Swine farming shifted the gut antibiotic resistome of local people.

Antibiotic resistance genes (ARGs) are prevalent in the livestock environment, but little is known about impacts of animal farming on the gut antibiotic resistome of local people. Here we conducted metagenomic sequencing to investigate gut microbiome and resistome of residents in a swine farming village as well as environmental relevance by comparing with a nearby non-farming village. Results showed a shift of gut microbiome towards unhealthy status in the residents of swine farming village, with an increased abundance and diversity in pathogens and ARGs. The resistome composition in human guts was more similar with that in swine feces and air than that in soil and water. Mobile gene elements were closely associated with the prevalence of gut resistome. Some plasmid-borne ARGs were colocalized in similar genetic contexts in gut and environmental samples. Metagenomic binning obtained 47 ARGs-carrying families in human guts, and therein Enterobacteriaceae posed the highest threats in antibiotic resistance and virulence. Several ARGs-carrying families were shared by gut and environmental samples (mainly in swine feces and air), and the ARGs were evolutionarily conservative within genera. The findings highlight that swine farming can shape gut resistome of local people with close linkage to farm environmental exposures.

Characteristics of antimicrobial residues in manure composts from swine farms: Residual patterns, removal efficiencies, and relation to purchased quantities and composting methods in Japan.

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.

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.

Infection Dynamics and Genomic Mutations of Hepatitis E Virus in Naturally Infected Pigs on a Farrow-to-Finish Farm in Japan: A Survey from 2012 to 2021.

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.

Occupational exposure in swine farm defines human skin and nasal microbiota.

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.

Environmental exposure to swine farms reshapes human gut microbiota.

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.

First detection and characterization of rat hepatitis E Virus (HEV-C1) in Japan.

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.

Swine manure facilitates the spread of antibiotic resistome including tigecycline-resistant tet(X) variants to farm workers and receiving environment.

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.

Airborne Spread of Methicillin Resistant Staphylococcus aureus From a Swine Farm.

Spread of livestock-associated methicillin resistant Staphylococcus aureus (LA-MRSA) to farmworkers has been recognized as a risk when working in LA-MRSA positive stables, due to LA-MRSA being present on airborne dust particles. Based on this, airborne spread of LA-MRSA through stable vents is a concern that is addressed in this study. The aim of the investigation was to quantify the airborne spread of LA-MRSA from a MRSA positive swine farm. In order to achieve this, a method for sampling large volumes of air was applied. The results were compared to meteorological data and bacteriological investigation of samples from the air inside the swine barn, soil outside the farm, and nasal samples from the individuals participating in the sampling process. MRSA was detected up to 300 m (the maximal measuring distance) from the swine farm in the air but only at low levels at distances above 50 meters (0.085 CFU/m3 at a distance of 50 m in the wind plume). MRSA was detected in sock samples obtained at the soil surfaces up to 400 m (the maximal measuring distance) from the farm building. The proportion of MRSA positive soil samples decreased from ~80 to 30% with increasing distance from the farm. A total of 25 human nasal samples were sampled after the farm visits after the participants had stayed in the surroundings of the farm for an average of 10.5 h. When leaving the farm, only two of the samples (8%) were LA-MRSA-positive both obtained from one individual who was the one who had sampled the ventilation shafts. In conclusion, airborne spread of MRSA from swine farms does not seem to be an important route for human contamination for individuals staying a whole working day outside a swine farm.

Using vermiwash to enhance performance of small-scale vermifiltration for swine farm wastewater.

Pollution caused by swine wastewater is a growing concern in many countries. In the developing countries, swine wastewater is not properly collected and treated, the wastewater from swine farm pollutes the ecosystem. Especially for small swine farms, they could not afford to have wastewater treatment system. Therefore, farmers need cheap, sustainable technology for future mixed farming. Vermifiltration by earthworm has been introduced to be an answer for enhancing wastewater treatment. Vermiwash is the liquid gathered from vermicomposting that has high microbial activities and nutrients. This study was carried out on a small pilot scale to investigate swine wastewater treatment efficiency of vermifiltration system with and without vermiwash and compared with the geofiltration system. Vermiwash was incubated in vermifiltration and geofiltration systems for 1 week before the treatment. The result showed improved efficiency of vermifiltration incubated with vermiwash in swine wastewater treatment for biological oxygen demand (BOD), chemical oxygen demand (COD) and total suspended solids (TSS) removal, which was highest followed by vermifiltration without incubated vermiwash, geofilter incubated with vermiwash and geofilter, respectively. Good performance of vermifiltration incubated with vermiwash compared with the geofilter treatment was demonstrated for removal of BOD (91.29 ± 9.89%, n = 10), COD (91.42 ± 6.34%, n = 10) and TSS (86.02 ± 10.45%, n = 10). Furthermore, the burrowing activity of the test earthworm (Eisenia fetida) promoted the aeration condition in vermifilter which led to more dissolved oxygen (DO) in effluent (61.28 ± 20.05%, n = 10). Moreover, the amount of copper (Cu) in effluent was decreased compared with influent by up to 88% in all treatment. After 10 weeks of the experiment, the vermicompost that was incubated with vermiwash and produced from earthworm on the top layer was analyzed and showed that nutrients (nitrogen, phosphorus) and soil organic carbon were increased with vermifilter treatment (47.65, 81.61 and 31.79%, respectively) compared with geofilter treatment. In addition, bioavailability of Cu in soil in form of exchangeable Cu was decreased by increasing the bound to organic matter fraction. Transformation of Cu during vermifiltration happened and alleviated the mobility and availability of Cu. Copper in exchangeable form can change into non-toxic form. Therefore, vermifiltration process incubated with vermiwash could reduce the dispersion of copper in swine waste. In conclusion, vermiwash could enhance performance of vermifiltration for swine farm wastewater treatment. The available fraction of copper in vermicompost produced from vermifiltration decreased. Therefore, the farmer could produce vermicompost as the biofertilizer for agricultural production. Using vermifiltration for wastewater treatment in small swine farm could be the eco-solution for nutrient recovery, water resource recycles and minimize pollution.

Occurrence and fate of androgens, progestogens and glucocorticoids in two swine farms with integrated wastewater treatment systems.

Steroid hormones are endocrine-disrupting chemicals that can cause adverse effects even at trace levels. The information about steroid hormones in animal wastes is still very limited. Here we investigated the occurrence and fate of fourteen androgens, twenty-one progestogens, and five glucocorticoids in Farm Luo Cheng (LC) and Farm Shui Tai (ST) with integrated wastewater treatment systems (WTSs) in South China. These two integrated systems have four stages: primary treatment (primary sedimentation tank), secondary biological treatment (biogas digester and up-flow anaerobic sludge reaction bed (UASB)), third-stage disinfection process, and fourth-stage dilution and further biodegradation process (oxidation fish ponds/lagoons). A total of 31 target steroid hormones were detected in the wastewater of the two swine farms, with concentrations ranging from 0.12 ng/L (medroxyprogesterone acetate, MPA) to 11,200 ng/L (5α-dihydroprogesterone, 5α-DHP). A total of 22 target steroid hormones were detected in feces, of which 19 were detected in Farm LC and 17 in Farm ST. Some of these detected steroids were synthetic chemicals, which might be parent chemicals from exogenous addition or their metabolites, or transformation products from other natural steroids. The steroids excretion of sows in swine farms were estimated, with some steroids such as androstenedione (AED, 41.5 µg/d), epiandrosterone (EADR, 268 µg/d), progesterone (P, 661 µg/d), and 5α-DHP (982µg/d) having much higher values than those from human bodies. Both WTSs in the swine farms could effectively remove the target steroid hormones, with the removal rates of most targets exceeding 90%. In comparison, the anaerobic digester-A2/O (anaerobic-anoxic-oxic)-lagoon system performed better in removing steroids than the up-flow anaerobic sludge reaction bed (UASB)-two-stage series (A/O)2-oxidation fish ponds system. However, there were still 22 steroid hormones, including 14 synthetic ones detected in the effluent, with the risk quotients of most synthetic steroids exceeding 1, showing high risks to aquatic organisms. The findings from this study showed that there is a wide presence of steroid hormones, especially some synthetic steroids in animal wastes, posing potential ecological risks, and these steroids should be removed before discharge to the environment.

Rapid Increase in the IS26-Mediated cfr Gene in E. coli Isolates with IncP and IncX4 Plasmids and Co-Existing cfr and mcr-1 Genes in a Swine Farm.

This paper aimed to investigate the molecular epidemiological features of the cfr gene in E. coli isolates in a typical swine farm during 2014-2017. A total of 617 E. coli isolates were screened for the cfr gene using PCR amplification. A susceptibility test, pulsed-field gel electrophoresis (PFGE), S1-PFGE, southern blotting hybridization, and the genetic context of the cfr gene were all used for analyzing all cfr-positive E. coli isolates. A conjugation experiment was conducted with the broth mating method using E. coli C600 as the recipient strain and 45 mcr-1-cfr-bearing E. coli isolates as the donor strain. Plasmids pHNEP124 and pHNEP129 were revealed by Illumina Miseq 2500. Eighty-five (13.7%) E. coli isolates were positive for the cfr gene and the prevalence of the cfr gene had significantly increased from 1.6% in 2014 to 29.1% in 2017. The Pulsed-Field Gel Electrophoresis (PFGE) analysis indicated that the spread of the cfr gene among E. coli isolates was mainly due to horizontal transfer. In addition, the cfr gene was primarily located on the plasmids between 28.8-kb to 60-kb in size, and the cfr gene was flanked by two copies of IS26 with the same orientation. Sequence analysis suggested that the plasmids pHNEP124 and pHNEP129 co-harboring the cfr and mcr-1 genes belonged to the plasmids IncP plasmid and IncX4 plasmid, respectively. In conclusion, this is the first study to report the high prevalence of the cfr gene among E. coli isolates and the first report of the complete genome sequence of IncP and IncX4 plasmids carrying the mcr-1 and cfr genes. The occurrence and dissemination of the cfr/mcr-1-carrying plasmids among E. coli isolates need further surveillance.

Genotypic and phenotypic situation of antimicrobial drug resistance of Escherichia coli in water and manure between biogas and non-biogas swine farms in central Thailand.

Currently, Thai livestock is rapidly expanding, especially the production of ruminants, chicken, and swine. The improper use of antibiotics will probably lead to an antimicrobial resistance problem. It has long been suspected that wastewater released from swine farms is a crucial aspect of the spread of antimicrobial resistance to the environment. Biogas systems are wastewater treatment systems commonly used on swine farms; however, little is known about the roles they play in the occurrence and transmission of resistant bacteria between biogas and non-biogas systems. This study collected pooled water, wastewater, and feces samples from five biogas farms and three non-biogas farms in Central Thailand. The samples were isolated to hemolytic E. coli (HEC) and non-hemolytic E. coli (NHEC) to test the drug resistance by using VITEK® 2 Compact (BioMérieux, USA) and detect resistant genes by using the polymerase chain reaction (PCR) technique to correlate the determined phenotypic and genotypic patterns. The results demonstrated that enumeration levels of E. coli ranged from 20.1 to 70.4 (MPN/100 ml), 105 to 107 (cfu/ml), and 105 to 109 (cfu/g), while they were 0-148.7 (MPN/100 ml), 105 to 107 (cfu/ml) and 105 to 109 (cfu/g) for water, wastewater and manure from biogas and non-biogas swine farms, respectively. The amount of E. coli in the sow feces samples was higher than the samples of nursery piglets on biogas farms at a 0.05 significant level (p < 0.05). The antimicrobial resistance indicated the relevant resistance characteristics of E. coli: the highest antimicrobial resistance was for ampicillin (AMP), followed by amoxicillin (AMX), tetracyclines (TET), chloramphenicol (C), and piperacillin (PIP), respectively. Multidrug resistance (MDR) of E. coli was 15 drugs: AMP-AMX-AMC-PIP-CEX-CEV-CPD-XNL-GM-IMP-SXT-C-TE (11.9%) and AMP-AMX-AMC-PIP-CEX-CEV-CPD-XNL-GM-IMP-SXT-C-ENR-MBR-TE (18.55%), which were the most commonly found in biogas and non-biogas swine farms, respectively. The blaTEM, tetA, sul2, and sul3 were dominantly resistant genes isolated from the water from both types of farm; while, blaTEM, aadA1, tetA, dfrA12, sul2, sul3, and cmlA were isolated from feces. The amount of E. coli in the final effluent from biogas swine farms was higher than the non-biogas swine farms; however, it was not significantly different at (p > 0.05). Furthermore, the findings of study found that genotypic characteristic of HEC showed similarity 100%. Thus, it was concluded that the levels of E. coli were accelerated in biogas wastewater treatment systems, and isolated E. coli demonstrated multidrug resistance. Even though E. coli was found in different locations, it showed relevant resistance characteristics. Therefore, regular monitoring of antimicrobial resistance on livestock farms is necessary for efficient management and drug uses on farms.

Coagulase-negative staphylococci carrying cfr and PVL genes, and MRSA/MSSA-CC398 in the swine farm environment.

This work aimed at characterizing four Staphylococcus aureus and 68 coagulase-negative staphylococci (CoNS), recovered from the air and liquid manure tank of two swine farms with intensive- and semi-extensive-production types, for their antimicrobial resistance pheno-/genotypes and their virulence gene content. Molecular typing was performed by spa typing, MLST, agr typing, and SCCmec typing, where applicable. Conjugation experiments were performed to assess the transferability of the linezolid resistance gene cfr, and its genetic environment was determined by Whole-Genome-Sequencing. The four S. aureus (intensive-production farm, IP-farm) were typed as t011-agrI-CC398-ST398, were scn-negative and two of them were methicillin-resistant (MRSA) with the mecA gene (SCCmec-V). Multidrug resistance was seen in 87 % of the CoNS. Statistically significant differences among the antimicrobial resistance rates of CoNS from the two farms were observed for cefoxitin, aminoglycosides, tetracycline, ciprofloxacin and trimethoprim-sulfamethoxazole. Eight methicillin-resistant CoNS, which were recovered from the IP-farm, carried the mecA gene. One S. simulans isolate was PVL-positive and three S. cohnii eta-positive. One S. equorum and one S. arlettae showed linezolid resistance and carried the cfr gene (IP-farm), which was non-transferable by conjugation into S. aureus. The cfr genetic context in both isolates was identical, with the lsa(B) gene located upstream of cfr. The environment of swine farms might contribute to the dissemination of CoNS that show multidrug resistance and harbor important virulence factors.

Rational budgeting approach as a nutrient management tool for mixed crop-swine farms in Korea.

OBJECTIVE: Due to rapid economic return, mixed crop-swine farming systems in Korea have become more intensive. Intensive farming practices often cause nutrient surpluses and lead to environmental pollution. Nutrient budgets can be used to evaluate the environmental impact and as a regulatory policy instrument for nutrient management. This study was conducted to select a nutrient budgeting approach applicable to the mixed crop-swine farms in Korea and suggest an effective manure treatment method to reduce on-farm nutrient production. METHODS: In this study, we compared current and ideal gross nutrient balance (GNB) approaches of Organisation for Economic Co-operation and Development and soil system budget (SSB) approach with reference to on-farm manure treatment processes. Data obtained from farm census and published literature were used to develop the farm nutrient budgets. RESULTS: The average nitrogen (N) and phosphorus (P) surpluses were approximately 11 times and over 7 times respectively higher in the GNB approaches than the SSB. After solid-liquid separation of manure, during liquid composting a change in aeration method from intermittent to continuous reduced the N and P loading about 50% and 47%, respectively. Although changing in solid composting method from turning only to turning+aeration improved the N removal efficiency by 30.5%, not much improvement in P removal efficiency was observed. CONCLUSION: Although the GNB approaches depict the impact of nutrients produced in the mixed crop-swine farms on the overall agricultural environment, the SSB approach shows the partitioning among different nutrient loss pathways and storage of nutrients within the soil system; thus, can help design sustainable nutrient management plans for the mixed cropswine farms. The study also suggests that continuous aeration for liquid composting and turning+aeration for solid composting can reduce nutrient loading to the soil.

Swine farming elevated the proliferation of Acinetobacter with the prevalence of antibiotic resistance genes in the groundwater.

Swine farming generates a large amount of wastes containing various contaminants, resulting in environmental contamination and human health problems. Here we investigated the contamination profiles of antibiotics and antibiotic resistance genes (ARGs) as well as microbial community in groundwater of the two villages with or without swine farms, and then assessed the human exposure risks of antibiotics, ARGs and indicator bacteria through drinking groundwater. The results showed that swine farming could lead to enhanced concentration levels of various veterinary antibiotics and ARGs in the groundwater in comparison to the reference village without swine farming. The microbial diversity of groundwater was significantly decreased with predominance of conditional pathogens Acinetobacter (up to 90%) in some wells of the swine farming village. Meanwhile, the abundance of Acinetobacter was significantly correlated to bacterial abundance, ARGs and integrons. The local residents could ingest various antibiotic residues and ARGs as well as pathogens, with daily intake of Acinetobacter up to approximately 10 billion CFU/resident through drinking groundwater contaminated by swine farming. The findings from this study suggest potential health risks of changing gut microbial community and resistome by drinking contaminated groundwater.

Salmonella spp. prevalence, antimicrobial resistance and risk factor determination in Colombian swine farms / Salmonella spp. prevalência, resistência antimicrobiana e determinação de fatores de risco em granjas suínas colombianas

To determine Salmonella spp. prevalence/seroprevalence, antimicrobial resistance patterns and risk factor identification associated with its presence in Colombian swine farms. 504 samples (Faeces, swabs and environment samples) were obtained from 21 farms distributed in four geographical regions in Colombia. Salmonella spp. microbiological and molecular detection were determined by two Salmonella spp. MDS3M™ and MALDI-TOF MS assays, respectively. In addition, for serological evaluation 231 serum samples were analyzed employing ELISA Salmonella Pigtype®-Salmonella Ab (QUIAGEN®). Additionally, 41 isolates were tested for antimicrobial susceptibility using broth microdilution technique (Panel B1016-180 Beckman Coulter NC72®) and verified with WHONET 2016 software. Risk factors were assessed from a survey and analyzed for statistical significance by U Mann-Whitney test. An 8.9% prevalence (n=45) and 38.1% (n=88) seroprevalence were determined. All isolates presented 100% antimicrobial susceptibility against amikacin. However, resistance against penicillin, tetracycline, cefuroxime and trimethoprim/sulfamethoxazole was present in more than 50% of evaluated strains. Risk factors associated with Salmonella spp. presence were surface water use, rough-surfaced on floors, presence of hoppers as feeders and worker's boots. Bacteria were present in animals and environmental samples from evaluated farms. Animal contact and/or exposure with the microorganism were also evident in obtained serological response. Bacteria presence depended on management practices and infrastructure, likewise antibiotic use, supplemented in the diet may have induced an increase in Salmonella spp. antimicrobial resistance.(AU)

Para determinar Salmonellaspp. prevalência/soroprevalência, padrões de resistência antimicrobiana e identificação de fatores de risco associados à sua presença em granjas suínas colombianas. Foram obtidas 504 amostras (fezes, zaragatoas e amostras do ambiente) de 21 fazendas distribuídas em quatro regiões geográficas da Colômbia. Salmonella spp., a detecção microbiológica e molecular foi determinada por 2 Salmonella spp. Ensaios MDS3M™ e MALDI-TOF MS, respectivamente. Além disso, para avaliação sorológica, foram analisadas 231 amostras de soro empregando ELISA Salmonella Pigtype® - Salmonella Ab (QUIAGEN®). Além disso, 41 isolados foram testados quanto à suscetibilidade antimicrobiana usando a técnica de microdiluição em caldo (Painel B1016-180 Beckman Coulter NC72®) e verificados com o software WHONET 2016. Os fatores de risco foram avaliados em uma pesquisa e analisados quanto à significância estatística pelo teste U Mann-Whitney. Foram determinadas prevalências de 8,9% (n=45) e 38,1% (n=88). Todos os isolados apresentaram 100% de suscetibilidade antimicrobiana à amicacina. No entanto, resistência à penicilina, tetraciclina, cefuroxima e trimetoprim/sulfametoxazol estava presente em mais de 50% das cepas avaliadas. Fatores de risco associados à Salmonella spp., presença de uso de água de superfície, superfície áspera no chão, presença de tremonhas como alimentadores e botas de trabalho. Bactérias estavam presentes em animais e amostras ambientais de fazendas avaliadas. O contato animal e/ou a exposição ao microrganismo também foram evidentes na resposta sorológica obtida. A presença de bactérias dependia de práticas de manejo e infraestrutura, assim como o uso de antibióticos suplementados na dieta pode ter induzido um aumento de Salmonella spp. resistência antimicrobiana.(AU)

Swine waste: A reservoir of high-risk blaNDM and mcr-1.

Multidrug resistance associated with pigs not only affects pig production but also threatens human health by influencing the farm surrounding and contaminating the food chain. This paper focused on the occurrence and prevalence of high-risk resistance genes (using blaNDM and mcr-1 as marker genes) in two Chinese swine farms, and investigated their fate and seasonal changes in piggery wastewater treatment systems (PWWTSs). Results revealed that blaNDM and mcr-1 were prevalent in both confined swine farms, and even prevailed through various processing stages of PWWTSs. Moreover, the abundance of blaNDM and mcr-1 in winter was higher than that in summer, with 0.01-1.01 logs variation in piggery wastewater. Of concern is that considerable amounts of blaNDM and mcr-1 were present in final effluent that is applied to farmland (up to 102-104copies/mL), raising the risk of propagation to indigenous bacteria. Worse still, those pig-derived isolates harboring the blaNDM/mcr-1 gene were confirmed to spread multidrug resistance to other bacteria, which further increased their dissemination potential in agricultural environment. This study highlights the prevalence of blaNDM and mcr-1 in swine farms, meanwhile, also emphasizes the necessary to mitigate the release and propagation of these high-risk genes from swine farms following land fertilization and wastewater usage.

Major environmental characteristics of swine husbandry that affect exposure to dust and airborne endotoxins.

Inhalation of organic dust or endotoxin in the dust is considered a major risk factor for occupational respiratory illnesses. Eighteen environmental characteristics associated with animal husbandry were surveyed at 36 swine farms in seven provinces throughout South Korea. Association of these factors with levels of indoor inhalable or respirable dust or endotoxin in each type of dust was analyzed using backward stepwise multiple linear regression models. Mean levels of inhalable and respirable dust were 0.5 ± 0.35 and 0.13 ± 0.12 mg/m3 air, respectively, and mean endotoxin levels were 676 ± 463 and 48.4 ± 68.2 EU/m3, respectively, in each dust. Factors negatively associated with inhalable dust levels included pig age, indoor farm temperature, number of pigs in the building, hr/week of indoor farm work, and partly slatted floor. Factors positively associated with inhalable dust levels included floor cleaning by manual scraping and slurry deposit duration. Factors negatively associated with the level of endotoxin in inhalable dust included pig age, temperature, number of pigs, hr/week of indoor farm work, and partly slatted floor. Factors negatively associated with respirable dust level included area of the confinement building, whereas factors positively associated with respirable dust level included the number of pigs and stocking density. Endotoxin levels in respirable dust were negatively associated with h/week of indoor farm work and partly slatted floor. Overall, data suggest that husbandry variables may be adjusted to control dust and airborne endotoxin levels in swine farms.

Occurrence and contamination profiles of antibiotic resistance genes from swine manure to receiving environments in Guangdong Province southern China.

Livestock farms are commonly regarded as the main sources of antibiotic resistance genes (ARGs), emerging pollutants with potential implications for human health, in the environment. This study investigated the occurrence and contamination profiles of nine ARGs of three types from swine manure to receiving environments (soil and water) in Guangdong Province, southern China. All ARGs occurred in 100% of swine manure samples. Moreover, the absolute concentration of total ARGs varied from 3.01 × 108 to 7.18 × 1014 copies/g, which was significantly higher than that in wastewater and manured soil (p < 0.05). Regarding the distribution characteristics of ARGs in swine manure, wastewater and manured soil, the tetracycline resistance gene tetO was predominant. ARGs in swine manure were relatively stable among swine growth periods after the nursery period. The ARG concentration did not differ significantly between manured and unmanured soil (p > 0.05). However, the number of ARGs (ermB, qnrS, acc(6')-Ib, tetM, tetO and tetQ) decreased but were not eliminated by wastewater treatment components (p < 0.05). Based on correlation analysis, the tetracycline resistance genes tetQ and tetW in swine manure and the macrolide resistance genes ermB and ermF in wastewater were more easily spread than were other ARGs onto soil when the substances were applied as fertilizers. Therefore, effective removal and a standard permissible environmental level of ARGs should be established to control the risk of spreading ARGs in the environment.