Contaminations of organic fertilizers with antibiotic residues, resistance genes, and mobile genetic elements mirroring antibiotic use in livestock?

Unraveling the determinants of antibiotic resistance evolution in farmland under fertilizations

Organic fertilization is a major driver potentiating soil antibiotic resistance in farmland. However, it remains unclear how bacterial antibiotic resistance evolves in fertilized soils and even spreads to crops. Compared with no fertilizer and commercial fertilizer treatments, organic fertilizers markedly increased the abundance of soil antibiotic resistance genes (ARGs) but the relatively weaker transfer of resistance genes from soil to crops. The introduction of organic fertilizers enriches the soil with nutrients, driving indigenous microorganisms towards a K-strategy. The pH, EC, and nutrients as key drivers influenced the ARGs abundance. The neutral (pH 7.2), low salt (TDS 1.4 %) and mesotrophic (carbon content 3.54 g/L) habitats similar to the soil environment conditioned by organic fertilizers. These environmental conditions clearly prolonged the persistence of resistant plasmids, and facilitated their dissemination to massive conjugators soil microbiome but not to plant endophytes. This suggested that organic fertilizers inhibited the spread of ARGs to crops. Moreover, the composition of conjugators showed differential selection of resistant plasmids by endophytes under these conditions. This study sheds light on the evolution and dissemination of antibiotic resistance in farmlands and can aid in the development of antimicrobial resistance control strategies in agriculture.

Residues of veterinary antibiotics in solid natural and organic fertilizers-method development and sample analysis

Livestock excrement is used around the world as natural fertilizers or, after processing, as organic fertilizers for crops and grasslands. But due to the presence of veterinary antibiotics in them, they may pose a threat not only to the natural environment, mainly to soil microorganisms, but also to human and animal health. This article describes a method for detecting 21 antibacterial substances in solid natural and organic fertilizers. Antibiotics from fertilizers were extracted with a mixture of acetonitrile and McIlvain-Na2EDTA buffer, twice. The extracts were purified by solid phase extraction technique on Strata-X cartridges and analyzed with the use UHPLC-MS/MS technique. The method was validated in accordance with EU Commission Implementing Regulation 2021/808; the obtained recovery ranged from 93.6 to 116.6% (depending on the analytes), and the linearity ranged from 50 to 1000 µg/kg. The developed method was used to analyze 73 samples of solid natural and organic fertilizers. Our research has shown that over 38% of natural fertilizers were contaminated with antibiotics, mainly doxycycline in concentrations reaching several dozen milligrams per kilogram of fertilizers. In the case of processed organic fertilizers, the presence of antibiotics was found in over 37% of the analyzed samples. The research results showed that the developed and validated analytical method may be useful for assessing the presence and content of antibacterial substances in solid natural and organic fertilizers.

Environmental microbiome diversity and stability is a barrier to antimicrobial resistance gene accumulation

When antimicrobial resistant bacteria (ARB) and genes (ARGs) reach novel habitats, they can become part of the habitat's microbiome in the long term if they are able to overcome the habitat's biotic resilience towards immigration. This process should become more difficult with increasing biodiversity, as exploitable niches in a given habitat are reduced for immigrants when more diverse competitors are present. Consequently, microbial diversity could provide a natural barrier towards antimicrobial resistance by reducing the persistence time of immigrating ARB and ARG. To test this hypothesis, a pan-European sampling campaign was performed for structured forest soil and dynamic riverbed environments of low anthropogenic impact. In soils, higher diversity, evenness and richness were significantly negatively correlated with relative abundance of >85% of ARGs. Furthermore, the number of detected ARGs per sample were inversely correlated with diversity. However, no such effects were present in the more dynamic riverbeds. Hence, microbiome diversity can serve as a barrier towards antimicrobial resistance dissemination in stationary, structured environments, where long-term, diversity-based resilience against immigration can evolve.

Treatment of anaerobically digested pig manure by applying membrane processes for nutrient recovery and antibiotics removal

A combination of membrane processes was applied to treat the digestate produced after the anaerobic treatment of pig manure in a biogas plant, aiming towards the recovery of nutrients and effective water treatment for potential reuse. Initially, coarse filtration (sieving and microfiltration) was used to remove particles larger than 1 µm, followed by ultrafiltration, to reduce the suspended solids concentrations below 1 g/L. Subsequently, selective electrodialysis is employed to recover the main nutrient ions, primarily ammonium and potassium. The ion-depleted digestate is then fed to a reverse osmosis unit, where clean water was recovered, yielding a by-product (concentrate) stream enriched in phosphates and organics content. The presence of antibiotics and the concentrations of heavy metals were monitored during all treatment stages to assess their behavior/removal in the various membrane processes. The results indicate that almost 51% of the digestate could be recovered as water free from ions and antibiotics, suitable for reuse in the biogas plant for process needs and irrigation purposes. The selective electrodialysis process can recover 51% of initial NH4+ content (corresponding to 96% of the electrodialysis feed), while the remainder largely ended up in the ultrafiltration concentrate. A similar behavior was observed for the case of K+, while approximately 68% of the phosphates content was retained by the coarse filtration process, with another 24% remaining in the ultrafiltration concentrate and the remaining 8% in the reverse osmosis concentrate. Most of the antibiotics and heavy metals were retained by the coarse and ultrafiltration steps, with smaller amounts detected in the reverse osmosis concentrate.

Tetracyclines contamination in European aquatic environments: A comprehensive review of occurrence, fate, and removal techniques

Tetracyclines are among the most commonly used antibiotics for the treatment of bacterial infections and the improvement of agricultural growth and feed efficiency. All compounds in the group of tetracyclines (tetracycline, chlorotetracycline, doxycycline, and oxytetracycline) are excreted in an unchanged form in urine at a rate of more than 70%. They enter the aquatic environment in altered and unaltered forms which affect aquatic micro- and macroorganisms. This study reviews the occurrence, fate, and removal techniques of tetracycline contamination in Europe. The average level of tetracycline contamination in water ranged from 0 to 20 ng/L. However, data regarding environmental contamination by tetracyclines are still insufficient. Despite the constant presence and impact of tetracyclines in the environment, there are no legal restrictions regarding the discharge of tetracyclines into the aquatic environment. To address these challenges, various removal techniques, including advanced oxidation, adsorption, and UV treatment, are being critically evaluated and compared. The summarized data contributes to a better understanding of the current state of Europe's waters and provides insight into potential strategies for future environmental management and policy development. Further research on the pollution and effects of tetracyclines in aquatic environments is therefore required.

Analysis of Resistance Gene Diversity in the Intestinal Microbiome of Broilers from Two Types of Broiler Farms in Hebei Province, China

The crucial reservoir of antibiotic resistance genes (ARGs) within the chicken intestinal microbiome poses a serious threat to both animal and human health. In China, the overuse of antibiotics has significantly contributed to the proliferation of ARGs in the chicken intestinal microbiome, which is a serious concern. However, there has been relatively little research on the diversity of resistance genes in the chicken intestinal microbiome since the implementation of the National Pilot Work Program for Action to Reduce the Use of Veterinary Antimicrobial Drugs in China. The objective of this study was to analyze the diversity of antibiotic resistance genes carried by the chicken intestinal microbiome in both standard farms (SFs), which implement antibiotic reduction and passed national acceptance, and nonstandard farms (NSFs), which do not implement antibiotic reductions, in Hebei Province. Fresh fecal samples of broiler chickens were collected from SFs (n = 4) and NSF (n = 1) and analyzed using high-throughput qPCR technology. Our findings revealed that all five farms exhibited a wide range of highly abundant ARGs, with a total of 201 ARGs and 7 MGEs detected in all fecal samples. The dominant ARGs identified conferred resistance to aminoglycosides, macrolide-lincosamide-streptomycin B (MLSB), and tetracycline antibiotics. Cellular protection mechanisms were found to be the primary resistance mechanism for these ARGs. The analysis of the co-occurrence network demonstrated a significant positive correlation between the abundance of MGEs and ARGs. The SF samples showed a significantly lower relative abundance of certain ARGs than the NSF samples (p < 0.05). The results of this study show that the abundance of ARGs demonstrated a downward trend after the implementation of the National Pilot Work Program for Action to Reduce the Usage of Veterinary Antimicrobial Drugs in Hebei Province, China.

Aged polyamide microplastics enhance the adsorption of trimethoprim in soil environments

Microplastics (MPs) in the environment typically age. However, the influence of aged MPs on the adsorption of antibiotics in soil remains unknown. In this study, the adsorption behavior of trimethoprim (TMP) on soil and soil containing aged polyamide (PA) was investigated using batch and stirred flow chamber experiments. The adsorption of TMP on the tested soil with and without PA was fast, with the k_a values ranging from 50.5 to 55.6 L (mg min)^-1. The adsorption of TMP on aged PA was more than 20 times larger than that on the tested soil, which resulted in an "enrichment effect." Furthermore, aged PA altered the pH of the reaction system, thereby enhancing the adsorption of TMP. Consequently, the K_d values of TMP for soil, soil containing 5%, and 10% aged PA were 5.64, 12.38, and 23.65 L kg^-1, respectively. The effect of aged PA on the adsorption of TMP on soil depended on pH values. However, TMP adsorption on soil containing 10% aged PA was constantly higher (p < 0.01) than that on soil with NaCl concentrations ranging from 0 to 50 mmol L^-1. These findings provide new insights into the effect of environmental MPs on the fate and transport of antibiotics in soil environments.

Prevalence of veterinary antibiotics in natural and organic fertilizers from animal food production and assessment of their potential ecological risk

BACKGROUND

Veterinary antibiotics are emerging contaminants and enter into soil principally by agricultural application of organic fertilizers. This article presents the results of the research obtained for the analyzed 70 samples of fertilizers (pig and poultry manure and slurry and digestate) for various classes of antibiotics.

RESULTS

Doxycycline, oxytetracycline, tetracycline, lincomycin, tiamulin and enrofloxacin were found in tested samples. Doxycycline was found as a dominant compound, and its highest concentration was 175 mg/kg in pig manure. This investigation indicated that fertilization with manure, especially animal feces, might be the primary source of antibiotics. Additionally, a risk assessment based on a risk quotient was carried out, which showed that the determined concentrations of antibiotics in fertilizers may pose a threat to soil microorganisms.

CONCLUSIONS

Results suggested that the ecological risk effects of antibiotic contamination on soil bases and their potential adverse risk on human health needs special attention. © 2023 Society of Chemical Industry.

Digestate from Agricultural Biogas Plants as a Reservoir of Antimicrobials and Antibiotic Resistance Genes-Implications for the Environment

Antimicrobials and antibiotic resistance genes (ARGs) in substrates processed during anaerobic digestion in agricultural biogas plants (BPs) can reach the digestate (_D), which is used as fertilizer. Antimicrobials and ARGs can be transferred to agricultural land, which increases their concentrations in the environment. The concentrations of 13 antibiotics in digestate samples from biogas plants (BPs) were investigated in this study. The abundance of ARGs encoding resistance to beta-lactams, tetracyclines, sulfonamides, fluoroquinolones, macrolide-lincosamide-streptogramin antibiotics, and the integrase genes were determined in the analyzed samples. The presence of cadmium, lead, nickel, chromium, zinc, and mercury was also examined. Antimicrobials were not eliminated during anaerobic digestion. Their concentrations differed in digestates obtained from different substrates and in liquid and solid fractions (ranging from 62.8 ng/g clarithromycin in the solid fraction of sewage sludge digestate to 1555.9 ng/L doxycycline in the liquid fraction of cattle manure digestate). Digestates obtained from plant-based substrates were characterized by high concentrations of ARGs (ranging from 5.73 × 10² copies/g_DcfxA to 2.98 × 10⁹ copies/g_Dsul1). The samples also contained mercury (0.5 mg/kg dry mass (dm)) and zinc (830 mg/kg dm). The results confirmed that digestate is a reservoir of ARGs (5.73 × 10² to 8.89 × 10¹⁰ copies/g_D) and heavy metals (HMs). In addition, high concentrations of integrase genes (10⁵ to 10⁷ copies/g_D) in the samples indicate that mobile genetic elements may be involved in the spread of antibiotic resistance. The study suggested that the risk of soil contamination with antibiotics, HMs, and ARGs is high in farms where digestate is used as fertilizer.

Responses of cherry radish to different types of microplastics in the presence of oxytetracycline

Croplands have become a hotspot for antibiotic and microplastic (MP) pollution. However, little is known regarding their combined effects on crops. In this study, the individual and combined effects of oxytetracycline (OTC) and three MPs (i.e., polypropylene (PP), polyamide (PA), and polyvinylchloride (PVC)) on cherry radish were investigated using pot experiments. Individually, OTC (50 mg kg^-1), PA (2%, w/w), and PP (2%, w/w) induced negligible effects on cherry radish biomass and the root/shoot ratio. However, PVC (2%, w/w) significantly inhibited cherry radish growth; that is, its shoot and root fresh weight decreased by 46.2% and 81.1%, respectively. In the combined exposure groups, OTC alleviated the adverse effects of PVC on the cherry radish leaf number and shoot fresh weight. This was linked to that OTC increased the content of photosynthetic pigments. Superoxide dismutase activity in cherry radish roots was inhibited to different extents in all treatment groups except for the PA and PVC treatments. Malondialdehyde (MDA) content in cherry radish roots increased in all treatment groups, suggesting that both OTC and MPs caused oxidative damage to cherry radish root cells, therefore inhibiting cherry radish root growth. However, the presence of OTC non-significantly changed the effects of MPs on cherry radish roots. Irrespective of OTC presence, MPs induced a reduction in the root/shoot ratio of cherry radish, suggesting that the inhibitory effect of MPs on cherry radish roots was stronger than that on shoots. These findings contribute to the evaluation of the phytotoxicity of antibiotics and MPs in soil-vegetable systems.

Impact of organic soil amendments in antibiotic levels, antibiotic resistance gene loads, and microbiome composition in corn fields and crops

The potential spreading of antibiotic resistance genes (ARG) into agricultural fields and crops represent a fundamental limitation on the use of organic fertilization in food production systems. We present here a study of the effect of spreading four types of organic soil amendments (raw pig slurry, liquid and solid fractions, and a digested derivative) on demonstrative plots in two consecutive productive cycles of corn harvest (Zea mays), using a mineral fertilizer as a control, following the application of organic amendments at 32-62 T per ha (150 kg total N/ha) and allowing 5-8 months between fertilization and harvest. A combination of qPCR and high-throughput 16S rDNA sequencing methods showed a small, but significant impact of the fertilizers in both ARG loads and microbiomes in soil samples, particularly after the second harvesting cycle. The slurry solid fraction showed the largest impact on both ARG loads and microbiome variation, whereas its digestion derivatives showed a much smaller impact. Soil samples with the highest ARG loads also presented increased levels of tetracyclines, indicating a potential dual hazard by ARG and antibiotic residues linked to some organic amendments. Unlike soils, no accumulation of ARG or antibiotics was observed in corn leaves (used as fodder) or grains, and no grain sample reached detection limits for neither parameter. These results support the use of organic soil amendments in corn crops, while proposing the reduction of the loads of ARGs and antibiotics from the fertilizers to greatly reduce their potential risk.

Metagenomic assembly reveals hosts and mobility of common antibiotic resistome in animal manure and commercial compost

BACKGROUND

Antibiotics and antibiotic resistance genes (ARGs) used in intensive animal farming threaten human health worldwide; however, the common resistome, ARG mobility, and ARG host composition in different animal manures and mixed manure composts remain unclear. In the present study, metagenomic assembly and cross-sample mapping were used to comprehensively decipher the common resistome and its potential mobility and hosts in animal manure and composts.

RESULTS

In total, 201 ARGs were shared among different animal (layer, broiler, swine, beef cow, and dairy cow) manures and accounted for 86-99% of total relative abundance of ARGs. Except for multidrug, sulfonamide, and trimethoprim resistance genes, the relative abundance of most ARGs in composts was significantly lower than that in animal manure. Procrustes analysis indicated that antibiotic residues positively correlated with ARG composition in manure but not in composts. More than 75% ARG subtypes were shared between plasmids and chromosomes in our samples. Transposases could play a pivotal role in mediating the transfer of ARGs between different phyla in animal manure and composting. Cross-sample mapping to contigs carrying ARGs showed that the hosts of common resistome in manure had preference on animal species, and the dominant genus of ARG host shifted from Enterococcus in manure to Pseudomonas in composts. The broad host range and linking with diverse mobile genetic elements (MGEs) were two key factors for ARGs, such as sul1 and aadA, which could survive during composting. The multidrug resistance genes represented the dominant ARGs in pathogenic antibiotic-resistant bacteria in manure but could be effectively controlled by composting.

CONCLUSIONS

Our experiments revealed the common resistome in animal manure, classified and relative quantified the ARG hosts, and assessed the mobility of ARGs. Composting can mitigate ARGs in animal manure by altering the bacterial hosts; however, persistent ARGs can escape from the removal because of diverse host range and MGEs. Our findings provide an overall background for source tracking, risk assessment, and control of livestock ARGs.

Uncovering antimicrobial resistance in three agricultural biogas plants using plant-based substrates

Antimicrobial resistance (AMR) is becoming an increasing global concern and the anaerobic digestion (AD) process represents a potential transmission route when digestates are used as fertilizing agents. AMR contaminants, e.g. antibiotic-resistant bacteria (ARB) and plasmid-mediated antibiotic resistance genes (ARGs) have been found in different substrates and AD systems, but not yet been investigated in plant-based substrates. AMR transfer from soils to vegetable microbiomes has been observed, and thus crop material potentially represents a so far neglected AMR load in agricultural AD processes, contributing to AMR spread. In order to test this hypothesis, this study examined the AMR situation throughout the process of three biogas plants using plant-based substrates only, or a mixture of plant-based and manure substrates. The evaluation included a combination of culture-independent and -dependent methods, i.e., identification of ARGs, plasmids, and pathogenic bacteria by DNA arrays, and phylogenetic classification of bacterial isolates and their phenotypic resistance pattern. To our knowledge, this is the first study on AMR in plant-based substrates and the corresponding biogas plant. The results showed that the bacterial community isolated from the investigated substrates and the AD processing facilities were mainly Gram-positive Bacillus spp. Apart from Pantoea agglomerans, no other Gram-negative species were found, either by bacteria culturing or by DNA typing array. In contrast, the presence of ARGs and plasmids clearly indicated the existence of Gram-negative pathogenic bacteria, in both substrate and AD process. Compared with substrates, digestates had lower levels of ARGs, plasmids, and culturable ARB. Thus, digestate could pose a lower risk of spreading AMR than substrates per se. In conclusion, plant-based substrates are associated with AMR, including culturable Gram-positive ARB and Gram-negative pathogenic bacteria-associated ARGs and plasmids. Thus, the AMR load from plant-based substrates should be taken into consideration in agricultural biogas processing.

ROCker Models for Reliable Detection and Typing of Short-Read Sequences Carrying β-Lactamase Genes

Identification of genes encoding β-lactamases (BLs) from short-read sequences remains challenging due to the high frequency of shared amino acid functional domains and motifs in proteins encoded by BL genes and related non-BL gene sequences. Divergent BL homologs can be frequently missed during similarity searches, which has important practical consequences for monitoring antibiotic resistance. To address this limitation, we built ROCker models that targeted broad classes (e.g., class A, B, C, and D) and individual families (e.g., TEM) of BLs and challenged them with mock 150-bp- and 250-bp-read data sets of known composition. ROCker identifies most-discriminant bit score thresholds in sliding windows along the sequence of the target protein sequence and hence can account for nondiscriminative domains shared by unrelated proteins. BL ROCker models showed a 0% false-positive rate (FPR), a 0% to 4% false-negative rate (FNR), and an up-to-50-fold-higher F1 score [2 × precision × recall/(precision + recall)] compared to alternative methods, such as similarity searches using BLASTx with various e-value thresholds and BL hidden Markov models, or tools like DeepARG, ShortBRED, and AMRFinder. The ROCker models and the underlying protein sequence reference data sets and phylogenetic trees for read placement are freely available through http://enve-omics.ce.gatech.edu/data/rocker-bla. Application of these BL ROCker models to metagenomics, metatranscriptomics, and high-throughput PCR gene amplicon data should facilitate the reliable detection and quantification of BL variants encoded by environmental or clinical isolates and microbiomes and more accurate assessment of the associated public health risk, compared to the current practice.

IMPORTANCE Resistance genes encoding β-lactamases (BLs) confer resistance to the widely prescribed antibiotic class β-lactams. Therefore, it is important to assess the prevalence of BL genes in clinical or environmental samples for monitoring the spreading of these genes into pathogens and estimating public health risk. However, detecting BLs in short-read sequence data is technically challenging. Our ROCker model-based bioinformatics approach showcases the reliable detection and typing of BLs in complex data sets and thus contributes toward solving an important problem in antibiotic resistance surveillance. The ROCker models developed substantially expand the toolbox for monitoring antibiotic resistance in clinical or environmental settings.

Occurrence of Antimicrobial Resistance in the Environment in Germany, Austria, and Switzerland: A Narrative Review of Existing Evidence

(1) Background: This study summarizes the current research on antibiotic resistance (AR) in the environment conducted in Austria, Germany, and Switzerland; (2) Methods: A narrative systematic literature review of epidemiological studies based on searches in EMBASE and CAB abstracts (up to 16 June2021) was conducted. Environmental reservoirs included water sources, wastewater, animal husbandry, wildlife, soil, and sediment; (3) Results: Four hundred and four records were screened, and 52 studies were included. Thirteen studies examined aquatic environments, and eleven investigated wastewater. Eight studies investigated both wildlife and animal husbandry. Less evidence was available for sediments, soil, and air. Considerable heterogeneity in research focus, study design, sampling, and measurement of resistance was observed. Resistance to all categories of antimicrobials in the WHO CIA list was identified. Resistance to critically important and highly important substances was reported most frequently; (4) Conclusions: The current research scope presents data-gathering efforts. Usage of a unified protocol for isolate collection, selecting sampling sites, and susceptibility testing is required to provide results that can be compared between the studies and reservoirs. Epidemiological, environmental, and ecological factors should be considered in surveys of the environmental dissemination of AR. Systematic epidemiological studies investigating AR at the interface of human, animal, and environmental health are needed.

Thermophilic 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.

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

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

Antibiotics and antibiotic resistance genes in anaerobic digesters and predicted concentrations in agroecosystems

In recent decades, the innovative practice of management and valorization of agrozootechnical waste as energy through anaerobic digestion (AD) has been rapidly growing. However, whether applying digestate to soil as biofertilizer can be a source of antibiotics (ABs) and antibiotic resistance genes (ARGs) has not been fully investigated so far. In this work the ARGs responsible for sulfamethoxazole (SMX) resistance (sul1, sul2), ciprofloxacin (CIP) resistance (qnrS, qepA, aac-(6')-Ib-cr) and the mobile genetic element intl1, together with the concentrations of the antibiotics SMX and CIP, were measured in several anaerobic digesters located in Central Italy. Based on these results, the concentrations of antibiotics and ARGs which can potentially reach soil through amendment with digestate were also estimated. The highest CIP and SMX concentrations were found during winter and spring in anaerobic digesters. The highest ARG abundances were found for the aac-(6')-Ib-cr and sul2 genes. The overall results showed that application of digestate to soil does not exclude AB contamination and spread of ARGs in agroecosystems, especially in the case of ciprofloxacin, owing to its high intrinsic persistence.

Antibiotic residues in substrates and output materials from biogas plants - Implications for agriculture

Bio-based fertilizers including farmyard manure, sewage sludge, meat and bone meal, composts, digestates and derived products are nutrient-rich fertilizers. They deliver organic matter but may pose the risk to contaminate soils by pollutants such as pharmaceuticals, heavy metals, resistance genes or pathogens. Manure and sewage sludge are increasingly used in biogas plants for energy production with the residue being used as fertilizer. It is therefore important to understand the fate of pharmaceuticals during anaerobic digestion. In the present study, 29 biogas plants from three countries were studied. The different input materials and output after digestion were analyzed for selected examples of antibiotics from three different classes, namely tetracyclines (TCs), sulfonamides (SAs) and fluoroquinolones (FQs). These classes are frequently found in animal manures and sewage sludge and display differing mobility and persistence. The results revealed that antibiotics could be detected in 81% of the substrates derived from animal manures and sewage sludge and in 83% of the digestates. Antibiotics were determined with the highest frequency of 100% in sewage sludge where especially ciprofloxacin and tetracycline were found. Highest concentrations were analyzed in poultry dung with in maximum of 8.6 and 8.2 mg/kg DW of enrofloxacin and tetracycline, respectively. After digestion, slightly lower concentrations of antibiotics were determined for most substrates. However, in one biogas plant using poultry dung as an input material a maximum concentration of 15.2 mg/kg DW of tetracycline was determined in the digestate, which after separation accounted for 29.8 mg/kg DW of tetracycline in the liquid phase.

Distribution of genetic elements associated with antibiotic resistance in treated and untreated animal husbandry waste and wastewater

Animal breeding for meat production based on swine, cattle, poultry, and aquaculture is an activity that generates several impacts on the environment, among them the spread of antibiotic resistance. There is a worldwide concern related to the massive use of antibiotics, which causes selective pressure on the microbial community, triggering bacteria that contain "antibiotic resistance genes." According to the survey here presented, antibiotic resistance-related genes such as tetracyclines (tet), erythromycin (erm), and sulfonamides (sul), as well as the genetic mobile element interferon (int), are the most reported genetic elements in qualitative and quantitative studies of swine, cattle, poultry, and aquaculture manure/wastewater. It has been observed that biological treatments based on waste composting and anaerobic digestion are effective in ARG removal, particularly for tet, bla, erm, and qnr (quinolone) genes. On the other hand, sul and intI genes were more persistent in such treatments. Tertiary treatments, such advanced oxidative processes, are suitable strategies to improve ARG reduction. In general temperature, hydraulic retention time, and penetration of sunlight are the main operational parameters for ARG reduction in treatments applied to animal waste, and therefore attention should be addressed to optimize their efficacy regarding ARG removal. Despite being reduced, the presence of ARG in treated effluents and in biosolids indicates that there is a potential risk of antibiotic resistance spread in nature, especially through the release of treated livestock waste into the environment.

Polyphasic study of antibiotic-resistant enterobacteria isolated from fresh produce in Germany and description of Enterobacter vonholyi sp. nov. isolated from marjoram and Enterobacter dykesii sp. nov. isolated from mung bean sprout

Forty-two antibiotic-resistant enterobacteria strains were isolated from fresh produce obtained from the northern German retail market. A polyphasic characterization based on both phenotypic and genotypic methods was used to identify predominant strains as Citrobacter (C.) gillenii, C. portucalensis, Enterobacter (En.) ludwigii, Escherichia (E.) coli and Klebsiella (K.) pneumoniae. 38.1% of the enterobacteria strains were resistant to tetracycline, while 23.8% and 9.5% of strains were resistant to streptomycin and chloramphenicol, respectively. A high percentage of Klebsiella (100%), Enterobacter (57.1%) and Citrobacter (42.9%) strains were also resistant to ampicillin, with some strains showing multiple resistances. For unequivocal species identification, the genomes of thirty strains were sequenced. Multilocus sequence analysis, average nucleotide identity and digital DNA-DNA hybridization showed that Enterobacter strains E1 and E13 were clearly clustered apart from Enterobacter species type strains below the species delineation cutoff values. Thus, strains E1^T (=DSM 111347^T, LMG 31875^T) represents a novel species proposed as Enterobacter dykesii sp. nov., while strain E13^T (=DSM 110788^T, LMG 31764^T) represent a novel species proposed as Enterobacter vonholyi sp. nov. Strains often possessed different serine β-lactamase genes, tet(A) and tet(D) tetracycline resistance genes and other acquired antibiotic resistance genes. Typical plasmid replicon types were determined. This study thus accurately identified the enterobacteria from fresh produce as species belonging to the genera Citrobacter, Enterobacter, Escherichia and Klebsiella, but also showed that these can carry potentially transferable antibiotic resistance genes and may thus contribute to the spread of these via the food route.

Dissemination of antibiotic resistance genes (ARGs) via integrons in Escherichia coli: A risk to human health

With the induction of various emerging environmental contaminants such as antibiotic resistance genes (ARGs), environment is considered as a key indicator for the spread of antimicrobial resistance (AMR). As such, the ARGs mediated environmental pollution raises a significant public health concern worldwide. Among various genetic mechanisms that are involved in the dissemination of ARGs, integrons play a vital role in the dissemination of ARGs. Integrons are mobile genetic elements that can capture and spread ARGs among environmental settings via transmissible plasmids and transposons. Most of the ARGs are found in Gram-negative bacteria and are primarily studied for their potential role in antibiotic resistance in clinical settings. As one of the most common microorganisms, Escherichia coli (E. coli) is widely studied as an indicator carrying drug-resistant genes, so this article aims to provide an in-depth study on the spread of ARGs via integrons associated with E. coli outside clinical settings and highlight their potential role as environmental contaminants. It also focuses on multiple but related aspects that do facilitate environmental pollution, i.e. ARGs from animal sources, water treatment plants situated at or near animal farms, agriculture fields, wild birds and animals. We believe that this updated study with summarized text, will facilitate the readers to understand the primary mechanisms as well as a variety of factors involved in the transmission and spread of ARGs among animals, humans, and the environment.

Whole Genome Sequencing of Escherichia coli From Store-Bought Produce

The role of agriculture in the transfer of drug resistant pathogens to humans is widely debated and poorly understood. Escherichia coli is a valuable indicator organism for contamination and carriage of antimicrobial resistance (AMR) in foods. Whilst whole genome sequences for E. coli from animals and associated meats are common, sequences from produce are scarce. Produce may acquire drug resistant E. coli from animal manure fertilizers, contaminated irrigation water and wildlife, particularly birds. Whole genome sequencing was used to characterize 120 tetracycline (TET) resistant E. coli from store-bought, ready-to-eat cilantro, arugula and mixed salad from two German cities. E. coli were recovered on the day of purchase and after 7 days of refrigeration. Cilantro was far more frequently contaminated with TET-resistant E. coli providing 102 (85%) sequenced strains. Phylogroup B1 dominated the collection (n = 84, 70%) with multi-locus sequence types B1-ST6186 (n = 37, 31%), C-ST165 (n = 17, 14%), B1-ST58 (n = 14, 12%), B1-ST641 (n = 8, 7%), and C-ST88 (n = 5, 4%) frequently identified. Notably, seven strains of diverse sequence type (ST) carried genetic indicators of ColV virulence plasmid carriage. A number of previously identified and novel integrons associated with insertion elements including IS26 were also identified. Storage may affect the lineages of E. coli isolated, however further studies are needed. Our study indicates produce predominantly carry E. coli with a commensal phylogroup and a variety of AMR and virulence-associated traits. Genomic surveillance of bacteria that contaminate produce should be a matter of public health importance in order to develop a holistic understanding of the environmental dimensions of AMR.

Exploring the profile of antimicrobial resistance genes harboring by bacteriophage in chicken feces

Bacteriophage may play an important role in antimicrobial resistance genes (ARGs) transmission. However, the contribution of bacteriophage to the spread of ARGs in environment, especially in poultry farm environment, is rarely known. In this study, the prevalence of ARGs in bacteriophage DNA was investigated in chicken feces from 30 different poultry farms in China. Then the abundance of the aac(6')-Ib-cr, bla_CTX-M, ermB, floR, mcr-1, sul1, tetM and intI1 genes was determined by qPCR in bacteriophage and compared with certain representative plasmid DNA samples. The results showed that 12 ARGs (aac(6')-Ib-cr, aph(3')-IIIa, bla_CTX-M, ermB, ermF, floR, mcr-1, qnrS, sul1, sul2, vanA, tetM genes) and class 1 integron gene intI1 were detected in bacteriophage DNA fraction. The sul1, tetM and aac(6')-Ib-cr genes were most prevalent with high detection rates of 77%, 61% and 55%, respectively. To our best knowledge, this study firstly reported the presence of the mcr-1 gene in bacteriophage DNA derived from farms environments. We found that the gene copy (GC) numbers of the aac(6')-Ib-cr, ermB and sul1 genes were as high as 5.47, 5.22 and 5.54 log₁₀ GC/g, respectively. Both the prevalence and abundance of ARGs in broiler fecal wastes were also generally higher than in laying hens. In addition, although the GC numbers of the aac(6')-Ib-cr, floR and tetM genes in plasmid DNA was higher than that in phage DNA fraction by 4.68, 3.59 and 3.9 orders of magnitude, respectively, the absolute abundances of the bla_CTX-M and mcr-1 genes in phage DNA were close to or even higher than that in plasmid DNA at farm SIL2, SIL4 and SIB1. As potential vessels for ARGs, bacteriophage could not be ignored due to their unique extracellular persistence in environments. Overall, this is the first comprehensive survey about bacteriophage carried ARGs from farms in different regions in China.

Characterization of the Pig Gut Microbiome and Antibiotic Resistome in Industrialized Feedlots in China

The gut microbiota is believed to be closely related to many important physical functions in the host. Comprehensive data on mammalian gut metagenomes has facilitated research on host-microbiome interaction mechanisms, but less is known about pig gut microbiome, especially the gut microbiome in industrialized feedlot pigs, compared with human microbiome. On the other hand, pig production, as an important source of food, is believed to exacerbate the antibiotic resistance in humans due to the abuse of antibiotics in pig production in various parts of the world. This study delineates an intricate picture of swine gut microbiome and antibiotic resistome in industrialized feedlots and may provide insight for the pig producing industry.

To characterize the diversity and richness and explore the function and structure of swine gut microbiome and resistome in common pig-farming feedlots, we sampled and metagenomic sequenced the feces of pigs from four different industrialized feedlots located in four distant provinces across China. Surprisingly, more than half of the nonredundant genes (1,937,648, 54.3%) in the current catalogue were newly found compared with the previously published reference gene catalogue (RGC) of the pig gut microbiome. Additionally, 16 high-completeness draft genomes were obtained by analyzing the dominant species on each feedlot. Notably, seven of these species often appeared in the human body sites. Despite a smaller number of nonredundant genes, our study identified more antibiotic resistance genes than those available in the RGC. Tetracycline, aminoglycoside, and multidrug resistance genes accounted for nearly 70% of the relative abundance in the current catalogue. Slightly higher sharing ratios were shown between the industrialized feedlot pig gut microbiomes and human gut microbiomes than that between the RGC and human counterpart (14.7% versus 12.6% in genes and 94.1% versus 87.7% in functional groups, respectively). Furthermore, a remarkably high number of the antibiotic resistance proteins (n =141) were identified to be shared by the pig, human, and mouse resistome, indicating the potential for horizontal transfer of resistance genes. Of the antibiotic resistance proteins shared by pigs and humans, 50 proteins were related to tetracycline resistance, and 49 were related to aminoglycoside resistance.

IMPORTANCE The gut microbiota is believed to be closely related to many important physical functions in the host. Comprehensive data on mammalian gut metagenomes has facilitated research on host-microbiome interaction mechanisms, but less is known about pig gut microbiome, especially the gut microbiome in industrialized feedlot pigs, compared with human microbiome. On the other hand, pig production, as an important source of food, is believed to exacerbate the antibiotic resistance in humans due to the abuse of antibiotics in pig production in various parts of the world. This study delineates an intricate picture of swine gut microbiome and antibiotic resistome in industrialized feedlots and may provide insight for the pig producing industry.

Fate of pharmaceuticals and antibiotic resistance genes in a full-scale on-farm livestock waste treatment plant

This study investigated, for the first time, the distribution and fate of 28 multiple-class veterinary pharmaceuticals and antibiotics (PhACs), and their corresponding antibiotic resistance genes (ARGs), in a full-scale on-farm livestock waste treatment plant. The plant relies on several technologies, including: anaerobic digestion (AD), solid-liquid separation, and two stages reverse osmosis (RO) of the liquid digestate. Tetracycline, fluoroquinolone, lincosamide and pleuromutilin antibiotics, together with anti-helmintic (flubendazole) and anti-inflammatory (flunixin) drugs were the most frequently detected compounds in livestock waste and in slaughterhouse sludge. This last fraction is used as co-substrate in the AD process and showed to be an important input source of PhACs and ARGs. In terms of treatment performance, AD exhibited moderate to low PhACs and ARGs reduction, while a large fraction (<50%) of the PhACs present in the digestate were distributed onto the solid fraction, after solid-liquid separation. Both solid and liquid digestates had relatively high copy numbers of ARGs. Finally, RO showed high rejection percentages for all PhACs (<90%), with concentrations in the low ng L^-1 range in permeates, for most target PhACs. Nevertheless, moderate copy numbers of ARGs were detected in permeates.

Environmental dimensions of antibiotic resistance: assessment of basic science gaps

Antibiotic resistance is one of the major problems facing medical practice in the 21st century. Historical approaches to managing antibiotic resistance have often focused on individual patients, specific pathogens and particular resistance phenotypes. However, it is increasingly recognized that antibiotic resistance is a complex ecological and evolutionary problem. As such, understanding the dynamics of antibiotic resistance requires integration of data on the diverse mobile genetic elements often associated with antibiotic resistance genes, and their dissemination by various mechanisms of horizontal gene transfer between bacterial cells and environments. Most important is understanding the fate and effects of antibiotics at sub-inhibitory concentrations, and co-selection. This opinion paper identifies key knowledge gaps in our understanding of resistance phenomena, and outlines research needs that should be addressed to help us manage resistance into the future.

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

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

Manure and Doxycycline Affect the Bacterial Community and Its Resistome in Lettuce Rhizosphere and Bulk Soil

Manure application to agricultural soil introduces antibiotic residues and increases the abundance of antibiotic-resistant bacteria (ARB) carrying antibiotic resistance genes (ARGs), often located on mobile genetic elements (MGEs). The rhizosphere is regarded as a hotspot of microbial activity and gene transfer, which can alter and prolong the effects of organic fertilizers containing antibiotics. However, not much is known about the influence of plants on the effects of doxycycline applied to soil via manure. In this study, the effects of manure spiked with or without doxycycline on the prokaryotic community composition as well as on the relative abundance of ARGs and MGEs in lettuce rhizosphere and bulk soil were investigated by means of a polyphasic cultivation-independent approach. Samples were taken 42 days after manure application, and total community DNA was extracted. Besides a pronounced manure effect, doxycycline spiking caused an additional enrichment of ARGs and MGEs. High-throughput quantitative PCR revealed an increase in tetracycline, aminoglycoside, and macrolide-lincosamide-streptogramin B (MLSB) resistance genes associated with the application of manure spiked with doxycycline. This effect was unexpectedly lower in the rhizosphere than in bulk soil, suggesting a faster dissipation of the antibiotic and a more resilient prokaryotic community in the rhizosphere. Interestingly, the tetracycline resistance gene tetA(P) was highly enriched in manure-treated bulk soil and rhizosphere, with highest values observed in doxycycline-treated bulk soil, concurring with an enrichment of Clostridia. Thus, the gene tetA(P) might be a suitable marker of soil contamination by ARB, ARGs, and antibiotics of manure origin. These findings illustrate that the effects of manure and doxycycline on ARGs and MGEs differ between rhizosphere and bulk soil, which needs to be considered when assessing risks for human health connected to the spread of ARGs in the environment.

Degradation of tetracyclines in manure-amended soil and their uptake by litchi (Litchi chinensis Sonn.)

The environmental and human health risk posed by veterinary antibiotics is of global concern. Antibiotic uptake by herbal plants has been studied, but little is known about perennial woody fruit crops. Litchi (Litchi chinensis Sonn.), a longevial fruit tree, is routinely fertilized with animal manure and, therefore, may be at risk of antibiotic uptake into its fruits. This study investigated the degradation of chlortetracycline and doxycycline present in manure used to amend orchard soil, and their subsequent assimilation by litchi plant, as affected by manure application rate. The results show that half-lives of chlortetracycline and doxycycline in soil were decreased by increased manure rate, with an average of 27 and 59 days, respectively. Chlortetracycline was readily transported to litchi shoots and increased with the growth of litchi plants. Doxycycline predominantly remained in the roots, and underwent growth dilution in the plants. The two tetracyclines could not be detected in fruits from litchi trees when applied with manures, at various rates, over 2 years. For litchi, chlortetracycline may pose human health risk through manure application, but doxycycline is unlikely to do so. Long-term field experiments are required to monitor antibiotic accumulation in fruits of perennial fruit trees fertilized with animal manure.

Assessment of Three Antimicrobial Residue Concentrations in Broiler Chicken Droppings as a Potential Risk Factor for Public Health and Environment

Tetracyclines, sulfonamides and amphenicols are broad spectrum antimicrobial drugs that are widely used in poultry farming. However, a high proportion of these drugs can be excreted at high concentrations in droppings, even after the end of a therapy course. This work intended to assess and compare concentrations of florfenicol (FF), florfenicol amine (FFa), chlortetracycline (CTC), 4-epi-chlortetracycline (4-epi-CTC), and sulfachloropyridazine (SCP) in broiler chicken droppings. To this end, 70 chickens were housed under controlled environmental conditions, and assigned to experimental groups that were treated with therapeutic doses of either 10% FF, 20% CTC, or 10% SCP. Consequently, we implemented and designed an in-house validation for three analytical methodologies, which allowed us to quantify the concentrations of these three antimicrobial drugs using liquid chromatography coupled to mass spectrometry (LC-MS/MS). Our results showed that FF and FFa concentrations were detected in chicken droppings up to day 10 after ceasing treatment, while CTC and 4-epi-CTC were detected up to day 25. As for SCP residues, these were detected up to day 21. Noticeably, CTC showed the longest excretion period, as well as the highest concentrations detected after the end of its administration using therapeutic doses.

The Transferable Resistome of Produce

Produce is increasingly recognized as a reservoir of human pathogens and transferable antibiotic resistance genes. This study aimed to explore methods to characterize the transferable resistome of bacteria associated with produce. Mixed salad, arugula, and cilantro purchased from supermarkets in Germany were analyzed by means of cultivation- and DNA-based methods. Before and after a nonselective enrichment step, tetracycline (TET)-resistant Escherichia coli were isolated and plasmids conferring TET resistance were captured by exogenous plasmid isolation. TET-resistant E. coli isolates, transconjugants, and total community DNA (TC-DNA) from the microbial fraction detached from leaves or after enrichment were analyzed for the presence of resistance genes, class 1 integrons, and various plasmids by real-time PCR and PCR-Southern blot hybridization. Real-time PCR primers were developed for IncI and IncF plasmids. TET-resistant E. coli isolated from arugula and cilantro carried IncF, IncI1, IncN, IncHI1, IncU, and IncX1 plasmids. Three isolates from cilantro were positive for IncN plasmids and blaCTX-M-1 From mixed salad and cilantro, IncF, IncI1, and IncP-1β plasmids were captured exogenously. Importantly, whereas direct detection of IncI and IncF plasmids in TC-DNA failed, these plasmids became detectable in DNA extracted from enrichment cultures. This confirms that cultivation-independent DNA-based methods are not always sufficiently sensitive to detect the transferable resistome in the rare microbiome. In summary, this study showed that an impressive diversity of self-transmissible multiple resistance plasmids was detected in bacteria associated with produce that is consumed raw, and exogenous capturing into E. coli suggests that they could transfer to gut bacteria as well.IMPORTANCE Produce is one of the most popular food commodities. Unfortunately, leafy greens can be a reservoir of transferable antibiotic resistance genes. We found that IncF and IncI plasmids were the most prevalent plasmid types in E. coli isolates from produce. This study highlights the importance of the rare microbiome associated with produce as a source of antibiotic resistance genes that might escape cultivation-independent detection, yet may be transferred to human pathogens or commensals.

Antibiotics and Antibiotic Resistance Genes in Bulk and Rhizosphere Soils Subject to Manure Amendment and Vegetable Cultivation

There is interest in understanding effects of amending soil with manure in a cultivation setting and if composting can provide benefits. Raw or composted manure from cattle administered with and without sulfamethazine, chlortetracycline, and tylosin was amended to loamy sand and silty clay loam soils, where lettuce ( L.), radish ( L.), and broccoli ( L. var. ) were cultivated and compared with those grown in soil amended with fertilizer as a control. Upon plant maturation, rhizosphere and bulk soils were analyzed for antibiotics, and 1, B, (W), and I1 genes were quantified. Antibiotic concentrations in compost-amended soils were below detection limits. For soils amended with manure containing antibiotics, sulfamethazine ranged from 1.1 to 3.1 μg kg in the bulk soils but was below detection limits in the rhizosphere soils. Chlortetracycline (2.8-9.3 μg kg) was two times lower in the rhizosphere than in the bulk soil. Levels of tylosin in the rhizosphere soil were similar to the bulk soil. Soil texture or vegetable type did not have significant influence on antibiotic concentration differences between the bulk and rhizosphere soils. Relative abundances of (W) and I1 in the fertilizer-amended soil were significantly lower than in those amended with manure or compost ( < 0.05), whereas B was not detected in any soils. Rhizosphere zone has no significant effect on the detected antibiotic resistance genes. It is suggested that plant roots may have a substantial effect on the fate of certain antibiotics in manure-amended fields, but less of an effect on antibiotic resistance and mobility genes.

Critical knowledge gaps and research needs related to the environmental dimensions of antibiotic resistance

There is growing understanding that the environment plays an important role both in the transmission of antibiotic resistant pathogens and in their evolution. Accordingly, researchers and stakeholders world-wide seek to further explore the mechanisms and drivers involved, quantify risks and identify suitable interventions. There is a clear value in establishing research needs and coordinating efforts within and across nations in order to best tackle this global challenge. At an international workshop in late September 2017, scientists from 14 countries with expertise on the environmental dimensions of antibiotic resistance gathered to define critical knowledge gaps. Four key areas were identified where research is urgently needed: 1) the relative contributions of different sources of antibiotics and antibiotic resistant bacteria into the environment; 2) the role of the environment, and particularly anthropogenic inputs, in the evolution of resistance; 3) the overall human and animal health impacts caused by exposure to environmental resistant bacteria; and 4) the efficacy and feasibility of different technological, social, economic and behavioral interventions to mitigate environmental antibiotic resistance.1.

Hops (Humulus lupulus L.) Bitter Acids: Modulation of Rumen Fermentation and Potential As an Alternative Growth Promoter

Antibiotics can improve ruminant growth and efficiency by altering rumen fermentation via selective inhibition of microorganisms. However, antibiotic use is increasingly restricted due to concerns about the spread of antibiotic-resistance. Plant-based antimicrobials are alternatives to antibiotics in animal production. The hops plant (Humulus lupulus L.) produces a range of bioactive secondary metabolites, including antimicrobial prenylated phloroglucinols, which are commonly called alpha- and beta-acids. These latter compounds can be considered phyto-ionophores, phytochemicals with a similar antimicrobial mechanism of action to ionophore antibiotics (e.g., monensin, lasalocid). Like ionophores, the hop beta-acids inhibit rumen bacteria possessing a classical Gram-positive cell envelope. This selective inhibition causes several effects on rumen fermentation that are beneficial to finishing cattle, such as decreased proteolysis, ammonia production, acetate: propionate ratio, and methane production. This article reviews the effects of hops and hop secondary metabolites on rumen fermentation, including the physiological mechanisms on specific rumen microorganisms, and consequences for the ruminant host and ruminant production. Further, we propose that hop beta-acids are useful model natural products for ruminants because of (1) the ionophore-like mechanism of action and spectrum of activity and (2) the literature available on the plant due to its use in brewing.

Lessons from the Environmental Antibiotic Resistome

Antibiotic resistance is a global public health issue of growing proportions. All antibiotics are susceptible to resistance. The evidence is now clear that the environment is the single largest source and reservoir of resistance. Soil, aquatic, atmospheric, animal-associated, and built ecosystems are home to microbes that harbor antibiotic resistance elements and the means to mobilize them. The diversity and abundance of resistance in the environment is consistent with the ancient origins of antibiotics and a variety of studies support a long natural history of associated resistance. The implications are clear: Understanding the evolution of resistance in the environment, its diversity, and mechanisms is essential to the management of our existing and future antibiotic resources.

In silico serine β-lactamases analysis reveals a huge potential resistome in environmental and pathogenic species

The secretion of antimicrobial compounds is an ancient mechanism with clear survival benefits for microbes competing with other microorganisms. Consequently, mechanisms that confer resistance are also ancient and may represent an underestimated reservoir in environmental bacteria. In this context, β-lactamases (BLs) are of great interest due to their long-term presence and diversification in the hospital environment, leading to the emergence of Gram-negative pathogens that are resistant to cephalosporins (extended spectrum BLs = ESBLs) and carbapenems (carbapenemases). In the current study, protein sequence databases were used to analyze BLs, and the results revealed a substantial number of unknown and functionally uncharacterized BLs in a multitude of environmental and pathogenic species. Together, these BLs represent an uncharacterized reservoir of potentially transferable resistance genes. Considering all available data, in silico approaches appear to more adequately reflect a given resistome than analyses of limited datasets. This approach leads to a more precise definition of BL clades and conserved motifs. Moreover, it may support the prediction of new resistance determinants and improve the tailored development of robust molecular diagnostics.