Background Mobile element variants(MEVs)have a significant and complex impact on genomic diversity and phe-notypic traits.However,the quantity,distribution,and relationship with gene expression and complex traits of M...Background Mobile element variants(MEVs)have a significant and complex impact on genomic diversity and phe-notypic traits.However,the quantity,distribution,and relationship with gene expression and complex traits of MEVs in the pig genome remain poorly understood.Results We constructed the most comprehensive porcine MEV library based on high-depth whole genome sequencing(WGS)data from 747 pigs across 59 breeds worldwide.This database identified a total of 147,993 poly-morphic MEVs,including 121,099 short interspersed nuclear elements(SINEs),26,053 long interspersed nuclear elements(LINEs),802 long terminal repeats(LTRs),and 39 other transposons,among which 54%are newly discovered.We found that MEVs are unevenly distributed across the genome and are strongly influenced by negative selec-tion effects.Importantly,we identified 514,530,and 584 candidate MEVs associated with population differentiation,domestication,and breed formation,respectively.For example,a significantly differentiated MEV is located in the ATRX intron between Asian and European pigs,whereas ATRX is also differentially expressed between Asian and European pigs in muscle tissue.In addition,we identified 4,169 expressed MEVs(eMEVs)significantly associated with gene expression and 6,914 splicing MEVs(sMEVs)associated with gene splicing based on RNA-seq data from 266 porcine liver tissues.These eMEVs and sMEVs explain 6.24%and 9.47%,respectively,of the observed cis-heritability and high-light the important role of MEVs in the regulation of gene expression.Finally,we provide a high-quality SNP–MEV reference haplotype panel to impute MEV genotypes from genome-wide SNPs.Notably,we identified a candidate MEV significantly associated with total teat number,demonstrating the functionality of this reference panel.Conclusions The present investigation demonstrated the importance of MEVs in pigs in terms of population diversity,gene expression and phenotypic traits,which may provide useful resources and theoretical support for pig genetics and breeding.展开更多
Exploiting mobile elements （MEs） to accomplish data collection in wireless sensor networks （WSNs） can improve the energy efficiency of sensor nodes, and prolong network lifetime. However, it will lead to large dat...Exploiting mobile elements （MEs） to accomplish data collection in wireless sensor networks （WSNs） can improve the energy efficiency of sensor nodes, and prolong network lifetime. However, it will lead to large data collection latency for the network, which is unacceptable for data-critical applications. In this paper, we address this problem by minimizing the traveling length of MEs. Our methods mainly consist of two steps： we first construct a virtual grid network and select the minimal stop point set （SPS） from it; then, we make optimal scheduling for the MEs based on the SPS in order to minimize their traveling length. Different implementations of genetic algorithm （GA） are used to solve the problem. Our methods are evaluated by extensive simulations. The results show that these methods can greatly reduce the traveling length of MEs, and decrease the data collection latency.展开更多
1 Introduction Genomic islands(GIs)promote co-evolution among different species,which are of significant importance for studying microbial functionality and evolution[1].To effectively identify genomic islands,numerou...1 Introduction Genomic islands(GIs)promote co-evolution among different species,which are of significant importance for studying microbial functionality and evolution[1].To effectively identify genomic islands,numerous algorithms have been developed.These methods detect candidate genomic islands either by recognizing differences in sequence composition between genomic islands and their host genomes or by analyzing multiple genomes through sequence alignment[2].However,it’s important to note that genomic islands are formed through horizontal gene transfer and typically contain functional genes,such as those related to pathogenicity,metabolic regulation,and antibiotic resistance,as well as mobile elements like insertion sequences(IS),integrative and conjugative elements(ICE),mobile genetic elements(MGE),and bacteriophages(phage).In turn,utilizing these mobile elements can aid in the identification of genomic islands.展开更多
Multidrug-resistant(MDR)Enterobacteriaceae critically threaten duck farming and public health.The phenotypes,genotypes,and associated mobile genetic elements(MGEs)of MDR Enterobacteriaceae isolated from 6 duck farms i...Multidrug-resistant(MDR)Enterobacteriaceae critically threaten duck farming and public health.The phenotypes,genotypes,and associated mobile genetic elements(MGEs)of MDR Enterobacteriaceae isolated from 6 duck farms in Zhejiang Province,China,were investigated.A total of 215 isolates were identified as Escherichia coli(64.65%),Klebsiella pneumoniae(12.09%),Proteus mirabilis(10.23%),Salmonella(8.84%),and Enterobacter cloacae(4.19%).Meanwhile,all isolates were resistant to at least two antibiotics.Most isolates carried tet(A)(85.12%),blaTEM(78.60%)and sul1(67.44%)resistance genes.Gene co-occurrence analysis showed that the resistance genes were associated with IS26 and integrons.A conjugative IncFII plasmid pSDM004 containing all the above MGEs was detected in Proteus mirabilis isolate SDM004.This isolate was resistant to 18 antibiotics and carried the blaNDM-5 gene.MGEs,especially plasmids,are the primary antibiotic resistance gene transmission route in duck farms.These findings provide a theoretical basis for the rational use of antibiotics in farms which are substantial for evaluating public health and food safety.展开更多
The Disuga Cu deposit,located in the eastern porphyry belt of the Zhongdian arc,southwest China,provides a window into magmatic-hydrothermal processes controlling porphyry Cu mineralization.Based on zircon U-Pb geochr...The Disuga Cu deposit,located in the eastern porphyry belt of the Zhongdian arc,southwest China,provides a window into magmatic-hydrothermal processes controlling porphyry Cu mineralization.Based on zircon U-Pb geochronology,hydrothermal mineral chemistry,short-wave infrared spectroscopy,and mass balance modeling,this study investigated the alteration zonation and element mobility in the Disuga Cu deposit.Zircon U-Pb ages of the ore-hosting quartz dioritic porphyries(222.4±3.1 and 219.3±2.4 Ma)are similar to those of Late Triassic subduction-related magmatism.High zircon-crystallization temperatures(727±26℃)and elevated oxygen fugacity(ΔFMQ+2.0)confirm these porphyries were favorable for mineralization.Hydrothermal sericite(Si=6.49 atoms per formula unit[apfu];Al^(Ⅵ)=3.39 apfu)and chlorite(Fe/(Fe+Mg)=0.59-0.63)compositions indicate an acidic reduced fluid.Three distinct hydrothermal stages were identified:(1)phyllic alteration(370℃);(2)propylitic alteration(315℃);and(3)low-temperature hydrothermal alteration(242℃).Mass balance calculations show that the Cu migration rate(155.6%/114.4%)in the propylitic/phyllic alteration zones was higher than that of Mo(14.3%;limited to the propylitic alteration zone).The alteration mineralization assemblages indicate the occurrence of deep potassic alteration zones and porphyry Cu-(Mo)mineralization in the Disuga area.展开更多
Due to its complicated matrix effects, rapid quantitative analysis of chromium in agricultural soils is difficult without the concentration gradient samples by laser-induced breakdown spectroscopy. To improve the anal...Due to its complicated matrix effects, rapid quantitative analysis of chromium in agricultural soils is difficult without the concentration gradient samples by laser-induced breakdown spectroscopy. To improve the analysis speed and accuracy, two calibration models are built with the support vector machine method： one considering the whole spectra and the other based on the segmental spectra input. Considering the results of the multiple linear regression analysis, three segmental spectra are chosen as the input variables of the support vector regression （SVR） model. Compared with the results of the SVR model with the whole spectra input, the relative standard error of prediction is reduced from 3.18% to 2.61% and the running time is saved due to the decrease in the number of input variables, showing the robustness in rapid soil analysis without the concentration gradient samples.展开更多
HighlightsA novel conjugative plasmid pHJ90-cfr carrying the multiresistance gene cfr was characterized in Proteus vulgaris.A new IS5-family member,ISPmi4,was identified for the first time.Both plasmids and ICEs were ...HighlightsA novel conjugative plasmid pHJ90-cfr carrying the multiresistance gene cfr was characterized in Proteus vulgaris.A new IS5-family member,ISPmi4,was identified for the first time.Both plasmids and ICEs were vital mobile genetic elements for horizontal transmission of cfr gene in Proteus species.展开更多
Antibiotic resistance genes(ARGs)are an emerging issue for drinkingwater safety.However,the seasonal variation of ARGs in drinking water distribution systems(DWDS)is still unclear.This work revealed the tempo-spatial ...Antibiotic resistance genes(ARGs)are an emerging issue for drinkingwater safety.However,the seasonal variation of ARGs in drinking water distribution systems(DWDS)is still unclear.This work revealed the tempo-spatial changes of microbial community,ARGs,mobile genetic elements(MGEs)co-occurring with ARGs,ARG hosts in DWDS bulk water by means of metagenome assembly.The microbial community and antibiotic resistome varied with sampling season and site.Temperature,ammonia,chlorite and total plate count(TPC)drove the variations of microbial community structure.Moreover,environmental parameters(total organic carbon(TOC),chlorite,TPC and hardness)shifted antibiotic resistome.ARGs and MGEs co-occurring with ARGs showed higher relative abundance in summer and autumn,which might be attributed to detached pipe biofilm.In particular,ARG-bacitracin and plasmid were the predominant ARG and MGE,respectively.ARG hosts changed with season and site and were more diverse in summer and autumn.In winter and spring,Limnohabitans and Mycobacterium were the major ARG hosts as well as the dominant genera in microbial community.In addition,in summer and autumn,high relative abundance of Achromobacter and Stenotrophomonas were the hosts harboring many kinds of ARGs and MGEs at site in a residential zone(0.4 km from the water treatment plant).Compared with MGEs,microbial community had a greater contribution to the variation of antibiotic resistome.This work gives new insights into the dynamics of ARGs in full-scale DWDS and the underlying factors.展开更多
The global increased antibiotic resistance level in pathogenic microbes has posed a significant threat to human health.Fresh vegetables have been recognized to be an important vehicle of antibiotic resistance genes(AR...The global increased antibiotic resistance level in pathogenic microbes has posed a significant threat to human health.Fresh vegetables have been recognized to be an important vehicle of antibiotic resistance genes(ARGs)from environments to human beings.Phyllosphere ARGs have been indicated to be changed with plant species,yet the influence of plant cultivar on the phyllospheric resistome is still unclear.Here,we detected the ARGs and bacterial communities in the phyllosphere of two cultivars of cilantros and their corresponding soils using high-throughput quantitative PCR technique and bacterial 16S rRNA gene-based high-throughput sequencing,respectively.We further identified the potential bacterial pathogens and analyzed the effects of plant cultivar on ARGs,mobile genetic elements(MGEs),microbiome and potential bacterial pathogens.The results showed that the cultivars did not affect the ARG abundance and composition,but significantly shaped the abundance of MGEs and the composition structure of bacteria in the phyllosphere.The relative abundance of potential bacterial pathogenswas significantly higher in the phyllosphere than that in soils.Mantel test showed that the ARG patterns were significantly correlated to the patterns of potential bacterial pathogens.Our results suggested that the horizontal gene transfer of ARGs in the phyllosphere might be different between the two cultivars of cilantro and highlighted the higher risk of phyllospheric microorganisms compared with those in soils.These findings extend our knowledge on the vegetable microbiomes,ARGs,and potential pathogens,suggesting more agricultural and hygiene protocols are needed to control the risk of foodborne ARGs.展开更多
To meet the rapidly growing global demand for aquaculture products,large amounts of antibiotics were used in aquaculture,which might accelerate the evolution of antibiotic-resistant bacteria(ARB)and the propagation of...To meet the rapidly growing global demand for aquaculture products,large amounts of antibiotics were used in aquaculture,which might accelerate the evolution of antibiotic-resistant bacteria(ARB)and the propagation of antibiotic genes(ARGs).In our research,we revealed the ARGs profiles,their co-occurrence with mobile genetic elements(MGEs),and potential hosts in sediments of a crab pond wastewater purification system based on metagenomic analysis.The residual antibiotic seems to increase the propagation of ARGs in the crab pond,but there was no clear relationship between a given antibiotic type and the corresponding resistance genes.The effect of aquaculture on sediment was not as profound as that of other anthropogentic activities,but increased the relative abundance of sulfon-amide resistance gene.A higher abundance of MGEs,especially plasmid,increased the po-tential ARGs dissemination risk in crab and purification ponds.Multidrug and sulfonamide resistance genes had greater potential to transfer because they were more frequently carried by MGEs.The horizontal gene transfer was likely to occur among a variety of microorgan-isms,and various ARGs hosts including Pseudomonas,Acinetobacter,Escherichia,and Klebsiella were identified.Bacterial community influenced the composition of ARG hosts,and Pro-teobacteria was the predominant hosts.Overall,our study provides novel insights into the environmental risk of ARGs in sediments of aquaculture wastewater treatment system.展开更多
Despite coastal mudflats serving as essential ecological zones interconnecting terrestrial/freshwater and marine systems,little is known about the profiles of antibiotic resistance genes(ARGs)in this area.In this stud...Despite coastal mudflats serving as essential ecological zones interconnecting terrestrial/freshwater and marine systems,little is known about the profiles of antibiotic resistance genes(ARGs)in this area.In this study,characteristics of typical ARGs,involving both intracellular(iARGs)and extracellular ARGs(eARGs)at different physical states,were explored in over 1000 km of coastal mudflats in Eastern China.Results indicated the presence of iARGs and eARGs at states of both freely present or attached by particles.The abundance of eARGs was significantly higher than that of iARGs(87.3%vs 12.7%),and their dominance was more significant than those in other habitats(52.7%-76.3%).ARG abundance,especially for eARGs,showed an increasing trend(p<0.05)from southern(Nantong)to northern(Lianyungang)coastalmudflats.Higher salinity facilitated the transformation from iARGs to eARGs,and smaller soil particle size was conducive to the persistence of eARGs in northern coastal mudflats.This study addresses the neglected function of coastal mudflats as eARGs reservoirs.展开更多
A study was conducted by collecting eight seepage water samples that drain through the sedimentary rocks, mainly sandstone and shale, to evaluate the hydro- geochemical characteristics. The collected samples were anal...A study was conducted by collecting eight seepage water samples that drain through the sedimentary rocks, mainly sandstone and shale, to evaluate the hydro- geochemical characteristics. The collected samples were analyzed for physico-chemical parameters using standard procedures. Three water types were identified in the Piper plot and the hydrogeochemical evolution starts from a Ca- C1 facies （type 1） via mixed Ca-Mg-C1 and Ca-Na-HCO3 facies （type 2） to Na-C1 facies （type 3）. Increasing trend of electrical conductivity （EC） values were observed from type 1 water to type 3 water. Lower ionic concentrations with an average EC value of 35.7 kts/cm in Ca-C1 facies indicate the recharge water by monsoonal rainfall, and ion exchange/weathering process is reflected in the mixing zone. Higher ionic concentration with an average EC value of 399 kts/cm is noted in Na-C1 facies, which indicates the ion exchange during water-rock interaction. Higher log pCO2 values are also found in this facies, revealing the longer residence time of seepage water in the rock matrix, which release more ions into the water. The relative mobility of elements during weathering suggest that the order of mobility in both sandstone and shale is Na 〉 Ca 〉 Mg 〉 K. It was observed that thehydrogeochemistry of seepage water is mainly controlled by the bedrock geology.展开更多
The occurrence of antibiotic resistance genes(ARGs)in various environments has drawn worldwide attention due to their potential risks.Previous studies have reported that a variety of substances can enhance the occurre...The occurrence of antibiotic resistance genes(ARGs)in various environments has drawn worldwide attention due to their potential risks.Previous studies have reported that a variety of substances can enhance the occurrence and dissemination of ARGs.However,few studies have compared the response of ARGs under the stress of different organicmatters in biologicalwastewater treatment systems.In this study,seven organic pollutantswere added into wastewater treatment bioreactors to investigate their impacts on the ARG occurrence in activated sludge.Based on high-throughput sequencing,it was found that the microbial communities and ARG patterns were significantly changed in the activated sludge exposed to these organic pollutants.Compared with the non-antibiotic refractory organic matters,antibiotics not only increased the abundance of ARGs but also significantly changed the ARG compositions.The increase of Gram-negative bacteria(e.g.,Archangium,Prosthecobacter and Dokdonella)carrying ARGs could be the main cause of ARG proliferation.In addition,significant co-occurrence relationships between ARGs and mobile genetic elements were also observed in the sludge samples,which may also affect the ARG diversity and abundance during the organic matter treatment in the bioreactors.Overall,these findings provide new information for better understanding the ARG occurrence and dissemination caused by organic pollutants in wastewater treatment systems.展开更多
Vibrio cholerae(V. cholerae) genome is equipped with a number of integrative mobile genetic element(IMGE) like prophages, plasmids, transposons or genomic islands, which provides fitness factors that help the pathogen...Vibrio cholerae(V. cholerae) genome is equipped with a number of integrative mobile genetic element(IMGE) like prophages, plasmids, transposons or genomic islands, which provides fitness factors that help the pathogen to survive in changing environmental conditions. Metagenomic analyses of clinical and environmental V. cholerae isolates revealed that dimer resolution sites(dif) harbor several structurally and functionally distinct IMGEs. All IMGEs present in the dif region exploit chromosomally encoded tyrosine recombinases, Xer C and Xer D, for integration. Integration takes place due to site-specific recombination between two specific DNA sequences; chromosomal sequence is called att B and IMGEs sequence is called att P. Different IMGEs present in the att P region have different attP structure but all of them are recognized by Xer C and Xer D enzymes and mediate either reversible or irreversible integration. Cholera toxin phage(CTXΦ), a lysogenic filamentous phage carrying the cholera toxin genes ctx AB, deserves special attention because it provides V. cholerae the crucial toxin and is always present in the dif region of all epidemic cholera isolates. Therefore, understanding the mechanisms of integration and dissemination of CTXΦ, genetic and ecological factors which support CTXΦ integration as well as production of virion from chromosomally integrated phage genome and interactions of CTXΦ with other genetic elements present in the genomes of V. cholerae is important for learning more about the biology of cholera pathogen.展开更多
Profiles and driving mechanisms of antibiotic resistome in the polar region are important for exploring the natural evolution of antibiotic resistance genes(ARGs).Here,we evaluated the profiles of antibiotic resistome...Profiles and driving mechanisms of antibiotic resistome in the polar region are important for exploring the natural evolution of antibiotic resistance genes(ARGs).Here,we evaluated the profiles of antibiotic resistome in multiple media on Inexpressible Island,Terra Nova Bay,Antarctica.Average concentrations of ARGs in intracellular DNA(iARGs)among water(3.98×10^(6)copies/L),soil(3.41×10^(7)copies/kg),and penguin guano(7.04×10^(7)copies/kg)were higher than those of ARGs in extracellular DNA(eARGs)among water(1.99×10^(4)copies/L),soil(1.75×10^(6)copies/kg),and penguin guano(8.02×10^(6)copies/kg).It was indicated that the transmission of ARGs across different media occurs with around 77.8%of iARGs from soil and 86.7%of iARGs from penguins observed in water,and 80.7%of iARGs and 56.7%of eARGs from penguins found in soil.Annual inputs of ARGs from Adélie penguins on Inexpressible Island have increased since 1983.Bacitracin,multidrug,and aminoglycoside resistance genes were the main ARGs among water,soil,and penguin guano.Primary medium-risk ARGs associated with human pathogenic bacteria were multidrug resistance genes,and main low-risk ARGs associated with mobile genetic elements(MGEs)were aminoglycoside resistance genes.Antibiotic-resistant bacteria(ARB)from soil and penguins were more phylogenetically related to aquatic antibiotic-resistant mesophiles than aquatic antibiotic-resistant psychrophiles.MGEs,ARB,bacterial diversities,antibiotics,and metals could explain total ARGs between water and soil.Intracellular MGEs were the most significant in-situ driver of iARGs in water,reflecting that horizontal gene transfer could facilitate the spread of ARGs in water.Penguins were important ex-situ drivers of environmental antibiotic resistome,which was linked with risky ARGs between water and soil.These findings highlight the major roles of natural drivers(e.g.,MGEs and penguins)in shaping environmental antibiotic resistome in polar areas,improving our understanding of the evolution of environmental microbiome.展开更多
Objective:Recent cholera outbreaks in Anhui Province have been linked to Vibrio cholerae O139,but information on these strains is limited.We established the first genomic dataset of local O139 strains to analyze the g...Objective:Recent cholera outbreaks in Anhui Province have been linked to Vibrio cholerae O139,but information on these strains is limited.We established the first genomic dataset of local O139 strains to analyze the genomic characteristics and evolution of antibiotic resistance.Methods:Thirty-four Vibrio cholerae O139 isolates from Anhui(2013–2024)were sequenced using nextgeneration sequencing.Genes for virulence,antimicrobial resistance,pathogenicity islands,and mobile genetic elements were predicted using ABRicate and other online tools.To construct a phylogenetic tree,124 publicly available O139 genomes were included in the single-nucleotide polymorphism analysis alongside the study isolates.Results:Strains formed two clusters that were genetically closer to China isolates than with those from Bangladesh and India.All strains harbored ctxA and ctxB,with partial deletions in virulence genes and pathogenicity islands;over 50%lacked vgrG-2 in the T6SS.Strains from 2022–2024 exhibited higher azithromycin but lower trimethoprimsulfamethoxazole resistance than those collected during 2013–2017.Conclusion:Vibrio cholerae O139 in Anhui are endemic to China,with limited virulence but strong colonization abilities.The increased azithromycin resistance rate may be driven by its clinical antimicrobial usage,suggesting its potential for continued antibiotic resistance evolution.展开更多
The clustered regularly interspaced short palindromic repeat(CRISPR)-Caspase(Cas)system acts as a natural defense of bacteria against invasion by mobile genetic elements,such as plasmids,transposons,and bacteriophages...The clustered regularly interspaced short palindromic repeat(CRISPR)-Caspase(Cas)system acts as a natural defense of bacteria against invasion by mobile genetic elements,such as plasmids,transposons,and bacteriophages.The review discusses the different classes and types of CRISPR-Cas systems in terms of principles of their action,limitations,and future perspectives.Also,the role of the CRISPR-Cas system as a new arsenal in fighting multidrug-resistant pathogens and clinically relevant pathogenic viruses and up-to-date clinical trials have been discussed and highlighted.Moreover,the utilization mode,regulation,and the link of CRISPR-Cas to quorum sensing for targeting cell chromosome or antimicrobial-resistant gene(s)of some clinically relevant pathogens,including Klebsiella pneumoniae,Escherichia coli,and Pseudomonas aeruginosa have been discussed.The information provided in this review can act as a platform for researchers for the future use of the CRISPR-Cas system as a smart antimicrobial agent for combating infections caused by life-threatening pathogens,particularly those with limited therapeutic options.展开更多
The ESKAPE pathogens and E.coli are of significant public health concern and are listed among the top priorities of the World Health Organization.These pathogens are equally important for animal and public health,but ...The ESKAPE pathogens and E.coli are of significant public health concern and are listed among the top priorities of the World Health Organization.These pathogens are equally important for animal and public health,but their interaction with animal,human,and environmental aspects needs to be sufficiently studied.We investigated the comprehensive molecular characterization of three ESKAPE pathogens and E.coli recovered from milk,farm workers,and environmental settings in Hainan province.Minimum inhibitory concentration(MIC),extended-spectrum b-lactamase production,and biofilm production were performed per set standard protocols.The isolates were further processed by PCR and sequencing to detect resistome,virulome,and mobilome.The study found four Enterobacteriaceae species(E.coli,n=32;K.pneumoniae,n=13;E.cloacae,n=3;E.aerogenes,n=1)among n=49 bacterial isolates from the study area.Most of the strains exhibited resistance against tetracycline(71.4%),ampicillin(61.2%),flor-fenicol(44.9%),and ciprofloxacin(42.9%),while none of the strains was resistant against meropenem and amikacin.The MDR and ESBL-production percentages were 55.1%and 34.7%,respectively.The resistance determinants for b-lactams(bla_(TEM),bla_(OXA-2),bla_(SHV),bla_(CTX-M)),aminoglycosides(aac(3')-IIa),quinolones(qnrB,qnrS),tetracyclines(tetA,tetD),florfenicol(floR),sulfonamides(sul1,sul2),trimethoprim(dfrA14),and MDR efflux pumps(oqxA,oqxB)were detected along with diverse plasmid replicon types and integrons(intl3,55.1%;intl1,18.4%).The detection of virulence determinants was noted at a higher rate,and most of the strains were identified as biofilm producers by genotype(85.7%).The current study findings revealed diversified resistance and virulence determinants along with mobilome in ESKAPE pathogens and E.coli,which may pose a significant threat to human health through the food chain and environmental exposure and need immediate attention.展开更多
Antibiotic resistance genes(ARGs)might have great effect on ecological security and human health.Oceans are important reservoirs that receive tremendous amounts of pollutants globally.However,information on the prolif...Antibiotic resistance genes(ARGs)might have great effect on ecological security and human health.Oceans are important reservoirs that receive tremendous amounts of pollutants globally.However,information on the proliferation of ARGs in seawater is still limited.This study performed field sampling to investigate the occurrence and distribution of ARGs in seawater of the South China Sea,which is the deepest and largest sea in China.The results showed that the total absolute abundances of ARGs in seawater samples ranged from 2.1×10^(3)to 2.3×10^(4)copies/mL,with an of 5.0×10^(3)copies/mL and a range of 2.2×10^(3)–1.8×10^(4)copies/mL for those with mobile genetic elements(MGEs).Genes resistant to multidrug,aminoglycoside,tetracycline,and fluoroquinolone antibiotics accounted for 77.3%–88.6%of total ARGs in seawater.Proteobacteria and Cyanobacteria represented 32.1%–56.2%and 30.4%–49.5%of microbial community,respectively.Prochlorococcus_MIT9313 and Clade_la were the prevalent genera in seawater of the South China Sea.Complex co-occurrence relationship existed among ARGs,MGEs,and bacteria.Anthropogenic activities had critical influence on ARGs and MGEs.Hospital wastewater,wastewater treatment plant effluent,sewage,aquaculture tailwater,and runoff were determined as the important sources of ARGs in seawater of the South China Sea based on positive matrix factorization analysis.展开更多
Metals are increasingly important risk factors for the evolution of antibiotic resistance in environments.The rapid development of antibiotic resistance is occurring at a global scale.We therefore stride into the post...Metals are increasingly important risk factors for the evolution of antibiotic resistance in environments.The rapid development of antibiotic resistance is occurring at a global scale.We therefore stride into the post-antibiotic era and have to battle antibiotic resistance in the Anthropocene.Metals are widely used and their pollution is widespread worldwide.More importantly,metal-induced co-selection greatly expands the environmental resistomes and increases the health risk of antibiotic resistance in environments.Here,we reviewed the metal-induced co-selection and their increasingly important roles in the development of antibiotic resistance.In particular,we highlight the metal-rich environments that maintain reservoirs for high-risk antibiotic resistance genes with horizontally transferable potentials.We also call for considerations and further investigations of other co-selective agents and the efficacy of metal-based interventions to better manage and combat the global antibiotic resistance crisis within the One Health framework.展开更多
基金National Key Research and Development Program of China(2022YFF1000103)Postdoctoral Fellowship Program of CPSF under Grant Number GZC20240620.
文摘Background Mobile element variants(MEVs)have a significant and complex impact on genomic diversity and phe-notypic traits.However,the quantity,distribution,and relationship with gene expression and complex traits of MEVs in the pig genome remain poorly understood.Results We constructed the most comprehensive porcine MEV library based on high-depth whole genome sequencing(WGS)data from 747 pigs across 59 breeds worldwide.This database identified a total of 147,993 poly-morphic MEVs,including 121,099 short interspersed nuclear elements(SINEs),26,053 long interspersed nuclear elements(LINEs),802 long terminal repeats(LTRs),and 39 other transposons,among which 54%are newly discovered.We found that MEVs are unevenly distributed across the genome and are strongly influenced by negative selec-tion effects.Importantly,we identified 514,530,and 584 candidate MEVs associated with population differentiation,domestication,and breed formation,respectively.For example,a significantly differentiated MEV is located in the ATRX intron between Asian and European pigs,whereas ATRX is also differentially expressed between Asian and European pigs in muscle tissue.In addition,we identified 4,169 expressed MEVs(eMEVs)significantly associated with gene expression and 6,914 splicing MEVs(sMEVs)associated with gene splicing based on RNA-seq data from 266 porcine liver tissues.These eMEVs and sMEVs explain 6.24%and 9.47%,respectively,of the observed cis-heritability and high-light the important role of MEVs in the regulation of gene expression.Finally,we provide a high-quality SNP–MEV reference haplotype panel to impute MEV genotypes from genome-wide SNPs.Notably,we identified a candidate MEV significantly associated with total teat number,demonstrating the functionality of this reference panel.Conclusions The present investigation demonstrated the importance of MEVs in pigs in terms of population diversity,gene expression and phenotypic traits,which may provide useful resources and theoretical support for pig genetics and breeding.
基金supported by Tianjin Municipal Information Industry Office (No. 082044012)
文摘Exploiting mobile elements （MEs） to accomplish data collection in wireless sensor networks （WSNs） can improve the energy efficiency of sensor nodes, and prolong network lifetime. However, it will lead to large data collection latency for the network, which is unacceptable for data-critical applications. In this paper, we address this problem by minimizing the traveling length of MEs. Our methods mainly consist of two steps： we first construct a virtual grid network and select the minimal stop point set （SPS） from it; then, we make optimal scheduling for the MEs based on the SPS in order to minimize their traveling length. Different implementations of genetic algorithm （GA） are used to solve the problem. Our methods are evaluated by extensive simulations. The results show that these methods can greatly reduce the traveling length of MEs, and decrease the data collection latency.
基金supported by the National Natural Science Foundation of China(Grant Nos.62172369,62302456)the Special Support Plan for High Level Talents in Zhejiang Province(2021R52019).
文摘1 Introduction Genomic islands(GIs)promote co-evolution among different species,which are of significant importance for studying microbial functionality and evolution[1].To effectively identify genomic islands,numerous algorithms have been developed.These methods detect candidate genomic islands either by recognizing differences in sequence composition between genomic islands and their host genomes or by analyzing multiple genomes through sequence alignment[2].However,it’s important to note that genomic islands are formed through horizontal gene transfer and typically contain functional genes,such as those related to pathogenicity,metabolic regulation,and antibiotic resistance,as well as mobile elements like insertion sequences(IS),integrative and conjugative elements(ICE),mobile genetic elements(MGE),and bacteriophages(phage).In turn,utilizing these mobile elements can aid in the identification of genomic islands.
基金supported by the National Natural Science Foundation of China(32172188)Science and Technology Cooperation Project of ZheJiang Province(2023SNJF058-3)。
文摘Multidrug-resistant(MDR)Enterobacteriaceae critically threaten duck farming and public health.The phenotypes,genotypes,and associated mobile genetic elements(MGEs)of MDR Enterobacteriaceae isolated from 6 duck farms in Zhejiang Province,China,were investigated.A total of 215 isolates were identified as Escherichia coli(64.65%),Klebsiella pneumoniae(12.09%),Proteus mirabilis(10.23%),Salmonella(8.84%),and Enterobacter cloacae(4.19%).Meanwhile,all isolates were resistant to at least two antibiotics.Most isolates carried tet(A)(85.12%),blaTEM(78.60%)and sul1(67.44%)resistance genes.Gene co-occurrence analysis showed that the resistance genes were associated with IS26 and integrons.A conjugative IncFII plasmid pSDM004 containing all the above MGEs was detected in Proteus mirabilis isolate SDM004.This isolate was resistant to 18 antibiotics and carried the blaNDM-5 gene.MGEs,especially plasmids,are the primary antibiotic resistance gene transmission route in duck farms.These findings provide a theoretical basis for the rational use of antibiotics in farms which are substantial for evaluating public health and food safety.
基金granted by the Deep Earth Probe and Mineral Resource Exploration-National Science and Technology Major Project(Grant No.2024ZD1001602)a Second Tibetan Plateau Scientific Expedition and Research project(Grant No.2021QZKK0301)+1 种基金the National Natural Science Foundation of China(Grant No.42022021)the Jiangxi Provincial Youth Fund(Grant No.20224BAB213051).
文摘The Disuga Cu deposit,located in the eastern porphyry belt of the Zhongdian arc,southwest China,provides a window into magmatic-hydrothermal processes controlling porphyry Cu mineralization.Based on zircon U-Pb geochronology,hydrothermal mineral chemistry,short-wave infrared spectroscopy,and mass balance modeling,this study investigated the alteration zonation and element mobility in the Disuga Cu deposit.Zircon U-Pb ages of the ore-hosting quartz dioritic porphyries(222.4±3.1 and 219.3±2.4 Ma)are similar to those of Late Triassic subduction-related magmatism.High zircon-crystallization temperatures(727±26℃)and elevated oxygen fugacity(ΔFMQ+2.0)confirm these porphyries were favorable for mineralization.Hydrothermal sericite(Si=6.49 atoms per formula unit[apfu];Al^(Ⅵ)=3.39 apfu)and chlorite(Fe/(Fe+Mg)=0.59-0.63)compositions indicate an acidic reduced fluid.Three distinct hydrothermal stages were identified:(1)phyllic alteration(370℃);(2)propylitic alteration(315℃);and(3)low-temperature hydrothermal alteration(242℃).Mass balance calculations show that the Cu migration rate(155.6%/114.4%)in the propylitic/phyllic alteration zones was higher than that of Mo(14.3%;limited to the propylitic alteration zone).The alteration mineralization assemblages indicate the occurrence of deep potassic alteration zones and porphyry Cu-(Mo)mineralization in the Disuga area.
基金Supported by the National High-Technology Research and Development Program of China under Grant Nos 2014AA06A513 and 2013AA065502the National Natural Science Foundation of China under Grant No 61378041the Anhui Province Outstanding Youth Science Fund of China under Grant No 1508085JGD02
文摘Due to its complicated matrix effects, rapid quantitative analysis of chromium in agricultural soils is difficult without the concentration gradient samples by laser-induced breakdown spectroscopy. To improve the analysis speed and accuracy, two calibration models are built with the support vector machine method： one considering the whole spectra and the other based on the segmental spectra input. Considering the results of the multiple linear regression analysis, three segmental spectra are chosen as the input variables of the support vector regression （SVR） model. Compared with the results of the SVR model with the whole spectra input, the relative standard error of prediction is reduced from 3.18% to 2.61% and the running time is saved due to the decrease in the number of input variables, showing the robustness in rapid soil analysis without the concentration gradient samples.
基金supported by the National Key Research and Development Program of China(2022YFF0710505)the Central Public-interest Scientific Institution Basal Research Fund,China(1610302022001)。
文摘HighlightsA novel conjugative plasmid pHJ90-cfr carrying the multiresistance gene cfr was characterized in Proteus vulgaris.A new IS5-family member,ISPmi4,was identified for the first time.Both plasmids and ICEs were vital mobile genetic elements for horizontal transmission of cfr gene in Proteus species.
基金supported by the National Key R&D Program of China(No.2019YFC0408700).
文摘Antibiotic resistance genes(ARGs)are an emerging issue for drinkingwater safety.However,the seasonal variation of ARGs in drinking water distribution systems(DWDS)is still unclear.This work revealed the tempo-spatial changes of microbial community,ARGs,mobile genetic elements(MGEs)co-occurring with ARGs,ARG hosts in DWDS bulk water by means of metagenome assembly.The microbial community and antibiotic resistome varied with sampling season and site.Temperature,ammonia,chlorite and total plate count(TPC)drove the variations of microbial community structure.Moreover,environmental parameters(total organic carbon(TOC),chlorite,TPC and hardness)shifted antibiotic resistome.ARGs and MGEs co-occurring with ARGs showed higher relative abundance in summer and autumn,which might be attributed to detached pipe biofilm.In particular,ARG-bacitracin and plasmid were the predominant ARG and MGE,respectively.ARG hosts changed with season and site and were more diverse in summer and autumn.In winter and spring,Limnohabitans and Mycobacterium were the major ARG hosts as well as the dominant genera in microbial community.In addition,in summer and autumn,high relative abundance of Achromobacter and Stenotrophomonas were the hosts harboring many kinds of ARGs and MGEs at site in a residential zone(0.4 km from the water treatment plant).Compared with MGEs,microbial community had a greater contribution to the variation of antibiotic resistome.This work gives new insights into the dynamics of ARGs in full-scale DWDS and the underlying factors.
基金supported by the National Key Research and Development Plan from Ministry of Science and Technology of the People’s Republic of China(No.2020YFC1806902)the Alliance of International Science Organizations(No.ANSO-PA-2020-18).
文摘The global increased antibiotic resistance level in pathogenic microbes has posed a significant threat to human health.Fresh vegetables have been recognized to be an important vehicle of antibiotic resistance genes(ARGs)from environments to human beings.Phyllosphere ARGs have been indicated to be changed with plant species,yet the influence of plant cultivar on the phyllospheric resistome is still unclear.Here,we detected the ARGs and bacterial communities in the phyllosphere of two cultivars of cilantros and their corresponding soils using high-throughput quantitative PCR technique and bacterial 16S rRNA gene-based high-throughput sequencing,respectively.We further identified the potential bacterial pathogens and analyzed the effects of plant cultivar on ARGs,mobile genetic elements(MGEs),microbiome and potential bacterial pathogens.The results showed that the cultivars did not affect the ARG abundance and composition,but significantly shaped the abundance of MGEs and the composition structure of bacteria in the phyllosphere.The relative abundance of potential bacterial pathogenswas significantly higher in the phyllosphere than that in soils.Mantel test showed that the ARG patterns were significantly correlated to the patterns of potential bacterial pathogens.Our results suggested that the horizontal gene transfer of ARGs in the phyllosphere might be different between the two cultivars of cilantro and highlighted the higher risk of phyllospheric microorganisms compared with those in soils.These findings extend our knowledge on the vegetable microbiomes,ARGs,and potential pathogens,suggesting more agricultural and hygiene protocols are needed to control the risk of foodborne ARGs.
基金This work was financially supported by the National Natural Science Foundation of China(No.51778006)the High-performance Computing Platform of Peking University。
文摘To meet the rapidly growing global demand for aquaculture products,large amounts of antibiotics were used in aquaculture,which might accelerate the evolution of antibiotic-resistant bacteria(ARB)and the propagation of antibiotic genes(ARGs).In our research,we revealed the ARGs profiles,their co-occurrence with mobile genetic elements(MGEs),and potential hosts in sediments of a crab pond wastewater purification system based on metagenomic analysis.The residual antibiotic seems to increase the propagation of ARGs in the crab pond,but there was no clear relationship between a given antibiotic type and the corresponding resistance genes.The effect of aquaculture on sediment was not as profound as that of other anthropogentic activities,but increased the relative abundance of sulfon-amide resistance gene.A higher abundance of MGEs,especially plasmid,increased the po-tential ARGs dissemination risk in crab and purification ponds.Multidrug and sulfonamide resistance genes had greater potential to transfer because they were more frequently carried by MGEs.The horizontal gene transfer was likely to occur among a variety of microorgan-isms,and various ARGs hosts including Pseudomonas,Acinetobacter,Escherichia,and Klebsiella were identified.Bacterial community influenced the composition of ARG hosts,and Pro-teobacteria was the predominant hosts.Overall,our study provides novel insights into the environmental risk of ARGs in sediments of aquaculture wastewater treatment system.
基金This study was supported by the National Natural Science Foundation of China(No.42177348)the Natural Science Foundation of Jiangsu Province(No.BK20201367)China Postdoctoral Science Foundation(No.2021M701663).
文摘Despite coastal mudflats serving as essential ecological zones interconnecting terrestrial/freshwater and marine systems,little is known about the profiles of antibiotic resistance genes(ARGs)in this area.In this study,characteristics of typical ARGs,involving both intracellular(iARGs)and extracellular ARGs(eARGs)at different physical states,were explored in over 1000 km of coastal mudflats in Eastern China.Results indicated the presence of iARGs and eARGs at states of both freely present or attached by particles.The abundance of eARGs was significantly higher than that of iARGs(87.3%vs 12.7%),and their dominance was more significant than those in other habitats(52.7%-76.3%).ARG abundance,especially for eARGs,showed an increasing trend(p<0.05)from southern(Nantong)to northern(Lianyungang)coastalmudflats.Higher salinity facilitated the transformation from iARGs to eARGs,and smaller soil particle size was conducive to the persistence of eARGs in northern coastal mudflats.This study addresses the neglected function of coastal mudflats as eARGs reservoirs.
基金University of Malaya for the rock analysis by payment basis through RPI fund
文摘A study was conducted by collecting eight seepage water samples that drain through the sedimentary rocks, mainly sandstone and shale, to evaluate the hydro- geochemical characteristics. The collected samples were analyzed for physico-chemical parameters using standard procedures. Three water types were identified in the Piper plot and the hydrogeochemical evolution starts from a Ca- C1 facies （type 1） via mixed Ca-Mg-C1 and Ca-Na-HCO3 facies （type 2） to Na-C1 facies （type 3）. Increasing trend of electrical conductivity （EC） values were observed from type 1 water to type 3 water. Lower ionic concentrations with an average EC value of 35.7 kts/cm in Ca-C1 facies indicate the recharge water by monsoonal rainfall, and ion exchange/weathering process is reflected in the mixing zone. Higher ionic concentration with an average EC value of 399 kts/cm is noted in Na-C1 facies, which indicates the ion exchange during water-rock interaction. Higher log pCO2 values are also found in this facies, revealing the longer residence time of seepage water in the rock matrix, which release more ions into the water. The relative mobility of elements during weathering suggest that the order of mobility in both sandstone and shale is Na 〉 Ca 〉 Mg 〉 K. It was observed that thehydrogeochemistry of seepage water is mainly controlled by the bedrock geology.
基金supported by the National Natural Science Foundation of China(No.51878333)the Natural Science Foundation of Jiangsu Province(No.BK20201260).
文摘The occurrence of antibiotic resistance genes(ARGs)in various environments has drawn worldwide attention due to their potential risks.Previous studies have reported that a variety of substances can enhance the occurrence and dissemination of ARGs.However,few studies have compared the response of ARGs under the stress of different organicmatters in biologicalwastewater treatment systems.In this study,seven organic pollutantswere added into wastewater treatment bioreactors to investigate their impacts on the ARG occurrence in activated sludge.Based on high-throughput sequencing,it was found that the microbial communities and ARG patterns were significantly changed in the activated sludge exposed to these organic pollutants.Compared with the non-antibiotic refractory organic matters,antibiotics not only increased the abundance of ARGs but also significantly changed the ARG compositions.The increase of Gram-negative bacteria(e.g.,Archangium,Prosthecobacter and Dokdonella)carrying ARGs could be the main cause of ARG proliferation.In addition,significant co-occurrence relationships between ARGs and mobile genetic elements were also observed in the sludge samples,which may also affect the ARG diversity and abundance during the organic matter treatment in the bioreactors.Overall,these findings provide new information for better understanding the ARG occurrence and dissemination caused by organic pollutants in wastewater treatment systems.
基金Supported by Research in the Laboratory of Das B and NairGB is funded in part by Department of Science Technology,No.SB/FT/LS-309/2012Government of India(GOI)and the Department of Biotechnology,No.BT/MB/THSTI/HMC-SFC/2011Research in the Laboratory of Bhadra RK is partly financiallysupported by Council of Scientific and Industrial Research,GOIand Indian Council of Medical Research,GOI
文摘Vibrio cholerae(V. cholerae) genome is equipped with a number of integrative mobile genetic element(IMGE) like prophages, plasmids, transposons or genomic islands, which provides fitness factors that help the pathogen to survive in changing environmental conditions. Metagenomic analyses of clinical and environmental V. cholerae isolates revealed that dimer resolution sites(dif) harbor several structurally and functionally distinct IMGEs. All IMGEs present in the dif region exploit chromosomally encoded tyrosine recombinases, Xer C and Xer D, for integration. Integration takes place due to site-specific recombination between two specific DNA sequences; chromosomal sequence is called att B and IMGEs sequence is called att P. Different IMGEs present in the att P region have different attP structure but all of them are recognized by Xer C and Xer D enzymes and mediate either reversible or irreversible integration. Cholera toxin phage(CTXΦ), a lysogenic filamentous phage carrying the cholera toxin genes ctx AB, deserves special attention because it provides V. cholerae the crucial toxin and is always present in the dif region of all epidemic cholera isolates. Therefore, understanding the mechanisms of integration and dissemination of CTXΦ, genetic and ecological factors which support CTXΦ integration as well as production of virion from chromosomally integrated phage genome and interactions of CTXΦ with other genetic elements present in the genomes of V. cholerae is important for learning more about the biology of cholera pathogen.
基金supported by Polar Research Institute of China.The members of the 35th Antarctic expedition team were acknowledged for their support and help in sampling.
文摘Profiles and driving mechanisms of antibiotic resistome in the polar region are important for exploring the natural evolution of antibiotic resistance genes(ARGs).Here,we evaluated the profiles of antibiotic resistome in multiple media on Inexpressible Island,Terra Nova Bay,Antarctica.Average concentrations of ARGs in intracellular DNA(iARGs)among water(3.98×10^(6)copies/L),soil(3.41×10^(7)copies/kg),and penguin guano(7.04×10^(7)copies/kg)were higher than those of ARGs in extracellular DNA(eARGs)among water(1.99×10^(4)copies/L),soil(1.75×10^(6)copies/kg),and penguin guano(8.02×10^(6)copies/kg).It was indicated that the transmission of ARGs across different media occurs with around 77.8%of iARGs from soil and 86.7%of iARGs from penguins observed in water,and 80.7%of iARGs and 56.7%of eARGs from penguins found in soil.Annual inputs of ARGs from Adélie penguins on Inexpressible Island have increased since 1983.Bacitracin,multidrug,and aminoglycoside resistance genes were the main ARGs among water,soil,and penguin guano.Primary medium-risk ARGs associated with human pathogenic bacteria were multidrug resistance genes,and main low-risk ARGs associated with mobile genetic elements(MGEs)were aminoglycoside resistance genes.Antibiotic-resistant bacteria(ARB)from soil and penguins were more phylogenetically related to aquatic antibiotic-resistant mesophiles than aquatic antibiotic-resistant psychrophiles.MGEs,ARB,bacterial diversities,antibiotics,and metals could explain total ARGs between water and soil.Intracellular MGEs were the most significant in-situ driver of iARGs in water,reflecting that horizontal gene transfer could facilitate the spread of ARGs in water.Penguins were important ex-situ drivers of environmental antibiotic resistome,which was linked with risky ARGs between water and soil.These findings highlight the major roles of natural drivers(e.g.,MGEs and penguins)in shaping environmental antibiotic resistome in polar areas,improving our understanding of the evolution of environmental microbiome.
基金Supported by the National Disease Control and Prevention Administration Public Health Talent Training Program(202303)the Open Fund of the State Key Laboratory of Tea Plant Biology and Utilization(SKLTOF20200131)+1 种基金the Scientific Research Projects of Health Commission of Anhui Province in 2022(AHWJ2022a022)the Scientific Research Projects of Health Commission of Anhui Province in 2023(AHWJ2023A20398).
文摘Objective:Recent cholera outbreaks in Anhui Province have been linked to Vibrio cholerae O139,but information on these strains is limited.We established the first genomic dataset of local O139 strains to analyze the genomic characteristics and evolution of antibiotic resistance.Methods:Thirty-four Vibrio cholerae O139 isolates from Anhui(2013–2024)were sequenced using nextgeneration sequencing.Genes for virulence,antimicrobial resistance,pathogenicity islands,and mobile genetic elements were predicted using ABRicate and other online tools.To construct a phylogenetic tree,124 publicly available O139 genomes were included in the single-nucleotide polymorphism analysis alongside the study isolates.Results:Strains formed two clusters that were genetically closer to China isolates than with those from Bangladesh and India.All strains harbored ctxA and ctxB,with partial deletions in virulence genes and pathogenicity islands;over 50%lacked vgrG-2 in the T6SS.Strains from 2022–2024 exhibited higher azithromycin but lower trimethoprimsulfamethoxazole resistance than those collected during 2013–2017.Conclusion:Vibrio cholerae O139 in Anhui are endemic to China,with limited virulence but strong colonization abilities.The increased azithromycin resistance rate may be driven by its clinical antimicrobial usage,suggesting its potential for continued antibiotic resistance evolution.
基金supported by the Large Research Group Project of the Deanship of Scientific Research at King Khalid University,Abha,Saudi Arabia(Project No.R.G.P.2/297/44).
文摘The clustered regularly interspaced short palindromic repeat(CRISPR)-Caspase(Cas)system acts as a natural defense of bacteria against invasion by mobile genetic elements,such as plasmids,transposons,and bacteriophages.The review discusses the different classes and types of CRISPR-Cas systems in terms of principles of their action,limitations,and future perspectives.Also,the role of the CRISPR-Cas system as a new arsenal in fighting multidrug-resistant pathogens and clinically relevant pathogenic viruses and up-to-date clinical trials have been discussed and highlighted.Moreover,the utilization mode,regulation,and the link of CRISPR-Cas to quorum sensing for targeting cell chromosome or antimicrobial-resistant gene(s)of some clinically relevant pathogens,including Klebsiella pneumoniae,Escherichia coli,and Pseudomonas aeruginosa have been discussed.The information provided in this review can act as a platform for researchers for the future use of the CRISPR-Cas system as a smart antimicrobial agent for combating infections caused by life-threatening pathogens,particularly those with limited therapeutic options.
基金supported by the Agricultural Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences(Grant number:25-LZIHPS-03)Hainan Provincial Key Laboratory Project of Tropical Animal Breeding and Disease Research(Grant number:HKL20200302)Key Research and Development Program of Hainan Province(Grant number:ZDYF2023XDNY038).
文摘The ESKAPE pathogens and E.coli are of significant public health concern and are listed among the top priorities of the World Health Organization.These pathogens are equally important for animal and public health,but their interaction with animal,human,and environmental aspects needs to be sufficiently studied.We investigated the comprehensive molecular characterization of three ESKAPE pathogens and E.coli recovered from milk,farm workers,and environmental settings in Hainan province.Minimum inhibitory concentration(MIC),extended-spectrum b-lactamase production,and biofilm production were performed per set standard protocols.The isolates were further processed by PCR and sequencing to detect resistome,virulome,and mobilome.The study found four Enterobacteriaceae species(E.coli,n=32;K.pneumoniae,n=13;E.cloacae,n=3;E.aerogenes,n=1)among n=49 bacterial isolates from the study area.Most of the strains exhibited resistance against tetracycline(71.4%),ampicillin(61.2%),flor-fenicol(44.9%),and ciprofloxacin(42.9%),while none of the strains was resistant against meropenem and amikacin.The MDR and ESBL-production percentages were 55.1%and 34.7%,respectively.The resistance determinants for b-lactams(bla_(TEM),bla_(OXA-2),bla_(SHV),bla_(CTX-M)),aminoglycosides(aac(3')-IIa),quinolones(qnrB,qnrS),tetracyclines(tetA,tetD),florfenicol(floR),sulfonamides(sul1,sul2),trimethoprim(dfrA14),and MDR efflux pumps(oqxA,oqxB)were detected along with diverse plasmid replicon types and integrons(intl3,55.1%;intl1,18.4%).The detection of virulence determinants was noted at a higher rate,and most of the strains were identified as biofilm producers by genotype(85.7%).The current study findings revealed diversified resistance and virulence determinants along with mobilome in ESKAPE pathogens and E.coli,which may pose a significant threat to human health through the food chain and environmental exposure and need immediate attention.
基金supported by the National Natural Science Foundation of China(No.42276155)the Taishan Scholars Program,Shandong Provincial Natural Science Foundation(No.ZR2020QD131)+1 种基金the Research Program of CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation(No.1189010002)the Key R&D Program of Shandong Province,China(No.2022CXPT019).
文摘Antibiotic resistance genes(ARGs)might have great effect on ecological security and human health.Oceans are important reservoirs that receive tremendous amounts of pollutants globally.However,information on the proliferation of ARGs in seawater is still limited.This study performed field sampling to investigate the occurrence and distribution of ARGs in seawater of the South China Sea,which is the deepest and largest sea in China.The results showed that the total absolute abundances of ARGs in seawater samples ranged from 2.1×10^(3)to 2.3×10^(4)copies/mL,with an of 5.0×10^(3)copies/mL and a range of 2.2×10^(3)–1.8×10^(4)copies/mL for those with mobile genetic elements(MGEs).Genes resistant to multidrug,aminoglycoside,tetracycline,and fluoroquinolone antibiotics accounted for 77.3%–88.6%of total ARGs in seawater.Proteobacteria and Cyanobacteria represented 32.1%–56.2%and 30.4%–49.5%of microbial community,respectively.Prochlorococcus_MIT9313 and Clade_la were the prevalent genera in seawater of the South China Sea.Complex co-occurrence relationship existed among ARGs,MGEs,and bacteria.Anthropogenic activities had critical influence on ARGs and MGEs.Hospital wastewater,wastewater treatment plant effluent,sewage,aquaculture tailwater,and runoff were determined as the important sources of ARGs in seawater of the South China Sea based on positive matrix factorization analysis.
基金supported by the National Natural Science Foundation of China(Grant Nos.41825017,42377392,and 42107407)the Fundamental Research Funds for the Central Universities(Grant No.265QZ2022006).
文摘Metals are increasingly important risk factors for the evolution of antibiotic resistance in environments.The rapid development of antibiotic resistance is occurring at a global scale.We therefore stride into the post-antibiotic era and have to battle antibiotic resistance in the Anthropocene.Metals are widely used and their pollution is widespread worldwide.More importantly,metal-induced co-selection greatly expands the environmental resistomes and increases the health risk of antibiotic resistance in environments.Here,we reviewed the metal-induced co-selection and their increasingly important roles in the development of antibiotic resistance.In particular,we highlight the metal-rich environments that maintain reservoirs for high-risk antibiotic resistance genes with horizontally transferable potentials.We also call for considerations and further investigations of other co-selective agents and the efficacy of metal-based interventions to better manage and combat the global antibiotic resistance crisis within the One Health framework.
