Size-related bacterial diversity and tetracycline resistance gene abundance in the air of concentrated poultry feeding operations

Genomic characterisation of bioaerosols within livestock facilities: A systematic review

Livestock facilities are widely regarded as reservoirs of infectious disease, owing to their abundance in particulate matter (PM) and microbial bioaerosols. Over the past decade, bioaerosol studies have increasingly utilised high throughput sequencing (HTS) to achieve superior throughput, taxonomic resolution, and the detection of unculturable organisms. However, the prevailing focus on amplicon sequencing has limited the identification of viruses and microbial taxa at the species-level. Herein, a literature search was conducted to identify methods capable of overcoming the aforementioned limitations. Screening 1531 international publications resulted in 29 eligible for review. Metagenomics capable of providing rich insights were identified in only three instances. Notably, long-read sequencing was not utilised for metagenomics. This review also identified that sample collection methods lack a uniform approach, highlighted by the differences in sampling equipment, flow rates and durations. Further heterogeneity was introduced by the unique sampling conditions, which makes it challenging to ground new findings within the established literature. For instance, winter was associated with increased microbial abundance and antimicrobial resistance, yet less alpha diversity. Researchers implementing metagenomics into the livestock environment should consider season, the microclimate, and livestock growth stage as influential upon their findings. Considering the increasing accessibility of long-read sequencing, future research should explore its viability within a novel uniform testing protocol for bioaerosol emissions.

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.

Bioaerosol-related studies in wastewater treatment plant with anaerobic-anoxic-oxic processes: Characterization, source analysis, control measures

Sewage in wastewater treatment plants (WWTPs) can produce fugitive bioaerosols that pose a health risk to employees and residents. This study aimed to fugitive bioaerosols from two WWTPs with anaerobic-anoxic-oxic (AAO) processes, and bioaerosols control measures were proposed based on the results of these studies. It was found that the bioaerosols were mainly composed of microorganisms from dominant genera such as Romboutsia, Rubellimicrobium, Sphingomonas, Acidea, Cryptotrichosporon and water-soluble ions dominated by SO₄^2-. Moreover, total suspended particulate (TSP), relative humidity (RH), wind speed (WS), Ca²⁺, NH₄⁺, Na⁺, Cl^-, NO₃^-, and K⁺ had positive effects on most dominant genera, while temperature (T) and SO₄^2- had negative effects on most dominant genera. The source analysis showed that the bioaerosols in the indoor treatment facility's fine screen room and sludge dewatering plant mainly originated from sewage or sludge, and those in the aeration tank of the outdoor treatment facility mainly originated from the background air of WWTPs . By combining the characteristics of bioaerosols and the results of source analysis, targeted control measures were proposed from three aspects: source reduction of bioaerosol fugitives, control of bioaerosol propagation, and collection and treatment systems. This study provides the theoretical basis and ideas for controlling bioaerosols in WWTPs with AAO processes.

Fecal antibiotic resistance genes were transferred through the distribution of soil-lettuce-snail food chain

Massive antibiotic resistance genes (ARG) were detected in the soil modified by manure, which may affect human life safety through the food chain. However, the transmission of ARGs through the soil-plant-animal food chain is still unclear. Therefore, this study used high-throughput quantitative PCR technology to explore the effects of pig manure application on ARGs and bacterial communities in soil, lettuce phyllosphere, and snail excrement. The results showed that a total of 384 ARGs and 48 MEGs were detected in all samples after 75 days of incubation. The diversity of ARGs and MGEs in soil components increased significantly by 87.04% and 40% with the addition of pig manure. The absolute abundance of ARGs in the phyllosphere of lettuce was significantly higher than that of the control group, with a growth rate of 212.5%. Six common ARGs were detected between the three components of the fertilization group, indicating that there was internal transmission of fecal ARGs between the trophic levels of the food chain. Firmicutes and Proteobacteria were identified as the dominant host bacteria in the food chain system, which were more likely to be used as carriers of ARGs to promote the spread of resistance in the food chain. The results were used to assess the potential ecological risks of livestock and poultry manure. It provides theoretical basis and scientific support for the formulation of ARG prevention and control policies.

Spatial distribution of airborne bacterial communities in caged poultry houses

Microbial aerosols in intensive broiler houses whose species and concentrations are closely related to human health are ubiquitous. Based on 16S rRNA gene sequencing, the aim of this study was to investigate the spatial distribution and diversity of bacterial aerosols in the air of broiler houses. Significant spatial variations in airborne bacterial concentrations were observed inside the poultry farmhouse. The results indicated that bacteria in the air samples could be grouped into a total of 1,674 OTUs. Alpha diversity analysis showed that the diversity of the microbial community at the entry of the broiler house was higher than that at the middle or the rear (p < 0.01). The Sankey diagram illustrated species dynamic changes in Proteobacteria, Firmicutes, and Actinobacteria among the different locations. From the aspect of LEfSe (LDA Effect Size) analysis, we discovered that the abundance of Planctomycetes was significantly higher in the entry than in the rear and middle. This study shows the spatial distribution of the entire bacterial community in intensive broiler houses, which offers a new perspective for studying airborne total bacteria in those environments.Implications: The bacteria contained in air aerosols from poultry houses are closely connected to animal health and production. This study aimed to investigate the spatial distribution and diversity of bacterial aerosols in the air of broiler houses. The results observed that bacterial aerosol concentrations in the examined broilers house varied greatly at different positions, and a significantly higher exposure to bacterial aerosol was observed at the middle than at the other positions (p < 0.05). The alpha diversity analysis showed that the diversity of the microbial community at the entry of the broiler house was higher than that at the middle or the rear (P<0.01). Sankey diagram illustrated species dynamic changes of Proteobacteria, Firmicutes and Actinobacteria among the different locations. The microbial communities in genus level in the samples of entry and rear were closer, while the species diversity of middle and rear samples in chicken house was highly similar (P>0.05). Altogether, results revealed that the effects of spatial factors on the diversity and abundance of bacteria in the air of closed-cage broiler houses, which poses a potential threat to the health of animals and workers in those environments.

Effects of different laying periods on airborne bacterial diversity and antibiotic resistance genes in layer hen houses

Poultry farms are a complex environment for close contact between humans and animals. Accumulating evidence has indicated that pathogens and drug resistance genes in chicken houses may pose a serious threat to public health and economic concerns. However, insufficient knowledge of the indoor aerosol microbiome and resistome profiles of layer hen houses hampers the understanding of their health effects. Environmental surveillance of antibiotic resistance may contribute to a better understanding and management of the human exposure risk of bioaerosols under the environmental conditions of chicken houses. In addition, the chicken house has a long operation cycle, and the bacterial diversity and antibiotic resistance genes of aerosols in different periods may be different. In this study, air samples were collected from 18 chicken houses on three farms, including the early laying period (EL), peak laying period (PL), and late laying period (LL). 16S rRNA gene sequencing and metagenomics were used to study the composition of the bacteria and resistome in aerosols of layer hen houses and the results showed that they varied with laying period. The highest alpha diversity of bacteria was observed in PL bioaerosols. The dominant bacterial phyla included Firmicutes, Bacteroidetes and Proteobacteria. Three potential pathogenic bacterial genera (Bacteroides, Corynebacterium and Fusobacterium) were found. The most abundant ARG type was aminoglycosides in all laying periods. In total, 22 possible ARG host genera were detected. ARG subtypes and abundance were both higher in LL. Network analysis also showed higher co-occurrence patterns between the bacteria and resistome in bioaerosols. The laying period plays an important role in the bacterial community and resistome in layer house aerosols.

One Health Approach to Tackle Microbial Contamination on Poultries-A Systematic Review

This study reports the search of available data published regarding microbial occupational exposure assessment in poultries, following the PRISMA methodology. Air collection through filtration was the most frequently used. The most commonly used passive sampling method was material collection such as dust, cages, soils, sediment, and wastewater. Regarding assays applied, the majority of studies comprised culture-based methods, but molecular tools were also frequently used. Screening for antimicrobial susceptibility was performed only for bacteria; cytotoxicity, virological and serological assays were also performed. Most of the selected studies focused on bacteria, although fungi, endotoxins, and β-glucans were also assessed. The only study concerning fungi and mycotoxins reported the carcinogenic mycotoxin AFB1. This study gives a comprehensive overview of microbial contamination in the poultry industry, emphasizing this setting as a potential reservoir of microbial pathogens threatening human, animal, and environmental health. Additionally, this research helps to provide a sampling and analysis protocol proposal to evaluate the microbiological contamination in these facilities. Few articles were found reporting fungal contamination in poultry farms worldwide. In addition, information concerning fungal resistance profile and mycotoxin contamination remain scarce. Overall, a One Health approach should be incorporated in exposure assessments and the knowledge gaps identified in this paper should be addressed in further research.

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.

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.

Short-term inhalation exposure evaluations of airborne antibiotic resistance genes in environments

Antibiotic resistance is a sword of Damocles that hangs over humans. In regards to airborne antibiotic resistance genes (AARGs), critical knowledge gaps still exist in the identification of hotspots and quantification of exposure levels in different environments. Here, we have studied the profiles of AARGs, mobile genetic elements (MGEs) and bacterial communities in various atmospheric environments by high throughput qPCR and 16S rRNA gene sequencing. We propose a new AARGs exposure dose calculation that uses short-term inhalation (STI). Swine farms and hospitals were high-risk areas where AARGs standardised abundance was more abundant than suburbs and urban areas. Additionally, resistance gene abundance in swine farm worker sputum was higher than that in healthy individuals in other environments. The correlation between AARGs with MGEs and bacteria was strong in suburbs but weak in livestock farms and hospitals. STI exposure analysis revealed that occupational intake of AARGs (via PM₁₀) in swine farms and hospitals were 110 and 29 times higher than in suburbs, were 1.5 × 10⁴, 5.6 × 10⁴ and 5.1 × 10² copies, i.e., 61.9%, 75.1% and 10.7% of the overall daily inhalation intake, respectively. Our study comprehensively compares environmental differences in AARGs to identify high-risk areas, and forwardly proposes the STI exposure dose of AARGs to guide risk assessment.

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.

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.

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.

Seasonal Variations in the Characteristics of Microbial Community Structure and Diversity in Atmospheric Particulate Matter from Clean Days and Smoggy Days in Beijing

Microorganisms are an important part of atmospheric particulate matter and are closely related to human health. In this paper, the variations in the characteristics of the chemical components and bacterial communities in PM₁₀ and PM_2.5 grouped according to season, pollution degree, particle size, and winter heating stage were studied. The influence of environmental factors on community structure was also analyzed. The results showed that seasonal variations were significant. NO₃^- contributed the most to the formation of particulate matter in spring and winter, while SO₄^2- contributed the most in summer and autumn. The community structures in summer and autumn were similar, while the community structure in spring was significantly different. The dominant phyla were similar among seasons, but their proportions were different. The dominant genera were no-rank_c_Cyanobacteria, Acidovorax, Escherichia-Shigella and Sphingomonas in spring; Massilia, Bacillus, Acinetobacter, Rhodococcus, and Brevibacillus in summer and autumn; and Rhodococcus in winter. The atmospheric microorganisms in Beijing mainly came from soil, water, and plants. The few pathogens detected were mainly affected by the microbial source on the sampling day, regardless of pollution level. RDA (redundancy analysis) showed that the bacterial community was positively correlated with the concentration of particulate matter and that the wind speed in spring was positively correlated with NO₃^- levels, NH₄⁺ levels, temperature, and relative humidity in summer and autumn, but there was no clear consistency among winter samples. This study comprehensively analyzed the variations in the characteristics of the airborne bacterial community in Beijing over one year and provided a reference for understanding the source, mechanism, and assessment of the health effects of different air qualities.

Seasonal and short-term variations of bacteria and pathogenic bacteria on road deposited sediments

The bacteria (including pathogenic bacteria) attached to road deposited sediments (RDS) may interrelate with the microbe in the atmosphere, soil and water through resuspension and wash-off, and is of great significance to human and ecological health. However, the characteristics of bacterial communities with different time scale on RDS were unknown to dates. Climate change prolonged the dry days between rain events in many areas, making the varied trend of bacterial communities might be more significant in short term. This study revealed the characteristics of bacterial communities on RDS in urban and suburban areas through seasonal and daily scale. The correlations between other factors (land use, particle size, and chemical components) and the bacterial communities were also analyzed. It was found that the season showed a higher association with the bacterial community diversity than land use and particle size in urban areas. The bacterial community diversity increased substantially throughout the short-term study period (41 days) and the variation of dominant bacteria could be fitted by quadratic function in suburbs. In addition, urbanization notably increased the bacterial community diversity, while the potential pathogenic bacteria were more abundant in the suburban areas, coarse RDS (>75 μm), and in spring. The chemical components on RDS showed special correlations with the relative abundance of dominant bacteria. The research findings would fill the knowledge gap on RDS bacterial communities and be helpful for the future research on the assembly process of bacterial communities.

Comparison of Bacterial Community Structure in PM2.5 within Broiler Houses under Different Rearing Systems in China

Background: In intensive poultry farming, high concentrations of indoor particulate matter (PM) impact production performance and welfare. In this study, PM2.5 level and bacterial community diversity were investigated in a multilayer cage house rearing system (CH) and a net flooring house rearing system (FH) during different growth stages to clarify the effects of the rearing systems on the diversity of airborne bacteria and help improve health management. Methods: The IC and high-throughput sequencing were used for ion composition and bacterial diversity analysis of PM2.5 collected from CH and FH. Results: The concentrations of NH3, CO2 and PM2.5 in CH were significantly lower than FH (p < 0.001) in both middle and late rearing stages. PM concentrations gradually increased with broiler growth only in FH. The water-soluble ions of PM2.5 samples had no significant difference between the two systems (p > 0.05). Firmicutes, Actinobacteria and Proteobacteria were the most abundant phyla in both the atmosphere and the broiler houses, but the composition was significantly different. The bacterial community in the broiler houses had strong correlations with temperature, humidity and PM of extremely high concentrations. Ions had stronger correlations with microbial community structure. Conclusions: The superiority of CH in environmental control over FH indicates that improved techniques in environmental control and breeding management can greatly reduce farming air pollution and improve the health management of broiler houses.

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.

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.

Abundance and diversity of antibiotic resistance genes possibly released to ambient air by experiments in biology laboratories

Antibiotic resistance genes (ARG) have been considered as a global emerging threat to public health systems. As special locations where both antibiotics and ARGs are directly used, biology laboratories are poorly studied but potential important emission sources where not only the environmental stress is strong but also obtaining resistance is much easier comparing to other well studied hot spots including farms, hospitals, wastewater treatment plants and landfills where antibiotics but not ARGs are used or discharged. Therefore, in this study, 11 Swiss biology laboratories working on different fields and located in the city center, suburb and rural area were studied to reveal the abundance and diversity of airborne ARGs in them and their surrounding areas with Colony-forming units (CFU) cultivation and quantitative Polymerase Chain Reaction (qPCR). Most biology laboratories did not discharge significant amounts or varieties of ARGs and cultivable bacteria via air. No correlation was found between the number of CFUs and the abundance of 16S rRNA, but two clusters of correlated airborne ARGs, the animal husbandry related cluster, and city and hospital related cluster were identified in this study. Although most biology laboratories may not be the emission sources of a wide variety of airborne ARGs, the ARGs in the animal husbandry related cluster which are abundant in the animal laboratories and aadA1 which is abundant in the laboratories working on other eukaryocytes need to be furtherly studied to make sure if they are potential health risks for the researchers.

Tracking antibiotic resistance genes (ARGs) during earthworm conversion of cow dung in northern China

Using cow dung to breed earthworms poses a risk of environmental transmission of antibiotic resistance genes (ARGs). The purpose of this study was to address the occurrence, persistence and environmental fate of ARGs during earthworm conversion of cow dung. The results showed that ARGs persisted through the whole process. Notably, earthworm conversion effectively reduced some ARGs in cow dung, but a definite concentration of ARGs still remained in earthworms and vermicompost (up to 10^-1 and 10^-2 copies/16S copies, respectively). We found that tet-ARGs were the most abundant in 15 earthworm farms (10^-6~10^-1 copies/16S copies) and some high-risk ARGs (i.e., bla_ampC, bla_OXA-1 and bla_TEM-1) were even prevalent in these farms. Interestingly, although ARGs differ widely in cow dung (10^-10~10^-1 copies/16S copies), the ARGs levels were comparable in vermicompost samples from different farms (10^-8~10^-2 copies/16S copies). Notably, earthworm conversion effectively reduced some ARGs in cow dung, but significant level of ARGs still remained in earthworms and vermicompost (up to 10^-1 and 10^-2 copies/16S copies, respectively). Nevertheless, the concentrations of some heavy metals (Cu, Zn and Ni), the abundance of mobile genetic elements (MGEs) and total nitrogen content were confirmed to be correlated to the enrichment of some ARGs. Overall, this study demonstrated the high prevalence of ARGs contamination in earthworm farms, and also highlighted the dissemination risk of ARGs during the earthworm conversion of cow dung.

Effects of Enterococcus faecalis administration on the community structure of airborne bacteria in weanling piglet and layer hen houses

Probiotics have been shown to improve microbial compositions in animal intestine and feces, but the effects of probiotic administration on airborne microbial composition in animal houses remain unclear. In this study, we investigated the effects of dietary Enterococcus faecalis on the bacterial community structure in the air of piglet and layer hen houses. Indoor air and feces from piglet and layer hen houses were sampled after supplementing E. faecalis in feed for 60 days, and bacterial community structures were analyzed using Illumina high-throughput sequencing technology. Results showed that Chao1, ACE, Shannon, and Simpson indices of bacterial diversity did not significantly change in feces or indoor air of piglet or layer hen after supplementation with E. faecalis (P > 0.05). However, E. faecalis administration resulted in a decrease in the relative abundance of Proteobacteria (P < 0.05). In addition, E. faecalis significantly reduced the relative abundance of opportunistic pathogens such as Acinetobacter, Escherichia, and Shigella (P < 0.05), and beneficial bacterial genus such as Lactobacillus was significantly enriched in both feces and indoor air (P < 0.05). These changes should be of benefit to livestock, farm workers, and the surrounding environment.

Role played by the environment in the emergence and spread of antimicrobial resistance (AMR) through the food chain

The role of food-producing environments in the emergence and spread of antimicrobial resistance (AMR) in EU plant-based food production, terrestrial animals (poultry, cattle and pigs) and aquaculture was assessed. Among the various sources and transmission routes identified, fertilisers of faecal origin, irrigation and surface water for plant-based food and water for aquaculture were considered of major importance. For terrestrial animal production, potential sources consist of feed, humans, water, air/dust, soil, wildlife, rodents, arthropods and equipment. Among those, evidence was found for introduction with feed and humans, for the other sources, the importance could not be assessed. Several ARB of highest priority for public health, such as carbapenem or extended-spectrum cephalosporin and/or fluoroquinolone-resistant Enterobacterales (including Salmonella enterica), fluoroquinolone-resistant Campylobacter spp., methicillin-resistant Staphylococcus aureus and glycopeptide-resistant Enterococcus faecium and E. faecalis were identified. Among highest priority ARGs bla CTX -M, bla VIM, bla NDM, bla OXA -48-like, bla OXA -23, mcr, armA, vanA, cfr and optrA were reported. These highest priority bacteria and genes were identified in different sources, at primary and post-harvest level, particularly faeces/manure, soil and water. For all sectors, reducing the occurrence of faecal microbial contamination of fertilisers, water, feed and the production environment and minimising persistence/recycling of ARB within animal production facilities is a priority. Proper implementation of good hygiene practices, biosecurity and food safety management systems is very important. Potential AMR-specific interventions are in the early stages of development. Many data gaps relating to sources and relevance of transmission routes, diversity of ARB and ARGs, effectiveness of mitigation measures were identified. Representative epidemiological and attribution studies on AMR and its effective control in food production environments at EU level, linked to One Health and environmental initiatives, are urgently required.

Spatiotemporal variations in the association between particulate matter and airborne bacteria based on the size-resolved respiratory tract deposition in concentrated layer feeding operations

Bacterial loading aggravates the health and environmental hazards of particulate matter (PM), particularly in concentrated animal feeding operations. Understanding the association between PM and airborne bacteria is conducive to accurately assessing occupational exposure, providing fundamental data for exposure mitigation via engineering solutions, and providing information regarding the physical properties influencing the transmission of airborne microorganisms at emission sources. In this work, we conducted a joint study to systematically determine the concentrations and size distributions of PM and airborne bacteria, and establish the quantitative relationship between PM and airborne bacteria in laying hen houses. The association between PM and airborne bacteria was expressed as the load of airborne bacteria on PM in terms of the identical particle size interval based on the size-resolved respiratory tract deposition. The concentrations and size distributions of PM and airborne bacteria in laying hen houses were affected by the in-house space (upper and lower), chicken activity (day and night), and outside temperature. The size distributions of PM and airborne bacteria indicated that the mass concentration of large particles decreased with increasing outside temperature, while the concentration of airborne bacteria loaded on the small particles increased with increasing outside temperature. The results indicated that particles with diameters ranging from 2.1 to 4.7 μm carried the most airborne bacteria. Therefore, particles with diameters ranging from 2.1 to 4.7 μm should be the focus of future experimental research on occupational exposure, air quality improvement, and the airborne transmission of PM and airborne microorganisms originating from concentrated layer feeding operations.

Dispersion of Antibiotic Resistance Genes (ARGs) from stored swine manure biogas digestate to the atmosphere

Biogas digestate is a reservoir of antibiotic resistance genes (ARGs) and could pose a high health risk to both human and animals if the host microorganisms of ARGs become aerosolized. The purpose of this study was to investigate the diversity and relative abundance characteristics of aerosol-loaded ARGs from biogas digestate during storage, and to explore whether the change of ARGs in biogas digestate directly affect the dispersion of aerosol-loaded ARGs. This study reported for the first time that 28 of 42 ARG subtypes detected in the biogas digestate could be dispersed to the atmosphere via aerosol dispersion in a lab-scale dynamic emission vessels experiment. The relative abundance or diversity of ARGs in aerosols were different from that in biogas digestate, and no significant correlation were observed between the relative abundance of ARGs in biogas digestate and aerosols. The dominant ARGs were tetracycline resistance genes in biogas digestate and β-lactam resistance genes in aerosols. The process of biogas digestate storage reduced the total relative abundance of targeted ARGs in biogas digestate, decreased by 0.35 copies/16S rRNA after 30 days of storage, but increased the abundance of some ARG subtypes, including tetM, tetX, tetQ, tetS, ermF and sul2. High-concerned ARGs, including NDM-1, mcr-1 and vancomycin resistance genes (including vanA, vanB, vanRA and vanSA), were found in biogas digestate, and NDM-1 and vanB were also detected in aerosols. These results indicated a potential risk of ARGs dispersion during biogas digestate storage. Further research on the dispersion of ARGs from biogas digestate is required to elucidate the emission mechanism and develop mitigation measures.

Prevalence of multi-resistant plasmids in hospital inhalable particulate matter (PM) and its impact on horizontal gene transfer

Antibiotic resistance is exacerbated by the exchange of antibiotic resistance genes (ARGs) between microbes from diverse habitats. Plasmids are important ARGs mobile elements and are spread by horizontal gene transfer (HGT). In this study, we demonstrated the presence of multi-resistant plasmids from inhalable particulate matter (PM) and its effect on gene horizontal transfer. Three transferable multi-resistant plasmids were identified from PM in a hospital, using conjugative mating assays and nanopore sequencing. pTAir-3 contained 26 horizontal transfer elements and 10 ARGs. Importantly pTAir-5 harbored carbapenem resistance gene (blaOXA) which shows homology to plasmids from human and pig commensal bacteria, thus indicating that PM is a media for antibiotic resistant plasmid spread. In addition, 125 μg/mL PM_2.5 and PM₁₀ significantly increased the conjugative transfer rate by 110% and 30%, respectively, and augmented reactive oxygen species (ROS) levels. Underlying mechanisms were revealed by identifying the upregulated expressional levels of genes related to ROS, SOS, cell membranes, pilus generation, and transposition via genome-wide RNA sequencing. The study highlights the airborne spread of multi-resistant plasmids and the impact of inhalable PM on the horizontal transfer of antibiotic resistance.

Prevalence of Cryptosporidium in pigs in China: A systematic review and meta-analysis

Cryptosporidium is an important zoonotic parasite that can infect a variety of hosts, including pigs and humans, through water and food. Many studies on Cryptosporidium infection in pigs have been reported worldwide. However, the meta-analysis of Cryptosporidium infection in pigs in China has not been published. This study retrieved articles related to Cryptosporidium in pigs in China by using four databases: Chinese National Knowledge Infrastructure (CNKI), PubMed, VIP Chinese journal database and Wanfang Data. We retrieved 40 studies related to Cryptosporidium infection in China, and those articles were harvested from the inception to 1 January 2020. We estimated that the overall prevalence of pigs with Cryptosporidium in the selected period was 12.2% (4,349/30,404). In the sampling year subgroup, the prevalence rate after 2010 was the lowest at 8.7% (2,087/18,100). In Northern China, the Cryptosporidium prevalence was 47.9% (34/71). By contrast, the prevalence of Cryptosporidium in Southwestern China was only 6.9% (778/6,445). The infection rate of Cryptosporidium in diarrhoea pigs of 15.6% (74/384) was higher than that in non-diarrhoea pigs at 10.8% (378/2,840). Among the four age groups, the prevalence of weaning pigs of 16.2% (530/3,243) was the highest, and the difference was significant (p < .05). The prevalence of Cryptosporidium in extensive farming was 25.7% (660/3,121), which was significantly higher than in intensive farming 8.7% (566/6,336), and the prevalence of infection was related to the farming modes (p < .05). We also analysed the impact of different geographic factor subgroups (longitude, latitude, precipitation, temperature, humidity, climate and altitude) on the prevalence of pigs. The results showed that cryptosporidiosis was widespread in pigs in China. We suggest that appropriate control schemes should be developed according to the differences in breeding patterns and geographic conditions in different regions, and effective management measures should be developed to reduce the spread between pigs.

Enhanced removal of antibiotic resistance genes and mobile genetic elements during sewage sludge composting covered with a semi-permeable membrane

Transmission of antibiotic resistance genes (ARGs) via air media, such as particulate matter, has been intensively investigated due to human exposure through inhalation. However, whether particulate matter originating from the atmospheric environment of composting plants can impact ARG abundance during composting is unknown. Here, we investigated the effects of the atmospheric environment of composting plants on ARG abundance during sewage sludge composting using semi-permeable membrane-covered thermophilic composting (smTC) and conventional thermophilic composting (cTC). After smTC treatment, the total abundances of ARGs and mobile genetic elements (MGEs) decreased by 42.1 % and 38.1 % compared with those of the initial phase, respectively, but they increased by 4.5- and 1.6-fold after cTC, respectively. This result suggested that smTC was more efficient at decreasing ARGs and MGEs than cTC, mainly due to a significant reduction in bacterial contamination from the atmospheric environment of composting plants that accelerated the resurgence of ARGs and MGEs. Furthermore, culture experiments demonstrated that the abundance and diversity of antibiotic-resistant bacteria during the mature phase of smTC were also significantly (P <  0.05) lower than those in the cTC treatment. Thus, covering composting with a semi-permeable membrane could decrease the risk of ARGs spreading.

Size resolved characteristics of urban and suburban bacterial bioaerosols in Japan as assessed by 16S rRNA amplicon sequencing

To study the size-resolved characteristics of airborne bacterial community composition, diversity, and abundance, outdoor aerosol samples were analysed by 16S rRNA gene-targeted quantitative PCR and amplicon sequencing with Illumina MiSeq. The samples were collected using size-resolved samplers between August and October 2016, at a suburban site in Toyama City and an urban site in Yokohama City, Japan. The bacterial communities were found to be dominated by Actinobacteria, Firmicutes, and Proteobacteria. At the genus level, we found a high abundance of human skin-associated bacteria, such as Propionibacterium, Staphylococcus, and Corynebacterium, in the urban site. Whereas, a high abundance of bacteria associated with soil and plants, such as Methylobacterium and Sphingomonas, was observed in the suburban site. Furthermore, our data revealed a shift in the bacterial community structure, diversity, and abundance of total bacteria at a threshold of 1.1-µm diameter. Interestingly, we observed that Legionella spp., the causal agents of legionellosis in humans, were mainly detected in > 2.1 µm coarse particles. Our data indicate that local environmental factors including built environments could influence the outdoor airborne bacterial community at each site. These results provide a basis for understanding the size-resolved properties of bacterial community composition, diversity, and abundance in outdoor aerosol samples and their potential influence on human health.

Characteristics of and variation in airborne ARGs among urban hospitals and adjacent urban and suburban communities: A metagenomic approach

Environmental antibiotic resistance genes (ARGs) have received much attention, while the characteristics of ARGs carried by particulate matter (PM) as a function of urban functional region are almost unknown. In this study, ARGs carried by PM_2.5 and PM₁₀ in an urban hospital, a nearby urban community and the nearest suburban community were detected using metagenomics. In total, 643 ARG subtypes belonging to 22 different ARG types were identified. The chloramphenicol exporter gene, sul1, bacA, and lnuA were the most abundant ARG subtypes in all air samples. The hospital exhibited higher ARG abundance and richness than the nearby communities. ARG profiles depended on functional region: hospital and suburban samples clustered separately, and samples from the nearby urban community interspersed among them. The representation of multidrug and quinolone resistance genes decayed with distance from the hospital to the urban community to the suburban community, indicating that hospital PM may be a hotspot for ARGs encoding proteins conferring multidrug and quinolone resistance. Airborne ARGs carried by PM in the hospital environment were more closely associated with clinically important pathogens than were those in nearby communities. In particular, carbapenemase genes, including bla_NDM,bla_KPC,bla_IMP,bla_VIM,and bla_OXA-48, were discovered in hospital PM. In the suburban community, crAssphage, a human host-specific bacteriophage, was applied to predict ARG abundance and found to be enriched due to anthropogenic pollution but showed no clear evidence for ARG selection. In the hospital and the nearby urban community, the drivers of ARGs were complex. Our results highlighted that PM ARGs were closely related to human activities and revealed a potential hotspot, which could provide new evidence for further research and consequently mitigate the formation of airborne ARGs and transfer risks.

Potential of industrial composting and anaerobic digestion for the removal of antibiotics, antibiotic resistance genes and heavy metals from chicken manure

Composting and anaerobic digestion techniques are widely used for manure recycling, but these methods have shown conflicting results in the removal of antibiotics, antibiotic resistance genes (ARGs), and heavy metals. In the present study, anaerobically digested chicken manure and various types of composted chicken manure were investigated on an industrial scale. Antibiotics, ARGs, and heavy metals had shown inconsistent results for anaerobic digestion and composting. The different composting processes either declined or completely removed the blaCTX-M, intl1 and oqxB genes. In addition, composting processes decreased the absolute abundance of aac6'-Ib and aadA genes, while increased the absolute abundance of qnrD, sul1, and tet(A) genes. On the other hand, anaerobic digestion of chicken manure increased the absolute abundance of ere(A) and tet(A). High throughput sequencing showed that Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria dominated the total bacterial composition of composted and anaerobically digested samples. Network analysis revealed the co-occurrence of ARGs and intl1. The redundancy analysis showed a significant correlation between some heavy metals and ARGs. Similarly, the bacterial composition showed a positive correlation with the prevalence of ARGs in treated manure. These findings suggest that bacterial community, heavy metals, and mobile genetic elements can play a significant role in the abundance and variation of ARGs during composting and anaerobic digestion. In conclusion, anaerobic digestion and composting methods at industrial scale need to be improved for the effective removal of antibiotics, ARGs and heavy metals from chicken manure.

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.

Diversity of tetracycline- and erythromycin-resistant bacteria in aerosols and manures from four types of animal farms in China

Confined animal feeding operations generate high levels of airborne antibiotic-resistant bacteria, including pathogenic strains that may pollute the local environment or pose a health risk to both animals and workers. However, the communities of airborne antibiotic-resistant bacteria in such operations are not fully understood, especially in fine particles that penetrate deeply into the respiratory system. To address these gaps, manures and aerosols from inside and outside of animal houses were collected, and the characteristics of antibiotic-resistant bacteria were analyzed using Illumina MiSeq sequencing to amplify the V3-V4 region of bacterial 16S rRNA. The results indicated that animal species was the main factor that influenced the bacterial community of both manure and aerosol samples, while antibiotic selection was the major factor that influenced the bacterial community of aerosol samples from the inside of animal houses. An obvious clustering difference was detected between manure and aerosol samples. No significant difference in both alpha- and beta-diversity indices was detected between fine and coarse particles. As a key genus, Staphylococcus was found to drive the difference in the bacterial community of tetracycline-resistant bacteria to total culturable bacteria and erythromycin-resistant bacteria and also the difference in the bacterial community from aerosol to manure samples. Current data would help in evaluating the risk to human and livestock health and tracing the source of airborne antibiotic-resistant bacteria in animal farms.

Antibiotic Pollution in the Environment: From Microbial Ecology to Public Policy

The ability to fight bacterial infections with antibiotics has been a longstanding cornerstone of modern medicine. However, wide-spread overuse and misuse of antibiotics has led to unintended consequences, which in turn require large-scale changes of policy for mitigation. In this review, we address two broad classes of corollaries of antibiotics overuse and misuse. Firstly, we discuss the spread of antibiotic resistance from hotspots of resistance evolution to the environment, with special concerns given to potential vectors of resistance transmission. Secondly, we outline the effects of antibiotic pollution independent of resistance evolution on natural microbial populations, as well as invertebrates and vertebrates. We close with an overview of current regional policies tasked with curbing the effects of antibiotics pollution and outline areas in which such policies are still under development.

Global Survey of Antibiotic Resistance Genes in Air

Despite its emerging significant public health concern, the presence of antibiotic resistance genes (ARGs) in urban air has not received significant attention. Here, we profiled relative abundances (as a fraction, normalized by 16S rRNA gene) of 30 ARG subtypes resistant to seven common classes of antibiotics, which are quinolones, β-lactams, macrolides, tetracyclines, sulfonamides, aminoglycosides, and vancomycins, in ambient total particulate matter (PM) using a novel protocol across 19 world cities. In addition, their longitudinal changes in PM_2.5 samples in Xi'an, China as an example were also studied. Geographically, the ARGs were detected to vary by nearly 100-fold in their abundances, for example, from 0.07 (Bandung, Indonesia) to 5.6 (San Francisco, USA). The β-lactam resistance gene blaTEM was found to be most abundant, seconded by quinolone resistance gene qepA; and their corresponding relative abundances have increased by 178% and 26%, respectively, from 2004 to 2014 in Xi'an. Independent of cities, gene network analysis indicates that airborne ARGs were differentially contributed by bacterial taxa. Results here reveal that urban air is being polluted by ARGs, and different cities are challenged with varying health risks associated with airborne ARG exposure. This work highlights the threat of urban airborne transmission of ARGs and the need of redefining our current air quality standards in terms with public health.

The abundance and diversity of antibiotic resistance genes in the atmospheric environment of composting plants

Composting is considered to reduce the introduction of antimicrobial resistance genes (ARGs) into the environment through land application of manure; however, the possible pollution of ARGs in the atmospheric environment of composting plants is unknown. In this study, 29 air samples including up- and downwind, composting, packaging, and office areas from 4 composting plants were collected. Dynamic concentrations of 22 subtypes of ARGs, class 1 integron (intl1), and 2 potential human pathogenic bacteria (HPB), and bacterial communities were investigated using droplet digital PCR and 16S rRNA gene sequencing, respectively. In this study, intl1 and 22 subtypes of ARGs (except tetQ) were detected in air of composting, packaging, office, and downwind areas. The highest concentration of 15 out of 22 subtypes of ARGs was detected in the packaging areas, and intl1 also had the maximum average concentration of 10⁴ copies/m³, with up to (1.78 ± 0.49) × 10^-2 copies/16S rRNA copy. Non-metric multi-dimensional scaling of ARGs, potential HPBs, and bacterial components all indicated that the bioaerosol pollutant pattern in packaging areas was most similar to that in composting areas, followed by office, downwind, and upwind areas. The co-occurrence between ARGs and bacterial taxa assessed by Procrustes test, mantel test, and network analysis implied that aerosolized ARG fragments from composting and packaging areas contributed to the compositions of ARG aerosols in office and downwind areas. The results presented here show that atmoshperic environments of composting plants harbor abundant and diverse ARGs, which highlight the urgent need for comprehensive evaluation of potential human health and ecological risks of composts during both production as well as land application.

Size-Resolved Endotoxin and Oxidative Potential of Ambient Particles in Beijing and Zürich

PM_2.5 pollution has become a global health concern, however its size-resolved health impact remains to be poorly elucidated. Here, ambient particulate matter (PM) were collected into 13 different size ranges (10 nm to 18 μm) and the mass, metal, endotoxin distributions, and related oxidative potential were investigated in two regions (Zürich, Switzerland and Beijing, China). Results showed that the two regions had remarkably different PM distribution patterns. Swiss urban samples had a mode around 40 nm with 23.3% of total PM mass, while Chinese samples featured two modes around 0.75 and 4.23 μm with 13.8-18.6% and 13.7-20.4% of total PM mass, respectively. Two peaks for endotoxin at 40-100 nm and 1-4 μm were observed in different regions. For PM-borne metals, Chinese samples had 67.6-100% of total Cd, As, and Pb in the size range of 0.1-1 μm, and Swiss samples had similar distributions of Cd and Pb but much lower total metals than Chinese samples. The PM oxidative potential varied greatly with sizes for different regions. Accordingly, the current practice, i.e., sole use of the mass concentration, could lead to inadequate health protection for one region, but unnecessary economic costs for another without achieving significant extra health benefits.

A review on airborne microorganisms in particulate matters: Composition, characteristics and influence factors

Airborne microorganisms (AM), vital components of particulate matters (PM), are widespread in the atmosphere. Since some AM have pathogenicity, they can lead to a wide range of diseases in human and other organisms, meanwhile, some AM act as cloud condensation nuclei and ice nuclei which let them can affect the climate. The inherent characteristics of AM play critical roles in many aspects which, in turn, can decide microbial traits. The uncertain factors bring various influences on AM, which make it difficult to elaborate effect trends as whole. Because of the potential roles of AM in environment and potent effects of factors on AM, detailed knowledge of them is of primary significance. This review highlights the issues of composition and characteristics of AM with size-distribution, species diversity, variation and so on, and summarizes the main factors which affect airborne microbial features. This general information is a knowledge base for further thorough researches of AM and relevant aspects. Besides, current knowledge gaps and new perspectives are offered to roundly understand the impacts and application of AM in nature and human health.

Metagenomic profiling of ARGs in airborne particulate matters during a severe smog event

Information is currently limited regarding the distribution of antibiotic resistance genes (ARGs) in smog and their correlations with airborne bacteria. This study characterized the diversity and abundance of ARGs in the particulate matters (PMs) of severe smog based on publicly available metagenomic data, and revealed the occurrence of 205 airborne ARG subtypes, including 31 dominant ones encoding resistance to 11 antibiotic types. Among the detectable ARGs, tetracycline, β-lactam and aminoglycoside resistance genes had the highest abundance, and smog and soil had similar composition characteristics of ARGs. During the smog event, the total abundance of airborne ARGs ranged from 4.90 to 38.07ppm in PM_2.5 samples, and from 7.61 to 38.49ppm in PM₁₀ samples, which were 1.6-7.7 times and 2.1-5.1 times of those in the non-smog day, respectively. The airborne ARGs showed complicated co-occurrence patterns, which were heavily influenced by the interaction of bacterial community, and physicochemical and meteorological factors. Lactobacillus and sulfonamide resistance gene sul1 were determined as keystones in the co-occurrence network of microbial taxa and airborne ARGs. The results may help to understand the distribution patterns of ARGs in smog for the potential health risk evaluation.

Riemerella anatipestifer M949_0459 gene is responsible for the bacterial resistance to tigecycline

Based on its important role in last-line therapeutics against multidrug-resistant bacteria, tigecycline has been increasingly important in treating infections. However, mounting reports on tigecycline-resistant bacterial strains isolated from different sources are of concern, and molecular mechanisms regarding tigecycline resistance are poorly understood. Riemerella anatipestifer is a Gram-negative, non-motile, non-spore-forming, rod-shaped bacterium, which causes fibrinous pericarditis, perihepatitis, and meningitis in infected ducks. We previously constructed a random transposon mutant library using Riemerella anatipestifer strain CH3, in present study, we described that Riemerella anatipestifer M949_0459 gene is responsible for the bacterial resistance to tigecycline. Using the minimum inhibitory concentration assay, a mutant strain showed significantly increased (about six-fold) tigecycline susceptibility. Subsequently, the knocked-down gene was identified as M949_0459, a putative flavin adenine dinucleotide-dependent oxidoreductase. To confirm the resistance function, M949_0459 gene was overexpressed in Escherichia coli strain BL21, and the minimum inhibitory concentration analysis showed that the gene product conferred resistance to tigecycline. Additionally, expression of the M949_0459 gene under treatment with tigecycline was measured with quantitative real-time PCR. Results showed that the mRNA expression of M949_0459 gene was elevated under tigecycline treatment with dose range of 1-10 mg/L, and peaked at 4 mg/L. Moreover, two kinds of efflux pump inhibitors, carbonyl cyanide m-chlorophenyl hydrazone and phenylalanine arginyl β-naphthylamide were tested, which showed no function on tigecycline resistance in the strain CH3. Our results may provide insights into molecular mechanisms for chemotherapy in combating Riemerella anatipestifer infections.

Lessons from the Environmental Antibiotic Resistome

Antibiotic resistance is a global public health issue of growing proportions. All antibiotics are susceptible to resistance. The evidence is now clear that the environment is the single largest source and reservoir of resistance. Soil, aquatic, atmospheric, animal-associated, and built ecosystems are home to microbes that harbor antibiotic resistance elements and the means to mobilize them. The diversity and abundance of resistance in the environment is consistent with the ancient origins of antibiotics and a variety of studies support a long natural history of associated resistance. The implications are clear: Understanding the evolution of resistance in the environment, its diversity, and mechanisms is essential to the management of our existing and future antibiotic resources.