Swine liquid manure: a hotspot of mobile genetic elements and antibiotic resistance genes

Environmental risks in swine biogas slurry-irrigated soils: A comprehensive analysis of antibiotic residues, resistome, and bacterial pathogens

Simple anaerobic digestion is insufficient to completely remove residual parent antibiotics and antibiotic resistance genes (ARGs) from animal manure. ARG prevalence in swine biogas slurry-irrigated soils threatens human health. However, comprehensive analysis of antibiotic residues, high-resolution resistance gene profiles, and pathogenic microbiomes in biogas slurry-irrigated soils is very limited. Here, we comprehensively determined the antibiotics, resistome, and potential pathogens distribution in these soils, using high-performance liquid chromatography-tandem mass spectrometry, high-throughput quantitative PCR, and 16S rRNA gene sequencing. The results revealed a significant enrichment of tetracyclines and fluoroquinolones antibiotics and ARGs in soils with prolonged biogas slurry irrigation, with a total of 12 antibiotics, 175 unique ARGs, and 9 mobile genetic elements (MGEs) detected. Quantification of veterinary antibiotic residues (especially chlortetracycline) showed significant correlations with multiple ARGs. The abundance of ARGs and MGEs was highest in the biogas slurry-irrigated soils, denoting a tight link between the application of biogas slurry and the spread of antibiotic resistance. The presence of 50 potential pathogenic bacterial genera, including 13 with multidrug resistance, was identified. Variation partitioning, combined with hierarchical partitioning analysis, indicated that Firmicutes, MGEs, and tetracyclines were the key drivers shaping the ARG profiles in biogas slurry-irrigated soils. The findings offer insights into the mechanisms of antibiotic residue and ARGs spread from the agricultural practice of biogas slurry irrigation, underscoring the necessity of sustainable soil management to mitigate the spread of antibiotic resistance.

Vancomycin resistance and virulence genes evaluation in Enterococci isolated from pork and wild boar meat

Enterococci are considered valuable sentinel Gram-positive bacteria for monitoring vancomycin antibiotic resistance due to their widespread presence and characteristics. The use of antimicrobials in farming animals has a role in the increasing of Antimicrobial Resistance (AMR) and the anthropogenic transformation of the landscape has forced wildlife into greater contact with humans and their livestock. The transmission of resistant bacteria by their meat products is a significant contributor to AMR development. The present study aimed to assess the prevalence of vancomycin resistant Enterococci spp. In antimicrobial-treated farmed pigs meat and in antimicrobial-free wild boars meat. A total of 341 Enterococci were isolated from 598 pork meat samples (57 %) and 173 Enterococci were isolated from 404 wild boar meat samples (42.8 %). Data found showed that low-resistance was detected more in wild boars meat Enterococci (52.6 %) than in pork meat once (48.4 %). However, the prevalence of resistance genes was at low level (33.9 % in pork meat Enterococci and 4.4 % in wild boar meat ones) and the only gene found was vanC1/C2, related to intrinsic AMR. Normally, Enterococci persist in the normal intestinal flora of animals including humans. However, the presence of resistance genes was frequently linked to the detection of pathogenic genes, mostly gelE in pork meat isolates and asa1 in wild boars meat isolates. Pathogenic bacteria can cause severe infections in human that can become more risky if associated to the presence of AMR. Pathogenic bacteria were characterized and a high presence of E. gallinarum and E. casseliflavus was found. Given the growing interest in wild game meat consumption the monitoring of AMR in these matrices is essential. Further surveillance studies are needed to fully evaluate the emergence and spread of vancomycin-resistant Enterococci (VRE) and pathogenic Enterococci from animal-derived food to humans, including the role of wildlife in this phenomenon. Giving the higher interest in wild animals meat consumption, it is important to better evaluate the spread of AMR phenomenon in the future and intensify hygienic control of wild animals derived food.

Tackling transmission of infectious diseases: A probiotic-based system as a remedy for the spread of pathogenic and resistant microbes

Built environments (BEs) currently represent the areas in which human beings spend most of their life. Consistently, microbes populating BEs mostly derive from human occupants and can be easily transferred from BE to occupants. The hospital microbiome is a paradigmatic example, representing a reservoir for harmful pathogens that can be transmitted to susceptible patients, causing the healthcare-associated infections (HAIs). Environmental cleaning is a crucial pillar in controlling BE pathogens and preventing related infections, and chemical disinfectants have been largely used so far towards this aim. However, despite their immediate effect, chemical-based disinfection is unable to prevent recontamination, has a high environmental impact, and can select/increase antimicrobial resistance (AMR) in treated microbes. To overcome these limitations, probiotic-based sanitation (PBS) strategies were recently proposed, built on the use of detergents added with selected probiotics able to displace surrounding pathogens by competitive exclusion. PBS was reported as an effective and low-impact alternative to chemical disinfection, providing stable rebalance of the BE microbiome and significantly reducing pathogens and HAIs compared to disinfectants, without exacerbating AMR and pollution concerns. This minireview summarizes the most significant results obtained by applying PBS in sanitary and non-sanitary settings, which overall suggest that PBS may effectively tackle the infectious risk meanwhile preventing the further spread of pathogenic and resistant microbes.

Deodorizing bacterial consortium: community analysis of biofilms and leachate water collected from an air biofiltration system in a piggery

Intensive livestock production is a source of water, soil, and air contamination. The first aspect that negatively affects the quality of life of residents in the vicinity of piggeries is malodorous aerosols, which are not only responsible for discomfort but can be an etiological factor in the development of various diseases during prolonged exposure. One of the proven and efficient ways to counteract odor emissions is the usage of air biofiltration. The purpose of this study was to qualitatively analyze the bacterial community colonizing the biofilm of a biofilter operating at an industrial piggery in Switzerland. The study material consisted of biofilm and leachate water samples. The microbiological analysis consisted of DNA isolation, amplification of the bacterial 16S rRNA gene fragment (V3-V4), preparation of a library for high-throughput sequencing, high-throughput NGS sequencing, filtering of the obtained sequencing reads, and evaluation of the species composition in the studied samples. The investigation revealed the presence of the following bacterial genera: Pseudochelatococcus, Methyloversatilis, Flexilinea, Deviosia, Chryseobacterium, Kribbia, Leadbetterella, Corynebacterium, Flavobacterium, Xantobacter, Tessaracoccus, Staphylococcus, Thiobacillus, Enhydrobacter, Proteiniclasticum, and Giesbergeria. Analysis of the microbial composition of biofilters provides the opportunity to improve the biofiltration process.

Occurrence and dissemination of antibiotic resistance genes in the Yellow River basin: focused on family farms

As an emerging contaminant, antibiotic resistance genes (ARGs) have attracted growing attention, owing to their widespread dissemination and potential risk in the farming environment. However, ARG pollution from family livestock farms in the Yellow River basin, one of the main irrigation water sources in the North China Plain, remains unclear. Herein, we targeted 21 typical family farms to assess the occurrence patterns of ARGs in livestock waste and its influence on ARGs in receiving environment by real-time quantitative PCR (qPCR). Results showed that common ARGs were highly prevalent in family livestock waste, and tet-ARGs and sul-ARGs were the most abundant in these family farms. Most ARG levels in fresh feces of different animals varied, as the trend of chicken farms (broilers > laying hens) > swine farms (piglets > fattening pigs > boars and sows) > cattle farms (dairy cattle > beef cattle). The effect of natural composting on removing ARGs for chicken manure was better than that for cattle manure, while lagoon storage was not effective in removing ARGs from family livestock wastewater. More troublesomely, considerable amounts of ARGs were discharged with manure application, further leading to the ARG increase in farmland soil (up to 58-119 times), which would exert adverse impacts on human health and ecological safety.

Review of antibiotic-resistant bacteria and antibiotic resistance genes within the one health framework

Background: The interdisciplinary One Health (OH) approach recognizes that human, animal, and environmental health are all interconnected. Its ultimate goal is to promote optimal health for all through the exploration of these relationships. Antibiotic resistance (AR) is a public health challenge that has been primarily addressed within the context of human health and clinical settings. However, it has become increasingly evident that antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) that confer resistance are transmitted and circulated within humans, animals, and the environment. Therefore, to effectively address this issue, antibiotic resistance must also be considered an environmental and livestock/wildlife problem. Objective: This review was carried out to provide a broad overview of the existence of ARB and ARGs in One Health settings. Methods: Relevant studies that placed emphasis on ARB and ARGs were reviewed and key findings were accessed that illustrate the importance of One Health as a measure to tackle growing public and environmental threats. Results: In this review, we delve into the complex interplay of the three components of OH in relation to ARB and ARGs. Antibiotics used in animal husbandry and plants to promote growth, treat, and prevent infectious diseases lead to the development of antibiotic-resistant bacteria in animals. These bacteria are transmitted from animals to humans through food and environmental exposure. The environment plays a critical role in the circulation and persistence of antibiotic-resistant bacteria and genes, posing a significant threat to human and animal health. This article also highlights how ARGs are spread in the environment through the transfer of genetic material between bacteria. This transfer can occur naturally or through human activities such as the use of antibiotics in agriculture and waste management practices. Conclusion: It is important to integrate the One Health approach into the public health system to effectively tackle the emergence and spread of ARB and genes that code for resistance to different antibiotics.

Local and Environmental Reservoirs of Salmonella enterica After Hurricane Florence Flooding

In many regions of the world, including the United States, human and animal fecal genetic markers have been found in flood waters. In this study, we use high-resolution whole genomic sequencing to examine the origin and distribution of Salmonella enterica after the 2018 Hurricane Florence flooding. We specifically asked whether S. enterica isolated from water samples collected near swine farms in North Carolina shortly after Hurricane Florence had evidence of swine origin. To investigate this, we isolated and fully sequenced 18 independent S. enterica strains from 10 locations (five flooded and five unflooded). We found that all strains have extremely similar chromosomes with only five single nucleotide polymorphisms (SNPs) and possessed two plasmids assigned bioinformatically to the incompatibility groups IncFIB and IncFII. The chromosomal core genome and the IncFIB plasmid are most closely related to environmental Salmonella strains isolated previously from the southeastern US. In contrast, the IncFII plasmid was found in environmental S. enterica strains whose genomes were more divergent, suggesting the IncFII plasmid is more promiscuous than the IncFIB type. We identified 65 antibiotic resistance genes (ARGs) in each of our 18 S. enterica isolates. All ARGs were located on the Salmonella chromosome, similar to other previously characterized environmental isolates. All isolates with different SNPs were resistant to a panel of commonly used antibiotics. These results highlight the importance of environmental sources of antibiotic-resistant S. enterica after extreme flood events.

Exploring the Microbial Community and Functional Characteristics of the Livestock Feces Using the Whole Metagenome Shotgun Sequencing

The foodborne illness is the important public health concerns, and the livestock feces are known to be one of the major reservoirs of foodborne pathogens. Also, it was reported that 45.5% of foodborne illness outbreaks have been associated with the animal products contaminated with the livestock feces. In addition, it has been known that the persistence of a pathogens depends on many potential virulent factors including the various virulent genes. Therefore, the first step to understanding the public health risk of livestock feces is to identify and describe microbial communities and potential virulent genes that contribute to bacterial pathogenicity. We used the whole metagenome shotgun sequencing to evaluate the prevalence of foodborne pathogens and to characterize the virulence associated genes in pig and chicken feces. Our data showed that the relative abundance of potential foodborne pathogens, such as Bacillus cereus was higher in chickens than pigs at the species level while the relative abundance of foodborne pathogens including Campylobacter coli was only detected in pigs. Also, the microbial functional characteristics of livestock feces revealed that the gene families related to "Biofilm formation and quorum sensing" were highly enriched in pigs than chicken. Moreover, the variety of gene families associated with "Resistance to antibiotics and toxic compounds" were detected in both animals. These results will help us to prepare the scientific action plans to improve awareness and understanding of the public health risks of livestock feces.

Exploring antibiotic resistance load in paddy-upland rotation fields amended with commercial organic and chemical/slow release fertilizer

Agricultural fertilization caused the dissemination of antibiotic resistance genes (ARGs) in agro-ecological environment, which poses a global threat to crop-food safety and human health. However, few studies are known about the influence of different agricultural fertilization modes on antibiotic resistome in the paddy-upland rotation soils. Therefore, we conducted a field experiment to compare the effect of different fertilization (chemical fertilizer, slow release fertilizer and commercial organic fertilizer replacement at various rates) on soil antibiotic resistome in paddy-upland rotation fields. Results revealed that a total of 100 ARG subtypes and 9 mobile genetic elements (MGEs) occurred in paddy-upland rotation soil, among which MDR-ARGs, MLSB-ARGs and tet-ARGs were the dominant resistance determinants. Long-term agricultural fertilization remarkably facilitated the vertical accumulation of ARGs, in particular that bla _ampC and tetO in relative abundance showed significant enrichment with increasing depth. It's worth noting that slow release fertilizer significantly increased soil ARGs, when comparable to manure with 20% replacing amount, but chemical fertilizer had only slight impact on soil ARGs. Fertilization modes affected soil microbial communities, mainly concentrated in the surface layer, while the proportion of Proteobacteria with the highest abundance decreased gradually with increasing depth. Furthermore, microbial community and MGEs were further proved to be essential factors in regulating the variability of ARGs of different fertilization modes by structural equation model, and had strong direct influence (λ = 0.61, p < 0.05; λ = 0. 55, p < 0.01). The results provided scientific guidance for reducing the spreading risk of ARGs and control ARG dissemination in agricultural fertilization.

High concentration of ammonia sensitizes the response of microbial electrolysis cells to tetracycline

Microbial electrolysis cell (MEC) is a promising technology for effective energy conversion of wastewater organics to biogas. Yet, in swine wastewater treatment, the complex contaminants including antibiotics may affect MEC performance, while the high ammonia concentration might increase this risk by increasing cell membrane permeability. In this work, the responses of MECs on tetracycline (TC) with low and high ammonia loadings (80 and 1000 mg L^-1) were fully investigated. The TC of 0 to 1 mg L^-1 slightly improved MEC performance in current production and electrochemical characteristics with low ammonia loading, while TC ≥ 4 mg L^-1 started to show negative effects. Generally, the high ammonia loading sensitized MECs to TC concentration, inducing the current and COD removal of MECs to sharply decline with TC ≥ 0.5 mg L^-1. The positive effect of high ammonia loading on MEC due to conductivity increase was counteracted with TC ≥ 1 mg L^-1. The co-contamination of TC and ammonia significantly decreased the bioactivity and biomass of anode biofilm. Although the high concentration of co-existing TC and ammonia inhibited MEC performance, the reactors still obtained positive energy feedback. The network analyses indicated that the effluent suspension contributed much to antibiotic resistance gene (ARG) transmission, while the microplastics (MPs) in wastewater greatly raised the risks of ARGs spreading. This work systematically examined the synergetic effects of TC and ammonia and the transmission of ARGs in MEC operation, which is conducive to expediting the application of MECs in swine wastewater treatment.

Current status and future perspective of antimicrobial-resistant bacteria and resistance genes in animal-breeding environments

The emergence and spread of antimicrobial-resistant bacteria (ARB) and antimicrobial resistance genes (ARGs) are a global public health concern. ARB are transmitted directly or indirectly from animals to humans. The importance of environmental transmission of ARB and ARGs has recently been demonstrated, given the relationships between compost, livestock wastewater, insects, and wildlife. In addition, companion animals and their surrounding environments (veterinary hospitals and homes with companion animals) should be considered owing to their close relationship with humans. This review discusses the current status and future perspectives of ARB and ARGs in animal-breeding environments.

Comparative analysis of antibiotic resistance genes on a pig farm and its neighboring fish ponds in a lakeside district

Antibiotics usage in animal production is considered a primary driver of the occurrence, supply and spread of antibiotic resistance genes (ARGs) in the environment. Pig farms and fish ponds are important breeding systems in food animal production. In this study, we compared and analyzed broad ARGs profiles, mobile genetic elements (MGEs) and bacterial communities in a representative pig farm and neighboring fish ponds around Poyang Lake, the largest freshwater lake in China. The factors influencing the distribution of ARGs were also explored. The results showed widespread detection of ARGs (from 57 to 110) among 283 targeted ARGs in the collected water samples. The differences in the number and relative abundance of ARGs observed from the pig farm and neighboring fish ponds revealed that ARG contamination was more serious on the pig farm than in the fish ponds and that the water treatment plant on the pig farm was not very effective. Based on the variance partition analysis (VPA), MGEs, bacterial communities and water quality indicators (WIs) codrive the relative abundance of ARGs. Based on network analysis, we found that total phosphorus and Tp614 were the most important WIs and MGEs affecting ARG abundance, respectively. Our findings provide fundamental data on farms in lakeside districts and provide insights into establishing standards for the discharge of aquaculture wastewater.

Prevalence of High-Risk β-Lactam Resistance Genes in Family Livestock Farms in Danjiangkou Reservoir Basin, Central China

The propagation of antibiotic resistance genes (ARGs) from domestic livestock manure is an unnegligible important environmental problem. There is an increasing need to understand the role of domestic livestock manure in causing antibiotic resistance in the environment to minimize risks to human health. Here, we targeted β-lactam resistance genes (bla genes), primarily discovered in clinical settings, to compare the high-risk ARG profile and their main spreading vectors of 26 family livestock farms in China and analyze the effects of domestic livestock manure on their receiving farmland environments. Results showed that the high-risk bla genes and their spreading carriers were widely prevalent in livestock and poultry manure from family farms. The bla_ampC gene encoding extended-spectrum AmpC β-lactamases, as well as its corresponding spreading carrier (class-1 integron), had the highest occurrence level. The bla gene abundance in family chicken farms was higher than that in family swine and cattle farms, while the bla gene contamination in the feces of laying hens or beef cattle was worse than that in corresponding broiler chickens or dairy cattle. Notably, the application from domestic livestock manure led to substantial emission of bla genes, which significantly increased the abundance of high-risk resistance genes in farmland soil by 12–46 times. This study demonstrated the prevalence and severity of high-risk resistance genes in domestic livestock and poultry manure; meanwhile, the discharge of bla genes also highlighted the need to mitigate the persistence and spread of these elevated high-risk genes in agricultural systems.

Effect of cattle farm exposure on oropharyngeal and gut microbial communities and antibiotic resistance genes in workers

Livestock farms are recognized as the main sources of antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) with potential implications for human health. In this study, we systematically analyzed microbiome composition, distribution of ARGs and mobile genetic elements (MGEs) in the oropharynx and gut of workers in cattle farms and surrounding villagers, cattle feces and farm air, and the relationship of microbial communities among farm air, cattle feces and farmworkers (oropharynx and gut). Exposure to the farm environment may have remodeled farmworkers' oropharynx and gut microbiota, with reduced microbial diversity (P < 0.05) and enrichment of some opportunistic pathogenic bacteria like Shigella, Streptococcus, and Neisseria in the oropharynx. Meanwhile, compared with villagers, ARG abundance in oropharynx of farmworkers increased significantly (P < 0.05), but, no significant difference in gut (P > 0.05). Microbial composition and ARG profile in farmworkers might be influenced by working time and work type, ARG abundance in farmworkers' gut was positively correlated with working time (P < 0.01), and higher ARG abundance was found in the oropharynx of drovers. The network analysis revealed that 4 MGEs (tnpA-01, tnpA-04, Tp614, and IS613), 5 phyla (e.g. Bacteroidetes, Fusobacteria, and TM7), and 6 genera were significantly associated with 37 ARGs (ρ > 0.6, P < 0.01). Overall, our results indicated that farm exposure may have affected the microbial composition and increased ARG abundance of farmworkers. Transmission of some ARGs may have occurred among the environment, animals and humans via host bacteria, which might pose a potential threat to human health.

Antibiotic Resistance: From Pig to Meat

Pork meat is in high demand worldwide and this is expected to increase. Pork is often raised in intensive conditions, which is conducive to the spread of infectious diseases. Vaccines, antibiotics, and other biosafety measures help mitigate the impact of infectious diseases. However, bacterial strains resistant to antibiotics are more and more frequently found in pig farms, animals, and the environment. It is now recognized that a holistic perspective is needed to sustainably fight antibiotic resistance, and that an integrated One Health approach is essential. With this in mind, this review tackles antibiotic resistance throughout the pork raising process, including their microbiome; many factors of their environment (agricultural workers, farms, rivers, etc.); and an overview of the impact of antibiotic resistance on pork meat, which is the end product available to consumers. Antibiotic resistance, while a natural process, is a public health concern. If we react, and act, collectively, it is expected to be, at least partially, reversible with judicious antibiotic usage and the development of innovative strategies and tools to foster animal health.