Mobile genetic elements facilitate the transmission of antibiotic resistance genes in multidrug-resistant Enterobacteriaceae from duck farms

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.

Monitoring the Heavy Element of Cr in Agricultural Soils Using a Mobile Laser-Induced Breakdown Spectroscopy System with Support Vector Machine

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.

Evaluation of hydrogeochemical characteristics and the impact of weathering in seepage water collected within the sedimentary formation

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.

Optimizing Data Collection Path in Sensor Networks with Mobile Elements

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.

Acquisition and dissemination mechanisms of CTXΦ in Vibrio cholerae : New paradigm for dif residents

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.

Occurrence and possible sources of antibiotic resistance genes in seawater of the South China Sea

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.

Plant cultivar determined bacterial community and potential risk of antibiotic resistance gene spread in the phyllosphere

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.

Seasonal variations of microbial community and antibiotic resistome in a suburb drinking water distribution system in a northern Chinese city

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.

Impact of different organic matters on the occurrence of antibiotic resistance genes in activated sludge

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.

Response of antibiotic and heavy metal resistance genes to the co-occurrence of gadolinium and sulfamethoxazole in activated sludge systems

With the increasing use of antibiotics and rare earth elements(REE)during the coronavirus disease(COVID-19)pandemic,the co-occurrence of sulfamethoxazole(SMX)and gadolinium(Gd)has increased in wastewater treatment plants(WWTPs).However,the effects of SMX and Gd exposure on the transmission of antibiotic resistance genes(ARGs)and heavy metal resistance genes(MRGs)remain unknown.This study investigated the impacts of SMX and Gd on the fate of ARGs and MRGs in an activated sludge system.The diversity and relative abundance of ARGs,MRGs,and mobile genetic elements(MGEs)were detected by metagenomic sequencing.The results revealed an increased abundance of ARGs but a decreased abundance of MRGs under the joint effect of SMX and Gd.In addition,Gd alone exerted adverse effects on the proliferation and spread of ARGs and MRGs.However,SMX alone resulted in an increase in the diversity of ARGs and MRGs and promoted the growth of Pseudomonas,Thauera,and Streptomyces in the activated sludge system.Interestingly,a positive correlation was observed between most ARGs and MGEs.These findings provide comprehensive insights into the effects of co-occurring REEs and antibiotics on the fate of ARGs,MRGs,and MGEs,providing evidence to assist in controlling the spread and proliferation of ARGs and MRGs in activated sludge systems.

Coastal mudflats as reservoirs of extracellular antibiotic resistance genes: Studies in Eastern China

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.

Fluid/melt in continental deep subduction zones: Compositions and related geochemical fractionations

Plate subduction is the most magnificent process in the Earth. Subduction zones are important sites for proceeding matter- and energy- transports between the Earth's surface and the interior, continental crust growth, and crust-mantle interactions. Besides, a number of geological processes in subduction zones are closely related to human beings' daily life, such as volcanic eruptions and earthquakes, formation of mineral deposits. Subduction process thus has long been the centric topic of Earth sciences. The finding in 1980 s that continental crust could be subducted to mantle depths is a revolutionary progress in plate tectonic theory. Compared to oceanic crust, continental crust is colder, drier, lighter, and much more geochemically/isotopically heterogeneous. Hence, continental subduction process would affect the structure, compositions and evolutions of the overlying mantle wedge even more. During continental subduction and subsequent exhumation, fluids and melts can be generated in the(de)hydration process and partial melting process, respectively. These melts/fluids play important roles in crust-mantle interactions, elemental migrations, isotopic fractionations, and mantle metasomatism. By summarizing recent research works on subduction zones in this paper, we present a review on the types, physicochemical conditions and compositions of fluids/melts, as well as the migration behaviors of fluid-related characteristic elements(Nb-Ta-V) and the fractionation behaviors of non-traditional stable isotopes(Li-Mg) in subduction zones. The aim of this paper is to provide the readers an update comprehensive overview of the melt/fluid activities in subduction zones and of Li-Mg isotope systematics in subduction-related rocks and minerals.

Collembolans accelerate the dispersal of antibiotic resistance genes in the soil ecosystem

Soils have become an important sink for antibiotic resistance genes(ARGs).To better understand the impacts of ARGs on the soil ecosystem,the transport of ARGs is a basic question.So far,however,the role of soil animals in the dispersal of ARGs is not understood.Here,two treatments(without collembolans and with collembolans)were established,each treatment included unamended and manure-amended soil,and soil samples were collected at 14,28 and 56 days after incubation.The effects of the collembolan Folsomia candida on dispersal of ARGs in the soil ecosystem were explored using high-throughput qPCR combined with Illumina sequencing.As the culture time increased,more shared ARGs and OTUs were detected between the unamended and manured soil,especially in the treatment with collembolans.Vancomycin,aminoglycoside and MLSB genes may have been more readily transported by the collembolan.On the 28th day after incubation,a high abundance of mobile genetic elements(MGEs)was found in the treatment with collembolans.These results clearly reveal that collembolans can accelerate the dispersal of ARGs in the soil ecosystem.Procrustes analysis and the Mantel test both indicate that soil bacterial communities were significantly correlated with ARG profiles.Furthermore,partial redundancy analysis indicates that soil bacterial communities can explain 41.28% of the variation in ARGs.These results suggest that the change of soil microbial community have an important contribution to the dispersal of ARGs by the collembolan.

Genetic factors related to the widespread dissemination of ST11 extensively drug-resistant carbapenemase-producing Klebsiella pneumoniae strains within hospital

Background:Carbapenemase-producing Klebsiella pneumoniae(CP-Kp)poses distinct clinical challenges due to extensively drug resistant(XDR)phenotype,and sequence type(ST)11 is the most dominant blaKPC-2-bearing CP-Kp clone in China.The purpose of this current retrospective study was to explore the genetic factors associated with the success of XDR CP-Kp ST11 strains circulated in the intensive care unit(ICU)of a Chinese tertiary hospital.Methods:Six ST11 XDR CP-Kp strains were identified between May and December 2014 and validated by minimum inhibitory concentration examination,polymerase chain reaction,and pyrosequencing.The six ST11 XDR CP-Kp,as well as three multi-drug resistant(MDR)and four susceptible strains,were sequenced using single-molecule real-time method.Comprehensively structural and functional analysis based on comparative genomics was performed to identify genomic characteristics of the XDR ST11 CP-Kp strains.Results:We found that ST11 XDR blaKPC-2-bearing CP-Kp strains isolated from inpatients spread in the ICU of the hospital.Functionally,genes associated with information storage and processing of the ST11 XDR CP-Kp strains were more abundant than those of MDR and susceptible strains,especially genes correlative with mobile genetic elements(MGEs)such as transposons and prophages.Structurally,eleven large-scale genetic regions taken for the unique genome in these ST11 XDR CP-Kp strains were identified as MGEs including transposons,integrons,prophages,genomic islands,and integrative and conjugative elements.Three of them were located on plasmids and eight on chromosomes;five of them were with antimicrobial resistance genes and eight with adaptation associated genes.Notably,a new blaKPC-2-bearingΔΔTn1721-blaKPC-2 transposon,probably transposed and truncated fromΔTn1721-blaKPC-2 by IS903D and ISKpn8,was identified in all six ST11 XDR CP-Kp strains.Conclusion:Our findings suggested that together with clonal spread,MGEs identified uniquely in the ST11 XDR CP-Kp strains might contribute to their formidable adaptability,which facilitated their widespread dissemination in hospital.

Source apportionment of atmospheric particulate carbon in Las Vegas,Nevada,USA

A study was conducted to quantify wintertime contributions of source types to carbonaceous PM2.5 at four urban sites in the Las Vegas Valley, one of the most rapidly growing urban areas in the southwestern United States. Twenty-four hour average ambient samples were collected for mass, ions, elements, organic carbon （OC）, elemental carbon （EC）, and trace organic markers analysis. Additional measurements were made to determine diurnal patterns in light-absorbing black carbon （BC） as a marker for combustion sources. Carbonaceous PM sources of on-road gasoline vehicles, on-road diesel vehicles, and off-road diesel engines were characterized with their chemical profiles, as well as fuel-based emission factors, using an In-Plume Sampling System. The Effective Variance Chemical Mass Balance （EV-CMB） source apportionment model was applied to the ambient samples collected, using source profiles developed in this study as well as profiles from other relevant studies. Four main sources contributed to PM2.5 carbon within the Las Vegas Valley： （1） paved road dust, （2） on-road gasoline vehicles, （3） residential wood combustion, and （4） on-road diesel vehicles. CMB estimated that on-road mixed fleet gasoline vehicles are the largest source for OC and EC at all the sites. The contribution of paved road dust to both OC and EC was 5-10% at the four sites. On-road diesel vehicles contribute 22% of the OC and 34% of the EC at a site near the city center, which is located immediately downwind of a major freeway. Residential wood combustion is a more important source than on-road diesel vehicles for two residential neighborhood sites, These results are consistent with our conceptual model, and the research methodology may be applied to studying other urban areas.

Metagenomic insights into the profile of antibiotic resistomes in sediments of aquaculture wastewater treatment system

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.