Microbial regulation of natural antibiotic resistance: Understanding the protist-bacteria interactions for evolution of soil resistome. - Related Documents




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644901.0000Microbial regulation of natural antibiotic resistance: Understanding the protist-bacteria interactions for evolution of soil resistome. The emergence, evolution and spread of antibiotic resistance genes (ARGs) in the environment represent a global threat to human health. Our knowledge of antibiotic resistance in human-impacted ecosystems is rapidly growing with antibiotic use, organic fertilization and wastewater irrigation identified as key selection pressures. However, the importance of biological interactions, especially predation and competition, as a potential driver of antibiotic resistance in the natural environment with limited anthropogenic disturbance remains largely overlooked. Stress-affected bacteria develop resistance to maximize competition and survival, and similarly bacteria may develop resistance to fight stress under the predation pressure of protists, an essential component of the soil microbiome. In this article, we summarized the major findings for the prevalence of natural ARGs on our planet and discussed the potential selection pressures driving the evolution and development of antibiotic resistance in natural settings. This is the first article that reviewed the potential links between protists and the antibiotic resistance of bacteria, and highlighted the importance of predation by protists as a crucial selection pressure of antibiotic resistance in the absence of anthropogenic disturbance. We conclude that an improved ecological understanding of the protists-bacteria interactions and other biological relationships would greatly expand our ability to predict and mitigate the environmental antibiotic resistance under the context of global change.202031818598
645010.9999Protist predation promotes antimicrobial resistance spread through antagonistic microbiome interactions. Antibiotic resistance has grown into a major public health threat. In this study, we reveal predation by protists as an overlooked driver of antibiotic resistance dissemination in the soil microbiome. While previous studies have primarily focused on the distribution of antibiotic resistance genes, our work sheds light on the pivotal role of soil protists in shaping antibiotic resistance dynamics. Using a combination of metagenomics and controlled experiments in this study, we demonstrate that protists cause an increase in antibiotic resistance. We mechanistically link this increase to a fostering of antimicrobial activity in the microbiome. Protist predation gives a competitive edge to bacteria capable of producing antagonistic secondary metabolites, which secondary metabolites promote in turn antibiotic-resistant bacteria. This study provides insights into the complex interplay between protists and soil microbiomes in regulating antibiotic resistance dynamics. This study highlights the importance of top-down control on the spread of antibiotic resistance and directly connects it to cross-kingdom interactions within the microbiome. Managing protist communities may become an important tool to control outbreaks of antibiotic resistance in the environment.202439259188
645520.9999Bacteriophages: Underestimated vehicles of antibiotic resistance genes in the soil. Bacteriophages (phages), the most abundant biological entities on Earth, have a significant effect on the composition and dynamics of microbial communities, biogeochemical cycles of global ecosystems, and bacterial evolution. A variety of antibiotic resistance genes (ARGs) have been identified in phage genomes in different soil samples. Phages can mediate the transfer of ARGs between bacteria via transduction. Recent studies have suggested that anthropogenic activities promote phage-mediated horizontal gene transfer events. Therefore, the role of phages in the dissemination of ARGs, which are a potential threat to human health, may be underestimated. However, the contribution of phages to the transfer of ARGs is still poorly understood. Considering the growing and wide concerns of antibiotic resistance, phages should be considered a research focus in the mobile resistome. This review aimed to provide an overview of phages as vehicles of ARGs in soil. Here, we summarized the current knowledge on the diversity and abundance of ARGs in soilborne phages and analyzed the contribution of phages to the horizontal transfer of ARGs. Finally, research deficiencies and future perspectives were discussed. This study provides a reference for preventing and controlling ARG pollution in agricultural systems.202235992716
645730.9999Antibiotics and Antibiotic Resistance in Agroecosystems: State of the Science. We propose a simple causal model depicting relationships involved in dissemination of antibiotics and antibiotic resistance in agroecosystems and potential effects on human health, functioning of natural ecosystems, and agricultural productivity. Available evidence for each causal link is briefly summarized, and key knowledge gaps are highlighted. A lack of quantitative estimates of human exposure to environmental bacteria, in general, and antibiotic-resistant bacteria, specifically, is a significant data gap hindering the assessment of effects on human health. The contribution of horizontal gene transfer to resistance in the environment and conditions that might foster the horizontal transfer of antibiotic resistance genes into human pathogens also need further research. Existing research has focused heavily on human health effects, with relatively little known about the effects of antibiotics and antibiotic resistance on natural and agricultural ecosystems. The proposed causal model is used to elucidate gaps in knowledge that must be addressed by the research community and may provide a useful starting point for the design and analysis of future research efforts.201627065386
768340.9998Antibiotic Resistomes in Plant Microbiomes. Microorganisms associated with plants may alter the traits of the human microbiome important for human health, but this alteration has largely been overlooked. The plant microbiome is an interface between plants and the environment, and provides many ecosystem functions such as improving nutrient uptake and protecting against biotic and abiotic stress. The plant microbiome also represents a major pathway by which humans are exposed to microbes and genes consumed with food, such as pathogenic bacteria, antibiotic-resistant bacteria, and antibiotic-resistance genes. In this review we highlight the main findings on the composition and function of the plant microbiome, and underline the potential of plant microbiomes in the dissemination of antibiotic resistance via food consumption or direct contact.201930890301
645850.9998Overview of Direct and Indirect Effects of Antibiotics on Terrestrial Organisms. Antibiotics (ABs) have made it possible to treat bacterial infections, which were in the past untreatable and consequently fatal. Regrettably, their use and abuse among humans and livestock led to antibiotic resistance, which has made them ineffective in many cases. The spread of antibiotic resistance genes (ARGs) and bacteria is not limited to nosocomial environments, but also involves water and soil ecosystems. The environmental presence of ABs and ARGs is a hot topic, and their direct and indirect effects, are still not well known or clarified. A particular concern is the presence of antibiotics in agroecosystems due to the application of agro-zootechnical waste (e.g., manure and biosolids), which can introduce antibiotic residues and ARGs to soils. This review provides an insight of recent findings of AB direct and indirect effects on terrestrial organisms, focusing on plant and invertebrates. Possible changing in viability and organism growth, AB bioaccumulation, and shifts in associated microbiome composition are reported. Oxidative stress responses of plants (such as reactive oxygen species production) to antibiotics are also described.202337760767
646760.9998The role of biofilms as environmental reservoirs of antibiotic resistance. Antibiotic resistance has become a significant and growing threat to public and environmental health. To face this problem both at local and global scales, a better understanding of the sources and mechanisms that contribute to the emergence and spread of antibiotic resistance is required. Recent studies demonstrate that aquatic ecosystems are reservoirs of resistant bacteria and antibiotic resistance genes as well as potential conduits for their transmission to human pathogens. Despite the wealth of information about antibiotic pollution and its effect on the aquatic microbial resistome, the contribution of environmental biofilms to the acquisition and spread of antibiotic resistance has not been fully explored in aquatic systems. Biofilms are structured multicellular communities embedded in a self-produced extracellular matrix that acts as a barrier to antibiotic diffusion. High population densities and proximity of cells in biofilms also increases the chances for genetic exchange among bacterial species converting biofilms in hot spots of antibiotic resistance. This review focuses on the potential effect of antibiotic pollution on biofilm microbial communities, with special emphasis on ecological and evolutionary processes underlying acquired resistance to these compounds.201526583011
644570.9998Microplastics: Disseminators of antibiotic resistance genes and pathogenic bacteria. Microplastics (MPs) are emerging pollutants that linger in the air, water, and land. Beyond their physical and chemical risks, there is growing evidence that MPs contribute to the worldwide antimicrobial resistance (AMR) dilemma by acting as carriers of harmful microbes and antibiotic resistance genes (ARGs). Despite an increase in research, the available literature is dispersed, and the part that MPs play in influencing microbial populations and fostering resistance is still not well understood. This review summarizes current research on how MPs contribute to the spread of antibiotic resistance. We concentrated on the ways in which MPs support horizontal gene transfer (HGT) processes such as conjugation, transformation, and transduction, assist biofilm development, and offer surfaces for microbial colonization. Evidence from a variety of settings suggests that MPs serve as vectors for opportunistic pathogens, such as the ESKAPE group, and ARGs, increasing the survival and movement of resistance determinants in ecosystems. Through the consolidation of current developments, this review emphasizes MPs as active resistance vectors instead of passive pollutants. We also point out important limitations, such as the lack of standardized procedures, inadequate risk assessment frameworks, and the absence of real-world exposure research. It is imperative that these issues be approached from a One Health standpoint in order to reduce the risks of both plastic pollution and antibiotic resistance.202541056605
401580.9998Bacteriophages as Environmental Reservoirs of Antibiotic Resistance. Although antibiotic resistance represents a significant and growing public health concern, the contribution of bacteriophages (phages) to the mobilization of antibiotic resistance genes (ARGs) in the environment has not been extensively studied. Recent studies, however, suggest that phages play an important role in the acquisition, maintenance, and spread of ARGs than previously expected. This Opinion article offers an update on the contribution of phages to environmental antibiotic resistance. A better understanding of the mechanisms and factors that promote antibiotic resistance may significantly contribute to the implementation of control strategies.201930905524
972090.9998Molecular Evolution and Origins of Antibiotic Resistance Genes. Antibiotic resistance is a global health crisis with bacteria resisting both natural and synthetic antibiotics. While all antibiotic classes face similar mechanistic and evolutionary forces, their origins shape distinct resistance pathways. Produced over millions of years, natural antibiotics drove the early emergence and coevolution of antibiotic resistance genes (ARGs), later spreading with clinical use. By contrast, synthetic antibiotics began without pre-existing ARGs, yet bacteria soon adapted novel approaches to overcome them. In this perspective, we examine recent findings on ARG evolution, including their distribution in environmental bacteria, host range, and underlying molecular mechanisms of ARGs for bacterial adaptation against these antibiotics. To address these questions, we emphasize the urgent need for comprehensive studies to uncover the full range, distribution, and evolution of ARGs. Understanding these processes not only aids in developing effective strategies to combat ARGs but also provides critical insights into protein chemistry and advances protein engineering approaches.202540457171
9642100.9998Towards the fate of antibiotics and the development of related resistance genes in stream biofilms. Antibiotics are ubiquitously found in natural surface waters and cause great harm to aquatic organisms. Stream biofilm is a complex and active community composed of algae, bacteria, fungi and other microorganisms, which mainly adheres to solid substances such as rocks and sediments. The durability and diverse structural and metabolic characteristics of biofilms make them a representative of microbial life in aquatic micrecosystems and can reflect major ecosystem processes. Microorganisms and extracellular polymeric substances in biofilms can adsorb and actively accumulate antibiotics. Therefore, biofilms are excellent biological indicators for detecting antibiotic in polluted aquatic environments, but the biotransformation potential of stream biofilms for antibiotics has not been fully explored in the aquatic environment. The characteristics of stream biofilm, such as high abundance and activity of bacterial community, wide contact area with pollutants, etc., which increases the opportunity of biotransformation of antibiotics in biofilm and contribute to bioremediation to improve ecosystem health. Recent studies have demonstrated that both exposure to high and sub-minimum inhibitory concentrations of antibiotics may drive the development of antibiotic resistance genes (ARGs) in natural stream biofilms, which are susceptible to the effects of antibiotic residues, microbial communities and mobile genetic elements, etc. On the basis of peer-reviewed papers, this review explores the distribution behavior of antibiotics in stream biofilms and the contribution of biofilms to the acquisition and spread of antibiotic resistance. Considering that antibiotics and ARGs alter the structure and ecological functions of natural microbial communities and pose a threat to river organisms and human health, our research findings provide comprehensive insights into the migration, transformation, and bioavailability of antibiotics in biofilms.202337454845
6446110.9998Ecological consequences of antimicrobial residues and bioactive chemicals on antimicrobial resistance in agroecosystems. BACKGROUND: The widespread use of antimicrobials in agriculture, coupled with bioactive chemicals like pesticides and growth-promoting agents, has accelerated the global crisis of antimicrobial resistance (AMR). Agroecosystems provides a platform in the evolution and dissemination of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs), which pose significant threats to both environmental and public health. AIM OF REVIEW: This review explores the ecological consequences of antimicrobial residues and bioactive chemicals in agroecosystems, with a focus on their role in shaping AMR. It delves into the mechanisms by which these substances enter agricultural environments, their interactions with soil microbiomes, and the subsequent impacts on microbial community structure. KEY SCIENTIFIC CONCEPTS OF REVIEW: Evidence indicates that the accumulation of antimicrobials promotes resistance gene transfer among microorganisms, potentially compromising ecosystem health and agricultural productivity. By synthesizing current research, we identify critical gaps in knowledge and propose strategies for mitigating the ecological risks associated with antimicrobial residues. Moreover, this review highlights the urgent need for integrated management approaches to preserve ecosystem health and combat the spread of AMR in agricultural settings.202539414225
6448120.9998The resistance within: Antibiotic disruption of the gut microbiome and resistome dynamics in infancy. Intestinal host-microbiota interactions during the first year of life are critical for infant development. Early-life antibiotic exposures disrupt stereotypical gut microbiota maturation and adversely affect childhood health. Furthermore, antibiotics increase the abundance of resistant bacteria and enrich the resistome-the compendium of antibiotic resistance genes-within the gut microbiota. Here, we discuss acute and persistent impacts of antibiotic exposure during infancy on pediatric health, the gut microbiome, and, particularly, the resistome. Reviewing our current understanding of antibiotic resistance acquisition and dissemination within and between microbiomes, we highlight open questions, which are imperative to resolve in the face of rising bacterial resistance.202235550670
7682130.9998Soil Amoebae Are Unexpected Hotspots of Environmental Antibiotics and Antibiotic Resistance Genes. Antibiotic resistance poses a significant threat to human health. While most studies focus on bacteria, interactions between antibiotics and other crucial microbial groups like protists remain uncertain. This study investigates how protists interact with antibiotics and examines how these interactions impact the fate of resistance genes. It reveals that amoebae exhibit high resistance to eight high-risk environmental antibiotics, accumulating significant quantities within their cells. Wild amoeboid strains from distant locations carry substantial antibiotic resistance genes (ARGs) and metal resistance genes (MRGs), with significant heterogeneity within a single species. Amoeboid symbionts and pathogens predominantly carry these genes. Paraburkholderia symbionts have reduced genomes and fewer resistance genes compared to free-living strains, while amoeba-endogenous Stenotrophomonas maltophilia does not exhibit a significantly reduced genome size. This suggests that the amoeboid hosts serve as a temporary medium facilitating its transmission. In summary, the study unveils that soil amoebae represent unexpected hotspots for antibiotics and resistance genes. Future research should assess the effects of antibiotics on often-overlooked protists and explore their role in spreading ARGs and MRGs in ecosystems. Incorporating protists into broader antibiotic resistance research is recommended, highlighting their significance within a One Health perspective.202439584452
9728140.9998Metagenomic analysis of metal(loid)s resistance genes and its environmental applications. Heavy metals are widely used to satiate the demands of growing industrialization and modern life. However, the presence of metal in large quantities in the ecosystem significantly impacts all life forms, particularly microorganisms. Many bacterial strains have developed metal resistance genes (MRG) to survive in extreme conditions through various mechanisms, such as active efflux, sequestration, permeability barriers, or co-resistance with antibiotic resistance genes. Metagenomic analysis is a powerful approach that enables the exploration of the functional repertoire and diversity of microorganisms, providing deeper insights into the mechanisms underlying the development of MRGs, and the active metabolites they produce to adapt to the polluted environments. With the advancement of these techniques, the knowledge can be further applied to environmental applications, such as bioremediation, biomonitoring, and synthetic biology. Bacteria with metal toxicity tolerance can be employed to enhance environmental sustainability and mitigate potential hazards.202540992856
6466150.9998The antibiotic resistome: gene flow in environments, animals and human beings. The antibiotic resistance is natural in bacteria and predates the human use of antibiotics. Numerous antibiotic resistance genes (ARGs) have been discovered to confer resistance to a wide range of antibiotics. The ARGs in natural environments are highly integrated and tightly regulated in specific bacterial metabolic networks. However, the antibiotic selection pressure conferred by the use of antibiotics in both human medicine and agriculture practice leads to a significant increase of antibiotic resistance and a steady accumulation of ARGs in bacteria. In this review, we summarized, with an emphasis on an ecological point of view, the important research progress regarding the collective ARGs (antibiotic resistome) in bacterial communities of natural environments, human and animals, i.e., in the one health settings.We propose that the resistance gene flow in nature is "from the natural environments" and "to the natural environments"; human and animals, as intermediate recipients and disseminators, contribute greatly to such a resistance gene "circulation."201728500429
6460160.9998Biocides as drivers of antibiotic resistance: A critical review of environmental implications and public health risks. The widespread and indiscriminate use of biocides poses significant threats to global health, socioeconomic development, and environmental sustainability by accelerating antibiotic resistance. Bacterial resistance development is highly complex and influenced significantly by environmental factors. Increased biocide usage in households, agriculture, livestock farming, industrial settings, and hospitals produces persistent chemical residues that pollute soil and aquatic environments. Such contaminants contribute to the selection and proliferation of resistant bacteria and antimicrobial resistance genes (ARGs), facilitating their dissemination among humans, animals, and ecosystems. In this review, we conduct a critical assessment of four significant issues pertaining to this topic. Specifically, (i) the role of biocides in exerting selective pressure within the environmental resistome, thereby promoting the proliferation of resistant microbial populations and contributing to the global spread of antimicrobial resistance genes (ARGs); (ii) the role of biocides in triggering transient phenotypic adaptations in bacteria, including efflux pump overexpression, membrane alterations, and reduced porin expression, which often result in cross-resistance to multiple antibiotics; (iii) the capacity of biocides to disrupt bacteria and make the genetic content accessible, releasing DNA into the environment that remains intact under certain conditions, facilitating horizontal gene transfer and the spread of resistance determinants; (iv) the capacity of biocides to disrupt bacterial cells, releasing intact DNA into the environment and enhancing horizontal gene transfer of resistance determinants; and (iv) the selective interactions between biocides and bacterial biofilms in the environment, strengthening biofilm cohesion, inducing resistance mechanisms, and creating reservoirs for resistant microorganisms and ARG dissemination. Collectively, this review highlights the critical environmental and public health implications of biocide use, emphasizing an urgent need for strategic interventions to mitigate their role in antibiotic resistance proliferation.202540230384
9641170.9998Microplastics pollution in the ocean: Potential carrier of resistant bacteria and resistance genes. Microplastics pollution in marine environments is concerning. Microplastics persist and accumulate in various sections of the ocean where they present opportunity for micropollutant accumulation and microbial colonisation. Even though biofilm formation on plastics was first reported in the 1970's, it is only in recent years were plastic associated biofilms have gained research attention. Plastic surfaces pose a problem as they are a niche ready for colonisation by diverse biofilm assemblages, composed of specific bacterial communities and putative pathogens prone to acquiring ARGs and resistance in the biofilm. However, the nature of antibiotic resistance on aquatic plastic debris is not yet fully understood and remains a concern. Given the inevitable increase of plastic production and waste generation, microplastics released into the environment may prove to be problematic. This review explores microplastic waste in the ocean and possible concerns that may arise from the presence of microplastics in conjunction with favourable conditions for the development and dispersal of antibiotic resistance in the ocean and food web.202134562691
6436180.9998Protist predation selects for the soil resistome. A key aspect of "One Health" is to comprehend how antibiotic resistomes evolve naturally. In this issue, Nguyen and colleagues pioneered an in situ investigation on the impact of protist predations on the soil microbial community and its antibiotic resistance genes (ARGs). They found that bacterivorous protists consistently increased the abundance of ARGs, such as tetracycline resistant genes. Indeed, antibiotic production is a common strategy for bacteria to evade protist predation. The rise of ARGs can be explained by the balance between antibiotic producers and resisters shaped by predatory selection. This work suggests that ARG enrichment due to biotic interactions may be less worrisome than previously thought. Unless, these ARGs are carried by or disseminated among pathogens. Therefore, it is essential to monitor the occurrence, dissemination and pathogenic hosts of ARGs, enhancing our capacity to combat antibiotic resistance.202438365252
6469190.9998From environment to clinic: the role of pesticides in antimicrobial resistance. Antimicrobial resistance (AMR) in pathogens has been associated mainly with excessive use of antibiotics. Most studies of resistance have focused on clinical pathogens; however, microorganisms are exposed to numerous anthropogenic substances. Few studies have sought to determine the effects of chemical substances on microorganisms. Exposure to these substances may contribute to increased rates of AMR. Understanding microorganism communities in natural environments and AMR mechanisms under the effects of anthropogenic substances, such as pesticides, is important to addressing the current crisis of antimicrobial resistance. This report draws attention to molecules, rather than antibiotics, that are commonly used in agrochemicals and may be involved in developing AMR in non-clinical environments, such as soil. This report examines pesticides as mediators for the appearance of AMR, and as a route for antibiotic resistance genes and antimicrobial resistant bacteria to the anthropic environment. Available evidence suggests that the natural environment may be a key dissemination route for antibiotic-resistant genes. Understanding the interrelationship of soil, water, and pesticides is fundamental to raising awareness of the need for environmental monitoring programs and overcoming the current crisis of AMR.202032973897