Antibiotic resistance,which is encoded by antibiotic-resistance genes(ARGs),has proliferated to become a growing threat to public health around the world.With technical advances,especially in the popularization of met...Antibiotic resistance,which is encoded by antibiotic-resistance genes(ARGs),has proliferated to become a growing threat to public health around the world.With technical advances,especially in the popularization of metagenomic sequencing,scientists have gained the ability to decipher the profiles of ARGs in diverse samples with high accuracy at an accelerated speed.To analyze thousands of ARGs in a highthroughput way,standardized and integrated pipelines are needed.The new version(v3.0)of the widely used ARGs online analysis pipeline(ARGs-OAP)has made significant improvements to both the reference database-the structured ARG(SARG)database-and the integrated analysis pipeline.SARG has been enhanced with sequence curation to improve annotation reliability,incorporate emerging resistance genotypes,and determine rigorous mechanism classification.The database has been further organized and visualized online in the format of a tree-like structure with a dictionary.It has also been divided into sub-databases for different application scenarios.In addition,the ARGs-OAP has been improved with adjusted quantification methods,simplified tool implementation,and multiple functions with userdefined reference databases.Moreover,the online platform now provides a diverse biostatistical analysis workflow with visualization packages for the efficient interpretation of ARG profiles.The ARGs-OAP v3.0 with an improved database and analysis pipeline will benefit academia,governmental management,and consultation regarding risk assessment of the environmental prevalence of ARGs.展开更多
The emergence and rapid spread of antimicrobial resistance is of global public health concern.The gut microbiota harboring diverse commensal and opportunistic bacteria that can acquire resistance via horizontal and ve...The emergence and rapid spread of antimicrobial resistance is of global public health concern.The gut microbiota harboring diverse commensal and opportunistic bacteria that can acquire resistance via horizontal and vertical gene transfers is considered an important reservoir and sink of antibiotic resistance genes(ARGs).In this review,we describe the reservoirs of gut ARGs and their dynamics in both animals and humans,use the One Health perspective to track the transmission of ARG-containing bacteria between humans,animals,and the environment,and assess the impact of antimicrobial resistance on human health and socioeconomic development.The gut resistome can evolve in an environment subject to various selective pressures,including antibiotic administration and environmental and lifestyle factors(e.g.,diet,age,gender,and living conditions),and interventions through probiotics.Strategies to reduce the abundance of clinically relevant antibiotic-resistant bacteria and their resistance determinants in various environmental niches are needed to ensure the mitigation of acquired antibiotic resistance.With the help of effective measures taken at the national,local,personal,and intestinal management,it will also result in preventing or minimizing the spread of infectious diseases.This review aims to improve our understanding of the correlations between intestinal microbiota and antimicrobial resistance and provide a basis for the development of management strategies to mitigate the antimicrobial resistance crisis.展开更多
Antibiotic resistance has been recognized as a major challenge worldwide for humans.“One Health”has been recognized as a key concept for containment of antibiotic resistance.Under the framework,the role of the envir...Antibiotic resistance has been recognized as a major challenge worldwide for humans.“One Health”has been recognized as a key concept for containment of antibiotic resistance.Under the framework,the role of the environment in the development of antibiotic resistance genes(ARGs)has become increasingly obvious.Despite numerous efforts,response to antibiotic re-sistance is considered to be inadequate,which is probably due to the lack of a clear roadmap.Here,we propose a“One Health”roadmap to combat antibiotic resistance in the environment through(1)understanding environmental resistome.The environmental gene pool has long been recognized as the single largest reservoir of both known and novel ARGs.(2)Standardizing ARG quantification.Systematic joint efforts based on standardized quantification are urgently needed to un-derstand the true tempospatial profiles of the environmental resistome.(3)Identifying mechanisms of resistome development.Horizontal gene transfer and co-selection have been recognized as the two main mechanisms contributing to the environmental resistome.(4)Establishing a risk-assessment framework.The first critical step for large-scale cost-effective targeted ARG management in the environment is the risk assessment to identify the priority ARGs for control.(5)Formulating regulatory standards.By correlating the environmental ARG profile with public health,we may identify the indicator ARGs that can be integrated into current environmental quality standards.(6)Developing control strategies.Systematic analysis of available control technologies is required to identify the most feasible ones to curtail the spread of ARGs in the environment.The proposed roadmap under the“One Health”framework provides a guide to tackle antibiotic resistance in the environment.展开更多
The recent outbreak of the 5th wave of COVID-19 in Hong Kong reminds us again that infectious diseases are one of the grand challenges to the public health today.The ability to rapidly monitor the spread of diseases i...The recent outbreak of the 5th wave of COVID-19 in Hong Kong reminds us again that infectious diseases are one of the grand challenges to the public health today.The ability to rapidly monitor the spread of diseases in a large scale is the key for prevention,intervention and control.Wastewater-Based Epidemiology(WBE)is based on pooled wastewater of a population.展开更多
基金supported by a Theme-based Research Scheme grant from the Research Grants Council of the Hong Kong Special Administrative Region,China(T21-705/20-N)。
文摘Antibiotic resistance,which is encoded by antibiotic-resistance genes(ARGs),has proliferated to become a growing threat to public health around the world.With technical advances,especially in the popularization of metagenomic sequencing,scientists have gained the ability to decipher the profiles of ARGs in diverse samples with high accuracy at an accelerated speed.To analyze thousands of ARGs in a highthroughput way,standardized and integrated pipelines are needed.The new version(v3.0)of the widely used ARGs online analysis pipeline(ARGs-OAP)has made significant improvements to both the reference database-the structured ARG(SARG)database-and the integrated analysis pipeline.SARG has been enhanced with sequence curation to improve annotation reliability,incorporate emerging resistance genotypes,and determine rigorous mechanism classification.The database has been further organized and visualized online in the format of a tree-like structure with a dictionary.It has also been divided into sub-databases for different application scenarios.In addition,the ARGs-OAP has been improved with adjusted quantification methods,simplified tool implementation,and multiple functions with userdefined reference databases.Moreover,the online platform now provides a diverse biostatistical analysis workflow with visualization packages for the efficient interpretation of ARG profiles.The ARGs-OAP v3.0 with an improved database and analysis pipeline will benefit academia,governmental management,and consultation regarding risk assessment of the environmental prevalence of ARGs.
基金supported by the National Natural Science Foundation of China (41977137 and 42307048)the International Atomic Energy Agency Research Project (D15022)+5 种基金Jiangsu Funding Program for Excellent Postdoctoral Talent (2022ZB460)the China Postdoctoral Science Foundation (2023M733593)Chinese Academy of Sciences President's International Fellowship Initiative (2020DC0005)Academy of Finland,Innovation Fund Denmark and the European Commission Horizon 2020 financed under the ERA-NET Aquatic Pollutants Joint Transnational Call (REWA,GA No 869178)the Center for Health Impacts of Agriculture (CHIA)of Michigan State Universitysupported by the fellowship of Alexander von Humboldt for experienced researchers,and Shennong Young Talents of the Ministry of Agriculture and Rural Affairs,China (SNYCQN006-2022).
文摘The emergence and rapid spread of antimicrobial resistance is of global public health concern.The gut microbiota harboring diverse commensal and opportunistic bacteria that can acquire resistance via horizontal and vertical gene transfers is considered an important reservoir and sink of antibiotic resistance genes(ARGs).In this review,we describe the reservoirs of gut ARGs and their dynamics in both animals and humans,use the One Health perspective to track the transmission of ARG-containing bacteria between humans,animals,and the environment,and assess the impact of antimicrobial resistance on human health and socioeconomic development.The gut resistome can evolve in an environment subject to various selective pressures,including antibiotic administration and environmental and lifestyle factors(e.g.,diet,age,gender,and living conditions),and interventions through probiotics.Strategies to reduce the abundance of clinically relevant antibiotic-resistant bacteria and their resistance determinants in various environmental niches are needed to ensure the mitigation of acquired antibiotic resistance.With the help of effective measures taken at the national,local,personal,and intestinal management,it will also result in preventing or minimizing the spread of infectious diseases.This review aims to improve our understanding of the correlations between intestinal microbiota and antimicrobial resistance and provide a basis for the development of management strategies to mitigate the antimicrobial resistance crisis.
基金supported by a Theme‐based Research Scheme grant from the Research Grants Council of the Hong Kong Special Administrative Region,China(Project no.T21‐705/20‐N).
文摘Antibiotic resistance has been recognized as a major challenge worldwide for humans.“One Health”has been recognized as a key concept for containment of antibiotic resistance.Under the framework,the role of the environment in the development of antibiotic resistance genes(ARGs)has become increasingly obvious.Despite numerous efforts,response to antibiotic re-sistance is considered to be inadequate,which is probably due to the lack of a clear roadmap.Here,we propose a“One Health”roadmap to combat antibiotic resistance in the environment through(1)understanding environmental resistome.The environmental gene pool has long been recognized as the single largest reservoir of both known and novel ARGs.(2)Standardizing ARG quantification.Systematic joint efforts based on standardized quantification are urgently needed to un-derstand the true tempospatial profiles of the environmental resistome.(3)Identifying mechanisms of resistome development.Horizontal gene transfer and co-selection have been recognized as the two main mechanisms contributing to the environmental resistome.(4)Establishing a risk-assessment framework.The first critical step for large-scale cost-effective targeted ARG management in the environment is the risk assessment to identify the priority ARGs for control.(5)Formulating regulatory standards.By correlating the environmental ARG profile with public health,we may identify the indicator ARGs that can be integrated into current environmental quality standards.(6)Developing control strategies.Systematic analysis of available control technologies is required to identify the most feasible ones to curtail the spread of ARGs in the environment.The proposed roadmap under the“One Health”framework provides a guide to tackle antibiotic resistance in the environment.
文摘The recent outbreak of the 5th wave of COVID-19 in Hong Kong reminds us again that infectious diseases are one of the grand challenges to the public health today.The ability to rapidly monitor the spread of diseases in a large scale is the key for prevention,intervention and control.Wastewater-Based Epidemiology(WBE)is based on pooled wastewater of a population.
