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

Underrated risk of antibiotic resistance genes dissemination mediated by bioaerosols released from anaerobic biological wastewater treatment system

Antibiotic resistance has been recognized as one of the most prevalent public health problems. The bioaerosol-mediated spread of antibiotic resistance genes (ARGs) is an important but underrated pathway. Therefore, this work investigated the comprehensive resistome and pathogen-induced risk in bioaerosols released from anaerobic ammonium oxidation (anammox) process under antibiotic stress. The results showed that the bioaerosol oxidation potential increased by 2.7 times after the addition of sulfamethoxazole (SMX) into the anammox system. Based on the metagenomic analyses, abundant ARGs were enriched in bioaerosols, especially novA, olec, msbA and patA. There were many antibiotic resistance contigs carrying at least two mobile genetic elements (MGEs) in bioaerosols. Compared to the control, SMX caused the significant increase in ARGs proportion in plasmids from 11.4 % to 19.4 %. Similarly, the abundance of the type IV secretion system protein encoding genes (mtrA and mtrB) increased by 30.2 % and 31.5 %, respectively, which was conducive to gene transfer between bacteria. In addition, SMX stress induced the reactive oxygen species (ROS) production and the upregulation of genes related to membrane protein and DNA replication, further facilitating ARGs transfer. The co-occurrence networks showed that Aquamicrobium and Microbacterium probably were the hosts of most ARGs. Notably, four abundant human pathogens were detected in bioaerosols from the anammox system, which raised concerns on the health risk of resistant bioaerosol diffusion. These findings reveal the potential of horizontal gene transfer through bioaerosols and provide a guidance for systematically assessing the risk of environmental antibiotic resistance and relevant pathogens.

Key Contribution and Risk of Airborne Antibiotic Resistance: Total Suspended Particles or Settled Dust?

The atmosphere is an important environmental medium in spreading antimicrobial resistance (AMR) in animal farming systems, yet the exposure risks associated with airborne pathways remain underexplored. This study employed metagenomic sequencing to investigate the airborne transmission of AMR in chicken farms (i.e., chicken feces, total suspended particles (TSP), and dust) and its exposure risks on the gut and nasal cavities of workers, office staff, and nearby villagers. Results revealed that TSP exhibited greater abundance, diversity, and transfer potential of antibiotic resistance genes (ARGs) compared to dust. The abundance of airborne resistome decreased with distance from the chicken house, and ARGs were estimated to spread up to 9.48 km within 1 h. While the gut resistome of workers and villagers showed limited differences, emerging tet(X) variants and high-risk dfrA remain future concerns. More nasal resistome was attributable to TSP compared to dust. Workers faced significantly higher inhalable exposures to antibiotic-resistant bacteria (ARB) and human pathogenic antibiotic-resistant bacteria (HPARB), exceeding those of office staff and villagers by an order of magnitude. We also compiled lists of high-risk and potential-risk airborne ARGs to inform monitoring. These findings highlight the need for regular air disinfection in animal farms and better protective measures for workers.

From air to insight: the evolution of airborne DNA sequencing technologies

Historically, the analysis of airborne biological organisms relied on microscopy and culture-based techniques. However, technological advances such as PCR and next-generation sequencing now provide researchers with the ability to gather vast amounts of data on airborne environmental DNA (eDNA). Studies typically involve capturing airborne biological material, followed by nucleic acid extraction, library preparation, sequencing and taxonomic identification to characterize the eDNA at a given location. These methods have diverse applications, including pathogen detection in agriculture and human health, air quality monitoring, bioterrorism detection and biodiversity monitoring. A variety of methods are used for airborne eDNA analysis, as no single pipeline meets all needs. This review outlines current methods for sampling, extraction, sequencing and bioinformatic analysis, highlighting how different approaches can influence the resulting data and their suitability for specific use cases. It also explores current applications of airborne eDNA sampling and identifies research gaps in the field.

Emission Dynamics and Public Health Implications of Airborne Pathogens and Antimicrobial Resistance from Urban Waste Collection Facilities

Airborne pathogens and antimicrobial resistance (AMR) present significant global health threats. Household waste collection facilities (WCFs), crucial initial nodes in urban waste management systems, have been understudied in regards to their role in emitting these hazards. This study investigated the abundance, composition, sources, driving mechanisms, and health risks associated with pathogens and AMR originating from WCFs in a major city, using culture-based analysis, high-throughput sequencing, and health risk modeling, respectively. The atmospheric escape rates of culturable bacteria (43.4%), fungi (71.7%), and antibiotic-resistant bacteria (ARB) (43.7%) were estimated based on the concentration differences between the interior and exterior of the WCFs by using SourceTracker2 analysis. Health risk assessments showed that annual infection risks for waste-handling workers ranged from 0.194 to 0.489, far exceeding the World Health Organization's acceptable limit of 10-4. Community exposure risks were notable up to 220 m downwind from WCFs, marking the maximum extent of pathogen dispersion. Our analysis suggests that approximately 6.3% of the megacity's area (equivalent to 400 km2) is within potential risk zones influenced by WCF emissions. These results underscore the critical need to evaluate and mitigate the public health risks posed by airborne pathogens and AMR emitted from WCFs in megacities globally.

Unveiling soil-borne antibiotic resistome and their associated risks: A comparative study of antibiotic and non-antibiotic pharmaceutical factories

Antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) are extensively documented within antibiotic pharmaceutical factories. Notably, non-antibiotic pharmaceuticals also represent a significant portion of the pharmaceuticals market. However, the comparative analyses of soil-borne ARG profiles and associated risks in different categories of pharmaceutical factories remain limited. This study conducted metagenomic sequencing on soil samples collected from both antibiotic and non-antibiotic pharmaceutical factories, alongside isolated ARB from soil, wastewater, groundwater, and air. Our results indicated the significant discrepancies in soil-borne ARG profiles, comprising abundance, diversity, and composition, in different categories of pharmaceutical factories (P < 0.05), which mainly driven by antibiotic residues. Significantly, bacterial pathogens were the important soil-borne ARG hosts, potentially posing risks to human health. In addition, the full-length nucleotide sequences of sul1, tetA, and TEM-1 were similar among soil, wastewater, groundwater, and air, suggesting the cross-media ARG dissemination within pharmaceutical settings. Through macrophage and Galleria mellonella infection models, the isolated antibiotic-resistant Escherichia coli strains possessed relatively high virulence. Overall, the findings provide valuable insights into the discrepancies in soil-borne ARG profiles and associated risks across different types of pharmaceutical factories, offering critical data for the targeted prevention and control of soil-borne ARG contamination in pharmaceutical production settings.

Antibiotic-resistant bacteria aerosol in a Caribbean coastal city: Pre- and post- COVID-19 lockdown

This study assessed the prevalence and spatial distribution of viable ultrafine and fine antibiotic-resistant bacteria aerosols (ARB) in the Metropolitan Area of Barranquilla, Colombia, pre- and post-lockdown (September 2019 to December 2020). Samples were systematically collected from urban, suburban, and rural sites using a six-stage viable cascade impactor. We employed logistic regression and Bayesian Neural Network Classifiers to analyze meteorological variables' influence on antibiotic resistance persistence. The lockdown led to a significant decrease (76 %) in overall bacterial aerosol concentrations, likely due to reduced human activity. The most significant reduction (82 %) was observed at Peace Square. Bacillus cereus was the most prevalent species, showing high concentrations at all sampling sites. Other species, like Leifsonia aquatica and Staphylococcus lentus, were linked to wastewater effluents and agricultural activities. Despite the overall decrease in bacterial aerosols, antibiotic-resistant bacteria remained high, particularly in highly impacted urban areas like the Barranquilla Riverwalk. Bacillus cereus exhibited resistance to multiple antibiotics, including commonly used ones like Ampicillin and Penicillin G. Resistance to newer antibiotics like Vancomycin was rare. Peace Square, a high-traffic urban area, showed elevated resistance rates in the deeper respiratory regions compared to other locations. Our findings indicate that while overall concentration levels decreased, the threat of antibiotic resistance in bacterial bioaerosols persists, emphasizing the need for continuous monitoring and targeted public health interventions in urban areas.

Bioaerosol emission characteristics and potential risks during composting: Focus on pathogens and antimicrobial resistance

In this study, we analyzed bioaerosol emission characteristics and potential risks of antimicrobial resistance (AMR) during composting using the impaction culture method and metagenomic sequencing. The results showed that the highly saturated water vapor in the emission gas mitigated particulate matter emission during the thermophilic period. About the bioaerosols, the airborne aerobic bacterial emissions were suppressed as composting enters the mature period, and the airborne fungi are usually present as single-cell or small-cell aggregates (< 3.3 µm). In addition, the microbial community structure in bioaerosols was stable and independent of composting time. Most importantly, the PM2.5 in bioaerosols contained large amounts of antibiotic resistance genes (ARGs), potential pathogens, and multidrug resistant pathogens, which were diverse and present in high concentrations. Among them, ARGs concentrations encoding 21 antibiotics ranged from - 4.50 to 0.70 ppm/m3 (Log10 ARGs). Among the 89 potential human pathogens detected, Escherichia coli, Salmonella enterica, Klebsiella pneumoniae, and Staphylococcus aureus were the only culturable potentially multidrug resistant pathogens carrying multiple ARGs encoding resistance at high concentrations (- 0.57 to 1.15 ppm/m3 (Log10 ARGs)), and were more likely to persist and multiply in oligotrophic environments. Our findings indicate that composting technology can transfer AMR from solid compost to gas phase and increase the risk of AMR transmission.

Antibiotic resistance in urban soils: Dynamics and mitigation strategies

Antibiotic resistance (AR) is a critical global health issue with significant clinical and economic implications. AR occurs when microorganisms develop mechanisms to withstand the effects of antibiotics, reducing treatment efficacy and increasing the risk of mortality and healthcare costs. While the connection between antibiotic use in clinical and agricultural settings and the emergence of AR is well-established, the role of urban soils as reservoirs and spreaders of AR is underexplored. This review examines the complex dynamics of AR in urban soils, highlighting the various sources of antibiotics, including domestic wastewater, industrial effluents, urban agricultural practices, but also microplastics and domestic animal excrements. The selective pressure exerted by these anthropogenic sources promotes the proliferation of antibiotic-resistant bacteria, particularly through horizontal gene transfer, which facilitates the transmission of resistance genes among soil microorganisms in urban environments. About that, the presence of antibiotics in urban soils poses a significant threat to public health by potentially transferring resistance genes to human pathogens through multiple pathways, including direct contact, food consumption, and water ingestion. Furthermore, AR in urban soils disrupts microbial community dynamics, impacting soil fertility, plant growth, and overall environmental quality. Therefore, this review aims to address gaps in understanding AR in urban soils, offering insights into its implications for human health and ecosystem integrity. By identifying these gaps and suggesting evidence-based strategies, this review proposes valid and sustainable solutions to mitigate and counteract the spread of AR in urban environments.

Antibiotic resistance and resistome risks of inhalable bioaerosols at aeration tank of a full-scale wastewater treatment plant

Antibiotic resistome could be aerosolized under wastewater aeration processes, however, their seasonal variation, mobility, hosts, aerosolization behavior, and risk, are largely unknown. Herein, the antibiotic resistant pollution associated with fine particulate matter (PM2.5) from the actual aeration tank (AerT), was analyzed using metagenomic assembly. The antibiotic resistance of AerT-PM2.5 was characterized by significant seasonality. Antibiotic resistance genes (ARGs) in AerT-PM2.5, exhibited higher enrichment and mobility and were harbored more by pathogens than those in upwind-PM2.5, regardless of sampling season. Mobile ARGs were mainly flanked by transposase. Totally, 18 pathogenic antibiotic-resistant bacteria (PARB) carried more than one ARG, including 9 PARB with multiple ARG types. Although wastewater exerted a dominant source contribution for the airborne ARGs (47.31-55.56 %) and PARB (46.18-64.32 %), aeration endowed differential aerosolization capacity for various ARGs and PARB from wastewater. Airborne antibiotic resistome was mainly determined by bacterial community and indirectly influenced by meteorological conditions (i.e., relative humidity). Higher PM2.5-borne resistome risk was observed in AerT than upwind, and the most serious resistome risk of AerT-PM2.5 was found in winter. This study emphasizes the importance of wastewater aeration processes in emission of airborne antibiotic resistome and offers referenced information for mitigating air pollution in wastewater treatment plants.

The dynamics and assembly patterns of airborne pathogen communities in the municipal food waste treatment system and its risk implications

While municipal solid waste (MSW) provides an ideal habitat for pathogen propagation, the dynamics and assembly of airborne pathogen communities in these environments remain largely unknown. Here, we combined amplicon and metagenomics with spatiotemporal sampling to study inhalable particulate matter-carried potential pathogenic bacteria at full-scale food waste treatment plants (FWTPs), alongside comparisons to urban air in the area. The results showed that pathogenic bacteria constituted a notable portion (64.5 % ± 20.6 %, n = 75) of the total bacterial communities in FWTPs-impacted air, with species and relative abundance 2-4 times higher than that of urban air, and contributed over 50 % of pathogens to the outdoor air. Airborne pathogen community structures were highly shaped by sampling sites (i.e. treatment units), but conserved across seasons (summer vs. winter) and particle sizes (PM2.5vs. PM10). Notably, Acinetobacter johnsonii-dominated pathogens (i.e. biofilm-related species) presented high levels of aerosolization and consistently occupied the upper-representative niches in all neutral models, highlighting their persistent exposure risk. Furthermore, pathogen community assembly was strongly driven by stochastic processes (58.8 %-96.8 %), while environmental variables explained only limited variations (3.4 %-28.7 %). In particular, the relative importance of stochastic processes clearly increased along an outdoor-to-indoor gradient (84.9 %-96.5 % vs. 71.3 %-76 %), which might be related to indoor anthropogenic activities that weaken microbial network stability and environmental filtering effects. This work enhances our knowledge of the dynamic behaviors and risk of airborne pathogen communities in MSW disposal and underscores the role of FWTPs in disseminating airborne pathogens.

Neglected contributors to the transmission of bacterial antibiotic resistance in drinking water: Extracellular antibiotic resistance genes and the natural transformation

Antibiotic resistance genes (ARGs) have increasingly gained recognition as an "emerging contaminant" that poses a threat to the biosafety of drinking water. However, previous researches have primarily focused on the intracellular state of ARGs and rarely investigated the ecological characteristics (e.g., distribution and origin), environmental behavior (spread), and risks of extracellular form (eARGs) within drinking water systems. Therefore, this review evaluated isolation strategies and extraction methods for recovering eARGs from drinking water, elucidated the distribution characteristics of eARGs, and examined their impact on the antibiotic resistome from source water to tap water. We emphasized that chlorination and biological treatments significantly contribute to the prevalence and persistence of eARGs in drinking water. Moreover, we highlighted the role of biological reactors (e.g., biofilter, biological activated carbon) and drinking water distribution systems in facilitating the natural transformation of eARGs while significantly contributing to bacterial antibiotic resistance (BAR) propagation. Finally, we summarized the current risk assessment systems for ARGs and critically address remaining challenging questions necessary for better forecasting health risks associated with eARGs in drinking water environments. Collectively, this review enhances the understanding of ecological characteristics and environmental behavior of eARGs in drinking water while providing important implications for controlling and reducing BAR contamination not only in drinking water but also in other aquatic environments.

Effects of massive desiccation of olive waste residues on air quality

New industries are proliferating in the recovery of agri-food wastes, such as those involved in the revaluation of alperujo, generated in the production of olive oil. Despite the potential environmental benefits, their activity is not exempt from new forms of emissions, aggravated by the massification of waste treatments. This work reports a six-month field campaign carried out in an alperujo desiccation plant which can serve as a proxy for these emerging industries in the Mediterranean countries. The study focused on air quality parameters, covering criteria pollutants, metals and microbiological load of particulate matter and the characterization of volatile organic compounds (VOCs). The results show a slight contribution of the factory to the NOx levels in the surroundings (3.0-12.5 μg/m3). Statistically significant effects were not observed for ozone, CO, SO2, or PM10. Concerning the levels of metals, concentrations were low and calculated health risk indexes indicated safe conditions in the area. The most abundant elements were Na (6.5 × 102 ng/m3), K (4.0 × 102 ng/m3), Al (2.7 × 102 ng/m3), Zn (2.1 × 102 ng/m3), Ca (2.16 × 102 ng/m3), Fe (3.6 × 101 ng/m3) and Mg (3.2 × 101 ng/m3). Bacterial counts, with a mean value of 15.9 CFU/m3, showed a seasonal shift, mainly explained by weather (air moisture and temperature) and PM2.5 concentration. The genomic analysis showed Cutibacterium as the dominant genus during the cold months while Bacillus predominated in the warm season. The VOCs with higher average concentrations were acetic acid (130 μg/m3), nonanoic acid (124 μg/m3), benzoic acid (29.7 μg/m3), octanoic acid (19.9 μg/m3) and nonanal (4.70 μg/m3), with the rest of compounds in concentrations below 4 μg/m3. Odorant pollutants with the greatest contribution to olfactory nuisance were aldehydes (from pentanaldehyde to decanaldehyde), acetic acid and phenol. Although the observable effects of the waste treatments were low, several parameters showed an influence on the environment which should be assessed to foresee and prevent long-term consequences.

Diel variations of airborne microbes and antibiotic resistance genes in Response to urban PM2.5 chemical properties during the heating season

Among the components of fine particulate matter (PM2.5), the contributions of airborne microorganisms and antibiotic resistance genes (ARGs) to health risks have been overlooked. Airborne microbial dynamics exhibit a unique diurnal cycle due to environmental influences. However, the specific roles of PM2.5 chemical properties resulting from fossil fuel combustion in driving circadian fluctuations in microbial populations and ARGs remain unclear. This study explored the interactions between toxic components and microbial communities during the heating period to understand the variations in ARGs. Bacterial and fungal communities showed a higher susceptibility to diel variations in PM2.5 compared to their chemical properties. Mantel tests revealed that chemical properties and microbial community interactions contribute differently to ARG variations, both directly and indirectly, during circadian fluctuations. Our findings highlight that, during the daytime, the enrichment of pathogenic microorganisms and ARGs increases the risk of PM2.5 toxicity. Conversely, during the nighttime, the utilization of water-soluble ions by the fungal community increased, leading to a significant increase in fungal biomass. Notably, Aspergillus exhibited a significant correlation with mobile genetic elements and ARGs, implying that this genus is a crucial driver of airborne ARGs. This study provides novel insights into the interplay between the chemical composition, microbial communities, and ARGs in PM, underscoring the urgent need for a comprehensive understanding of effective air pollution control strategies.

Metagenomic airborne resistome from urban hot spots through the One Health lens

Human activities are a significant contributor to the spread of antibiotic resistance genes (ARGs), which pose a serious threat to human health. These ARGs can be transmitted through various pathways, including air, within the context of One Health. This study used metagenomics to monitor the resistomes in urban air from two critical locations: a wastewater treatment plant and a hospital, both indoor and outdoor. The presence of cell-like structures was confirmed through fluorescence microscopy. The metagenomic analysis revealed a wide variety of ARGs and a high diversity of antibiotic-resistant bacteria in the airborne particles collected. The wastewater treatment plant showed higher relative abundances with 32 ARG hits per Gb and m3, followed by the main entrance of the hospital (indoor) with ≈5 ARG hits per Gb and m3. The hospital entrance exhibited the highest ARG richness, with a total of 152 different ARGs classified into nine categories of antibiotic resistance. Common commensal and pathogenic bacteria carrying ARGs, such as Moraxella, Staphylococcus and Micrococcus, were detected in the indoor airborne particles of the hospital. Interestingly, no ARGs were shared among all the samples analysed, indicating a highly variable dynamic of airborne resistomes. Furthermore, the study found no ARGs in the airborne viral fractions analysed, suggesting that airborne viruses play a negligible role in the dissemination of ARGs.

Dissemination of antibiotic resistance genes from aboveground sources to groundwater in livestock farms

Antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) are prevalent in various environments on livestock farms, including livestock waste, soil, and groundwater. Contamination of groundwater by ARB and ARGs in livestock farms is a growing concern as it may have potentially huge risks to human health. However, the source of groundwater-borne ARB and ARGs in animal farms remains largely unknown. In this study, different types of samples including groundwater and its potential contamination sources from aboveground (pig feces, wastewater, and soil) from both working and abandoned swine feedlots in southern China were collected and subjected to metagenomic sequencing and ARB isolation. The source tracking based on metagenomic analysis revealed that 56-95 % of ARGs in groundwater was attributable to aboveground sources. Using metagenomic assembly, we found that 45 ARGs predominantly conferring resistance to aminoglycosides, sulfonamides, and tetracyclines could be transferred from the aboveground sources to groundwater, mostly through plasmid-mediated horizontal gene transfer. Furthermore, the full-length nucleotide sequences of sul1, tetA, and TEM-1 detected in ARB isolates exhibited the close evolutionary relationships between aboveground sources and groundwater. Some isolated strains of antibiotic-resistant Pseudomonas spp. from aboveground sources and groundwater had the high similarity (average nucleotide identity > 99 %). Notably, the groundwater-borne ARGs were identified as mainly carried by bacterial pathogens, potentially posing risks to human and animal health. Overall, this study underscores the dissemination of ARGs from aboveground sources to groundwater in animal farms and associated risks.

Carbonaceous particulate matter promotes the horizontal transfer of antibiotic resistance genes

There is growing concern about the transfer of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in airborne particulate matter. In this study, we investigated the effects of various types of carbonaceous particulate matter (CPM) on the transfer of ARGs in vitro. The results showed that CPM promoted the transfer of ARGs, which was related to the concentration and particle size. Compared with the control group, the transfer frequency was 95.5, 74.7, 65.4, 14.7, and 3.8 times higher in G (graphene), CB (carbon black), NGP (nanographite powder), GP1.6 (graphite powder 1.6 micron), and GP45 (graphite powder 45 micron) groups, respectively. Moreover, the transfer frequency gradually increased with the increase in CPM concentration, while there was a negative relationship between the CPM particle size and conjugative transfer frequency. In addition, the results showed that CPM could promote the transfer of ARGs by increasing ROS, as well as activating the SOS response and expression of conjugative transfer-related genes (trbBp, trfAp, korA, kroB, and trbA). These findings are indicative of the potential risk of CPM for the transfer of ARGs in the environment, enriching our understanding of environmental pollution and further raising awareness of environmental protection.

Food waste compost and digestate as novel fertilizers: Impacts on antibiotic resistome and potential risks in a soil-vegetable system

As a novel agricultural practice, the reuse of food waste compost and digestate as fertilizers leads to a circular economy, but inevitably introduces bio-contaminants such as antibiotic resistance genes (ARGs) into the agroecosystem. Moreover, heavy metal and antibiotic contamination in farmland soil may exert selective pressures on the evolution of ARGs, posing threats to human health. This study investigated the fate, influencing mechanisms and potential risks of ARGs in a soil-vegetable system under different food waste fertilization and remediation treatments and soil contamination conditions. Application of food waste fertilizers significantly promoted the pakchoi growth, but resulted in the spread of ARGs from fertilizers to pakchoi. A total of 56, 80, 84, 41, and 73 ARGs, mobile genetic elements (MGEs) and metal resistance genes (MRGs) were detected in the rhizosphere soil (RS), bulk soil (BS), control soil (CS), root endophytes (RE), and leaf endophytes (LE), respectively. Notably, 7 genes were shared in the above five subgroups, indicating a specific soil-root-endophytes transmission pathway. 36 genes were uniquely detected in the LE, which may originate from airborne ARGs. The combined application of biochar and fertilizers reduced the occurrence of ARGs and MGEs to some extent, showing the remediation effect of biochar. The average abundance of ARGs in the RS, BS and CS was 3.15 × 10-2, 1.31 × 10-2 and 2.35 × 10-1, respectively. Rhizosphere effects may reduce the abundance of ARGs in soil. The distribution pattern of ARGs was influenced by the types of soil, endophyte and contaminant. MGEs is the key driver shaping ARGs dynamics. Soil properties and pakchoi growth status may affect the bacterial composition, and consequently regulate ARGs fate, while endophytic ARGs were more impacted by biotic factors. Moreover, the average daily doses of ARGs from pakchoi consumption is 107-109 copies/d/kg, and its potential health risks should be emphasized.

Contribution of sulfur-containing precursors to release of hydrogen sulfide in sludge composting

Hydrogen sulfide (H2S) production during composting can impact the environment and human health. Especially during the thermophilic phase, H2S is discharged in large quantities. However, in sludge composting, the contributions of different sulfur-containing precursors to H2S fluxes, key functional microorganisms, and key environmental parameters for reducing H2S flux remain unclear. Analysis of cysteine (Cys), methionine (Met), and sulfate (SO42-) concentrations, multiple stepwise regression analysis, and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation analysis of metagenomes showed that Cys was the main contributor to the production of H2S and that Met was among the main sources during the first three days of composting, while the SO42- contribution to H2S was negligible. Fifteen functional genera involved in the conversion of precursors to H2S were identified by co-occurrence network analysis. Only Bacillus showed high temperature resistance (>50 °C) and the ability to reduce H2S. Redundancy analysis showed that total carbon (64.0 %) and pH (23.3 %) had significant effects on functional bacteria. H2S had a quadratic relationship with sulfur-containing precursors. All microbial network sulfur-containing precursors metabolism modules showed a highly significant relationship with Cys.

Antibiotic resistance genes associated with size-segregated bioaerosols from wastewater treatment plants: A review

The antibiotic-resistant pollution in size-segregated bioaerosols from wastewater treatment plants (WWTPs) is of increasing concern due to its public health risks, but an elaborate review is still lacking. This work overviewed the profile, mobility, pathogenic hosts, source, and risks of antibiotic resistance genes (ARGs) in size-segregated bioaerosols from WWTPs. The dominant ARG type in size-segregated bioaerosols from WWTPs was multidrug resistance genes. Treatment units that equipped with mechanical facilities and aeration devices, such as grilles, grit chambers, biochemical reaction tanks, and sludge treatment units, were the primary sources of bioaerosol antibiotic resistome in WWTPs. Higher enrichment of antibiotic resistome in particulate matter with an aerodynamic diameter of <2.5 μm, was found along the upwind-downwind-WWTPs gradient. Only a small portion of ARGs in inhalable bioaerosols from WWTPs were flanked by mobile genetic elements. The pathogens with multiple drug resistance had been found in size-segregated bioaerosols from WWTPs. Different ARGs or antibiotic resistant bacteria have different aerosolization potential associated with bioaerosols from various treatment processes. The validation of pathogenic antibiotic resistance bacteria, deeper investigation of ARG mobility, emission mechanism of antibiotic resistome, and development of treatment technologies, should be systematically considered in future.

Resistomes in freshwater bioaerosols and their impact on drinking and recreational water safety: A perspective

Antibiotic resistance genes (ARGs) are widespread environmental pollutants of biological origin that pose a significant threat to human, animal, and plant health, as well as to ecosystems. ARGs are found in soil, water, air, and waste, and several pathways for global dissemination in the environment have been described. However, studies on airborne ARG transport through atmospheric particles are limited. The ARGs in microorganisms inhabiting an environment are referred to as the "resistome". A global search was conducted of air-resistome studies by retrieving bioaerosol ARG-related papers published in the last 30 years from PubMed. We found that there is no dedicated methodology for isolating ARGs in bioaerosols; instead, conventional methods for microbial culture and metagenomic analysis are used in combination with standard aerosol sampling techniques. There is a dearth of information on the bioaerosol resistomes of freshwater environments and their impact on freshwater sources used for drinking and recreational activities. More studies of aerobiome freshwater environments are needed to ensure the safe use of water and sanitation. In this review we outline and synthesize the few studies that address the freshwater air microbiome (from tap water, bathroom showers, rivers, lakes, and swimming pools) and their resistomes, as well as the likely impacts on drinking and recreational waters. We also discuss current knowledge gaps for the freshwater airborne resistome. This review will stimulate new investigations of the atmospheric microbiome, particularly in areas where both air and water quality are of public health concern.

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.

Pathogenic Bacteria Are the Primary Determinants Shaping PM2.5-Borne Resistomes in the Municipal Food Waste Treatment System

Bioaerosol pollution poses a substantial threat to human health during municipal food waste (FW) recycling. However, bioaerosol-borne antibiotic-resistant genes (ARGs) have received little attention. Herein, 48 metagenomic data were applied to study the prevalence of PM2.5-borne ARGs in and around full-scale food waste treatment plants (FWTPs). Overall, FWTP PM2.5 (2.82 ± 1.47 copies/16S rRNA gene) harbored comparable total abundance of ARGs to that of municipal wastewater treatment plant PM2.5 (WWTP), but was significantly enriched with the multidrug type (e.g., AdeC/I/J; p < 0.05), especially the abundant multidrug ARGs could serve as effective indicators to define resistome profiles of FWTPs (Random Forest accuracy >92%). FWTP PM2.5 exhibited a decreasing enrichment of total ARGs along the FWTP-downwind-boundary gradient, eventually reaching levels comparable to urban PM2.5 (1.46 ± 0.21 copies/16S rRNA gene, N = 12). The combined analysis of source-tracking, metagenome-assembled genomes (MAGs), and culture-based testing provides strong evidence that Acinetobacter johnsonii-dominated pathogens contributed significantly to shaping and disseminating multidrug ARGs, while abiotic factors (i.e., SO42-) indirectly participated in these processes, which deserves more attention in developing strategies to mitigate airborne ARGs. In addition, the exposure level of FWTP PM2.5-borne resistant pathogens was about 5-11 times higher than those in urban PM2.5, and could be more severe than hospital PM2.5 in certain scenarios (<41.53%). This work highlights the importance of FWTP in disseminating airborne multidrug ARGs and the need for re-evaluating the air pollution induced by municipal FWTP in public health terms.

New approach to soil management focusing on soil health and air quality: one earth one life (critical review)

Soil plays a key role in ecosphere and air quality regulation. Obsolete environmental technologies lead to soil quality loss, air, water, and land systems pollution. Pedosphere and plants are intertwined with the air quality. Ionized O2 is capable to intensify atmosphere turbulence, providing particulate matter (PM2.5) coalescence and dry deposition. Addressing environmental quality, a Biogeosystem Technique (BGT*) heuristic transcendental (nonstandard and not direct imitation of nature) methodology has been developed. A BGT* main focus is an enrichment of Earth's biogeochemical cycles through land use and air cleaning. An intra-soil processing, which provides the soil multilevel architecture, is one of the BGT* ingredients. A next BGT* implementation is intra-soil pulse continuously discrete watering for optimal soil water regime and freshwater saving up to 10-20 times. The BGT* comprises intra-soil dispersed environmentally safe recycling of the PM sediments, heavy metals (HMs) and other pollutants, controlling biofilm-mediated microbial community interactions in the soil. This provides abundant biogeochemical cycle formation and better functioning of the humic substances, biological preparation, and microbial biofilms as a soil-biological starter, ensuring priority plants and trees nutrition, growth and resistance to phytopathogens. A higher underground and aboveground soil biological product increases a reversible C biological sequestration from the atmosphere. An additional light O2 ions photosynthetic production ensures a PM2.5 and PM0.1 coalescence and strengthens an intra-soil transformation of PM sediments into nutrients and improves atmosphere quality. The BGT* provides PM and HMs intra-soil passivation, increases soil biological productivity, stabilizes a climate system of the earth and promotes a green circular economy.

Assessment of risk of exposure to Campylobacter species and their antibiotic-resistant genes from selected rivers in the Eastern Cape, South Africa

Contaminated rivers play a critical role in the transmission of Campylobacter and antibiotic-resistant genes (ARGs) in many parts of the world. South Africa is a water-scarce country which relies on its freshwater systems such as rivers for recreation, irrigation, and domestic activities. This study assesses the potential human exposure to Campylobacter and its ARGs from rivers through the ingestion route in two South African rivers. The concentration of viable Campylobacter and ARGs in selected rivers was determined using quantitative PCR. The concentrations were then used to estimate the number of gene copies a person could ingest after swimming in the contaminated water for 1 h (intake burden). The human intake burden of Campylobacter 16 S rRNA copies per 1-h swimming event ranged from 7.1 × 105-3.7 × 106 copies/h for the Bloukrans River, and 9.9 × 101-2.3 × 105 copies/h for the Swartkops River. The intake burden of Campylobacter ARGs ranged from 1.64 × 104-5.8 × 105 copies/h for cmeB; 1.0 × 103-5.7 × 104 copies/h for tetO for the Bloukrans River, and 3.6 × 102-1.551 × 105 copies/h (cmeB) and 9.98 × 102-5.7 × 104 copies/h (tetO) for the Swartkops River. Ingestion of water from contaminated rivers during recreation, cultural, or religious activities may lead to human exposure to ARGs, posing a health risk. In many communities in the world, rivers play an important role in the social and cultural lives of people, and so it is important to monitor the quality of river water. Studies such as these will help prevent the spread of antibiotic-resistant genes and waterborne diseases caused by pathogens such as Campylobacter.

Atmospheric antibiotic resistome driven by air pollutants

The atmosphere is an important reservoir and habitat for antibiotic resistance genes (ARGs) and is a main pathway to cause potential health risks through inhalation and ingestion. However, the distribution characteristics of ARGs in the atmosphere and whether they were driven by atmospheric pollutants remain unclear. We annotated 392 public air metagenomic data worldwide and identified 1863 ARGs, mainly conferring to tetracycline, MLS, and multidrug resistance. We quantified these ARG's risk to human health and identified their principal pathogenic hosts, Burkholderia and Staphylococcus. Additionally, we found that bacteria in particulate contaminated air carry more ARGs than in chemically polluted air. This study revealed the influence of typical pollutants in the global atmosphere on the dissemination and risk of ARGs, providing a theoretical basis for the prevention and mitigation of the global risks associated with ARGs.

Particle-size stratification of airborne antibiotic resistant genes, mobile genetic elements, and bacterial pathogens within layer and broiler farms in Beijing, China

The particle-size distribution of antimicrobial resistant (AMR) elements is crucial in evaluating their environmental behavior and health risks, and exposure to the fecal microbiome via particle mass (PM) is an important route of transmission of AMR from livestock to humans. However, few studies have explored the association between air and fecal AMR in farm environments from the perspective of particle-size stratification. We collected feces and PMs of different sizes from layer and broiler farms, quantified antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and human pathogenic bacteria (HPB) using Droplet digital PCR (ddPCR), and analyzed the bacterial communities based on 16S rRNA sequencing. The particle-size distributions of 16S rRNA and AMR elements were similar and generally increased with larger particle sizes in chicken farms. In broiler farms, we observed a bimodal distribution with two peaks at 5.8-9.0 μm and 3.3-4.7 μm. The dominant airborne bacterial phyla were Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes. The dominant phyla in the feces were the same as those in the air, but the order of relative abundance varied. The particle-size distributions of specific bacterial genera differed between the animal-farm types. Overall, the degree of association between feces and different particulates increased with increasing particle size. The microbial communities in the coarse particles were similar to those in fecal samples. Escherichia coli, Staphylococcus spp., Campylobacter spp., and sul 2 (sulfonamide ARGs) tended to attach to small particles. We highlight the particle size-specific relationship between fecal and air microbes involving ARGs, MGEs, and HPB and provide valuable information for comprehensively assessing the transmission of fecal microorganisms through the airpath and its environmental and occupational health risks.

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.

Association between particulate matter (PM)2·5 air pollution and clinical antibiotic resistance: a global analysis

BACKGROUND

Antibiotic resistance is an increasing global issue, causing millions of deaths worldwide every year. Particulate matter (PM)2·5 has diverse elements of antibiotic resistance that increase its spread after inhalation. However, understanding of the contribution of PM2·5 to global antibiotic resistance is poor. Through univariate and multivariable analysis, we aimed to present the first global estimates of antibiotic resistance and burden of premature deaths attributable to antibiotic resistance resulting from PM2·5 pollution.

METHODS

For this global analysis, data on multiple potential predictors (ie, air pollution, antibiotic use, sanitation services, economics, health expenditure, population, education, climate, year, and region) were collected in 116 countries from 2000 to 2018 to estimate the effect of PM2·5 on antibiotic resistance via univariate and multivariable analysis. Data were obtained from ResistanceMap, European Centre for Disease Prevention and Control Surveillance Atlas (antimicrobial-resistance sources), and PLISA Health Information Platform for the Americas. Future global aggregate antibiotic resistance and premature mortality trends derived from PM2·5 in different scenarios (eg, 50% reduced antibiotic use or PM2·5 controlled to 5 μg/m3) were projected until 2050.

FINDINGS

The final dataset included more than 11·5 million tested isolates. Raw antibiotic-resistance data included nine pathogens and 43 types of antibiotic agents. Significant correlations between PM2·5 and antibiotic resistance were consistent globally in most antibiotic-resistant bacteria (R2=0·42-0·76, p<0·0001), and correlations have strengthened over time. Antibiotic resistance derived from PM2·5 caused an estimated 0·48 (95% CI 0·34-0·60) million premature deaths and 18·2 (13·4-23·0) million years of life lost in 2018 worldwide, corresponding to an annual welfare loss of US$395 (290-500) billion due to premature deaths. The 5 μg/m3 target of concentration of PM2·5 in the air quality guidelines set by WHO, if reached in 2050, was estimated to reduce antibiotic resistance by 16·8% (95% CI 15·3-18·3) and avoid 23·4% (21·2-25·6) of premature deaths attributable to antibiotic resistance, equivalent to a saving of $640 (580-671) billion.

INTERPRETATION

This analysis is the first to describe the association between PM2·5 and clinical antibiotic resistance globally. Results provide new pathways for antibiotic-resistance control from an environmental perspective.

FUNDING

National Natural Science Foundation of China, Fundamental Research Funds for the Central Universities, Zhejiang University Global Partnership Fund, and China Postdoctoral Science Foundation.

The exposure risks associated with pathogens and antibiotic resistance genes in bioaerosol from municipal landfill and surrounding area

Pathogenic microbes with antibiotic resistance can thrive on municipal solid waste as nutrients and be aerosolized and transported to vicinities during waste disposal processes. However, the characterization of pathogenic bioaerosols and assessment of their exposure risks are lacking. Herein, particle size, concentration, activity, antibiotic resistance, and pathogenicity of airborne microorganisms were assessed in different sectors of a typical landfill. Results showed that active sector in downwind direction has the highest bioaerosol level (1234 CFU/m³), while residential area has the highest activity (14.82 mg/L). Botanical deodorizer from mist cannon can effectively remove bioaerosol. Most bioaerosols can be inhaled into respiratory system till bronchi with sizes ranging from 2.1-3.3 and 3.3-4.7 µm. Pathogenic bacteria (Bacilli, Bacillus, and Burkholderia-Paraburkholderia) and allergenic fungi (Aspergillus, Cladosporium, and Curvularia) prevailed in landfill. Although high abundance of microbial volatile organic compounds (mVOCs) producing bioaerosols were detected, these mVOCs contributed little to odor issues in landfill. Notably, surrounding areas have higher levels of antibiotic-resistance genes (ARGs) than inner landfill with tetC, acrB, acrF, mdtF, and bacA as dominant ones. Most ARGs were significantly correlated with bacterial community, while environmental parameters mainly influenced fungal prevalence. These findings can assist in reducing and preventing respiratory allergy or infection risks in occupational environments relating to waste management.

The dynamics and transmission of antibiotic resistance associated with plant microbiomes

Antibiotic resistance genes (ARGs) have been widely found and studied in soil and water environments. However, the propagation of ARGs in plant microbiomes has attracted insufficient attention. Plant microbiomes, especially the rhizosphere microorganisms, are closely connected with water, soil, and air, which allows ARGs to spread widely in ecosystems and pose a threat to human health after entering the human body with bacteria. Therefore, it is necessary to deeply understand and explore the dynamics and the transmission of ARGs in rhizosphere microorganisms and endophytes of plants. In this review, the transmission and influencing factors of ARGs in the microorganisms associated with plants, especially the influence of root exudates on plant microbiomes, are analyzed. Notably, the role of intrinsic genes of plants in determining root exudates and their potential effects on ARGs are proposed and analyzed. The important role of phyllosphere microorganisms and endophytes in the transmission of ARGs and co-resistance of antibiotics and other substances are also emphasized. The proliferation and transmission of ARGs associated with plant microbiomes addressed in this review is conducive to revealing the fate of ARGs in plant microorganisms and alleviating ARG pollution.

Viability and transcriptional responses of multidrug resistant E. coli to chromium stress

The viability of multidrug resistant (MDR) bacteria in environment is critical for the spread of antimicrobial resistance. In this study, two Escherichia coli strains, MDR LM13 and susceptible ATCC25922, were used to elucidate differences in their viability and transcriptional responses to hexavalent chromium (Cr(VI)) stress. The results show that the viability of LM13 was notably higher than that of ATCC25922 under 2-20 mg/L Cr(VI) exposure with bacteriostatic rates of 3.1%-57%, respectively, for LM13 and 0.9%-93.1%, respectively, for ATCC25922. The levels of reactive oxygen species and superoxide dismutase in ATCC25922 were much higher than those in LM13 under Cr(VI) exposure. Additionally, 514 and 765 differentially expressed genes were identified from the transcriptomes of the two strains (log₂|FC| > 1, p < 0.05). Among them, 134 up-regulated genes were enriched in LM13 in response to external pressure, but only 48 genes were annotated in ATCC25922. Furthermore, the expression levels of antibiotic resistance genes, insertion sequences, DNA and RNA methyltransferases, and toxin-antitoxin systems were generally higher in LM13 than in ATCC25922. This work shows that MDR LM13 has a stronger viability under Cr(VI) stress, and therefore may promote the dissemination of MDR bacteria in environment.

Antibiotic Resistance Genes in Aerosols: Baseline from Kuwait

Antimicrobial resistance (AMR) is one of the biggest threats to human health worldwide. The World Health Organization (WHO, Geneva, Switzerland) has launched the "One-Health" approach, which encourages assessment of antibiotic-resistant genes (ARGs) within environments shared by human-animals-plants-microbes to constrain and alleviate the development of AMR. Aerosols as a medium to disseminate ARGs, have received minimal attention. In the present study, we investigated the distribution and abundance of ARGs in indoor and outdoor aerosols collected from an urban location in Kuwait and the interior of three hospitals. The high throughput quantitative polymerase chain reaction (HT-qPCR) approach was used for this purpose. The results demonstrate the presence of aminoglycoside, beta-lactam, fluoroquinolone, tetracycline, macrolide-lincosamide-streptogramin B (MLSB), multidrug-resistant (MDR) and vancomycin-resistant genes in the aerosols. The most dominant drug class was beta-lactam and the genes were IMP-2-group (0.85), Per-2 group (0.65), OXA-54 (0.57), QnrS (0.50) and OXA-55 (0.55) in the urban non-clinical settings. The indoor aerosols possessed a richer diversity (Observed, Chao1, Shannon's and Pielou's evenness) of ARGs compared to the outdoors. Seasonal variations (autumn vs. winter) in relative abundances and types of ARGs were also recorded (R² of 0.132 at p < 0.08). The presence of ARGs was found in both the inhalable (2.1 µm, 1.1 µm, 0.7 µm and < 0.3 µm) and respirable (>9.0 µm, 5.8 µm, 4.7 µm and 3.3 µm) size fractions within hospital aerosols. All the ARGs are of pathogenic bacterial origin and are hosted by pathogenic forms. The findings present baseline data and underpin the need for detailed investigations looking at aerosol as a vehicle for ARG dissemination among human and non-human terrestrial biota.

Seasonal variation characteristics of inhalable bacteria in bioaerosols and antibiotic resistance genes in Harbin

Bioaerosols have received extensive attention due to their impact on climate, ecological environment, and human health. This study aimed to reveal the driving factors that structure bacterial community composition and the transmission route of antibiotic resistance genes (ARGs) in PM_2.5. The results showed that the bacterial concentration in spring (8.76 × 10⁵ copies/m³) was significantly higher than that in summer (1.03 × 10⁵ copies/m³) and winter (4.74 × 10⁴ copies/m³). Low temperatures and air pollution in winter negatively affected bacterial concentrations. Keystone taxa were identified by network analysis. Although about 50 % of the keystone taxa had low relative abundances, the strong impact of complex interactions between keystone taxa and other taxa on bacterial community structure deserved attention. The bacterial community assembly was dominated by stochastic processes (79.3 %). Interactions between bacteria and environmental filtering together affected bacterial community composition. Vertical gene transfer played an important role in the transmission of airborne ARGs. Given the potential integration and expression of ARGs in recipients, the human exposure risk due to high concentrations of ARGs and mobile genetic elements cannot be ignored. This study highlights human exposure to inhalable bacterial pathogens and ARGs in urban areas.

Metagenomic analysis of microbiological risk in bioaerosols during biowaste valorization using Musca domestica

Bioconversion using insects has gradually become a promising technology for biowaste management and protein production. However, knowledge about microbiological risk of insect related bioaerosols is sparse and conventional methods failed to provide higher resolved information of environmental microbe. In this study, a metagenomic analysis including microorganisms, antibiotic resistance genes (ARGs), virulence factor genes (VFGs), mobile gene elements (MGEs), and endotoxin distribution in bioaerosols during biowaste conversion via Musca domestica revealed that bioaerosols in Fly rearing room possess the highest ARGs abundances and MGEs diversity. Through a metagenome-assembled genomes (MAGs)-based pipeline, compelling evidence of ARGs/VFGs host assignment and ARG-VFG co-occurrence pattern were provided from metagenomic perspective. Bioaerosols in Bioconversion and Maggot separation zone were identified to own high density of MAGs carrying both ARGs and VFGs. Bacteria in Proteobacteria, Actinobacteriota, and Firmicutes phyla were predominate hosts of ARGs and VFGs. Multidrug-Motility, Multidrug-Adherence, and Beta lactam-Motility pairs were the most common ARG-VFG co-occurrence pattern in this study. Results obtained are of great significance for microbiological risk assessment during housefly biowaste conversion process.

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.

Animal farms are hot spots for airborne antimicrobial resistance

Animal farms are known reservoirs for environmental antimicrobial resistance (AMR). However, knowledge of AMR burden in the air around animal farms remains disproportionately limited. In this study, we characterized the airborne AMR based on the quantitative information of 30 antimicrobial resistance genes (ARGs), four mobile genetic elements (MGEs), and four human pathogenic bacteria (HPBs) involving four animal species from 20 farms. By comparing these genes with those in animal feces, the distinguishing features of airborne AMR were revealed, which included high enrichment of ARGs and their potential mobility to host HPBs. We found that depending on the antimicrobial class, the mean concentration of airborne ARGs in the animal farms ranged from 10² to 10⁴ copies/m³ and was accompanied by a considerable intensity of MGEs and HPBs (approximately 10³ copies/m³). Although significant correlations were observed between the ARGs and bacterial communities of air and fecal samples, the abundance of target genes was generally high in fine inhalable particles (PM2.5), with an enrichment ratio of up to 10² in swine and cattle farms. The potential transferability of airborne ARGs was universally strengthened, embodied by a pronounced co-occurrence of ARGs-MGEs in air compared with that in feces. Exposure analysis showed that animal farmworkers may inhale approximately 10⁴ copies of human pathogenic bacteria-associated genera per day potentially carrying highly transferable ARGs, including multidrug resistant Staphylococcus aureus. Moreover, PM2.5 inhalation posed higher human daily intake burdens of some ARGs than those associated with drinking water intake. Overall, our findings highlight the severity of animal-related airborne AMR and the subsequent inhalation exposure, thus improving our understanding of the airborne flow of AMR genes from animals to humans. These findings could help develop strategies to mitigate the human exposure and dissemination of ARGs across different media.

Airborne bacterial communities in the poultry farm and their relevance with environmental factors and antibiotic resistance genes

The accelerating occurrence and environmental dissemination of bacteria, gas pollutants and antibiotic resistance genes (ARGs) in aerosols of poultry farms have become emerging environmental issues due to their potential threat to animals, workers, and the communities located near such farms. Here, aerosol samples were gathered from inside and outside of the chicken house in winter with a transportable high-flow bioaerosol sampler. Then, 16S rRNA gene amplicon sequencing was used to categorize the bacteria in air samples, and the abundance of 12 ARG subtypes was researched via the real-time quantitative polymerase chain reaction (qPCR). Results indicated that the bacterial richness and diversity and total absolute abundance of ARGs were similar in the bioaerosols from indoor and downwind site of the poultry farm. The zoonotic pathogens, Staphylococcus and Corynebacterium, were detected both inside and outside of the chicken house, and the four most abundant target genes were bla_TEM, tetQ, ermB and sul1 in aerosols. Moreover, the correlation between the bacterial communities and environmental factors, such as NH₃ and H₂S concentrations, wind speed, temperature and relative humidity, was analyzed. The result revealed that the indoor bacteria community was positively associated with temperature and concentrations of air pollutants (NH₃ and H₂S), and could spread from confinement buildings to the ambient atmosphere through wind. In addition, the network analysis result showed that the airborne bacteria might significantly contribute in shaping the ARGs' profiles in bioaerosol from inside and outside of the poultry house. Overall, our results revealed the airborne bacterial communities and their associated influencing factors in the micro-environment (inside of the chicken house and nearby the boundary of the farm), and brought a new perspective for studying the gas pollutants and bioaerosol from poultry farms in winter.

Municipal solid waste, an overlooked route of transmission for the severe acute respiratory syndrome coronavirus 2: a review

Municipal solid waste could potentially transmit human pathogens during the collection, transport, handling, and disposal of waste. Workers and residents living in the vicinity of municipal solid waste collection or disposal sites are particularly susceptible, especially unprotected workers and waste pickers. Recent evidence suggests that municipal solid waste-mediated transmission can spread the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to humans. Such risks, however, have received little attention from public health authorities so far and may present an under-investigated transmission route for SARS-CoV-2 and other infectious agents during pandemics. In this review, we provide a retrospective analysis of the challenges, practices, and policies on municipal solid waste management during the current pandemic, and scrutinize the recent case reports on the municipal solid waste-mediated transmission of the coronavirus disease 2019 (COVID-19). We found abrupt changes in quantity and composition of municipal solid wastes during the COVID-19. We detail pathways of exposure to SARS-CoV-2 and other pathogens carried on municipal solid wastes. We disclose evidence of pathogenic transmission by municipal solid waste to humans and animals. Assessments of current policies, gaps, and voluntary actions taken on municipal solid waste handling and disposal in the current pandemic are presented. We propose risk mitigation strategies and research priorities to alleviate the risk for humans and vectors exposed to municipal solid wastes.

Airborne fungi and human exposure in different areas of composting facilities

Airborne fungi can pose serious health concerns in humans; however, the area-specific abundance and composition of airborne fungal microbiota discharged from composting facilities remain unclear. In the present study, we collected air samples from composting, packaging, office, and downwind areas of four commercial composting facilities. The characteristics of airborne fungi, including pathogen/allergen-containing genera, and their corresponding human exposure in different areas of composting facilities were analyzed using high-throughput sequencing and ddPCR. High fungal concentrations and richness were detected in the air of the packaging area. In all four areas, Ascomycota, Basidiomycota, and Mucoromycota were observed to be the primary fungal phyla, with Cladosporium, Alternaria, and Aspergillus as the consistently dominant fungal genera. A large number of endemic airborne fungi were found in the composting and packaging areas, which also shared the most common airborne fungi as well as pathogen/allergen-containing genera. The packaging area contributed substantially to airborne fungi in the office and downwind areas. Area-specific human exposure to broad airborne fungal compositions was revealed, especially regarding the pathogen/allergen-containing genera. Current results provide valuable data for a comprehensive understanding of area-specific airborne fungi in composting facilities and highlight the importance of assessing the inhaled exposure to airborne fungi in evaluating their following health risks.

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).

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.

Inhalable Antibiotic Resistome from Wastewater Treatment Plants to Urban Areas: Bacterial Hosts, Dissemination Risks, and Source Contributions

Antibiotic resistance genes (ARGs) are commonly detected in the atmosphere, but questions remain regarding their sources and relative contributions, bacterial hosts, and corresponding human health risks. Here, we conducted a qPCR- and metagenomics-based investigation of inhalable fine particulate matter (PM_2.5) at a large wastewater treatment plant (WWTP) and in the ambient air of Hong Kong, together with an in-depth analysis of published data of other potential sources in the area. PM_2.5 was observed with increasing enrichment of total ARGs along the coastal-urban-WWTP gradient and clinically relevant ARGs commonly identified in urban and WWTP sites, illustrating anthropogenic impacts on the atmospheric accumulation of ARGs. With certain kinds of putative antibiotic-resistant pathogens detected in urban and WWTP PM_2.5, a comparable proportion of ARGs that co-occurred with MGEs was found between the atmosphere and WWTP matrices. Despite similar emission rates of bacteria and ARGs within each WWTP matrix, about 11-13% of the bacteria and >57% of the relevant ARGs in urban and WWTP PM_2.5 were attributable to WWTPs. Our study highlights the importance of WWTPs in disseminating bacteria and ARGs to the ambient air from a quantitative perspective and, thus, the need to control potential sources of inhalation exposure to protect the health of urban populations.

Air path of antimicrobial resistance related genes from layer farms: Emission inventory, atmospheric transport, and human exposure

Animal husbandry is a significant contributor to increased environmental antimicrobial resistance (AMR), but little is known regarding the dissemination of AMR from animal farms via airborne transmission. Here, we connected the air path of AMR related genes tailored to layer poultry farms from source of escape to end of sedimentation. The emission inventories of 8 AMR related genes from all 163-layer poultry farms around Beijing city were quantified. We developed the atmospheric transport model with a gene degradation module to estimate the spatiotemporal distribution of airborne AMR, and also assessed their corresponding regional exposure and sedimentation. Total emissions of 16 S rDNA and AMR related genes from layer houses ranged from 10¹⁵ to 10¹⁶ copies year^-1. Those layer-sourced genes contributed 1-14.6% of antimicrobial resistant genes, 4.9% of Staphylococcus spp. and 2.2% of CintI1 to the corresponding annual genetic burden of Beijing's urban air. The average exposure of the Beijing residents to layer-sourced airborne 16 S rDNA was 1.39 × 10⁴ copies year^-1 person^-1, approximately 87% of them would be deposited in the upper respiratory tract. The findings highlight that air medium represents an important dissemination pathway of animal-sourced genes to AMR burden in humans and environment.

Characteristics of airborne bacterial communities and antibiotic resistance genes under different air quality levels

Pathogenic bacteria and antibiotic resistance genes (ARGs) in bioaerosols are major threats to human health. In this study, the microbial community structure and ARG distribution characteristics of airborne bacteria in total suspended particulates (TSP) and PM_2.5 were investigated under different air quality levels in Xinxiang, Central China. The results revealed that with the deterioration of air quality, the concentrations of airborne bacteria in both TSP and PM_2.5 decreased; however, the relative amounts of pathogenic bacteria increased. The predominant genera in pathogenic bacteria of Bacillus, Sphingomonas, Corynebacterium, Rhodococcus, and Staphylococcus were identified in both TSP and PM_2.5. Although the airborne bacteria concentrations and absolute abundances of ARGs in TSP were higher than those in PM_2.5 under identical air quality conditions, the bacterial community structure and relative amounts of pathogenic bacteria were similar. In addition, the relationship between environmental factors of ions, metal elements, and meteorological parameters and the community structures of airborne bacteria and pathogenic bacteria were also analyzed. The effects of soluble ions and metal elements on several dominant genera of total bacteria and pathogenic bacteria differed, probably due to the strong tolerance of pathogenic bacteria to harsh atmospheric environments Different subtypes of ARGs showed various distribution characteristics with variations in air quality. The deterioration of air quality can inhibit the dissemination of ARGs, as the minimum values of all ARGs and class 1 integrase intI1 were observed under Severely Polluted conditions. This study provides a comprehensive understanding of the effect of air pollution levels on the airborne bacteria community composition and ARG distribution.

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.