Antibiotic resistance and its environmental component are gaining more attention as part of combating the growing healthcare crisis. The One Health framework, promulgated by many global health agencies, recognizes tha...Antibiotic resistance and its environmental component are gaining more attention as part of combating the growing healthcare crisis. The One Health framework, promulgated by many global health agencies, recognizes that antimicrobial resistance is a truly inter-domain problem in which human health, animal agriculture, and the environment are the core and interrelated components.This prospectus presents the status and issues relevant to the environmental component of antibiotic resistance, namely, the needs for advancing surveillance methodology: the environmental reservoirs and sources of resistance, namely, urban wastewater treatment plants, aquaculture production systems, soil receiving manure and biosolid, and the atmosphere which includes longer range dispersal.Recently, much work has been done describing antibiotic resistance genes in various environments;now quantitative, mechanistic,and hypothesis-driven studies are needed to identify practices that reduce real risks and maintain the effectiveness of our current antibiotics as long as possible. Advanced deployable detection methods for antibiotic resistance in diverse environmental samples are needed in order to provide the surveillance information to identify risks and define barriers that can reduce risks. Also needed are practices that reduce antibiotic use and thereby reduce selection for resistance, as well as practices that limit the dispersal of or destroy antibiotic-resistant bacteria or their resistance genes that are feasible for these varied environmental domains.展开更多
Economic losses and market constraints caused by bacterial diseases such as colibacillosis due to avian pathogenic Escherichia coli and necrotic enteritis due to Clostridium perfringens remain major problems for poult...Economic losses and market constraints caused by bacterial diseases such as colibacillosis due to avian pathogenic Escherichia coli and necrotic enteritis due to Clostridium perfringens remain major problems for poultry producers,despite substantial efforts in prevention and control.Antibiotics have been used not only for the treatment and prevention of such diseases,but also for growth promotion.Consequently,these practices have been linked to the selection and spread of antimicrobial resistant bacteria which constitute a significant global threat to humans,ani-mals,and the environment.To break down the antimicrobial resistance(AMR),poultry producers are restricting the antimicrobial use(AMU)while adopting the antibiotic-free(ABF)and organic production practices to satisfy consum-ers’demands.However,it is not well understood how ABF and organic poultry production practices influence AMR profiles in the poultry gut microbiome.Various Gram-negative(Salmonella enterica serovars,Campylobacter jejuni/coli,E.coli)and Gram-positive(Enterococcus spp.,Staphylococcus spp.and C.perfringens)bacteria harboring multiple AMR determinants have been reported in poultry including organically-and ABF-raised chickens.In this review,we discussed major poultry production systems(conventional,ABF and organic)and their impacts on AMR in some potential pathogenic Gram-negative and Gram-positive bacteria which could allow identifying issues and opportuni-ties to develop efficient and safe production practices in controlling pathogens.展开更多
Wastewater treatment plants(WWTPs)represent one of biotechnology's largest and most critical applications,playing a pivotal role in environmental protection and public health.In WWTPs,activated sludge(AS)plays a m...Wastewater treatment plants(WWTPs)represent one of biotechnology's largest and most critical applications,playing a pivotal role in environmental protection and public health.In WWTPs,activated sludge(AS)plays a major role in removing contaminants and pathogens from wastewater.While metagenomics has advanced our understanding of microbial communities,it still faces challenges in revealing the genomic heterogeneity of cells,uncovering the microbial dark matter,and establishing precise links between genetic elements and their host cells as a bulk method.These issues could be largely resolved by single-cell sequencing,which can offer unprecedented resolution to show the unique genetic information.Here we show the high-throughput single-cell sequencing to the AS microbiome.The single-amplified genomes(SAGs)of 15,110 individual cells were clustered into 2,454 SAG bins.We find that 27.5%of the genomes in the AS microbial community represent potential novel species,highlighting the presence of microbial dark matter.Furthermore,we identified 1,137 antibiotic resistance genes(ARGs),10,450 plasmid fragments,and 1,343 phage contigs,with shared plasmid and phage groups broadly distributed among hosts,indicating a high frequency of horizontal gene transfer(HGT)within the AS microbiome.Complementary analysis using 1,529 metagenome-assembled genomes from the AS samples allowed for the taxonomic classification of 98 SAG bins,which were previously unclassified.Our study establishes the feasibility of single-cell sequencing in characterizing the AS microbiome,providing novel insights into its ecological dynamics,and deepening our understanding of HGT processes,particularly those involving ARGs.Additionally,this valuable tool could monitor the distribution,spread,and pathogenic hosts of ARGs both within AS environments and between AS and other environments,which will ultimately contribute to developing a health risk evaluation system for diverse environments within a One Health framework.展开更多
Environmental pollution is escalating due to rapid global development that often prioritizes human needs over planetary health.Despite global efforts to mitigate legacy pollutants,the continuous introduction of new su...Environmental pollution is escalating due to rapid global development that often prioritizes human needs over planetary health.Despite global efforts to mitigate legacy pollutants,the continuous introduction of new substances remains a major threat to both people and the planet.In response,global initiatives are focusing on risk assessment and regulation of emerging contaminants,as demonstrated by the ongoing efforts to establish the UN’s Intergovernmental Science-Policy Panel on Chemicals,Waste,and Pollution Prevention.This review identifies the sources and impacts of emerging contaminants on planetary health,emphasizing the importance of adopting a One Health approach.Strategies for monitoring and addressing these pollutants are discussed,underscoring the need for robust and socially equitable environmental policies at both regional and international levels.Urgent actions are needed to transition toward sustainable pollution management practices to safeguard our planet for future generations.展开更多
基金funded by the National Natural Science Foundation of China (No. 21677149)the Outstanding Youth Fund of the Natural Science Foundation of Jiangsu Province, China (No. BK20150050)+6 种基金the Innovative Project of Chinese Academy of Sciences (No. ISSASIP1616)funded by the Center for Health Impacts of Agriculture (CHIA) of Michigan State University, USAfunded by Agriculture and AgriFood Canada, the Canadian Genomics Research Development Initiative (GRDI-AMR)the Canadian Institute for Health Research (CIHR) through the Joint Programming Initiative on Antimicrobial Resistance (JPIAMR)the National Funds from FCT—Fundacao para a Ciência e a Tecnologia, Portugal (No. UID/Multi/ 50016/2013)funded by Academy of Finland and the Joint Programming Initiative “Water Challenges for a Changing World” (Water JPI)funded by the Collaborative Research Fund of Hong Kong (CRF), China (No. C6033-14G)
文摘Antibiotic resistance and its environmental component are gaining more attention as part of combating the growing healthcare crisis. The One Health framework, promulgated by many global health agencies, recognizes that antimicrobial resistance is a truly inter-domain problem in which human health, animal agriculture, and the environment are the core and interrelated components.This prospectus presents the status and issues relevant to the environmental component of antibiotic resistance, namely, the needs for advancing surveillance methodology: the environmental reservoirs and sources of resistance, namely, urban wastewater treatment plants, aquaculture production systems, soil receiving manure and biosolid, and the atmosphere which includes longer range dispersal.Recently, much work has been done describing antibiotic resistance genes in various environments;now quantitative, mechanistic,and hypothesis-driven studies are needed to identify practices that reduce real risks and maintain the effectiveness of our current antibiotics as long as possible. Advanced deployable detection methods for antibiotic resistance in diverse environmental samples are needed in order to provide the surveillance information to identify risks and define barriers that can reduce risks. Also needed are practices that reduce antibiotic use and thereby reduce selection for resistance, as well as practices that limit the dispersal of or destroy antibiotic-resistant bacteria or their resistance genes that are feasible for these varied environmental domains.
基金supported by Agriculture and Agri-Food Canada to M.S.Diarra through the Genomics Research and Development Initiative (PSS#1858 J-001262) and A-Base (PSS#3441,J-002363) projects on “Mitigating Antimicrobial Resistance”.
文摘Economic losses and market constraints caused by bacterial diseases such as colibacillosis due to avian pathogenic Escherichia coli and necrotic enteritis due to Clostridium perfringens remain major problems for poultry producers,despite substantial efforts in prevention and control.Antibiotics have been used not only for the treatment and prevention of such diseases,but also for growth promotion.Consequently,these practices have been linked to the selection and spread of antimicrobial resistant bacteria which constitute a significant global threat to humans,ani-mals,and the environment.To break down the antimicrobial resistance(AMR),poultry producers are restricting the antimicrobial use(AMU)while adopting the antibiotic-free(ABF)and organic production practices to satisfy consum-ers’demands.However,it is not well understood how ABF and organic poultry production practices influence AMR profiles in the poultry gut microbiome.Various Gram-negative(Salmonella enterica serovars,Campylobacter jejuni/coli,E.coli)and Gram-positive(Enterococcus spp.,Staphylococcus spp.and C.perfringens)bacteria harboring multiple AMR determinants have been reported in poultry including organically-and ABF-raised chickens.In this review,we discussed major poultry production systems(conventional,ABF and organic)and their impacts on AMR in some potential pathogenic Gram-negative and Gram-positive bacteria which could allow identifying issues and opportuni-ties to develop efficient and safe production practices in controlling pathogens.
基金supported by the Themebased Research Scheme(T21-705/20-N)and Shenzhen ScienceTechnology Program(Sustainable Development Project,KCXFZ20230731093959008).
文摘Wastewater treatment plants(WWTPs)represent one of biotechnology's largest and most critical applications,playing a pivotal role in environmental protection and public health.In WWTPs,activated sludge(AS)plays a major role in removing contaminants and pathogens from wastewater.While metagenomics has advanced our understanding of microbial communities,it still faces challenges in revealing the genomic heterogeneity of cells,uncovering the microbial dark matter,and establishing precise links between genetic elements and their host cells as a bulk method.These issues could be largely resolved by single-cell sequencing,which can offer unprecedented resolution to show the unique genetic information.Here we show the high-throughput single-cell sequencing to the AS microbiome.The single-amplified genomes(SAGs)of 15,110 individual cells were clustered into 2,454 SAG bins.We find that 27.5%of the genomes in the AS microbial community represent potential novel species,highlighting the presence of microbial dark matter.Furthermore,we identified 1,137 antibiotic resistance genes(ARGs),10,450 plasmid fragments,and 1,343 phage contigs,with shared plasmid and phage groups broadly distributed among hosts,indicating a high frequency of horizontal gene transfer(HGT)within the AS microbiome.Complementary analysis using 1,529 metagenome-assembled genomes from the AS samples allowed for the taxonomic classification of 98 SAG bins,which were previously unclassified.Our study establishes the feasibility of single-cell sequencing in characterizing the AS microbiome,providing novel insights into its ecological dynamics,and deepening our understanding of HGT processes,particularly those involving ARGs.Additionally,this valuable tool could monitor the distribution,spread,and pathogenic hosts of ARGs both within AS environments and between AS and other environments,which will ultimately contribute to developing a health risk evaluation system for diverse environments within a One Health framework.
基金funded by the National Key Research and Development Program of China(2020YFC1807000)the Strategic Priority Research Program of the Chinese Academy of Sciences(no.XDA28030501)+9 种基金the National Natural Science Foundation of China(41991333,41977137,42090060)the International Atomic Energy Agency Research Project(D15022)the Youth Innovation Promotion Association of Chinese Academy of Sciences(2011225[Fang Wang],Y201859[H.Wang],2013201[J.Su],2021309[Y.Song],Y2022084[M.Ye])Chinese Academy of Sciences President’s International Fellowship Initiative(2020DC0005,2022DC0001,2024DC0009)the Institute of Soil Science,Chinese Academy of Sciences(ISSAS2419)the Research Group Linkage project from Alexander von Humboldt foundation,the Center for Health Impacts of Agriculture(CHIA)of Michigan State University,and the URI STEEP Superfund Center(grant#P42ES027706)Fang Wang was partly supported 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)J.P.and T.R.S.were supported by the Canada Research Chair program.B.W.B.was supported by a Royal Society of New Zealand Catalyst International Leaders fellowship.K.K.B.was supported by Innovation Fund Denmark and the European Commission Horizon 2020 financed under the ERA-NET Aquatic Pollutants Joint Transnational Call(REWA,GA no.869178)S.A.H.was partly supported by a grant from the National Institute of Environmental Health Sciences,National Institutes of Health grant number P42ES04911-29(Project 4)T.R.S.thanks CESAM by FCT/MCTES(UIDP/50017/2020+UIDB/50017/2020+LA/P/0094/2020)。
文摘Environmental pollution is escalating due to rapid global development that often prioritizes human needs over planetary health.Despite global efforts to mitigate legacy pollutants,the continuous introduction of new substances remains a major threat to both people and the planet.In response,global initiatives are focusing on risk assessment and regulation of emerging contaminants,as demonstrated by the ongoing efforts to establish the UN’s Intergovernmental Science-Policy Panel on Chemicals,Waste,and Pollution Prevention.This review identifies the sources and impacts of emerging contaminants on planetary health,emphasizing the importance of adopting a One Health approach.Strategies for monitoring and addressing these pollutants are discussed,underscoring the need for robust and socially equitable environmental policies at both regional and international levels.Urgent actions are needed to transition toward sustainable pollution management practices to safeguard our planet for future generations.
