Monitoring airborne biotic contaminants in the indoor environment of pig and poultry confinement buildings

Microbial dynamics and climatic interactions in pig sheds: Insights into airborne microbes and particulate matter concentrations

Emissions of airborne pollutants from livestock buildings affect indoor air quality, the health and well-being of farmers, animals and the environment. This study aimed to evaluate the microbial count within pig sheds and its relationship with meteorological variables (temperature, relative humidity and air velocity) and particulate matter (PM10 and PM2.5) and microbial diversity. Sampling was conducted both inside and outside of two pig sheds over three seasons (summer, rainy and winter), with regular monitoring at fortnightly intervals. Results showed that the bacterial and fungal counts ranged from 0.07 to 3.98 x 103 cfu/m3 inside the sheds and 0.01 to 1.82 x 103 cfu/m3 outside. Seasonal variations were observed, with higher concentrations of particulate matter detected during the winter season, followed by summer. Climatic variables such as temperature, air velocity and relative humidity demonstrated significant impacts on the abundance of Enterobacteriaceae and fungi, while air velocity specifically influenced the presence of mesophilic bacteria and staphylococci. Importantly, no significant disparities were found between microbial counts and particulate matter levels. Staphylococcaceae emerged as the predominant bacterial family, while Aspergillus and Cladosporium spp. were the dominant fungal species within the pig sheds. The average levels of airborne bacteria and fungi in pig sheds were found to be within the recommended range, which can be attributed to the loose housing design and lower animal population on the farms.

Distribution characteristics and potential risks of bioaerosols during scattered farming

In most economically underdeveloped areas, scattered farming and human‒livestock cohabitation are common. However, production of bioaerosols and their potential harm in these areas have not been previously researched. In this study, bioaerosol characteristics were analyzed in scattered farming areas in rural Northwest China. The highest bacteria, fungi, and Enterobacteria concentrations were 125609 ± 467 CFU/m³, 25175 ± 10305 CFU/m³, and 4167 ± 592 CFU/m³, respectively. Most bioaerosols had particle sizes >3.3 μm. A total of 71 bacterial genera and 16 fungal genera of potential pathogens were identified, including zoonotic potential pathogenic genera. Moreover, our findings showed that the scattered farming pattern of human‒animal cohabitation can affect the indoor air environment in the surrounding area, leading to chronic respiratory diseases in the occupants. Therefore, relevant government departments and farmers should enhance their awareness of bioaerosol risks and consider measures that may be taken to reduce them.

Bioaerosols in swine confinement buildings: A metaproteomic view

Swine confinement buildings represent workplaces with high biological air pollution. It is suspected that individual components of inhalable air are causatives of chronic respiratory disease that are regularly detected among workers. In order to understand the relationship between exposure and stress, it is necessary to study the components of bioaerosols in more detail. For this purpose, bioaerosols from pig barns were collected on quartz filters and analysed via a combinatorial approach of 16S rRNA amplicon sequencing and metaproteomics. The study reveals the presence of peptides from pigs, their feed and microorganisms. The proportion of fungal peptides detected is considered to be underrepresented compared to bacterial peptides. In addition, the metaproteomic workflow enabled functional predictions about the discovered peptides. Housekeeping proteins were found in particular, but also evidence for the presence of bacterial virulence factors (e.g., serralysin-like metalloprotease) as well as plant (e.g., chitinase) and fungal allergens (e.g., alt a10). Metaproteomic analyses can thus be used to identify factors that may be relevant to the health of pig farmers. Accordingly, such studies could be used in the future to assess the adverse health potential of an occupationally relevant bioaerosol and help consider defined protective strategies for workers.

Methionine influences the profile of intestinal antibiotic resistome through inhibiting the growth of Escherichia coli

Antibiotic resistance genes (ARGs) are a new type of environmental pollutant. However, studies have mainly focused on the distribution characteristics of ARGs in the livestock environment, lacking of studies on the composition of ARGs in the intestinal tract of animals and the effect of nutrients on intestinal ARGs and microbial communities. Reducing antimicrobial resistance and maintaining optimal animal health and performance are urgently needed. Methionine is an essential amino acid which plays a critical role in the growth and reproductive performance of animals. In this study, feeding experiment, in vitro fermentation and bacterial culture experiment were performed to explore the influence of methionine on the intestinal resistome of sows. We found that dietary 0.2 % methionine supplementation decreased the total abundance of intestinal ARGs, which was further confirmed by in vitro fecal microbial fermentation of sows. Metagenome binning analysis identified that Escherichia coli was the major ARG host, which carried 60-113 ARGs and 134-286 virulence factors, indicating that Escherichia coli in the pig intestine is not only a core ARG host, but also an important pathogen. In addition, we found that methionine supplementation inhibited the growth of Escherichia coli, indicating that dietary methionine may reduce the resistome risk in sow intestine by inhibiting core ARG hosts such as Escherichia coli. These findings reveal that dietary methionine application plays a critical role in intestinal antibiotic resistance, providing a new idea for preventing and controlling environmental pollution by antibiotic-resistant microbes.

Effects of ex situ conservation on diversity and function of the gut microbiota of the Tibetan wild ass (Equus kiang)

Ex situ conservation is the main method for the protection of endangered wildlife. To explore the effect of ex situ conservation on the gut microbiota of the kiang (Equus kiang), metagenomic sequencing combined with bioinformatics analysis was used to investigate the composition and function of the gut microbiota of the kiang. The results showed that ex situ conservation not only protected wildlife, but also affected the composition and function of gut microbiota, as well as the health of animals. In the zoo, the ratio of the relative abundance of Firmicutes to that of Bacteroidetes (F/B) is higher, clusters of potentially pathogenic bacteria (such as Catonella, Catonella, and Mycoplasma) are more numerous, the abundance of resistance genes is higher, and the abundance of metabolic functions is increased. The dynamic changes of the gut microbiota also played an important role in the nutritional absorption, energy metabolism, and environmental adaptation of the kiang. Improving the rearing environment and increasing food diversity play important roles for increasing the diversity of gut microbiota, reducing the spread of potentially pathogenic bacteria, and reducing diseases. In the wild, especially in winter and in food-deficient areas, food supplementation can enhance the gut microbial homeostasis of wild animals and reduce the impact of crises. In depth studies of the gut microbial function of wildlife have important implications for improving ex situ conservation.

Copper in different forms and tetracycline affect behavior and risk of antibiotic resistome in thermophilic anaerobic digestion of cattle manure

The metagenomics-based behavior and risk of antibiotic resistance genes (ARGs) were investigated during cattle manure thermophilic anaerobic digestion with tetracycline and copper, namely, bulk-copper oxide, nano-copper oxide, and copper sulfate, which are common feed additives. Although bulk-copper oxide reduced ARGs' diversity, it enriched high-risk ARGs the most than the other two copper species, while copper sulfate could strongly mitigate the ARG risk by decreasing their abundances. Compared to corresponding individual effects, copper and tetracycline combinations may decrease ARGs' co-occurrence potential by 22.0%, and particularly, tetracycline combined separately with copper sulfate and nano-copper oxide reduces the ARGs' risk in abundance (by 7.2%) and human health (by 4.0%). These were mainly driven by bioavailable copper, volatile fatty acids, and pH, as well as the main potential hosts in phyla Firmicutes, Coprothermobacterota, and Euryarchaeota. Notably, the twin risks of pathogenicity and ARGs should be emphasized due to the ARGs' positive correlation with human pathogens of Clostridioides difficile and Arcobacter peruensis. These findings are important for understanding the potential ARGs' risk in treatments of livestock wastes containing feed additives of different sizes and speciation.

Characteristics of aerosols from swine farms: A review of the past two-decade progress

With the rapid development of large-scale and intensive swine production, the emission of aerosols from swine farms has become a growing concern, attracting extensive attention. While aerosols are found in various environments, those from swine farms are distinguished from human habitats, such as residential, suburban, and urban areas. In order to gain a comprehensive understanding of aerosols from swine farms, this paper reviewed relevant studies conducted between 2000 and 2022. The main components, concentrations, and size distribution of the aerosols were systematically reviewed. The differences between aerosols from swine farms and human living and working environments were compared. Finally, the sources, influencing factors, and reduction technologies for aerosols from swine farms were thoroughly elucidated. The results demonstrated that the concentrations of aerosols inside swine farms varied considerably, and most exceeded safety thresholds. However, further exploration is needed to fully understand the difference in airborne microorganism community structure and particles with small sizes (<1 μm) between swine farms and human living and working environments. More airborne bacterial and viruses were adhered to large particles in swine houses, while the proportion of airborne fungi in the respirable fraction was similar to that of human living and working environments. In addition, swine farms have a higher abundance and diversity of potential pathogens, airborne resistant microorganisms and resistant genes compared to the human living and working environments. The aerosols of swine farms mainly originated from sources such as manure, feed, swine hair and skin, secondary production, and waste treatment. According to the source analysis and factors influencing aerosols in swine farms, various technologies could be employed to mitigate aerosol emissions, and some end-of-pipe technologies need to be further improved before they are widely applied. Swine farms are advised not to increase aerosol concentration in human living and working environments, in order to decrease the impact of aerosols from swine farms on human health and restrain the spread of airborne potential pathogens. This review provides critical insights into aerosols of swine farms, offering guidance for taking appropriate measures to enhance air quality inside and surrounding swine farms.

Microbiological Indoor and Outdoor Air Quality in Chicken Fattening Houses

This study was conducted at one of the largest poultry companies in Kuwait during November and December 2019 to evaluate the microbiological threats of Escherichia coli (APEC), Salmonella spp., and Aspergillus fumigatus to chickens in fattening houses by counting and identifying the microorganisms by culturing and pyrosequencing analysis. During the fattening cycle, the temperature and humidity ranged between 23.6°C and 29°C and 64.1% and 87.1%, respectively. The total bacterial population and Aspergillus fumigatus measured in the indoor and outdoor air exhibited a linear relationship during the fattening cycle. The total bacterial and Aspergillus concentrations determined during the cycle ranged between 150 and 2000 CFU/m³ and 0 and 1000 CFU/m³, respectively. E. coli and Salmonella spp. concentrations determined during the cycle ranged between 1 and 220 CFU/m³ and 4 and 110 CFU/m³, respectively. Pyrosequencing analysis of the air inside the houses at the end of the cycle revealed extensive biodiversity in the microorganisms, detecting 32 bacterial genera and 14 species. The identified species belonging to the genera Corynebacterium, Haemophilus, Streptococcus, Veillonella, and Aspergillus were identified as potentially affecting human and broiler health. The emission of potentially pathogenic bacteria to the outdoor environment from chicken housing can pose a considerable risk to human health and environmental microbial pollution. This study could guide the development of integrated control devices for monitoring microbes in broiler production facilities during chicken collection for transport to slaughterhouses.

Effect of sulfamethazine on the horizontal transfer of plasmid-mediated antibiotic resistance genes and its mechanism of action

As a new type of environmental pollutant, antibiotic resistance genes (ARGs) pose a huge challenge to global health. Horizontal gene transfer (HGT) represents an important route for the spread of ARGs. The widespread use of sulfamethazine (SM2) as a broad-spectrum bacteriostatic agent leads to high residual levels in the environment, thereby increasing the spread of ARGs. Therefore, we chose to study the effect of SM2 on the HGT of ARGs mediated by plasmid RP4 from Escherichia coli (E. coli) HB101 to E. coli NK5449 as well as its mechanism of action. The results showed that compared with the control group, SM2 at concentrations of 10 mg/L and 200 mg/L promoted the HGT of ARGs, but transfer frequency decreased at concentrations of 100 mg/L and 500 mg/L. The transfer frequency at 200 mg/L was 3.04 × 10^-5, which was 1.34-fold of the control group. The mechanism of SM2 improving conjugation transfer is via enhancement of the mRNA expression of conjugation genes (trbBP, trfAP) and oxidative stress genes, inhibition of the mRNA expression of vertical transfer genes, up regulation of the outer membrane protein genes (ompC, ompA), promotion of the formation of cell pores, and improvement of the permeability of cell membrane to promote the conjugation transfer of plasmid RP4. The results of this study provide theoretical support for studying the spread of ARGs in the environment.

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.

Full-length 16S rRNA gene sequencing and machine learning reveal the bacterial composition of inhalable particles from two different breeding stages in a piggery

Bacterial loading aggravates the harm of particulate matter (PM) to public health and ecological systems, especially in operations of concentrated animal production. This study aimed to explore the characteristics and influencing factors of bacterial components of inhalable particles at a piggery. The morphology and elemental composition of coarse particles (PM₁₀, aerodynamic diameter ≤ 10 µm) and fine particles (PM_2.5, aerodynamic diameter ≤ 2.5 µm) were analyzed. Full-length 16 S rRNA sequencing technology was used to identify bacterial components according to breeding stage, particle size, and diurnal rhythm. Machine learning (ML) algorithms were used to further explore the relationship between bacteria and the environment. The results showed that the morphology of particles in the piggery differed, and the morphologies of the suspected bacterial components were elliptical deposited particles. Full-length 16 S rRNA indicated that most of the airborne bacteria in the fattening and gestation houses were bacilli. The analysis of beta diversity and difference between samples showed that the relative abundance of some bacteria in PM_2.5 was significantly higher than that in PM₁₀ at the same pig house (P < 0.01). There were significant differences in the bacterial composition of inhalable particles between the fattening and gestation houses (P < 0.01). The aggregated boosted tree (ABT) model showed that PM_2.5 had a great influence on airborne bacteria among air pollutants. Fast expectation-maximization microbial source tracking (FEAST) showed that feces was a major potential source of airborne bacteria in pig houses (contribution 52.64-80.58 %). These results will provide a scientific basis for exploring the potential risks of airborne bacteria in a piggery to human and animal health.

Aerosolization behavior of antimicrobial resistance in animal farms: a field study from feces to fine particulate matter

Antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) in animal feces can be released into the atmosphere via aerosolization, posing a high health risk to farm workers. So far, little attention has been paid to the characterization of the aerosolization process. In this study, fecal and fine particulate matter (PM2.5) samples were collected from 20 animal farms involving swine, cattle, layers, and broilers, and the ARGs, ARB, and human pathogenic bacteria (HPB) were loaded in these two media. The results showed that approximately 70% of ARGs, 60% of ARBs, and 43% of HPBs were found to be preferential aerosolization. The bioaerosolization index (BI) of target 30 ARGs varied from 0.04 to 460.07, and the highest value was detected from tetW. The highest BI values of erythromycin- and tetracycline-resistant bacteria were for Kocuria (13119) and Staphylococcus (24746), respectively, and the distribution of BI in the two types of dominant ARB was similar. Regarding the bioaerosolization behavior of HPB, Clostridium saccharolyticum WM1 was the most easily aerosolized pathogen in swine and broiler farms, and Brucella abortus strain CNM 20040339 had the highest value in cattle and layer farms. Notably, the highest BI values for ARGs, ARB, and HPB were universally detected on chicken farms. Most ARGs, ARB, and HPB positively correlated with animal age, stocking density, and breeding area. Temperature and relative humidity have significant effects on the aerosolization behavior of targets, and the effects of these two parameters on the same target are usually opposite. The results of this study provide a basis for a better understanding of the contribution of animal feces to airborne ARGs and HPBs in farms, as well as for controlling the transport of the fecal microbiome to the environment through the aerosolization pathway.

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.

Research progress on distribution and exposure risk of microbial aerosols in animal houses

Environmental aerosols in animal houses are closely related to the productive performance and health level of animals living in the houses. Preferable housing environments can improve animal welfare and production efficiency, so it is necessary to monitor and study these environments. In recent years, there have been many large-scale outbreaks of respiratory diseases related to biological aerosols, especially the novel coronavirus that has been sweeping the world. This has attracted much attention to the mode of aerosol transmission. With the rapid development of large-scale and intensive breeding, microbial aerosols have gradually become the main factor of environmental pollution in animal houses. They not only lead to a large-scale outbreak of infectious diseases, but they also have a certain impact on the health of animals and employees in the houses and increase the difficulty of prevention and control of animal-borne diseases. This paper reviews the distribution, harm, and control measures of microbial aerosols in animal house environments in order to improve people's understanding of them.

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.

Seasonal dynamics in bacterial communities of closed-cage broiler houses

The bacteria contained in air aerosols from poultry houses are closely connected to animal health and production. This study aimed to investigate the seasonal factors on microbial aerosol concentration, particle size and bacterial spectrum composition inside a closed-cage broiler house. Then, 16S rDNA sequencing technology was applied to analyze the characteristics of bacterial abundance and diversity. The results indicated that the concentration of bacterial aerosol in the broiler house varied significantly in different seasons, with a concentration range of 5.87–15.77 × 10³ CFU/m³, and the highest and lowest concentrations in the summer and winter, respectively. Microbiological analysis showed that the proportion of Gram-negative bacteria in autumn was significantly higher than that in summer (P < 0.05). In addition, the floral structure of potential pathogenic bacterial genera also differed by season. Escherichia-Shigella, Streptococcus, Acinetobacter, Pseudomonas were identified in the bacterial aerosols. Importantly, the relative abundance of Firmicutes in spring and autumn was much higher. In contrast, the relative abundance of Proteobacteria in spring and autumn was lower than that in summer and winter. Altogether, results revealed the effects of seasonal factors on the diversity and abundance of bacteria and the distribution characteristics of major opportunistic pathogens in the air of closed-cage broiler houses. These results will provide important information for exploring the potential risk of aerosols from poultry houses all four seasons.

Conifer Needle Phyllosphere as a Potential Passive Monitor of Bioaerosolised Antibiotic Resistance Genes

Monitoring antibiotic resistance genes (ARGs) is vital to the One Health approach to tackling the antibiotic resistance crisis. It has been suggested that conifer needles can be used as passive bioaerosol samplers. Here, the use of conifer needles as biomonitors of ARGs in bioaerosols was assessed as a proof-of-concept. Needles were collected from trees surrounding pig farms, villages, and forest sites in Québec, Canada. Needles were homogenised and DNA was extracted. Results of qPCR analyses showed biomass estimates were consistent across samples. Number and quantity of ARGs was significantly lower in forest sites when compared to the farm and village, comprising a distinct resistome. Consistent with previous findings, the most common ARGs were tetracyclines and sulfonamides, which were found close to agricultural activities. Although results were limited, there is great potential for using the conifer phyllosphere as a passive bioaerosol sampler. This method represents an accessible way to promote ARG surveillance over long distances from point sources.

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.

Cow Farmers’ Homes Host More Diverse Airborne Bacterial Communities Than Pig Farmers’ Homes and Suburban Homes

Living on a farm has been linked to a lower risk of immunoregulatory disorders, such as asthma, allergy, and inflammatory bowel disease. It is hypothesized that a decrease in the diversity and composition of indoor microbial communities is a sensible explanation for the upsurge in immunoregulatory diseases, with airborne bacteria contributing to this protective effect. However, the composition of this potentially beneficial microbial community in various farm and suburban indoor environments is still to be characterized. We collected settled airborne dust from stables and the associated farmers’ homes and from suburban homes using electrostatic dust collectors (EDCs) over a period of 14 days. Then, quantitative PCR (qPCR) was used to assess bacterial abundance. The V3–V4 region of the bacterial 16S rRNA gene was amplified and sequenced using Ilumina MiSeq in order to assess microbial diversity. The Divisive Amplicon Denoising Algorithm (DADA2) algorithm was used for the inference of amplicon sequence variants from amplicon data. Airborne bacteria were significantly more abundant in farmers’ indoor environments than in suburban homes (p < 0.001). Cow farmers’ homes had significantly higher bacterial diversity than pig farmers’ and suburban homes (p < 0.001). Bacterial taxa, such as Firmicutes, Prevotellaceae, Lachnospiraceae, and Lactobacillus were significantly more abundant in farmers’ homes than suburban homes, and the same was true for beneficial intestinal bacterial species, such as Lactobacillus amylovorus, Eubacterium hallii, and Faecalibacterium prausnitzii. Furthermore, we found a higher similarity between bacterial communities in individual farmers’ homes and their associated cow stables than for pig stables. Our findings contribute with important knowledge on bacterial composition, abundance, and diversity in different environments, which is highly valuable in the discussion on how microbial exposure may contribute to the development of immune-mediated diseases in both children and adults.

The Distribution Characteristics of Aerosol Bacteria in Different Types of Pig Houses

Simple Summary

Microbial aerosols from pig houses can be released into the environment, posing a serious threat to biosafety and public health. At present, there are few studies on the structural characteristics of aerosol bacteria in piggeries at different growth stages. It is important to understand the characteristics of aerosol bacteria in pig houses to solve the problems of air pollution and disease control in pig houses at different growth stages. In this study, bacterial aerosol concentrations and bacterial communities were compared in pig houses at different growth stages in Hebei Province, China. It was found that bacterial concentrations, community richness, and diversity in the air increased with the age of pigs. There are many pathogenic bacteria in the microbial aerosols of piggery. Our study highlights the importance of more comprehensive research and analysis of microbial aerosols in pig houses. Precautions for air pollution should be instituted in pig houses, including wearing masks, rigorous disinfection, and hygiene procedures.

Abstract

With the development of modern pig raising technology, the increasing density of animals in pig houses leads to the accumulation of microbial aerosols in pig houses. It is an important prerequisite to grasp the characteristics of bacteria in aerosols in different pig houses to solve the problems of air pollution and disease prevention and control in different pig houses. This work investigated the effects of growth stages on bacterial aerosol concentrations and bacterial communities in pig houses. Three traditional types of closed pig houses were studied: farrowing (FAR) houses, weaning (WEA) houses, and fattening (FAT) houses. The Andersen six-stage sampler and high-volume air sampler were used to assess the concentrations and size distribution of airborne bacteria, and 16S rRNA gene sequencing was used to identify the bacterial communities. We found that the airborne bacterial concentration, community richness, and diversity index increased with pig age. We found that Acinetobacter, Erysipelothrix, Streptococcus, Moraxella, and Aerococcus in the microbial aerosols of pig houses have the potential risk of causing disease. These differences lead us to believe that disinfection strategies for pig houses should involve a situational focus on environmental aerosol composition on a case-by-case basis.

Particulate Matter in Swine Barns: A Comprehensive Review

Particulate matter (PM) represents an air quality management challenge for confined swine production systems. Due to the limited space and ventilation rate, PM can reach relatively high concentrations in swine barns. PM in swine barns possesses different physical, chemical, and biological characteristics than that in the atmosphere and other indoor environments. As a result, it exerts different environmental and health effects and creates some unique challenges regarding PM measurement and mitigation. Numerous research efforts have been made, generating massive data and information. However, relevant review reports are sporadic. This study aims to provide an updated comprehensive review of swine barn PM, focusing on publications since 1990. It covers various topics including PM characteristics, sources, measurement methods, and in-barn mitigation technologies. As PM in swine barns is primarily of biological origins, bioaerosols are reviewed in great detail. Relevant topics include bacterial/fungal counts, viruses, microbial community composition, antibiotic-resistant bacteria, antibiotic resistance genes, endotoxins, and (1→3)-β-D-glucans. For each topic, existing knowledge is summarized and discussed and knowledge gaps are identified. Overall, PM in swine barns is complicated in chemical and biological composition and highly variable in mass concentrations, size, and microbial abundance. Feed, feces, and skins constitute the major PM sources. Regarding in-barn PM mitigation, four technologies (oil/water sprinkling, ionization, alternation of feed and feeders, and recirculating air filtration) are dominant. However, none of them have been widely used in commercial barns. A collective discussion of major knowledge gaps and future research needs is offered at the end of the report.

The fate and behavior mechanism of antibiotic resistance genes and microbial communities in anaerobic reactors treating oxytetracycline manufacturing wastewater

In this study, two parallel-operated expanded granular sludge bed (EGSB) reactors, one used to treat oxytetracycline (OTC) manufacturing wastewater with gradual increase of OTC concentration as experimental reactor and the other fed with the same wastewater without OTC as control reactor, were operated to investigate the behavior of antibiotics resistance genes (ARGs) and mobile genetic elements (MGEs) and their possible relationships with bacterial community among influent, sludge and effluent environments. Though the average absolute abundance of ARGs slightly decreased (0.26 - log), the ARGs' relative abundance normalized to 16S-rRNA gene copy numbers showed a significant upward trend in effluent (2 multiples - increase) and the absolute and relative abundances both extremely increased in anaerobic sludge, indicating that anaerobic treatment process cannot reduce ARGs efficiently, inversely can increase the risk of ARGs through the proliferation of antibiotics resistance bacteria (ARB) under the suppression of OTC. MGEs, bacterial communities and OTC concentration mainly impacted the ARGs profiles, which contributed 88.4% to the variation of ARGs. The differences and correlations of hosts in influent, effluent and sludge were further confirmed by network analysis. Overall, this study enhanced the understanding of the prevalence and transfer of ARGs in OTC production effluents during anaerobic treatment.

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.

Abundance, diversity and diffusion of antibiotic resistance genes in cat feces and dog feces

The ARG profiles in pet feces, such as cat and dog feces, and their potential threat to environmental safety are still unclear. In this study, ARGs in 45 cat and 28 dog fecal samples were detected, and a diffusion experiment was performed to assess the risk of ARGs diffusion into the air. The results showed that the abundances of ARGs in cat feces and dog feces were high, and the abundance in dog feces (0.89 ± 0.17 copies/bacterial cell) was significantly higher than that in cat feces (0.46 ± 0.09 copies/bacterial cell) (P < 0.05). The bacterial community, especially Firmicutes and Desulfobacterota in cat feces, and Proteobacteria in dog feces, was the main factor affecting the variation in the ARG profiles, contributing to 31.6% and 32.4% of the variation in cat feces and dog feces, respectively. Physicochemical factors (especially NH₄⁺-N) and age also indirectly affected the variation in the ARG profiles by affecting the bacterial community. In addition, the ARGs in cat feces and dog feces diffused into the air, but there was no evidence that this diffusion posed a threat to environmental safety and human health. These results can provide reference data for healthy animal breeding and the prevention and control of ARG pollution.

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.

Effects of Clostridium butyricum on Growth Performance, Gut Microbiota and Intestinal Barrier Function of Broilers

This study was conducted to evaluate the effects of Clostridium butyricum dietary supplementation on the growth, antioxidant, immune response, gut microbiota, and intestinal barrier function of broilers under high stocking density (HSD) stress. A total of 324 1-day-old Arbor Acres male broilers were randomly assigned to three treatments with six replicates, each replicate including 18 chickens (18 birds/m²). The experiment lasted 6 weeks. The three treatments were basal diet (control, CON), basal diet supplemented with 1 × 10⁹ colony forming units (cfu)/kg C. butyricum (CB), and basal diet supplemented with 10 mg/kg virginiamycin (antibiotic, ANT). The results showed that the body weight (BW) and average daily gain (ADG) of broilers in the CB group were significantly higher than those in the CON group in three periods (p < 0.05). The total antioxidant capacity (T-AOC) and the superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px) activity in serum of the CB group were significantly increased compared with those in the CON and ANT groups at 42 days (p < 0.05). At 42 days, the serum immunoglobulin M (IgM) and immunoglobulin G (IgG) levels of the CB group were significantly higher than those of the CON group. Compared with the CON group, interleukin-1β (IL-1β) in the CB group was significantly decreased in the starter and grower stages (p < 0.05), but there was no significant difference between the two treatment groups (p > 0.05). C. butyricum significantly decreased the high stocking density-induced expression levels of IL-1β and tumor necrosis factor-α (TNF-α) in the ileum of broilers at different stages. Additionally, C. butyricum could increase the expressions of claudin-1 and zonula occludens-1 (ZO-1) in intestinal tissue. Moreover, C. butyricum significantly increased the Sobs and Shannon indices in the CB group compared with the ANT group (p < 0.05), while the Ace index in the CB group was significantly higher than that of the CON group (p < 0.05). Furthermore, by using 16S rRNA gene sequencing, the proportion of Bacteroides in the CB group was increased compared to those in the CON and ANT groups at the genus level. In conclusion, C. butyricum supplemented into feed could improve the growth performance and feed utilization of broilers by promoting immune and intestinal barrier function and benefiting the cecal microflora.

Airborne Bacterial Community Composition According to Their Origin in Tenerife, Canary Islands

Microorganisms are ubiquitous in the environment, and the atmosphere is no exception. However, airborne bacterial communities are some of the least studied. Increasing our knowledge about these communities and how environmental factors shape them is key to understanding disease outbreaks and transmission routes. We describe airborne bacterial communities at two different sites in Tenerife, La Laguna (urban, 600 m.a.s.l.) and Izaña (high mountain, 2,400 m.a.s.l.), and how they change throughout the year. Illumina MiSeq sequencing was used to target 16S rRNA genes in 293 samples. Results indicated a predominance of Proteobacteria at both sites (>65%), followed by Bacteroidetes, Actinobacteria, and Firmicutes. Gammaproteobacteria were the most frequent within the Proteobacteria phylum during spring and winter, while Alphaproteobacteria dominated in the fall and summer. Within the 519 genera identified, Cellvibrio was the most frequent during spring (35.75%) and winter (30.73%); Limnobacter (24.49%) and Blastomonas (19.88%) dominated in the summer; and Sediminibacterium represented 10.26 and 12.41% of fall and winter samples, respectively. Sphingomonas was also identified in 17.15% of the fall samples. These five genera were more abundant at the high mountain site, while other common airborne bacteria were more frequent at the urban site (Kocuria, Delftia, Mesorhizobium, and Methylobacterium). Diversity values showed different patterns for both sites, with higher values during the cooler seasons in Izaña, whereas the opposite was observed in La Laguna. Regarding wind back trajectories, Tropical air masses were significantly different from African ones at both sites, showing the highest diversity and characterized by genera regularly associated with humans (Pseudomonas, Sphingomonas, and Cloacibacterium), as well as others related to extreme conditions (Alicyclobacillus) or typically associated with animals (Lachnospiraceae). Marine and African air masses were consistent and very similar in their microbial composition. By contrast, European trajectories were dominated by Cellvibrio, Pseudomonas, Pseudoxanthomonas, and Sediminibacterium. These data contribute to our current state of knowledge in the field of atmospheric microbiology. However, future studies are needed to increase our understanding of the influence of different environmental factors on atmospheric microbial dispersion and the potential impact of airborne microorganisms on ecosystems and public health.

Revealing the distribution characteristics of antibiotic resistance genes and bacterial communities in animal-aerosol-human in a chicken farm: From One-Health perspective

Antibiotics in breeding industry can enter the environment through multiple pathways, thus accelerating the emergence and spread of antibiotic resistance genes (ARGs), among which aerosol transmission is easily achieved and often overlooked. To elucidate the role of aerosols in this situation, the present study investigated the distribution characteristics of 107 ARG subtypes (targeting to eight different ARG types) and nine mobile genetic elements (MGEs) and bacterial community in animal (chicken cloaca), environment (aerosols) and human (nasopharynx) of a chicken farm (n = 42) in Henan Province. In total, 116 ARG subtypes and MGEs were identified in the poultry farm. The total bacterial concentration of aerosols inside the chicken house (3.117 × 104 CFU/m3) exceeded the corresponding limit. The microbial communities in the samples of cloaca swab (C) and the workers' nasopharyngeal swab (N) were closer, while the abundance distribution of ARGs/ MGEs in cloacal swab (C) and aerosol (AI) in chicken house were much similar. There were certain consistency of the microbial community structure and the distribution of ARGs among the three groups of chicken cloaca, air aerosol, and workers' nasopharynx. Our results highlighted that animal breeding does have a certain impact on the surrounding environment and human, and aerosols play an important role in this process.

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.

Evaluation of the microbiome composition in particulate matter inside and outside of pig houses

Particulate matter (PM) produced in pig houses may contain microbes which can spread by airborne transmission, and PM and microbes in PM adversely affect human and animal health. To investigate the microbiome in PM from pig houses, nine PM samples were collected in summer 2020 inside and outside of pig houses located in Jangseong-gun, Jeollanam-do Province, Korea, comprising three PM samples from within a nursery pig house (I-NPH), three samples from within a finishing pig house (I-FPH), and three samples from outside of the pig houses (O-PH). Microbiomes were analyzed using 16S rRNA gene amplicon sequencing. Firmicutes was the most dominant phylum and accounted for 64.8%–97.5% of total sequences in all the samples, followed by Proteobacteria (1.4%–21.8%) and Bacteroidetes (0.3%–13.7%). In total, 31 genera were represented by > 0.3% of all sequences, and only Lactobacillus, Turicibacter, and Aerococcus differed significantly among the three PM sample types. All three genera were more abundant in the I-FPH samples than in the O-PH samples. Alpha diversity indices did not differ significantly among the three PM types, and a principal coordinate analysis suggested that overall microbial communities were similar across PM types. The concentration of PM did not significantly differ among the three PM types, and no significant correlation of PM concentration with the abundance of any potential pathogen was observed. The present study demonstrates that microbial composition in PM inside and outside of pig houses is similar, indicating that most microbe-containing PM inside pig houses leaks to the outside from where it, along with microbe-containing PM on the outside, may re-enter the pig houses. Our results may provide useful insights regarding strategies to mitigate potential risk associated with pig farming PM and pathogens in PM.

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.

Distribution characteristics of bioaerosols inside pig houses and the respiratory tract of pigs

Particulate matter (PM) is a carrier of many substances. Microorganisms are vital constituents contained in PM, and their varieties and concentrations are closely connected to human health and animal production. This study aimed to investigate the distribution characteristics of bioaerosols inside a pig house and in the respiratory tract of pigs. Environmental indices inside a nursery pig house were monitored in winter, including temperature, relative humidity, total suspended particulate (TSP), PM₁₀, PM_2.5, NH₃, CO₂, CO and NO. The concentrations of airborne culturable bacteria, fungi and Escherichia coli were detected. Then, 16S rRNA sequencing technology was applied to identify different-sized bioaerosols and bacteria in the respiratory tract of piglets. The results showed that the concentration of airborne culturable bacteria inside the pig house was significantly higher than that outside, and no significant difference was found among culturable fungi and Escherichia coli. The 16S rRNA results showed that the bacterial aerosols presented high similarity to the bacteria in the respiratory tract of piglets. The airborne bacterial aerosols within the size range of 1.1-3.3 µm showed high similarity to the bacteria in the lower respiratory tract (bronchus and lung) of piglets. In addition, four potential pathogenic bacterial genera (Escherichia-Shigella, Streptococcus, Acinetobacter, Pseudomonas) were identified both in the bacterial aerosols and the respiratory tract of piglets. These results will provide a significant scientific basis for exploring the potential risk of aerosols from animal houses to human and animal health.

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.

Profiles of bacteria/phage-comediated ARGs in pig farm wastewater treatment plants in China: Association with mobile genetic elements, bacterial communities and environmental factors

In this study, the profiles of bacteria/phage-comediated antibiotic resistance genes (b/pARGs) were monitored in water samples collected from 45 pig farm wastewater treatment plants (WWTPs) in seven different regions of China. We found that 8 major types and 112 subtypes of b/pARGs were detected in all the water samples, and the detected number ranged from 53 to 92. The absolute abundances of bARGs and pARGs in the influent were as high as 10⁹ copies/mL and 10⁶ copies/mL, respectively. Anaerobic anoxic/oxic (AAO) and anaerobic short-cut nitrification/denitrification (ASND) treatment plants can effectively reduce the absolute abundance and amount of b/pARGs. Anaerobic treatment plants cannot reduce the absolute abundance of pARGs, and even increase the amount of pARGs. Mobile genetic elements (MGEs), bacterial communities and environmental factors were important factors impacting the b/pARG profile. Among these factors, the bacterial community was the major driver that impacted the bARG profile, while bacterial community and MGEs were the major codrivers impacting the pARG profile. This study was the first to investigate the profiles of b/pARGs in pig farm WWTPs in China on such a large scale, providing a reference for the prevention and control of ARG pollution in agricultural environments.

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

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

Antibiotics and their alternatives in Artificial Breeding in livestock

Antibiotics are mandatory components of semen extenders for the control of bacterial contamination and growth. The increasing rate of worldwide resistance to conventional antibiotics in semen preservation media requires the development of new antimicrobial alternatives. This review provides an update on this topic and also highlights the improvement of hygiene in Artificial Insemination centers in order to prevent the development of bacterial resistance. Ideas are shared on future diagnostic tools for bacterial contamination in Artificial Breeding. Finally, new methods to remove or reduce bacteria in semen will be discussed.

Research and Technological Advances Regarding the Study of the Spread of Antimicrobial Resistance Genes and Antimicrobial-Resistant Bacteria Related to Animal Husbandry

The extensive use of antimicrobials in animal farms poses serious safety hazards to both the environment and public health, and this trend is likely to continue. Antimicrobial resistance genes (ARGs) are a class of emerging pollutants that are difficult to remove once introduced. Understanding the environmental transfer of antimicrobial-resistant bacteria (ARB) and ARGs is pivotal for creating control measures. In this review, we summarize the research progress on the spread and detection of ARB and ARG pollution related to animal husbandry. Molecular methods such as high-throughput sequencing have greatly enriched the information about ARB communities. However, it remains challenging to delineate mechanisms regarding ARG induction, transmission, and tempo-spatial changes in the whole process, from animal husbandry to multiple ecosystems. As a result, future research should be more focused on the mechanisms of ARG induction, transmission, and control. We also expect that future research will rely more heavily on metagenomic -analysis, metatranscriptomic sequencing, and multi-omics technologies

The persistence of antimicrobial resistance and related environmental factors in abandoned and working swine feedlots

Swine feedlots that have operated in the absence of adequate disposal facilities are being demolished under the new environmental protection policies in China. The environmental behavior and transmission risks of antimicrobial resistance genes (ARGs) are unclear for these abandoned swine feedlots. We examined 40 soil samples that originated from the soils adjacent to two abandoned and two working swine feedlots to explore: 1) the distribution patterns and vertical transmission of 17 ARGs and two integron genes and 2) the bacterial community as well as their correlation with environmental factors and target genes. We found that seven and nine out of forty-eight subtypes of veterinary antimicrobials (VAs) were detected in the soil near abandoned feedlots and working feedlots, respectively. Three tet genes (tetM, tetO and tetW) were particularly enriched in the soil adjacent to both abandoned and working feedlots. The tetM gene was a "hub" on the network of the topsoil. The relative abundance of Firmicutes ranged from 2.5 to 9% in the soil near two Beijing feedlots and was significantly higher than that in the upstream blank control (CK soil) (ANOVA, p < 0.05). Overall, the ARG distribution patterns in the soils adjacent to abandoned swine feedlots were similar to the working feedlots. This study offers basic information on the prevalence and transmission risk of ARGs in abandoned swine feedlots and provides a reference for the restoration and reuse of demolished feedlots.

The correlation between antibiotic resistance gene abundance and microbial community resistance in pig farm wastewater and surrounding rivers

Antimicrobial resistance gene (ARG) abundance and microbial resistance (MR) are often used as important indicators of pollution risk; however, the relationship between ARGs abundance and MR in pig farm wastewater remains unknown. In this study, the raw pig farm wastewater, effluent water, upstream river water, domestic wastewater and downstream river water samples were collected. The concentration of 20 subtypes of ARGs and 2 integrons, minimal inhibit concentration (MIC), and bacterial communities were investigated. In this study, 20 subtypes of ARGs and integrons were detected in all sampling sites. The highest abundance of 17 of the 20 subtypes of ARGs was detected in raw pig farm wastewater, and ermA had the maximum average abundance of 10⁸ copies/mL, with up to 2.41 ± 0.12 × 10⁸ copies/mL. There was no significant correlation between MR to three antibiotics (ciprofloxacin, streptomycin and tetracycline hydrochloride) and the abundance of their corresponding ARGs (P > 0.05), and a large difference was detected between the types of ARGs co-occur bacteria and resistance co-occur bacteria in the 5 sampling sites. And the pig farm wastewater treatment (WWT) could effectively reduce the ARGs and MR to the 3 antibiotics. The results presented here show that there may be no obvious correlation between ARGs and MCR in pig farm wastewater and surrounding rivers, which may be due to various environmental factors, highlighting the urgent need for a comprehensive evaluation of relationship between ARGs abundance and MR.

Microbiome composition of airborne particulate matter from livestock farms and their effect on innate immune receptors and cells

Patients with respiratory diseases in rural areas have been reported to have enhanced responsiveness to ambient particulate matter (PM). In addition to the physical and chemical components, ambient PM can contain microorganisms or parts thereof, referred here as BioPM, that can also contribute to the adverse health effects. This study aimed to characterize the microbial composition of BioPM originating from livestock, and to investigate whether these BioPM can trigger the activation of innate receptors and cells. Coarse (PM_2.5-10 μm) and fine (PM_<2.5 μm) BioPM samples were collected from indoor chicken, pig and goat farms using the versatile aerosol concentration enrichment system (VACES) connected to a Biosampler. The fungal and bacterial communities were assessed with an amplicon based approach using Next Generation Sequencing (NGS). In parallel, HEK-Blue cells expressing different pattern recognition receptors (Toll like receptors (TLR) 2, 3, 4, 5, 7, 8, 9 and NOD 1, 2) and a human monocytic cell line (MM6) were exposed to BioPM samples from these sites. Distinct airborne microbiota profiles associated with the corresponding animal farm were observed. Moreover, the various BioPM contained mainly ligands for TLR2 and TLR4 resulting in a concentration-dependent increase of pro-inflammatory cytokine secreted by MM6 cells. In addition, we show for the first time that only the pig-derived BioPM induced TLR5 activation. These findings suggest that animal farm specific BioPM trigger distinct inflammatory responses, which may contribute to airway diseases in humans.

A Metataxonomic Tool to Investigate the Diversity of Treponema

The genus Treponema contains a number of human and animal pathogenic as well as symbiotic bacteria that are found in vastly different anatomical and environmental habitats. Our understanding of the species range, evolution, and biology of these important bacteria is still limited. To explore the diversity of treponemes, we established, validated, and tested a novel metataxonomic approach. As the informative nature of the hypervariable regions of the 16S rRNA gene differ, we first analyzed each variable region independently. Considering the in silico results obtained, we established and validated the sequencing of the V4-region of the 16S rRNA gene using known mixtures of Treponema species as well as a selected number of clinical samples. The metataxonomic approach was able to identify Treponema to a near-species level. We demonstrate that using a spirochete-specific enrichment, our method is applicable to complex microbial communities and large variety of biological samples. The metataxonomic approach described provides a useful method to unravel the full diversity and range of Treponema in various ecosystems.

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.

The Indoor-Air Microbiota of Pig Farms Drives the Composition of the Pig Farmers' Nasal Microbiota in a Season-Dependent and Farm-Specific Manner

Prior studies have demonstrated an influence of the built environment on the human nasal microbiota. However, very little is known about the influences of working on a pig farm on the human nasal microbiota. We longitudinally collected samples from 30 pig farms (air and nasal swabs from humans and pigs) in Switzerland from 2014 to 2015. As controls, nasal swabs from cow farmers and individuals with no contact with farm animals were included. An analysis of the microbiota for all samples (n = 609) was performed based on 16S rRNA gene sequencing (MiSeq) and included the investigations of source-sink dynamics. The numbers of indoor airborne particles and bacterial loads in pig farms were also investigated and were highest in winter. Similarly, the microbiota analyses revealed that the alpha diversity values of the nares of pig farmers were increased in winter in contrast to those of samples from the nonexposed controls, which displayed low alpha diversity values throughout the seasons. Source-sink analyses revealed that bacteria from the noses of pigs are more commonly coidentified within the pig farmers' microbiota in winter but to a less extent in summer. In addition, in winter, there was a stronger intrasimilarity for samples that originated from the same farm than for samples from different farms, and this farm specificity was partially or completely lost in spring, summer, and fall. In conclusion, in contrast to nonexposed controls, a pig farmer's nasal microbiota is dynamic, as the indoor-air microbiota of pig farms drives the composition of the pig farmer's nasal microbiota in a season-dependent manner.IMPORTANCE The airborne microbiota of pig farms poses a potential health hazard and impacts both livestock and humans working in this environment. Therefore, a more thorough understanding of the microbiota composition and dynamics in this setting is needed. This study was of a prospective design (12 months) and used samples from different sites. This means that the microbiota of air, animals (pigs), and humans was simultaneously investigated. Our findings highlight that the potential health hazard might be particularly high in winter compared to that in summer.

Production Phase Affects the Bioaerosol MicrobialComposition and Functional Potential in SwineConfinement Buildings

Bioaerosols from swine confinement buildings (SCBs) pose a challenge to public health,and microorganisms within the SCBs bioaerosols originate from swine feces, of which the microbialcomposition is associated with the production phase. The present study adopted the wholemetagenome shotgun sequencing approach, to assess the effects of the production phase on thecomposition and functional potential of microbial populations in SCBs bioaerosols. Most annotatedproteins were assigned into domain bacteria, within which the predominant phylum was Firmicutes.The taxonomical profiles of bioaerosols from different types of piggeries showed that buildingshousing weaning piglets (WP) exhibited higher abundances of Bacteroidetes and Proteobacteria thanbuildings housing finishing pigs (FP), gestating sows (GS), farrowing sows (FS), and breeding boars(BB). Regarding the functional potential, the WP bioaerosol had more genes involved in the proteinturnover and fewer genes involved in the carbohydrate metabolism than bioaerosols from othertypes of SCBs. Furthermore, production phase influenced the antibiotic resistance genes (ARGs)profile of the SCBs bioaerosols. Bioaerosol microbiome of BB, shared a high similarity with GS, andWP bioaerosol microbiome was more similar to FP than other types of SCBs. Our study suggeststhat the production phase plays a key role in the SCBs bioaerosol microbiome.

Prevalence of Antibiotic Resistance Genes in Air-Conditioning Systems in Hospitals, Farms, and Residences

High-throughput quantitative PCR combined with Illumina sequencing and network analysis were used to characterize the antibiotic resistance gene (ARG) profiles in air-conditioning filters from different environments. In total, 177 ARGs comprising 10 ARG types were determined. The detectable numbers and the relative abundance of ARGs in hospitals and farms were significantly higher than those in city and village residences. Compared to hospitals, farms had a higher level of tetracycline, multidrug, integrase, and macrolide⁻lincosamide⁻streptogramin (MLS) B resistance genes but a lower level of beta-lactam resistance genes. The bl3_cpha gene was the most abundant resistance gene subtype in hospital samples with an abundance of 2.01 × 10^-4 copies/16S rRNA, while a level of only 5.08 × 10^-12 copies/16S rRNA was observed in farm samples. There was no significant difference in bacterial diversity among the hospitals, farms, and residences, and Proteobacteria was the most abundant phylum. Network analysis revealed that Proteobacteria and Actinobacteria were possible hosts of the beta-lactam, MLSB, aminoglycoside, multidrug, sulfonamide, and tetracycline resistance genes. The results demonstrate that ARGs exist in indoor environments and that farms and hospitals are important sources. This study provides a useful reference for understanding the distribution patterns and risk management of ARGs in indoor environments.

Analyses of Aerosol Concentrations and Bacterial Community Structures for Closed Cage Broiler Houses at Different Broiler Growth Stages in Winter

The aim of the present study was to analyze the aerosol concentrations and microbial community structures in closed cage broiler houses at different broiler growth stages to assess the dynamic pattern of microbial aerosols in closed cage systems. Our results revealed that the total concentration of bacterial aerosols gradually increased during the growth cycle of broilers. High-throughput sequencing of 16S rDNA revealed that microbial compositions differed tremendously during different growth stages, although Firmicutes and Proteobacteria were the dominant taxa in samples from all broiler growth stages. At the genus level, dominant phylotypes displayed great variation during different growth stages. Escherichia and Shigella were the most dominant taxa throughout the growth cycle, increasing from 4.3 to 12.4% as the broilers grew. The alpha index revealed that the microbial diversity displayed significant differences between the different growth stages and that the bacterial community had the highest diversity when broilers were 22 days old. High-throughput sequencing analyses revealed that environmental microbes and opportunistic pathogens had relatively high abundances during the winter growth period. The data revealed the composition and aerodynamic diameters of microbial aerosols in closed cage broiler houses at different broiler growth stages in winter. The results also enabled us to elucidate the dynamic pattern of microbial aerosols in broiler houses in response to bacterial communities. Our results may provide a basis for developing technologies for air quality control in caged poultry houses.

Detection and analysis of fine particulate matter and microbial aerosol in chicken houses in Shandong Province, China

Bacteria and fungi are primary constituents of airborne microbes in fine particulate matter and harmful to health. To evaluate the environmental quality of different poultry houses in Shandong Province, China, the airborne aerobic bacteria, airborne fungi, and airborne Escherichia coli were collected by the Andersen-6 air microorganism sampler. The fine particulate matter was collected by a ZR-3920 ambient air particulate matter sampler, and bacterial and fungal diversities and relative abundances analyzed using high-throughput sequencing. Results showed that the concentrations of airborne aerobic bacteria, airborne fungi, and airborne Escherichia coli in poultry houses were 0.167 to 4.484 × 104 CFU/m3, 0.236 to 4.735 × 103 CFU/m3, and 0 to 33.0 CFU/m3, respectively. 11.4 to 34.3% of aerobic bacteria and 16.8 to 37.5% of fungi were distributed at levels 5 and 6 (0.6 to 2.1 μm, the particle sizes similar to fine particulate matter) in the Andersen sampler. The concentration of fine particulate matter in the poultry houses was 114 to 230 μg/m3, which was higher than the safety value 10 specified by WHO. In fine particulate matter, the main bacteria at phylum level were Firmicutes, Bacteroidetes, and Proteobacteria, whereas the dominant phylum of fungus was Ascomycota and Basidiomycota. Importantly, the relative abundances of Escherichia and Corynebacterium in the broiler houses were greater than those in layer houses. However, the percentages of Aspergillus and Penicillium were 13.5 and 0.56%, with a relatively high level in the layer houses. Altogether, results revealed that the ambient air quality in the poultry houses sampled had a relatively high abundance of conditional pathogenic bacteria and concentration of fine particulate matter, which could threaten the health of animals and workers in those environments.