Impact of dairy manure pre-application treatment on manure composition, soil dynamics of antibiotic resistance genes, and abundance of antibiotic-resistance genes on vegetables at harvest

Differential drivers on the occurrence of antibiotic resistance genes in agricultural soils and crops: Evidence from the different fertilization regimes

Organic fertilizer application caused bacterial resistance contamination in farming systems has been widely documented, and long-term fertilization will exacerbate the migration of antibiotic resistance genes (ARGs) to crops and humans. However, it remains unclear whether a combined pattern of chemical and organic fertilizer application can arrest the high prevalence of ARGs in soil-crop. Here we investigated the ARGs occurrence under different fertilization regimes, and explored the mechanisms by which micro-ecological shifts and geochemical factors in modulating the ARGs fate in soil and crop. The results showed that the soil ARGs abundance was highest under 100% organic fertilizer, while the highest ARGs abundance in crops was observed at 100% chemical fertilizer. Application of organic fertilizers with more than 50% ration intensified the soil accumulation and migration of tetA, sul1, sul2 and macA genes. And, multidrug_transporter, macA and sul1 were co-shared in soil and crop, where ARGs potential hosts differed complete in the two, suggesting that these ARGs may be transferred across media by horizontal transfer. Procrustes analysis revealed that soil microbial community was significantly correlated with ARG hosts, and soil microbial evolutionary pathway was congruent with antibiotic resistance, suggesting that fertilizers affect soil ARGs abundance mainly by altering soil microbial composition and their ecological evolutionary trajectories. While, no significant correlation was observed between endophytes and crop ARG host. Structural equations demonstrated that soil nutrients and crop growth characteristics contributed largely to the prevalence of crop ARGs. This outcome will provide new insights into the high prevalence of ARGs in soil and crop, and offer fertilizer recommendations for effectively curbing antibiotic-resistance contamination in farming systems.

Ceftiofur in swine manure contributes to reducing pathogens and antibiotic resistance genes during composting

Aerobic composting is a common way for the disposal of feces produced in animal husbandry, and can reduce the release of antibiotic resistance genes (ARGs) from feces into the environment. In this study, we collected samples from two distinct treatments of swine manure compost with and without ceftiofur (CEF), and identified the ARGs, mobile genetic elements (MGEs), and bacterial community by metagenomic sequencing. The impacts of CEF on the bacterial community composition and fate of ARGs and MGEs were investigated. With increasing composting temperature and pH, the concentration of CEF in the manure decreased rapidly, with a degradation half-life of 1.12 d and a 100% removal rate after 10 d of aerobic composting. Metagenomics demonstrated that CEF in the manure might inhibit the growth of Firmicutes and Proteobacteria, thereby reducing some ARGs and MGEs hosted by these two bacteria, which was further confirmed by the variations of ARGs and MGEs. A further redundancy analysis suggested that pH and temperature are key environmental factors affecting ARG removal during composting, and intI1 and bacterial communities also have significant influence on ARG abundance. These results are of great significance for promoting the removal of some ARGs from animal manure by controlling some key environmental factors and the type of antibiotics used in animals.

Interplay among manures, vegetable types, and tetracycline resistance genes in rhizosphere microbiome

The rapid global emergence of antibiotic resistance genes (ARGs) is a substantial public health concern. Livestock manure serves as a key reservoir for tetracycline resistance genes (TRGs), serving as a means of their transmission to soil and vegetables upon utilization as a fertilizer, consequently posing a risk to human health. The dynamics and transfer of TRGs among microorganisms in vegetables and fauna are being investigated. However, the impact of different vegetable species on acquisition of TRGs from various manure sources remains unclear. This study investigated the rhizospheres of three vegetables (carrots, tomatoes, and cucumbers) grown with chicken, sheep, and pig manure to assess TRGs and bacterial community compositions via qPCR and high-throughput sequencing techniques. Our findings revealed that tomatoes exhibited the highest accumulation of TRGs, followed by cucumbers and carrots. Pig manure resulted in the highest TRG levels, compared to chicken and sheep manure, in that order. Bacterial community analyses revealed distinct effects of manure sources and the selective behavior of individual vegetable species in shaping bacterial communities, explaining 12.2% of TRG variation. Firmicutes had a positive correlation with most TRGs and the intl1 gene among the dominant phyla. Notably, both the types of vegetables and manures significantly influenced the abundance of the intl1 gene and soil properties, exhibiting strong correlations with TRGs and elucidating 30% and 17.7% of TRG variance, respectively. Our study delineated vegetables accumulating TRGs from manure-amended soils, resulting in significant risk to human health. Moreover, we elucidated the pivotal roles of bacterial communities, soil characteristics, and the intl1 gene in TRG fate and dissemination. These insights emphasize the need for integrated strategies to reduce selection pressure and disrupt TRG transmission routes, ultimately curbing the transmission of tetracycline resistance genes to vegetables.

Environment, animals, and food as reservoirs of antibiotic-resistant bacteria for humans: One health or more?

Antimicrobial resistance (AMR) is a major public health challenge. For several years, AMR has been addressed through a One Health approach that links human health, animal health, and environmental quality. In this review, we discuss AMR in different reservoirs with a focus on the environment. Anthropogenic activities produce effluents (sewage, manure, and industrial wastes) that contaminate soils and aquatic environments with antibiotic-resistant bacteria (ARB), antibiotic-resistant genes (ARGs), and selective agents such as antibiotics, biocides, and heavy metals. Livestock treated with antibiotics can also contaminate food with ARB. In high-income countries (HICs), effective sanitation infrastructure and limited pharmaceutical industries result in more controlled discharges associated with human activities. Hence, studies using genome-based typing methods have revealed that, although rare inter-reservoir transmission events have been reported, human acquisition in HICs occurs primarily through person-to-person transmission. The situation is different in low- and middle-income countries (LMICs) where high population density, poorer sanitation and animal farming practices are more conducive to inter-reservoir transmissions. In addition, environmental bacteria can be a source of ARGs that, when transferred to pathogenic species under antibiotic selection pressure in environmental hotspots, produce new antibiotic-resistant strains that can potentially spread in the human community through human-to-human transmission. The keys to reducing AMR in the environment are (i) better treatment of human waste by improving wastewater treatment plants (WWTPs) in HICs and improving sanitation infrastructure in LMICs, (ii) reducing the use of antibiotics by humans and animals, (iii) prioritizing the use of less environmentally harmful antibiotics, and (iv) better control of pharmaceutical industry waste.

Modelling the impact of wastewater flows and management practices on antimicrobial resistance in dairy farms

Dairy slurry is a major source of environmental contamination with antimicrobial resistant genes and bacteria. We developed mathematical models and conducted on-farm research to explore the impact of wastewater flows and management practices on antimicrobial resistance (AMR) in slurry. Temporal fluctuations in cephalosporin-resistant Escherichia coli were observed and attributed to farm activities, specifically the disposal of spent copper and zinc footbath into the slurry system. Our model revealed that resistance should be more frequently observed with relevant determinants encoded chromosomally rather than on plasmids, which was supported by reanalysis of sequenced genomes from the farm. Additionally, lower resistance levels were predicted in conditions with lower growth and higher death rates. The use of muck heap effluent for washing dirty channels did not explain the fluctuations in cephalosporin resistance. These results highlight farm-specific opportunities to reduce AMR pollution, beyond antibiotic use reduction, including careful disposal or recycling of waste antimicrobial metals.

Metagenomic insights into the impact of litter from poultry Concentrated Animal Feeding Operations (CAFOs) to adjacent soil and water microbial communities

In recent decades, human food consumption has led to an increased demand for animal-based foods, particularly chicken meat production. The state of Georgia, USA is one of the top broiler chicken producers in the United States, where animals are raised in Concentrated Animal Feeding Operations (CAFOs). Without proper management, CAFOs could negatively impact the environment and become a public health risk as a source of water and air pollution and/or by spreading antimicrobial resistance genes. In this study, we used metagenome sequencing to investigate the impact of the application of the CAFO's litter on adjacent soils and downstream creek waters in terms of microbial diversity and antimicrobial resistance profile changes. Our data indicate that while a few microbial groups increased in abundance within a short period of time after litter application, these populations subsequently decreased to levels similar to those found prior to the litter application or to below the detection limit of our metagenome sequencing effort. Microbial taxonomic composition analyses, relative abundance of Metagenome-Assembled Genomes (MAGs) and detection of Antimicrobial Resistance Genes (ARGs) allow us to conclude that this practice of litter application had a negligible effect on the microbiome or resistome profile of these soils and nearby waterways, likely due to its dilution in the field and/or outcompetition by indigenous microbes, revealing a minimal impact of these poultry facilities on the natural microbial communities.

Agroecosystem exploration for Antimicrobial Resistance in Ahmedabad, India: A Study Protocol

Introduction

Antimicrobial resistance (AMR) has emerged as one of the leading threats to public health. AMR possesses a multidimensional challenge that has social, economic, and environmental dimensions that encompass the food production system, influencing human and animal health. The One Health approach highlights the inextricable linkage and interdependence between the health of people, animal, agriculture, and the environment. Antibiotic use in any of these areas can potentially impact the health of others. There is a dearth of evidence on AMR from the natural environment, such as the plant-based agriculture sector. Antibiotics, antibiotic-resistant bacteria (ARB), and related AMR genes (ARGs) are assumed to present in the natural environment and disseminate resistance to fresh produce/vegetables and thus to human health upon consumption. Therefore, this study aims to investigate the role of vegetables in the spread of AMR through an agroecosystem exploration in Ahmedabad, India.

Protocol

The present study will be executed in Ahmedabad, located in Gujarat state in the Western part of India, by adopting a mixed-method approach. First, a systematic review will be conducted to document the prevalence of ARB and ARGs on fresh produce in South Asia. Second, agriculture farmland surveys will be used to collect the general farming practices and the data on common vegetables consumed raw by the households in Ahmedabad. Third, vegetable and soil samples will be collected from the selected agriculture farms and analyzed for the presence or absence of ARB and ARGs using standard microbiological and molecular methods.

Discussion

The analysis will help to understand the spread of ARB/ARGs through the agroecosystem. This is anticipated to provide an insight into the current state of ARB/ARGs contamination of fresh produce/vegetables and will assist in identifying the relevant strategies for effectively controlling and preventing the spread of AMR.

Physico-chemical assessment of on-farm bioconversion of organic waste in dairy farms in context to sustainability and circular bioeconomy

On a milk-producing dairy farm, milk production is correlated with manure production and the number of cattle, and manure is widely used as a soil fertilizer. However, excessive dairy manure production is linked with greenhouse gas emissions and water quality issues. On-farm planning of manure storage and application to enhance soil nutrients are essential in a circular economy to reduce environmental impact, where manure is not landfilled and incinerated. Instead, it creates a nutrient resource for crops and soil. Dairy manure, which is rich in nutrients, is a valuable fertilizer that contains many nutrients such as nitrogen (N), organic matter (OM), phosphorous (P), Potassium (K) and micronutrients. In this work, a pilot field research was conducted between 2016 and 2018 in various parts of California, USA (San Joaquin Valley, Sacramento Valley, Shasta Cascade, and the North Coast of California) to assess physio-chemical characteristics of solid fractions of dairy manure among various dairy farms. A total of 156 samples were collected from the gut (n = 107) and toe (n = 49) of the manure piles across California for determining total solid (TS), volatile solid (VS), temperature, moisture content and carbon-nitrogen ratio (C: N). Here, using the observations of field study and analysis, we show that C: N, OM and MC of solid fractions of dairy manure vary significantly among dairy farms. The average C: N ratio of manure (26-32) among various regions was close to an ideal C: N value of 24:1 for soil microbes to stimulate nutrient release to crops. Manure pH ranged between 7.0 and 8.0, which was close to an optimal pH range for common crops (6.0-8.0). Moreover, considering less cost and surplus availability, manure will likely continue providing a cost-effective organic fertilizer resource compared to commercial chemical fertilizers.

Do contaminants compromise the use of recycled nutrients in organic agriculture? A review and synthesis of current knowledge on contaminant concentrations, fate in the environment and risk assessment

Use of nutrients recycled from societal waste streams in agriculture is part of the circular economy, and in line with organic farming principles. Nevertheless, diverse contaminants in waste streams create doubts among organic farmers about potential risks for soil health. Here, we gather the current knowledge on contaminant levels in waste streams and recycled nutrient sources, and discuss associated risks. For potentially toxic elements (PTEs), the input of zinc (Zn) and copper (Cu) from mineral feed supplements remains of concern, while concentrations of PTEs in many waste streams have decreased substantially in Europe. The same applies to organic contaminants, although new chemical groups such as flame retardants are of emerging concern and globally contamination levels differ strongly. Compared to inorganic fertilizers, application of organic fertilizers derived from human or animal feces is associated with an increased risk for environmental dissemination of antibiotic resistance. The risk depends on the quality of the organic fertilizers, which varies between geographical regions, but farmland application of sewage sludge appears to be a safe practice as shown by some studies (e.g. from Sweden). Microplastic concentrations in agricultural soils show a wide spread and our understanding of its toxicity is limited, hampering a sound risk assessment. Methods for assessing public health risks for organic contaminants must include emerging contaminants and potential interactions of multiple compounds. Evidence from long-term field experiments suggests that soils may be more resilient and capable to degrade or stabilize pollutants than often assumed. In view of the need to source nutrients for expanding areas under organic farming, we discuss inputs originating from conventional farms vs. non-agricultural (i.e. societal) inputs. Closing nutrient cycles between agriculture and society is feasible in many cases, without being compromised by contaminants, and should be enhanced, aided by improved source control, waste treatment and sound risk assessments.

The soil-microbe-plant resistome: A focus on the source-pathway-receptor continuum

The One World, One Health concept implies that antibiotic resistance (AR) in the soil-microbe-plant resistome is intricately linked to the human resistome. However, the literature is mainly confined to sources and types of AR in soils or microbes, but comprehensive reviews tracking AR in the soil-microbe-plant resistome are limited. The present review applies the source-pathway-receptor concept to understand the sources, behaviour, and health hazards of the soil-microbe-plant resistome. The results showed that the soil-microbe-plant system harbours various antibiotic-resistance genes (ARGs), antibiotic-resistant bacteria (ARB), and mobile genetic elements (MGEs). Anthropogenic sources and drivers include soil application of solid waste, wastewater, biosolids, and industrial waste. Water-, wind-, and human-driven processes and horizontal gene transfer circulate AR in the soil-microbe-plant resistome. The AR in bulk soil, soil components that include soil microorganisms, soil meso- and macro-organisms, and possible mechanisms of AR transfer to soil components and ultimately to plants are discussed. The health risks of the soil-microbe-plant resistome are less studied, but potential impacts include (1) the transfer of AR to previously susceptible organisms and other resistomes, including the human resistome. Overall, the study tracks the behaviour and health risks of AR in the soil-plant system. Future research should focus on (1) ecological risks of AR at different levels of biological organization, (2) partitioning of AR among various phases of the soil-plant system, (3) physico-chemical parameters controlling the fate of AR, and (4) increasing research from low-income regions particularly Africa as most of the available literature is from developed countries.

Impacts of irrigation with treated livestock wastewater on the accumulation characteristic of ARGs in the farmland soil: a case study in Hohhot, China

Irrigation with treated livestock wastewater (TWW) is a promising strategy for reusing resources. However, TWW irrigation might introduce antibiotic resistant genes (ARGs) into the soil, posing environmental risks associated with antibiotic resistance. This study focuses on investigating the influence of irrigation amounts and duration on the fate of ARGs and identifies key factors driving their changes. The results showed that there were 13 ARGs in TWW, while only 5 ARGs were detected in irrigated soil. That is some introduced ARGs from TWW could not persistently exist in the soil. After 1-year irrigation, an increase in irrigation amount from 0.016 t/m2 to 0.048 t/m2 significantly enhanced the abundance of tetC by 29.81%, while ermB and sul2 decreased by 45.37% and 76.47%, respectively (p < 0.01). After 2-year irrigation, the abundance of tetC, ermB, ermF, dfrA1, and total ARGs significantly increased (p < 0.05) when the irrigation amount increased. The abundances of ARGs after 2-year irrigation were found to be 2.5-34.4 times higher than 1 year. Obviously, the irrigation years intensified the positive correlation between ARGs abundance and irrigation amount. TetC and ermF were the dominant genes resulting in the accumulation of ARGs. TWW irrigation increased the content of organic matter and total nitrogen in the soil, which affected microbial community structure. The changes of the potential host were the determining factors driving the ARGs abundance. Our study demonstrated that continuous TWW irrigation for 2 years led to a substantial accumulation of ARGs in soil.

A review on the effects of discharging conventionally treated livestock waste to the environmental resistome

Globally, animal production has developed rapidly as a consequence of the ongoing population growth, to support food security. This has consequently led to an extensive use of antibiotics to promote growth and prevent diseases in animals. However, most antibiotics are not fully metabolized by these animals, leading to their excretion within urine and faeces, thus making these wastes a major reservoir of antibiotics residues, antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB) in the environment. Farmers normally depend on conventional treatment methods to mitigate the environmental impact of animal waste; however, these methods are not fully efficient to remove the environmental resistome. The present study reviewed the variability of residual antibiotics, ARB, as well as ARGs in the conventionally treated waste and assessed how discharging it could increase resistome in the receiving environments. Wherein, considering the efficiency and environmental safety, an addition of pre-treatments steps with these conventional treatment methods could enhance the removal of antibiotic resistance agents from livestock waste.

Influence of the Antibiotic Oxytetracycline on the Morphometric Characteristics and Endophytic Bacterial Community of Lettuce (Lactuca sativa L.)

Antibiotics enter the soil with compost prepared from livestock manures and other sources. There is concern that they may influence plant growth and cause antibiotic resistance in soil and plant endospheric microbiomes. In the present work, lettuce plants were cultivated in soil and hydroponics spiked with oxytetracycline (0, 15, and 300 mg × kg-1 and 0, 15, and 50 mg × L-1, respectively) during a 28-day greenhouse experiment. It was revealed that the antibiotic reduced the chlorophyll content, the biomass, and the length of the roots and stems by 1.4-4.7, 1.8-39, 2.5-3.2, and 1.8-6.3 times in soil and in hydroponics. The copy numbers of the tet(A) and tet(X) genes were revealed to be 4.51 × 103-1.58 × 105 and 8.36 × 106-1.07 × 108 copies × g-1, respectively, suggesting the potential migration of these genes from soil/hydroponics to plant roots and leaves. According to a non-metric multidimensional scaling (NMDS) analysis of the 16S rRNA amplicon sequencing data, endospheric bacterial communities were similar in leaves and roots independent of the growing substrate and antibiotic concentration. While soil bacterial communities were unaffected by the presence of antibiotics, hydroponic communities exhibited dependency, likely attributable to the absence of the mitigating effect of soil particle absorption.

Dual Activation of Peroxymonosulfate Using MnFe2O4/g-C3N4 and Visible Light for the Efficient Degradation of Steroid Hormones: Performance, Mechanisms, and Environmental Impacts

Single activation of peroxymonosulfate (PMS) in a homogeneous system is sometimes insufficient for producing reactive oxygen species (ROS) for water treatment applications. In this work, manganese spinel ferrite and graphitic carbon nitride (MnFe2O4/g-C3N4; MnF) were successfully used as an activator for PMS under visible light irradiation to remove the four-most-detected-hormone-contaminated water under different environmental conditions. The incorporation of g-C3N4 in the nanocomposites led to material enhancements, including increased crystallinity, reduced particle agglomeration, amplified magnetism, improved recyclability, and increased active surface area, thereby facilitating the PMS activation and electron transfer processes. The dominant active radical species included singlet oxygen (1O2) and superoxide anions (O2•-), which were more susceptible to the estrogen molecular structure than testosterone due to the higher electron-rich moieties. The self-scavenging effect occurred at high PMS concentrations, whereas elevated constituent ion concentrations can be both inhibitors and promoters due to the generation of secondary radicals. The MnF/PMS/vis system degradation byproducts and possible pathways of 17β-estradiol and 17α-methyltestosterone were identified. The impact of hormone-treated water on Oryza sativa L. seed germination, shoot length, and root length was found to be lower than that of untreated water. However, the viability of both ELT3 and Sertoli TM4 cells was affected only at higher water compositions. Our results confirmed that MnF and visible light could be potential PMS activators due to their superior degradation performance and ability to produce safer treated water.

Long-term impacts of conservation pasture management in manuresheds on system-level microbiome and antibiotic resistance genes

Animal manure improves soil fertility and organic carbon, but long-term deposition may contribute to antibiotic resistance genes (ARGs) entering the soil-water environment. Additionally, long-term impacts of applying animal manure to soil on the soil-water microbiome, a crucial factor in soil health and fertility, are not well understood. The aim of this study is to assess: (1) impacts of long-term conservation practices on the distribution of ARGs and microbial dynamics in soil, and runoff; and (2) associations between bacterial taxa, heavy metals, soil health indicators, and ARGs in manures, soils, and surface runoff in a study following 15 years of continuous management. This management strategy consists of two conventional and three conservation systems, all receiving annual poultry litter. High throughput sequencing of the 16S ribosomal RNA was carried out on samples of cattle manure, poultry litter, soil, and runoff collected from each manureshed. In addition, four representative ARGs (intl1, sul1, ermB, and blactx-m-32) were quantified from manures, soil, and runoff using quantitative PCR. Results revealed that conventional practice increased soil ARGs, and microbial diversity compared to conservation systems. Further, ARGs were strongly correlated with each other in cattle manure and soil, but not in runoff. After 15-years of conservation practices, relationships existed between heavy metals and ARGs. In the soil, Cu, Fe and Mn were positively linked to intl1, sul1, and ermB, but trends varied in runoff. These findings were further supported by network analyses that indicated complex co-occurrence patterns between bacteria taxa, ARGs, and physicochemical parameters. Overall, this study provides system-level linkages of microbial communities, ARGs, and physicochemical conditions based on long-term conservation practices at the soil-water-animal nexus.

Microbial Risks Caused by Livestock Excrement: Current Research Status and Prospects

Livestock excrement is a major pollutant yielded from husbandry and it has been constantly imported into various related environments. Livestock excrement comprises a variety of microorganisms including certain units with health risks and these microorganisms are transferred synchronically during the management and utilization processes of livestock excrement. The livestock excrement microbiome is extensively affecting the microbiome of humans and the relevant environments and it could be altered by related environmental factors as well. The zoonotic microorganisms, extremely zoonotic pathogens, and antibiotic-resistant microorganisms are posing threats to human health and environmental safety. In this review, we highlight the main feature of the microbiome of livestock excrement and elucidate the composition and structure of the repertoire of microbes, how these microbes transfer from different spots, and they then affect the microbiomes of related habitants as a whole. Overall, the environmental problems caused by the microbiome of livestock excrement and the potential risks it may cause are summarized from the microbial perspective and the strategies for prediction, prevention, and management are discussed so as to provide a reference for further studies regarding potential microbial risks of livestock excrement microbes.

The impact of antibiotic residues on resistance patterns in leek at harvest

When crops are cultivated on fields fertilized with animal manure, the risk exists that plants may take up antibiotic residues and may be exposed to antibiotic resistance genes and antibiotic resistant bacteria. During cultivation in a greenhouse pot experiment, leek (Allium porrum) was fertilized with either pig slurry or mineral fertilizer and exposed to either no antibiotics, doxycycline (10,000 μg/kg manure), sulfadiazine (1000 μg/kg manure), or lincomycin (1000 μg/kg manure). At harvest, 4.5 months later, lincomycin, sulfadiazine or doxycycline were not detected in any of the leek samples nor in their corresponding soil samples. Further, antimicrobial susceptibility testing was performed on 181 Bacillus cereus group isolates and 52 Pseudomonas aeruginosa isolates from the grown leek. For the B. cereus group isolates, only a small shift in MIC50 for lincomycin was observed among isolates from the lincomycin and control treatment. For P. aeruginosa, only in the setup with doxycycline treatment a higher MIC50 for doxycycline was observed compared to the control, specifically the isolates selected from growth media supplemented with 8 mg/L doxycycline. Nine antibiotic resistance genes (tet(B), tet(L), tet(M), tet(O), tet(Q), tet(W), erm(B), erm(F) and sul2) were investigated at harvest in the leek and soil samples. In the leek samples, none of the antibiotic resistance genes were detected. In the soil samples fertilized with pig slurry, the genes erm(B), erm(F), tet(M), sul2, tet(W) and tet(O) were detected in significantly higher copy numbers in the lincomycin treatment as compared to the other antibiotic treatments. This could be due to a shift in soil microbiota induced by the addition of lincomycin. The results of this study indicate that consumption of leek carries a low risk of exposure to antibiotic residues or antibiotic resistance to doxycycline, sulfadiazine or lincomycin.

Composting reduces the risks of antibiotic resistance genes in maize seeds posed by gentamicin fermentation waste

Using high-throughput quantitative PCR and next generation sequencing, the impact of land application of raw and composted gentamicin fermentation waste (GFW) on antibiotic resistance genes (ARGs) in maize seeds was studied in a three-year field trial. The raw and composted GFW changed both the bacterial community composition and the ARGs diversity in the maize seeds compared to non-amended controls and chemical fertilizer. The abundance of ARGs after raw GFW amendment was significantly higher than other treatments because of a high abundance of aadA1, qacEdeltal and aph(2')-Id-02; probably induced by gentamicin selection pressure in maize tissues. Meanwhile, the potential host of these three ARGs, pathogenic bacteria Tenacibaculum, also increased significantly in maize seeds after the application of raw GFW. But our result proved that composting could weaken the risk posed by GFW. We further reveal that the key biotic driver for shaping the ARG profiles in maize seeds is bacterial community followed by heavy metal resistance genes, and ARGs are more likely located on bacterial chromosomes. Our findings provide new insight into ARGs dispersal mechanism in maize seeds after long-term GFW application, demonstrate the potential benefits of composting the GFW to reduce risks as well as the potential efficient management method to GFW.

Comparison of soil and grass microbiomes and resistomes reveals grass as a greater antimicrobial resistance reservoir than soil

Grasslands cover a large proportion of global agricultural landmass used to feed herbivores and ruminants and link the environment to the food chain via animals onto humans. However, most scientific studies of antimicrobial resistance and microbiomes at the environmental - animal nexus have focused on soil or vegetables rather than grasslands. Based on previous microbiome phyllosphere-soil studies we hypothesised that the microbiome and resistomes across soil and grass would have a core of shared taxa and antimicrobial resistance genes (ARGs), but that in addition each would also have a minority of unique signatures. Our data indicated grass contained a wider variety and higher relative abundance of ARGs and mobile genetic elements (MGEs) than soil with or without slurry amendments. The microbiomes of soil and grass were similar in content but varied in the composition proportionality. While there were commonalities across many of the ARGs present in soil and on grass their correlations with MGEs and bacteria differed, suggesting a source other than soil is also relevant for the resistome of grass. The variations in the relative abundances of ARGs in soil and on grass also indicated that either the MGEs or the bacteria carrying the ARGs comprised a higher relative abundance on grass than in soil. We conclude that while soil may be a source of some of these genes it cannot be the source for all ARGs and MGEs. Our data identifies grass as a more diverse and abundant reservoir of ARGs and MGEs in the environment than soil, which is significant to human and animal health when viewed in the context of grazing food animals.

Facultative pathogenic bacteria and antibiotic resistance genes in swine livestock manure and clinical wastewater: A molecular biology comparison

Manure contains vast amounts of biological contaminants of veterinary origin. Only few studies analyse clinically critical resistance genes against reserve antibiotics in manure. In general, resistances against these high priority antibiotics involve a high potential health risk. Therefore, their spread in the soil as well as the aquatic environment has to be prevented. Manures of 29 different swine livestock were analysed. Abundances of facultative pathogenic bacteria including representatives of the clinically critical ESKAPE-pathogens (P. aeruginosa, K. pneumoniae, A. baumannii, E. faecium) and E. coli were investigated via qPCR. Antibiotic resistance genes against commonly used veterinary antibiotics (ermB, tetM, sul1) as well as various resistance genes against important (mecA, vanA) and reserve antibiotics (bla_NDM, bla_KPC3, mcr-1), which are identified by the WHO, were also obtained by qPCR analysis. The manures of all swine livestock contained facultative pathogenic bacteria and commonly known resistance genes against antibiotics used in veterinary therapies, but more important also a significant amount of clinically critical resistance genes against reserve antibiotics for human medicine. To illustrate the impact the occurrence of these clinically critical resistance genes, comparative measurements were taken of the total wastewater of a large tertiary care hospital (n = 8). Both manure as well as raw hospital wastewaters were contaminated with significant abundances of gene markers for facultative pathogens and with critical resistance genes of reserve antibiotics associated with genetic mobile elements for horizontal gene transfer. Hence, both compartments bear an exceptional potential risk for the dissemination of facultative pathogens and critical antibiotic resistance genes.

Antimicrobial Resistance and Its Drivers-A Review

Antimicrobial resistance (AMR) is a critical issue in health care in terms of mortality, quality of services, and financial damage. In the battle against AMR, it is crucial to recognize the impacts of all four domains, namely, mankind, livestock, agriculture, and the ecosystem. Many sociocultural and financial practices that are widespread in the world have made resistance management extremely complicated. Several pathways, including hospital effluent, agricultural waste, and wastewater treatment facilities, have been identified as potential routes for the spread of resistant bacteria and their resistance genes in soil and surrounding ecosystems. The overuse of uncontrolled antibiotics and improper treatment and recycled wastewater are among the contributors to AMR. Health-care organizations have begun to address AMR, although they are currently in the early stages. In this review, we provide a brief overview of AMR development processes, the worldwide burden and drivers of AMR, current knowledge gaps, monitoring methodologies, and global mitigation measures in the development and spread of AMR in the environment.

Impact of mesophilic anaerobic digestion and post-treatment of digestates on the transfer of conjugative antimicrobial resistance plasmids

Manure is a major source of antimicrobial-resistant bacteria and resistance genes carried by mobile genetic elements such as plasmids. In France, the number of on-farm biogas plants has increased significantly in recent years. Our study investigated the impact of mesophilic anaerobic digestion (AD) and the post-treatment of digestates on the fate of conjugative plasmids, along with their potential transfer of antimicrobial resistance. Samples of raw manure, digestates and post-treated digestates were collected from three on-farm biogas plants. Conjugative plasmids were captured using the Escherichia coli CV601 recipient strain and media supplemented with rifampicin and kanamycin - to which the recipient strain is resistant - and tetracycline, sulfamethoxazole, gentamicin, trimethoprim, amoxicillin, cefotaxime, ciprofloxacin or colistin. Putative transconjugants were identified and characterised by disc diffusion and whole genome sequencing. The results showed that the antimicrobial resistance genes transferred from the different matrices conferred resistance to tetracyclines, sulphonamides, trimethoprim, and/or streptomycin. Transconjugants were obtained from raw manure samples but not from digestates or post-digestates, suggesting that mesophilic AD processes may produce fewer conjugative plasmids potentially able to be transferred to Enterobacterales.

Distribution of quinolone and macrolide resistance genes and their co-occurrence with heavy metal resistance genes in vegetable soils with long-term application of manure

The spread of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) has become an increasingly serious global public health issue. This study investigated the distribution characteristics and influencing factors of ARB and ARGs in greenhouse vegetable soils with long-term application of manure. Five typical ARGs, four heavy metal resistance genes (MRGs), and two mobile genetic elements (MGEs) were quantified by real-time quantitative polymerase chain reaction (qPCR). The amount of ARB in manure-improved soil greatly exceeded that in control soil, and the bacterial resistance rate decreased significantly with increases in antibiotic concentrations. In addition, the resistance rate of ARB to enrofloxacin (ENR) was lower than that of tylosin (TYL). Real-time qPCR results showed that long-term application of manure enhanced the relative abundance of ARGs in vegetable soils, and the content and proportion of quinolone resistance genes were higher than those of macrolide resistance genes. Redundancy analysis (RDA) showed that qepA and qnrS significantly correlated with total and available amounts of Cu and Zn, highlighting that certain heavy metals can influence persistence of ARGs. Integrase gene intI1 correlated significantly with the relative abundance of qepA, qnrS, and ermF, suggesting that intI1 played an important role in the horizontal transfer of ARGs. Furthermore, there was a weakly but not significantly positive correlation between specific detected MRGs and ARGs and MGEs. The results of this study enhance understanding the potential for increasing ARGs in manure-applied soil, assessing ecological risk and reducing the spread of ARGs.

Metagenomic insights into the antibiotic resistomes of typical Chinese dairy farm environments

Antibiotic resistance genes (ARGs) in the environment pose a threat to human and animal health. Dairy cows are important livestock in China; however, a comprehensive understanding of antibiotic resistance in their production environment has not been well clarified. In this study, we used metagenomic methods to analyze the resistomes, microbiomes, and potential ARG bacterial hosts in typical dairy farm environments (including feces, wastewater, and soil). The ARGs resistant to tetracyclines, MLS, β-lactams, aminoglycoside, and multidrug was dominant in the dairy farm ecosystem. The abundance and diversity of total ARGs in dairy feces and wastewater were significantly higher than in soil (P &lt; 0.05). The same environmental samples from different dairy have similar resistomes and microbiomes. A high detection rate of tet(X) in wastewater and feces (100% and 71.4%, respectively), high abundance (range from 5.74 to 68.99 copies/Gb), and the finding of tet(X5) challenged the clinical application of the last antibiotics resort of tigecycline. Network analysis identified Bacteroides as the dominant genus in feces and wastewater, which harbored the greatest abundance of their respective total ARG coverage and shared ARGs. These results improved our understanding of ARG profiles and their bacterial hosts in dairy farm environments and provided a basis for further surveillance.

Long-term manure inputs induce a deep selection on agroecosystem soil antibiotic resistome

Although the enrichment of antibiotic resistance genes (ARGs) in diverse organic soils have been explored, understanding of the ecological processes governing the composition of ARGs in long-term organically fertilized soils still remains limited across typical agricultural regions. Thus, the distribution and assembly of ARG profile in three typical agricultural soils (black soil, fluvo-aquic soil, and red soil) under long-term contrasting fertilization regimes (chemical-only vs organic-only) were investigated using high-throughput qPCR (HT-qPCR). The application of organic manure significantly increased the abundance and number of ARGs across soils, as compared to those with chemical fertilizer. Organic manure application enriched the abundance of mobile genetic elements (MGEs), which were positively associated with ARGs. In addition, it is long-term organic fertilizer that enriched the number and abundance of opportunist and specialist ARGs in the fluvo-aquic and red soils, but not black soils. The number and abundance of most generalist ARGs did not change significantly among different fertilization or soil types. The assembly process of the ARG profiles tends to be more deterministic in organically fertilized soils than in chemically fertilized soils. These results suggest that long-term organic fertilizer application may contribute to the persistence and health risk of the soil antibiotic resistomes (especially specialist ARGs).

Metagenomic tracking of antibiotic resistance genes through a pre-harvest vegetable production system: an integrated lab-, microcosm- and greenhouse-scale analysis

Prior research demonstrated the potential for agricultural production systems to contribute to the environmental spread of antibiotic resistance genes (ARGs). However, there is a need for integrated assessment of critical management points for minimizing this potential. Shotgun metagenomic sequencing data were analysed to comprehensively compare total ARG profiles characteristic of amendments (manure or compost) derived from either beef or dairy cattle (with and without dosing antibiotics according to conventional practice), soil (loamy sand or silty clay loam) and vegetable (lettuce or radish) samples collected across studies carried out at laboratory-, microcosm- and greenhouse-scale. Vegetables carried the greatest diversity of ARGs (n = 838) as well as the most ARG-mobile genetic element co-occurrences (n = 945). Radishes grown in manure- or compost-amended soils harboured a higher relative abundance of total (0.91 and 0.91 ARGs/16S rRNA gene) and clinically relevant ARGs than vegetables from other experimental conditions (average: 0.36 ARGs/16S rRNA gene). Lettuce carried the highest relative abundance of pathogen gene markers among the metagenomes examined. Total ARG relative abundances were highest on vegetables grown in loamy sand receiving antibiotic-treated beef amendments. The findings emphasize that additional barriers, such as post-harvest processes, merit further study to minimize potential exposure to consumers.

The overlap of soil and vegetable microbes drives the transfer of antibiotic resistance genes from manure-amended soil to vegetables

Livestock manure, as a major source of antibiotic resistance genes (ARGs), could further transfer ARGs from soil to vegetables when it's used as fertilizer in field and then pose threat to human health. Meanwhile, manure inputs and vegetable planting also affect soil bacterial communities, but these effects on the transmission of ARGs from soil to vegetable is still lacking. Here, lettuce and endive were cultivated in manure-amended soils using pot experiment. The distribution of bacterial community, ARGs and intI1 gene were studied in manure-amended soil and vegetable roots and leaves at harvest. High-throughput sequencing analysis demonstrated that planting vegetables exerted significant effect on soil bacterial communities, which partly explained the decrease of certain ARGs and the intI1 gene in planted soil than in control soil. ARGs in vegetable and soil were interconnected. The bacterial community compositions among root endophyte, leaf endophyte, and phyllosphere were varied by Hierarchical clustering analysis. Higher abundance of shared bacterial taxa was found between root endophytes and soil microbes, which could lead to a relative higher detection frequency of ARGs in root endophyte. Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes were dominant in the plant endophyte and phyllosphere microbes and had intensive correlations with ARGs. Taken together, our findings provided valuable insights into the role of bacterial community structure in the dissemination of ARGs from manure-amended soil to vegetables.

Fate of Clostridia and other spore-forming Firmicute bacteria during feedstock anaerobic digestion and aerobic composting

Pathogenic spore-forming Firmicutes are commonly present in animal and human wastes that are used as fertilizers in crop production. Pre-treatments of organic waste prior to land application offer the potential to abate enteric microorganisms, and therefore reduce the risk of contamination of crops or adjacent water resources with pathogens carried in these materials. The inactivation and reduction of gram-positive spore formers such as Clostridium spp., Clostridioides spp. and Bacillus spp. from animal and human waste can be challenging given the recalcitrance of the spores these bacteria produce. Given the significance of these organisms to human and animal health, information concerning spore-forming bacteria inactivation during anaerobic digestion (AD) and aerobic composting (AC) is required as the basis for recommending safe organic waste management practices. In this review, an assessment of the inactivation of spore-forming Firmicutes during AD and AC was conducted to provide guidance for practical management of organic matrices of animal or human origin. Temperature and pH may be the main factors contributing to the inactivation of spore-forming Firmicutes during batch lab-scale AD (log reduction <0.5-5 log). In continuous digesters, wet AD systems do not effectively inactivate spore-forming Firmicutes even under thermopholic conditions (log reduction -1.09 - 0.98), but dry AD systems could be a feasible management practice to inactivate spore-forming Firmicutes from organic materials with high solid content (log reduction 1.77-3.1). In contrast, composting is an effective treatment to abate spore-forming Firmicutes (log reduction 1.7-6.5) when thermophilic conditions last at least six consecutive days. Temperature, moisture content and composting scale are the key operating conditions influencing the inactivation of spore-forming Firmicutes during composting. Where possible, undertaking AD with subsequent composting to ensure the biosafety of digestate before its downstream processing and recycling is recommended to abate recalcitrant bacteria in digestate.

Fate of bacterial community, antibiotic resistance genes and gentamicin residues in soil after three-year amendment using gentamicin fermentation waste

Over a three-year field trial, the impacts of composted and raw gentamicin fermentation waste (GFW) application to land on residual soil gentamicin levels, physicochemical properties, bacterial community composition, and antibiotic resistance genes (ARGs) were assessed. In the saline-alkali soil tested, GFW application decreased electrical conductivity (EC) and pH. Importantly, there was no measurable long-term accumulation of gentamicin as a result of GFW addition. Changes in the abundance of Bacillus was primarily associated with degradation of gentamicin in soil, whereas wider (i.e. more general) shifts in bacterial communities over the treatments was linked to alteration of soil physicochemical properties, particularly pH, total nitrogen, dissolved organic carbon, EC, NO₃^--N and NH₄⁺-N. Compared with other treatments, soils receiving composted GFW harbored more types of ARGs and significantly higher (P < 0.05) abundances of mobile genes elements (MGEs) (especially IncQ and Int1) and aminoglycoside ARGs (especially aminoglycoside phosphotransferases genes, APH). Finally, the abundances of ARGs in soils receiving raw and composted GFW were 59.60% and 50.26% higher than that in soils only receiving chemical fertilizer, respectively. Specifically, the abundances of APH, especially strB, were significantly higher than other kinds of ARGs (P < 0.05). The results of linear regression and partial least squares path model showed that MGEs, including plasmids, integrons, and transposons, along with soil properties (EC and NH₄⁺-N) were the main factors associated with change in ARGs. Furthermore, different MGEs were involved in different transfer mechanisms of specific ARGs. Our findings demonstrated the potential risks of using raw and composted GFW as fertilizer, and suggest potential solutions to this problem.

Influence of Dairy Cows Bedding Material on the Microbial Structure and Antibiotic Resistance Genes of Milk

The presence of pathogenic bacteria and antibiotic resistance genes (ARGs) in milk are among the most important issues related to the safety of dairy products and the health of consumers. However, despite that dairy cow are housed for long periods of time on different beddings, the effect of different bedding materials on the microbiota and presence of ARGs is unclear. In this study, the composition of microorganisms, and the presence of mastitis pathogens and 33 ARGs targeting seven antibiotics in raw milk produced from farms using sand bedding, rice husk bedding, and recycled manure solids (RMS) bedding were compared by amplicon sequencing and real-time quantitative PCR. The results showed that the microbial composition of milk was related to the microbiota of bedding. None of the mastitis pathogens were detected in milk from cows housed on sand bedding (S-M). The proportion of ARGs was highest in the S-M group and lowest in the milk from cows housed on RMS bedding (RMS-M) group. In general, the content of ARGs in RMS-M was the lowest, however, the RMS bedding may pose a threat to the breast health of dairy cows.

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.

From gut to mud: dissemination of antimicrobial resistance between animal and agricultural niches

With increasing reports on antimicrobial resistance (AMR) in humans, animals and the environment, we are at risk of returning to a pre-antibiotic era. Therefore, AMR is recognized as one of the major global health threats of this century. Antibiotics are used extensively in farming systems to treat and prevent infections in food animals or to increase their growth. Besides the risk of a transfer of AMR between the human and the animal sector, there is another yet largely overlooked sector in the One Health triad. Human-dominated ecosystems such as agricultural soils are a major sink for antibiotics and AMR originating from livestock farming. This review summarizes current knowledge on the prevalence of AMR at the interface of animal and agricultural production and discusses the potential implications for human health. Soil resistomes are augmented by the application of manure from treated livestock. Subsequent transfer of AMR into plant microbiomes may likely play a critical role in human exposure to antibiotic resistance in the environment. Based on the knowledge that is currently available we advocate that more attention should be paid to the role of environmental resistomes in the AMR crisis.

Characteristics and Global Occurrence of Human Pathogens Harboring Antimicrobial Resistance in Food Crops: A Scoping Review

Background

The role of the crop environment as a conduit for antimicrobial resistance (AMR) through soil, water, and plants has received less attention than other sectors. Food crops may provide a link between the agro-environmental reservoir of AMR and acquisition by humans, adding to existing food safety hazards associated with microbial contamination of food crops.

Objectives

The objectives of this review were: (1) to use a systematic methodology to characterize AMR in food crop value chains globally, and (2) to identify knowledge gaps in understanding exposure risks to humans.

Methods

Four bibliographic databases were searched using synonyms of AMR in food crop value chains. Following two-stage screening, phenotypic results were extracted and categorized into primary and secondary combinations of acquired resistance in microbes of concern based on established prioritization. Occurrence of these pathogen-AMR phenotype combinations were summarized by sample group, value chain stage, and world region. Sub-analyses on antimicrobial resistance genes (ARG) focused on extended-spectrum beta-lactamase and tetracycline resistance genes.

Results

Screening of 4,455 citations yielded 196 studies originating from 49 countries, predominantly in Asia (89 studies) and Africa (38). Observations of pathogen-phenotype combinations of interest were reported in a subset of 133 studies (68%). Primary combinations, which include resistance to antimicrobials of critical importance to human medicine varied from 3% (carbapenem resistance) to 13% (fluoroquinolones), whereas secondary combinations, which include resistance to antimicrobials also used in agriculture ranged from 14% (aminoglycoside resistance) to 20% (aminopenicillins). Salad crops, vegetables, and culinary herbs were the most sampled crops with almost twice as many studies testing post-harvest samples. Sub-analysis of ARG found similar patterns corresponding to phenotypic results.

Discussion

These results suggest that acquired AMR in opportunistic and obligate human pathogens is disseminated throughout food crop value chains in multiple world regions. However, few longitudinal studies exist and substantial heterogeneity in sampling methods currently limit quantification of exposure risks to consumers. This review highlights the need to include agriculturally-derived AMR in monitoring food safety risks from plant-based foods, and the challenges facing its surveillance.

Transport of Veterinary Antibiotics in Farmland Soil: Effects of Dissolved Organic Matter

The application of manure as a fertiliser to farmland is regarded as a major source of veterinary antibiotic (VA) contamination in the environment. The frequent detection of such emerging contaminants and their potential adverse impacts on the ecosystem and human health have provoked increasing concern for VA transport and fate. Extrinsic dissolved organic matter (DOM) may be introduced into farmland soil along with Vas, and thus exert significant effects on the transport of VAs via hydrological processes upon rainfall. The leaching of VAs can be either enhanced or reduced by DOM, depending on the nature, mobility, and interactions of VAs with DOM of different origins. From the aspect of the diversity and reactivity of DOM, the state-of-the-art knowledge of DOM−VA interactions and their resulting effects on the sorption−desorption and leaching of VAs in farmland soil was reviewed. Spectroscopic techniques for examining the extent of binding and reactive components of DOM with VAs are summarized and their usefulness is highlighted. Models for simulating VA transport under the effects of DOM were also reviewed. It is suggested that distinct impacts of DOM of various organic fertiliser/amendment origins should be considered for predicting the transport of VAs in farmland soil.

Environmental contamination in a high-income country (France) by antibiotics, antibiotic-resistant bacteria, and antibiotic resistance genes: Status and possible causes

Antimicrobial resistance (AMR) is a major global public health concern, shared by a large number of human and animal health actors. Within the framework of a One Health approach, actions should be implemented in the environmental realm, as well as the human and animal realms. The Government of France commissioned a report to provide policy and decision makers with an evidential basis for recommending or taking future actions to mitigate AMR in the environment. We first examined the mechanisms that underlie the emergence and persistence of antimicrobial resistance in the environment. This report drew up an inventory of the contamination of aquatic and terrestrial environments by AMR and antibiotics, anticipating that the findings will be representative of some other high-income countries. Effluents of wastewater treatment plants were identified as the major source of contamination on French territory, with spreading of organic waste products as a more diffuse and incidental contamination of aquatic environments. A limitation of this review is the heterogeneity of available data in space and time, as well as the lack of data for certain sources. Comparing the French Measured Environmental Concentrations (MECs) with predicted no effect concentrations (PNECs), fluoroquinolones and trimethoprim were identified as representing high and medium risk of favoring the selection of resistant bacteria in treated wastewater and in the most contaminated rivers. All other antibiotic molecules analyzed (erythromycin, clarithromycin, azithromycin, tetracycline) were at low risk of resistance selection in those environments. However, the heterogeneity of the data available impairs their full exploitation. Consequently, we listed indicators to survey AMR and antibiotics in the environment and recommended the harmonization of sampling strategies and endpoints for analyses. Finally, the objectives and methods used for the present work could comprise a useful example for how national authorities of countries sharing common socio-geographic characteristics with France could seek to better understand and define the environmental dimension of AMR in their particular settings.

Contamination of hay and haylage with enteric bacteria and selected antibiotic resistance genes following fertilization with dairy manure or biosolids

The present study evaluated if enteric bacteria or antibiotic resistance genes carried in fecal amendments contaminate the hay at harvest, representing a potential route of exposure to ruminants that consume the hay. In field experiments, dairy manure was applied to a hay field for three successive growing seasons, and biosolids applied to a hay field for one growing season. Various enteric bacteria in the amendments were enumerated by viable plate count, and selected gene targets were quantified by qPCR. Key findings include the following: At harvest, hay receiving dairy manure or biosolids did not carry more viable enteric bacteria than did hay from unamended control plots. Fermentation of hay did not result in a detectable increase in viable enteric bacteria. The application of dairy manure or biosolids did result in a few gene targets being more abundant on hay at the first harvest. Fermentation of hay did result in an increase in the abundance of gene targets, but this occurred both with hay from amended and control plots. Overall, application of fecal amendments will result in an increase in the abundance of some gene targets associated with antibiotic resistance on first cut hay.

Effects of tetracycline antibiotics in chicken manure on soil microbes and antibiotic resistance genes (ARGs)

China is the world's largest livestock and poultry breeding country, but also the largest use of veterinary antibiotics. When a large amount of chicken manure is applied to the soil, it will cause the number of antibiotic residues and resistant bacteria to increase, which will bring about the pollution of antibiotic resistance genes (ARGs) in the soil, and then increase the risk of environmental pollution and human health. Field experiments were conducted to study the changes of soil tetracycline antibiotic residues, resistant bacteria and resistance genes treated with different types and dosage of chicken manure (no chicken manure, (CK), low fresh chicken manure treatment (300 kg·667 m^-2), high fresh chicken manure treatment (600 kg·667 m^-2), low decomposed chicken manure treatment (300 kg·667 m^-2) and high decomposed chicken manure treatment (600 kg·667 m^-2)). After one-year application of chicken manure, content of soil organic matter increased by 1.0%-3.2% compared with the control. The activity of soil catalase significantly increased by 84.3-91.5%, 81.9-102.9% in fresh and decomposed chicken manure treatments compared with the control, respectively. The amount of soil resistant bacteria under the same treatment was in the order of Anti-OTC > Anti-TC > Anti-CTC. After one-year application of chicken manure, the total tetracycline amount in the soil was increased by 168.5-217.9% compared with the control. The amount of antibiotic residue in soil treated with fresh chicken manure was 3.0-9.1% higher than that treated with decomposed chicken manure. The abundance of ARGs in the soil was in the order of that treated with high fresh chicken manure > low fresh chicken manure > high decomposed chicken manure > low decomposed chicken manure. The risk of tetracycline antibiotics to soil ecological environment may be greatly reduced after chicken manure decomposed.

The vertical migration of antibiotic-resistant genes and pathogens in soil and vegetables after the application of different fertilizers

The prevalence of bacterial resistance caused by the application of animal manure has become an important environmental issue. Herein, the vertical migration of antibiotic resistance genes (ARGs) and pathogens in soil and vegetables after the application of different fertilizers was explored. The results showed that the application of composted manure considerably enhanced the abundance of most ARGs and pathogens, especially in surface soil and pakchoi roots. Moreover, the soil ARGs increased partially from log 1.93 to log 4.65 after the application of composted manure, and six pathogens were simultaneously detected. It was observed that the increase in soil depth decreased most ARGs and pathogens by log 1.04-2.24 and 53.98 %~85.54 %, respectively. This indicated that ARGs and pathogens still existed in the deep soil (80-100 cm). Moreover, total organic carbon had a significant influence on the pathogen distribution, whereas bacterial communities primarily drove the vertical migration of ARGs rather than environmental factors. Although most of the ARG-host associations observed in the surface soil were disappeared in deep soil as revealed by network analysis, some co-occurrence pattern still occurred in deep soil, suggesting that some ARGs might be carried to deep soil by their host bacteria. These results were novel in describing the vertical migration of ARGs in the environment after the application of different fertilizers, providing ideas for curbing their migration to crops.

Impact of chicken litter pre-application treatment on the abundance, field persistence, and transfer of antibiotic resistant bacteria and antibiotic resistance genes to vegetables

Treatment of manures prior to land application can potentially reduce the abundance of antibiotic resistance genes and thus the risk of contaminating crops or water resources. In this study, raw and composted chicken litter were applied to field plots that were cropped to carrots, lettuce and radishes. Vegetables were washed per normal culinary practice before downstream analysis. The impact of composting on manure microbial composition, persistence of antibiotic resistant bacteria in soil following application, and distribution of antibiotic resistance genes and bacteria on washed vegetables were determined. A subset of samples that were thought likely to reveal the most significant effects were chosen for shotgun sequencing. The absolute abundance of all target genes detected by qPCR decreased after composting except sul1, intI1, incW and erm(F) that remained stable. The shotgun sequencing revealed that some integron integrases were enriched by composting. Composting significantly reduced the abundance of enteric bacteria, including those carrying antibiotic resistance. Manure-amended soil showed significantly higher abundances of sul1, str(A), str(B), erm(B), aad(A), intI1 and incW compared to unmanured soil. At harvest, those genes that were detected in soil samples before the application of manure (intI1, sul1, strA and strB) were quantifiable by qPCR on vegetables, with a larger number of gene targets detected on the radishes than in the carrots or lettuce. Shotgun metagenomic sequencing suggested that the increase of antibiotic resistance genes on radishes produced in soil receiving raw manure may be due to changes to soil microbial communities following manure application, rather than transfer to the radishes of enteric bacteria. Overall, under field conditions there was limited evidence for transfer of antibiotic resistance genes from composted or raw manure to vegetables that then persisted through washing.

The fate of antibiotic resistance genes and their influential factors during excess sludge composting in a full-scale plant

The alteration of antibiotic resistance genes (ARGs) during sludge composting has been less studied in a full-scale plant, causing the miss of practical implications for understanding/managing ARGs. Therefore, this study tracked the changes of ARGs and microbial communities in a full-scale plant engaged in excess sludge composting and then explored the key factors regulating ARGs through a series of analyses. After composting, the absolute and relative abundance of ARGs decreased by 91.90% and 66.57%, respectively. Additionally, pathway analysis showed that MGEs, composting physicochemical properties were the most vital factors directly influencing ARGs. Finally, network analysis indicated that Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria were the main hosts of ARGs. Based on these findings, it can be known that full-scale composting could reduce ARGs risk to an extent.

The risk of transmitting antibiotic resistance through endophytic bacteria

Antibiotic resistance is a global human health threat distributed across humans, animals, plants, and the environment. Under the One-Health concept (humans, animals, and environment), the contamination of water bodies and soil by antibiotic-resistant bacteria cannot be dissociated from its potential transmission to humans. Edible plants can be colonized by a vast diversity of bacteria, representing an important link between the environment and humans in the One-Health triad. Based on multiple examples of bacterial groups that comprise endophytes reported in edible plants, and that have close phylogenetic proximity with human opportunistic pathogens, we argue that plants exposed to human-derived biological contamination may represent a path of transmission of antibiotic resistance to humans.

Co-composting materials can further affect the attenuation of antibiotic resistome in soil application

This study investigated the effects of representative co-substrate (corncob particles) and additive (brick granules) alone on antibiotic resistome of swine manure during composting and subsequent compost application. For relative abundances, four antibiotic resistance gene (ARG) types encoding resistance to aminoglycoside, multidrug, florfenicol-chloramphenicol-amphenicol-fluoroquinolone-quinolone, and sulfonamide increased remarkably during composting, whereas all the ARG types decreased after compost application. Interestingly, much more ARG subtypes (50.1% in total) were reduced in corncob addition treatment. Meanwhile, the addition of corncob particles lowered the relative abundance and diversity of ARGs more significantly. Microbial community exhibited conspicuous changes across the manure, compost, and soil samples where the dominant genera were completely different. Procrustes test proved the co-occurrence and driving effect of microbial community on resistome variation, especially in corncob addition treatment during composting. Network analysis demonstrated that the dissipation of the dominant genera such as Ruminofilibacter, Luteimonas, and Pseudidiomarina in the composts after application contributed greatly to the reduction in ARG relative abundance. Besides, the low abundance of mobile genetic elements (MGEs) in soil also accounted for the attenuation of ARGs to some extent. Our findings clearly proved that co-composting materials can further affect the attenuation of antibiotic resistome in soil application, which can help in understanding the spread and control of ARGs during agricultural process.

Post-digestate composting shifts microbial composition and degrades antimicrobial resistance genes

Post-digestate treatments may reduce the risk linked to Antibiotic Resistant Genes (ARGs) release with digestate direct land application. Thus, this study aimed to evaluate post-digestate composting and co-composting with biogas production feedstock (maize silage, food processing waste, and poultry litter) effect on abundance of selected ARGs: erm(B), tet(K), tet(M), tet(O), and tet(S) genes. More than 80% of all ARGs were removed after 90 days of composting but removals from co-composting were lower. Bacteroidetes, Firmicutes, and Proteobacteria dominated fresh digestate, and a network analysis indicated that these were potential hosts of ARGs. The emergence of Actinobacteria (dominant), Planctomycetes, and Verrucomicrobia phyla during composting shifted the microbial composition. Moreover, canonical correspondence analysis showed trace elements explaining 90% variations in ARGs abundance. The study illustrates significance of post-digestate composting in mitigating ARGs release, and effectiveness could be linked to shift in microbial composition and trace elements release.

Antibiotics: An overview on the environmental occurrence, toxicity, degradation, and removal methods

Antibiotics, as antimicrobial drugs, have been widely applied as human and veterinary medicines. Recently, many antibiotics have been detected in the environments due to their mass production, widespread use, but a lack of adequate treatment processes. The environmental occurrence of antibiotics has received worldwide attention due to their potential harm to the ecosystem and human health. Research status of antibiotics in the environment field is presented by bibliometrics. Herein, we provided a comprehensive overview on the following important issues: (1) occurrence of antibiotics in different environmental compartments, such as wastewater, surface water, and soil; (2) toxicity of antibiotics toward non-target organisms, including aquatic and terrestrial organisms; (3) current treatment technologies for the degradation and removal of antibiotics, including adsorption, hydrolysis, photodegradation and oxidation, and biodegradation. It was found that macrolides, fluoroquinolones, tetracyclines, and sulfonamides were most frequently detected in the environment. Compared to surface and groundwaters, wastewater contained a high concentration of antibiotic residues. Both antibiotics and their metabolites exhibited toxicity to non-target organisms, especially aquatic organisms (e.g., algae and fish). Fluoroquinolones, tetracyclines, and sulfonamides can be removed through abiotic process, such as adsorption, photodegradation, and oxidation. Fluoroquinolones and sulfonamides can directly undergo biodegradation. Further studies on the chronic effects of antibiotics at environmentally relevant concentrations on the ecosystem were urgently needed to fully understand the hazards of antibiotics and help the government to establish the permissible limits. Biodegradation is a promising technology; it has numerous advantages such as cost-effectiveness and environmental friendliness.

Animal manures application increases the abundances of antibiotic resistance genes in soil-lettuce system associated with shared bacterial distributions

An increasing amount of animal manures is being used in agriculture, and the effect of animal manures application on the abundance of antibiotics resistance genes (ARGs) in soil-plant system has attracted widespread attention. However, the impacts of animal manures application on the various types of bacterial distribution that occur in soil-lettuce system are unclear. To address this topic, the effects of poultry manure, swine manure or chemical fertilizer application on ARG abundance and the distribution of shared bacteria were investigated in this study. In a lettuce pot experiment, 13 ARGs and 2 MGEs were quantified by qPCR, and bacterial communities in the soil, lettuce endosphere and lettuce phyllosphere were analysed by 16S rRNA sequence analysis. The results showed that the application of poultry or swine manure significantly increased ARG abundance in the soil, a result attributed mainly to increases in the abundances of tetG and tetC. The application of poultry manure, swine manure and chemical fertilizer significantly increased ARG abundance in the lettuce endosphere, and tetG abundance was significantly increased in the poultry and swine manure groups. However, animal manures application did not significantly increase ARG abundance in the lettuce phyllosphere. Flavobacteriaceae, Sphingomonadaceae and 11 other bacterial families were the shared bacteria in the soil, lettuce endosphere, and phyllosphere. The Streptomycetaceae and Methylobacteriaceae were significantly positively correlated with intI1 in both the soil and endosphere. Chemical fertilizer application increased both the proportions of Sphingomonadaceae and tetX abundance, which were positively correlated in the endosphere. Comamonadaceae and Flavobacteriaceae were not detected in the lettuce endosphere under swine manure application. Cu was related to Flavobacteriaceae in the lettuce endosphere. Overall, poultry and swine manure application significantly increased ARG abundance in the soil-lettuce system, which might be due to the shared bacterial distribution.

Dissipation of antibiotic resistance genes in manure-amended agricultural soil

Soil antibiotic resistance due to animal manure application is of great concern in recent years. Little is known about the fate of antibiotic resistance genes (ARGs) in agricultural soils associated with long-term manure application. Here we used soil microcosms to investigate the dissipation of ARGs and the change of bacterial community in agricultural soil originated from a vegetable field which had received 24 years' swine manure application. Soil microcosms were conducted at different soil moistures and with or without biochar over a testing period of two years in lab. Results showed that continuous manure application induced an accumulation of ARGs in soil, wherein the dissipation of ARGs differed from those in non-manure amended soil. ARGs persisted in soils at least two years, although their abundance declined gradually. Meanwhile, soil moisture and biochar had significant impact on the fate of ARGs. ARGs dissipated faster in soil with higher moisture. Biochar amendment contributed to the maintenance of bacterial diversity. Within the two years of simulation experiment, biochar enhanced soil ARG retention as they dissipated slowly in the soil amended with biochar. Succession of microbial community may have sustained the transfer and resilience of ARGs. This study provides insight into the dissipation of antibiotic resistance genes in manure-applied agricultural soil.

Proliferation of antibiotic-resistant microorganisms and associated genes during composting: An overview of the potential impacts on public health, management and future

Antibiotic residues together with non-antibiotic drugs and heavy metals act as a selective pressure for the spread of antibiotic-resistant microorganisms (ARMs), antibiotic-resistant genes (ARGs), and mobile genetic elements (MGEs) during composting of livestock manure. ARMs, ARGs and MGEs have become emerging contaminants since they are regularly implicated in the majority of compost produced from livestock manure. The prevalence of these contaminants in agricultural soil receiving compost has drawn huge attention globally due to the risks they pose to the total environment. Although a large body of literature exists on the application of composting methods in minimizing the relative abundance of these contaminants, there is a paucity of information on the robustness, limitations and opportunities and threats of various composting protocols currently deployed. To address this knowledge gap, the current review compiled literature on the origin and mechanisms of the proliferation of ARMs, ARGs, and MGEs during composting of livestock manure. The effectiveness of current composting protocols in the reduction or removal of emerging contaminants was evaluated. Furthermore, the potential environmental impacts and human health risks of these contaminants following land application of compost were also presented. Finally, we propose some strategic approaches for the reduction of ARGs and MGEs during composting of livestock manure.

A review targeting veterinary antibiotics removal from livestock manure management systems and future outlook

Veterinary antibiotics (VAs) contamination has been considered as a worldwide environmental and health concern in recent decades. This paper reviewed the variability of contents of VAs and their release from the animal breeding industry into the surrounding environment along with the performance of the manure treatment technologies. The data collected revealed that VAs were mostly excreted in animal feces and observed in manure, soil, water, and sediment. The findings illustrate the disparity of VAs in excretion rates, consumption, and their residues in the environment with relatively high distribution for tetracyclines, fluoroquinolones, and sulfonamides. Anaerobic digestion has a capacity to remove of 73% VAs while manure composting and constructed wetlands can remove 84.7%, and 90% VAs. Due to the profound effect of antibiotics on the environment, further research and intensive management strategies for livestock manure need to be designed to improve the removal efficiency and manure management technologies.