Airborne microbial communities in the atmospheric environment of urban hospitals in China

Method for detection of pathogenic bacteria from indoor air microbiome samples using high-throughput amplicon sequencing

The exposure of the air microbiome in indoor air posed a detrimental health effect to the building occupants compared to the outdoor air. Indoor air in hospitals has been identified as a reservoir for various pathogenic microbes. The conventional culture-dependent method has been widely used to access the microbial community in the air. However, it has limited capability in enumerating the complex air microbiome communities, as some of the air microbiomes are uncultivable, slow-growers, and require specific media for cultivation. Here, we utilized a culture-independent method via amplicon sequencing to target the V3 region of 16S rRNA from the pool of total genomic DNA extracted from the dust samples taken from hospital interiors. This method will help occupational health practitioners, researchers, and health authorities to efficiently and comprehensively monitor the presence of harmful air microbiome thus take appropriate action in controlling and minimizing the health risks to the hospital occupants. Key features;•Culture-independent methods offer fast, comprehensive, and unbias profiles of pathogenic and non-pathogenic bacteria from the air microbiomes.•Unlike the culture-dependent method, amplicon sequencing allows bacteria identification to the lowest taxonomy levels.

Expanding the focus of the One Health concept: links between the Earth-system processes of the planetary boundaries framework and antibiotic resistance

The scientific community warns that our impact on planet Earth is so acute that we are crossing several of the planetary boundaries that demarcate the safe operating space for humankind. Besides, there is mounting evidence of serious effects on people's health derived from the ongoing environmental degradation. Regarding human health, the spread of antibiotic resistant bacteria is one of the most critical public health issues worldwide. Relevantly, antibiotic resistance has been claimed to be the quintessential One Health issue. The One Health concept links human, animal, and environmental health, but it is frequently only focused on the risk of zoonotic pathogens to public health or, to a lesser extent, the impact of contaminants on human health, i.e., adverse effects on human health coming from the other two One Health "compartments". It is recurrently claimed that antibiotic resistance must be approached from a One Health perspective, but such statement often only refers to the connection between the use of antibiotics in veterinary practice and the antibiotic resistance crisis, or the impact of contaminants (antibiotics, heavy metals, disinfectants, etc.) on antibiotic resistance. Nonetheless, the nine Earth-system processes considered in the planetary boundaries framework can be directly or indirectly linked to antibiotic resistance. Here, some of the main links between those processes and the dissemination of antibiotic resistance are described. The ultimate goal is to expand the focus of the One Health concept by pointing out the links between critical Earth-system processes and the One Health quintessential issue, i.e., antibiotic resistance.

Metagenomic insights into isolable bacterial communities and antimicrobial resistance in airborne dust from pig farms

This study aims to investigate bacterial communities and antimicrobial resistance (AMR) in airborne dust from pig farms. Airborne dust, pig feces and feed were collected from nine pig farms in Thailand. Airborne dust samples were collected from upwind and downwind (25 meters from pig house), and inside (in the middle of the pig house) of the selected pig house. Pig feces and feed samples were individually collected from the pen floor and feed trough from the same pig house where airborne dust was collected. A direct total bacteria count on each sampling plate was conducted and averaged. The ESKAPE pathogens together with Escherichia coli, Salmonella, and Streptococcus were examined. A total of 163 bacterial isolates were collected and tested for MICs. Pooled bacteria from the inside airborne dust samples were analyzed using Metagenomic Sequencing. The highest bacterial concentration (1.9-11.2 × 103 CFU/m3) was found inside pig houses. Staphylococcus (n = 37) and Enterococcus (n = 36) were most frequent bacterial species. Salmonella (n = 3) were exclusively isolated from feed and feces. Target bacteria showed a variety of resistance phenotypes, and the same bacterial species with the same resistance phenotype were found in airborne dust, feed and fecal from each farm. Metagenomic Sequencing analysis revealed 1,652 bacterial species across all pig farms, of which the predominant bacterial phylum was Bacillota. One hundred fifty-nine AMR genes of 12 different antibiotic classes were identified, with aminoglycoside resistance genes (24%) being the most prevalent. A total of 251 different plasmids were discovered, and the same plasmid was detected in multiple farms. In conclusion, the phenotypic and metagenomic results demonstrated that airborne dust from pig farms contained a diverse array of bacterial species and genes encoding resistance to a range of clinically important antimicrobial agents, indicating the significant role in the spread of AMR bacterial pathogens with potential hazards to human health. Policy measurements to address AMR in airborne dust from livestock farms are mandatory.

Systematic evaluation of the impact of standard storage conditions on plasmid conjugation behavior in wastewater samples

Filter mating experiment is widely used to study the conjugation behavior of plasmids and associated antibiotic resistance in environmental settings, however, the influence and biases brought by sample storage conditions (temperature and duration) were not yet systematically elaborated. This study systematically investigated the influence of standard storage conditions (4 °C, -20 °C, -80 °C) on plasmid conjugation behavior in influent (Inf) and activated sludge (AS) samples from sewage treatment plants (STP). The findings revealed a significant reduction in conjugation efficiency under all the tested storage conditions except for 1-week storage at 4 °C. Notably, storing at -80 °C maintained conjugation activities in activated sludge more effectively compared to -20 °C. However, the preservation performance was less effective for influent samples, which consist mainly of anaerobe-dominant communities. Systematic loss of IncH-type plasmids was observed in influent samples stored at 4 °C and -20 °C. Correspondingly, the plasmid-carrying resistome genotypes detected in the influent samples showed a clear downward trend with the increase in storage duration when stored at 4 °C and -20 °C. A relatively uniform composition in terms of incompatibility type and resistome profile was observed across activated sludge samples, regardless of the varied storage conditions. This study highlights the critical impact of storage conditions on plasmid conjugation behavior and resistome composition, offering valuable insights for optimal sample handling in resistome research.

Pollution characteristics and potential health effects of airborne microplastics and culturable microorganisms during urban haze in Harbin, China

In this study, active sampling technology was used to collect microplastics (MPs) and microorganisms simultaneously on haze days in Harbin, China. Airborne MPs concentrations in Junior high school (162.4 ± 44.6 particles/m3) with high vehicular and pedestrian traffic was higher than those in University (63.2 ± 21.8 particles/m3) and Park (12.8 ± 5.5 particles/m3). More airborne MPs were detected in the night samples than in the morning and noon samples. The majority (69.06 %) of airborne MPs measured less than 100 μm, with fibers (69.4 %) being the predominant form. Polyesters and polyethylene were the dominant polymers. In addition, airborne MPs concentrations were positively correlated with microorganisms and PM10 concentrations, and the health hazards associated with microorganisms and MPs exposure via inhalation far exceeded those associated with skin contact, which can serve as a theoretical foundation for considering MPs as indicators of air quality in the future.

Pathogenic bacteria and fungi in bioaerosols from specialized hospitals in Shandong province, East China

Bacteria and fungi are abundant and ubiquitous in bioaerosols in hospital environments. Understanding the distribution and diversity of microbial communities within bioaerosols is critical for mitigating their detrimental effects. Our knowledge on the composition of bacteria or fungi in bioaerosols is limited, especially the potential pathogens present in fine particulate matter (PM2.5) from specialized hospitals. Thirty p.m.2.5 filter samples were collected from five hospitals (i.e., oral, dermatology, chest, eye, and general hospitals) in Shandong Province, East China. The diversity of bacteria and fungi was analyzed at the species level using single-molecule real-time sequencing of the 16 S and internal transcribed spacer 1 (ITS) ribosomal genes, respectively. Significant differences were detected across sampling sites in terms of microbial diversity and community composition in PM2.5 as well as pollution concentrations. The range of PM2.5 concentrations observed in hospital halls was higher, ranging from 39.0 to 46.2 μg/m3, compared to the wards where the concentrations ranged from 10.7 to 25.2 μg/m3. Furthermore, microbial variations in PM2.5 bioaerosols were associated with hospital type. The most dominant pathogens identified were Vibrio metschnikovii, Staphylococcus epidermidis, Staphylococcus haemolyticus, Fusarium pseudensiforme, and Aspergillus ruber. Among these, A. ruber was identified as an opportunistic fungus in a hospital setting for the first time. Nine potentially novel strains of F. pseudensiforme, showing 84.5%-92.0% ITS sequence similarity to known Fusarium isolates, were identified in PM2.5 samples from all hospitals (excluding an eye hospital). This study highlights the importance of hospital environments in shaping microbial aerosol communities. To the best of our knowledge, this is the first study to provide insights into the bacterial and fungal biodiversity of PM2.5 in specialized hospitals, enriching research in healthcare environmental microbiology and carrying significant public health implications.

Dynamic human exposure to airborne bacteria-associated antibiotic resistomes revealed by longitudinal personal monitoring data

Airborne antibiotic-resistant bacteria (ARB) can critically impact human health. We performed resistome profiling of 283 personal airborne exposure samples from 15 participants spanning 890 days and 66 locations. We found a greater diversity and abundance of airborne bacteria community and antibiotic resistomes in spring than in winter, and temperature contributed largely to the difference. A total of 1123 bacterial genera were detected, with 16 genera dominating. Of which, 7/16 were annotated as major antibiotic resistance gene (ARG) hosts. The participants were exposed to a highly dynamic collection of ARGs, including 322 subtypes conferring resistance to 18 antibiotic classes dominated by multidrug, macrolide-lincosamide-streptogramin, β-lactam, and fosfomycin. Unlike the overall community-level bacteria exposure, an extremely high abundance of specific ARG subtypes, including lunA and qacG, were found in some samples. Staphylococcus was the predominant genus in the bacterial community, serving as a primary bacterial host for the ARGs. The annotation of ARG-carrying contigs indicated that humans and companion animals were major reservoirs for ARG-carrying Staphylococcus. This study contextualized airborne antibiotic resistomes in the precision medicine framework through longitudinal personal monitoring, which can have broad implications for human health.

Comprehensive profiling and risk assessment of antibiotic resistance genes in a drinking water watershed by integrated analysis of air-water-soil

The prevalence of antibiotic resistance genes (ARGs) in diverse habitats threatens public health. Watersheds represent critical freshwater ecosystems that interact with both the soil and atmosphere. However, a holistic understanding of ARGs distribution across these environmental media is currently inadequate. We profiled ARGs and bacterial communities in air-water-soil in the same watershed area during four seasons using high-throughput qPCR and 16S rRNA gene sequencing. Our findings demonstrated that aminoglycoside resistance genes (58.5%) were dominant in water, and multidrug resistance genes (55.2% and 54.2%) were dominant in soil and air. Five ARGs and nineteen bacterial genera were consistently detected in all samples, were named as shared genes or bacteria. Co-occurrence Network analysis revealed the co-occurrence module of resistance genes, mobile genetic elements (MGEs), and potential bacterial hosts, indicating that shared genes and bacteria may persist and co-spread across different environmental media. The risk assessment framework, based on ARGs' abundance, detection rate, and mobility, identified 33 high-risk ARGs. This is essential to evaluate the health risks of ARGs and to develop strategies to limit the threat of antibiotic resistance. Our study offers new insights into the risks associated with ARGs in the environment and suggests that ARGs may depend on specific bacterial cohabitants that co-exist with MGEs to facilitate their spread across environmental interfaces.

Metagenomic and Machine Learning Meta-Analyses Characterize Airborne Resistome Features and Their Hosts in China Megacities

Urban ambient air contains a cocktail of antibiotic resistance genes (ARGs) emitted from various anthropogenic sites. However, what is largely unknown is whether the airborne ARGs exhibit site-specificity or their pathogenic hosts persistently exist in the air. Here, by retrieving 1.2 Tb metagenomic sequences (n = 136), we examined the airborne ARGs from hospitals, municipal wastewater treatment plants (WWTPs) and landfills, public transit centers, and urban sites located in seven of China's megacities. As validated by the multiple machine learning-based classification and optimization, ARGs' site-specificity was found to be the most apparent in hospital air, with featured resistances to clinical-used rifamycin and (glyco)peptides, whereas the more environmentally prevalent ARGs (e.g., resistance to sulfonamide and tetracycline) were identified being more specific to the nonclinical ambient air settings. Nearly all metagenome-assembled genomes (MAGs) that possessed the site-featured resistances were identified as pathogenic taxa, which occupied the upper-representative niches in all the neutrally distributed airborne microbial community (P < 0.01, m = 0.22-0.50, R2 = 0.41-0.86). These niche-favored putative resistant pathogens highlighted the enduring antibiotic resistance hazards in the studied urban air. These findings are critical, albeit the least appreciated until our study, to gauge the airborne dimension of resistomes' features and fates in urban atmospheric environments.

From air to airway: Dynamics and risk of inhalable bacteria in municipal solid waste treatment systems

Municipal solid waste treatment (MSWT) system emits a cocktail of microorganisms that jeopardize environmental and public health. However, the dynamics and risks of airborne microbiota associated with MSWT are poorly understood. Here, we analyzed the bacterial community of inhalable air particulates (PM10, n = 71) and the potentially exposed on-site workers' throat swabs (n = 30) along with waste treatment chain in Shanghai, the largest city of China. Overall, the airborne bacteria varied largely in composition and abundance during the treatment (P < 0.05), especially in winter. Compared to the air conditions, MSWT-sources that contributed to 15 ∼ 70% of airborne bacteria more heavily influenced the PM10-laden bacterial communities (PLS-SEM, β = 0.40, P < 0.05). Moreover, our year-span analysis found PM10 as an important media spreading pathogens (104 ∼ 108 copies/day) into on-site workers. The machine-learning identified Lactobacillus and Streptococcus as pharynx-niched featured biomarker in summer and Rhodococcus and Capnocytophaga in winter (RandomForest, ntree = 500, mtry = 10, cross = 10, OOB = 0%), which closely related to their airborne counterparts (Procrustes test, P < 0.05), suggesting that MSWT a dynamic hotspot of airborne bacteria with the pronounced inhalable risks to the neighboring communities.

Monodisperse Fluorescent Polystyrene Microspheres for Staphylococcus aureus Aerosol Simulation

Staphylococcus aureus (SA) is one of the most common causes of hospital-acquired infections and foodborne illnesses and is commonly found in nature in air, dust, and water. The spread and transmission of SA aerosols in the air has the potential to cause epidemic transmission among humans and between humans and animals. To effectively provide the timely warning of SA aerosols in the atmosphere, the identification and detection of SA aerosol concentrations are required. Due to their homogeneous physicochemical properties, highly monodisperse submicron polystyrene (PS) microspheres can be used as one of the simulants of SA aerosols. In this study, 800 nm monodisperse fluorescent PS (f-PS) microspheres with fluorescence spectra and particle size distribution similar to those of SA were prepared. The 800 nm monodisperse f-PS microspheres had a fluorescence characteristic peak at 465 nm; in aerosols, 800 nm monodisperse f-PS microspheres with a similar particle size distribution to that of SA were further verified, mainly in the range of 500 nm-1000 nm; finally, it was found that the f-PS microspheres still possessed similar fluorescence characteristics after 180 days. The f-PS microspheres prepared in this study are very close to SA in terms of particle size and fluorescence properties, providing a new idea for aerosol analogs of SA.

Airborne bacterial community and antibiotic resistome in the swine farming environment: Metagenomic insights into livestock relevance, pathogen hosts and public risks

Globally extensive use of antibiotics has accelerated antimicrobial resistance (AMR) in the environment. As one of the biggest antibiotic consumers, livestock farms are hotspots in AMR prevalence, especially those in the atmosphere can transmit over long distances and pose inhalation risks to the public. Here, we collected total suspended particulates in swine farms and ambient air of an intensive swine farming area. Bacterial communities and antibiotic resistomes were analyzed using amplicon and metagenomic sequencing approaches. AMR risks and inhalation exposure to potential human-pathogenic antibiotic-resistant bacteria (HPARB) were subsequently estimated with comparison to the reported hospital samples. The results show that swine farms shaped the airborne bacterial community by increasing abundances, reducing diversities and shifting compositions. Swine feces contributed 77% of bacteria to swine farm air, and about 35% to ambient air. Airborne antibiotic resistomes in swine farms mainly conferred resistance to tetracyclines, aminoglycosides and lincosamides, and over 48% were originated from swine feces. Distinct to the hospital air, Firmicutes were dominant bacteria in swine farming environments with conditional pathogens including Clostridium, Streptococcus and Aerococcus being major hosts of antibiotic resistance genes (ARGs). Therein, genomes of S. alactolyticus carrying (transposase/recombinase-associated) ARGs and virulence factor genes were retrieved from the metagenomes of all swine feces and swine farm air samples, but they were not detected in any hospital air samples. This suggests the indication of S. alactolyticus in swine farming environments with potential hazards to human health. Swine farm air faced higher AMR risks than hospital air and swine feces. The inhalation intake of HPARB by a swine farm worker was about three orders of magnitude higher than a person who works in the hospital. Consequently, this study depicted atmospheric transmission of bacteria and antibiotic resistomes from swine feces to the environment.

Evolution and improvement options of ecological environmental quality in the world's largest emerging urban green heart as revealed by a new assessment framework

Large ecological green spaces in cities are often designated as Urban Green Hearts (GHs) to support the ecological and recreational needs of urbanites. While GHs protection and sustainable development have been a high priority for urban planning and management, ecological environment quality (EEQ) of GHs has rarely been monitored and assessed. Here, we proposed a comprehensive assessment framework for EEQ based on entropy weights and rank-sum ratios methods, and applied the framework to the world's largest GH, Changsha-Zhuzhou-Xiangtan urban agglomeration Green Heart (CZT-GH), and its 5 km and 10 km buffer zones to examine the spatial-temporal dynamics of its EEQ from 2000 to 2019. Compared with the buffer zones, the EEQ in the CZT-GH was the best, with an annual average of 44.92 % of the area being High-grades EEQ. The restoration trend of EEQ was most conspicuous in only 8.4 % of CZT-GH, a small fraction compared with 25.1 % and 66.5 % of the CZT-GH showing deterioration trend and no change, respectively. Five factors were identified that calls for management attention: land use and cover change, spatial heterogeneity in vegetation restoration, temporal fluctuation in air quality improvement, comprehensive EEQ assessment and restoration, and capacity to cope with ecological risks. The approach, issues identified, and management measures proposed in this study should be applicable to GHs in general. The generic EEQ assessment framework and approaches developed in this study are generic and objective and therefore can be easily adapted to other regions; the procedures used to quantify the spatial and temporal changes of EEQ and identify underlying management issues provide essential information for formulating adaptive management measures of EEQ in general. SYNOPSIS: Taking the largest urban Green Heart as a case study, we established and applied a new general ecological environment quality (EEQ) evaluation system to monitor EEQ changes, identify issues, and propose management options.

Detection of multidrug resistant pathogenic bacteria and novel complex class 1 integrons in campus atmospheric particulate matters

Recent advances provided overwhelming evidence that atmospheric particulate matters carry a substantial amount of antibiotic resistance genes (ARGs). It has also been documented that polluted air facilitates transmission of bacterial pathogenesis and antimicrobial resistance (AMR). These investigations generally used culture-independent approaches which reveal sophisticated microbiomic and resistomic compositions in particulate matters, while culture-dependent methods directly demonstrating presence of live, functional bacteria has not been fully applied. In recent years, efforts undertaken worldwide managed to reduce air particulate matter pollution, leading to cleaner air in many parts of world, including China. Whether atmospheric particulate matters may still function as vehicles for pathogenic bacteria and AMR in improving air conditions is turning into an interesting question to address. In attempt to answer this question, a culture-dependent approach is used to find out the putative role of atmospheric particulate matters in relatively 'clean' air to transmit pathogenic bacteria and AMR in this work. By harvesting particulate matters in an unindustrialized and less-polluted university campus, culturing and identifying bacteria in particulate matters, and characterizing pathogenesis and AMR properties of these bacteria, interesting findings were made that even in relatively 'clean' air, antibiotic-resistant pathogenic bacteria are prevalent; and that mobile genetic elements including integrons are widespread. In particular, in air samples collected, multidrug-resistant hemolytic Bacillus strains that may pose significant health threat could be identified. Complex class 1 integrons, two of which carry novel antibiotic resistant gene cassette arrays, were also found for the first time in airborne bacteria, suggesting the danger of horizontal transfer of AMR in air. In conclusion, using culture-dependent methods, this work shows that atmospheric particulate matters are viable vehicles for the transmission of bacterial pathogenesis and AMR, and that even in relatively 'clean' air, the threat of airborne antibiotic-resistant pathogens is significant.

City-scale distribution of airborne antibiotic resistance genes

Concerns around urban air quality have been increasing worldwide due to large-scale urbanization. A large volume of work has been focused on the chemical pollutants in the air and their impacts on human health. However, the profile of airborne microbial contaminants, especially antibiotic resistance genes (ARGs), is largely understudied. Here, high-throughput quantitative PCR (HT-qPCR) was employed to explore the temporal and spatial distribution of airborne ARGs from 11 sites with various functional zones and different urbanization levels within Xiamen, China. A total of 104 unique ARGs and 23 mobile genetic elements (MGEs) were detected across all samples. Temporal shift was observed in the distribution of ARG profiles, with significantly higher relative abundance of ARGs detected in summer than that in spring. Temperature is the key predictor of the total relative abundance of ARGs and MGEs in summer, while PM_2.5 and PM₁₀ were the two most important factors affecting the abundance in spring. Our findings suggest that urban aerosols accommodate rich and dynamic ARGs and MGEs, and emphasize the role of temperature, air quality and anthropogenic activities in shaping the profile of ARGs.

Comparison of bacterial community structure in PM2.5 during hazy and non-hazy periods in Guilin, South China

In recent years, significant efforts have been made to study changes in the levels of air pollutants at regional and urban scales, and changes in bioaerosols during air pollution events have attracted increasing attention. In this study, the bacterial structure of PM_2.5 was analysed under different environmental conditions during hazy and non-hazy periods in Guilin. A total of 32 PM_2.5 samples were collected in December 2020 and July 2021, and the microbial community structures were analysed using high-throughput sequencing methods. The results show that air pollution and climate change alter the species distribution and community diversity of bacteria in PM_2.5, particularly Sphingomonas and Pseudomonas. The structure of the bacterial community composition is related to diurnal variation, vertical height, and urban area and their interactions with various environmental factors. This is a comprehensive study that characterises the variability of bacteria associated with PM_2.5 in a variety of environments, highlighting the impacts of environmental effects on the atmospheric microbial community. The results will contribute to our understanding of haze trends in China, particularly the relationship between bioaerosol communities and the urban environment.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s10453-022-09777-0.

Charting the landscape of the environmental exposome

The exposome depicts the total exposures in the lifetime of an organism. Human exposome comprises exposures from environmental and humanistic sources. Biological, chemical, and physical environmental exposures pose potential health threats, especially to susceptible populations. Although still in its nascent stage, we are beginning to recognize the vast and dynamic nature of the exposome. In this review, we systematically summarize the biological and chemical environmental exposomes in three broad environmental matrices-air, soil, and water; each contains several distinct subcategories, along with a brief introduction to the physical exposome. Disease-related environmental exposures are highlighted, and humans are also a major source of disease-related biological exposures. We further discuss the interactions between biological, chemical, and physical exposomes. Finally, we propose a list of outstanding challenges under the exposome research framework that need to be addressed to move the field forward. Taken together, we present a detailed landscape of environmental exposome to prime researchers to join this exciting new field.

Associations between air pollutants and risk of respiratory infection: patient-based bacterial culture in sputum

Air pollution is a crucial risk factor for respiratory infection. However, the relationships between air pollution and respiratory infection based on pathogen detection are scarcely explored in the available literature. We detected respiratory infections through patient-based bacterial culture in sputum, obtained hourly data of all six pollutants (PM_2.5, PM₁₀, SO₂, NO, CO, and O₃) from four air quality monitoring stations, and assessed the relationships of air pollutants and respiratory bacterial infection and multi-drug-resistant bacteria. Air pollution remains a challenge for Mianyang, China, especially PM_2.5 and PM₁₀, and there are seasonal differences; pollution is the heaviest in winter and the lowest in summer. A total of 4237 pathogenic bacteria were detected, and the positive rate of multi-drug-resistant bacteria was 0.38%. Similar seasonal differences were found with respect to respiratory infection. In a single-pollutant model, all pollutants were significantly associated with respiratory bacterial infection, but only O₃ was significantly associated with multi-drug-resistant bacteria. In multi-pollutant models (adjusted for one pollutant), the relationships of air pollutants with respiratory bacterial infection remained significant, while PM_2.5, PM₁₀, and O₃ were significantly associated with the risk of infection with multi-drug-resistant bacteria. When adjusted for other five pollutants, only O₃ was significantly associated with respiratory bacterial infection and the risk of infection with multi-drug-resistant bacteria, showing that O₃ is an independent risk factor for respiratory bacterial infection and infection with multi-drug-resistant bacteria. In summary, this study highlights the adverse effects of air pollution on respiratory infection and the risk of infection with multi-drug-resistant bacteria, which may provide a basis for the formulation of environmental policy to prevent respiratory infections.

Distribution of typical antibiotic resistance genes in underlying surface sediments from urban commercial public squares and their potential hosts

Increasing attention has been paid to antibiotic resistance genes (ARGs) in environments. However, no available literature could be found on ARGs contamination in urban underlying surface sediments. In this study, sediments from commercial public squares around Nanjing (China) were selected for the investigation of target ARGs distribution, showing that intracellular ARGs (iARGs) in particles were the dominant with their relative abundances in descending order of 4.82 × 10^-2 copies/16S rRNA (<0.063 mm), 4.18 × 10^-2 copies/16S rRNA (0.063-0.125 mm), 3.70 × 10^-2 copies/16S rRNA (0.25-0.5 mm), 3.44 × 10^-2 copies/16S rRNA (0.5-1 mm), 3.20 × 10^-2 copies/16S rRNA (0.125-0.25 mm) and 9.53 × 10^-3 copies/16S rRNA (1-2 mm), which was different with that of extracellular ARGs (eARGs). The influence of street sweeping on ARGs levels indicated that the species and relative abundances for both iARGs and eARGs in sediments from different sites were not consistent with the corresponding population densities. The correlation between ARGs and dominant bacterial communities implied that both Firmicutes and Bacteroidetes were positively correlated with ARGs (P < 0.01). The role of solar UV disinfection demonstrated that UV irradiation could inactivate antibiotic resistance bacteria (ARB) slightly with 0.5-1.0 log reduction, implying a considerable risk of ARB after solar irradiation. Our results suggested that it would need the more effective sweeping modes for the cleaning of small particles (<0.25 mm) and the higher disinfection to ARGs potential hosts (like Firmicutes and Blastocatella).

Antibiotic resistance of airborne bacterial populations in a hospital environment

Bacteria in a hospital environment potentially cause hospital-acquired infections (HAIs), particularly in immunocompromised individuals. Treatments of HAIs with antibiotics, however, are ineffective due to the emergence of antibiotic-resistant bacteria (ARB). This study aims to identify airborne bacteria in a tertiary hospital in Malaysia and screen for their resistance to commonly used broad-spectrum antibiotics. Airborne bacteria were sampled using active sampling at the respiratory ward (RW), physician clinic (PC) and emergency department (ED). Physical parameters of the areas were recorded, following the Industry Code of Practice on Indoor Air Quality 2010 (ICOP IAQ 2010). Bacterial identification was based on morphological and biochemical tests. Antibiotic resistance screening was carried out using the Kirby-Bauer disk diffusion method. Results showed that the highest bacterial population was found in the highest density occupancy area, PC (1024 ± 54 CFU/m³), and exceeded the acceptable limit. Micrococcus spp., Staphylococcus aureus, α- and β-Streptococcus spp., Bacillus spp. and Clostridium spp. colonies were identified at the sampling locations. The antibiotic resistance screening showed a vast percentage of resistance amongst the bacterial colonies, with resistance to ampicillin observed as the highest percentage (Micrococcus spp.: 95.2%, S. aureus: 100%, Streptococcus spp.: 75%, Bacillus spp.: 100% and Clostridium spp.: 100%). This study provides awareness to healthcare practitioners and the public on the status of the emergence of ARB in a hospital environment. Early detection of bacterial populations and good management of hospital environments are important prevention measures for HAI.

Bacterial and fungal communities in indoor aerosols from two Kuwaiti hospitals

The airborne transmission of COVID-19 has drawn immense attention to bioaerosols. The topic is highly relevant in the indoor hospital environment where vulnerable patients are treated and healthcare workers are exposed to various pathogenic and non-pathogenic microbes. Knowledge of the microbial communities in such settings will enable precautionary measures to prevent any hospital-mediated outbreak and better assess occupational exposure of the healthcare workers. This study presents a baseline of the bacterial and fungal population of two major hospitals in Kuwait dealing with COVID patients, and in a non-hospital setting through targeted amplicon sequencing. The predominant bacteria of bioaerosols were Variovorax (9.44%), Parvibaculum (8.27%), Pseudonocardia (8.04%), Taonella (5.74%), Arthrospira (4.58%), Comamonas (3.84%), Methylibium (3.13%), Sphingobium (4.46%), Zoogloea (2.20%), and Sphingopyxis (2.56%). ESKAPEE pathogens, such as Pseudomonas, Acinetobacter, Staphylococcus, Enterococcus, and Escherichia, were also found in lower abundances. The fungi were represented by Wilcoxinia rehmii (64.38%), Aspergillus ruber (9.11%), Penicillium desertorum (3.89%), Leptobacillium leptobactrum (3.20%), Humicola grisea (2.99%), Ganoderma sichuanense (1.42%), Malassezia restricta (0.74%), Heterophoma sylvatica (0.49%), Fusarium proliferatum (0.46%), and Saccharomyces cerevisiae (0.23%). Some common and unique operational taxonomic units (OTUs) of bacteria and fungi were also recorded at each site; this inter-site variability shows that exhaled air can be a source of this variation. The alpha-diversity indices suggested variance in species richness and abundance in hospitals than in non-hospital sites. The community structure of bacteria varied spatially (ANOSIM r 2 = 0.181-0.243; p < 0.05) between the hospital and non-hospital sites, whereas fungi were more or less homogenous. Key taxa specific to the hospitals were Defluvicoccales, fungi, Ganodermataceae, Heterophoma, and H. sylvatica compared to Actinobacteria, Leptobacillium, L. leptobacillium, and Cordycipitaceae at the non-hospital site (LefSe, FDR q ≤ 0.05). The hospital/non-hospital MD index > 1 indicated shifts in the microbial communities of indoor air in hospitals. These findings highlight the need for regular surveillance of indoor hospital environments to prevent future outbreaks.

Critical review of antibiotic resistance genes in the atmosphere

We conducted a critical review to establish what is known about the sources, characteristics, and dissemination of ARGs in the atmosphere. We identified 52 papers that reported direct measurements of bacterial ARGs in air samples and met other inclusion criteria. The settings of the studies fell into the following categories: urban, rural, hospital, industrial, wastewater treatment plants (WWTPs), composting and landfill sites, and indoor environments. Certain genes were commonly studied and generally abundant: sul1, intI1, β-lactam ARGs, and tetracycline ARGs. Abundances of total ARGs varied by season and setting, with air in urban areas having higher ARG abundance than rural areas during the summer and vice versa during the winter. There was greater consistency in the types and abundances of ARGs throughout the seasons in urban areas. Human activity within indoor environments was also linked to increased ARG content (abundance, diversity, and concentration) in the air. Several studies found that human exposure to ARGs through inhalation was comparable to exposure through drinking water or ingesting soil. Detection of ARGs in air is a developing field, and differences in sampling and analysis methods reflect the many possible approaches to studying ARGs in air and make direct comparisons between studies difficult. Methodologies need to be standardized to facilitate identification of the dominant ARGs in the air, determine their major sources, and quantify the role of atmospheric transport in dissemination of ARGs in the environment. With such knowledge we can develop better policies and guidelines to limit the spread of antimicrobial resistance.

Effects of Yellow Light on Airborne Microbial Composition and on the Transcriptome of Typical Marker Strain in Ward

Airborne diseases are transmitted by pathogens in the air. The complex microbial environment in wards is usually considered a major cause of nosocomial infection of various diseases which greatly influences the health of patients with chronic diseases, whereas the illuminant of wards impacts on the microbe especially the disease marker strain is seldom studied. In the present study, high-throughput sequencing was used to study the effect of yellow light on airborne microbial composition, and changes of transcriptome of marker strains Escherichia coli, Staphylococcus aureus and Pseudomonas aeruginosa, which were isolated from wards, were further studied after the irradiation by yellow light. High-throughput sequencing results indicated that yellow light significantly decreased α-diversity. The relative abundance of Firmicutes at the phylum level, and Clostridium sensu stricto 1, Paraclostridium at the genus level were significantly reduced. RNA sequencing results declared that yellow light significantly downregulated the genes associated with flagella, heme transport system and carbohydrate, amino acid metabolism in E. coli, and the genes related to arginine biosynthesis and the biosynthesis of isoleucine, leucine, and valine in S. aureus. Meanwhile, yellow light significantly upregulated the genes relating to porphyrin metabolism in P. aeruginosa. In conclusion, our work reveals the impacts of yellow light on the microbe in wards, pointing out the application value of yellow light in the prevention of infectious diseases in clinical practice.

A Review of Current Bacterial Resistance to Antibiotics in Food Animals

The overuse of antibiotics in food animals has led to the development of bacterial resistance and the widespread of resistant bacteria in the world. Antibiotic-resistant bacteria (ARB) and antibiotic-resistant genes (ARGs) in food animals are currently considered emerging contaminants, which are a serious threat to public health globally. The current situation of ARB and ARGs from food animal farms, manure, and the wastewater was firstly covered in this review. Potential risks to public health were also highlighted, as well as strategies (including novel technologies, alternatives, and administration) to fight against bacterial resistance. This review can provide an avenue for further research, development, and application of novel antibacterial agents to reduce the adverse effects of antibiotic resistance in food animal farms.

Spatial distribution of antibiotic resistance genes of the Zaohe-Weihe Rivers, China: exerting a bottleneck in the hyporheic zone

The hyporheic zone (HZ) is an active biogeochemical region where groundwater and surface water mix and a potential reservoir for antibiotic resistance genes (ARGs). In this paper, the relative abundance and spatial distribution of ARGs in the HZ media were investigated, taking into consideration both the five speciation of six metals and the local characteristics. The samples of surface water, groundwater, and sediment were collected from Zaohe-Weihe Rivers of Xi'an City, which is a representative city with characteristics of the northwest region of China. Of 271 ARGs associated with 9 antibiotics, 228 ARGs were detected, with a total detection rate of 84%. Sulfonamide and aminoglycoside ARGs were the dominant types of ARGs. The top 6 ARGs and mobile genetic elements (MGEs) in terms of abundance were tnpA-04, cepA, sul1, aadA2-03, sul2 and intI1. The results of principal component analysis (PCA) showed that the distribution characteristics of ARGs were not associated with the sampling sites but with the environmental medias. Similarity in the water phases and significant differences in the water and sediment phases were found. The redundancy analysis (RDA) identified the key factors controlling ARG pollution, including dissolved oxygen (DO) in surface water, total nitrogen (TN) in groundwater, and total organic carbon (TOC) in sediment. In terms of the speciation of heavy metals, we further revealed the promotion effect between ARGs and heavy metals, especially the residual fraction of Ni. In terms of horizontal transfer mechanism, ARGs were significantly correlated with tnpA-03 in water phase and tnpA-04 in sediment. In the three media, intI1 and ARGs all show a significant correlation. These findings showed that hyporheic zone exerted a bottleneck effect on the distribution and transfer of ARGs.

Seasonal and vegetational variations of culturable bacteria concentrations in air from urban forest parks: a case study in Hunan, China

It is important to investigate the airborne bacterial air quality in urban forest parks as tree bacteriostasis practices are being increasingly advocated as measures to improve the air quality and public health in urban green spaces around the world. The aim of the study was to quantitatively investigate airborne culturable bacteria (ACB) concentration levels based on field measurements in every season in five selected forest communities and the uncovered space in an urban forest park, as well as the effects of several factors on the culturability of airborne bacteria. Results suggested that the airborne bacterial levels of all the forest communities reached the clean air quality standard with regard to the airborne bacteria content, with the highest concentration of ACB showing in the uncovered space (1658 ± 1298 CFU/m³) and the lowest showing in the mixed community (907 ± 567 CFU/m³). The temporal distribution analysis showed that the airborne bacteria were mostly concentrated in summer, as well as in the morning and afternoon. The bacteriostatic rates of the mixed community were significantly different with seasonal variation (p < 0.05). Spearman's correlations revealed that the concentration of ACB was significantly positively correlated with the season, wind speed (WS), temperature (T), ultraviolet light (UV), negative air ion (NAI), and total suspended particles (TSP) (p<0.05) but significantly negatively correlated with the forest community type (p < 0.05). Overall, the selection of tree species plays a key role in shaping the forest structure and improving air quality, and the urban forest highlights key priorities for future efforts toward a cleaner, healthier, and more diverse regional forest environment.

Inhalable antibiotic resistomes emitted from hospitals: metagenomic insights into bacterial hosts, clinical relevance, and environmental risks

BACKGROUND

Threats of antimicrobial resistance (AMR) to human health are on the rise worldwide. Airborne fine particulate matter (PM2.5), especially those emitted from hospitals, could serve as a substantial yet lesser-known environmental medium of inhalable antibiotic resistomes. A genome-centric understanding of the hosting bacterial taxa, mobility potential, and consequent risks of the resistomes is needed to reveal the health relevance of PM2.5-associated AMR from clinical settings.

RESULTS

Compared to urban ambient air PM2.5, the hospital samples harbored nearly twice the abundance of antibiotic resistantance genes (ARGs, ~ 0.2 log10(ARGs/16S rRNA gene)) in the summer and winter sampled. The profiled resistome was closely correlated with the human-source-influenced (~ 30% of the contribution) bacterial community (Procrustes test, P < 0.001), reflecting the potential antibiotic-resistant bacteria (PARB), such as the human commensals Staphylococcus spp. and Corynebacterium spp. Despite the reduced abundance and diversity of the assembled metagenomes from summer to winter, the high horizontal transfer potential of ARGs, such as the clinically relevant blaOXA and bacA, in the human virulent PARB remained unaffected in the hospital air PM samples. The occurring patterns of β-lactam resistance genes and their hosting genomes in the studied hospital-emitting PM2.5 were closely related to the in-ward β-lactam-resistant infections (SEM, std = 0.62, P < 0.01). Featured with more abundant potentially virulent PARB (2.89 genome copies/m3-air), the hospital samples had significantly higher resistome risk index scores than the urban ambient air samples, indicating that daily human exposure to virulent PARB via the inhalation of PM2.5 was ten times greater than from the ingestion of drinking water.

CONCLUSIONS

The significance of AMR in the studied hospital-emitting PM2.5 was highlighted by the greater abundance of ARGs, the prevalence of potentially virulent PARB, and the close association with hospital in-ward β-lactam infections. A larger-scale multi-source comparison of genome-resolved antibiotic resistomes is needed to provide a more holistic understanding to evaluate the importance of airborne AMR from the "One-Health" perspective. Video Abstract.

Seasonal disparities and source tracking of airborne antibiotic resistance genes in Handan, China

The transmission of airborne antibiotic resistance genes (ARGs) loaded on particle is a significant global public health concern. Up to date, the dispersal pattern of airborne ARGs remains unclear despite their critical role in multiregional transmission. In this study, airborne ARGs loaded on fine particulate matter (PM_2.5) and source tracking based on the airflow trajectories were performed by the potential source contribution function (PSCF) and concentration weighted trajectory (CWT) model. The results show that the absolute abundance of ARG subtypes were generally twice times higher in the winter season than that in the summer season, which could be attributable to winter haze events with high particulate matter concentrations in Handan. Exogenous input from serious haze events and local release of ARGs loaded on PM_2.5 of air masses may cause higher levels of ARGs in the winter. Moreover, based on the positive correlation between the abundance of ARGs and PM_2.5 concentration, a source tracing model of airborne ARGs was proposed to the estimate of ARGs release and dissemination. This study highlights airborne ARGs transmission loaded on PM_2.5 of air masses, which facilitating the global spread of antibiotic resistance.

The air-borne antibiotic resistome: Occurrence, health risks, and future directions

Antibiotic resistance comprising of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) is an emerging problem causing global human health risks. Several reviews exist on antibiotic resistance in various environmental compartments excluding the air-borne resistome. An increasing body of recent evidence exists on the air-borne resistome comprising of antibiotic resistance in air-borne bioaerosols from various environmental compartments. However, a comprehensive review on the sources, dissemination, behavior, fate, and human exposure and health risks of the air-borne resistome is still lacking. Therefore, the current review uses the source-pathway-receptor-impact-mitigation framework to investigate the air-borne resistome. The nature and sources of antibiotic resistance in the air-borne resistome are discussed. The dissemination pathways, and environmental and anthropogenic drivers accounting for the transfer of antibiotic resistance from sources to the receptors are highlighted. The human exposure and health risks posed by air-borne resistome are presented. A health risk assessment and mitigation strategy is discussed. Finally, future research directions including key knowledge gaps are summarized.

A review of the emergence of antibiotic resistance in bioaerosols and its monitoring methods

Despite significant public health concerns regarding infectious diseases in air environments, potentially harmful microbiological indicators, such as antibiotic resistance genes (ARGs) in bioaerosols, have not received significant attention. Traditionally, bioaerosol studies have focused on the characterization of microbial communities; however, a more serious problem has recently arisen due to the presence of ARGs in bioaerosols, leading to an increased prevalence of horizontal gene transfer (HGT). This constitutes a process by which bacteria transfer genes to other environmental media and consequently cause infectious disease. Antibiotic resistance in water and soil environments has been extensively investigated in the past few years by applying advanced molecular and biotechnological methods. However, ARGs in bioaerosols have not received much attention. In addition, ARG and HGT profiling in air environments is greatly limited in field studies due to the absence of suitable methodological approaches. Therefore, this study comprehensively describes recent findings from published studies and some of the appropriate molecular and biotechnological methods for monitoring antibiotic resistance in bioaerosols. In addition, this review discusses the main knowledge gaps regarding current methodological issues and future research directions.

Spread of airborne antibiotic resistance from animal farms to the environment: Dispersal pattern and exposure risk

Animal farms have been considered as the critical reservoir of antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB). Spread of antibiotic resistance from animal farms to the surrounding environments via aerosols has become a growing concern. Here we investigated the dispersal pattern and exposure risk of airborne ARGs (especially in zoonotic pathogens) in the environment of chicken and dairy farms. Aerosol, dust and animal feces samples were collected from the livestock houses and surrounding environments (upwind and downwind areas) for assessing ARG profiles. Antibiotic resistance phenotype and genotype of airborne Staphylococcus spp. was especially analyzed to reveal the exposure risk of airborne ARGs. Results showed that airborne ARGs were detected from upwind (50 m/100 m) and downwind (50 m/100 m/150 m) air environment, wherein at least 30% of bacterial taxa dispersed from the animal houses. Moreover, atmospheric dispersion modeling showed that airborne ARGs can disperse from the animal houses to a distance of 10 km along the wind direction. Clinically important pathogens were identified in airborne culturable bacteria. Genus of Staphylococcus, Sphingomonas and Acinetobacter were potential bacterial host of airborne ARGs. Airborne Staphylococcus spp. were isolated from the environment of chicken farm (n = 148) and dairy farm (n = 87). It is notable that all isolates from chicken-related environment were multidrug-resistance (>3 clinical-relevant antibiotics), with more than 80% of them carrying methicillin resistance gene (mecA) and associated ARGs and MGEs. Presence of numerous ARGs and diverse pathogens in dust from animal houses and the downwind residential areas indicated the accumulation of animal feces origin ARGs in bioaerosols. Employees and local residents in the chick farming environment are exposed to chicken originated ARGs and multidrug resistant Staphylococcus spp. via inhalation. This study highlights the potential exposure risks of airborne ARGs and antibiotic resistant pathogens to human health.

Rainfall facilitates the transmission and proliferation of antibiotic resistance genes from ambient air to soil

Antibiotic resistance is common in bacterial communities and appears to be correlated with human activities. However, the source of antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) in remote regions remains unclear. In this study, we examined the abundance of ARGs in fine particulate matter (PM_2.5) as a carrier throughout the rainfall process (4 mm rain/h) to observe the effects of rainfall on the transmission of ARGs. The results suggested that rainwater served as a reservoir that facilitated the spread of ARGs and that wind and particulate matter (PM) concentrations might be meteorological parameters that influence the distribution of ARGs in rainwater. In addition, soil microcosm experiments were performed to investigate the influence of rainfall on antibiotic resistance in soils with different environmental backgrounds. Rainwater facilitated the proliferation of ARGs and mobile genetic elements (MGEs) from ambient air to soil, and this influence was more obvious in heavy metal-contaminated soil. This is the first study to investigate the routes by which rainfall acts as a mobile reservoir to facilitate the transmission and proliferation of ARGs, and the results indicate the potential source of ARGs in remote regions where humans rarely interfere.

Microbial aerosol particles in four seasons of sanitary landfill site: Molecular approaches, traceability and risk assessment

Landfill sites are regarded as prominent sources of bioaerosols for the surrounding atmosphere. The present study focused on the emission of airborne bacteria and fungi in four seasons of a sanitary landfill site. The main species found in bioaerosols were assayed using high-throughput sequencing. The SourceTracker method was utilized to identify the sources of the bioaerosols present at the boundary of the landfill site. Furthermore, the health consequences of the exposure to bioaerosols were evaluated based on the average daily dose rates. Results showed that the concentrations of airborne bacteria in the operation area (OPA) and the leakage treatment area (LTA) were in the range of (4684 ± 477)-(10883 ± 1395) CFU/m³ and (3179 ± 453)-(9051 ± 738) CFU/m³, respectively. The average emission levels of fungal aerosols were 4026 CFU/m³ for OPA and 1295 CFU/m³ for LTA. The landfill site received the maximum bioaerosol load during summer and the minimum during winter. Approximately 41.39%- 86.24% of the airborne bacteria had a particle size of 1.1 to 4.7 µm, whereas 48.27%- 66.45% of the airborne fungi had a particle size of more than 4.7 µm. Bacillus sp., Brevibacillus sp., and Paenibacillus sp. were abundant in the bacterial population, whereas Penicillium sp. and Aspergillus sp. dominated the fungal population. Bioaerosols released from the working area and treatment of leachate were the two main sources that emerged in the surrounding air of the landfill site boundary. The exposure risks during summer and autumn were higher than those in spring and winter.

Concentrations, Size Distribution, and Community Structure Characteristics of Culturable Airborne Antibiotic-Resistant Bacteria in Xinxiang, Central China

Antimicrobial resistance is considered an important threat to global health and has recently attracted significant attention from the public. In this study, the concentrations and size distribution characteristics of culturable airborne total bacteria (TB) and four antibiotic-resistant bacteria (tetracycline-resistant bacteria (TRB), ciprofloxacin-resistant bacteria (CRB), erythromycin-resistant bacteria (ERB), and ampicillin-resistant bacteria (ARB)) were investigated for approximately one year to explore their variations under different seasons, diurnal periods, and air quality levels. The concentrations of TB and four antibiotic-resistant bacteria in winter and night were higher than during other seasons and diurnal periods. Their maximum concentrations were detected from air under moderate pollution or heavy pollution. PM2.5, PM10, SO2, and NO2 were positively related to TB and four antibiotic-resistant bacteria (p < 0.01), whereas O3 and wind speed were negatively related to them (p < 0.05). The particle size of TB and four antibiotic-resistant bacteria were mainly distributed in stage V (1.1–2.2 µm). Bacillus was the dominant genus of ARB (75.97%) and CRB (25.67%). Staphylococcus and Macrococcus were the dominant genera of TRB (46.05%) and ERB (47.67%), respectively. The opportunistic pathogens of Micrococcus, Sphingomonas, Enterococcus, Rhodococcus, and Stenotrophomonas were also identified. This study provides important references for understanding the threat of bioaerosols to human health.

Seasonal Variation Characteristics of Bacteria and Fungi in PM2.5 in Typical Basin Cities of Xi’an and Linfen, China

Microorganisms existing in airborne fine particulate matter (PM2.5) have key implications in biogeochemical cycling and human health. In this study, PM2.5 samples, collected in the typical basin cities of Xi’an and Linfen, China, were analyzed through high-throughput sequencing to understand microbial seasonal variation characteristics and ecological functions. For bacteria, the highest richness and diversity were identified in autumn. The bacterial phyla were dominated by Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes. Metabolism was the most abundant pathway, with the highest relative abundance found in autumn. Pathogenic bacteria (Pseudomonas, Acinetobacter, Serratia, and Delftia) were positively correlated with most disease-related pathways. Besides, C cycling dominated in spring and summer, while N cycling dominated in autumn and winter. The relative abundance of S cycling was highest during winter in Linfen. For fungi, the highest richness was found in summer. Basidiomycota and Ascomycota mainly constituted the fungal phyla. Moreover, temperature (T) and sulfur dioxide (SO2) in Xi’an, and T, SO2, and nitrogen dioxide (NO2) in Linfen were the key factors affecting microbial community structures, which were associated with different pollution characteristics in Xi’an and Linfen. Overall, these results provide an important reference for the research into airborne microbial seasonal variations, along with their ecological functions and health impacts.

Development of a size-selective sampler combined with an adenosine triphosphate bioluminescence assay for the rapid measurement of bioaerosols

In this study, a size-selective bioaerosol sampler was built and combined with adenosine triphosphate (ATP) bioluminescence assay for measuring the bioaerosol concentration more rapidly and easily. The ATP bioaerosol sampler consisted of a respirable cyclone, an impactor to collect bioaerosols onto the head of a swab used for ATP bioluminescence assay, a swab holder, and a sampling pump. The collection efficiency of the impactor was tested using aerosolized sodium chloride particles and then the particle diameter corresponding to the collection efficiency of 50% (cut-off diameter) was evaluated. The experimental cut-off diameter was 0.44 μm. The correlations between ATP bioluminescence (relative light unit; RLU) from commercially available swabs (UltraSnap and SuperSnap, Hygiena, LLC, U.S.A.) and colony forming unit (CFU) were examined using Escherichia coli (E. coli) suspension and then the conversion equations from RLU to CFU were obtained. From the correlation results, the R² values of UltraSnap and SuperSnap were 0.53 and 0.81, respectively. The conversion equations were the linear function and the slopes of UltraSnap and SuperSnap were 633.6 and 277.78, respectively. In the lab and field tests, the ATP bioaerosol sampler and a conventional Andersen impactor were tested and the results were compared. In the lab tests, concentrations of aerosolized E. coli collected using the sampler were highly correlated to those from the Anderson impactor (R² = 0.85). In the field tests, the concentrations measured using the ATP bioaerosol sampler were higher than those from the Andersen impactor due to the limitations of the colony counting method. These findings confirm the feasibility of developing a sampler for rapid measurement of bioaerosol concentrations, offering a compact device for measuring exposure to bioaerosols, and an easy-to-use methodological concept for efficient air quality management.

A metagenomic-based method to study hospital air dust resistome

As a symbol of the defense mechanisms that bacteria have evolved over time, the genes that make bacteria resist antibiotics are overwhelmingly present in the environment. Currently, bacterial antibiotic resistance genes (ARGs) in the air are a serious concern. Previous studies have identified bacterial communities and summarized putative routes of transmissions for some dominant hospital-associated pathogens from hospital indoor samples. However, little is known about the possible indoor air ARG transportation. In this study, we mainly surveyed air-conditioner air dust samples under different airflow conditions and analyzed these samples using a metagenomic-based method. The results show air dust samples exhibited a complex resistome, and the average concentration is 0.00042 copies/16S rRNA gene, which is comparable to some other environments. The hospital air-conditioners can form resistome over time and accumulate pathogens. In addition, our results indicate that the Outpatient hall is one of the main ARG transmission sources, which can distribute ARGs to other departments (explains >80% resistome). We believe that the management should focus on ARG carrier genera such as Staphylococcus, Micrococcus, Streptococcus, and Enterococcus in this hospital and our novel evidence-based network strategy proves that plasmid-mediated ARG transfer can occur frequently. Overall, these results provide insights into the characteristics of air dust resistome and possible route for how ARGs are spread in air.

A novel constructed carbonate-mineralized functional bacterial consortium for high-efficiency cadmium biomineralization

A stable, urease-producing consortium (UPC) was constructed for high-efficiency cadmium (Cd) ion mineralization via a short-term and efficient acclimation process (five acclimation transfers). 16S rRNA gene high-throughput sequencing and quantitative polymerase chain reaction (qPCR) analyses of the urease subunit C (ureC) gene suggested that the three functional genera, all belonging to the phylum Firmicutes, rapidly increased during the process and finally composed the UPC (70.22-75.41 % of Sporosarcina, 13.83-20.66 % of norank_f_Bacillaceae, and 5.91-13.69 % of unclassified_f_Bacillaceae). The UPC exhibited good adaptability to a wide range of environmental conditions (a pH range of 4.0-11.0, temperature range of 10-45 °C, and Cd concentration range of 0-200 mg L^-1). After 8 h of incubation, 92.87 % of Cd at an initial concentration of 100 mg L^-1 was mineralized by UPC, exhibiting a great improvement as compared to the first acclimated consortium (C-1). Furthermore, although the acclimated consortium had been successively transferred 21 times, the Cd biomineralization efficiency remained stable, and this was consistent with the observed stable microbial community structure. X-ray diffraction (XRD) spectra revealed that Cd was mineralized in a (Ca0.67, Cd0.33)CO₃ phase. This research obtained a promising microbial resource for the biomineralization of Cd or other hazardous heavy metal contaminants.

Significant higher airborne antibiotic resistance genes and the associated inhalation risk in the indoor than the outdoor

Inhalation of airborne antibiotic resistance genes (ARGs) can lead to antimicrobial resistance and potential health risk. In modern society, increasing individuals stay more indoors, however, studies regarding the exposure to airborne ARGs in indoor environments and the associated risks remain limited. Here, we compared the variance of aerosol-associated ARGs, bacterial microbiomes, and their daily intake (DI) burden in dormitory, office, and outdoor environments in a university in Tianjin. The results indicated that compared to outdoor aerosols, indoors exhibited significantly higher absolute abundance of both ARG subtypes and mobile genetic elements (MGEs) (1-7 orders of magnitude), 16S rRNA genes (2-3 orders), and total culturable bacteria (1-3 orders). Furthermore, we observed that significantly different airborne bacterial communities are the major drivers contributing to the variance of aerosol-associated ARGs in indoor and outdoor aerosols. Notably, the high abundances of total bacteria, potential pathogenic genera, and ARGs (particularly those harbored by pathogens) in indoor and outdoor aerosols, especially in indoors, may pose an increased exposure risk via inhalation. The successful isolation of human pathogens such as Elizabethkingia anopheles, Klebsiella pneumonia, and Delftia lacustris resistant to the "last-resort" antibiotics carbapenems and polymyxin B from indoor aerosols further indicated an increased exposure risk in indoors. Together, this study highlights the potential risks associated with ARGs and their inhalation to human health in indoor environments.

Bioaerosols in the Athens Metro: Metagenetic insights into the PM10 microbiome in a naturally ventilated subway station

To date, few studies have examined the aerosol microbial content in Metro transportation systems. Here we characterised the aerosol microbial abundance, diversity and composition in the Athens underground railway system. PM₁₀ filter samples were collected from the naturally ventilated Athens Metro Line 3 station "Nomismatokopio". Quantitative PCR of the 16S rRNA gene and high throughput amplicon sequencing of the 16S rRNA gene and internal transcribed spacer (ITS) region was performed on DNA extracted from PM₁₀ samples. Results showed that, despite the bacterial abundance (mean = 2.82 × 10⁵ 16S rRNA genes/m³ of air) being, on average, higher during day-time and weekdays, compared to night-time and weekends, respectively, the differences were not statistically significant. The average PM₁₀ mass concentration on the platform was 107 μg/m³. However, there was no significant correlation between 16S rRNA gene abundance and overall PM₁₀ levels. The Athens Metro air microbiome was mostly dominated by bacterial and fungal taxa of environmental origin (e.g. Paracoccus, Sphingomonas, Cladosporium, Mycosphaerella, Antrodia) with a lower contribution of human commensal bacteria (e.g. Corynebacterium, Staphylococcus). This study highlights the importance of both outdoor air and commuters as sources in shaping aerosol microbial communities. To our knowledge, this is the first study to characterise the mycobiome diversity in the air of a Metro environment based on amplicon sequencing of the ITS region. In conclusion, this study presents the first microbial characterisation of PM₁₀ in the Athens Metro, contributing to the growing body of microbiome exploration within urban transit networks. Moreover, this study shows the vulnerability of public transport to airborne disease transmission.

Airborne bacterial communities of outdoor environments and their associated influencing factors

Microbial entities (such bacteria, fungi, archaea and viruses) within outdoor aerosols have been scarcely studied compared with indoor aerosols and nonbiological components, and only during the last few decades have their studies increased. Bacteria represent an important part of the microbial abundance and diversity in a wide variety of rural and urban outdoor bioaerosols. Currently, airborne bacterial communities are mainly sampled in two aerosol size fractions (2.5 and 10 µm) and characterized by culture-dependent (plate-counting) and culture-independent (DNA sequencing) approaches. Studies have revealed a large diversity of bacteria in bioaerosols, highlighting Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes as ubiquitous phyla. Seasonal variations in and dispersion of bacterial communities have also been observed between geographical locations as has their correlation with specific atmospheric factors. Several investigations have also suggested the relevance of airborne bacteria in the public health and agriculture sectors as well as remediation and atmospheric processes. However, although factors influencing airborne bacterial communities and standardized procedures for their assessment have recently been proposed, the use of bacterial taxa as microbial indicators of specific bioaerosol sources and seasonality have not been broadly explored. Thus, in this review, we summarize and discuss recent advances in the study of airborne bacterial communities in outdoor environments and the possible factors influencing their abundance, diversity, and seasonal variation. Furthermore, airborne bacterial activity and bioprospecting in different fields (e.g., the textile industry, the food industry, medicine, and bioremediation) are discussed. We expect that this review will reveal the relevance and influencing factors of airborne bacteria in outdoor environments as well as stimulate new investigations on the atmospheric microbiome, particularly in areas where air quality is a public concern.

Exploring the disparity of inhalable bacterial communities and antibiotic resistance genes between hazy days and non-hazy days in a cold megacity in Northeast China

The physicochemical properties of inhalable particles during hazy days have been extensively studied, but their biological health threats have not been well-explored. This study aimed to explore the impacts of haze pollution on airborne bacteria and antibiotic-resistance genes (ARGs) by conducting a comparative study of the bacterial community structure and functions, pathogenic compositions, and ARGs between hazy days and non-hazy days in a cold megacity in Northeast China. The results suggested that bacterial communities were shaped by local weather and customs. In this study, cold-resistant and Chinese sauerkraut-related bacterial compositions were identified as predominant genera. In the comparative analysis, higher proportions of gram-negative bacteria and pathogens were detected on hazy days than on non-hazy days. Pollutants on hazy days provided more nutrients (sulfate, nitrate and ammonium) for bacterial metabolism but also caused more bacterial cell damage and death than on non-hazy days. This study also detected increases in the sub-types and average absolute abundance of airborne resistance genes on hazy days compared to non-hazy days. The results of this study revealed that particle pollution promotes the dissemination and exchange of pathogenic bacteria and ARGs among large urban populations, which leads to a higher potential for human inhalation exposure.

Pollution profiles of antibiotic resistance genes associated with airborne opportunistic pathogens from typical area, Pearl River Estuary and their exposure risk to human

To reveal the selective pressures of near-shore human activities on marine and continental bioaerosols, the pollution profile and potential exposure risk of airborne pathogens and antibiotic-resistance genes (ARGs) in Pearl River Estuaries (113.52 ^oE, 22.69 ^oN), a transitional zone between marine and continental environments, were fully explored. The results showed that the total bacteria among bioaerosols varied largely with average pollution levels of 1.86 × 10⁵ and 4.35 × 10⁴ cfu m^-3 in spring and summer, respectively, and were high than those of airborne fungi. The predominant aerodynamic diameters of bioaerosols were in respirable size range (<4.7 µm), and the microbes communities' diversity and abundance varied significantly. Besides, many opportunistic pathogenic bacteria (Burkholderia-Paraburkholderia, Staphylococcus and Acinetobacter) and fungi (Alternaria, Penicillium and Cladosporium) were dominant in bioaerosol samples. Of 21 ARGs subtypes detected, the tetracycline resistance gene tetA was the most abundant, followed by aminoglycoside resistance gene and mobile genetic elements. Correlation analysis revealed that the changes of pathogens community contributed significantly to the prevalence of ARGs in bioaerosol. Based on the average daily dose rates of microorganisms and human direct intake of ARGs, health risk of bioaerosols from the Pearl River Estuaries were also evaluated. In summary, the presence of opportunistic pathogens and diversity of ARGs strengthens the call to consider the bioaerosol in air quality monitoring and risk assessment in the future.

Municipal Solid Waste Treatment System Increases Ambient Airborne Bacteria and Antibiotic Resistance Genes

Landfill and incineration are the primary disposal practices for municipal solid waste (MSW) and have been considered as the critical reservoir of antibiotic resistance genes (ARGs). However, the possible transmission of ARGs from the municipal solid waste treatment system (MSWT system) to ambient air is still unclear. In this study, we collected inside and ambient air samples (PM₁₀ and PM_2.5) and potential source samples (leachate and solid waste) in the MSWT system. The results showed that the MSWT system contributed to the increased ambient airborne bacteria and associated ARGs. Forty-one antibiotic-resistant bacteria (ARB) harboring bla_TEM-1 were isolated, and the full-length nucleotide sequences of the bla_TEM-1 gene (harbored by identical bacillus) from air (downwind samples) were 100% identical with those in the leachate and solid waste, indicating that the MSWT system was the important source of disperse bacteria and associated ARGs in the ambient air. The daily intake (DI) burden level of ARGs via PM inhalation was comparable with that via ingestion of drinking water but lower than the DI level via ingestion of raw vegetables. The antibiotic-resistant opportunistic pathogen Bacillus cereus was isolated from air, with a relatively high DI level of Bacillus via inhalation (10⁴-10⁶ copies/day) in the MSWT system. This study highlights the key pathway of airborne ARGs to human exposure.

Seasonal variations of microbial assemblage in fine particulate matter from a nursery pig house

The microorganisms contained in PM_2.5 from livestock houses can spread over long distances through airborne transmission. As such, the potential bacterial pathogens and fungal allergens within can pose a formidable threat to nearby residents' health and the overall environment. However, little is known about the microbial assemblage contained in PM_2.5 from pig houses. In this study, 16S and 18S rRNA gene sequencing was employed to analyze the bacterial and fungal assemblage contained in PM_2.5 from a nursery pig house across four seasons, respectively. The results showed that alpha diversity was higher in summer and autumn compared to the spring and winter. The bacterial and fungal assemblage varied according to season. At the phylum level, the dominant bacteria and fungi were Firmicutes and Basidiomycota, respectively, across the four seasons. At the genus level, a total of five potential bacterial pathogen and 20 potential fungal allergen genera were identified across the samples. The most abundant bacterial pathogen and fungal allergen genera were observed in summer and autumn, respectively, but neither had a significant correlation with PM_2.5 concentration. Moreover, microbial diversity and the relative abundance of fungal allergen genera were positively correlated with temperature and relative humidity. It can be concluded that microbial diversity and assemblage varied significantly among the seasons in a nursery pig house, and this can be useful in exploring the potential risks of PM_2.5 from pig houses across all four seasons.

Airborne bacterial communities and antibiotic resistance gene dynamics in PM2.5 during rainfall

The biotoxicity and public health effects of airborne bacteria and antibiotic resistance genes (ARGs) in fine particulate matter (PM_2.5) are being increasingly recognized. The characteristics of bacterial community composition and ARGs in PM_2.5 under different rainfall conditions were studied based on the on-site synchronous measurements in downtown Beijing. Marked differences were evident in the bacterial community characteristics of PM_2.5 before, during, and after rain events (p < 0.05). The rain intensities affected the bacterial community abundance in PM_2.5 and heavy rain had greater washing effects. The Proteobacteria (phylum level), α-Proteobacteria (class level), Pseudomonadales (order level), Pseudomonadaceae (family level), and Cyanobacteria (genus level) were the dominant bacterial taxa associated with PM_2.5 in Beijing during rain events. However, the bacteria at each level that displayed the biggest percentage variance was not the dominant type under different rain intensities. The ermB, tetW, and mphE genes were the primary ARGs, with abundances of 18 to 30 copies/m³, which was a relatively smaller value than other observations. Real-time monitoring of the meteorological condition of rain events and physicochemical properties of PM_2.5 were used to identify the main factors during rainfall. The bacterial community was sensitive to the ionic and metal element components of PM_2.5 during rainfall. The abundance of ARGs was closely correlated with some groups of the bacterial community, which were also close to the initial value before the rain. Statistical analysis demonstrated that temperature, relative humidity, and duration of rain were the primary meteorological factors for the biological characteristics. The ionic species, rather than metal elements, in PM_2.5 were the sensitive factors for the bacteria community and ARGs, which varied at the phylum, class, order, family, and genus levels. The observations provide insights for the biological risk assessment in an urban rainfall water and the potential health impact on citizens.

Effects of antibiotics on microbial community structure and microbial functions in constructed wetlands treated with artificial root exudates

In the rhizosphere, plant root exudates can mediate the toxicity of antibiotics on microorganisms, yet the mechanisms are poorly understood. To simulate the antibiotic contamination of global rivers and lakes, the current study investigated the effects of two antibiotics (ofloxacin at 8.69 × 10⁴ ng L^-1 and tetracycline at 8.62 × 10⁴ ng L^-1) and their binary combination (8.24 × 10⁴ ng L^-1 ofloxacin and 7.11 × 10⁴ ng L^-1 tetracycline) on bacterial communities in micro-polluted constructed wetlands with and without artificial root exudates. The two antibiotics had no significant effects on the removal of excess carbon and nitrogen from the microcosms treated with and without exudates. Furthermore, with regard to bacterial community structure, antibiotic exposure increased the bacterial richness of bulk and exudate treated microcosms (P < 0.05). However, a significant increase (P < 0.05) in bacterial diversity elicited by ofloxacin and antibiotic mixture exposure was only observed in microcosms with exudates. In exudate treated microcosms, ofloxacin promoted the relative abundance of Arthrobacter spp., which are ofloxacin-resistant bacterial species, which significantly varied from what was observed in microcosms free of exudates. Moreover, tetracycline, ofloxacin and their combination all significantly increased the relative abundance of nitrogen cycling bacteria Rhizobacter spp. and Rhizobium spp., and decreased the relative abundance of antibiotic-resistant bacteria Pseudomonas spp. Simultaneously, with regard to bacterial community functions, the functional profiles (Kyoto Encyclopedia of Genes and Genomes) showed that the pathways of amino acid and carbohydrate metabolism were enhanced by antibiotics in microcosms with exudates. The findings illustrate that antibiotics not only alter the bacterial structure and composition but also change their functional properties in constructed wetlands, and these interruption effects could be affected by root exudates of plants, which may further reveal the ecological implication of plants in constructed wetlands.

Quantification of Airborne Resistant Organisms With Temporal and Spatial Diversity in Bangladesh: Protocol for a Cross-Sectional Study

BACKGROUND

Antimicrobial resistance is a widespread, alarming issue in global health and a significant contributor to human death and illness, especially in low and middle-income countries like Bangladesh. Despite extensive work conducted in environmental settings, there is a scarcity of knowledge about the presence of resistant organisms in the air.

OBJECTIVE

The objective of this protocol is to quantify and characterize the airborne resistomes in Bangladesh, which will be a guide to identify high-risk environments for multidrug-resistant pathogens with their spatiotemporal diversity.

METHODS

This is a cross-sectional study with an environmental, systematic, and grid sampling strategy focused on collecting air samples from different outdoor environments during the dry and wet seasons. The four environmental compartments are the frequent human exposure sites in both urban and rural settings: urban residential areas (n=20), live bird markets (n=20), rural households (n=20), and poultry farms (n=20). We obtained air samples from 80 locations in two seasons by using an active microbial air sampler. From each location, five air samples were collected in different media to yield the total bacterial count of 3rd generation cephalosporin (3GC) resistant Enterobacteriaceae, carbapenem-resistant Enterobacteriaceae, vancomycin-resistant Enterococci and methicillin-resistant Staphylococcus aureus.

RESULTS

The study started in January 2018, and the collection of air samples was completed in November 2018. We have received 800 air samples from 80 study locations in both dry and wet seasons. Currently, the laboratory analysis is ongoing, and we expect to receive the preliminary results by October 2019. We will publish the complete result as soon as we clean and analyze the data and draft the manuscript.

CONCLUSIONS

The existence of resistant bacteria in the air like those producing extended-spectrum beta-lactamases, carbapenem-resistant Enterobacteriaceae, vancomycin-resistant Enterococci, and methicillin-resistant Staphylococcus aureus will justify our hypothesis that the outdoor environment (air) in Bangladesh acts as a reservoir for bacteria that carry genes conferring resistance to antibiotics. To our knowledge, this is the first study to explore the presence of superbugs in the air in commonly exposed areas in Bangladesh.

INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID)

DERR1-10.2196/14574.