Antibiotic resistance gene profile changes in cropland soil after manure application and rainfall. - Related Documents




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765101.0000Antibiotic resistance gene profile changes in cropland soil after manure application and rainfall. Land application of manure introduces gastrointestinal microbes into the environment, including bacteria carrying antibiotic resistance genes (ARGs). Measuring soil ARGs is important for active stewardship efforts to minimize gene flow from agricultural production systems; however, the variety of sampling protocols and target genes makes it difficult to compare ARG results between studies. We used polymerase chain reaction (PCR) methods to characterize and/or quantify 27 ARG targets in soils from 20 replicate, long-term no-till plots, before and after swine manure application and simulated rainfall and runoff. All samples were negative for the 10 b-lactamase genes assayed. For tetracycline resistance, only source manure and post-application soil samples were positive. The mean number of macrolide, sulfonamide, and integrase genes increased in post-application soils when compared with source manure, but at plot level only, 1/20, 5/20, and 11/20 plots post-application showed an increase in erm(B), sulI, and intI1, respectively. Results confirmed the potential for temporary blooms of ARGs after manure application, likely linked to soil moisture levels. Results highlight uneven distribution of ARG targets, even within the same soil type and at the farm plot level. This heterogeneity presents a challenge for separating effects of manure application from background ARG noise under field conditions and needs to be considered when designing studies to evaluate the impact of best management practices to reduce ARG or for surveillance. We propose expressing normalized quantitative PCR (qPCR) ARG values as the number of ARG targets per 100,000 16S ribosomal RNA genes for ease of interpretation and to align with incidence rate data.202033016404
765210.9999Safely coupling livestock and crop production systems: how rapidly do antibiotic resistance genes dissipate in soil following a commercial application of swine or dairy manure? Animal manures recycled onto crop production land carry antibiotic-resistant bacteria. The present study evaluated the fate in soil of selected genes associated with antibiotic resistance or genetic mobility in field plots cropped to vegetables and managed according to normal farming practice. Referenced to unmanured soil, fertilization with swine or dairy manure increased the relative abundance of the gene targets sul1, erm(B), str(B), int1, and IncW repA. Following manure application in the spring of 2012, gene copy number decayed exponentially, reaching background levels by the fall of 2012. In contrast, gene copy number following manure application in the fall of 2012 or spring of 2013 increased significantly in the weeks following application and then declined. In both cases, the relative abundance of gene copy numbers had not returned to background levels by the fall of 2013. Overall, these results suggest that under conditions characteristic of agriculture in a humid continental climate, a 1-year period following a commercial application of raw manure is sufficient to ensure that an additional soil burden of antibiotic resistance genes approaches background. The relative abundance of several gene targets exceeded background during the growing season following a spring application or an application done the previous fall. Results from the present study reinforce the advisability of treating manure prior to use in crop production systems.201424632259
765420.9998Impact of fertilizing with raw or anaerobically digested sewage sludge on the abundance of antibiotic-resistant coliforms, antibiotic resistance genes, and pathogenic bacteria in soil and on vegetables at harvest. The consumption of crops fertilized with human waste represents a potential route of exposure to antibiotic-resistant fecal bacteria. The present study evaluated the abundance of bacteria and antibiotic resistance genes by using both culture-dependent and molecular methods. Various vegetables (lettuce, carrots, radish, and tomatoes) were sown into field plots fertilized inorganically or with class B biosolids or untreated municipal sewage sludge and harvested when of marketable quality. Analysis of viable pathogenic bacteria or antibiotic-resistant coliform bacteria by plate counts did not reveal significant treatment effects of fertilization with class B biosolids or untreated sewage sludge on the vegetables. Numerous targeted genes associated with antibiotic resistance and mobile genetic elements were detected by PCR in soil and on vegetables at harvest from plots that received no organic amendment. However, in the season of application, vegetables harvested from plots treated with either material carried gene targets not detected in the absence of amendment. Several gene targets evaluated by using quantitative PCR (qPCR) were considerably more abundant on vegetables harvested from sewage sludge-treated plots than on vegetables from control plots in the season of application, whereas vegetables harvested the following year revealed no treatment effect. Overall, the results of the present study suggest that producing vegetable crops in ground fertilized with human waste without appropriate delay or pretreatment will result in an additional burden of antibiotic resistance genes on harvested crops. Managing human exposure to antibiotic resistance genes carried in human waste must be undertaken through judicious agricultural practice.201425172864
738730.9998Bloom of resident antibiotic-resistant bacteria in soil following manure fertilization. The increasing prevalence of antibiotic-resistant bacteria is a global threat to public health. Agricultural use of antibiotics is believed to contribute to the spread of antibiotic resistance, but the mechanisms by which many agricultural practices influence resistance remain obscure. Although manure from dairy farms is a common soil amendment in crop production, its impact on the soil microbiome and resistome is not known. To gain insight into this impact, we cultured bacteria from soil before and at 10 time points after application of manure from cows that had not received antibiotic treatment. Soil treated with manure contained a higher abundance of β-lactam-resistant bacteria than soil treated with inorganic fertilizer. Functional metagenomics identified β-lactam-resistance genes in treated and untreated soil, and indicated that the higher frequency of resistant bacteria in manure-amended soil was attributable to enrichment of resident soil bacteria that harbor β-lactamases. Quantitative PCR indicated that manure treatment enriched the blaCEP-04 gene, which is highly similar (96%) to a gene found previously in a Pseudomonas sp. Analysis of 16S rRNA genes indicated that the abundance of Pseudomonas spp. increased in manure-amended soil. Populations of other soil bacteria that commonly harbor β-lactamases, including Janthinobacterium sp. and Psychrobacter pulmonis, also increased in response to manure treatment. These results indicate that manure amendment induced a bloom of certain antibiotic-resistant bacteria in soil that was independent of antibiotic exposure of the cows from which the manure was derived. Our data illustrate the unintended consequences that can result from agricultural practices, and demonstrate the need for empirical analysis of the agroecosystem.201425288759
740940.9998Longitudinal screening of antibiotic residues, antibiotic resistance genes and zoonotic bacteria in soils fertilized with pig manure. Fertilization with animal manure is one of the main routes responsible for the introduction of antibiotic residues, antibiotic resistance genes, and zoonotic bacteria into the environment. The aim of this study was to assess the effect of the use of pig (swine) manure as a fertilizer on the presence and fate of six antibiotic residues, nine antibiotic resistance genes, and bacteria (zoonotic bacteria Salmonella spp. and Campylobacter spp. and E. coli as indicator for Gram-negative bacterial species of the microbiota of livestock) on five fields. To the best of our knowledge, the present study is the first to assess a multitude of antibiotic residues and resistance to several classes of antibiotics in pig manure and in fertilized soil over time in a region with an intensive pig industry (Flanders, Belgium). The fields were sampled at five consecutive time points, starting before fertilization up to harvest. Low concentrations of antibiotic residues could be observed in the soils until harvest. The antibiotic resistance genes studied were already present at background levels in the soil environment prior to fertilization, but after fertilization with pig manure, an increase in relative abundance was observed for most of them, followed by a decline back to background levels by harvest-time on all of the fields studied. No apparent differences regarding the presence of antibiotic resistance genes in soils were observed between those fertilized with manure that either contained antibiotic residues or not. With regard to dissemination of resistance, the results presented in this study confirm that fertilization with animal manure directly adds resistance genes to the soil. In addition, it shows that this direct mechanism may be more important than possible selective pressure in soil-dwelling bacteria exerted by antibiotic residues present in the manure. These results also indicate that zoonotic bacteria detected in the manure could be detected in the soil environment directly after fertilization, but not after 1 month. In conclusion, although some antibiotic residues may be present in both manure and soil at concentrations to exert selective pressure, it seems that antibiotic resistance is mostly introduced directly to soil through fertilization with animal manure.202032410188
707150.9998Impacts of multi-year field exposure of agricultural soil to macrolide antibiotics on the abundance of antibiotic resistance genes and selected mobile genetic elements. Exposure of environmental bacteria to antibiotics may be increasing the global resistome. Antibiotic residues are entrained into agricultural soil through the application of animal and human wastes, and irrigation with reclaimed water. The impact of a mixture of three macrolide antibiotics on the abundance of selected genes associated with antibiotic resistance and genetic mobility were determined in a long-term field experiment undertaken in London, Canada. Replicated plots received annual applications of a mixture of erythromycin, clarithromycin and azithromycin every spring since 2010. Each antibiotic was added directly to the soil at a concentration of either 0.1 or 10 mg kg soil(-1) and all plots were cropped to soybeans. By means of qPCR, no gene targets were enriched in soil exposed to the 0.1 mg kg soil(-1) dose compared to untreated control. In contrast, the relative abundance of several gene targets including int1, sul2 and mphE increased significantly with the annual exposure to the 10 mg kg soil(-1) dose. By means of high-throughput qPCR, numerous gene targets associated with resistance to aminoglycosides, sulfonamides, trimethoprim, streptomycin, quaternary ammonium chemicals as well as mobile genetic elements (tnpA, IS26 and IS6100) were detected in soil exposed to 10 mg kg soil(-1), but not the lower dose. Overall, exposure of soil to macrolide antibiotics increased the relative abundance of numerous gene targets associated with resistance to macrolides and other antibiotics, and mobile genetic elements. This occurred at an exposure dose that is unrealistically high, but did not occur at the lower more realistic exposure dose.202032330714
741260.9998Effect of composting and storage on the microbiome and resistome of cattle manure from a commercial dairy farm in Poland. Manure from food-producing animals, rich in antibiotic-resistant bacteria and antibiotic resistance genes (ARGs), poses significant environmental and healthcare risks. Despite global efforts, most manure is not adequately processed before use on fields, escalating the spread of antimicrobial resistance. This study examined how different cattle manure treatments, including composting and storage, affect its microbiome and resistome. The changes occurring in the microbiome and resistome of the treated manure samples were compared with those of raw samples by high-throughput qPCR for ARGs tracking and sequencing of the V3-V4 variable region of the 16S rRNA gene to indicate bacterial community composition. We identified 203 ARGs and mobile genetic elements (MGEs) in raw manure. Post-treatment reduced these to 76 in composted and 51 in stored samples. Notably, beta-lactam, cross-resistance to macrolides, lincosamides and streptogramin B (MLSB), and vancomycin resistance genes decreased, while genes linked to MGEs, integrons, and sulfonamide resistance increased after composting. Overall, total resistance gene abundance significantly dropped with both treatments. During composting, the relative abundance of genes was lower midway than at the end. Moreover, higher biodiversity was observed in samples after composting than storage. Our current research shows that both composting and storage effectively reduce ARGs in cattle manure. However, it is challenging to determine which method is superior, as different groups of resistance genes react differently to each treatment, even though a notable overall reduction in ARGs is observed.202438616224
711970.9998Assessing the benefits of composting poultry manure in reducing antimicrobial residues, pathogenic bacteria, and antimicrobial resistance genes: a field-scale study. The poultry industry in the European Union produces 13 million tons of manure annually, which represents a major health and environmental challenge. Composting is an environmental-friendly technique for the management of manure, but there are few studies about antibiotic residues and antimicrobial resistances at a field scale. The goal of this study was to determine if the composting of poultry manure at a field scale would result in the reduction of antibiotic residues, pathogenic bacteria, and antibiotic resistance genes (ARGs) in the final fertilizer product. A 10-week composting of poultry manure spiked with enrofloxacin, doxycycline, and ciprofloxacin was performed. The determination of antibiotics residues and 22 selected ARGs was carried out together with the identification of bacteria by metagenomics. In the case of ciprofloxacin and doxycycline, a 90% decrease was observed after composting for 3 weeks. Sixteen ARGs were detected at the beginning of the experiment; 12 of them decreased from week 0 to week 10 (reduction of 73.7-99.99%). The presence of potentially pathogenic bacteria, such as, Campylobacter coli or commensal bacteria such as Escherichia coli decreases along the composting process. In conclusion, 10-week composting of poultry manure promotes the reduction of antibiotic residues and most of the ARGs and pathogenic bacteria.202032399873
741380.9998Fecal antibiotic resistance genes were transferred through the distribution of soil-lettuce-snail food chain. Massive antibiotic resistance genes (ARG) were detected in the soil modified by manure, which may affect human life safety through the food chain. However, the transmission of ARGs through the soil-plant-animal food chain is still unclear. Therefore, this study used high-throughput quantitative PCR technology to explore the effects of pig manure application on ARGs and bacterial communities in soil, lettuce phyllosphere, and snail excrement. The results showed that a total of 384 ARGs and 48 MEGs were detected in all samples after 75 days of incubation. The diversity of ARGs and MGEs in soil components increased significantly by 87.04% and 40% with the addition of pig manure. The absolute abundance of ARGs in the phyllosphere of lettuce was significantly higher than that of the control group, with a growth rate of 212.5%. Six common ARGs were detected between the three components of the fertilization group, indicating that there was internal transmission of fecal ARGs between the trophic levels of the food chain. Firmicutes and Proteobacteria were identified as the dominant host bacteria in the food chain system, which were more likely to be used as carriers of ARGs to promote the spread of resistance in the food chain. The results were used to assess the potential ecological risks of livestock and poultry manure. It provides theoretical basis and scientific support for the formulation of ARG prevention and control policies.202337434056
738990.9998Temporal changes of antibiotic-resistance genes and bacterial communities in two contrasting soils treated with cattle manure. The emerging environmental spread of antibiotic-resistance genes (ARGs) and their subsequent acquisition by clinically relevant microorganisms is a major threat to public health. Animal manure has been recognized as an important reservoir of ARGs; however, the dissemination of manure-derived ARGs and the impacts of manure application on the soil resistome remain obscure. Here, we conducted a microcosm study to assess the temporal succession of total bacteria and a broad spectrum of ARGs in two contrasting soils following manure application from cattle that had not been treated with antibiotics. High-capacity quantitative PCR detected 52 unique ARGs across all the samples, with β-lactamase as the most dominant ARG type. Several genes of soil indigenous bacteria conferring resistance to β-lactam, which could not be detected in manure, were found to be highly enriched in manure-treated soils, and the level of enrichment was maintained over the entire course of 140 days. The enriched β-lactam resistance genes had significantly positive relationships with the relative abundance of the integrase intI1 gene, suggesting an increasing mobility potential in manure-treated soils. The changes in ARG patterns were accompanied by a significant effect of cattle manure on the total bacterial community compositions. Our study indicates that even in the absence of selective pressure imposed by agricultural use of antibiotics, manure application could still strongly impact the abundance, diversity and mobility potential of a broad spectrum of soil ARGs. Our findings are important for reliable prediction of ARG behaviors in soil environment and development of appropriate strategies to minimize their dissemination.201626712351
7411100.9998Thermophilic Composting of Human Feces: Development of Bacterial Community Composition and Antimicrobial Resistance Gene Pool. In times of climate change, practicing sustainable, climate-resilient, and productive agriculture is of primordial importance. Compost from different resources, now treated as wastes, could be one form of sustainable fertilizer creating a resilience of agriculture to the adverse effects of climate change. However, the safety of the produced compost regarding human pathogens, pharmaceuticals, and related resistance genes must be considered. We have assessed the effect of thermophilic composting of dry toilet contents, green cuttings, and straw, with and without biochar, on fecal indicators, the bacterial community, and antibiotic resistance genes (ARGs). Mature compost samples were analyzed regarding fecal indicator organisms, revealing low levels of Escherichia coli that are in line with German regulations for fertilizers. However, one finding of Salmonella spp. exceeded the threshold value. Cultivation of bacteria from the mature compost resulted in 200 isolates with 36.5% of biosafety level 2 (BSL-2) species. The majority is known as opportunistic pathogens that likewise occur in different environments. A quarter of the isolated BSL-2 strains exhibited multiresistance to different classes of antibiotics. Molecular analysis of total DNA before and after composting revealed changes in bacterial community composition and ARGs. 16S rRNA gene amplicon sequencing showed a decline of the two most abundant phyla Proteobacteria (start: 36-48%, end: 27-30%) and Firmicutes (start: 13-33%, end: 12-16%), whereas the abundance of Chloroflexi, Gemmatimonadetes, and Planctomycetes rose. Groups containing many human pathogens decreased during composting, like Pseudomonadales, Bacilli with Bacillus spp., or Staphylococcaceae and Enterococcaceae. Gene-specific PCR showed a decline in the number of detectable ARGs from 15 before to 8 after composting. The results reveal the importance of sufficiently high temperatures lasting for a sufficiently long period during the thermophilic phase of composting for reducing Salmonella to levels matching the criteria for fertilizers. However, most severe human pathogens that were targeted by isolation conditions were not detected. Cultivation-independent analyses also indicated a decline in bacterial orders comprising many pathogenic bacteria, as well as a decrease in ARGs. In summary, thermophilic composting could be a promising approach for producing hygienically safe organic fertilizer from ecological sanitation.202235250940
3674110.9998New Estimation of Antibiotic Resistance Genes in Sediment Along the Haihe River and Bohai Bay in China: A Comparison Between Single and Successive DNA Extraction Methods. Sediment is thought to be a vital reservoir for antibiotic resistance genes (ARGs). Often, studies describing and comparing ARGs and their potential hosts in sediment are based on single DNA extractions. To date, however, no study has been conducted to assess the influence of DNA extraction efficiency on ARGs in sediment. To determine whether the abundance of ARGs is underestimated, we performed five successive extraction cycles with a widely used commercial kit in 10 sediment samples collected from the Haihe River and Bohai Bay. Our results showed that accumulated DNA yields after five extractions were 1.8-3.1 times higher than that by single DNA extractions. High-throughput sequencing showed that insufficient DNA extraction could generate PCR bias and skew community structure characterization in sediment. The relative abundances of some pathogenic bacteria, such as Enterobacteriales, Lactobacillales, and Streptomycetales, were significantly different between single and successive DNA extraction samples. In addition, real-time fluorescent quantitative PCR (qPCR) showed that ARGs, intI1, and 16S rRNA gene abundance strongly increased with increasing extraction cycles. Among the measured ARGs, sulfonamide resistance genes and multidrug resistance genes were dominant subtypes in the study region. Nevertheless, different subtypes of ARGs did not respond equally to the additional extraction cycles; some continued to have linear growth trends, and some tended to level off. Additionally, more correlations between ARGs and bacterial communities were observed in the successive DNA extraction samples than in the single DNA extraction samples. It is suggested that 3-4 additional extraction cycles are required in future studies when extracting DNA from sediment samples. Taken together, our results highlight that performing successive DNA extractions on sediment samples optimizes the extractable DNA yield and can lead to a better picture of the abundance of ARGs and their potential hosts in sediments.202134616375
7386120.9998Regulation of Antibiotic Resistance Genes on Agricultural Land Is Dependent on Both Choice of Organic Amendment and Prevalence of Predatory Bacteria. Antibiotic resistance genes (ARGs) are widespread in the environment, and soils, specifically, are hotspots for microorganisms with inherent antibiotic resistance. Manure and sludge used as fertilizers in agricultural production have been shown to contain vast amounts of ARGs, and due to continued applications, ARGs accumulate in agricultural soils. Some soils, however, harbor a resilience capacity that could depend on specific soil properties, as well as the presence of predatory bacteria that are able to hydrolyse living bacteria, including bacteria of clinical importance. The objectives of this study were to (i) investigate if the antibiotic resistance profile of the soil microbiota could be differently affected by the addition of cow manure, chicken manure, and sludge, and (ii) investigate if the amendments had an effect on the presence of predatory bacteria. The three organic amendments were mixed separately with a field soil, divided into pots, and incubated in a greenhouse for 28 days. Droplet digital PCR (ddPCR) was used to quantify three ARGs, two predatory bacteria, and total number of bacteria. In this study, we demonstrated that the choice of organic amendment significantly affected the antibiotic resistance profile of soil, and promoted the growth of predatory bacteria, while the total number of bacteria was unaffected.202439200050
7127130.9998Comparison of antibiotic resistance genes in swine manure storage pits of Iowa, USA. Antimicrobial resistance (AMR) can develop in deep-pit swine manure storage when bacteria are selectively pressured by unmetabolized antibiotics. Subsequent manure application on row crops is then a source of AMR into soil and downstream runoff water. Therefore, understanding the patterns of diverse antibiotic resistance genes (ARGs) in manure among different farms is important for both interpreting the results of the detection of these genes from previous studies and for the use of these genes as bioindicators of manure borne antibiotic resistance in the environment. Previous studies of manure-associated ARGs are based on limited samples of manures. To better understand the distribution of ARGs between manures, we characterized manures from 48 geographically independent swine farms across Iowa. The objectives of this study were to characterize the distribution of ARGs among these manures and to evaluate what factors in manure management may influence the presence of ARGs in manures. Our analysis included quantification of two commonly found ARGs in swine manure, ermB and tetM. Additionally, we characterized a broader suite of 31 ARGs which allowed for simultaneous assays of the presence or absence of multiple genes. We found the company integrator had a significant effect on both ermB (P=0.0007) and tetM gene concentrations (P=0.0425). Our broad analysis on ARG profiles found that the tet(36) gene was broadly present in swine manures, followed by the detection of tetT, tetM, erm(35), ermF, ermB, str, aadD, and intl3 in samples from 14 farms. Finally, we provide a comparison of methods to detect ARGs in manures, specifically comparing conventional and high-throughput qPCR and discuss their role in ARG environmental monitoring efforts. Results of this study provide insight into commonalities of ARG presence in manure holding pits and provide supporting evidence that company integrator decisions may impact ARG concentrations.202339816658
7124140.9998Changes in diversity of cultured bacteria resistant to erythromycin and tetracycline in swine manure during simulated composting and lagoon storage. This study investigated the impact of composting and lagoon storage on survival and change in diversity of tetracycline-resistant (Tc(r) ) and erythromycin-resistant (Em(r) ) bacteria and the resistance genes they carry in swine manure. Treatments were arranged as a 2 × 2 factorial design: composting vs lagoon storage and 0 vs 1% Surround WP Crop Protectant (a clay product) in three replicates. After 48 days of treatments, resistant bacteria were enumerated by selective plating and identified by 16S rRNA gene sequencing. The erm and the tet gene(s) carried by the resistant isolates were screened using class-specific PCR assays. The plate counts of Tc(r) and Em(r) bacteria decreased by 4-7 logs by composting, but only by 1-2 logs by the lagoon treatment. During the treatments, Acinetobacter gave way to Pseudomonas and Providencia as the largest resistant genera. The clay product had little effect on survival or diversity of resistant bacteria. Of six classes of erm and seven classes of tet genes tested, changes in prevalence were also noted. The results indicate that composting can dramatically shift Tc(r) and Em(r) bacterial populations, and composting can be an effective and practical approach to decrease dissemination of antibiotic resistance from swine farms to the environment. SIGNIFICANCE AND IMPACT OF THE STUDY: The presented research provided evidence that composting is much more effective than lagoon storage in dramatically decreasing culturable bacteria resistant to erythromycin and tetracycline in swine manure. Considerable diversity changes of resistant bacteria were also demonstrated during composting or lagoon storage. Overall, Acinetobacter was the major resistant genus in untreated swine manure, but pseudomonads and Providencia became the major resistant genera after the treatments. This is the first study that investigated diversity changes of cultured bacteria resistant to these two antibiotics during composting and lagoon storage of swine manure. New genes encoding resistance to the two antibiotics were also implied in the cultured isolates.201526031793
7183150.9998Evaluation of five antibiotic resistance genes in wastewater treatment systems of swine farms by real-time PCR. Antibiotics are widely used in livestock for infection treatment and growth promotion. Wastes from animal husbandry are a potential environmental source of antibiotic-insensitive pathogens, and the removal efficiency of the resistance genotypes in current wastewater treatment plants (WWTPs) is unknown. In this study, quantitative PCR was used for evaluating antibiotic resistance genes in wastewater treatment processes. Six wastewater treatment plants in different swine farms were included in this study, and five antibiotic resistance genes (ARGs) were tested for each treatment procedure. All of the tested ARGs including tetA, tetW, sulI, sulII, and blaTEM genes were detected in six swine farms with considerable amounts. The results showed that antibiotic resistance is prevalent in livestock farming. The ARG levels were varied by wastewater treatment procedure, frequently with the highest level at anaerobic treatment tank and lowest in the activated sludge unit and the effluents. After normalizing the ARG levels to 16S rRNA gene copies, the results showed that ARGs in WWTP units fluctuated partly with the quantity of bacteria. Regardless of its importance in biodegradation, the anaerobic procedure may facilitate bacterial growth thus increasing the sustainability of the antibiotic resistance genotypes. After comparing the copy numbers in influx and efflux samples, the mean removal efficiency of ARGs ranged between 33.30 and 97.56%. The results suggested that treatments in the WWTP could partially reduce the spread of antibiotic-resistant bacteria, and additional procedures such as sedimentation may not critically affect the removal efficiency.201425064719
7414160.9998Structure of the manure resistome and the associated mobilome for assessing the risk of antimicrobial resistance transmission to crops. In this study, the impact of bovine and poultry manure on the quantitative and qualitative composition of antibiotic resistance genes (ARGs) and the environmental mobilome associated with antimicrobial resistance in soil and crops was determined with the use of next generation sequencing methods. The aim of the study was to perform a metagenomic analysis of manure to estimate the risk of the transmission of ARGs and bacterial drug resistance carriers to fertilized soil and crops. The total copy number of ARGs was nearly four times higher in poultry manure (555 ppm) than in bovine manure (140 ppm), and this relationship was also noted in fertilized soil. Poultry manure induced a much greater increase in the concentrations of ARGs in the soil environment (196.4 ppm) than bovine manure (137.8 ppm) immediately after supplementation. The application of poultry manure led to the highest increase in the abundance of genes encoding resistance to tetracyclines (9%), aminoglycosides (3.5%), sulfonamides (3%), bacitracin (2%), chloramphenicol (2%), and macrolide-lincosamide-streptogramin antibiotics (1%). Heavy metals were stronger promoters of antibiotic resistance in the environment than antibiotics. Antibiotics exerted a greater influence on maintaining the diversity of ARGs than on increasing their abundance in soil. Large quantities of insertion sequences (IS), including those associated with the mobility of ARGs in the population of ESKAPEE pathogens, are introduced to soil with manure. These IS remain stable for up to several months, which indicates that manure, in particular poultry manure, significantly increases the risk of rapid ARG transfer to the environment. Manure also largely contributes to an increase in the diversity of the resistome and mobilome in the metagenome of bacteria isolated from crops. Bacteria of the phylum Proteobacteria appear to play a major role in the transmission of multiple ARGs in crops grown for human and animal consumption.202234864022
7262170.9998Soil texture-depending effects of doxycycline and streptomycin applied with manure on the bacterial community composition and resistome. Veterinary antibiotics, bacteria carrying antibiotic resistance determinants located on mobile genetic elements and nutrients are spread on agricultural soil using manure as fertilizer. However, systematic quantitative studies linking antibiotic concentrations and antimicrobial resistance genes (ARGs) in manure and the environment are scarce but needed to assess environmental risks. In this microcosm study, a sandy and a loamy soil were mixed with manure spiked with streptomycin or doxycycline at five concentrations. Total-community DNA was extracted on days 28 and 92, and the abundances of ARGs (aadA, strA, tet(A), tet(M), tet(W), tet(Q), sul1, qacE/qacEΔ1) and class 1 and 2 integron integrase genes (intI1 and intI2) were determined by qPCR relative to 16S rRNA genes. Effects on the bacterial community composition were evaluated by denaturing gradient gel electrophoresis of 16S rRNA gene amplicons. Manure application to the soils strongly increased the relative abundance of most tested genes. Antibiotics caused further enrichments which decreased over time and were mostly seen at high concentrations. Strikingly, the effects on relative gene abundances and soil bacterial community composition were more pronounced in sandy soil. The concept of defining antibiotic threshold concentrations for environmental risk assessments remains challenging due to the various influencing factors.201829087461
7120180.9998Impact of liquid hog manure applications on antibiotic resistance genes concentration in soil and drainage water in field crops. Agricultural practices such as manure applications could contribute to the spread of antibiotic resistance genes (ARGs) within the environment. Our objective was to assess the impact of certain fertilization methods (mineral or manure) and tillage practices (reduced or conventional) on the presence of ARGs and bacteria in soil and drainage water under wheat and grain corn crops. Targeted ARGs tet(T), sul1, and bla(CTX-M-1) in liquid hog manure, soil, and water samples were quantified by qPCR. Conventional PCR was used to detect mcr-1 and mcr-2. ARGs in control plots were detected despite the absence of manure, representing an environmental reservoir of resistant microorganisms. The manure application rate higher than 39 m(3)/ha increased tet(T) and sul1 gene concentrations in soil for more than 180 days. Tillage practices had no impact on ARG concentrations in soil and water samples. The bla(CTX-M-1) gene was only detected in seven water samples in 2016, but no link was established with the treatments. The mcr-1 and mcr-2 genes were not detected in all tested samples. This study demonstrated that tet(T) and sul1 gene concentrations increased in soil after liquid hog manure application as well as in drainage water in the next weeks.202032330390
7063190.9998Impact 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. Manuring ground used for crop production is an important agricultural practice. Should antibiotic-resistant enteric bacteria carried in the manure be transferred to crops that are consumed raw, their consumption by humans or animals will represent a route of exposure to antibiotic resistance genes. Treatment of manures prior to land application is a potential management option to reduce the abundance of antibiotic resistance genes entrained with manure application. In this study, dairy manure that was untreated, anaerobically digested, mechanically dewatered or composted was applied to field plots that were then cropped to lettuce, carrots and radishes. The impact of treatment on manure composition, persistence of antibiotic resistance gene targets in soil following application, and distribution of antibiotic resistance genes and bacteria on vegetables at harvest was determined. Composted manure had the lowest abundance of antibiotic resistance gene targets compared to the other manures. There was no significant difference in the persistence characteristics of antibiotic resistance genes following land application of the various manures. Compared to unmanured soil, antibiotic resistance genes were detected more frequently in soil receiving raw or digested manure, whereas they were not in soil receiving composted manure. The present study suggests that vegetables grown in ground receiving raw or digested manure are at risk of contamination with manure-borne antibiotic resistant bacteria, whereas vegetables grown in ground receiving composted manure are less so.201728076772