risk of infectious disease transmission in public washrooms causes concern particularly in the context of the COVID-19 pandemic. This systematic review aims to assess the risk of transmission of viral or bacterial infections through inhalation, surface contact, and faecal-oral routes in public washrooms in healthcare and non-healthcare environments.

METHODS

We systematically reviewed environmental sampling, laboratory, and epidemiological studies on viral and bacterial infection transmission in washrooms using PubMed and Scopus. The review focused on indoor, publicly accessible washrooms.

RESULTS

Thirty-eight studies from 13 countries were identified, including 14 studies carried out in healthcare settings, 10 in laboratories or experimental chambers, and 14 studies in restaurants, workplaces, commercial and academic environments. Thirty-three studies involved surface sampling, 15 air sampling, 8 water sampling, and 5 studies were risk assessments or outbreak investigations. Infectious disease transmission was studied in relation with: (a) toilets with flushing mechanisms; (b) hand drying systems; and (c) water taps, sinks and drains. A wide range of enteric, skin and soil bacteria and enteric and respiratory viruses were identified in public washrooms, potentially posing a risk of infection transmission. Studies on COVID-19 transmission only examined washroom contamination in healthcare settings.

CONCLUSION

Open-lid toilet flushing, ineffective handwashing or hand drying, substandard or infrequent surface cleaning, blocked drains, and uncovered rubbish bins can result in widespread bacterial and/or viral contamination in washrooms. However, only a few cases of infectious diseases mostly related to faecal-oral transmission originating from washrooms in restaurants were reported. Although there is a risk of microbial aerosolisation from toilet flushing and the use of hand drying systems, we found no evidence of airborne transmission of enteric or respiratory pathogens, including COVID-19, in public washrooms. Appropriate hand hygiene, surface cleaning and disinfection, and washroom maintenance and ventilation are likely to minimise the risk of infectious disease transmission.

Comparative effects of environmental factors on bacterial communities in two types of indoor dust: Potential risks to university students

University students are constantly exposed to potential bacterial pathogens and environmental pollutants in indoor environment because they spend most of their time indoors. University dormitory and printing shop are two typical indoor environments frequented by university students. However, little is known about the characteristics of bacterial community as well as the effect of indoor environmental factors on them. 16S rRNA gene sequencing was used to reveal the bacterial community in indoor dust, electronic devices were recorded during dust sampling, and polybrominated diphenyl ethers (PBDEs) were detected by gas chromatography mass spectrometry (GC-MS). Proteobacteria, Actinobacteria and Firmicutes were leading phyla, and Acinetobacter, Paracoccus and Kocuria were dominating genera. The predominant genera showed Acinetobacter > Paracoccus > unidentified Corynebacteriaceae in indoor dusts from university dormitories, whereas Paracoccus > unidentified Cyanobacteria > Acinetobacter in printing shops. The occurrence of Acinetobacter, Kocuria, Corynebacterium, Pseudomonas, and Bacillus suggested the health risks of potential pathogenic bacteria to university students. Significant differences of microbial composition and diversity were proved between university dormitories and printing shops. Chemoheterotrophy and aerobic chemoheterotrophy were dominant bacterial functions, and the seven primary bacterial functions displayed university dormitory > printing shop. BDE 138 and BDE 66 were main environmental parameters affecting the indoor dust bacterial community in university dormitory, while printer and BDE 47 played dominating role in shaping microorganism in printing shop. The complex biotic (potential bacterial pathogens) and abiotic factors (electronic equipment and chemical pollutants) in indoor dusts may pose potential health risks to university students.

Hyperosmolarity adversely impacts recombinant protein synthesis by Yarrowia lipolytica-molecular background revealed by quantitative proteomics

Abstract

In this research, we were interested in answering a question whether subjecting a Yarrowia lipolytica strain overproducing a recombinant secretory protein (rs-Prot) to pre-optimized stress factors may enhance synthesis of the rs-Prot. Increased osmolarity (3 Osm kg⁻¹) was the primary stress factor implemented alone or in combination with decreased temperature (20 °C), known to promote synthesis of rs-Prots. The treatments were executed in batch bioreactor cultures, and the cellular response was studied in terms of culture progression, gene expression and global proteomics, to get insight into molecular bases underlying an awaken reaction. Primarily, we observed that hyperosmolarity executed by high sorbitol concentration does not enhance synthesis of the rs-Prot but increases its transcription. Expectedly, hyperosmolarity induced synthesis of polyols at the expense of citric acid synthesis and growth, which was severely limited. A number of stress-related proteins were upregulated, including heat-shock proteins (HSPs) and aldo–keto reductases, as observed at transcriptomics and proteomics levels. Concerted downregulation of central carbon metabolism, including glycolysis, tricarboxylic acid cycle and fatty acid synthesis, highlighted redirection of carbon fluxes. Elevated abundance of HSPs and osmolytes did not outbalance the severe limitation of protein synthesis, marked by orchestrated downregulation of translation (elongation factors, several aa-tRNA synthetases), amino acid biosynthesis and ribosome biogenesis in response to the hyperosmolarity. Altogether we settled that increased osmolarity is not beneficial for rs-Prots synthesis in Y. lipolytica, even though some elements of the response could assist this process. Insight into global changes in the yeast proteome under the treatments is provided.

Key points

• Temp enhances, but Osm decreases rs-Prots synthesis by Y. lipolytica.

• Enhanced abundance of HSPs and osmolytes is overweighted by limited translation.

• Global proteome under Osm, Temp and Osm Temp treatments was studied.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00253-021-11731-y.

Differences between the Leaf Mycobiome of Coffea arabica and Wild Coffee Species and Their Modulation by Caffeine/Chlorogenic Acid Content

The study of microbes associated with the coffee tree has been gaining strength in recent years. In this work, we compared the leaf mycobiome of the traditional crop Coffea arabica with wild species Coffea racemosa and Coffea stenophylla using ITS sequencing for qualitative information and real-time PCR for quantitative information, seeking to relate the mycobiomes with the content of caffeine and chlorogenic acid in leaves. Dothideomycetes, Wallemiomycetes, and Tremellomycetes are the dominant classes of fungi. The core leaf mycobiome among the three Coffea species is formed by Hannaella, Cladosporium, Cryptococcus, Erythrobasidium, and Alternaria. A network analysis showed that Phoma, an important C. arabica pathogen, is negatively related to six fungal species present in C. racemosa and C. stenophylla and absent in C. arabica. Finally, C. arabica have more than 35 times the concentration of caffeine and 2.5 times the concentration of chlorogenic acid than C. stenophylla and C. racemosa. The relationship between caffeine/chlorogenic acid content, the leaf mycobiome, and genotype pathogen resistance is discussed.

Metagenomic insights into the microbial communities of inert and oligotrophic outdoor pier surfaces of a coastal city

BACKGROUND

Studies of the microbiomes on surfaces in built environment have largely focused on indoor spaces, while outdoor spaces have received far less attention. Piers are engineered infrastructures commonly found in coastal areas, and due to their unique locations at the interface between terrestrial and aquatic ecosystems, pier surfaces are likely to harbor interesting microbiology. In this study, the microbiomes on the metal and concrete surfaces at nine piers located along the coastline of Hong Kong were investigated by metagenomic sequencing. The roles played by different physical attributes and environmental factors in shaping the taxonomic composition and functional traits of the pier surface microbiomes were determined. Metagenome-assembled genomes were reconstructed and their putative biosynthetic gene clusters were characterized in detail.

RESULTS

Surface material was found to be the strongest factor in structuring the taxonomic and functional compositions of the pier surface microbiomes. Corrosion-related bacteria were significantly enriched on metal surfaces, consistent with the pitting corrosion observed. The differential enrichment of taxa mediating biodegradation suggests differences between the metal and concrete surfaces in terms of specific xenobiotics being potentially degraded. Genome-centric analysis detected the presence of many novel species, with the majority of them belonging to the phylum Proteobacteria. Genomic characterization showed that the potential metabolic functions and secondary biosynthetic capacity were largely correlated with taxonomy, rather than surface attributes and geography.

CONCLUSIONS

Pier surfaces are a rich reservoir of abundant novel bacterial species. Members of the surface microbial communities use different mechanisms to counter the stresses under oligotrophic conditions. A better understanding of the outdoor surface microbiomes located in different environments should enhance the ability to maintain outdoor surfaces of infrastructures. Video Abstract.

Forensic Analysis of Human Microbiome in Skin and Body Fluids Based on Geographic Location

High-throughput DNA sequencing technologies have facilitated the in silico forensic analysis of human microbiome. Specific microbial species or communities obtained from the crime scene provide evidence of human contacts and their body fluids. The microbial community is influenced by geographic, ethnic, lifestyle, and environmental factors such as urbanization. An understanding of the effects of these external stressors on the human microbiome and determination of stable and changing elements are important in selecting appropriate targets for investigation. In this study, the Forensic Microbiome Database (FMD) (http://www.fmd.jcvi.org) containing the microbiome data of various locations in the human body in 35 countries was used. We focused on skin, saliva, vaginal fluid, and stool and found that the microbiome distribution differed according to the body part as well as the geographic location. In the case of skin samples, Staphylococcus species were higher than Corynebacterium species among Asians compared with Americans. Holdemanella and Fusobacterium were specific in the saliva of Koreans and Japanese populations. Lactobacillus was found in the vaginal fluids of individuals in all countries, whereas Serratia and Enterobacter were endemic to Bolivia and Congo, respectively. This study is the first attempt to collate and describe the observed variation in microbiomes from the forensic microbiome database. As additional microbiome databases are reported by studies worldwide, the diversity of the applications may exceed and expand beyond the initial identification of the host.

At the Interface of Life and Death: Post-mortem and Other Applications of Vaginal, Skin, and Salivary Microbiome Analysis in Forensics

Microbial forensics represents a promising tool to strengthen traditional forensic investigative methods and fill related knowledge gaps. Large-scale microbiome studies indicate that microbial fingerprinting can assist forensics in areas such as trace evidence, source tracking, geolocation, and circumstances of death. Nevertheless, the majority of forensic microbiome studies focus on soil and internal organ samples, whereas the microbiome of skin, mouth, and especially vaginal samples that are routinely collected in sexual assault and femicide cases remain underexplored. This review discusses the current and emerging insights into vaginal, skin, and salivary microbiome-modulating factors during life (e.g., lifestyle and health status) and after death (e.g., environmental influences and post-mortem interval) based on next-generation sequencing. We specifically highlight the key aspects of female reproductive tract, skin, and mouth microbiome samples relevant in forensics. To fill the current knowledge gaps, future research should focus on the degree to which the post-mortem succession rate and profiles of vaginal, skin, and saliva microbiota are sensitive to abiotic and biotic factors, presence or absence of oxygen and other gases, and the nutrient richness of the environment. Application of this microbiome-related knowledge could provide valuable complementary data to strengthen forensic cases, for example, to shed light on the circumstances surrounding death with (post-mortem) microbial fingerprinting. Overall, this review synthesizes the present knowledge and aims to provide a framework to adequately comprehend the hurdles and potential application of vaginal, skin, and salivary post-mortem microbiomes in forensic investigations.

Detection of SARS-CoV-2 RNA on contact surfaces within shared sanitation facilities

Contamination of contact surfaces with SARS-CoV-2 has been reported as a potential route for the transmission of COVID-19. This could be a major issue in developing countries where access to basic sanitation is poor, leading to the sharing of toilet facilities. In this study, we report SARS-CoV-2 contamination of key contact surfaces in shared toilets and the probabilistic risks of COVID-19 infections based on detection and quantification of the nucleic acid on the surfaces. We observed that 54-69% of the contact surfaces were contaminated, with SARS-CoV-2 loads ranging from 28.1 to 132.7 gene copies per cm². Toilet seats had the highest contamination, which could be attributed to shedding of the virus in feces and urine. We observed a significant reduction in viral loads on the contaminated surfaces after cleaning, showing the potential of effective cleaning on the reduction of contamination. The pattern of contamination indicates that the most contaminated surfaces are those that are either commonly touched by users of the shared toilets or easily contaminated with feces and urine. These surfaces were the toilet seats, cistern handles and tap handles. The likelihood (probability) of infection with COVID-19 on these surfaces was highest on the toilet seat (1.76 × 10^-4(1.58 × 10^-6)) for one time use of the toilet. These findings highlight the potential risks for COVID-19 infections in the event that intact infectious viral particles are deposited on these contact surfaces. Therefore, this study shows that shared toilet facilities in densely populated areas could lead to an increase in risks of COVID-19 infections. This calls for the implementation of risk reduction measures, such as regular washing of hands with soap, strict adherence to wearing face masks, and effective and regular cleaning of shared facilities.

Bacterial communities of indoor surface of stingless bee nests

Microbes have been identified as fundamental for the good health of bees, acting as pathogens, protective agent against infection/inorganic toxic compounds, degradation of recalcitrant secondary plant metabolites, definition of social group membership, carbohydrate metabolism, honey and bee pollen production. However, study of microbiota associated with bees have been largely confined to the honeybees and solitary bees. Here, I characterized the microbiota of indoor surface nest of four brazilian stingless bee species (Apidae: Meliponini) with different construction behaviors and populations. Bees that use predominantly plant material to build the nest (Frieseomelitta varia and Tetragonisca angustula) have a microbiome dominated by bacteria found in the phylloplane and flowers such as Pseudomonas sp. and Sphingomonas sp. Species that use mud and feces (Trigona spinipes) possess a microbiome dominated by coliforms such as Escherichia coli and Alcaligenes faecalis. Melipona quadrifasciata, which uses both mud / feces and plant resin, showed a hybrid microbiome with microbes found in soil, feces and plant material. These findings indicate that indoor surface microbiome varies widely among bees and reflects the materials used in the construction of the nests.

Detection of SARS-CoV-2 RNA on contact surfaces within shared sanitation facilities

Contamination of contact surfaces with SARS-CoV-2 has been reported as a potential route for the transmission of COVID-19. This could be a major issue in developing countries where access to basic sanitation is poor, leading to the sharing of toilet facilities. In this study, we report SARS-CoV-2 contamination of key contact surfaces in shared toilets and the probabilistic risks of COVID-19 infections based on detection and quantification of the nucleic acid on the surfaces. We observed that 54-69% of the contact surfaces were contaminated, with SARS-CoV-2 loads ranging from 28.1 to 132.7 gene copies per cm². Toilet seats had the highest contamination, which could be attributed to shedding of the virus in feces and urine. We observed a significant reduction in viral loads on the contaminated surfaces after cleaning, showing the potential of effective cleaning on the reduction of contamination. The pattern of contamination indicates that the most contaminated surfaces are those that are either commonly touched by users of the shared toilets or easily contaminated with feces and urine. These surfaces were the toilet seats, cistern handles and tap handles. The likelihood (probability) of infection with COVID-19 on these surfaces was highest on the toilet seat (1.76 × 10^-4(1.58 × 10^-6)) for one time use of the toilet. These findings highlight the potential risks for COVID-19 infections in the event that intact infectious viral particles are deposited on these contact surfaces. Therefore, this study shows that shared toilet facilities in densely populated areas could lead to an increase in risks of COVID-19 infections. This calls for the implementation of risk reduction measures, such as regular washing of hands with soap, strict adherence to wearing face masks, and effective and regular cleaning of shared facilities.

Assessment of bio-contaminants during COVID-19 outbreak from the indoor environment of Hail city, Kingdom of Saudi Arabia

Biocontaminants are minute particles derived from different biological materials. Indoor biocontaminants are associated with major public health problems. In Gulf countries, it is more precarious due to the harsh climatic conditions, including high ambient temperatures and relative humidity. In addition, due to COVID-19 pandemic, most of the time public is inside their home. Therefore, the aim of the study was to determine the load of biocontaminants in the indoor environment of Hail city. The results showed that most of the bacteria are gram-positive and higher in polymicrobial (87.1%) than monomicrobial (62.7%) association. There was no significant association with sample collection time and types of isolates. The most abundant microbes found in all samples were Staphylococcus aureus followed by Bacillus spp. Among Gram-negative bacterial isolates, E. coli was most common in tested indoor air samples. The study will be useful to find the biocontaminants associated with risk factors and their impact on human health in indoor environment, especially during the COVID-19 pandemic. These results indicate the need to implement health care awareness programs in the region to improve indoor air quality.

Identifying background microbiomes in an evidence recovery laboratory: A preliminary study

16S rRNA profiling of bacterial communities may have forensic utility in the identification or association of individuals involved with criminal activities. Microbial profiling of evidence may, in the future, be performed within environments currently utilised for human DNA recovery, such as a forensic biology laboratory. It would be important to establish the background microbiome of such an environment to determine the potential presence of human or environmental microbial signatures to assist forensic scientists in the appropriate interpretation of target microbial communities. This study sampled various surfaces of an Evidence Recovery Laboratory (ERL) on three occasions including (a) before a monthly deep-clean, (b) immediately following the deep-clean, and (c) immediately after the laboratory's use by a single participant for the purposes of routine item examinations. Microbial profiles were also generated for the involved participant and researcher for comparison purposes. Additionally, human nuclear DNA was profiled for each of the samples collected, using standard forensic profiling techniques, to provide a prospective link to the presence or absence of a background microbial signature within the ERL after its use. Taxonomic distributions across ERL samples revealed no consistent signature of any of the items sampled over time, however, major phyla noted within all ERL samples across the three timepoints were consistent with those found in human skin microbiomes. PCoA plots based on the Unweighted Unifrac metric revealed some clustering between participant microbial reference samples and surfaces of the ERL after use, suggesting that despite a lack of direct contact, and adherence to standard operating procedures (SOPs) suitable for human DNA recovery, microbiomes may be deposited into a forensic setting over time. The reference samples collected from the involved participant and researcher generated full STR profiles. Human DNA was observed to varying degrees in samples taken from the ERL across each of the sampling timepoints. There was no correlation observed between samples that contained or did not contain detectable quantities of human nuclear DNA and microbial profile outputs.

Forensic Microbiome Database: A Tool for Forensic Geolocation Meta-Analysis Using Publicly Available 16S rRNA Microbiome Sequencing

The human microbiome has been proposed as a tool to investigate different forensic questions, including for the identification of multiple personal information. However, the fragmented state of the publicly available data has retarded the development of analysis techniques and, therefore, the implementation of microbiomes as a forensic tool. To address this, we introduce the forensic microbiome database (FMD), which is a collection of 16S rRNA data and associated metadata generated from publicly available data. The raw data was further normalized and processed using a pipeline to create a standardized data set for downstream analysis. We present a website allowing for the exploration of geolocation signals in the FMD. The website allows users to investigate the taxonomic differences between microbiomes harvested from different locations and to predict the geolocation of their data based on the FMD sequences. All the results are presented in dynamic graphics to allow for a rapid and intuitive investigation of the taxonomic distributions underpinning the geolocation signals and prediction between locations. Apart from the forensic aspect, the database also allows exploration and comparison of microbiome samples from different geolocation and between different body sites. The goal of the FMD is to provide the scientific and non-scientific communities with data and tools to explore the possibilities of microbiomes to answer forensic questions and serve as a model for any future such databases.

The Impacts of the Occupants on the Bacterial Communities of Classrooms

In modern societies, people spend most of their time in the built environment which harbors unique microbial assemblages with the potential to influence human health. However, how the occupants of buildings influence indoor microbial communities remains under-researched. Here, we investigated the diversities of the bacterial communities of a typical Chinese middle school to demonstrate the effects of occupant activities on bacterial communities inside classrooms. The results showed that samples taken from classrooms exhibited higher microbial diversity compared to samples collected from public areas such as gym and restaurant, suggesting the occupant activities could increase the diversities of the indoor microbial communities. Moreover, we also found that the duration of occupation strongly influence the presence/absence of phylogenetic lineages of the bacterial communities, the type of occupants, on the other hand, affect the relative abundances of bacterial taxa. In addition, samples taken from classrooms with longer occupation time exhibited a better fit to the Sloan Neutral Community Model for Prokaryotes, suggesting that room occupation influences the assembly process of microbial communities. In conclusion, our study demonstrates that the duration of occupation and the type of occupants influence the microbiome of the built environment.

A new UVC-LED system for disinfection of pathogens generated by toilet flushing

A new disinfection system utilizing UVC-LED irradiation was developed. The system was affixed to the toilet seat, and it was challenged by three bacteria strains. Different configurations were tested: 3-LEDs, 5-LEDs (two variants), and 8-LEDs. To determine the arrangement designs of LEDs with the optimum efficacy, two variants of 5-LEDs configurations were additionally considered-uniform and concentrated (2-sided) distributions. It was noticed that disinfection efficacy initially increased with the number of LEDs, but with 8-LEDs, the trend became almost non-obvious for surface disinfection and just marginally increased for airborne disinfection. The mean efficiencies for the surface disinfection ranged from 55.17 ± 23.89% to 72.80 ± 4.13% for E. coli; 36.65 ± 2.99% to 50.05 ± 13.38% for S. typhimurium; and 8.81 ± 3.23% to 39.43 ± 9.33% for S. epidermidis. Likewise, the mean efficiencies for airborne disinfection ranged from 42.17 ± 8.18% to 70.70 ± 4.80%; 40.40 ± 17.90% to 58.31 ± 13.87%; and 24.16 ± 3.81% to 42.79 ± 10.20% for E. coli; S. typhimurium; and S. epidermidis, respectively. Furthermore, the efficacy of the uniform irradiation was nearly twice that of the concentrated irradiation for surface disinfection and 17.70% higher for airborne disinfection, when tested against E coli. Collectively, these very promising results showcased that this compact, sustainable, and localized disinfection system has a high potential for the next generation of disinfection devices.

Improving Public Toilet Environment and Hygiene Practices in an Asian City: Voices From Hong Kong Residents

Toilet hygiene is an important preventive measure for infectious diseases, including severe acute respiratory syndrome (SARS) and COVID-19. This study explored public's opinions on improving toilet environment and hygiene practices in Hong Kong. A mixed-method approach was applied. We conducted 4 focus groups plus 3 individual interviews among the Hong Kong Chinese, followed by a questionnaire survey with 300 respondents recruited from various districts. Difference in response distributions between groups with different demographics was tested by Pearson χ² test. Instead of advocating for advanced toilet facilities, respondents were mostly concerned about basic hygiene issues. Malfunctioning facilities resulting from poor toilet management, such as clogged toilets, stained facilities, and problematic flushing systems, were most cited as barriers to toilet hygiene practices. Three quarters of the survey respondents expressed concerns over worn and poorly maintained toilets, shortage of janitors, and cleansing supplies. However, respondents who were older (P < .001), less educated (P < .001), and had lower income (P = .001) were significantly more likely to find hygiene conditions in public toilets satisfactory. The findings reflected the substandard of the current provisions as a developed city in Asia. Enhanced efforts by the government to maintain basic toilet supplies and facilities is the key to improving public compliance to toilet hygiene practices.

Outdoor Atmospheric Microbial Diversity Is Associated With Urban Landscape Structure and Differs From Indoor-Transit Systems as Revealed by Mobile Monitoring and Three-Dimensional Spatial Analysis

Microbes are abundant inhabitants of the near-surface atmosphere in urban areas. The distribution of microbial communities may benefit or hinder human wellbeing and ecosystem function. Surveys of airborne microbial diversity are uncommon in both natural and built environments and those that investigate diversity are stationary in the city, thus missing continuous exposure to microbes that covary with three-dimensional urban structure. Individuals in cities are generally mobile and would be exposed to diverse urban structures outdoors and within indoor-transit systems in a day. We used mobile monitoring of microbial diversity and geographic information system spatial analysis, across Philadelphia, Pennsylvania, USA in outdoor and indoor-transit (subways and train cars) environments. This study identifies to the role of the three-dimensional urban landscape in structuring atmospheric microbiomes and employs mobile monitoring over ~1,920 kilometers to measure continuous biodiversity. We found more diverse communities outdoors that significantly differ from indoor-transit air in microbial community structure, function, likely source environment, and potentially pathogenic fraction of the community. Variation in the structure of the urban landscape was associated with diversity and function of the near-surface atmospheric microbiome in outdoor samples.

Microbial, environmental and anthropogenic factors influencing the indoor microbiome of the built environment

A built environment is a human-made environment providing surroundings for human occupancy, activities, and settlement. It is supposed to safeguard humans from all undesirable and harmful pollutants; however, indoor concentrations of some pollutants are much greater than that of the outdoors. Bioaerosols infiltrate from the outdoors in addition to many indoor sources of bioaerosols including the use of various chemicals as well as activities like cooking, smoking, cleaning, or even normal movement. They are also associated with a number of serious health concerns. Various ecological factors associated with the generation, the persistence as well as the dispersal of these microbial components of indoor bioaerosols, are discussed in this review, that have not been considered all together till now. The factors like microbial taxa, environmental factors, and anthropogenic activities (human occupancy, activities, and impact of urbanization) are addressed in the review. Effects of both indoor environmental factors like architectural design, lighting, ventilation, temperature, humidity, indoor/outdoor ratio, particulate matter, indoor chemistry as well as outdoor environmental factors like geography, seasons, and meteorology on the microbial concentrations have been discussed. Efforts are underway to design selective pressures for microbes to create a healthy symbiotic built microbiome as the "right" indoor microbiome is a "healthy" indoor microbiome.

Bioburden in sleeping environments from Portuguese dwellings

A wider characterization of indoor air quality during sleep is still lacking in the literature. This study intends to assess bioburden before and after sleeping periods in Portuguese dwellings through active methods (air sampling) coupled with passive methods, such as electrostatic dust cloths (EDC); and investigate associations between before and after sleeping and bioburden. In addition, and driven by the lack of information regarding fungi azole-resistance in Portuguese dwellings, a screening with supplemented media was also performed. The most prevalent genera of airborne bacteria identified in the indoor air of the bedrooms were Micrococcus (41%), Staphylococcus (15%) and Neisseria (9%). The major indoor bacterial species isolated in all ten studied bedrooms were Micrococcus luteus (30%), Staphylococcus aureus (13%) and Micrococcus varians (11%). Our results highlight that our bodies are the source of the majority of the bacteria found in the indoor air of our homes. Regarding air fungal contamination, Chrysosporium spp. presented the highest prevalence both in after the sleeping period (40.8%) and before the sleeping period (28.8%) followed by Penicillium spp. (23.47% morning; 23.6% night) and Chrysonilia spp. (12.4% morning; 20.3% night). Several Aspergillus sections were identified in air and EDC samples. However, none of the fungal species/strains (Aspergillus sections Fumigati, Flavi, Nidulantes and Circumdati) were amplified by qPCR in the analyzed EDC. The correlations observed suggest reduced susceptibility to antifungal drugs of some fungal species found in sleeping environments. Toxigenic fungal species and indicators of harmful fungal contamination were observed in sleeping environments.

Bacterial Contamination Analysis of Residential Toilet Room Environment and Delivery of Residual Bacterial Growth Prevention Efficacy on Residential Toilet Permeable Surfaces Using Toilet Air Freshener Product

Toilet malodor is one of the most concerned malodor in residential houses, so that many technologies and products have been developed by which is aiming to remove or reduce such toilet malodor. Toilet malodour is generated from human faecal matters left inside of toilet bowl and from that deposited outside of toilet bowl such as toilet floors. In order to remove or prevent the malodor generated outside of toilet bowl, it is effective to do more frequent cleaning of toilet room surfaces or place a deodorizer which mask the malodour by perfume. We developed a toilet deodorizer which is preventing malodor generation outside of toilet bowl more effectively by delivering antibacterial efficacy on toilet room permeable surfaces. We analyzed microbiological quality of residential toilet rooms and found that toilet floor is the most contaminated location by bacteria, so that we developed a test method using materials frequently used for residential toilet floors such as vinyl cushion and using bacteria commonly found in toilet room environment. As the results, we found the product can provide bacterial growth prevention efficacy on permeable materials and prevent toilet malodor effectively.

Shared bacterial communities between soil, stored drinking water, and hands in rural Bangladeshi households

Understanding household-level transmission pathways of fecal pathogens can provide insight for developing effective strategies to reduce diarrheal illness in low- and middle-income countries. We applied whole bacterial community analysis to investigate pathways of bacterial transmission in 50 rural Bangladeshi households. SourceTracker was used to quantify the shared microbial community in household reservoirs (stored drinking water, soil, and hands) and estimate the percentage of fecal-associated bacteria from child and mothers' feces in these reservoirs. Among the reservoirs studied, most bacterial transfer occurred between mothers' and children's hands and between mothers' hands and stored water. The relative percentage of human fecal-associated bacteria in all household reservoirs was low. We also quantified the number of identical amplicon sequence variants within and between individual households to assess bacterial community exchange in the domestic environment. Intra-household sharing of bacteria between mothers' and children's hands and between hands and soil was significantly greater than inter-household sharing.

Methicillin Resistant Staphylococcus aureus and public fomites: a review

Staphylococcus genus is a Gram-positive coccus normally associated with skin and mucous membranes of warm-blooded animals. It is part of the commensal human microflora, or found in animals, or contaminating surfaces in the community and hospital settings. Staphylococcus aureus is the most pathogenic species belonging to this genus, as it possesses a collection of virulence factors that are expressed solely to evade the immune system. The increase in the misuse of antimicrobial agents predisposed S. aureus to develop antibiotic resistance, including the resistance to methicillin which led to the emergence of Methicillin-Resistant S. aureus (MRSA). MRSA is considered one of the most dangerous nosocomial pathogens causing many hard to treat infections in hospitals and was named as Hospital Associated MRSA (HA-MRSA). Over the past 20-25 years, MRSA was isolated from community settings and thus Community Associated MRSA (CA-MRSA) has emerged. Inside hospitals, MRSA has been isolated from fomites in contact with patients, as well as staff's protective and personal items. This review highlights the worldwide prevalence of MRSA on fomites within the contexts of hospital and community settings.

A Landscape of Opportunities for Microbial Ecology Research

Microbes encompass tremendous biodiversity, provide support to all living forms, including humans, and play an important role in many ecosystem services. The rules that govern microorganism community assembly are increasingly revealed due to key advances in molecular and analytical methods but their understanding remain a key challenge in microbial ecology. The existence of biogeographic patterns within microbial communities has been established and explained in relation to landscape-scale processes, including selection, drift, dispersal and mutation. The effect of habitat patchiness on microorganisms' assembly rules remains though incompletely understood. Here, we review how landscape ecology principles can be adapted to explore new perspectives on the mechanisms that determine microbial community structure. To provide a general overview, we characterize microbial landscapes, the spatial and temporal scales of the mechanisms that drive microbial assembly and the feedback between microorganisms and landscape structure. We provide evidence for the effects of landscape heterogeneity, landscape fragmentation and landscape dynamics on microbial community structure, and show that predictions made for macro-organisms at least partly also apply to microorganisms. We explain why emerging metacommunity approaches in microbial ecology should include explicit characterization of landscape structure in their development and interpretation. We also explain how biotic interactions, such as competition, prey-predator or mutualist relations may influence the microbial landscape and may be involved in the above-mentioned feedback process. However, we argue that the application of landscape ecology to the microbial world cannot simply involve transposing existing theoretical frameworks. This is due to the particularity of these organisms, in terms of size, generation time, and for some of them, tight interaction with hosts. These characteristics imply dealing with unusual and dependent space and time scales of effect. Evolutionary processes have also a strong importance in microorganisms' response to their landscapes. Lastly, microorganisms' activity and distribution induce feedback effects on the landscape that have to be taken into account. The transposition of the landscape ecology framework to microorganisms provides many challenging research directions for microbial ecology.

Assessing the Risk of Transfer of Microorganisms at the International Space Station Due to Cargo Delivery by Commercial Resupply Vehicles

BACKGROUND

With increasing numbers of interplanetary missions, there is a need to establish robust protocols to ensure the protection of extraterrestrial planets being visited from contamination by terrestrial life forms. The current study is the first report comparing the commercial resupply vehicle (CRV) microbiome with the International Space Station (ISS) microbiome to understand the risks of contamination, thus serving as a model system for future planetary missions.

RESULTS

Samples obtained from the internal surfaces and ground support equipment of three CRV missions were subjected to various molecular techniques for microbial diversity analysis. In total, 25 samples were collected with eight defined locations from each CRV mission prior to launch. In general, the internal surfaces of vehicles were clean, with an order of magnitude fewer microbes compared to ground support equipment. The first CRV mission had a larger microbial population than subsequent CRV missions, which were clean as compared to the initial CRV locations sampled. Cultivation assays showed the presence of Actinobacteria, Proteobacteria, Firmicutes, and Bacteroidetes and members of Ascomycota and Basidiomycota. As expected, shotgun metagenome analyses revealed the presence of more microbial taxa compared to cultivation-based assays. The internal locations of the CRV microbiome reportedly showed the presence of microorganisms capable of tolerating ultraviolet radiation (e.g., Bacillus firmus) and clustered separately from the ISS microbiome.

CONCLUSIONS

The metagenome sequence comparison of the CRV microbiome with the ISS microbiome revealed significant differences showing that CRV microbiomes were a negligible part of the ISS environmental microbiome. These findings suggest that the maintenance protocols in cleaning CRV surfaces are highly effective in controlling the contaminating microbial population during cargo transfer to the ISS via the CRV route.

Infant Skin Bacterial Communities Vary by Skin Site and Infant Age across Populations in Mexico and the United States

This study contributes to the sparse literature on the infant skin microbiome in general, and the virtually nonexistent literature on the infant skin microbiome in a field setting. While microbiome research often addresses patterns at a national scale, this study addresses the influence of population-level factors, such as maternal socioeconomic status and contact with caregivers, on infant skin bacterial communities. This approach strengthens our understanding of how local variables influence the infant skin microbiome, and paves the way for additional studies to combine biological sample collection with questionnaires to adequately capture how specific behaviors dictate infant microbial exposures. Work in this realm has implications for infant care and health, as well as for investigating how the microbial communities of different body sites develop over time, with applications to specific health outcomes associated with the skin microbiome (e.g., immune system development or atopic dermatitis).

Daily practices put humans in close contact with the surrounding environment, and differences in these practices have an impact on human physiology, development, and health. There is mounting evidence that the microbiome represents an interface that mediates interactions between the human body and the environment. In particular, the skin microbiome serves as the primary interface with the external environment and aids in host immune function by contributing as the first line of defense against pathogens. Despite these important connections, we have only a basic understanding of how the skin microbiome is first established, or which environmental factors contribute to its development. To this end, this study compared the skin bacterial communities of infants (n = 47) living in four populations in Mexico and the United States that span the socioeconomic gradient, where we predicted that variation in physical and social environments would shape the infant skin microbiome. Results of 16S rRNA bacterial gene sequencing on 119 samples (armpit, hand, and forehead) showed that infant skin bacterial diversity and composition are shaped by population-level factors, including those related to socioeconomic status and household composition, and vary by skin site and infant age. Differences in infant-environment interactions, including with other people, appear to vary across the populations, likely influencing infant microbial exposures and, in turn, the composition of infant skin bacterial communities. These findings suggest that variation in microbial exposures stemming from the local environment in infancy can impact the establishment of the skin microbiome across body sites, with implications for developmental and health outcomes.

IMPORTANCE This study contributes to the sparse literature on the infant skin microbiome in general, and the virtually nonexistent literature on the infant skin microbiome in a field setting. While microbiome research often addresses patterns at a national scale, this study addresses the influence of population-level factors, such as maternal socioeconomic status and contact with caregivers, on infant skin bacterial communities. This approach strengthens our understanding of how local variables influence the infant skin microbiome, and paves the way for additional studies to combine biological sample collection with questionnaires to adequately capture how specific behaviors dictate infant microbial exposures. Work in this realm has implications for infant care and health, as well as for investigating how the microbial communities of different body sites develop over time, with applications to specific health outcomes associated with the skin microbiome (e.g., immune system development or atopic dermatitis).