Human migration activities drive the fluctuation of ARGs: Case study of landfills in Nanjing, eastern China

Winged resistance: Storks and gulls increase carriage of antibiotic resistance by shifting from paddy fields to landfills

Waterbirds are vectors for the dissemination of antimicrobial resistance across environments, with some species increasingly reliant on highly anthropized habitats for feeding. However, data on the impact of their feeding habits on the carriage of antibiotic resistance genes (ARGs) are still scarce. To fill this gap, we examined the microbiota (16S rRNA amplicon gene sequencing) and the prevalence of ARG (high-throughput qPCR of 47 genes) in faeces from white storks (Ciconia ciconia) and lesser black-backed gulls (Larus fuscus) feeding in highly (landfill) and less (paddy fields) polluted habitats. Faecal bacterial richness and diversity were higher in gulls feeding upon landfills and showed a greater abundance of potential pathogens, such as Staphylococcus. In contrast, faecal bacterial communities from storks were similar regardless of habitat preferences, maybe due to a less intense habitat use compared to gulls. In addition, birds feeding in the landfill carried a higher burden of ARGs compared to the surrounding soil and surface waters. Network analysis revealed strong correlations between ARGs and potential pathogens, particularly between tetM (resistance to tetracyclines), blaCMY (beta-lactam resistance), sul1 (sulfonamide resistance) and members of the genera Streptococcus, Peptostreptococcus, and Peptoclostridium. Our work demonstrates how transitioning from paddy fields to landfills fosters the carriage of ARGs and potential pathogens in the bird gut, shedding light on the ecological role of these avian vectors in antimicrobial resistance dissemination.

Antibiotic resistance genes and heavy metals in landfill: A review

Landfill is reservoir containing antibiotic resistance genes (ARGs) that pose a threat to human life and health. Heavy metals impose lasting effects on ARGs. This review investigated and analyzed the distribution, composition, and abundance of heavy metals and ARGs in landfill. The abundance ranges of ARGs detected in refuse and leachate were similar. The composition of ARG varied with sampling depth in refuse. ARG in leachate varies with the distribution of ARG in the refuse. The ARG of sulI was associated with 11 metals (Co, Pb, Mn, Zn, Cu, Cr, Ni, Sb, As, Cd, and Al). The effects of the total metal concentration on ARG abundance were masked by many factors. Low heavy metal concentrations showed positive effects on ARG diffusion; conversely, high heavy metal concentrations showed negative effects. Organic matter had a selective pressure effect on microorganisms and could provide energy for the diffusion of ARGs. Complexes of heavy metals and organic matter were common in landfill. Therefore, the hypothesis was proposed that organic matter and heavy metals have combined effects on the horizontal gene transfer (HGT) of ARGs during landfill stabilization. This work provides a new basis to better understand the HGT of ARGs in landfill.

Microbial organic fertilizer prepared by co-composting of Trichoderma dregs mitigates dissemination of resistance, virulence genes, and bacterial pathogens in soil and rhizosphere

The use of manure, mycelium dregs and other waste as organic fertilizer is the main source of antibiotic resistance genes (ARGs) and pathogens in farmland. Composting of waste may effectively remove ARGs and pathogens. However, the profiles and drivers of changes in metal resistance genes (MRGs), biocide resistance genes (BRGs), and virulence genes (VGs) in soil-crop rhizosphere systems after compost application remain largely unknown. Here, we prepared two kinds of microbial organic fertilizers (MOF) by using Trichoderma dregs (TDs) and organic fertilizer mixing method (MOF1) and TDs co-composting method (MOF2). The effects of different types and doses of MOF on resistance genes, VGs and pathogens in soil-rhizosphere system and their potential mechanisms were studied. The results showed that co-composting of TDs promoted the decomposition of organic carbon and decreased the absolute abundance of ARGs and mobile genetic elements (MGEs) by 53.4-65.0%. MOF1 application significantly increased the abundance and diversity of soil ARGs, BRGs, and VGs, while low and medium doses of MOF2 significantly decreased their abundance and diversity in soil and rhizosphere. Patterns of positive co-occurrence between MGEs and VGs/MRGs/BRGs/ARGs were observed through statistical analysis and gene arrangements. ARGs/MRGs reductions in MOF2 soil were directly driven by weakened horizontal gene transfer triggered by MGEs. Furthermore, MOF2 reduced soil BRGs/VGs levels by shifting bacterial communities (e.g., reduced bacterial host) or improving soil property. Our study provided new insights into the rational use of waste to minimize the spread of resistomes and VGs in soil.

Microbial contamination risk of landfilled waste with different ages

Landfills are reservoirs of antibiotic resistance genes (ARGs) and pathogens, and humans are exposed to these pollutants during extensive excavation of old landfills. However, the microbial contamination risk of landfilled waste with different ages has not been assessed. In this study, human bacterial pathogens (HBPs), ARGs, and virulence factors (VFs) were systematically determined using metagenomic analysis. Results showed that the abundance of HBPs, ARGs, and VFs increased with landfill age, the percentage of HBPs in refuse with deposit age of 10-12 years (Y10) was 23.75 ± 0.49%, which was higher than that in fresh refuse (Y0, 17.99 ± 0.14%) and refuse with deposit age of 5-6 years (Y5, 19.14 ± 0.15%), indicating that old refuse had higher microbial contamination risk than fresh refuse. Multidrug, macrolide, lincosamide, streptogramine, and tetracycline resistance genes were the primary ARGs, whereas lipooligosaccharides, type IV pili, and polar flagella were the dominant VFs in refuse. The HBPs showed a significant positive correlation with ARGs and VFs. Listeria monocytogenes, Salmonella enterica, Streptococcus pneumoniae, Acinetobacter baumannii, and Escherichia coli possibly possess both multiple ARGs and VFs and could be listed as high-risk HBPs in refuse. Mobile genetic elements, especially transposons, showed positive correlations with most ARGs and VFs, and they were identified as the primary factors accounting for the variations in ARGs and VFs. These findings will help understand the spread of ARGs and VFs in landfills and evaluate the potential risk of microbiological contamination in refuse of different landfill ages, thus providing guidance for preventing disease infection during landfill excavations.

The Source and Distribution of Tetracycline Antibiotics in China: A Review

In recent years, antibiotics have been listed as a new class of environmental pollutants. Tetracycline antibiotics (TCs) used in human medical treatment, animal husbandry and agricultural production are the most widely used antibiotics. Due to their wide range of activities and low cost, their annual consumption is increasing. TCs cannot be completely metabolized by humans and animals. They can be abused or overused, causing the continuous accumulation of TCs in the ecological environment and potential negative effects on non-target organisms. These TCs may spread into the food chain and pose a serious threat to human health and the ecology. Based on the Chinese environment, the residues of TCs in feces, sewage, sludge, soil and water were comprehensively summarized, as well as the potential transmission capacity of air. This paper collected the concentrations of TCs in different media in the Chinese environment, contributing to the collection of a TC pollutant database in China, and facilitating the monitoring and treatment of pollutants in the future.

Vertical distribution of antibiotics and antibiotic resistance genes in a representative municipal solid waste landfill, China

The vertical distribution of sulfonamides (SAs), tetracyclines (TCs), macrolides (MLs), and their related antibiotic resistance genes (ARGs) were comprehensively investigated and characterized in a representative municipal solid waste (MSW) landfill in China. The total concentrations of target antibiotics in the MSW landfill were SAs > TCs > MLs. The abundances of mexF (10.78 ± 0.65 log₁₀copies/g) and sul genes (9.15 ± 0.54 log₁₀copies/g) were relatively high, while the tet genes (7.19 ± 0.77 log₁₀copies/g) were the lowest. Both the abundance of antibiotics and genes fluctuated with landfill depth, and the ARGs of the same antibiotics were consistent with depth change. Intl1 and sul genes (sul1, sul2) were tightly connected, and a close relationship also existed between tet genes (tetM, tetQ) and MLs resistance genes (ermB, mefA). High-throughput sequencing showed the dominant genera were Sporosarcina (38%) and Thiobacillus (17%) at sampling points A and C, while the microbial community varied with depth increase at point B were Brevundimonas (20%), Sporosarcina (20%), Pseudomonas (24%), Lysobacter (28%), and Thioalkalimicrobium (14%), respectively. Network analysis further visualized the relationship among antibiotics, genes, and microbial communities and the results indicated the non-random connection among them and the possible host of the target gene. Even at 12.0 m below the landfill surface, the pollution of antibiotics resistance was still serious, which posed difficulties for subsequent landfill remediation and pollution control.

Antibiotics and antibiotic resistance genes in landfills: A review

Landfill are important reservoirs of antibiotics and antibiotic resistance genes (ARGs). They harbor diverse contaminants, such as heavy metals and persistent organic chemicals, complex microbial consortia, and anaerobic degradation processes, which facilitate the occurrence, development, and transfer of ARGs and antibiotic resistant bacteria (ARB). The main concern is that antibiotics and developed ARGs and ARB may transfer to the local environment via leachate and landfill leakage. In this paper, we provide an overview of established studies on antibiotics and ARGs in landfills, summarize the origins and distribution of antibiotics and ARGs, discuss the linkages among various antibiotics, ARGs, and bacterial communities as well as the influencing factors of ARGs, and evaluate the current treatment processes of antibiotics and ARGs. Finally, future research is proposed to fill the current knowledge gaps, which include mechanisms for the development and transmission of antibiotic resistance, as well as efficient treatment approaches for antibiotic resistance.

Relationship between water quality, heavy metals and antibiotic resistance genes among three freshwater lakes

Urban recreational lakes are impacted by consistent anthropogenic activities and are significant sources of heavy metals and antibiotic resistance genes (ARGs). In this study, three urban lakes of varying size and anthropogenic impact in Nanjing, China, were investigated for the abundance of ten ARGs, six physicochemical factors and four heavy metals. Correlations between heavy metals and physicochemical parameters against ARGs were performed to investigate the presence of ARGs in the lakes. The water quality data indicated that the lakes were on par with levels 3 and 4 of the Chinese surface water environmental standards, signifying disturbing pollution levels in the lakes. The lakes were dominant with high amounts of sul1, sul2 and strA genes, and the sum of these three genes appropriated over 38.9-84.4% in all three lakes, while the sum of tetM, tetQ and ermB genes occupied a minor proportion (0.1-1.4%). High levels of vancomycin resistance genes were found in the three lakes. Spearman analysis indicated that Chlα, cadmium, lead and copper had a significant positive correlation with sul2 and strB. The results of redundancy analysis displayed that Chlα and co-selection with certain heavy metals were the major factors driving the propagation of specific genes in three lakes. We believe our study contributes by adding further knowledge to existing antibiotic resistance gene abundance studies in recreational urban lakes with significant anthropogenic impacts.

Effects of coexistence of tetracycline, copper and microplastics on the fate of antibiotic resistance genes in manured soil

The coexistence of antibiotics, heavy metals and microplastics is becoming commonplace and may affect antibiotic resistance in manured soil. The current understanding of the role of microplastics in soil with combined pollution of antibiotics, heavy metals and antibiotic resistance genes (ARGs) is limited. Here, the effects of the coexistence of tetracycline (TC), Cu and environmental microplastics (EM) on the fate of nine ARGs and three heavy metal resistance genes in agricultural soil were investigated by batch and microcosm experiments. EM were obtained by exposing virgin microplastics to soil environments for 80 days, which exhibited higher adsorption affinity for Cu and TC than soil particles and virgin microplastics. 1% EM in soil increased bioavailable concentrations of TC and Cu by 79-138% and 88-135%, respectively, and decreased TC dissipation from 11.79 mg kg^-1 to 3.08 mg kg^-1. Correspondingly, the total relative abundances of target ARGs increased by 219-348%. The significant correlations of tetG, tetB, tetQ, sul2, sul1 and intl1 with bioavailable fractions of TC and Cu in soil environments were revealed by network analysis. Moreover, scanning electron micrographs showed the special plastisphere around EM. Attributed to the biofilm generation and higher pollutant accumulation in the plastisphere, EM could be the source of antibiotic-resistant bacteria and ARGs in soil environments. Structure equation models further identified that indirect effects of EM acted a major role in the propagation of ARGs by altering soil properties, soil microbial diversity and intl1 abundance. This study revealed that EM could increase the stimulative effects of Cu and TC on antibiotic resistance and magnify the environmental risk of manure application in soil environments.

Contributions of meat waste decomposition to the abundance and diversity of pathogens and antibiotic-resistance genes in the atmosphere

Airborne transmission of antibiotic-resistance genes (ARGs) in landfill and acquisition of antibiotic resistance by pathogenic bacteria are posing potential threat to human and environmental health. However, little is known about contribution of waste decomposition to airborne ARGs and pathogens during landfilling of household waste. Herein, the dynamic changes of microbial communities and ARGs were comparatively investigated in leachate and bioaerosol during the decomposition of chicken, fish, and pork wastes. Results found that chicken and pork decomposition could result in emitting high abundance of bioaerosol and pathogen, while fish fermentation will lead to high airborne microbial activity. The main pathogens were Bacilli, Burkholderia-Paraburkholderia and Mycobacterium in bioaerosols, but were Wohlfahrtiimonas, Peptoniphilus and Fusobacterium in leachate, suggesting that the ability of aerosolization of bacteria in leachate was independent of their abundance and diversity. Whereas, diversity and relative abundance of ARGs in leachate were significantly higher than bioaerosol. Moreover, the relative abundance of ARGs in leachate and bioaerosols was not completely relevant. The changes of pathogenic community contributed significantly to the prevalence of ARGs in bioaerosol and leachate. The results will define the contribution of household waste decomposition to airborne pathogen and ARG distribution and provide foundation for airborne bacterial exposure risk and control in landfill.

Antibiotic resistance genes are enriched with prolonged age of refuse in small and medium-sized landfill systems

Landfills are sites for the disposal of waste over decades. The dynamics of contaminants during landfill treatment influence the functions and environmental risks of the landfill systems, but the patterns of these dynamics are not fully characterized, especially for antibiotic resistant genes (ARGs), an emerging contaminant of global concern. Here, seventeen typical ARG subtypes were quantitatively investigated in refuse samples from small and medium-sized landfills with ages of <3 years, ~5 years, and 8-10 years. The abundance of ARGs, including tetM, tetX, blaPER, emrB, sul1 and sul2, increased significantly (p < 0.05), approaching 8- to 304-fold on average, from refuse of < 3years to that of 8-10 years, while there was no obvious change (p > 0.05) in abundance for other ARGs, including tetQ, tetW, ampC, blaCTX-M, blaSHV, emrA, mefA, qnrD, qnrS, and mexF. Accordingly, resistance to tetracyclines, macrolides, and sulfonamides increased with landfill age, while resistance to β-lactams and quinolones remained unchanged. The increase in ARG abundance with increasing refuse age was probably related with the increased horizontal gene transfer (HGT) (indicated by the increased abundance of mobile gene elements) and the enhanced co-selective pressure (suggested by the increased contents of heavy metals). These results indicated a potential risk from ARG enrichment with an increase in refuse age in small and medium-sized landfills, which should be managed to ensure landfill safety.

Rainfall Influences Occurrence of Pharmaceutical and Personal Care Products in Landfill Leachates: Evidence from Seasonal Variations and Extreme Rainfall Episodes

Unused or expired pharmaceutical and personal care products (PPCPs) are usually discharged into municipal solid wastes, then travel to landfills, and eventually percolate into leachates. However, knowledge of their occurrence and temporal dynamics in leachates is limited, making landfill leachate an underappreciated emission source of PPCPs. Furthermore, the differences in PPCP variations in landfill leachates emphasize the necessity for identifying the influencing factors and elucidating the mechanisms for PPCP fluctuations. In this study, successive monthly monitoring of PPCPs in leachates throughout an entire year was performed to determine their seasonal variations and identify their influencing factors. Furthermore, five pairs of additional sampling campaigns were conducted before and after rainfall events during wet seasons to elucidate the influencing mechanisms. The results showed that there was a distinct seasonal variation in PPCPs in landfill leachates-elevated levels during the wet period (from April to September, with a mean concentration of 17.0 μg/L for total monitored PPCPs)-when compared to other months (mean concentration of 3.8 μg/L). Rainfall played a considerable role in mediating PPCP concentrations in leachates. The PPCP responses to five rainfall episodes further verified the influence of rainfall and demonstrated that the tendency to PPCP concentration increase was related to rainfall precipitation. Torrential rain events (i.e., 24 h cumulative precipitation of 50-99.9 mm) led to the most significant increases in PPCP concentrations in landfill leachates. In addition, the hydrophilicity of PPCPs contributed to the different fluctuations during the 1 year investigation and different responses to rainfall. To the best of our knowledge, this study provides the first direct evidence supporting the influence of rainfall on PPCPs in landfill leachates, which can help better understand the occurrence and behavior of emerging contaminants in this underappreciated emission source.

The changes in antibiotic resistance genes during 86 years of the soil ripening process without anthropogenic activities

This study aimed to reveal the baseline of natural variations in antibiotic resistance genes (ARGs) in soil without anthropogenic activities over the decades. Nine soil samples with different time of soil formation were taken from the Yancheng Wetland National Nature Reserve, China. ARGs and mobile genetic elements (MGEs) were characterized using metagenomic analysis. A total of 196 and 192 subtypes of ARGs were detected in bulk soil and rhizosphere, respectively. The diversity and abundance of ARGs were stable during 69 years probably due to the alkaline pH soil environment but not due to antibiotics. Increases in ARGs after 86 years were probably attributed to more migrant birds inhabited compared with other sampling sites. Multidrug was the most abundant type, and largely shared by soil samples. It was further shown that soil samples could not be clearly distinguished, suggesting a slow process of succession of ARGs in the mudflat. The variation partitioning analysis revealed that the ARG profile was driven by the comprehensive effects exhibited by the bacterial community, MGEs, and environmental factors. Besides, pathogenic bacteria containing ARGs mediated by migrant birds in the area with 86 years of soil formation history nearing human settlements needed special attention. This study revealed the slow variations in ARGs in the soil ripening process without anthropogenic activities over decades, and it provided information for assessing the effect of human activities on the occurrence and dissemination of ARGs.

Polycyclic aromatic hydrocarbons, antibiotic resistance genes, toxicity in the exposed to anthropogenic pressure soils of the Southern Russia

The influence of anthropogenic pollution, particularly with polycyclic aromatic hydrocarbons (PAHs) on soil toxicity and spread of antibiotic resistance genes (ARGs) is extremely important nowadays. We studied 20 soil samples from a technogenically polluted site, municipal solid wastes (MSW) landfills, and rural settlements in the southwestern part of the Rostov Region of Russia. A close correlation was established between the results of biosensor testing for integral toxicity, the content of genes for the biodegradation of hydrocarbons, and the concentration of PAHs in soils. The relation between the quantitative content of ARGs and the qualitative and quantitative composition of PAHs has not been registered. Soils subjected to different types of the anthropogenic pressure differed in PAHs composition. The technogenic soils are the most polluted ones. These soils are enriched with 5 ring PAHs and carry the maximum variety of assayed ARGs, despite the fact that they do not receive household or medical waste.

Associations between human bacterial pathogens and ARGs are magnified in leachates as landfill ages

Landfills constitute the largest treatment and disposal reservoirs of anthropogenic waste on earth and they are continuously releasing antibiotic resistance genes (ARGs) to the environment for decades via leachates. Little is known about the association between ARGs and human bacterial pathogens as a function of time. Here, we quantified 10 subtypes of ARGs, integrons, and human bacterial pathogens (HBPs). Except for the ARGs encoding resistance to sulfonamides, the subtypes encoding resistance to beta-lactams, macrolides, and aminoglycosides were not related to integrons (Spearman, P > 0.05). Over time presence of ARGs became increasingly more correlated with the presence of human bacterial pathogens (Procrustes test; R = 0.81, P < 0.05), which were primarily identified as the Proteobacteria, Actinobacteria, and Firmicutes. Rather than the prevalence of integrons, dynamics of the bacterial community, including the increased nitrogen metabolism activity of Proteobacteria and decreased bacterial diversity were assumed to lead to a magnified association between HBPs and target ARGs (Varpart; > 13%).

Screening of Bacterial Endophytes Able to Promote Plant Growth and Increase Salinity Tolerance

Bacterial endophytes can colonize plant tissues without harming the plant. Instead, they are often able to increase plant growth and tolerance to environmental stresses. In this work, new strains of bacterial endophytes were isolated from three economically important crop plants (sorghum, cucumber and tomato) grown in three different regions in soils with different management. All bacterial strains were identified by 16S rRNA sequencing and characterized for plant beneficial traits. Based on physiological activities, we selected eight strains that were further tested for their antibiotic resistance profile and for the ability to efficiently colonize the interior of sorghum plants. According to the results of the re-inoculation test, five strains were used to inoculate sorghum seeds. Then, plant growth promotion activity was assessed on sorghum plants exposed to salinity stress. Only two bacterial endophytes increased plant biomass, but three of them delayed or reduced plant salinity stress symptoms. These five strains were then characterized for the ability to produce the enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase, which is involved in the increase of stress tolerance. Pseudomonas brassicacearum SVB6R1 was the only strain that was able to produce this enzyme, suggesting that ACC deaminase is not the only physiological trait involved in conferring plant tolerance to salt stress in these bacterial strains.

Prevalence of fluoroquinolone, macrolide and sulfonamide-related resistance genes in landfills from East China, mainly driven by MGEs

Landfills are one of the most important reservoirs of antibiotic resistance genes (ARGs), and ARG pollution in landfills has been well investigated. However, the various factors contributing to the widespread prevalence of ARGs in landfills have rarely been explored. Here, we quantified three classes of antibiotics, six kinds of heavy metals, eight types of ARGs, and five varieties of mobile genetic elements (MGEs) in refuse samples from 10 landfills in Zhejiang Province, China. Compared with sulfonamides and macrolides, fluoroquinolones were present at much higher concentrations in all refuse samples, reaching a concentration of 1406.85 μg/kg in the Jiaxing region. The relative abundances of qnrD, qnrS, mexF, ermA, ermB, mefA, sul1, and sul2 in most landfills were >10^-4 copies per 16S rRNA, suggesting the presence of highly contaminated ARGs. No significant correlations between most target antibiotics and their corresponding ARGs were found. Variation partitioning analysis indicated that MGEs could be the determining factor in the spread of ARGs in landfills. This research not only reveals high levels of ARGs and the ubiquitous presence of antibiotics in refuse, but also provides guidance for controlling the spread of ARGs in landfills.

Pharmaceutical exposure changed antibiotic resistance genes and bacterial communities in soil-surface- and overhead-irrigated greenhouse lettuce

New classes of emerging contaminants such as pharmaceuticals, antibiotic resistant bacteria (ARB), and antibiotic resistance genes (ARGs) have received increasing attention due to rapid increases of their abundance in agroecosystems. As food consumption is a direct exposure pathway of pharmaceuticals, ARB, and ARGs to humans, it is important to understand changes of bacterial communities and ARG profiles in food crops produced with contaminated soils and waters. This study examined the level and type of ARGs and bacterial community composition in soil, and lettuce shoots and roots under soil-surface or overhead irrigation with pharmaceuticals-contaminated water, using high throughput qPCR and 16S rRNA amplicon sequencing techniques, respectively. In total 52 ARG subtypes were detected in the soil, lettuce shoot and root samples, with mobile genetic elements (MGEs), and macrolide-lincosamide-streptogramin B (MLSB) and multidrug resistance (MDR) genes as dominant types. The overall abundance and diversity of ARGs and bacteria associated with lettuce shoots under soil-surface irrigation were lower than those under overhead irrigation, indicating soil-surface irrigation may have lower risks of producing food crops with high abundance of ARGs. ARG profiles and bacterial communities were sensitive to pharmaceutical exposure, but no consistent patterns of changes were observed. MGE intl1 was consistently more abundant with pharmaceutical exposure than in the absence of pharmaceuticals. Pharmaceutical exposure enriched Proteobacteria (specifically Methylophilaceae) and decreased bacterial alpha diversity. Finally, there were significant interplays among bacteria community, antibiotic concentrations, and ARG abundance possibly involving hotspots including Sphingomonadaceae, Pirellulaceae, and Chitinophagaceae, MGEs (intl1 and tnpA_1) and MDR genes (mexF and oprJ).

Validated predictive modelling of sulfonamide and beta-lactam resistance genes in landfill leachates

The spread of antimicrobial resistance via landfill leachates jeopardizes millions of people's health, which can be exacerbated due to the unclear quantitative relationships between leachate characteristics and occurrences of antibiotic resistance genes (ARGs). Here, in parallel with sampling raw leachates from a real landfill, we constructed a lab-scale landfill and collected its leachates for 260 days. All leachate samples were analyzed for the abundance of integrons, sulfonamide resistance (sulR; sul1 and sul2) and beta-lactams resistance (blaR; bla_OXA, bla_CTX-M, and bla_TEM) genes. The enrichment of sulR subtypes was closely associated with the integrons' prevalence during the landfilling process (0.65-0.75 log₁₀(copies/mL)), which can be explained by the multiple linear regression that contained intl1, pH, and nitrogen compounds as variables. The predicted abundance of sulR genes (6.06 ± 0.6 log₁₀(copies/mL)) was statistically the same as the observed value in raw leachates (P = 0.73). The abundance of blaR genes decreased from 5.0 to 2.5 log₁₀(copies/mL) during the experiment (P < 0.001); and a locally weighted regression of blaR genes with integrons, COD and total nitrogen accurately predicted blaR genes abundance in raw leachate (Bootstrap = 10,000, P = 0.67). The partial least squares path modelling (PLS-PM) showed that variations of blaR genes in the lab and raw leachates shared an identical pattern (PLS-PM, Bootstrap = 10,000, P > 0.05), which was influenced by integrons and environmental factors with the coefficients of -0.11 and 0.39, respectively. We believe the validated models are highly useful tools to streamline the strategies for monitoring and prediction of ARGs.

Differential Drivers of Antimicrobial Resistance across the World

Antimicrobial resistance (AMR) is one of the greatest threats faced by humankind. The development of resistance in clinical and hospital settings has been well documented ever since the initial discovery of penicillin and the subsequent introduction of sulfonamides as clinical antibiotics. In contrast, the environmental (i.e., community-acquired) dimensions of resistance dissemination have been only more recently delineated. The global spread of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) between air, water, soil, and food is now well documented, while the factors that affect ARB and ARG dissemination (e.g., water and air quality, antibiotic fluxes, urbanization, sanitation practices) in these and other environmental matrices are just now beginning to be more fully appreciated. In this Account, we discuss how the global perpetuation of resistance is dictated by highly interconnected socioeconomic risk factors and illustrate that development status should be more fully considered when developing global strategies to address AMR. We first differentiate low to middle income countries (LMICs) and high-income countries (HICs), then we summarize the modes of action of commercially available antibiotics, and then discuss the four primary mechanisms by which bacteria develop resistance to those antibiotics. Resistance is disseminated via both vertical gene transfer (VGT; parent to offspring) as well as by horizontal gene transfer (HGT; cell to cell transference of genetic material). A key challenge hindering attempts to control resistance dissemination is the presence of native, environmental bacteria that can harbor ARGs. Such environmental "resistomes" have potential to transfer resistance to pathogens via HGT. Of particular concern is the development of resistance to antibiotics of last-resort such as the cephalosporins, carbapenems, and polymyxins. We then illustrate how antibiotic use differs in LMICs relative to HICs in terms of the volumes of antibiotics used and their fate within local environments. Antibiotic use in HICs has remained flat over the past 15 years, while in LMICs use over the same period has increased substantially as a result of economic improvements and changes in diet. These use and fate differences impact local citizens and thus the local dissemination of AMR. Various physical, social, and economic circumstances within LMICs potentially favor AMR dissemination. We focus on three physical factors: changing population density, sanitation infrastructure, and solid-waste disposal. We show that high population densities in cities within LMICs that suffer from poor sanitation and solid-waste disposal can potentially impact the dissemination of resistance. In the final section, we discuss potential monitoring approaches to quantify the spread of resistance both within LMICs as well as in HICs. We posit that culture-based approaches, molecular approaches, and cutting-edge nanotechnology-based methods for monitoring ARB and ARGs should be considered both within HICs and, as appropriate, within LMICs.

Comparing polyvalent bacteriophage and bacteriophage cocktails for controlling antibiotic-resistant bacteria in soil-plant system

Antibiotic resistant pathogenic bacteria (ARPB) residual in soil-plant system has caused serious threat against public health and environmental safety. Being capable of targeted lysing host bacteria, phage therapy has been proposed as promising method to control the ARPB contamination in environments. In this study, microcosm trials were performed to investigate the impact of various phage treatments on the dissipation of tetracycline resistant Escherichia coli K-12 and chloramphenicol resistant Pseudomonas aeruginosa PAO1 in soil-carrot system. After 70 days of incubation, all the four phage treatments significantly decreased the abundance of the pathogenic bacteria and the corresponding antibiotic resistance genes (tetW and cmlA) in the soil-carrot system (p < 0.05), following the order of the cocktail phage treatment (phages ΦYSZ1 + ΦYSZ2) > the polyvalent phage (ΦYSZ3 phage with broad host range) treatment > host-specific phage (ΦYSZ2 and ΦYSZ1) treatments > the control. In addition, the polyvalent phage treatment also exerted positive impact on the diversity and stability of the bacterial community in the system, suggesting that this is an environmentally friendly technique with broad applications in the biocontrol of ARPB/ARGs in soil-plant system.

Effect of long-term manure slurry application on the occurrence of antibiotic resistance genes in arable purple soil (entisol)

The application of animal manure is a highly recommended traditional agricultural practice for soils of relatively low fertility. However, for the farmland purple soils that are widely distributed in the upper Yangtze River region, little knowledge has been established in previous studies about the changes in the antibiotic resistome upon manure amendment. In the present study, the impact of long-term pig manure slurry application on the occurrence of antibiotic resistance genes (ARGs) and bacterial community was assessed in arable calcareous purple soil using high-throughput quantitative polymerase chain reaction and Illumina sequencing. Four treatments, including a non-fertilization control (CK) and pig manure (OM), OM plus mineral N fertilizer (OMN) and OM plus mineral NPK fertilizer (OMNPK) treatments were investigated. Across all the soil samples receiving different treatments, a total of 139 unique ARGs and 6 mobile genetic element genes were detected, with multidrug and beta-lactam the two most dominant types of ARGs. The results of the principal coordinate analysis (PCoA) suggest that the profiles of soil ARGs in the two treatments of OM combined with mineral fertilizer(s) (i.e., OMN and OMNPK) were similar to those in the control treatment, while the soil receiving only pig manure application had a different pattern of ARGs from the soils in the other three treatments. A clear reduction of soil ARGs was observed in the OM treatment. Significant and positive relationships were found not only among ARGs but also between mobile genetic elements (MGEs) and ARGs. However, no significant relationships were detected between ARG patterns and bacterial community composition. These results imply that the long-term application of pig manure slurry to purple soil does not lead to the prevalence of ARGs; however, the potential for the horizontal transfer of ARGs in calcareous purple soil should not be ignored.

'Agricultural Waste to Treasure' - Biochar and eggshell to impede soil antibiotics/antibiotic resistant bacteria (genes) from accumulating in Solanum tuberosum L

Soil contamination with antibiotics and antibiotic resistant bacteria/genes (ARB/ARGs) has becoming an emerging environmental problem. Moreover, the mixed pollutants' transfer and accumulation from soil to tuberous vegetables has posed a great threat against food security and human health. In this work, the application of two absorbing materials (maize biochar and sulfate modified eggshell) was able to reduce the poisonous effect of soil antibiotics on potato root system by stimulate the dissipation of water-soluble antibiotics in soil; and also improve food quality by increasing potato starch, protein, fat, and vitamins. Meanwhile, both amendments could effectively decrease the classes and the accumulative abundance of ARB and ARGs (sulI, sulII, catI, catII, ermA, ermB) in the edible parts of potato. The lowest abundance of ARGs was detected in the biochar application treatment, with the accumulative ARG level of 8.9 × 10² and 7.2 × 10² copies mL^-1 in potato peel (sull + catI + ermA) and tuberous root (sulI), respectively. It is the first study to demonstrate the feasibility of biochar and eggshell derived from agricultural wastes as green absorbing materials to reduce soil antibiotic, ARB, and ARGs accumulation risk in tuberous vegetable.

Simulated discharge of treated landfill leachates reveals a fueled development of antibiotic resistance in receiving tidal river

Around 350 million tons of solid waste is disposed of in landfills every year globally, with millions of cubic meters of landfill leachates released into neighboring environment. However, to date, little is known about the variations of antimicrobial resistance (AMR) in on-site leachate treatment systems and its development in leachate-receiving water environment. Here, we quantified 7 subtypes of antibiotic resistance genes (ARGs), 3 types of culturable antibiotic resistant bacteria (ARB) and 6 subtypes of mobile genetic elements (MGEs) in the effluents from a combined leachate treatment process, including biological treatment (MBR), physical separation (UF), ultraviolet (UV) disinfection and advanced oxidation process (AOP). The contents of ARGs, ARB and MGEs were generally enriched by the MBR, but then decreased significantly along with the tertiary treatment process. However, in the effluent-receiving water samples, the abundance of dominant ARGs (i.e. ermB, sul1, bla_TEM) increased by 1.5 orders of magnitude within 96 h, alongside a general increase of MGEs (~10.0 log₁₀(copies/mL) and total ARB (~1100 CFU/mL). Structural correlation analyses reveal that target ARGs were closely associated with MGEs, particularly in effluent-receiving samples (Procrustes test; M² = 0.49, R = 0.71, P = 0.001); and occurrences of ARB were majorly affected by ARG's distribution and environmental conditions (e.g. nitrogen speciation) in effluent and recipient groups, respectively. This study indicates that current treatment technologies and operation protocols are not feasible in countering the development of AMR in effluent-receiving water environment, particularly in tidal rivers that are capable of retaining contaminants for a long residence time.

Human dissemination of genes and microorganisms in Earth's Critical Zone

Earth's Critical Zone sustains terrestrial life and consists of the thin planetary surface layer between unaltered rock and the atmospheric boundary. Within this zone, flows of energy and materials are mediated by physical processes and by the actions of diverse organisms. Human activities significantly influence these physical and biological processes, affecting the atmosphere, shallow lithosphere, hydrosphere, and biosphere. The role of organisms includes an additional class of biogeochemical cycling, this being the flow and transformation of genetic information. This is particularly the case for the microorganisms that govern carbon and nitrogen cycling. These biological processes are mediated by the expression of functional genes and their translation into enzymes that catalyze geochemical reactions. Understanding human effects on microbial activity, fitness and distribution is an important component of Critical Zone science, but is highly challenging to investigate across the enormous physical scales of impact ranging from individual organisms to the planet. One arena where this might be tractable is by studying the dynamics and dissemination of genes for antibiotic resistance and the organisms that carry such genes. Here we explore the transport and transformation of microbial genes and cells through Earth's Critical Zone. We do so by examining the origins and rise of antibiotic resistance genes, their subsequent dissemination, and the ongoing colonization of diverse ecosystems by resistant organisms.

Fluoroquinolones and β-lactam antibiotics and antibiotic resistance genes in autumn leachates of seven major municipal solid waste landfills in China

Landfills are reservoirs of antibiotics, heavy metals, disinfectants and other emerging contaminants, and they are closely associated with the increasing prevalence of antibiotic-resistance genes (ARGs). In this study, two classes of clinical use antibiotics, i.e., fluoroquinolones (FQs) and β-lactams (BLs), twelve subtypes of their parallel ARGs, and five mobile genetic elements (MGEs), were measured in municipal solid waste (MSW) landfill leachates from seven mega-cities in China. The highest concentration of FQs was detected in Shanghai (48,326.67 ng/L), and the highest concentration of BLs was detected in Hangzhou (1304 ng/L). In landfill leachates in Suzhou, the total contents of targeted ARGs subtypes ((1.44 ± 4.64) × 10^-4 (ARGs/16S)) and MGEs (7.88 × 10^-2 ± 1.18 × 10^-1 (ARGs/16S)) were the highest. The relative abundance of ARGs and MGEs was significantly correlated with the contents of As and Cr, and the presence of MGEs was highly correlated with the content of Cd (r = -0.438, p = 0.475). Linear regression analysis showed that MGEs are closely associated with the abundance of genes resistant to FQs and BLs. These results suggest that the occurrences of FQs and BLs ARGs in the landfills of China are substantially influenced by heavy metals and MGEs. Regional differences concerning the antibiotics and ARGs contents in leachates were observed across seven mega-cities, and FQs were significantly correlated with the local population level (p < 0.01). Further, the nitrogen input to the landfills contributes significantly to the elevated levels of target ARGs.

Changes in tetracycline partitioning and bacteria/phage-comediated ARGs in microplastic-contaminated greenhouse soil facilitated by sophorolipid

The emerging mixed contamination of antibiotics and microplastics in greenhouse soil has made the control of antibiotic resistant gene (ARG) transmission a novel challenge. In this work, surfactant sophorolipid was applied to enhance the dissipation of tetracycline (TC) and tet genes in the presence of microplastics in greenhouse soil. During 49days of incubation, soil bacteria and phages were both found to be the crucial reservoirs of ARGs. Meanwhile, microplastic's presence significantly inhibited the dissipation of TC and ARGs in the soil. However, sophorolipid application was proved to outweigh the negative impact caused by microplastic existence, and lead to the highest dissipation of soil TC and ARGs. Significant positive correlation was detected between the dissipation rate of water-soluble and exchangeable TC content and bacteria/phage co-mediated ARG levels. This also held true between the two fractions of soil TC and the ratio of ARG level in the bacteria to that in the phages (B_ARGs/P_ARGs). The opposite impacts of microplastic presence and sophorolipid amendment on the TC/ARG dissipation found in this work provides new information for understanding ARG transmission between bacteria and phages in the mixed contaminated greenhouse soil.

Antibiotic Resistance Genes and Associated Microbial Community Conditions in Aging Landfill Systems

Landfills receive about 350 million tons of municipal solid wastes (MSWs) per year globally, including antibiotics and other coselecting agents that impact antimicrobial resistance (AMR). However, little is known about AMR in landfills, especially as a function of landfill ages. Here we quantified antibiotics, heavy metals, and AMR genes (ARGs) in refuse and leachates from landfills of different age (<3, 10, and >20 years). Antibiotics levels were consistently lower in refuse and leachates from older landfills, whereas ARG levels in leachates significantly increased with landfill age (One-way ANOVA, F = 10.8, P < 0.01). Heavy metals whose contents increased as landfills age (one-way ANOVA, F = 12.3, P < 0.01) were significantly correlated with elevated levels of ARGs (Mantel test, R = 0.66, P < 0.01) in leachates, which implies greater AMR exposure risks around older landfills. To further explain ARGs distributional mechanisms with age, microbial communities, mobile genetic elements (MGEs) and environmental factors were contrasted between refuse and leachate samples. Microbial communities in the refuse were closely correlated with ARG contents (Procrustes test; M² = 0.37, R = 0.86, P < 0.001), whereas ARG in leachates were more associated with MGEs.

Isothermal assay targeting class 1 integrase gene for environmental surveillance of antibiotic resistance markers

Antimicrobial resistance genes (ARGs) present in the environment pose a risk to human health due to potential for transfer to human pathogens. Surveillance is an integral part of mitigating environmental dissemination. Quantification of the mobile genetic element class 1 integron-integrase gene (intI1) has been proposed as a surrogate to measuring multiple ARGs. Measurement of such indicator genes can be further simplified by adopting emerging nucleic acids methods such as loop mediated isothermal amplification (LAMP). In this study, LAMP assays were designed and tested for estimating relative abundance of the intI1 gene, which included design of a universal bacteria 16S rRNA gene assay. Following validation of sensitivity and specificity with known bacterial strains, the assays were tested using DNA extracted from river and lake samples. Results showed a significant Pearson correlation (R² = 0.8) between the intI1 gene LAMP assay and ARG relative abundance (measured via qPCR). To demonstrate the ruggedness of the LAMP assays, experiments were also run in the hands of relatively "untrained" personnel by volunteer undergraduate students at a local community college using a hand-held real-time DNA analysis device - Gene-Z. Overall, results support use of the intI1 gene as an indicator of ARGs and the LAMP assays exhibit the opportunity for volunteers to monitor environmental samples for anthropogenic pollution outside of a specialized laboratory.

Feasibility of sulfate-calcined eggshells for removing pathogenic bacteria and antibiotic resistance genes from landfill leachates

High abundance of human pathogen and antibiotic resistance genes (ARGs) in landfill leachate has become an emerging threat against human health. Therefore, sulfate- and calcination-modified eggshells as green agricultural bioresource were applied to test the feasibility of removing pathogenic bacteria and ARGs from leachate. The highest removal of Escherichia coli (E. coil) and gentamycin resistant gene (gmrA) from artificial contaminated landfill leachate was achieved by the application of eggshell with combined treatment of sulfate and calcination. The 16S and gmrA gene copies of E. coil declined significantly from 1.78E8±8.7E6 and 4.12E8±5.9E6 copies mL^-1 to 1.32E7±2.6E6 and 2.69E7±7.2E6 copies mL^-1, respectively, within 24h dynamic adsorption equilibrium process (p<0.05). Moreover, according to the Langmuir kinetic model, the greatest adsorption amount (1.56×10⁹ CFU E. coil per gram of modified eggshells) could be obtained at neutral pH of 7.5. The optimal adsorption eggshells were then screened to the further application in three typical landfill leachates in Nanjing, eastern China. Significant decrease in species and abundance of pathogenic bacteria and ARGs (tet, sul, erm, qnr, and ampC) indicated its great efficiency to purify landfill leachates. This study demonstrated that sulfate-calcined eggshells can be an environmentally-friendly and highly efficient bioadsorbent to the management of reducing dissemination risk of pathogen and ARGs in landfill leachate.