Fungicide exposure accelerated horizontal transfer of antibiotic resistance genes via plasmid-mediated conjugation

Dissemination mechanisms of unique antibiotic resistance genes from flowback water to soil revealed by combined Illumina and Nanopore sequencing

As a byproduct of shale gas extraction, flowback water (FW) is produced in large quantities globally. Due to the unique interactions between pollutants and microorganisms, FW always harbor multiple antibiotic resistance genes (ARGs) that have been confirmed in our previous findings, potentially serving as a point source for ARGs released into the environment. However, whether ARGs in FW can disseminate or integrate into the environmental resistome remains unclear. In this study, unique ARGs from FW were identified, and the ARG profiles in soil and FW-spiked soil were compared using a combination of Illumina and Nanopore sequencing. The results indicated that the total abundance of the soil resistome increased by 30.8 % in soil contaminated with FW. Of this increase, 11.1 % was attributable to the integration of exogenous ARGs from FW into the soil resistome. Sequence alignment at the gene level further confirmed the successful integration of 20 unique ARG sequences classified as multidrug and vancomycin resistance genes into the soil resistome. These 20 ARG sequences were detected only in the FW. Multiple lines of evidence indicated that horizontal gene transfer dominated ARG dissemination in soil contaminated by FW. This conclusion is supported by the discrepancy between changes in mobile ARGs and host abundance, the upregulation of oxidative stress-related genes (SOD1 and SOD2) and the SOS response (lexA and recA), as well as the upregulation of genes related to quorum sensing (virD4, virB9, and virB3) and naked DNA uptake (pilD, pilT, and pilQ).

Exposure to bisphenol compounds accelerates the conjugative transfer of antibiotic resistance plasmid

Antimicrobial resistance poses the most formidable challenge to public health, with plasmid-mediated horizontal gene transfer playing a pivotal role in its global spread. Bisphenol compounds (BPs), a group of environmental contaminants with endocrine-disrupting properties, are extensively used in various plastic products and can be transmitted to food. However, the impact of BPs on the plasmid-mediated horizontal transfer of antibiotic resistance genes (ARGs) has not yet been elucidated. Herein, we demonstrate that BPs could promote the conjugative transfer frequency of RP4-7 and clinically multidrug-resistant plasmids. Furthermore, the promoting effect of BPs on the plasmid transfer was also confirmed in a murine model. Microbial diversity analysis of transconjugants indicated an increase in α diversity in the BPAF-treated group, along with the declined richness of some beneficial bacteria and elevated richness of Faecalibaculum rodentium, which might serve as an intermediate repository for resistance plasmids. The underlying mechanisms driving the enhanced conjugative transfer upon BPAF treatment include exacerbated oxidative stress, disrupted membrane homeostasis, augmented energy metabolism, and the increased expression of conjugation-related genes. Collectively, our findings highlight the potential risk associated with the exacerbated dissemination of AMR both in vitro and in vivo caused by BPs exposure.

Mechanisms and influencing factors of horizontal gene transfer in composting system: A review

Organic solid wastes such as livestock manure and sewage sludge are important sources and repositories of antibiotic resistance genes (ARGs). Composting, a solid waste treatment technology, has demonstrated efficacy in degrading various antibiotics and reducing ARGs. However, some recalcitrant ARGs (e.g., sul1, sul2) will enrich during the composting maturation period. These ARGs persist in compost products and spread through horizontal gene transfer (HGT). We analyzed the reasons behind the increase of ARGs during the maturation phase. It was found that the proliferation of ARG-host bacteria and HGT process play an important role. This article revealed that microbial physiological responses, environmental factors, pollutants, and quorum sensing (QS) can all influence the HGT process in composting systems. We examined the influence of these factors on HGT in the compost system and summarized potential mechanisms by analyzing the alterations in microbial communities. We comprehensively summarized the HGT hazards that these factors may present in composting systems. Finally, we summarized methods to inhibit HGT in compost, such as using additives, quorum sensing inhibitors (QSIs), microbial inoculation, and predicting HGT events. Overall, the HGT mechanism and driving force in complex composting systems are still insufficiently studied. In view of the current situation, using predictions to assess the risk of HGT in composting may be advisable.

A feasible regulation strategy for conjugation of antibiotic resistance genes based on different bacterial quorum sensing inhibition methods

The dissemination of antibiotic resistance genes (ARGs) poses global environmental issues, and plasmid-mediated conjugation contributes substantially to the spread of ARGs. Quorum sensing (QS), an important cell-cell communication system that coordinates group behaviors, has potential as a feasible regulation pathway to inhibit the conjugation process. We examined the promoting effects of QS signal on conjugation, and this study is the first to report that QS inhibitors 2(3H)-benzofuranone and acylase I effectively repressed conjugation frequency of RP4 plasmid to 0.32- and 0.13-fold compared with the control respectively. The investigation of underlying mechanisms of QS inhibitors revealed a significant decrease in cellular contact and the formation of transfer channels. The downregulation of sdiA gene regulating the expression of QS signal receptor contribute to conjugation inhibition. Importantly, the expression of genes related to the formation of conjugative pili, which plays a role in plasmid mating bridge formation was downregulated, indicating QS inhibitors affect conjugation mainly through regulation of the mating pair formation system. Furthermore, 2(3H)-benzofuranone and acylase I achieved 84.07% and 66.05% inhibitory effect on plasmid spread in activated sludge reactors. Collectively, our findings demonstrate the feasibility of using different bacteria quorum quenching methods to control the spread of ARGs.

Evolution of the Black solider fly larvae gut antibiotic resistome during kitchen waste disposal

Kitchen waste (KW) is an important reservoir of antibiotic resistance genes (ARGs). Black solider fly larvae (BSFL) are extensively employed in KW disposal, closely linking to their robust gut microbes. However, antibiotic resistome in BSFL gut during the KW disposal processes and the mechanism remain unclear. In the present study, the antibiotic resistome in BSFL gut within the 12 days KW disposal processes were investigated. Results showed that, ARGs abundance initially increased and subsequently decreased, the five most prevalent core ARG classes were tetracycline, aminoglycoside, cephalosporin, lincosamide and multidrug. A total of 7 MGE types were observed and the horizontal gene transfer (HGT) of ARGs was predominantly mediated by plasmids. Host microbes were mainly categorized into Proteobacteria (98.12 %) and their assemblies were mainly classified into the deterministic processes. To elucidate the driving mechanisms, the mantel test and the structural equation model (SEM) were developed. Results indicated that microbial functions (0.912, p < 0.0001) and microbial community (1.014, p = 0.036), consistently showed very significant relationships with the patterns of ARGs, which presented higher direct effects than indirect effects. Overall, this study makes an initial contribution to a more deepgoing comprehension of the gut antibiotic resistome of BSFL during KW disposal.

Multivariate statistical analysis of surface water quality in the capibaribe river (Pernambuco state, Northeast Brazil): Contributions to water management

Assessing the quality of surface waters is essential for identifying changes in freshwater ecosystems and supporting the planning/proposing of measures to mitigate polluting sources. However, many studies involving the identification of pathogenic bacteria and/or their resistance profile to antimicrobial agents need a more holistic approach to conditioning or modulating factors. Thus, we apply different multivariate statistical techniques to the data set from the Capibaribe River's surface water, one of the most important in the Northeast of Brazil. Our data, taken together, suggest that the waters of the Capibaribe River have been suffering impacts associated with different human activities. Due to its flow crossing a large urban area, different sources are contributing to the contamination/pollution of its aquatic ecosystem, whose multivariate analysis allowed us to identify site-dependent characteristics that reflect the degree and type of human influence. The study of physical-chemical and chemical parameters reveals the influence of the high load of effluents (industrial and domestic) on the chemical and microbiological quality of the waters sampled at the SS4 site. On the other hand, the antimicrobial resistance profile of the isolates evaluated, especially at SS1, SS2, and SS3 sites, provides a comprehensive sample of the "resistome" present in the fecal content of thousands of people living in the region surrounding the Capibaribe River. The presence of enterobacteria in water indicates contamination of fecal origin. It represents a public health problem since the waters of the Capibaribe River can be a source of dissemination and persistence of bacteria resistant to humans and the environment. In conclusion, our study provides a more comprehensive understanding of the relationships between surface water, basic sanitation, antibiotic exposure, bacterial gene transfer, and human colonization, whether in the context of the region studied or other locations.

Effects of glyphosate on antibiotic resistance in soil bacteria and its potential significance: A review

The evolution and spread of antibiotic resistance are problems with important consequences for bacterial disease treatment. Antibiotic use in animal production and the subsequent export of antibiotic resistance elements in animal manure to soil is a concern. Recent reports suggest that exposure of pathogenic bacteria to glyphosate increases antibiotic resistance. We review these reports and identify soil processes likely to affect the persistence of glyphosate, antibiotic resistance elements, and their interactions. The herbicide molecular target of glyphosate is not shared by antibiotics, indicating that target-site cross-resistance cannot account for increased antibiotic resistance. The mechanisms of bacterial resistance to glyphosate and antibiotics differ, and bacterial tolerance or resistance to glyphosate does not coincide with increased resistance to antibiotics. Glyphosate in the presence of antibiotics can increase the activity of efflux pumps, which confer tolerance to glyphosate, allowing for an increased frequency of mutation for antibiotic resistance. Such effects are not unique to glyphosate, as other herbicides and chemical pollutants can have the same effect, although glyphosate is used in much larger quantities on agricultural soils than most other chemicals. Most evidence indicates that glyphosate is not mutagenic in bacteria. Some studies suggest that glyphosate enhances genetic exchange of antibiotic-resistance elements through effects on membrane permeability. Glyphosate and antibiotics are often present together in manure-treated soil for at least part of the crop-growing season, and initial studies indicate that glyphosate may increase abundance of antibiotic resistance genes in soil, but longer term investigations under realistic field conditions are needed. Although there are demonstratable interactions among glyphosate, bacteria, and antibiotic resistance, there is limited evidence that normal use of glyphosate poses a substantial risk for increased occurrence of antibiotic-resistant, bacterial pathogens. Longer term field studies using environmentally relevant concentrations of glyphosate and antibiotics are needed.

Sewerage surveillance tracking characteristics of human antibiotic resistance genes in sewer system

Sewage surveillance is widely applied to track valid human excretion information and identify public health conditions during corona virus disease 2019 (COVID-19) pandemic. This approach can be applied to monitor the antibiotic resistance level in sewers and to assess the risk of spreading antibiotic resistance in municipal wastewater systems. However, there is still little information about human antibiotic resistance occurrence characteristics in sewer system. This study conducted a field trial for whole year to advance understanding on spatial and temporal occurrence of antibiotic resistance genes (ARGs) in gravity sewerage. The spatial distribution of ARGs along the drainage pipe line (from human settlements to wastewater treatement pant (WWTP)) was insignificant, which may be affected by irregular human emission alongside the pipeline. The correlation between ARGs and antibiotics in sewage was insignificant. The temporal distribution showed that the effect of temperature on ARGs abundance was evident, the ARGs abundance in sewage was generally higher during the cold season. Metagenomic analysis revealed that the detected ARGs were mainly distributed in Proteobacteria (47.51 %) and Antinobacteria (20.11 %). Potential hosts of ARGs in sewage were mainly identified as human gut microorganisms, including human pathogenic bacteria, such as Prevotella, Kocuria, and Propionibacterium, etc. This study provides a new insight into the sewerage surveillance tracking characteristics of human ARGs in sewer system, and suggesting that the sewage-carried ARGs surveillance is a promising method for assessment and management of antibiotic resistance level on population size.

Water temperature disturbance alters the conjugate transfer of antibiotic resistance genes via affecting ROS content and intercellular aggregation

Spread of antibiotic resistance genes (ARGs) in aquatic ecosystems poses a significant global challenge to public health. The potential effects of water temperature perturbation induced by specific water environment changes on ARGs transmission are still unclear. The conjugate transfer of plasmid-mediated ARGs under water temperature perturbation was investigated in this study. The conjugate transfer frequency (CTF) was only 7.16 × 10-7 at a constant water temperature of 5 °C, and it reached 2.18 × 10-5 at 30 °C. Interestingly, compared to the constant 5 °C, the water temperature perturbations (cooling and warming models between 5-30 °C) significantly promoted the CTF. Intracellular reactive oxygen species was a dominant factor, which not only directly affected the CTF of ARGs, but also functioned indirectly via influencing the cell membrane permeability and cell adhesion. Compared to the constant 5 °C, water temperature perturbations significantly elevated the gene expression associated with intercellular contact, cell membrane permeability, oxidative stress responses, and energy driven force for CTF. Furthermore, based on the mathematical model predictions, the stabilization times of acquiring plasmid maintenance were shortened to 184 h and 190 h under cooling and warming model, respectively, thus the water temperature perturbations promoted the ARGs transmission in natural conditions compared with the constant low temperature conditions.

Investigation of the impact of widely used pesticides on conjugative transfer of multidrug resistance plasmids

Plasmid-mediated conjugative transfer has emerged as a major driver accounting for the dissemination of antibiotic resistance genes (ARGs). In addition to the use of antimicrobial agents, there is growing evidence that non-antibiotic factors also play an important role. Pesticides are widely used to protect crops against vectors of diseases, and are indispensable agents in agricultural production, whereas the impact of pesticide pollution on the transmission of antimicrobial resistance remains poorly understood. Here we reveal that the pesticides at environmentally relevant concentrations, especially cyromazine (Cyr) and kresoxim-methyl (Kre), greatly facilitate the conjugative transfer of antibiotic-resistance plasmids carrying clinically important ARGs. Mechanistic studies indicate that Cyr and Kre treatments trigger reactive oxygen species (ROS) production and SOS response, increase membrane permeability, upregulate bacterial proton motive force (PMF) and promote ATP supply. Further non-targeted metabolomics and biochemical analysis demonstrate that the addition of Cyr and Kre accelerates tricarboxylic acid (TCA) cycle and electron transport chain (ETC), thereby activating bacterial energy metabolism. In the constructed soil model, we prove that two pesticides contribute to the dissemination of resistance plasmids in the soil microbiota. 16S rRNA sequencing analyses indicate that pesticides alter transconjugant microbial communities, and enable more opportunistic pathogens, such as Pseudomonas and Enterobacter, to acquire the multidrug resistance plasmids. Collectively, our work indicates the potential risk in accelerating the spread of antimicrobial resistance owing to pesticide pollution, highlighting the importance of continuous surveillance of pesticide residues in complex environmental settings.

The occurrence of banana Fusarium wilt aggravates antibiotic resistance genes dissemination in soil

The spread of antibiotic resistance genes (ARGs) and subsequent soil-borne disease outbreaks are major threats to soil health and sustainable crop production. However, the relationship between occurrences of soil-borne diseases and the transmission of soil ARGs remains unclear. Here, soil ARGs, mobile genetic elements and microbial communities from co-located disease suppressive and conducive banana orchards were deciphered using metagenomics and metatranscriptomics approaches. In total, 23 ARG types, with 399 subtypes, were detected using a metagenomics approach, whereas 23 ARG types, with 452 subtypes, were discovered using a metatranscriptomics method. Furthermore, the metagenomics analysis revealed that the ARG total abundance levels were greater in rhizospheres (0.45 ARGs/16S rRNA on average) compared with bulk (0.32 ARGs/16S rRNA on average) soils. Interestingly, metatranscriptomics revealed that the total ARG abundances were greater in disease-conducive (8.85 ARGs/16S rRNA on average) soils than disease suppressive (1.45 ARGs/16S rRNA on average) soils. Mobile genetic elements showed the same trends as ARGs. Network and binning analyses indicated that Mycobacterium, Streptomyces, and Blastomonas are the main potential hosts of ARGs. Furthermore, Bacillus was significantly and negatively correlated with Fusarium (P < 0.05, r = -0.84) and hosts of ARGs (i.e., Mycobacterium, Streptomyces, and Blastomonas). By comparing metagenomic and metatranscriptomic analyses，this study demonstrated that metatranscriptomics may be more sensitive in indicating ARGs activities in soil. Our findings enable the more accurate assessment of the transmission risk of ARGs. The data provide a new perspective for recognizing soil health, in which soil-borne disease outbreaks appear to be associated with ARG spread, whereas beneficial microbe enrichment may mitigate wilt disease and ARG transmission.

Beta-blocker drives the conjugative transfer of multidrug resistance genes in pure and complex biological systems

Drug resistance poses a high risk to human health. Extensive use of non-antibiotic drugs contributes to antibiotic resistance genes (ARGs) transfer. However, how they affect the spread of broad-host plasmids in complex biological systems remains unknown. This study investigated the effect of metoprolol on the transfer frequency and host range of ARGs in both intrageneric and intergeneric pure culture systems, as well as in anammox microbiome. The results showed that environmental concentrations of metoprolol significantly promoted the intrageneric and intergeneric conjugative transfer. Initially, metoprolol induced excessive oxidative stress, resulting in high cell membrane permeability and bacterial SOS response. Meanwhile, more pili formation increased the adhesion and contact between bacteria, and the abundance of conjugation-related genes also increased significantly. Activation of the electron transport chain provided more ATP for this energy-consuming process. The underlying mechanism was further verified in the complex anammox conjugative system. Metoprolol induced the enrichment of ARGs and mobile genetic elements. The enhanced bacterial interaction and energy generation facilitated the high conjugative transfer frequency of ARGs. In addition, plasmid-borne ARGs tended to transfer to opportunistic pathogens. This work raises public concerns about the health and ecological risks of non-antibiotic drugs.

Disentangling abiotic and biotic effects of treated wastewater on stream biofilm resistomes enables the discovery of a new planctomycete beta-lactamase

BACKGROUND

Environmental reservoirs of antibiotic resistance pose a threat to human and animal health. Aquatic biofilms impacted by wastewater effluent (WW) are known environmental reservoirs for antibiotic resistance; however, the relative importance of biotic factors and abiotic factors from WW on the abundance of antibiotic resistance genes (ARGs) within aquatic biofilms remains unclear. Additionally, experimental evidence is limited within complex aquatic microbial communities as to whether genes bearing low sequence similarity to validated reference ARGs are functional as ARGs.

RESULTS

To disentangle the effects of abiotic and biotic factors on ARG abundances, natural biofilms were previously grown in flume systems with different proportions of stream water and either ultrafiltered or non-ultrafiltered WW. In this study, we conducted deep shotgun metagenomic sequencing of 75 biofilm, stream, and WW samples from these flume systems and compared the taxonomic and functional microbiome and resistome composition. Statistical analysis revealed an alignment of the resistome and microbiome composition and a significant association with experimental treatment. Several ARG classes exhibited an increase in normalized metagenomic abundances in biofilms grown with increasing percentages of non-ultrafiltered WW. In contrast, sulfonamide and extended-spectrum beta-lactamase ARGs showed greater abundances in biofilms grown in ultrafiltered WW compared to non-ultrafiltered WW. Overall, our results pointed toward the dominance of biotic factors over abiotic factors in determining ARG abundances in WW-impacted stream biofilms and suggested gene family-specific mechanisms for ARGs that exhibited divergent abundance patterns. To investigate one of these specific ARG families experimentally, we biochemically characterized a new beta-lactamase from the Planctomycetota (Phycisphaeraceae). This beta-lactamase displayed activity in the cleavage of cephalosporin analog despite sharing a low sequence identity with known ARGs.

CONCLUSIONS

This discovery of a functional planctomycete beta-lactamase ARG is noteworthy, not only because it was the first beta-lactamase to be biochemically characterized from this phylum, but also because it was not detected by standard homology-based ARG tools. In summary, this study conducted a metagenomic analysis of the relative importance of biotic and abiotic factors in the context of WW discharge and their impact on both known and new ARGs in aquatic biofilms. Video Abstract.

Insight into the mechanisms of combined toxicity of cadmium and flotation agents in luminescent bacteria: Role of micro/nano particles

Currently, risk assessment and pollution management in mines primarily focus on toxic metals, with the flotation agents being overlooked. However, the combined effects of metals and flotation agents in mines remain largely unknown. Therefore, this study aimed to evaluate the combined effects of Cd and two organic flotation agents (ethyl xanthate (EX) and diethyldithiocarbamate (DDTC)), and the associated mechanisms. The results showed that Cd + EX and Cd + DDTC exhibited synergistic toxicity. The EC50 values for luminescent bacteria were 1.6 mg/L and 1.0 mg/L at toxicity unit ratios of 0.3 and 1, respectively. The synergistic effects were closely related with the formation of Cd(EX)2 and Cd(DDTC)2 micro/nano particles, with nano-particles exhibiting higher toxicity. We observed severe cell membrane damage and cell shrinkage of the luminescent bacteria, which were probably caused by secondary harm to cells through the released CS2 during their decomposition inside cells. In addition, these particles induced toxicity by altering cellular levels of biochemical markers and the transcriptional levels of transport proteins and lipoproteins, leading to cell membrane impairment and DNA damage. This study has demonstrated that particulates formed by Cd and flotation agents contribute to the majority of the toxicity of the binary mixture. This study helps to better understand the complex ecological risk of inorganic metals and organic flotation agents in realistic mining environments.

Ubiquitous nanocolloids suppress the conjugative transfer of plasmid-mediated antibiotic resistance in aqueous environment

Nanocolloids (Nc) are widespread in natural water environment, whereas the potential effects of Nc on dissemination of antibiotic resistance remain largely unknown. In this study, Nc collected from the Yellow River in Henan province was tested for its ability to influence the conjugative transfer of resistant plasmid in aqueous environment. The results revealed that the conjugative transfer of RP4 plasmid between Escherichia coli was down-regulated by 52%-91% upon exposure to 1-10 mg/L Nc and the reduction became constant when the dose became higher (20-200 mg/L). Despite the exposure of Nc activated the anti-oxidation and SOS response in bacteria through up-regulating genes involved in glutathione biosynthesis and DNA recombination, the inhibition on the synthesis and secretion of extracellular polysaccharide induced the prevention of cell-cell contact, leading to the reduction of plasmid transfer. This was evidenced by the decreased bacterial adhesion and lowered levels of genes and metabolites relevant to transmembrane transport and D-glucose phosphorylation, as clarified in phenotypic, transcriptomics and metabolomics analysis of E. coli. The significant down-regulation of glycolysis/gluconeogenesis and TCA cycle was associated with the shortage of ATP induced by Nc. The up-regulation of global regulatory genes (korA and trbA) and the reduction of plasmid genes (trfAp, trbBp, and traG) expression also contributed to the suppressed conjugation of RP4 plasmid. The obtained findings remind that the role of ubiquitous colloidal particles is nonnegligible when practically and comprehensively assessing the risk of antibiotic resistance in the environment.

Regulation of intracellular process by two-component systems: Exploring the mechanism of plasmid-mediated conjugative transfer

Plasmid-mediated conjugative transfer facilitates the dissemination of antibiotic resistance, yet the comprehensive regulatory mechanisms governing this process remain elusive. Herein, we established pure bacteria and activated sludge conjugation system to investigate the regulatory mechanisms of conjugative transfer, leveraging metformin as an exogenous agent. Transcriptomic analysis unveiled that substantial upregulation of genes associated with the two-component system (e.g., AcrB/AcrA, EnvZ/Omp, and CpxA/CpxR) upon exposure to metformin. Furthermore, downstream regulators of the two-component system, including reactive oxygen species (ROS), cytoplasmic membrane permeability, and adenosine triphosphate (ATP) production, were enhanced by 1.7, 1.4 and 1.1 times, respectively, compared to the control group under 0.1 mg/L metformin exposure. Moreover, flow sorting and high-throughput sequencing revealed increased microbial community diversity among transconjugants in activated sludge systems. Notably, the antibacterial potential of human pathogenic bacteria (e.g., Bacteroides, Escherichia-Shigella, and Lactobacillus) was augmented, posing a potential threat to human health. Our findings shed light on the spread of antibiotic resistance bacteria and assess the ecological risks associated with plasmid-mediated conjugative transfer in wastewater treatment systems.

The potential of antifungal peptides derived from Lactiplantibacillus plantarum WYH for biocontrol of Aspergillus flavus contamination

Aspergillus flavus is a notorious fungus that contaminates food crops with toxic aflatoxins, posing a serious threat to human health and the agricultural economy. To overcome the inadequacy of traditional control methods and meet consumer preferences for natural-sources additives, there is an urgent demand for novel biocontrol agents that are safe and efficient. This study aims to investigate the antifungal properties of a novel antifungal agent derived from the biologically safe Lactiplantibacillus plantarum WYH. Firstly, antifungal peptides (AFPs) with a molecular weight of less than 3kD, exhibiting remarkable temperature stability and effectively retarding fungal growth in a dose-dependent manner specifically against A. flavus, were concentrated from the fermentation supernatant of L. plantarum WYH and were named as AFPs-WYH. Further analysis demonstrated that AFPs-WYH might exert antifungal effects through the induction of oxidative stress, disruption of mitochondrial function, alteration of membrane permeability, and cell apoptosis in A. flavus. To further validate our findings, a transcriptomics analysis was conducted on A. flavus treated with 2 and 5 mg/mL of AFPs-WYH, which elucidated the potential effect of AFPs-WYH administration on the regulation of genes involved in impairing fungal development and preventing aflatoxin biosynthesis pathways. Overall, AFPs-WYH reduced the A. flavus proliferation and affected the AFB1 biosynthesis, exhibiting a promising potential for food industry applications as a biopreservative and biocontrol agent.

Tebuconazole promotes spread of a multidrug-resistant plasmid into soil bacteria to form new resistant bacterial strains

The development of antibiotic resistance threatens human and environmental health. Non-antibiotic stressors, including fungicides, may contribute to the spread of antibiotic resistance genes (ARGs). We determined the promoting effects of tebuconazole on ARG dissemination using a donor, Escherichia coli MG1655, containing a multidrug-resistant fluorescent plasmid (RP4) and a recipient (E. coli HB101). The donor was then incorporated into the soil to test whether tebuconazole could accelerate the spread of RP4 into indigenous bacteria. Tebuconazole promoted the transfer of the RP4 plasmid from the donor into the recipient via overproduction of reactive oxygen species (ROS), enhancement of cell membrane permeability and regulation of related genes. The dissemination of the RP4 plasmid from the donor to soil bacteria was significantly enhanced by tebuconazole. RP4 plasmid could be propagated into more genera of bacteria in tebuconazole-contaminated soil as the exposure time increased. These findings demonstrate that the fungicide tebuconazole promotes the spread of the RP4 plasmid into indigenous soil bacteria, revealing the potential risk of tebuconazole residues enhancing the dissemination of ARGs in soil environments.

The role of water matrix on antibiotic resistance genes transmission in substrate layer from stormwater bioretention cells

Recently, extensive attention has been paid to antibiotic resistance genes (ARGs) transmission. However, little available literature could be found about ARGs transmission in stormwater bioretention cells, especially the role of water matrix on ARGs transmission. Batch experiments were conducted to investigate target ARGs (blaTEM, tetR and aphA) transmission behaviors in substrate layer from stormwater bioretention cells under different water matrices, including nutrient elements (e.g., carbon, nitrogen and phosphorus), water environmental conditions (dissolved oxygen (DO), pH and salinity, etc.) and pollution factors (like heavy metals, antibiotics and disinfectants), showing that ARGs conjugation frequency increased sharply with the enhancement of water matrices (expect DO and pH), while there were obvious increasing tendencies for all ARGs transformation frequencies under only the pollution factor. The correlation between dominant bacteria and ARGs transmission implied that conjugation and transformation of ARGs were mainly determined by Firmicutes, Bacteroidota, Latescibacterota, Chloroflexi and Cyanobacteria at the phylum level, and by Sphingomonas, Ensifer, IMCC26256, Rubellimicrobium, Saccharimonadales, Vicinamibacteraceae, Nocardioides, JG30-KF-CM66 at the genus level. The mentioned dominant bacteria were responsible for intracellular reactive oxygen species (ROS) and cell membrane permeability (CMP) in the substrate layer, where the amplification of intracellular ROS variation were the largest with 144 and 147 % under the condition of TP and salinity, respectively, and the one of CMP variation were the highest more than 165 % under various pollution factors. Furthermore, both increasing DO and reducing salinity could be potential approaches for the inhibition of ARGs transmission in bioretention cells taking into account the simultaneous removal of conventional pollutants.

Mechanisms Underlying the Overlooked Chiral Fungicide-Driven Enantioselective Proliferation of Antibiotic Resistance in Earthworm Intestinal Microbiome

From a "One Health" perspective, the global threat of antibiotic resistance genes (ARGs) is associated with modern agriculture practices including agrochemicals application. Chiral fungicides account for a considerable proportion of wildly used agrochemicals; however, whether and how their enantiomers lead to differential proliferation of antibiotic resistance in agricultural environments remain overlooked. Focused on the soil-earthworm ecosystem, we for the first time deciphered the mechanisms underlying the enantioselective proliferation of antibiotic resistance driven by the enantiomers of a typical chiral fungicide mandipropamid (i.e., R-MDP and S-MDP) utilizing a multiomic approach. Time-series metagenomic analysis revealed that R-MDP led to a significant enhancement of ARGs with potential mobility (particularly the plasmid-borne ARGs) in the earthworm intestinal microbiome. We further demonstrated that R-MDP induced a concentration-dependent facilitation of plasmid-mediated ARG transfer among microbes. In addition, transcriptomic analysis with verification identified the key aspects involved, where R-MDP enhanced cell membrane permeability, transfer ability, biofilm formation and quorum sensing, rebalanced energy production, and decreased cell mobility versus S-MDP. Overall, the findings provide novel insights into the enantioselective disruption of microbiome and resistome in earthworm gut by chiral fungicides and offer significant contributions to the comprehensive risk assessment of chiral agrochemicals in agroecosystems.

Key taxa and mobilome-mediated responses co-reshape the soil antibiotic resistome under dazomet fumigation stress

Agrochemicals are emergingly being implicated in the widespread dissemination of antibiotic resistance genes (ARGs) in agroecosystems. However, minimal research exists on the disturbance of fumigant on soil ARGs. Focusing on a typical fumigant dazomet in a simulated soil microcosm, we characterized the dazomet-triggered timely response and longstanding dynamic of ARGs at one-fold and two-fold field recommended doses using metagenome and quantitative PCR. Dazomet treatments reduced 13.17%-69.98% of absolute abundance of 16S rRNA gene and targeted ARGs, but, awfully, boosted diversity and relative abundance of ARGs up to 1.33-1.60 and 1.62-1.90 folds, respectively. Approximately 77.28% of changes in relative abundance of ARGs could be explained by bacterial community and mobile genetic elements (MGEs). Mechanistically, primary hosts of ARGs shifted from Proteobacteria (control) to Firmicutes and Actinobacteria (treatments) accompanied with corresponding changes in their abundance by combining community analysis, host tracking analysis and antibiotic resistant bacteria assay. Meanwhile, dazomet exposure significantly increased the incidence of MGEs and stimulated the conjugation of antibiotic-resistant plasmid. In addition, absolute abundance of targeted ARGs gradually recovered in the post-fumigation stage. Collectively, our results elucidate the dazomet-triggered emergence and spread of soil ARGs and highlight the importance of navigating toward rational use of fumigant in agricultural fields.

Comprehensive insights into antibiotic resistance gene migration in microalgal-bacterial consortia: Mechanisms, factors, and perspectives

With the overuse of antibiotics, antibiotic resistance gene (ARG) prevalence is gradually increasing. ARGs are considered emerging contaminants that are broadly concentrated and dispersed in most aquatic environments. Recently, interest in microalgal-bacterial biotreatment of antibiotics has increased, as eukaryotes are not the primary target of antimicrobial drugs. Moreover, research has shown that microalgal-bacterial consortia can minimize the transmission of antibiotic resistance in the environment. Unfortunately, reviews surrounding the ARG migration mechanism in microalgal-bacterial consortia have not yet been performed. This review briefly introduces the migration of ARGs in aquatic environments. Additionally, an in-depth summary of horizontal gene transfer (HGT) between cyanobacteria and bacteria and from bacteria to eukaryotic microalgae is presented. Factors influencing gene transfer in microalgal-bacterial consortia are discussed systematically, including bacteriophage abundance, environmental conditions (temperature, pH, and nutrient availability), and other selective pressure conditions including nanomaterials, heavy metals, and pharmaceuticals and personal care products. Furthermore, considering that quorum sensing could be involved in DNA transformation by affecting secondary metabolites, current knowledge surrounding quorum sensing regulation of HGT of ARGs is summarized. In summary, this review gives valuable information to promote the development of practical and innovative techniques for ARG removal by microalgal-bacterial consortia.

Chlorothalonil drives the antibiotic resistome in earthworm guts

Earthworms are recognized as carriers of pollutants; however, how fungicide residues affect microbiota and antibiotic resistance genes (ARGs) in earthworm guts has remained unclear. In this work, changes in the earthworm gut microbiome and resistome were investigated after chlorothalonil (CTL) application. Earthworm activity accelerated the dissipation of CTL in soil, while metagenomic analysis revealed that CTL altered the ARG profile, leading to an increased abundance of ARGs in earthworm guts, particularly with respect to ARG subtypes CRP and OXA-427. CTL also reduced bacterial diversity and elevated the relative abundance of the phylum Proteobacteria, including a potential ARG host, Aeromonas, which is a known pathogen. Various bacterial genera from the Actinobacteria and Proteobacteria phyla were identified as broad-spectrum hosts for ARGs in earthworm guts. CTL could increase the abundance of multidrug efflux pump genes and enhance the abundance of mobile genetic elements, especially plasmids. Various co-occurrence patterns between plasmids and ARGs were also found after CTL treatments. It is concluded that CTL may act as a selective stress for ARGs and lead to an increase in their abundance by facilitating the proliferation of potential ARG hosts and enhancing plasmid-mediated horizontal transfer frequency of ARGs in earthworm guts.

Cultivating antimicrobial resistance: how intensive agriculture ploughs the way for antibiotic resistance

Antimicrobial resistance (AMR) is a growing threat to public health, global food security and animal welfare. Despite efforts in antibiotic stewardship, AMR continues to rise worldwide. Anthropogenic activities, particularly intensive agriculture, play an integral role in the dissemination of AMR genes within natural microbial communities - which current antibiotic stewardship typically overlooks. In this review, we examine the impact of anthropogenically induced temperature fluctuations, increased soil salinity, soil fertility loss, and contaminants such as metals and pesticides on the de novo evolution and dissemination of AMR in the environment. These stressors can select for AMR - even in the absence of antibiotics - via mechanisms such as cross-resistance, co-resistance and co-regulation. Moreover, anthropogenic stressors can prime bacterial physiology against stress, potentially widening the window of opportunity for the de novo evolution of AMR. However, research to date is typically limited to the study of single isolated bacterial species - we lack data on how intensive agricultural practices drive AMR over evolutionary timescales in more complex microbial communities. Furthermore, a multidisciplinary approach to fighting AMR is urgently needed, as it is clear that the drivers of AMR extend far beyond the clinical environment.

Augmented dissemination of antibiotic resistance elicited by non-antibiotic factors

The emergence and rapid spread of antibiotic resistance seriously compromise the clinical efficacy of current antibiotic therapies, representing a serious public health threat worldwide. Generally, drug-susceptible bacteria can acquire antibiotic resistance through genetic mutation or gene transfer, among which horizontal gene transfer (HGT) plays a dominant role. It is widely acknowledged that the sub-inhibitory concentrations of antibiotics are the key drivers in promoting the transmission of antibiotic resistance. However, accumulating evidence in recent years has shown that in addition to antibiotics, non-antibiotics can also accelerate the horizontal transfer of antibiotic resistance genes (ARGs). Nevertheless, the roles and potential mechanisms of non-antibiotic factors in the transmission of ARGs remain largely underestimated. In this review, we depict the four pathways of HGT and their differences, including conjugation, transformation, transduction and vesiduction. We summarize non-antibiotic factors accounting for the enhanced horizontal transfer of ARGs and their underlying molecular mechanisms. Finally, we discuss the limitations and implications of current studies.

Current and Future Flow Cytometry Applications Contributing to Antimicrobial Resistance Control

Antimicrobial resistance is a global threat to human health and welfare, food safety, and environmental health. The rapid detection and quantification of antimicrobial resistance are important for both infectious disease control and public health threat assessment. Technologies such as flow cytometry can provide clinicians with the early information, they need for appropriate antibiotic treatment. At the same time, cytometry platforms facilitate the measurement of antibiotic-resistant bacteria in environments impacted by human activities, enabling assessment of their impact on watersheds and soils. This review focuses on the latest applications of flow cytometry for the detection of pathogens and antibiotic-resistant bacteria in both clinical and environmental samples. Novel antimicrobial susceptibility testing frameworks embedding flow cytometry assays can contribute to the implementation of global antimicrobial resistance surveillance systems that are needed for science-based decisions and actions.