Bloom of resident antibiotic-resistant bacteria in soil following manure fertilization

Reducing tetracycline resistance genes in wheat soil using natural quorum sensing inhibitors: A new approach for mitigating antibiotic resistance gene contamination

The distribution and transmission of antibiotic resistance genes (ARGs) in agricultural soils constitute a significant threat to food safety and human health. Natural quorum sensing inhibitors (QSIs), with advantages such as low plant toxicity and low application costs, present a potential approach for mitigating ARG contamination by targeting bacterial quorum sensing systems. This study explored the impacts and mechanisms of three natural QSIs (vanillin, catechin, and tannin) on the abundance of tetracycline resistance genes (TRGs) in both rhizosphere and non-rhizosphere soils. Results illustrated a notable reduction in TRG abundance across three natural QSI treatments, with catechin displaying the most pronounced effect in the rhizosphere soil. Furthermore, the application of natural QSIs had a significant influence on the bacterial community structure and population dynamics, particularly evident in the alterations induced by catechin on bacterial interactions within the soil ecosystem. Natural QSIs inhibited the production of N-acyl homoserine lactone (AHL) signaling molecules. The primary environmental factors driving changes in bacterial community were identified as pH and NO3--N content. Through mechanisms involving the modulations of AHL concentrations and soil environmental factors, natural QSIs were found to impact bacterial population, ultimately leading to a decrease in TRG abundance. Importantly, the application of natural QSIs did not exhibit adverse effects on plant phenotypic traits. These findings serve as a useful reference for implementing natural QSIs to effectively control soil ARG contamination.

Effects of Organic Soil Amendments on Antimicrobial-Resistant Bacteria in Urban Agriculture Environments

Biological soil amendments of animal origin (BSAAOs) are widely used in urban agriculture to improve soil quality. Although BSAAO use is regulated due to risks for introducing foodborne pathogens, effects on antimicrobial-resistant (AMR) bacteria are not well established. Here, we aimed to explore the impacts of BSAAOs on levels of resident AMR bacteria in leafy vegetable production environments (i.e., kale, lettuce, chard, cabbage) across urban farms and community gardens in the greater Washington D.C. area (n = 7 sites). Leaf tissue (LT), root zone soil (RZS; amended soil in crop beds), and bulk soil (BS; site perimeter) were collected and analyzed for concentrations of total heterotrophic bacteria (THB), ampicillin (Amp) or tetracycline (Tet) resistant THB, and coliforms. As expected, amended plots harbored significantly higher concentrations of THB than bulk soil (P < 0.001). The increases in total bacteria associated with reduced fractions of Tet-resistant bacteria (P = 0.008), as well as case-specific trends for reduced fractions of Amp-resistant bacteria and coliforms. Site-to-site variation in concentrations of AMR bacteria in soil and vegetable samples reflected differences in land history and crop management, while within-site variation was associated with specific amendment sources, as well as vegetable type and cultivar. Representative isolates of the AMR bacteria and coliforms were further screened for multidrug resistance (MDR) phenotypes, and a high frequency was observed for the former. In amended soils, as the soil pH (range 6.56-7.80) positively correlated with the fraction of Tet-resistant bacteria (rho = 0.529; P < 0.001), crop management strategies targeting pH may have applications to control related risks. Overall, our findings demonstrate that soil amendments promote soil bacteria concentrations and have important implications for limiting the spread of AMR bacteria, at least in the urban landscape.

Impact of aeration rate on the transfer range of antibiotic-resistant plasmids during manure composting

Conjugative plasmids are important vectors of mobile antibiotic resvistance genes (ARGs), facilitating their horizontal transfer within the environment. While composting is recognized as an effective method to reduce antibiotics and ARGs in animal manure, its impact on the bacterial host communities containing antibiotic-resistant plasmids remains unclear. In this study, we investigated the permissiveness of bacterial community during composting when challenged with multidrug-resistant conjugative RP4 plasmids, employing Pseudomonas putida as the donor strain. Ultimately, this represents the first exploration of the effects of aeration rates on the range of RP4 plasmid transfer hosts. Transconjugants were analyzed through fluorescent reporter gene-based fluorescence-activated cell sorting and Illumina sequencing. Overall, aeration rates were found to influence various physicochemical parameters of compost, including temperature, pH, total organic matter, total nitrogen, and potassium. Regarding RP4 plasmid host bacteria, the dominant phylum was determined to shift from Bacteroidetes in the raw material to Proteobacteria in the compost. Notably, a moderate-intensity aeration rate (0.05 L/min/L) was found to be more effective in reducing the diversity and richness of the RP4 plasmid host bacterial community. Following composting, the total percentage of dominant transconjugant-related genera decreased by 66.15-76.62%. Ultimately, this study determined that the aeration rate negatively impacts RP4 plasmid host abundance primarily through alterations to the environmental factors during composting. In summary, these findings enhance our understanding of plasmid host bacterial communities under varying composting aeration rates and offer novel insights into preventing the dissemination of ARGs from animal manure to farmland.

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.

Occurrence and dissemination of antibiotics and antibiotic resistance in aquatic environment and its ecological implications: a review

The occurrence of antibiotics and antibiotic-resistant bacteria (ARBs), genes (ARGs), and mobile genetic elements (MGEs) in aquatic systems is growing global public health concern. These emerging micropollutants, stemming from improper wastewater treatment and disposal, highlight the complex and evolving nature of environmental pollution. Current literature reveals potential biases, such as a geographical focus on specific regions, leading to an insufficient understanding of the global distribution and dynamics of antibiotic resistance in aquatic systems. There is methodological inconsistency across studies, making it challenging to compare findings. Potential biases include sample collection inconsistencies, detection sensitivity variances, and data interpretation variability. Gaps in understanding include the need for comprehensive, standardized long-term monitoring programs, elucidating the environmental fate and transformation of antibiotics and resistance genes. This review summarizes current knowledge on the occurrence and dissemination of emerging micropollutants, their ecological impacts, and the global health implications of antimicrobial resistance. It highlights the need for interdisciplinary collaborations among researchers, policymakers, and stakeholders to address the challenges posed by antibiotic resistance in aquatic resistance in aquatic systems effectively. This review highlights widespread antibiotic and antibiotic resistance in aquatic environment, driven by human and agricultural activities. It underscores the ecological consequences, including disrupted microbial communities and altered ecosystem functions. The findings call for urgent measures to mitigate antibiotics pollution and manage antibiotic resistance spread in water bodies.

Transmission of antibiotic resistance through organic amendments in arable land: A 3-year field study with pigeonpea-wheat cropping system

The worldwide emergence of antimicrobial resistance (AMR) poses a substantial risk to human health and environmental stability. In agriculture, organic amendments (derived from organic sources such as manure, and plant residues) are beneficial in restoring soil properties and providing essential nutrients to crops but raise concerns about harboring antibiotic resistance, which emphasizes the need for vigilant monitoring and strategic interventions in their application. The current study assessed the impact of farming practices (organic and conventional) in a three-year field experiment with pigeonpea-wheat cropping system, focusing on the transmission of AMR using culture-dependent and -independent approaches, and soil nutrient content. Markers for antibiotic resistance genes (ARGs) (aminoglycoside-aacA, β-lactam-blaTEM, chloramphenicol-cmlA1, macrolide-ermB, sulfonamides-sul1, sul2, and tetracycline-tetO) and integrons (intl1 and intl2) were targeted using qPCR. Manure amendments, particularly FYM1, exhibited a higher abundance of copies of ARGs compared to the rhizospheric soil. Organic farming was associated with higher copies of intl2, sul1, blaTEM, and tetO genes, while conventional farming showed increased copies of sul2 and ermB genes in the rhizosphere. Significant positive correlations were observed among soil nutrient contents, ARGs, and MGEs. The notable prevalence of ARGs linked to manure amendments serves as a cautionary note, demanding responsible management practices.

Mobile genetic elements mediate the cross-media transmission of antibiotic resistance genes from pig farms and their risks

Manure composting in traditional small-scale pig farms leads to the migration and diffusion of antibiotics and antibiotics resistance genes (ARGs) along the chain of transmission to the surrounding environment, increasing the risk of environmental resistance. Understanding the transmission patterns, driving factors, and health risks of ARGs on small-scale pig farms is important for effective control of ARGs transmission. This study was conducted on a small pig farm and its surrounding environment. The cross-media transmission of ARGs and their risks in the farming habitat were investigated using Metagenomic annotation and qPCR quantitative detection. The results indicate that ARGs in farms spread with manure pile-soil-channel sediment-mudflat sediment. Pig farm manure contributed 22.49 % of the mudflat sediment ARGs. Mobile genetic elements mediate the spread of ARGs across different media. Among them, tnpA and IS26 have the highest degree. Transmission of high-risk ARGs sul1 and tetM resulted in a 50 % and 116 % increase in host risk for sediment, respectively. This study provides a basis for farm manure management and control of the ARGs spread.

Assessment of antibiotic-resistant infection risks associated with reclaimed wastewater irrigation in intensive tomato cultivation

Agricultural irrigation using reclaimed urban wastewater (RWW) represents a sustainable practice to meet the ever-increasing water stress in modern societies. However, the occurrence of residual antibiotics and antibiotic resistant bacteria (ARB) in RWW is an important human health concern. This study applied for the first time a novel Simple-Death dose-response model to the field data of Escherichia coli and Pseudomonas spp. collected from three greenhouses for cultivation of tomatoes irrigated with RWW. The model estimates the risk of infection by enteropathogenic E. coli associated with consumption of tomatoes and the risk of eye-infection caused by Pseudomonas aeruginosa in cultivation soil through hand-to-eye contacts. The fraction of antibiotic resistant (AR)-E. coli measured in irrigation water and AR-Pseudomonas spp. in soil was incorporated in the model to estimate the survival of ARB and antibiotic susceptible bacteria in the presence of trace level of antibiotics in human body. The results showed that the risk of E. coli infection through consumption of tomatoes irrigated with RWW is within the WHO and USEPA recommended risk threshold (<10-4); Pseudomonas aeruginosa eye-infection risk is at or below the acceptable risk level. The presence of residual antibiotic in human body reduced the overall risk probabilities of infections but selectively enhanced the survival of ARB in comparison to their susceptible counterparts, which resulted in antibiotic untreatable infection. Therefore, the outcomes of this study call for a new risk threshold for antibiotic untreatable infections and highlight the key importance of adopting work safety measures for better human health protection.

Nano-CeO2 activates physical and chemical defenses of garlic (Allium sativum L.) for reducing antibiotic resistance genes in plant endosphere

The transmission of manure- and wastewater-borne antibiotic-resistant bacteria (ARB) to plants contributes to the proliferation of antimicrobial resistance in agriculture, necessitating effective strategies for preventing the spread of antibiotic resistance genes (ARGs) from ARB in the environment to humans. Nanomaterials are potential candidates for efficiently controlling the dissemination of ARGs. The present study investigated the abundance of ARGs in hydroponically grown garlic (Allium sativum L.) following nano-CeO2 (nCeO2) application. Specifically, root exposure to nCeO2 (1, 2.5, 5, 10 mg L-1, 18 days) reduced ARG abundance in the endosphere of bulbs and leaves. The accumulation of ARGs (cat, tet, and aph(3')-Ia) in garlic bulbs decreased by 24.2-32.5 % after nCeO2 exposure at 10 mg L-1. Notably, the lignification extent of garlic stem-disc was enhanced by 10 mg L-1 nCeO2, thereby accelerating the formation of an apoplastic barrier to impede the upward transfer of ARG-harboring bacteria to garlic bulbs. Besides, nCeO2 upregulated the gene expression related to alliin biosynthesis and increased allicin content by 15.9-16.2 %, promoting a potent antimicrobial defense for reducing ARG-harboring bacteria. The potential exposure risks associated with ARGs and Ce were evaluated according to the estimated daily intake (EDI). The EDI of ARGs exhibited a decrease exceeding 95 %, while the EDI of Ce remained below the estimated oral reference dose. Consequently, through stimulating physical and chemical defenses, nCeO2 contributed to a reduced EDI of ARGs and Ce, highlighting its potential for controlling ARGs in plant endosphere within the framework of nano-enabled agrotechnology.

Effect of poultry litter soil amendment on antibiotic-resistant Escherichia coli

Given the high cost and non-renewability of mineral-based fertilizers, there is increasing interest in the innovative use of manure-based materials, such as poultry litter (PL). However, manure-based fertilizers add both nutrients and microbes to the soil, including antibiotic-resistant Escherichia coli (AREc). PL soil amendment impact on AREc in corn fields was evaluated in a randomized field experiment (May-October 2017). Two winter cropping systems (fallow and cover crop) were assigned to whole plots, with three spring-applied fertilizer treatments (untreated control [UC], PL, and commercial fertilizer [CF]) assigned to subplots. Soil was collected from 0 to 15 cm on days 0, 7, 28, 70, 98, and 172 post-treatment applications. Samples were cultured for the enumeration and prevalence of generic, tetracycline-resistant (TETr), third-generation cephalosporin-resistant (3GCr) E. coli isolates, and extended spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae. PL soil amendment significantly (p < 0.05) increased the levels of generic E. coli, TETr E. coli, and 3GCr E. coli on days 7 and 28 compared to UC or CF. Beyond day 28, AREc did not significantly (p > 0.05) differ by fertilizer treatment and returned to baseline on day 70. ESBL-producing Enterobacteriaceae were detected from 16 samples, mostly on day 70. Cover crop significantly decreased TETr E. coli concentration on day 28, with no significant effects on the prevalence of 3GCr E. coli and ESBL-producing Enterobacteriaceae compared to no cover crop. All ESBL-producing Enterobacteriaceae and 79% of the 3GCr E. coli isolates were positive for blaCTX-M gene by polymerase chain reaction. Results show that PL soil amendment transiently increases the levels of AREc compared to mineral fertilizer.

Effect 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.

The Use and Impact of Antibiotics in Plant Agriculture: A Review

Growers have depended on the specificity and efficacy of streptomycin and oxytetracycline as a part of their plant disease arsenal since the middle of the 20th century. With climate change intensifying plant bacterial epidemics, the established success of these antibiotics remains threatened. Our strong reliance on certain antibiotics for devastating diseases eventually gave way to resistance development. Although antibiotics in plant agriculture equal to less than 0.5% of overall antibiotic use in the United States, it is still imperative for humans to continue to monitor usage, environmental residues, and resistance in bacterial populations. This review provides an overview of the history and use, resistance and mitigation, regulation, environmental impact, and economics of antibiotics in plant agriculture. Bacterial issues, such as the ongoing Huanglongbing (citrus greening) epidemic in Florida citrus production, may need antibiotics for adequate control. Therefore, preserving the efficacy of our current antibiotics by utilizing more targeted application methods, such as trunk injection, should be a major focus. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Manure application amplified the co-selection of quaternary ammonium disinfectant and antibiotic on soil antibiotic resistome

Disinfectants and antibiotics are widely used for the prevention and control of bacterial infectious diseases. Frequent disinfection is thought to exacerbate antibiotic resistance. However, little is known about how disinfectants and antibiotics co-induce changes in the soil antibiotic resistance genes (ARGs). This study determined the ARG profiles and bacterial community dynamics between unamended soil and manure-amended soil exposed to benzalkonium chloride (C12) (BC, 10 mg kg-1) disinfectant and sulfamethazine (SMZ, 1 mg kg-1), using high-throughput quantitative PCR and 16 S rRNA gene sequencing. Manure application enriched the soil in terms of ARGs abundance and diversity, which synergistically amplified the co-selection effect of BC and SMZ on soil antibiotic resistome. Compared with the control treatment, BC and SMZ exposure had a smaller impact on the bacterial infectious diseases and antimicrobial resistance-related functions in manure-amended soil, in which bacterial communities with greater tolerance to antimicrobial substances were constructed. Manure application increased the proportion of rank I ARGs and potential human pathogenic bacteria, while BC and SMZ exposure increased the drug-resistant pathogens transmission risk. This study validated that BC and SMZ aggravated the antimicrobial resistance under manure application, providing a reference for managing the spread risk of antimicrobial resistance in agricultural activities.

Soil type and moisture content alter soil microbial responses to manure from cattle administered antibiotics

Growing concerns about the global antimicrobial resistance crisis require a better understanding of how antibiotic resistance persists in soil and how antibiotic exposure impacts soil microbial communities. In agroecosystems, these responses are complex because environmental factors may influence how soil microbial communities respond to manure and antibiotic exposure. The study aimed to determine how soil type and moisture alter responses of microbial communities to additions of manure from cattle treated with antibiotics. Soil microcosms were constructed using two soil types at 15, 30, or 45% moisture. Microcosms received biweekly additions of manure from cattle given cephapirin or pirlimycin, antibiotic-free manure, or no manure. While soil type and moisture had the largest effects on microbiome structure, impacts of manure treatments on community structure and individual ARG abundances were observed across varying soil conditions. Activity was also affected, as respiration increased in the cephapirin treatment but decreased with pirlimycin. Manure from cattle antibiotics also increased NH4+ and decreased NO3- availability in some scenarios, but the effects were heavily influenced by soil type and moisture. Overall, this work demonstrates that environmental conditions can alter how manure from cattle administered antibiotics impact the soil microbiome. A nuanced approach that considers environmental variability may benefit the long-term management of antibiotic resistance in soil systems.

Deciphering the biotic and abiotic drivers of coalescence asymmetry between soil and manure microbiomes

Manure application improves soil fertility, yet its implications on the success of invasion of manure-borne microorganisms in the soil are poorly understood. Here, we assessed the importance of abiotic and biotic factors in modulating the extent to which manure-borne fungal and bacterial communities can invade resident soil microbial communities. For this purpose, we applied varying frequencies of two different amounts of manure to nine soils differing in physico-chemical properties, as well as in land-use history, over 180 days and monitored changes in bacterial and fungal communities. Variance partitioning revealed differential contributions of abiotic and biotic factors to invasion success, which together accounted for up to 82 % of the variance explained. We showed that the effects of interactions between biotic and abiotic factors increased with coalescence frequency and manure amount for the bacterial and fungal communities, respectively. Both abiotic and biotic factors were important for modulating coalescence asymmetry for the bacterial community, whereas abiotic factors had a greater effect on the fungal community. These results provide new insights into the drivers of coalescence events between manure and resident soil microbial communities. Moreover, our findings highlight the roles of the mixing ratio and frequency of coalescence events in modulating the survival of manure-borne microorganisms.

Effects of environmentally relevant concentrations of oxytetracycline and sulfadiazine on the bacterial communities, antibiotic resistance genes, and functional genes are different between maize rhizosphere and bulk soil

Antibiotic contamination in soil has become a major concern worldwide. At present, it is not clear how two co-existed antibiotics with environmentally relevant concentrations would affect soil bacterial community structure, the abundances of antibiotic resistance genes (ARGs) and functional genes, and whether the effects of antibiotics would differ between rhizosphere and bulk soil. We conducted a greenhouse pot experiment to grow maize in a loess soil treated with oxytetracycline (OTC) or sulfadiazine (SDZ) or both at an environmentally relevant concentration (1 mg kg-1) to investigate the effects of OTC and SDZ on the rhizosphere and bulk soil bacterial communities, abundances of ARGs and carbon (C)-, nitrogen (N)-, and phosphorus (P)-cycling functional genes, and on plant growth and plant N and P nutrition. The results show that the effects of environmentally relevant concentrations of OTC and SDZ on bacterial communities and abundances of ARGs and functional genes differ between maize rhizosphere and bulk soil. The effects of two antibiotics resulted in a higher absolute abundances of accA, tet(34), tnpA-04, and sul2 in the rhizosphere soil than in the bulk soil and different bacterial community compositions and biomarkers in the rhizosphere soil and the bulk soil. However, OTC had a stronger inhibitory effect on the abundances of a few functional genes in the bulk soil than SDZ did, and their combination had no synergistic effect on plant growth, ARGs, and functional genes. The role of co-existed OTC and SDZ decreased shoot height and increased root N concentration. The results demonstrate that environmentally relevant concentrations of antibiotics shift soil microbial community structure, increase the abundances of ARGs, and reduce the abundances of functional genes. Furthermore, soil contamination with antibiotics can diminish agricultural production via phytotoxic effects on crops, and combined effects of antibiotics on plant growth and nutrient uptake should be considered.

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

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

Persistence and potential risks of tetracyclines and their transformation products in two typical different animal manure composting treatments

Abundant residues of tetracyclines in animal manures and manure-derived organic fertilizers can pose a substantial risk to environments. However, our knowledge on the residual levels and potential risk of tetracyclines and their transformation products (TPs) in manure and manure-derived organic fertilizers produced by different composting treatments is still limited. Herein, the occurrence and distribution of four veterinary tetracyclines (tetracycline, oxytetracycline, chlortetracycline, and doxycycline) and ten of their TPs were investigated in paired samples of fresh manure and manure-derived organic fertilizers. Tetracyclines and TPs were frequently detected in manure and manure-derived organic fertilizer samples in ranging from 130 to 118,137 μg·kg-1 and 54.6 to 104,891 μg·kg-1, respectively. Notably, the TPs concentrations of tetracycline and chlortetracycline were comparable to those of the parent compounds, with 4-epimers being always dominant and retained antibacterial potency. Based on paired-sampling strategy, the removal efficiency of tetracyclines and TPs in thermophilic composting was higher than that in manure storage. Toxicological data in the soil environment and the data derived from equilibrium partitioning method, indicated that tetracyclines and some TPs like 4-epitetracycline, 4-epichlortetracycline and isochlortetracycline could pose median to high ecological risk to terrestrial organisms. Total concentrations of TPs in manure-derived organic fertilizers were significantly correlated with the absolute abundance of tet(X) family genes, which provide evidence to evaluate the effects of TPs on the levels of antibiotic resistance in the environment. Among them, the 4-epitetracycline could pose ecological risk and retain antibacterial potency. Our findings emphasize the importance of monitoring and controlling the prevalence of tetracyclines and their TPs in livestock-related environments.

Field-based evidence for the enrichment of intrinsic antibiotic resistome stimulated by plant-derived fertilizer in agricultural soil

Animal manures have been demonstrated to enhance antibiotic resistance in agricultural soils. However, little is known about the effects of plant-derived fertilizer on soil antibiotic resistome. Herein, metagenomic sequencing was used to investigate the effects of a plant-derived fertilizer processed from sugarcane and beet on soil antibiotic resistance genes (ARGs) in a soybean field along crop growth stages. ARG profiles in the soils amended by plant-derived fertilizer were compared with those in the soils amended by chicken manure. The abundance and diversity of total ARGs in the soils amended by plant-derived fertilizer were significantly (P < 0.05) elevated at the sprout stage, to a level comparable to that in the manured soils. Whereas, unlike chicken manure mainly introducing manure-borne ARGs to soil, the plant-derived fertilizer was indicated to mainly enrich multidrug resistance genes in soil by nourishing indigenous bacteria. ARGs with abundances in amended soils significantly (P < 0.05) higher than in unamended soils at the sprout stage of soybean were considered as enriched ARGs. Decrease in the abundance of the enriched ARGs was observed in both the amended soils from the sprout to the harvest. Network analysis further identified Proteobacteria and Bacteroidetes as the primary bacterial taxa involved in the temporal variation of the enriched ARGs in the soils amended by plant-derived fertilizer, while in manured soils were Firmicutes and Actinobacteria. As revealed by multivariate statistical analyses, variation of the enriched ARGs in the soils amended by plant-derived fertilizer was majorly attributed to the response of co-occurred bacteria to depleting nutrients, which was different from the failed establishment of manure-borne bacteria in the manured soils. Our study provided field-based evidence that plant-derived fertilizer stimulated the intrinsic antibiotic resistome, and proposed attention to the un-perceived risk since some clinically relevant ARGs originate and evolve from natural resistome.

Tracing COVID-19 drugs in the environment: Are we focusing on the right environmental compartment?

The Coronavirus Disease 2019 (COVID-19) pandemic led to over 770 million confirmed cases, straining public healthcare systems and necessitating extensive and prolonged use of synthetic chemical drugs around the globe for medical treatment and symptom relief. Concerns have arisen regarding the massive release of active pharmaceutical ingredients (APIs) and their metabolites into the environment, particularly through domestic sewage. While discussions surrounding this issue have primarily centered on their discharge into aquatic environments, particularly through treated effluent from municipal wastewater treatment plants (WWTPs), one often overlooked aspect is the terrestrial environment as a significant receptor of pharmaceutical-laden waste. This occurs through the disposal of sewage sludge, for instance, by applying biosolids to land or non-compliant disposal of sewage sludge, in addition to the routine disposal of expired and unused medications in municipal solid wastes. In this article, we surveyed sixteen approved pharmaceuticals for treating COVID-19 and bacterial co-infections, along with their primary metabolites. For this, we delved into their physiochemical properties, ecological toxicities, environmental persistence, and fate within municipal WWTPs. Emphasis was given on lipophilic substances with log Kow >3.0, which are more likely to be found in sewage sludge at significant factions (25.2%-75.0%) of their inputs in raw sewage and subsequently enter the terrestrial environment through land application of biosolids, e.g., 43% in the United States and as high as 96% in Ireland or non-compliant practices of sewage sludge disposal in developing communities, such as open dumping and land application without prior anaerobic digestion. The available evidence underscores the importance of adequately treating and disposing of sewage sludge before its final disposal or land application in an epidemic or pandemic scenario, as mismanaged sewage sludge could be a significant vector for releasing pharmaceutical compounds and their metabolites into the terrestrial environment.

Swine-manure composts induce the enrichment of antibiotic-resistant bacteria but not antibiotic resistance genes in soils

Composting is a common and effective strategy for reducing antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) from animal manure. However, it is unclear whether the advantages of composting for the control of ARGs and ARB can be further increased in land application. This study investigated the fate of ARB and ARGs after land application of swine-manure composts (SMCs) to three different soil types (red soil, loess and black soil). The results showed that although the SMCs caused an increase in the abundance of total ARGs in the soil in the short period, they significantly reduced (p < 0.01) the abundance of total ARGs after 82 days compared to the control. The decay rate of ARGs reflected by the half-life times (t1/2) varied by soil type, with red soil being the longest. The SMCs mainly introduced ermF, tetG and tetX into the soils, while these ARGs quickly declined to the control level. Notably, SMCs increased the number of ARB in the soils, especially for cefotaxime-resistant bacteria. Although SMCs only affected the microbiome significantly during the early stage (p < 0.05), it took a much longer time for the microbiome to recover compared to the control. Statistical analysis indicated that changes in the microbial community contributed more to the fate of ARGs during SMCs land application than other factors. Overall, it is proposed that the advantages of ARGs control in the composting process for swine manure can be further increased in land application, but it can still bring some risks in regard to ARB.

Uncovering the prevalence and drivers of antibiotic resistance genes in soils across different land-use types

The emergence and spread of antibiotic resistance genes (ARGs) in soil due to animal excreta and organic waste is a major threat to human health and ecosystems, and global efforts are required to tackle the issue. However, there is limited knowledge of the variation in ARG prevalence and diversity resulting from different land-use patterns and underlying driving factors in soils. This study aimed to comprehensively characterize the profile of ARGs and mobile genetic elements and their drivers in soil samples collected from 11 provinces across China, representing three different land-use types, using high-throughput quantitative polymerase chain reaction and 16S rRNA amplicon sequencing. Our results showed that agricultural soil had the highest abundance and diversity of ARGs, followed by tea plantation and forest land. A total of 124 unique ARGs were detected in all samples, with shared subtypes among different land-use patterns indicating a common origin or high transmission frequency. Moreover, significant differences in ARG distribution were observed among different geographical regions, with the greatest enrichment of ARGs found in southern China. Biotic and abiotic factors, including soil properties, climatic factors, and bacterial diversity, were identified as the primary drivers associated with ARG abundance, explaining 71.8% of total ARG variation. The findings of our study demonstrate that different land-use patterns are associated with variations in ARG abundance in soil, with agricultural practices posing the greatest risk to human health and ecosystems regarding ARGs. Our identification of biotic and abiotic drivers of ARG abundance provides valuable insights into strategies for mitigating the spread of these genes. This study emphasizes the need for coordinated and integrated approaches to address the global antimicrobial resistance crisis.

Dynamics of Extended-spectrum Beta-lactamase-producing, Third-generation Cephalosporin-resistant and Tetracycline-resistant Escherichia coli in Feedlot Cattle With or Without Tylosin Administration

The impact of in-feed use of tylosin in feedlot cattle on Gram-negative foodborne bacteria is unknown. We evaluated the effect of continuous in-feed tylosin use on the concentration and prevalence of tetracycline-resistant (TETr)-, third-generation cephalosporin-resistant (3GCr)-, and extended-spectrum β-lactamase-producing (ESBLs) E. coli in feedlot cattle. A cohort of weaned calves (10 animals/group) were randomized to receive a feed ration with or without tylosin. Fecal samples, regularly collected over the entire feeding period, and pen surface and feed samples, collected at the end of the feeding period, were cultured on selective media. Enumeration and binary outcomes were analyzed by mixed effects linear regression or logistic regression, respectively, using treatment and days on feed as fixed factors, and animal ID as a random variable. Tylosin supplementation did not affect the fecal concentrations of TETrE. coli or fecal prevalence of 3GCrE. coli. However, cattle in the tylosin group were 1.5 times more likely (Odds ratio = 1.5: 95% confidence interval: 1.1-2.0) to harbor ESBLs E. coli than the control cattle. Regardless of tylosin treatment, fecal concentrations of TETrE. coli and the prevalence of 3GCr- and ESBLs-E. coli increased over time. Tylosin-supplemented feed did not affect the prevalence of TETrE. coli; 3GCr and ESBLs-E. coli were not detected from the feed samples. Most of the 3GCr- and ESBLs-E. coli isolates carried the blaCTX-M-15 gene, widely detected among ESBLs-E. coli human isolates. In summary, although in-feed tylosin use in feedlot cattle did not select for TETr- and 3GCr-E. coli, it increased the likelihood of detecting ESBL-producing E. coli. Furthermore, the study indicated that the feedlot production setting gradually increases the levels of E. coli resistant to the critically and/or important antibiotics for public health, indicating an increased risk of their dissemination beyond the feedlot environment.

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

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

Molecular characterization of Vibrio species isolated from dairy and water samples

Vibrio species can cause foodborne infections and lead to serious gastrointestinal illnesses. The purpose of this research was to detect the Vibrio cholerae and Vibrio parahaemolyticus in raw milk, dairy products, and water samples. Also, it investigated the virulence factors, antibiotic resistance and biofilm formation in isolated bacteria. Conventional and molecular approaches were used to identify the isolates in this study. Vibrio species were detected in 5% of the samples. Vibrio cholerae and Vibrio parahaemolyticus were isolated from 1.25 and 1.5%, respectively, of the total samples. Penicillin resistance was detected in all strains of Vibrio cholerae and Vibrio parahaemolyticus, with a MAR index ranging from 0.16 to 0.5. Four isolates were moderate biofilm producer and three of them were MDR. When Vibrio cholerae was screened for virulence genes, ctxAB, hlyA, and tcpA were found in 80, 60, and 80% of isolates, respectively. However, tdh + /trh + associated-virulence genes were found in 33.3% of Vibrio parahaemolyticus isolates.

Impact of soil supplemented with pig manure on the abundance of antibiotic resistant bacteria and their associated genes

This study was conducted to evaluate the abundance of antibiotic resistant bacteria and their resistance genes from agriculture soil supplemented with pig manure. Uncultivable soil sample was supplemented with pig manure samples under microcosm experimental conditions and plated on Luria-Bertani (LB) agar incorporated with commercial antibiotics. The supplementation of soil with 15% pig manure resulted in the highest increase in the population of antibiotic resistant bacteria (ARB)/multiple antibiotic resistant bacteria (MARB). Seven genera that included Pseudomonas, Escherichia, Providencia, Salmonella, Bacillus, Alcaligenes and Paenalcaligenes were the cultivable ARB identified. A total of ten antibiotic resistant bacteria genes (ARGs) frequently used in clinical or veterinary settings and two mobile genetic elements (MGEs) (Class 1 and Class 2 integrons) were detected. Eight heavy metal, copper, cadmium, chromium, manganese, lead, zinc, iron, and cobalt were found in all of the manure samples at different concentrations. Tetracycline resistance genes were widely distributed with prevalence of 50%, while aminoglycoside and quinolone-resistance gene had 16% and 13%, respectively. Eighteen ARB isolates carried more than two ARGs in their genome. Class 1 integron was detected among all the 18 ARB with prevalence of 90-100%, while Class 2 integron was detected among 11 ARB. The two classes of integron were found among 10 ARB. Undoubtedly, pig manure collected from farms in Akure metropolis are rich in ARB and their abundance might play a vital role in the dissemination of resistance genes among clinically-relevant pathogens.

Tackling Soil ARG-Carrying Pathogens with Global-Scale Metagenomics

Antibiotic overuse and the subsequent environmental contamination of residual antibiotics poses a public health crisis via an acceleration in the spread of antibiotic resistance genes (ARGs) through horizontal gene transfer. Although the occurrence, distribution, and driving factors of ARGs in soils have been widely investigated, little is known about the antibiotic resistance of soilborne pathogens at a global scale. To explore this gap, contigs from 1643 globally sourced metagnomes are assembled, yielding 407 ARG-carrying pathogens (APs) with at least one ARG; APs are detected in 1443 samples (sample detection rate of 87.8%). The richness of APs is greater in agricultural soils (with a median of 20) than in non-agricultural ecosystems. Agricultural soils possess a high prevalence of clinical APs affiliated with Escherichia, Enterobacter, Streptococcus, and Enterococcus. The APs detected in agricultural soils tend to coexist with multidrug resistance genes and bacA. A global map of soil AP richness is generated, where anthropogenic and climatic factors explained AP hot spots in East Asia, South Asia, and the eastern United States. The results herein advance this understanding of the global distribution of soil APs and determine regions prioritized to control soilborne APs worldwide.

Cattle-compost-soil: The transfer of antibiotic resistance in livestock agriculture

Antibiotic resistance is a major global health threat. Agricultural use of antibiotics is considered to be a main contributor to the issue, influencing both animals and humans as defined by the One Health approach. The purpose of the present study was to determine the abundance of antibiotic-resistant bacterial populations and the overall bacterial diversity of cattle farm soils that have been treated with animal manure compost. Soil and manure samples were collected from different sites at Tullimba farm, NSW. Cultures were grown from these samples in the presence of 11 commonly used antibiotics and antibiotic-resistant bacteria (ARB) colonies were identified. Soil and manure bacterial diversity was also determined using 16S ribosomal RNA next-generation sequencing. Results showed that ARB abundance was greatest in fresh manure and significantly lower in composted manure. However, the application of composted manure on paddock soil led to a significant increase in soil ARB abundance. Of the antibiotics tested, the number of ARB in each sample was greatest for antibiotics that inhibited the bacterial cell wall and protein synthesis. Collectively, these results suggest that the transfer of antibiotic resistance from composted animal manure to soil may not be solely mediated through the application of live bacteria and highlight the need for further research into the mechanism of antibiotic resistance transfer.

One Health and Global Health View of Antimicrobial Susceptibility through the "Eye" of Aeromonas: Systematic Review and Meta-Analysis

Antimicrobial resistance (AMR) is one of the most pressing public health concerns; therefore, it is imperative to advance our understanding of the factors influencing AMR from Global and One Health perspectives. To address this, Aeromonas populations were identified using 16S rRNA gene libraries among human, agriculture, aquaculture, drinking water, surface water, and wastewater samples, supporting its use as indicator bacteria to study AMR. A systematic review and meta-analysis was then performed from Global and One Health perspectives, including data from 221 articles describing 15 891 isolates from 57 countries. The interconnectedness of different environments was evident as minimal differences were identified between sectors among 21 different antimicrobials. However, resistance to critically important antibiotics (aztreonam and cefepime) was significantly higher among wastewater populations compared with clinical isolates. Additionally, isolates from untreated wastewater typically exhibited increased AMR compared with those from treated wastewater. Furthermore, aquaculture was associated with increased AMR to ciprofloxacin and tetracycline compared with wild-caught seafood. Using the World Health Organization AWaRe classifications, countries with lower consumption of "Access" compared to "Watch" drugs from 2000 to 2015 demonstrated higher AMR levels. The current analysis revealed negative correlations between AMR and anthropogenic factors, such as environmental performance indices and socioeconomic standing. Environmental health and sanitation were two of the environmental factors most strongly correlated with AMR. The current analysis highlights the negative impacts of "Watch" drug overconsumption, anthropogenic activity, absence of wastewater infrastructure, and aquaculture on AMR, thus stressing the need for proper infrastructure and global regulations to combat this growing problem.

Soil and Phytomicrobiome for Plant Disease Suppression and Management under Climate Change: A Review

The phytomicrobiome plays a crucial role in soil and ecosystem health, encompassing both beneficial members providing critical ecosystem goods and services and pathogens threatening food safety and security. The potential benefits of harnessing the power of the phytomicrobiome for plant disease suppression and management are indisputable and of interest in agriculture but also in forestry and landscaping. Indeed, plant diseases can be mitigated by in situ manipulations of resident microorganisms through agronomic practices (such as minimum tillage, crop rotation, cover cropping, organic mulching, etc.) as well as by applying microbial inoculants. However, numerous challenges, such as the lack of standardized methods for microbiome analysis and the difficulty in translating research findings into practical applications are at stake. Moreover, climate change is affecting the distribution, abundance, and virulence of many plant pathogens, while also altering the phytomicrobiome functioning, further compounding disease management strategies. Here, we will first review literature demonstrating how agricultural practices have been found effective in promoting soil health and enhancing disease suppressiveness and mitigation through a shift of the phytomicrobiome. Challenges and barriers to the identification and use of the phytomicrobiome for plant disease management will then be discussed before focusing on the potential impacts of climate change on the phytomicrobiome functioning and disease outcome.

Metagenomics reveals the abundance and accumulation trend of antibiotic resistance gene profile under long-term no tillage in a rainfed agroecosystem

Widespread soil resistance can seriously endanger sustainable food production and soil health. Conservation tillage is a promising practice for improving soil structure and health. However, the impact of long-term no-tillage on the presence of antibiotic resistance genes in agricultural soils remains unexplored. Based on the long-term (>11 yr) tillage experimental fields that include both conservation tillage practices [no tillage (ZT)] and conventional tillage practices [plough tillage (PT)], we investigated the accumulation trend of antibiotic resistance genes (ARGs) in farmland soils under long-term no-tillage conditions. We aimed to provide a scientific basis for formulating agricultural production strategies to promote ecological environment safety and human health. In comparison to PT, ZT led to a considerable reduction in the relative abundance of both antibiotic resistance genes and antibiotic target gene families in the soil. Furthermore, the abundance of all ARGs were considerably lower in the ZT soil. The classification of drug resistance showed that ZT substantially decreased the relative abundance of Ethambutol (59.97%), β-lactams (44.87%), Fosfomycin (35.82%), Sulfonamides (34.64%), Polymyxins (33.67%), MLSB (32.78%), Chloramphenicol (28.57%), Multi-drug resistance (26.22%), Efflux pump (23.46%), Aminoglycosides (16.79%), Trimethoprim (13.21%), Isoniazid (11.34%), Fluoroquinolone (6.21%) resistance genes, compared to PT soil. In addition, the abundance of the bacterial phyla Proteobacteria, Actinobacteria, Acidobacteria, and Gemmatimonadetes decreased considerably. The Mantel test indicated that long-term ZT practices substantially increased the abundance of beneficial microbial flora and inhibited the enrichment of ARGs in soil by improving soil microbial diversity, metabolic activity, increasing SOC, TN, and available Zn, and decreasing pH. Overall, long-term no-tillage practices inhibit the accumulation of antibiotic resistance genes in farmland soil, which is a promising agricultural management measure to reduce the accumulation risk of soil ARGs.

Long-term field application of manure induces deep selection of antibiotic resistomes in leaf endophytes of Chinese cabbage

Antibiotic resistomes in leaf endophytes of vegetables threaten human health through the food chain. However, little is known about the ability of long-term manure fertilization to impact the deep selection of antibiotic resistance genes (ARGs) in leaf endophytes of vegetables planted in different types of soils. Here, by high-throughput quantitative PCR, we characterized the ARGs of leaf endophytes of Chinese cabbage (Brassica pekinensis (Lour.) Rupr.) grown in long-term (14 year) manure-amended acidic, neutral and calcareous soils. In total, 87 ARGs and 4 mobile genetic elements (MGEs) were detected in all the samples. Manure fertilization significantly increased the ARG numbers and normalized abundance in leaf endophytes, especially in acidic soil. Moreover, in acidic soil, manure application also led to a higher increase in the normalized abundance of opportunist and specialist ARGs, and more opportunist and specialist ARGs posed a high risk according to their risk ranks. Random forest analysis revealed that Proteobacteria and MGEs were the major drivers affecting the normalized abundance of opportunist and specialist ARGs in both acidic and neutral soils, respectively. In calcareous soil, Cyanobacteria and Actinobacteria were the most important contributors. Collectively, this study expands our knowledge about the deep selection of plant resistomes under long-term manure application.

Evaluating the long-term portrayal of antibiotic resistance in major U.S. newspapers

BACKGROUND

Popular media play a critical role in informing the public about antibiotic resistance, which has remained a health concern for over seven decades. Media attention increases the notoriety of antibiotic resistance and shapes the public's perception of its severity, causes, and solutions. Therefore, it is critical the media accurately portray scientific knowledge that may shape personal and policy responses to antibiotic resistance.

METHODS

We analyzed articles from two major U.S. newspapers, The New York Times and Los Angeles Times, from 1940 to 2019 to assess trends in sentiment and lexicon surrounding antibiotic and antimicrobial resistance.

RESULTS

We observed a gradual increase in the number of relevant articles about resistance, although far fewer than other topics with comparable mortality rates. We found a consistently threatening portrayal of antibiotic resistance as a crisis, reflected in the usage of terms such as "superbug" to refer to some pathogens. Governmental agencies responsible for determining antibiotic usage policies were infrequently mentioned in articles. Blame for resistance was almost exclusively attributed to inappropriate antibiotic use, mainly in animals, rather than appropriate uses of antibiotics.

CONCLUSIONS

Collectively, our results provide insights into how popular media can more accurately inform the public about antibiotic resistance. Potential changes include increasing news coverage, avoiding fear-mongering, and adequately conveying the multiple uses of antibiotics that can potentiate resistance.

Resistome profiling reveals transmission dynamics of antimicrobial resistance genes from poultry litter to soil and plant

Poultry farming is a major livelihood in South and Southeast Asian economies where it is undergoing rapid intensification to meet the growing human demand for dietary protein. Intensification of poultry production systems is commonly supported by increased antimicrobial drug use, risking greater selection and dissemination of antimicrobial resistance genes (ARGs). Transmission of ARGs through food chains is an emerging threat. Here, we investigated transmission of ARGs from chicken (broiler and layer) litter to soil and Sorghum bicolor (L.) Moench plants based on field and pot experiments. The results demonstrate ARGs transmission from poultry litter to plant systems under field as well as experimental pot conditions. The most common ARGs could be tracked for transmission from litter to soil to plants were identified as detected were cmx, ErmX, ErmF, lnuB, TEM-98 and TEM-99, while common microorganisms included Escherichia coli, Staphylococcus aureus, Enterococcus faecium, Pseudomonas aeruginosa, and Vibrio cholerae. Using next generation sequencing and digital PCR assays we detected ARGs transmitted from poultry litter in both the roots and stems of S. bicolor (L.) Moench plants. Poultry litter is frequently used as a fertiliser because of its high nitrogen content; our studies show that ARGs can transmit from litter to plants and illustrates the risks posed to the environment by antimicrobial treatment of poultry. This knowledge is useful for formulating intervention strategies that can reduce or prevent ARGs transmission from one value chain to another, improving understanding of impacts on human and environmental health. The research outcome will help in further understanding the transmission and risks posed by ARGs from poultry to environmental and human/animal health.

Antimicrobial Resistance of Escherichia coli Isolates from Livestock and the Environment in Extensive Smallholder Livestock Production Systems in Ethiopia

The objective of this study was to characterize the distribution of antimicrobial resistance (AMR) of Escherichia coli (E. coli) isolated from livestock feces and soil in smallholder livestock systems. A cross-sectional study was carried out sampling 77 randomly selected households in four districts representing two agroecologies and production systems. E. coli was isolated and the susceptibility to 15 antimicrobials was assessed. Of 462 E. coli isolates tested, resistance to at least one antimicrobial was detected in 52% (43.7-60.8) of isolates from cattle fecal samples, 34% (95% CI, 26.2-41.8) from sheep samples, 58% (95% CI, 47.9-68.2) from goat samples and 53% (95% CI, 43.2-62.4) from soil samples. AMR patterns for E. coli from livestock and soil showed some similarities, with the highest prevalence of resistance detected against streptomycin (33%), followed by amoxycillin/clavulanate (23%) and tetracycline (8%). The odds of detecting E. coli resistance to ≥2 antimicrobials in livestock fecal samples were nearly three times (Odd Ratio-OR: 2.9; 95% CI, 1.72-5.17; p = 0.000) higher in lowland pastoral than in highland mixed crop-livestock production systems. These findings provide insights into the status of resistance in livestock and soil, and associated risk factors in low-resource settings in Ethiopia.

The dynamics and transmission of antibiotic resistance associated with plant microbiomes

Antibiotic resistance genes (ARGs) have been widely found and studied in soil and water environments. However, the propagation of ARGs in plant microbiomes has attracted insufficient attention. Plant microbiomes, especially the rhizosphere microorganisms, are closely connected with water, soil, and air, which allows ARGs to spread widely in ecosystems and pose a threat to human health after entering the human body with bacteria. Therefore, it is necessary to deeply understand and explore the dynamics and the transmission of ARGs in rhizosphere microorganisms and endophytes of plants. In this review, the transmission and influencing factors of ARGs in the microorganisms associated with plants, especially the influence of root exudates on plant microbiomes, are analyzed. Notably, the role of intrinsic genes of plants in determining root exudates and their potential effects on ARGs are proposed and analyzed. The important role of phyllosphere microorganisms and endophytes in the transmission of ARGs and co-resistance of antibiotics and other substances are also emphasized. The proliferation and transmission of ARGs associated with plant microbiomes addressed in this review is conducive to revealing the fate of ARGs in plant microorganisms and alleviating ARG pollution.

ResFinderFG v2.0: a database of antibiotic resistance genes obtained by functional metagenomics

Metagenomics can be used to monitor the spread of antibiotic resistance genes (ARGs). ARGs found in databases such as ResFinder and CARD primarily originate from culturable and pathogenic bacteria, while ARGs from non-culturable and non-pathogenic bacteria remain understudied. Functional metagenomics is based on phenotypic gene selection and can identify ARGs from non-culturable bacteria with a potentially low identity shared with known ARGs. In 2016, the ResFinderFG v1.0 database was created to collect ARGs from functional metagenomics studies. Here, we present the second version of the database, ResFinderFG v2.0, which is available on the Center of Genomic Epidemiology web server (https://cge.food.dtu.dk/services/ResFinderFG/). It comprises 3913 ARGs identified by functional metagenomics from 50 carefully curated datasets. We assessed its potential to detect ARGs in comparison to other popular databases in gut, soil and water (marine + freshwater) Global Microbial Gene Catalogues (https://gmgc.embl.de). ResFinderFG v2.0 allowed for the detection of ARGs that were not detected using other databases. These included ARGs conferring resistance to beta-lactams, cycline, phenicol, glycopeptide/cycloserine and trimethoprim/sulfonamide. Thus, ResFinderFG v2.0 can be used to identify ARGs differing from those found in conventional databases and therefore improve the description of resistomes.

Progressive Sub-MIC Exposure of Klebsiella pneumoniae 43816 to Cephalothin Induces the Evolution of Beta-Lactam Resistance without Acquisition of Beta-Lactamase Genes

Bacterial exposure to antibiotic concentrations below the minimum inhibitory concentration (MIC) may result in a selection window allowing for the rapid evolution of resistance. These sub-MIC concentrations are commonly found in soils and water supplies in the greater environment. This study aimed to evaluate the adaptive genetic changes in Klebsiella pneumoniae 43816 after prolonged but increasing sub-MIC levels of the common antibiotic cephalothin over a fourteen-day period. Over the course of the experiment, antibiotic concentrations increased from 0.5 μg/mL to 7.5 μg/mL. At the end of this extended exposure, the final adapted bacterial culture exhibited clinical resistance to both cephalothin and tetracycline, altered cellular and colony morphology, and a highly mucoid phenotype. Cephalothin resistance exceeded 125 μg/mL without the acquisition of beta-lactamase genes. Whole genome sequencing identified a series of genetic changes that could be mapped over the fourteen-day exposure period to the onset of antibiotic resistance. Specifically, mutations in the rpoB subunit of RNA Polymerase, the tetR/acrR regulator, and the wcaJ sugar transferase each fix at specific timepoints in the exposure regimen where the MIC susceptibility dramatically increased. These mutations indicate that alterations in the secretion of colanic acid and attachment of colonic acid to LPS may contribute to the resistant phenotype. These data demonstrate that very low sub-MIC concentrations of antibiotics can have dramatic impacts on the bacterial evolution of resistance. Additionally, this study demonstrates that beta-lactam resistance can be achieved through sequential accumulation of specific mutations without the acquisition of a beta-lactamase gene.

Potential reservoirs of antimicrobial resistance in livestock waste and treated wastewater that can be disseminated to agricultural land

Livestock manure, dairy lagoon effluent, and treated wastewater are known reservoirs of antibiotic resistance genes (ARGs), antibiotic-resistant bacteria (ARB), and virulence factor genes (VFGs), and their application to agricultural farmland could be a serious public health threat. However, their dissemination to agricultural lands and impact on important geochemical pathways such as the nitrogen (N) cycle have not been jointly explored. In this study, shotgun metagenomic sequencing and analyses were performed to examine the diversity and composition of microbial communities, ARGs, VFGs, and N cycling genes in different livestock manure/lagoon and treated wastewater collected from concentrated animal feeding operations (CAFOs) and a municipal wastewater treatment plant along the west coast of the United States. Multivariate analysis showed that diversity indices of bacterial taxa from the different microbiomes were not significantly different based on InvSimpson (P = 0.05), but differences in ARG mechanisms were observed between swine manure and other microbiome sources. Comparative resistome profiling showed that ARGs in microbiome samples belonged to four core resistance classes: aminoglycosides (40-55 %), tetracyclines (30-45 %), beta-lactam-resistance (20-35 %), macrolides (18-30 %), and >50 % of the VFGs that the 24 microbiomes harbored were phyletically affiliated with two bacteria, Bacteroidetes fragilis and Enterobacter aerogenes. Network analysis based on Spearman correlation showed co-occurrence patterns between several genes such as transporter-gene and regulator, efflux pump and involved-in-polymyxin- resistance, aminoglycoside, beta-lactam, and macrolide with VFGs and bacterial taxa such as Firmicutes, Candidatus Themoplasmatota, Actinobacteria, and Bacteroidetes. Metabolic reconstruction of metagenome-assembled genome (MAGs) analysis showed that the most prevalent drug resistance mechanisms were associated with carbapenem resistance, multidrug resistance (MDR), and efflux pump. Bacteroidales was the main taxa involved in dissimilatory nitrate reduction (DNRA) in dairy lagoon effluent. This study demonstrates that the dissemination of waste from these sources can increase the spread of ARGs, ARB, and VFGs into agricultural lands, negatively impacting both soil and human health.

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

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

Knowledge and Practices of Cypriot Bovine Farmers towards Effective and Safe Manure Management

Manure from bovine farms is commonly used as an organic fertiliser. However, if not properly managed, it can spread significant biological and chemical hazards, threatening both human and animal health. The effectiveness of risk control hugely relies on farmers' knowledge regarding safe manure management and on the application of suitable management practices. This study aims to evaluate the knowledge and practices of Cypriot bovine farmers towards safer manure management, from its generation to its final use, in line with the One Health approach. Factors affecting farmers' knowledge and applied practices are also investigated through a questionnaire survey. The questionnaire was developed and sent to all eligible bovine farmers in Cyprus (n = 353), and 30% (n = 105) of them returned the completed questionnaire. Results revealed there are some gaps in farmers' knowledge. The use of manure for fertilising crops dominated. Only half of the farmers stored manure in appropriate facilities, with 28.5% of them using a dedicated area with cement floors and 21.5% utilising leakproof tanks. The majority (65.7%) stored manure for more than three months before its use as a fertiliser in a dried form. In multiple regression analysis, education level and farming purpose were significant determinants of farmer knowledge. In conclusion, Cypriot farmers' knowledge must be reinforced to ensure proper manure management. The results highlight the importance of providing relevant training to farmers. Although the current practices partially decrease manure pathogens, interventions to promote the use of more effective treatment methods, such as biogas transformation and composting, would be beneficial.

Does increasing the organic fertilizer application rate always boost the antibiotic resistance level in agricultural soils?

The amendment of organic fertilizer derived from livestock manure or biosolids is a significant driver of increasing antibiotic resistance in agricultural soils; however, it remains unclear whether increasing organic fertilizer application rates consistently enhances soil antibiotic resistance levels. Herein, we collected soils with long-term amendment with three types of organic fertilizers at four application rates (15, 30, 45, and 60 t/ha/y) and found that the higher the fertilization rate, the higher the antibiotic resistance gene (ARG) abundance. However, when the fertilization rate exceeded 45 t/ha/y, the ARG abundance ceased to significantly increase. Moreover, the soil ARG abundance was positively correlated with total nitrogen (TN) content and bacterial abundance, especially Firmicutes, and negatively affected by pH and bacterial diversity. Soil TN/bacterial abundance and pH/bacterial diversity reached maximum and minimum values at the 45 t/ha/y fertilization rate, respectively. Meanwhile, at this fertilization rate, Firmicutes enrichment peaked. Therefore, an organic fertilization rate of 45 t/ha/y appeared to represent the threshold for soil antibiotic resistance in this study. The underlying mechanism for this threshold was closely related to soil TN, pH, bacterial abundance, and diversity. Taken together, the findings of this study advance the current understanding regarding the soil resistome under different fertilization rates, while also providing novel insights into organic fertilizer management in agricultural practices.

Bacteria of Zoonotic Interest Identified on Edible Freshwater Fish Imported to Australia

Previous research has shown that freshwater edible fish imported into Australia are not compliant with Australian importation guidelines and as a result may be high risk for bacterial contamination. In the present study, the outer surface of imported freshwater fish were swabbed, cultured, confirmatory tests performed and antimicrobial patterns investigated. Channidae fish (Sp. A/n = 66) were contaminated with zoonotic Salmonella sp./Staphylococcus aureus (n = 1/66) and other bacteria implicated in cases of opportunistic human infection, these being Pseudomonas sp. (including P. mendocina and P. pseudoalcaligenes (n = 34/66)); Micrococcus sp. (n = 32/66); Comamonas testosteroni (n = 27/66) and Rhizobium radiobacter (n = 3/66). Pangasiidae fish (Species B/n = 47) were contaminated with zoonotic Vibrio fluvialis (n = 10/47); Salmonella sp. (n = 6/47) and environmental bacteria Micrococcus sp. (n = 3/47). One sample was resistant to all antimicrobials tested and is considered to be Methicillin Resistant S. aureus. Mud, natural diet, or vegetation identified in Sp. A fish/or packaging were significantly associated with the presence of Pseudomonas spp. The study also showed that visibly clean fish (Sp. B) may harbour zoonotic bacteria and that certain types of bacteria are common to fish groups, preparations, and contaminants. Further investigations are required to support the development of appropriate food safety recommendations in Australia.

Awaking the dormant virome in the rhizosphere

The rhizosphere is a vital soil compartment providing key plant-beneficial functions. However, little is known about the mechanisms driving viral diversity in the rhizosphere. Viruses can establish lytic or lysogenic interactions with their bacterial hosts. In the latter, they assume a dormant state integrated in the host genome and can be awakened by different perturbations that impact host cell physiology, triggering a viral bloom, which is potentially a fundamental mechanism driving soil viral diversity, as 22%-68% of soil bacteria are predicted to harbour dormant viruses. Here we assessed the viral bloom response in rhizospheric viromes by exposing them to three contrasting soil perturbation agents: earthworms, herbicide and antibiotic pollutant. The viromes were next screened for rhizosphere-relevant genes and also used as inoculant on microcosms incubations to test their impacts on pristine microbiomes. Our results show that while post-perturbation viromes diverged from control conditions, viral communities exposed to both herbicide and antibiotic pollutant were more similar to each other than those influenced by earthworms. The latter also favoured an increase in viral populations harbouring genes involved in plant-beneficial functions. Post-perturbation viromes inoculated on soil microcosms changed the diversity of pristine microbiomes, suggesting that viromes are important components of the soil ecological memory driving eco-evolutionary processes that determine future microbiome trajectories according to past events. Our findings demonstrate that viromes are active players in the rhizosphere and need to be considered in efforts to understand and control the microbial processes towards sustainable crop production.

Global profiling of antibiotic resistomes in maize rhizospheres

The spreading of antimicrobial resistance (AMR) in crops and food products represents a global concern. In this study, we conducted a survey of resistomes in maize rhizosphere from Michigan, California, the Netherlands, and South Africa, and investigated potential associations with host bacteria and soil management practices in the crop field. For comparison, relative abundance of antibiotic resistance genes (ARGs) is normalized to the size of individual metagenomes. Michigan maize rhizosphere metagenomes showed the highest abundance and diversity of ARGs, with the detection of blaTEM-116, blaACT-4/-6, and FosA2, exhibiting high similarity (≥ 99.0%) to those in animal and human pathogens. This was probably related to the decade-long application of manure/composted manure from antibiotic-treated animals. Moreover, RbpA, vanRO, mtrA, and dfrB were prevalently found across most studied regions, implying their intrinsic origins. Further analysis revealed that RbpA, vanRO, and mtrA are mainly harbored by native Actinobacteria with low mobility since mobile genetic elements were rarely found in their flanking regions. Notably, a group of dfrB genes are adjacent to the recombination binding sites (attC), which together constitute mobile gene cassettes, promoting the transmission from soil bacteria to human pathogens. These results suggest that maize rhizosphere resistomes can be distinctive and affected by many factors, particularly those relevant to agricultural practices.

Soil antibiotic resistance genes accumulate at different rates over four decades of manure application

Manure can be a source of antibiotic resistance genes (ARGs) that enter the soil. However, previous studies assessing ARG persistence in soil have generally lacked continuity over sampling times, consistency of location, and assessing the impact of discontinuing manure application. We evaluated both short- and long-term ARG accumulation dynamics in soil with a 40-year known history of manure use. Manure application caused a greater abundance of tetracycline, macrolide, and sulfonamide ARGs in the soil. There was an initial spike in ARG abundance resulting from manure bacteria harboring ARGs being introduced to soil, followed by resident soil bacteria out-competing them, which led to ARG dissipation within a year. However, over four decades, annual manure application caused linear or exponential ARG accumulation, and bacteria associated with ARGs differed compared to those in the short term. Eleven years after discontinuing manure application, most soil ARG levels declined but remained elevated. We systematically explored the historical accumulation of ARGs in manured soil, and provide insight into factors that affect their persistence.

Co-occurrence of antibiotic and metal resistance in long-term sewage sludge-amended soils: influence of application rates and pedo-climatic conditions

Urban sewage sludge (USS) is increasingly being used as an alternative organic amendment in agriculture. Because USS originates mostly from human excreta, partially metabolized pharmaceuticals have also been considered in risk assessment studies after reuse. In this regard, we investigated the cumulative effect of five annual USS applications on the spread of antibiotic-resistant bacteria (ARB) and their subsequent resistance to toxic metals in two unvegetated soils. Eventually, USS contained bacterial strains resistant to all addressed antibiotics with indices of resistance varying between 0.25 for gentamicin to 38% for ampicillin and azithromycin. Sludge-amended soils showed also the emergence of resistome for all tested antibiotics compared to non-treated controls. In this regard, the increase of sludge dose generally correlated with ARB counts, while soil texture had no influence. On the other hand, the multi-antibiotic resistance (MAR) of 52 isolates selected from USS and different soil treatments was investigated for 10 most prescribed antibiotics. Nine isolates showed significant MAR index (≥ 0.3) and co-resistance to Cd, As and Be as well. However, events including an extreme flash flood and the termination of USS applications significantly disrupted ARB communities in all soil treatments. In any case, this study highlighted the risks of ARB spread in sludge-amended soils and a greater concern with the recent exacerbation of antibiotic overuse following COVID-19 outbreak.

Nutrient concentrations affect the antimicrobial resistance profiles of cattle manures

Antimicrobial resistance (AMR) in cattle is widespread because of the increased use of antibiotics to combat microbial diseases and enhance milk production. The cattle excreta released into the environment can be a potent source of contamination in spreading antibiotic resistance, especially upon its application in agriculture. However, the correlation of AMR profile of manure with other physico-chemical parameters is limited. Therefore, the study aimed to generate AMR profiles for manure samples collected from 25 different sites of two agriculturally important states in India, Madhya Pradesh and Uttar Pradesh. Samples were tested for physico-chemical parameters, viz., electrical conductivity, pH, total nitrogen (N), total phosphorus (P), and total potassium (K). Bacterial community analysis was done by culture-dependent and culture-independent methods. The influence of feeding practices, nutrient concentration, and bacterial abundance on antibiotic resistance profiles was observed in collected manure samples. Manures of intensive feeding animals harbored highly resistant profiles of bacteria as compared to natural grazing cattle.

Impacts of organic materials amendment on the soil antibiotic resistome in subtropical paddy fields

The organic material amendment has been proven to change the soil antibiotic resistance genes (ARGs) profile, which may threaten human health through the food chain, but the effects and mechanisms of different organic materials on ARGs in paddy soils are less explored. In this study, a field experiment was set up with the treatments of conventional chemical fertilization (NPK) and common organic material amendment [rice straw (RS), swine manure (SM), and biochar (BC)] to explore the effects and mechanisms. In total, 84 unique ARGs were found across the soil samples with different organic material amendments, and they conferred resistance to the major antibiotic classes. Compared with NPK, SM significantly increased the detected number and relative abundance of ARGs. A higher detected number of ARGs than NPK was observed in BC, whereas BC had a lower relative abundance of ARGs than NPK. Compared with NPK, a detected number decrease was observed in RS, although abundance showed no significant differences. Compared with other treatments, a higher detected number and relative abundance of mobile genetic elements (MGEs) were observed in BC, indicating a higher potential for horizontal gene transfer. There were significantly positive relationships between the relative abundances of total ARGs and MGEs and the bacterial abundance. The network analysis suggested the important role of MGEs and bacterial communities in shaping the ARGs profile. Mantel test and redundancy analysis (RDA) suggested that soil carbon, nitrogen, and C/N were the major chemical drivers of the ARGs profile. The risk of ARGs spreading to the food chain should be considered when applying SM and biochar, which shifted the ARGs and MGEs profiles, respectively. Pre-treatment measures need to be studied to reduce the dissemination of ARGs in paddy fields.

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

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