Fate of integrons, antibiotic resistance genes and associated microbial community in food waste and its large-scale biotreatment systems

Mitigated dissemination of antibiotic resistance genes by nanoscale zero-valent iron and iron oxides during anaerobic digestion: Roles of microbial succession and regulation

Nanoscale zero-valent iron (ZVI) and the oxides have been documented as an effective approach for mitigating the dissemination of antibiotic resistance genes (ARGs) during anaerobic digestion (AD). However, the mechanism of ARGs dissemination mitigated by nanoscale ZVI and iron oxides remain unclear. Here, we investigated the influencing mechanisms of nanoscale ZVI and iron oxides on ARGs dissemination during AD. qPCR results indicated that nanoscale ZVI and iron oxides significantly declined the total ARGs abundances, and the strongest inhibiting effect was observed by 10 g/L nanoscale ZVI. Mantel test showed ARGs distribution was positively correlated with physiochemical properties, integrons and microbial community, among which microbial community primarily contributed to ARGs dissemination (39.74%). Furthermore, redundancy and null model analyses suggested the dominant and potential ARGs host was Fastidiosipila, and homogeneous selection in the determinism factors was the largest factor for driving Fastidiosipila variation, confirming the inhibition of Fastidiosipila was primary reason for mitigating ARGs dissemination by nanoscale ZVI and iron oxides. These results were related to the inhibition of ARGs transfer related functions. This work provides novel evidence for mitigating ARGs dissemination through regulating microbial succession and regulation induced by ZVI and iron oxides.

An overview of the occurrence, impact of process parameters, and the fate of antibiotic resistance genes during anaerobic digestion processes

Antibiotic resistance genes (ARGs) have emerged as a significant global health threat, contributing to fatalities worldwide. Wastewater treatment plants (WWTPs) and livestock farms serve as primary reservoirs for these genes due to the limited efficacy of existing treatment methods and microbial adaptation to environmental stressors. Anaerobic digestion (AD) stands as a prevalent biological treatment for managing sewage sludge and manure in these settings. Given the agricultural utility of AD digestate as biofertilizers, understanding ARGs' fate within AD processes is essential to devise effective mitigation strategies. However, understanding the impact of various factors on ARGs occurrence, dissemination, and fate remains limited. This review article explores various AD treatment parameters and correlates to various resistance mechanisms and hotspots of ARGs in the environment. It further evaluates the dissemination and occurrence of ARGs in AD feedstocks and provides a comprehensive understanding of the fate of ARGs in AD systems. This review explores the influence of key AD parameters such as feedstock properties, pretreatments, additives, and operational strategies on ARGs. Results show that properties such as high solid content and optimum co-digestion ratios can enhance ARG removal, while the presence of heavy metals, microplastics, and antibiotics could elevate ARG abundance. Also, operational enhancements, such as employing two-stage digestion, have shown promise in improving ARG removal. However, certain pretreatment methods, like thermal hydrolysis, may exhibit a rebounding effect on ARG levels. Overall, this review systematically addresses current challenges and offers future perspectives associated with the fate of ARGs in AD systems.

Review in anaerobic digestion of food waste

Due to the special property of food waste (FW), anaerobic digestion of food waste is facing many challenges like foaming, acidification, ammonia nitrogen and (NH4+-N) inhibition which resulted in a low biogas yield. A better understanding on the problems exiting in the FW anaerobic digestion would enhance the bio-energy recovery and increase the stable operation. Meanwhile, to overcome the bottle necks, pretreatment, co-digestion and additives is proposed as well as the solutions to improve biogas yield in FW digestion system. At last, future research directions regarding FW anaerobic digestion were proposed.

The pH-specific response of soil resistome to triclocarban and arsenic co-contamination

Heavy metals as well as disinfectants affect the spread of antibiotic resistance genes (ARGs) in soil microbes, however, their cumulative impacts on the proliferation of ARGs are not well studied. In addition, both the chemical stability/availability and ARG profiles are affected by the soil pH, but it has never been considered in the systematic evaluation of soil resistome. In the present study, a microcosm experiment was conducted to study the combined effects of arsenic and triclocarban on the resistome in soil samples with variable pH (pH 4-7). The simultaneous additions of arsenic and triclocarban increase the ARG abundance at pH > 6, because of the intensive co-selective pressures triggered by the increase in concentrations of available arsenic and triclocarban. The occurrence of multidrug ARGs increases with the addition of arsenic and triclocarban, due to the preferred selection of their functional flexibility. The presence of arsenic and triclocarban is strongly related to the spread of MGEs affecting the soil resistome. Furthermore, pH alters the patterns of microbial inhabitants, increasing the relative abundance of Bacteroidota and Proteobacteria and contributing to the prevalence of tetracycline and sulfonamide ARGs at neutral pH. These findings have insight that the effects of arsenic and triclocarban co-contamination on the soil antibiotic resistome is pH dependent.

Pathogenic Bacteria Are the Primary Determinants Shaping PM2.5-Borne Resistomes in the Municipal Food Waste Treatment System

Bioaerosol pollution poses a substantial threat to human health during municipal food waste (FW) recycling. However, bioaerosol-borne antibiotic-resistant genes (ARGs) have received little attention. Herein, 48 metagenomic data were applied to study the prevalence of PM2.5-borne ARGs in and around full-scale food waste treatment plants (FWTPs). Overall, FWTP PM2.5 (2.82 ± 1.47 copies/16S rRNA gene) harbored comparable total abundance of ARGs to that of municipal wastewater treatment plant PM2.5 (WWTP), but was significantly enriched with the multidrug type (e.g., AdeC/I/J; p < 0.05), especially the abundant multidrug ARGs could serve as effective indicators to define resistome profiles of FWTPs (Random Forest accuracy >92%). FWTP PM2.5 exhibited a decreasing enrichment of total ARGs along the FWTP-downwind-boundary gradient, eventually reaching levels comparable to urban PM2.5 (1.46 ± 0.21 copies/16S rRNA gene, N = 12). The combined analysis of source-tracking, metagenome-assembled genomes (MAGs), and culture-based testing provides strong evidence that Acinetobacter johnsonii-dominated pathogens contributed significantly to shaping and disseminating multidrug ARGs, while abiotic factors (i.e., SO42-) indirectly participated in these processes, which deserves more attention in developing strategies to mitigate airborne ARGs. In addition, the exposure level of FWTP PM2.5-borne resistant pathogens was about 5-11 times higher than those in urban PM2.5, and could be more severe than hospital PM2.5 in certain scenarios (<41.53%). This work highlights the importance of FWTP in disseminating airborne multidrug ARGs and the need for re-evaluating the air pollution induced by municipal FWTP in public health terms.

Dynamics of antibiotic resistance genes and bacterial community during pig manure, kitchen waste, and sewage sludge composting

Organic solid wastes (OSWs) are important reservoirs for antibiotic resistance genes (ARGs). Aerobic composting transforms OSWs into fertilizers. In this study, we investigated ARGs dynamics and their driving mechanisms in three OSW composts: pig manure (PM), kitchen waste (KC), and sewage sludge (SG). The dominant ARGs were different in each OSW, namely tetracycline, aminoglycoside, and macrolide resistance (PM); tetracyclines and aminoglycosides (KC); and sulfonamides (SG). ARGs abundance decreased in PM (71%) but increased in KC (5.9-fold) and SG (1.3-fold). Interestingly, the ARGs abundance was generally similar in all final composts, which was contributed to the similar bacterial community in final composts. In particular, sulfonamide and β-lactam resistant genes removed (100%) in PM, while sulfonamide in KC (38-fold) and tetracycline in SG (5-fold) increased the most. Additionally, ARGs abundance rebounded during the maturation period in all treatments. Firmicutes, Proteobacteria, and Actinobacteria were the main ARGs hosts. Several persistent and high-risk genes included tetW, aadA, aadE, tetX, strB, tetA, mefA, intl1, and intl2. The structural equation models showed ARGs removal was mainly affected by physicochemical parameters and bacterial communities in PM, the ARGs enrichment in KC composting correlated with increased mobile genetic elements (MGEs). In general, thermophilic aerobic composting can inhibit the vertical gene transfer (VGT) of pig manure and horizontal gene transfer (HGT) of sludge, but it increases the HGT of kitchen waste, resulting in a dramatic increase of ARGs in KC compost. More attention should be paid to the ARGs risk of kitchen waste composting.

Incomplete degradation of aromatic-aliphatic copolymer leads to proliferation of microplastics and antibiotic resistance genes

Biodegradable plastics (BDPs) have attracted extensive attention as an alternative to conventional plastics. BDPs could be mineralized by composting, while the quality of compost affected by the presence of BDPs and the residual microplastics (MPs) has not been well evaluated. This study aimed to explore the MPs release potential and environmental implications of commercial BDPs (aromatic-aliphatic copolymer) films in uncontrolled composting. Results showed that the molecular weight of BDPs decreased by >60% within 60 d. However, the non-extracted organic matter and wet-sieving measurements indicated that MPs continuously released and accumulated during regular composting. The average MPs release potential (0.1-5 mm) was 134.6 ± 18.1 particles/mg (BDPs), which resulted in 103-104 particles/g dw in compost. The plastisphere of MPs showed a significantly higher (0.95-16.76 times) abundance of antibiotic resistance genes (ARGs), which resulted in the rising (1.34-2.24 times) of ARGs in compost heaps, in comparison to the control groups. Overall, BDPs promote the spread of ARGs through the selective enrichment of bacteria and horizontal transfer from released MPs. These findings confirmed that BDPs could enhance the release potential of MPs and the dissemination of ARGs, which would promote the holistic understanding and environmental risk of BDPs.

From air to airway: Dynamics and risk of inhalable bacteria in municipal solid waste treatment systems

Municipal solid waste treatment (MSWT) system emits a cocktail of microorganisms that jeopardize environmental and public health. However, the dynamics and risks of airborne microbiota associated with MSWT are poorly understood. Here, we analyzed the bacterial community of inhalable air particulates (PM10, n = 71) and the potentially exposed on-site workers' throat swabs (n = 30) along with waste treatment chain in Shanghai, the largest city of China. Overall, the airborne bacteria varied largely in composition and abundance during the treatment (P < 0.05), especially in winter. Compared to the air conditions, MSWT-sources that contributed to 15 ∼ 70% of airborne bacteria more heavily influenced the PM10-laden bacterial communities (PLS-SEM, β = 0.40, P < 0.05). Moreover, our year-span analysis found PM10 as an important media spreading pathogens (104 ∼ 108 copies/day) into on-site workers. The machine-learning identified Lactobacillus and Streptococcus as pharynx-niched featured biomarker in summer and Rhodococcus and Capnocytophaga in winter (RandomForest, ntree = 500, mtry = 10, cross = 10, OOB = 0%), which closely related to their airborne counterparts (Procrustes test, P < 0.05), suggesting that MSWT a dynamic hotspot of airborne bacteria with the pronounced inhalable risks to the neighboring communities.

The migration regularity and removal mechanism of antibiotic resistance genes during in situ enzymatic hydrolysis and anaerobic digestion of food waste

This study developed a high efficiency compound enzyme (fungal mash) produced in situ from food waste (FW) used for improving hydrolysis and anaerobic digestion (AD) efficiency of FW. Results showed that the soluble COD and methane yield were respectively increased by 67.80% and 16.58% after 24 h in situ enzymatic hydrolysis of food waste by fungal mash. Furthermore, most of target ARGs in FW were also reduced by 45-94% after 24 h in situ enzymatic hydrolysis, while the total tested ARGs and intI1 were respectively further removed by 44-55% and 21-73% in subsequent AD process. In-depth analysis showed that fungal mash could effectively reduce potential hosts and control the horizontal transfer of ARGs during the in situ enzymatic hydrolysis and AD process. Ultimately, correlation analysis and redundancy analysis indicated that the evolution of bacterial communities and changes in intI1 where the common driving forces for the fate of ARGs.

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) coastal mudflats. 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.

Comparative insight into the effects of different carbon source supplement on antibiotic resistance genes during whole-run and short-cut nitrification-denitrification processes

Mature landfill leachate is known for nitrogen-removal challenging and meantime was considered as an important sink of antibiotic resistance genes (ARGs). The added external carbon sources, enabling the short-cut nitrification and denitrification, may facilitate the proliferation of bacteria that possibly carry ARGs. However, this speculation has yet to be studied. Here, we explored the effects of glucose, sodium acetate, and methanol supplements on ARGs during whole-run and short-cut treatment processes. The results showed that sodium acetate supplement during short-cut process efficiently reduced the abundances of total ARGs (0.84-1.99 copies/16S rRNA) and integrons (0.59-1.20 copies/16S rRNA), which were highly enhanced by methanol addition during whole-run treatment process (total ARGs: 3.60-11.01 copies/16S rRNA, integrons: 1.20-4.69 copies/16S rRNA). Indirect gradient analysis showed that the variation of ARGs was not correlated with the supplement of different external carbon source. Correlation analysis indicated that dominant intl1 (55.99 ± 17.61% of integrons) showed positively significant correlations with all detected ARGs expect for sul2 and ermB (p < 0.05), suggesting the significant role on ARGs dissemination. Redundancy analysis illustrated that the potential hosts of intl1, intl2, sul1, tetQ, tetM, mefA, and mexF were dominant Bacteroidetes and Actinobacteria. Interestingly, the numbers and significant extent of correlations under the supplement of sodium acetate during short-cut denitrification process were obviously declined, and it was in accordance with ARGs reduced by sodium acetate supplement, suggesting sodium acetate displayed the efficient ARGs reduction during short-cut process. In summary, this study provides a comparative understanding of the effects on ARGs by different carbon source supplements during nitrification-denitrification processes of leachate; sodium acetate is the optimal carbon source.

Leaching risk of antibiotic resistance contamination from organic waste compost in rural areas

Composting is an important decentralized technology for treating multiple biodegradable organic wastes in rural areas. However, compared to industrial composting (i.e., time and temperature protocols), rural composting is less well-controlled, and the risk of antibiotic resistance genes (ARGs) in these composts needs to be determined. We performed a quantitative determination of ARGs and both prokaryotes and eukaryotes to investigate the liquid-solid leaching ratio and the relationship between ARGs and microbial communities in solid and water extracts of composts collected from rural areas. We observed a high level of sulfonamides resistance genes and tetracyclines resistance genes (10^-4-10^-2 copies/16S copies). Tet-C and tet-X show the strongest leaching potential in rural organic waste composts with complex hosts in solid and liquid phases. This study showed high ARG abundances in compost solid and water extracts, highlighting the leaching risk of compost ARGs when exposed to runoff or groundwater during open storage and field application.

Characteristics of antibiotic resistance gene distribution in rainfall runoff and combined sewer overflow

Rainfall runoff and combined sewer overflow (CSO) converge with organic waste, nutrients, and microbes from the ground and wastewater. These pollutants promote the spread and transformation of antibiotic resistance genes (ARGs). In this study, four rainfall runoff and one CSO outfall were chosen, and samples were collected to explore the occurrence and distribution of ARGs. The ARGs were extracted from suspended solids and analyzed using metagenomic sequencing. A total of 888 ARG subtypes, belonging to 17 ARG types, were detected in all samples. Eleven ARG types were shared by all the samples. Multidrug resistance genes had the highest relative abundance. Their total relative abundance reached 1.07 ratio (ARG copy number/16S rRNA gene copy number) and comprised 46.6% of all the ARGs. In all samples, the CSO outfall had the highest total relative abundance (8.25 × 10^-1 ratio) of ARGs, with a ratio ranging ND (not detected)-3.78 × 10^-1 ratio. Furthermore, the relationship between ARG types and environmental factors was determined using redundancy analysis. The results showed that chemical organic demand (COD) and bacterial abundance were positively correlated with most ARG types, including multidrug, bacitracin, aminoglycoside, β-lactam, tetracycline, and sulfonamide. NH₃-N, TN, and TP were positively correlated with rifamycin, fosmidomycin, and vancomycin resistance genes. The relationship among the ARG subtypes was investigated using network analyses. The multidrug resistance gene subtypes had the highest frequency of co-occurrence. This study provides insights into the occurrence and distribution of ARGs under non-point source pollution and may contribute to the control of ARGs.

Multi-omics methods reveal that putrescine and cadaverine cause different degrees of enrichment of high-risk resistomes and opportunistic pathogens in the water and sediment of the Yellow River

Contamination of antibiotic resistomes due to animal carcass decay has become a serious environmental concern. However, the relationship between main metabolite compounds of corpse decomposition (i.e., putrescine and cadaverine) and antibiotic resistomes remains unclear. To tackle this issue, the response of antibiotic resistance genes (ARGs) and microbiome in aquatic environment to excess putrescine, cadaverine and a mixture of both based on laboratory simulation experiment was investigated by high-throughput quantitative PCR and amplicon sequencing methods. Our results showed putrescine and cadaverine led to the increasing of TC (total carbon) and TN (total nitrogen) both in water and sediment. Under the exposure of putrescine and cadaverine, the total abundance of mobile genetic elements (MGEs) and most ARGs in water was higher than in sediment. In particular, putrescine and cadaverine caused significantly different decreases in alpha diversity of microbial community in water and sediment compared with the control group. Microbial community structures both in water and sediment were also significantly affected by cadaverine and putrescine. Furthermore, putrescine and cadaverine led to different degrees of increases of high-risk ARGs (like mecA) and opportunistic pathogens (like Delftia) in sediment, promoting the prevalence of antibiotic resistant bacteria. In conclusion, our findings revealed the influences of main metabolites of carcass decay on microbiome and resistomes, providing references for risk assessment and pollution management.

Exploring the abundance and influencing factors of antimicrobial resistance genes in manure plasmidome from swine farms

Plasmids play a critical role in the dissemination of antimicrobial resistance genes (ARGs), however, a systematical understanding of ARGs originated from plasmids in swine production is currently lacking. Herein, quantitative polymerase chain reaction was applied to determine the prevalence of ten ARGs and the class1 integron gene intI1 of plasmid source in swine manure from 44 farms in Sichuan, Hubei and Hebei provinces, China. All assayed ARGs were observed in plasmid DNA samples, and the average absolute abundance of aac(6')-Ib-cr, bla_NDM, bla_CTX-M, optrA, ermB, floR, mcr-1, qnrS, tetM, sul1 and intI1 were 7.09, 2.90, 4.67, 6.62, 7.55, 7.14, 4.08, 4.85, 7.16, 7.11 and 8.07 of 10 log copies/gram, respectively. IntI1 showed a high correlation (r > 0.8, P < 0.01) with the abundance of aac(6')-Ib-cr and sul1 in swine manure. Moreover, the farm scale (i.e., herd population) and geographical location were not found to be critical factors influencing the absolute abundance of ARGs of plasmid DNA in swine farms. However, the concentrations of florfenicol, Cu, Zn, Fe, total phosphorus (TP) and total potassium (TK) demonstrated a significant correlation with the abundance of several ARGs. Particularly, Cu and Zn had high correlations with optrA and bla_CTX-M, respectively. Our results demonstrated that antibiotics, heavy metals and environmental nutrients are likely jointly contributing to the long-term persistence of ARGs in swine production. This study provides insights into the abundance and influencing factors of ARGs from swine manure, which is of significance for assessing and reducing the public health risks in livestock production.

Impact of hydrophilic functional groups of macromolecular organic fractions on food waste digestate dewaterability

：Deterioration of dewaterability is one of challenges faced by anaerobic digestion (AD) of food waste (FW). The underlying mechanism of the effect of AD on digestate dewaterability remains unclear. Thus, the effect of hydrophilic functional groups of macromolecular organic on FW digestate dewaterability in different stages during AD was studied. Results showed that the dewaterability first improved at the acidification stage, and then worsened at the gasification and stabilization stages. The correlations between normalized capillary suction time (NCST), bound moisture (BM) and extracellular protein (extra-PN) were significant (R = 0.736, p < 0.05, R = 0.637, p < 0.05). Macromolecular extra-PN that enhance the bonding between organic fractions and moisture via peptide bonds. In addition, carbonyl, phenolic and amide groups increased after AD, resulting in the enhancement of the digestate hydrophilicity. Furthermore, the evolution of microbial community during AD resulting in the wrapping of BM by increased organic fractions. Therefore, higher organic fractions with hydrophilic functional groups in digestate strongly hinder moisture removal. The findings obtained deepen our understanding of hydrophilic functional groups of macromolecular organic affecting FW digestate dewaterability and provide strong supports to treatment and disposal of FW digestate.

Removal behavior and key drivers of antibiotic resistance genes in two full-scale leachate treatment plants

Leachate is a critical reservoir of antibiotic resistance genes (ARGs) and its proper treatment is closely related to human health and ecosystem safety. Here, we used high-throughput qPCR to explore the removal behavior of ARGs in two full-scale leachate treatment plants (LTPs) where biological treatment and membrane filtration processes were integrated. A total of 286 ARGs and 55 mobile genetic elements (MGEs) were detected, with aminoglycoside, multidrug and MLSB resistance genes being the most prevalent and abundant. Anaerobic digestion was found to be an important pretreatment process for leachate, while anoxic/aerobic tanks in membrane bioreactor (MBR) acted as incubators for ARGs due to their significant proliferation effect on ARGs. Integrated membrane filtration (UF-NF-RO) excelled in ARGs removal with absolute abundances reduced by 3 to 6 orders of magnitude, from about 10⁹ copies/mL in raw leachate to 10³-10⁵ copies/mL in effluents. Our results also showed that leachate treatment processes significantly altered the composition of ARGs and bacterial communities. Procrustes analysis and network analysis revealed strong associations between microbes and ARGs, with several hub genes and bacterial genera identified. Structural equation models (SEMs) indicated that bacterial composition, MGEs and basic water properties were the key drivers shaping ARGs dynamics in the raw leachate, biological system and filtration system, respectively. Notably, several pathogens (e.g., Klebsiella, Vibrio, Aeromonas) were closely correlated with ARGs in raw leachate and may amplify the dissemination risks of ARGs. Moreover, insertion sequences in biological systems would accelerate the horizontal gene transfer of ARGs. In short, this study provides new insights into the mechanisms of ARGs removal and dissemination behavior in industrial-scale LTPs.

Temporal variation of antibiotic resistome and pathogens in food waste during short-term storage

The massive food wastes pose a growing health concern for spreading of antibiotic resistance and pathogens due to food spoilage. However, little is known about these microbial hazards during collection, classification, and transportation before eventual treatment. Here, we profiled the temporal variations of antibiotic resistance genes (ARGs), pathogens, bacterial and fungal communities across four typical food wastes (vegetable, fish, meat, and rice) during storage at room temperature in summer (maximum 28-29 °C) of typical southeast city in China. A total of 171 ARGs and 32 mobile genetic elements were detected, and the absolute abundance of ARGs significantly increased by up to 126-fold with the storage time. Additionally, five bacterial pathogens containing virulence factor genes were detected, and Klebsiella pneumoniae was persistently detected throughout the storage time in all food types except rice. Moreover, fungal pathogens (e.g., Aspergillus, Penicillium, and Fusarium) were also frequently detected. Notably, animal food wastes were demonstrated to harbor higher abundance of ARGs and more types of pathogens, indicating a higher level of hazard. Mobile genetic elements and food types were demonstrated to mainly impact ARG profiles and pathogens, respectively. This work provides a comprehensive understanding of the microbial hazards associated with food waste recycling, and will contribute to optimize the food waste management to ensure biosecurity and benefit human health.

Spread of antimicrobial resistance genes via pig manure from organic and conventional farms in the presence or absence of antibiotic use

AIMS

Antibiotic resistant bacteria affect human and animal health. Hence, their environmental spread represents a potential hazard for mankind. Livestock farming is suspected to be a key factor for spreading antibiotic resistance; consumers expect organic farming to imply less environmental health risk. This study aimed to assess the role of manure from organic and conventional farms for spreading antimicrobial resistance (AMR) genes.

METHODS AND RESULTS

AMR-genes- namely tet(A), tet(B), tet(M), sul2, and qacE/qacEΔ1 (potentially associated with multiresistance) were quantified by qPCR. Antimicrobial use during the study period was qualitatively assessed from official records in a binary mode (yes/no). Median concentrations were between 6.44 log copy-equivalents/g for tet(A) and 7.85 for tet(M) in organic liquid manure, and between 7.48 for tet(A) and 8.3 for sul2 in organic farmyard manure. In conventional manure, median concentrations were 6.67 log copy-equivalents/g for sul2, 6.89 for tet(A), 6.77 for tet(B) and 8.36 for tet(M). Integron-associated qac-genes reached median concentrations of 7.06 log copy-equivalents/g in organic liquid manure, 7.13 in conventional manure and 8.18 in organic farmyard manure. Use of tetracyclines or sulfonamides increased concentrations of tet(A) and tet(M), or of sul2, respectively. Comparing farms that did not apply tetracyclines during the study, the relative abundance of tet(A) and tet(M) was still higher for conventional piggeries than for organic ones.

CONCLUSIONS

Relative abundances of antimicrobial resistance genes were higher in conventional farms, compared to organic ones. Antibiotic use was linked to the relative abundance of AMR-genes. However, due to the bacterial load, absolute concentrations of AMR-genes were comparable between fertilizers of organic and conventional farms.

SIGNIFICANCE AND IMPACT OF STUDY

To our knowledge, this is the first absolute quantification of AMR-genes in manure from organic farms. Our study underlines the importance of long-term-reduction in the use of antimicrobial agents in order to minimize antibiotic resistance.

Migration of antibiotic resistance genes and evolution of flora structure in the Xenopus tropicalis intestinal tract with combined exposure to roxithromycin and oxytetracycline

The intestinal flora is one of the most important environments for antibiotic resistance development, owing to its diverse mix of bacteria. An excellent medicine model organism, Xenopus tropicalis, was selected to investigate the spread of antibiotic resistance genes (ARGs) in the intestinal bacterial community with single or combined exposure to roxithromycin (ROX) and oxytetracycline (OTC). Seventeen resistance genes (tetA, tetB, tetE, tetM, tetO, tetS, tetX, ermF, msrA, mefA, ereA, ereB, mphA, mphB, intI1, intI2, intI3) were detected in the intestines of Xenopus tropicalis living in three testing tanks (ROX tanks, OTC tanks, ROX + OTC tanks) and a blank tank for 20 days. The results showed that the relative abundance of total ARGs increased obviously in the tank with single stress but decreased in the tank with combined stress, and the genes encoding the macrolide antibiotic efflux pump (msrA), phosphatase (mphB) and integron (intI2, intI3) were the most sensitive. With the aid of AFM scanning, DNA was found to be scattered short chain in the blank, became extended or curled and then compacted with the stress from a single antibiotic, and was compacted and then fragmented with combined stress, which might be the reason for the variation of the abundance of ARGs with stress. The ratio of Firmicutes/Bacteroides related to diseases was increased by ROX and OTC. The very significant correlation between intI2 and intI3 with tetS (p ≤ 0.001) hinted at a high risk of ARG transmission in the intestines. Collectively, our results suggested that the relative abundance of intestinal ARGs could be changed depending on the intestinal microbiome and DNA structures upon exposure to antibiotics at environmental concentrations.

Short-term biodrying achieves compost maturity and significantly reduces antibiotic resistance genes during semi-continuous food waste composting inoculated with mature compost

Food waste (FW) is important object of resource utilization and source of antibiotic resistance genes (ARGs). This study investigated the effects of biodrying combined with inoculating mature compost (B&M) on the composting efficiency, succession of bacterial communities and their links with metabolism functions as well as the fate of ARGs during FW composting. The results showed that B&M could rapidly raise and maintain high relative abundance of Bacillaceae (66.59-94.44%) as well as composting temperature (45.86-65.86 ℃), so as to achieve the final maturity of FW composting in a short time by regulating microbial carbohydrate (14.02-15.31%) and amino acid metabolism (10.33-12.47%). Network analysis demonstrated that high temperature could effectively inhibit the proliferation and spread of potential bacterial hosts of ARGs and integrons including Lactobacillaceae, Enterobacteriaceae, Leuconostocaceae and Corynebacteriaceae during the first two days of composting. As a result, B&M significantly reduced the absolute (72.09-99.47%) and relative abundances (0.31-2.44 logs) of nearly all ARGs especially ermB, tetM, bla_CTX-M and bla_OXA. Present study deepened the knowledge of ARGs variation, succession and metabolism functions of bacterial communities when B&M processes were used for FW composting, suggesting a promising technology for reducing the transmission risk of ARGs and reaching maturity of FW composting.

Metatranscriptomic insight into the effects of antibiotic exposure on performance during anaerobic co-digestion of food waste and sludge

Antibiotics are inevitably entered into anaerobic co-digestion (AcoD) system of food waste (FW) and sludge along with the addition of abundant antibiotic-containing activated sludge. However, the in-depth insights into antibiotics affecting AcoD performance have not comprehensively studied. In present study, the results showed that tetracycline (TC), sulfamethoxazole (SMZ) and erythromycin (ERY) inhibited and delayed methane production except for 5 mg/L ERY. By comparison, TC and SMZ significantly inhibited the cumulative methane yields (one-way ANOVA, p < 0.01), and the inhibition effects were magnified as the antibiotic level increased. Physicochemical and methane yield analysis indicated antibiotics inhibited hydrolysis process and delayed methanogenesis process, which was in line with the declined abundance of acetogenic Proteiniphilum and hydrogenotrophic Methanobacterium during AcoD. Furthermore, metatranscriptomic analysis demonstrated the microbial activities of major organic and energy metabolism were down-regulated under antibiotics exposure, thereby down-regulating the expressions of key coenzymes (coenzymes M, F420, methanofuran) biosynthesis for methanogenesis and methane metabolism. The declined methanogenesis activity was completely consistent with the inhibited activity of dominant Methanosarcina and methane production, proving the importance of Methanosarcina on methane production. This study provides new metatranscriptomic evidence into the effects of antibiotics on methanogenesis during AcoD.

Dissemination of antibiotic resistance under antibiotics pressure during anaerobic co-digestion of food waste and sludge: Insights of driving factors, genetic expression, and regulation mechanism

This study revealed the effects and regulation mechanisms on antibiotic resistance genes (ARGs) dissemination during anaerobic co-digestion (AcoD) of food waste and sludge under the exposure of tetracycline, sulfamethoxazole (SMZ) and erythromycin (ERY). Results indicated antibiotics significantly increased the abundance of ARGs, and selectively enriched integron gene, suggesting antibiotics promoted the dissemination of ARGs. Procrustes analysis indicated that bacterial community, integrons and physicochemical properties displayed significant correlations with ARGs, and they respectively contributed 10.61%, 6.94% and 2.97% of explanations on ARGs variation. Especially, the maximum combined contribution (48.6%) of bacterial community and integrons, implying their significances on ARGs alteration. Metatranscriptomic analysis further demonstrated antibiotics upregulated the expressions of total ARGs and virulence factors, raising potential risks. The proposed mechanisms for ARGs dissemination facilitated by antibiotics might be attributed to the changes of ARGs-regulated functions for inducing DNA/cell damage and DNA conjugation during AcoD.

Underrepresented high diversity of class 1 integrons in the environment uncovered by PacBio sequencing using a new primer

Class 1 integrons (CL1s) are one of the major contributors to the horizontal transfer of antibiotic resistance genes (ARGs). However, our knowledge of CL1 in the environment is still very limited due to the limitations of the current PCR primers and the sequencing methods adopted. This study developed a new primer coupled with PacBio sequencing to investigate the underrepresented diversity of CL1s in a mixed environmental sample (i.e. activated sludge from wastewater treatment plant and pig feces from animal farm). The new primer successfully uncovered 20 extra ARGs subtypes and 57% (422/739) more unique integron array structures than the previous primers. Compared to the whole genome database, CL1s revealed in the environment in this study were of much greater diversity, having 93% (900/967) novel array structures. Antibiotic resistance is the predominant function (78.3% genes) carried by CL1, and a vast majority (98.6% genes) of them confer resistance to aminoglycoside, beta-lactam, trimethoprim, or chloramphenicol. Additionally, 78.5% unique CL1 arrays carried more than one ARGs, and 25.9% of them carried ARGs of clinical relevance with high transferability potential posing threat to the general public. Our results indicated the importance of CL1s in the spread of ARGs. Overall, combining PacBio sequencing with the new primer designed in this study largely broadened our knowledge of CL1s in the environment and their significance in the environmental proliferation of ARGs.

The variation of antibiotic resistance genes and their links with microbial communities during full-scale food waste leachate biotreatment processes

The prevalence of antibiotic resistance genes (ARGs) has been widely reported in various environments. However, little is known of them in food waste (FW) leachate with high organic content and how their distribution is influenced by biotreatment processes. Here, twelve ARGs, two integrase genes and bacterial communities were investigated during two full-scale FW biotreatment processes. High ARGs abundances (absolute: 1.03 × 10⁷-2.82 × 10⁹copies/mL; relative: 0.076-2.778copies/16S rRNA) were observed across all samples. Although biotreatment effectively reduced absolute abundance of ARGs, additional bacteria acquiring ARGs caused an increase in their relative abundance, which further increased the transmission risk of ARGs. mexF, blaCTX-M, sul1 played crucial roles and sul1 might be considered as an indicator for the prediction of total ARGs. It is worrying that the discharge (effluent and sludge) included highly abundant ARGs (5.09 × 10¹⁴-4.83 × 10¹⁵copies/d), integrons (1.11 × 10¹⁴-6.04 × 10¹⁴copies/d) and potential pathogens (such as Pseudomonas and Streptococcus), which should be given more attentions. blaCTX-M and tetQ possessed most potential hosts, Proteobacteria-L and Firmicutes-W were predominant contributors of ARGs-hosts at genus level. This study suggested FW leachate biotreatment systems could be reservoirs of ARGs and facilitated the proliferation of them. The exploration of effective removal methods and formulation of emission standard are necessary for future ARGs mitigation.

Role of anaerobic sludge digestion in handling antibiotic resistant bacteria and antibiotic resistance genes - A review

Currently, anaerobic sludge digestion (ASD) is considered not only for treating residual sewage sludge and energy recovery but also for the reduction of antibiotic resistance genes (ARGs). The current review highlights the reasons why antibiotic resistant bacteria (ARB) and ARGs exist in ASD and how ASD performs in the reduction of ARB and ARGs. ARGs and ARB have been detected in ASD with some reports indicating some of the ARGs can be completely removed during the ASD process, while other studies reported the enrichment of ARB and ARGs after ASD. This paper reviews the performance of ASD based on operational parameters as well as environmental chemistry. More studies are needed to improve the performance of ASD in reducing ARGs that are difficult to handle and also differentiate between extracellular (eARGs) and intracellular ARGs (iARGs) to achieve more accurate quantification of the ARGs.

Comparison of an integrated short-cut biological nitrogen removal process with magnetic coagulation treating swine wastewater and food waste digestate

An integration of two processes, magnetic coagulation (MC) and short-cut biological nitrogen removal (SBNR), coupled with a sequencing batch membrane bioreactor (SMBR) controlled by an automatic real-time control strategy (RTC), was developed to treat different characteristics of high strength wastewater. The treatment efficiency and microbial community-diversity of the proposed method was evaluated and investigated using swine wastewater and food waste (FW) digestate. The MC showed high removal of TSS (89.1 ± 1.5%, 92.21 ± 1.8%), turbidity (90.58 ± 2.1%, 95.1 ± 2.1%), TP (88.5 ± 1.9%, 92.1 ± 1.5%), phosphate (87.76 ± 1.6%, 91.22 ± 1.5%), and SMBR achieved stable and excellent removal of COD (96.05 ± 0.2%, 97.39 ± 0.2%), TN (97.30 ± 0.3%, 97.44 ± 0.3%) andNH₄⁺-N (99.07 ± 0.2%, 98.54 ± 0.2%) for swine wastewater and FW digestate, respectively. The effluent COD andNH₄⁺-N concentrations were found to meet their discharge standards. The microbial community comparison showed similar diversity and richness, and genus Diaphorobacter and Thaurea were dominant in denitritation, and Nitrosomonas was dominant in nitritation treating both swine wastewater and FW digestate.

Insight into the evolution of microbial community and antibiotic resistance genes in anammox process induced by copper after recovery from oxytetracycline stress

The influence of copper ion (Cu²⁺) on anaerobic ammonium oxidation (anammox) performance and microbial community structures after oxytetracycline (OTC) stress recovery were assessed. Experimental results demonstrated that anammox performance were stressed by 1.0 mg L^-1 Cu²⁺ and inhibitions were reversible with total nitrogen removal rate higher than 3.08 ± 0.2 kg N m^-3 d^-1. The residual OTC in the anammox sludge could combine with Cu²⁺ introduced and thereby retarded inhibition on performance in the presence of 2.0 mg L^-1 Cu²⁺. Moreover, the positive relation of dominant bacterium Ca. Anammoxoglobus with the abundance of functional genes and parts of antibiotic resistance genes were observed, suggesting that regain of performance was the results of the gradual domestication of latent resistant species after inhibition. This investigation reveals new insights into resistance of anammox performance for Cu²⁺ and OTC.

Does lipid stress affect performance, fate of antibiotic resistance genes and microbial dynamics during anaerobic digestion of food waste?

The dissemination of antibiotic resistance genes (ARGs) in food waste (FW) disposal can pose severe threats to public health. Lipid is a primary composition in FW, while whether lipid stress can affect ARGs dynamics during anaerobic digestion (AD) process of FW is uncertain. This study focused on the impacts of lipid stress on methane production, fate of ARGs and its microbial mechanisms during AD of FW. Results showed that high lipid content increased methane yield but prolonged hydrolysis and lag time of methane production compared to AD of FW without oil. Moreover, variations of ARGs were more susceptible to lipid stress. Lipid stress could facilitate the reduction of total ARGs abundances compared to the group without oil, particularly restraining the proliferation of sul1, aadA1 and mefA in AD systems (P < 0.05). Mantel test suggested that integrons (intl1 and intl2) were significantly correlated with all detected ARGs (r: 0.33, P < 0.05), indicating that horizontal gene transfer mediated by integrons could be the driving force on ARGs dissemination. Network analysis suggested that Firmicutes, Bacteroidetes, Synergistetes and Proteobacteria were the main potential hosts of ARGs. In addition, under the lipid stress, the reduction of host bacteria was responsible for the elimination of several specific ARGs, thereby affecting ARGs profiles. These findings firstly deciphered ARGs dynamics and their driving factors responding to lipid stress during anaerobic biological treatment of FW.

Antibiotic and metal resistance genes are closely linked with nitrogen-processing functions in municipal solid waste landfills

Landfilled antibiotics and metals were related to the occurrences of their resistance genes, whose decade-long development in leachates with the dynamic landfilling environmental conditions, especially with the varying nitrogen contents, has yet to be studied. Here, we sampled leachates from five representative municipal solid waste landfills in China. The total concentrations of antibiotics (5000 - 50000 ng/L) and metals (10 - 60 mg/L) in leachates were significantly different among different sites and they were only closely related to sulfonamide and tetracycline resistance genes (P < 0.05). Regarding the abundance of subtype resistance genes, sul1 and ermB were dominant antibiotic resistance genes (ARGs) and terc, arsc, and mer were dominant heavy metal resistance genes (HMRGs); and meanwhile the observed huge variations of these genes appeared to be related to environmental factors like nitrate and pH (P < 0.05). The GeoChip results further indicated that more than 85% of sequenced ARGs/HMRGs and nitrogen processing genes, particularly of the denitrification genes, were hosted by the same bacterial species, such as Pseudomonas sp. and Bacillus sp., which belonged to the predominant phylum in leachates. These results extended our knowledge about the linkages among ARGs, HMRGs and nitrogen-processing functions in leachates.

Volatile fatty acids production from waste activated sludge during anaerobic fermentation: The effect of superfine sand

Superfine sand in waste activated sludge (WAS) increased the uncertainty of anaerobic fermentation. Experiments showed that VFAs production from WAS was positively affected by superfine sand, with an increase from 2513 mg COD/L in the control (without superfine sand) to 3002 mg COD/L with superfine sand. A mechanism study demonstrated that the main factor responsible for the improved VFAs accumulation in response to superfine sand was acetic acid, which increased by nearly 30%. Further investigation exhibited that the process of solubilization and acidification were facilitated by superfine sand and the abundance of anaerobic functional microorganisms was greatly increased. Moreover, the activities of acetate kinase (AK) as well as the quantity of AK encoding gene were greatly promoted by superfine sand. The heat release during WAS anaerobic fermentation with superfine sand was higher than that without superfine sand (25.8 × 10^-3 versus 24.7 × 10^-3 W·min at about 70 min).