Antibiotic resistance (AMR) poses a significant global health challenge, with swine farms recognized as major reservoirs of antibiotic resistance genes (ARGs). Recently, bacterial membrane vesicles (BMVs) have emerged as novel carriers mediating horizontal gene transfer. However, little is known about the ARGs carried by BMVs in swine farm environments and their transfer potential. This study investigated the distribution, sources, and microbiological origins of BMVs in three key microbial habitats of swine farms (feces, soil, and fecal wastewater), along with the ARGs and mobile genetic elements (MGEs) they harbor. Characterization of BMVs revealed particle sizes ranging from 20 to 500 nm and concentrations from 108 to 1012 particles/g, containing DNA and proteins. Metagenomic sequencing identified BMVs predominantly composed of members of the Proteobacteria phyla, including Pseudomonadaceae, Moraxellaceae, and Enterobacteriaceae, carrying diverse functional genes encompassing resistance to 14 common antibiotics and 74,340 virulence genes. Notably, multidrug resistance, tetracycline, and chloramphenicol resistance genes were particularly abundant. Furthermore, BMVs harbored various MGEs, primarily plasmids, and demonstrated the ability to protect their DNA cargo from degradation and facilitate horizontal gene transfer, including the transmission of resistance genes. In conclusion, this study reveals widespread presence of BMVs carrying ARGs and potential virulence genes in swine farm feces, soil, and fecal wastewater. These findings not only provide new insights into the role of extracellular DNA in the environment but also highlight concerns regarding the gene transfer potential mediated by BMVs and associated health risks.

Antimicrobial resistance (AMR) is a major threat to global public health, and antibiotic resistance genes (ARGs) are widely distributed across humans, animals, and environment. Farming environments are emerging as a key research area for ARGs and antibiotic resistant bacteria (ARB). While the skin is an important reservoir of ARGs and ARB, transmission mechanisms between farming environments and human skin remain unclear. Previous studies confirmed that swine farm environmental exposures alter skin microbiome, but the timeline of these changes is ill defined. To improve understanding of these changes and to determine the specific time, we designed a cohort study of swine farm workers and students through collected skin and environmental samples to explore the impact of daily occupational exposure in swine farm on human skin microbiome. Results indicated that exposure to livestock-associated environments where microorganisms are richer than school environment can reshape the human skin microbiome and antibiotic resistome. Exposure of 5 h was sufficient to modify the microbiome and ARG structure in workers\' skin by enriching microorganisms and ARGs. These changes were preserved once formed. Further analysis indicated that ARGs carried by host microorganisms may transfer between the environment with workers\' skin and have the potential to expand to the general population using farm workers as an ARG vector. These results raised concerns about potential transmission of ARGs to the broader community. Therefore, it is necessary to take corresponding intervention measures in the production process to reduce the possibility of ARGs and ARB transmission.

UNASSIGNED: To update recent information on contamination levels of mycotoxins in South Korea.
UNASSIGNED: A total of 208 samples sourced from the feeds of swine farms were collected. The contamination levels of mycotoxins, which are aflatoxin (Afla), ochratoxin A (OTA), deoxynivalenol (DON), zearalenone (ZEN), fumonisin (FUM), and T-2 toxin, were investigated by enzyme-linked immunosorbent assays (ELISAs).
UNASSIGNED: The detection levels of the total samples were 78.91% for DON, 75.24% for Afla, 47.02% for ZEN, 68.31% for FUM, and 5.94% for OTA and T-2, which were not detected at all. Most of the analyzed mycotoxins showed significant high occurrences in 47.02%-78.91% of the swine feed samples. 11 of the 152 alfa-positive samples exceeded the maximum residue limit (MRL) of Afla proposed by the Korean regulation. In the analysis of mycotoxin detection levels by growth stage, ZEN was found in the nursery stage at a remarkably high concentration level (126.46 ± 63.76 ppb), exceeding the MRL of ZEN for piglets proposed by the European Commission. This mycotoxin was also found in the samples from the gestation barn (89.04 ± 46.05 ppb) and the farrowing house (105.58 ± 94.12) at a high concentration level. Afla was found in the nursery stage at a high concentration (8.00 ± 2.22 ppb), approaching the MRL (10 ppb) of Afla proposed by the Korean regulation.
UNASSIGNED: These results indicate that many swine farms in South Korea are still exposed to mycotoxin risk, and special attention and surveillance are necessary for these mycotoxin risks in swine farms.

Present study provides first comprehensive results on the residual levels of 19 antimicrobial (AM) residues in 12 Japanese swine manure composting facilities that use open or enclosed types of treatment methods. Tilmicosin (14000 μg/kg d.w.) and tiamulin (15000 μg/kg d.w.) were present in the highest concentrations in manure composts. Morantel (MRT) had the highest detection frequency (100%) in compost, suggesting its ubiquitous usage and resistance to degradation during composting. Sulfamethoxazole had low detection frequencies and concentrations, likely due to limited partitioning to the solid phase. A positive correlation (p < 0.05) between purchasing quantities and residue levels in manure composts was detected for fluoroquinolones (FQs). The removal efficiencies of AMs in enclosed-type facilities were lower and more inconsistent than those in open-type facilities. Tetracyclines (TCs), lincomycin, and trimethoprim were easily removed from open-type facilities, whereas FQs and MRT persisted in both facilities. After discontinuing the usage of oxytetracycline (OTC), TCs concentrations reduced drastically in input materials, remained pseudo-persistent in composts for up to 4 months, suggesting a time lag for composting and were not detected (<10 µg/kg) after 4 months of OTC withdrawal. This study emphasizes on the effectiveness of manure composting methods in reducing AM residues in swine waste.

Hepatitis E virus (HEV) causes acute or chronic hepatitis in humans. Pigs are the primary reservoir for zoonotic HEV genotypes 3 and 4 worldwide. This study investigated the infection dynamics and genomic mutations of HEV in domestic pigs on a farrow-to-finish pig farm in Japan between 2012 and 2021. A high prevalence of anti-HEV IgG antibodies was noted among pigs on this farm in 2012, when the survey started, and persisted for at least nine years. During 2012-2021, HEV RNA was detected in both serum and fecal samples, indicating active viral replication. Environmental samples, including slurry samples in manure pits, feces on the floor, floor and wall swabs in pens, and dust samples, also tested positive for HEV RNA, suggesting potential sources of infection within the farm environment. Indeed, pigs raised in HEV-contaminated houses had a higher rate of HEV infection than those in an HEV-free house. All 104 HEV strains belonged to subgenotype 3b, showing a gradual decrease in nucleotide identities over time. The 2012 (swEJM1201802S) and 2021 (swEJM2100729F) HEV strains shared 97.9% sequence identity over the entire genome. Importantly, the swEJM2100729F strain efficiently propagated in human hepatoma cells, demonstrating its infectivity. These findings contribute to our understanding of the prevalence, transmission dynamics, and genetic characteristics of HEV in domestic pigs, emphasizing the potential risks associated with HEV infections and are crucial for developing effective strategies to mitigate the risk of HEV infection in both animals and humans.

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.

Anthropogenic environments take an active part in shaping the human microbiome. Herein, we studied skin and nasal microbiota dynamics in response to the exposure in confined and controlled swine farms to decipher the impact of occupational exposure on microbiome formation. The microbiota of volunteers was longitudinally profiled in a 9-months survey, in which the volunteers underwent occupational exposure during 3-month internships in swine farms. By high-throughput sequencing, we showed that occupational exposure compositionally and functionally reshaped the volunteers\' skin and nasal microbiota. The exposure in farm A reduced the microbial diversity of skin and nasal microbiota, whereas the microbiota of skin and nose increased after exposure in farm B. The exposure in different farms resulted in compositionally different microbial patterns, as the abundance of Actinobacteria sharply increased at expense of Firmicutes after exposure in farm A, yet Proteobacteria became the most predominant in the volunteers in farm B. The remodeled microbiota composition due to exposure in farm A appeared to stall and persist, whereas the microbiota of volunteers in farm B showed better resilience to revert to the pre-exposure state within 9 months after the exposure. Several metabolic pathways, for example, the styrene, aminobenzoate, and N-glycan biosynthesis, were significantly altered through our PICRUSt analysis, and notably, the function of beta-lactam resistance was predicted to enrich after exposure in farm A yet decrease in farm B. We proposed that the differently modified microbiota patterns might be coordinated by microbial and non-microbial factors in different swine farms, which were always environment-specific. This study highlights the active role of occupational exposure in defining the skin and nasal microbiota and sheds light on the dynamics of microbial patterns in response to environmental conversion.

The gut microbiota can change to varying degrees because of changes in the environment. In the present study, we performed microbial amplicon sequencing on the feces of people who had long-term exposure to swine farms (F) and that of people living in normal environments (S) to investigate the impact of the environment on the human gut microbiota. A total of 1,283,503 high-quality ordered sequences were obtained, which provided different levels of microbial classification and statistics. We found that different environments did not alter the richness and diversity of the microbial communities in participants, but caused significant changes in the proportion of some bacteria. The main bacterial phyla found in group F participants were Firmicutes (69.44-89.03%), Actinobacteria (1.7-18.95%), and Bacteroidetes (1.17-22.35%); those found in group S participants were Firmicutes (49.93-95.04%), Bacteroidetes (0.62-39.59%), and Proteobacteria (0.98-11.95%). Additionally, because of changes in phylum proportions, the Bugbase phenotypic classification predicted an increase in the proportion of Gram-positive bacteria in group F and an increase in the proportion of Gram-negative bacteria in group S. In conclusion, our findings suggest that human exposure to swine farms can reshape the gut microbiota, resulting in changes in the microbial abundances. This change can potentially reduce the odds of developing bowel disease and contribute to the prevention of intestinal diseases, providing a theoretical basis for improving human health.

Rat hepatitis E virus (HEV-C1) in the Orthohepevirus C species has been reported to cause zoonotic infection and hepatitis in humans. HEV-C1 strains have been detected from wild rats in many countries in Europe, Asia, and North America. However, in Japan, no HEV-C1 strains have been identified. In the present study, 5 (1.2%) of 428 wild rats (Rattus norvegicus or R. rattus) were positive for anti-HEV-C1 IgG. Although all 428 rat sera were negative for HEV-C1 RNA, it was detectable in 20 (19.8%) of 101 rat fecal samples collected on a swine farm, where HEV (genotype 3b, HEV-3b) was prevalent and wild rats were present. In addition, HEV-C1 RNA was detectable in the intestinal contents and liver tissues of 7 (18.9%) of 37 additional rats captured on the same farm. The HEV-C1 strain (ratEJM1703495L) obtained in this study shared only 75.8-84.7% identity with reported HEV-C1 strains over the entire genome but propagated efficiently in cultured cells. HEV-3b strains were detected in the rats\' intestinal contents, with 97.3-99.5% identity to those in pigs on the same farm, but were undetectable in rat liver tissues, suggesting that wild rats do not support the replication of HEV-3b of swine origin.

The prevalence of antibiotic resistance genes (ARGs) in livestock and poultry manure is a severe threat to human health. However, the comprehensive characterization of antibiotic resistance in swine, workers, and the receiving environment is still lacking in the actual breeding environment. Hence, the ARG profile and the potential bacterial hosts producing among swine manure (including sows, piglets, finishing pigs, and nursery pigs), worker feces, and the receiving environment (including sediment and vegetable soil) were comprehensively analyzed based on the metagenomic method. The results showed that swine manure exhibited the high levels of richness and diversity of ARGs. Inactivating tetracycline resistance genes such as tet(X), tet(X1), and tet(X10) were prevalent on swine farms. Workers and the environment were the primary recipients of ARGs, and shared ARGs accounted for at least 90% of their ARG abundances. Network analysis revealed that Escherichia, Acinetobacter, and Erysipelothrix were the most dominant genera co-occurring with specific shared ARGs. The abundance of coexisting ARGs in swine at different developmental stages accounted for 76.4% to 90.8% of the shared ARGs in swine, workers, and environmental samples. The Mantel test revealed that Firmicutes and Proteobacteria had a significant correlation with the ARG profiles. In addition, variation partitioning analysis (VPA) showed that the joint effects of mobile genetic elements (MGEs) and bacterial communities accounted for 24.7% of the resistome variation and played a significant role in the ARG profiles. These results improve our understanding of the transmission and persistence of ARGs in the actual breeding environment.