The fate of antibiotic resistance genes and their association with bacterial and archaeal communities during advanced treatment of pig farm wastewater

Current perspectives on microalgae and extracellular polymers for reducing antibiotic resistance genes in livestock wastewater

Antibiotic resistance genes (ARGs) in livestock wastewater resulting from excessive antibiotics used in animal farming pose significant environmental and public health risks. Conventional treatment methods are often costly, inefficient, and may inadvertently promote ARG transmission. Microalgae, with their long genetic distance from bacteria and strong ability to utilize wastewater nutrients, offer a sustainable solution for ARG mitigation. This review studied the abundance and characterization of ARGs in livestock wastewater, highlighted microalgal-based removal mechanisms of ARGs, including phagocytosis, competition, and absorption by extracellular polymeric substances (EPS), and explored factors influencing their efficacy. Notably, the microalgae-EPS system reduced ARGs by 0.62-3.00 log, demonstrating significant potential in wastewater treatment. Key challenges, such as optimizing algal species, understanding EPS-ARG interactions, targeted reduction of host bacteria, and scaling technologies, were discussed. This work provides critical insights for advancing microalgal-based strategies for ARG removal, promoting environmentally friendly and efficient wastewater management.

Different combinations of operating temperature and solids retention time during two-phase anaerobic digestion impacts removal of antibiotic resistance genes

Two-phase anaerobic digestion (AD) performance is significantly influenced by operating parameters such as temperature and solids retention time (SRT), while their impact on antibiotic resistance genes (ARGs) during the acidogenic (AP) and methanogenic (MP) phases remains unclear. This study assessed the abundance of eight ARGs in full-scale two-phase AD, then operated lab-scale two-phase AD systems to evaluate temperature combinations (thermophilic-thermophilic, thermophilic-mesophilic, mesophilic-thermophilic, and mesophilic-mesophilic) at a constant SRT (AP = 2/MP = 13d) and to further assess different SRTs (AP = 2/MP = 13d and AP = 4/MP = 11d). qPCR results revealed that full-scale two-phase AD reduced total ARGs abundance by 87.70 ± 0.50 %. In lab-scale tests, the thermophilic-thermophilic configuration achieved nearly complete ARGs removal (97.61 ± 0.21 %), while the combination of AP = 4/MP = 11d had the highest removal efficiency (83.39 ± 1.17 %). Network analysis indicated that Firmicutes, Bacteroidota, and Proteobacteria were the primary ARG hosts, with Firmicutes dominant. These findings highlight the optimal operating parameters in two-phase AD for maximizing ARGs removal.

Mapping the heterogeneous removal landscape of wastewater virome in effluents of different advanced wastewater treatment systems of swine farm

In advanced wastewater treatment plants on pig farms, meticulous design aims to eliminate intrinsic pollutants such as organic matter, heavy metals, and biological contaminants. In our field survey across Southern China, a notable disparity in wastewater treatment procedures among various farming facilities lies in the utilization of terminal chemical oxidation post-sedimentation tank. However, recent focus in wastewater surveillance has predominantly centered on antibiotic resistance genes, leaving the efficacy of virus removal in different effluent systems largely unexplored. To profile virus composition at the effluent, assess the virus elimination efficiency of chemical oxidation at the effluent end, and the potential environmental driver of virus abundance, we deployed a meta-transcriptomics approach to first determine the total virome in effluent specimens of terminal clean water tank system (CWT) and terminal chemical oxidation system (TCO) in Southern China pig farms, respectively. From these data, 172 viruses were identified, with a median reads per million (RPM) of 27,789 in CWT and 19,982 in TCO. Through the integration of analyses encompassing the co-occurrence patterns within viral communities, the ecology of viral diversity, and a comparative assessment of average variation degrees, we have empirically demonstrated that the procedure of TCO may perturb viral communities and diminish their abundance, particularly impacting RNA viral communities. However, despite the diminished abundance, pathogenic viruses such as PEDV and PRRSV persisted in the effluent following chemical deoxidation at a moderate RPM value, indicating a substantial in situ presence at effluent. Our environmental driver modeling, employing GLM and mantel tests, substantiated the intricate nature of virus community variation within the effluent, influenced heterogeneously by diverse factors. Notably, pond temperature emerged as the foremost determinant, while fishing farming exhibited a positive correlation with virus diversity (p < 0.05). This revelation of the cryptic persistence of virus communities in wastewater effluent expands our understanding of the varied responses of different virus categories to oxidation. Such insights transcend mere virus characterization, offering valuable implications for enhancing biosafety measures in farming practices and informing wastewater-based epidemiological surveillance.

Seasonal dynamics of antibiotic resistance genes and mobile genetic elements in a subtropical coastal ecosystem: Implications for environmental health risks

Antibiotic resistance poses a considerable global public health concern, leading to heightened rates of illness and mortality. However, the impact of seasonal variations and environmental factors on the health risks associated with antibiotic resistance genes (ARGs) and their assembly mechanisms is not fully understood. Based on metagenomic sequencing, this study investigated the antibiotic resistome, mobile genetic elements (MGEs), and microbiomes in a subtropical coastal ecosystem of the Beibu Gulf, China, over autumn and winter, and explored the factors influencing seasonal changes in ARG and MGE abundance and diversity. Results indicated that ARG abundance and diversity were higher in winter than in autumn, with beta-lactam and multidrug resistance genes being the most diverse and abundant, respectively. Similarly, MGE abundance and diversity increased in winter and were strongly correlated with ARGs. In contrast, more pronounced associations between microbial communities, especially archaea, and the antibiotic resistome were observed in autumn than in winter. The co-occurrence network identified multiple interactions between MGEs and various multidrug efflux pumps in winter, suggesting a potential for ARG dissemination. Multivariate correlation analyses and path modeling indicated that environmental factors driving microbial community changes predominantly influenced antibiotic resistome assembly in autumn, while the relative importance of MGEs increased significantly in winter. These findings suggest an elevated health risk associated with antimicrobial resistance in the Beibu Gulf during winter, attributed to the dissemination of ARGs by horizontal gene transfer. The observed seasonal variations highlight the dynamic nature of antibiotic resistance dissemination in coastal ecosystems, emphasizing the need for comprehensive surveillance and management measures to address the growing threat of antimicrobial resistance in vulnerable environments.

Identification and characterisation of two functional antibiotic MATE efflux pumps in the archaeon Halorubrum amylolyticum

Multidrug efflux pumps have been found to play a crucial role in drug resistance in bacteria and eukaryotes. In this study, we investigated the presence of functional multidrug and toxic compound extrusion (MATE) efflux pumps, inferred from whole genome sequencing, in the halophilic archaeon Halorubrum amylolyticum CSM52 using Hoechst 33342 dye accumulation and antimicrobial sensitivity tests in the presence and absence of efflux pump inhibitors (EPIs). The whole genome sequence of H. amylolyticum CSM52 contained two putative MATE-type efflux pump genes, which may contribute to the inherent resistance to conventional antimicrobial agents reported in archaea. Antimicrobial susceptibility of the wild-type H. amylolyticum CSM52 testing revealed a lack of sensitivity to a wide range of antimicrobials, including glycopeptides, aminoglycosides, macrolides, fluoroquinolones, tetracycline, and chloramphenicol. However, the presence of EPIs, such as thioridazine, fluoxetine, and chlorpromazine, significantly increased the susceptibility of H. amylolyticum CSM52 to a number of these antimicrobials, indicating the potential involvement of efflux pumps in the observed resistance. A molecular modelling study with EPIs and substrate antimicrobials provided important insights into the molecular interactions with the putative transporter. It suggests that the occupancy of the transporter channel by EPIs has the potential to impact the efflux of antimicrobials. Phylogenetic analysis of the amino acid sequences of both MATE pumps showed low similarity with bacterial representatives, suggesting the presence of novel and distinct MATE efflux pumps in archaea. Our findings provide the first experimental evidence of active antibiotic efflux mechanisms in archaea and their potential roles in antimicrobial resistance, broadening our understanding of mechanisms of archaeal antimicrobial resistance, an overlooked aspect of AMR research.

Travertine deposition rather than tourism activity is the primary contributor to the microplastic risks in alpine karst lakes

Microplastics (MPs) are emerging as anthropogenic vectors to form plastisphere, facilitating microbiome colonization and pathogenic dissemination, thus contributing to environmental and health crises across various ecosystems. However, a knowledge gap persists regarding MPs risks and their driving factors in certain unique and vulnerable ecosystems, such as Karst travertine lakes, some of which are renowned World Natural Heritage Sites under ever-increasing tourism pressure. We hypothesized that tourism activities serve as the most important factor of MPs pollution, whereas intrinsic features, including travertine deposition can exacerbate potential environmental risks. Thus, metagenomic approaches were employed to investigate the geographical distribution of the microbiome, antibiotic resistance genes (ARGs), virulence factor genes (VFGs), and their combined environmental risks in Jiuzhaigou and Huanglong, two famous tourism destinations in Southwest China. The plastisphere risks were higher in Huanglong, contradicting our hypothesis that Jiuzhaigou would face more crucial antibiotic risks due to its higher tourist activities. Specifically, the levels of Lipopolysaccharide Lewis and fosD increased by sevenfold and 20-fold, respectively, from upstream to downstream in Huanglong, whereas in Jiuzhaigou, no significant accrual was observed. Structural equation modeling results showed that travertine deposition was the primary contributor to MPs risks in alpine karstic lakes. Our findings suggest that tourism has low impact on MPs risks, possibly because of proper management, and that travertine deposition might act as an MPs hotspot, emphasizing the importance of considering the unique aspects of travertine lakes in mitigating MPs pollution and promoting the sustainable development of World Natural Heritage Sites.

Seasonal hydrological dynamics affected the diversity and assembly process of the antibiotic resistome in a canal network

The significant threat of antibiotic resistance genes (ARGs) to aquatic environments health has been widely acknowledged. To date, several studies have focused on the distribution and diversity of ARGs in a single river while their profiles in complex river networks are largely known. Here, the spatiotemporal dynamics of ARG profiles in a canal network were examined using high-throughput quantitative PCR, and the underlying assembly processes and its main environmental influencing factors were elucidated using multiple statistical analyses. The results demonstrated significant seasonal dynamics with greater richness and relative abundance of ARGs observed during the dry season compared to the wet season. ARG profiles exhibited a pronounced distance-decay pattern in the dry season, whereas no such pattern was evident in the wet season. Null model analysis indicated that deterministic processes, in contrast to stochastic processes, had a significant impact on shaping the ARG profiles. Furthermore, it was found that Firmicutes and pH emerged as the foremost factors influencing these profiles. This study enhanced our comprehension of the variations in ARG profiles within canal networks, which may contribute to the design of efficient management approaches aimed at restraining the propagation of ARGs.

Variations in antibiotic resistomes associated with archaeal, bacterial, and viral communities affected by integrated rice-fish farming in the paddy field ecosystem

Antibiotic resistance genes (ARGs) serving as a newly recognized pollutant that poses potential risks to global human health, which in the paddy soil can be potentially altered by different agricultural production patterns. To elucidate the impacts and mechanisms of the widely used and sustainable agricultural production pattern, namely integrated rice-fish farming, on the antibiotic resistomes, we applied metagenomic sequencing to assess ARGs, mobile genetic elements (MGEs), bacteria, archaea, and viruses in paddy soil. There were 20 types and 359 subtypes of ARGs identified in paddy soil. The integrated rice-fish farming reduced the ARG and MGE diversities and the abundances of dominant ARGs and MGEs. Significantly decreased ARGs were mainly antibiotic deactivation and regulator types and primarily ranked level IV based on their potential threat to human health. The integrated rice-fish farming decreased the alpha diversities and altered microbial community compositions. MGEs, bacteria, archaea, and virus exhibited significant correlations with ARGs, while integrated rice-fish farming effectively changed their interrelationships. Viruses, bacteria, and MGEs played crucial roles in affecting the ARGs by the integrated rice-fish farming. The most crucial pathway by which integrated rice-fish farming affected ARGs was through the modulation of viral communities, thereby directly or indirectly influencing ARG abundance. Our research contributed to the control and restoration of ARGs pollution from a new perspective and providing theoretical support for the development of clean and sustainable agricultural production.

Phages in sludge from the A/O wastewater treatment process play an important role in the transmission of ARGs

Phages can influence the horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs) through transduction, but their profiles and effects on the transmission of ARGs are unclear, especially in complex swine sludge. In this study, we investigated the characterization of phage and ARG profiles in sludge generated from anoxic/oxic (A/O) wastewater treatment processes on swine farms using metagenomes and viromes. The results demonstrated that 205-221 subtypes of ARGs could be identified in swine sludge, among which sul1, tet(M), and floR were the dominant ARGs, indicating that sludge is an important reservoir of ARGs, especially in sludge (S) tanks. The greater abundance of mobile genetic elements (MGEs) in the S tank could significantly contribute to the greater abundance of ARGs there compared to the anoxic (A) and oxic (O) tanks (P < 0.05). However, when we compared the abundances of ARGs and MGEs in the A and O tanks, we observed opposite significant differences (P < 0.05), suggesting that MGEs are not the only factor influencing the abundance of ARGs. The high proportion of lysogenic phages in sludge from the S tank can also have a major impact on the ARG profile. Siphoviridae, Myoviridae, and Podoviridae were the dominant phage families in sludge, and a network diagram of bacteria-ARG-phages revealed that dominant phages and bacteria acted simultaneously as potential hosts for ARGs, which may have led to phage-mediated HGT of ARGs. Therefore, the risk of phage-mediated HGT of ARGs cannot be overlooked.

Insights into microbial contamination and antibiotic resistome traits in pork wholesale market: An evaluation of the disinfection effect of sodium hypochlorite

Chlorine and its derivatives, such as sodium hypochlorite (NaClO) and chlorine dioxide, are frequently employed as disinfectants throughout the pork supply chain in China. Nevertheless, the extensive use of NaClO has the potential to cause the creation of 'chlorine-tolerant bacteria' and accelerate the evolution of antibiotic resistance. This study evaluated the efficacy of NaClO disinfection by examining alterations in the microbiome and resistome of a pork wholesale market (PWM), and bacteria isolation and analysis were performed to validate the findings. As expected, the taxonomic compositions of bacteria was significantly different before and after disinfection. Notably, Salmonella enterica (S. enterica), Salmonella bongori (S. bongori), Escherichia coli (E. coli), Klebsiella pneumoniae (K. pneumoniae), and Pseudomonas aeruginosa (P. aeruginosa) were observed on all surfaces, indicating that the application of NaClO disinfection treatment in PWM environments for pathogenic bacteria is limited. Correlations were identified between antibiotic resistance genes (ARGs) associated with aminoglycosides (aph(3'')-I, aph(6')-I), quinolone (qnrB, abaQ), polymyxin (arnA, mcr-4) and disinfectant resistance genes (emrA/BD, mdtA/B/C/E/F). Furthermore, correlations were found between risk Rank I ARGs associated with aminoglycoside (aph(3')-I), tetracycline (tetH), beta_lactam (TEM-171), and disinfectant resistance genes (mdtB/C/E/F, emrA, acrB, qacG). Importantly, we found that Acinetobacter and Salmonella were the main hosts of disinfectant resistance genes. The resistance mechanisms of the ARGs identified in PWM were dominated by antibiotic deactivation (38.7%), antibiotic efflux (27.2%), and antibiotic target protection (14.4%). The proportion of genes encoding efflux pumps in the PWM resistome increased after disinfection. Microbial cultures demonstrated that the traits of microbial contamination and antibiotic resistane were consistent with those observed by metagenomic sequencing. This study highlights the possibility of cross-resistance between NaClO disinfectants and antibiotics, which should not be ignored.

Simultaneous extraction and detection of DNA and RNA from viruses, prokaryotes, and eukaryotes in wastewater using a modified COPMAN

Wastewater surveillance can offer a comprehensive grasp of infectious disease prevalence and human health because wastewater contains various human-derived microbial pathogens, including viruses, bacteria, and fungi. However, methods capable of simultaneous detection of multiple groups of targets in the automated systems and large-scale surveillance are still under development. Here, we demonstrated the modification, involving the addition of bead-beating, to the existing COPMAN (COagulation and Proteolysis method using MAgnetic beads for detection of Nucleic acids in wastewater) enabled enhanced detection of various microorganisms, including SARS-CoV-2. The modified method, termed bead-beating COPMAN (BB-COPMAN), was evaluated through spike-and-recovery experiments and comparative analysis against three previously reported methods for simultaneous DNA/RNA detection. Our study targeted a range of microorganisms, including enveloped and non-enveloped RNA viruses (SARS-CoV-2, PMMoV), a DNA virus (crAssphage), archaea, gram-negative and gram-positive bacteria (E. coli, Lachnospiraceae), antibiotic resistance gene (ampC), and fungi (Candida albicans). The recovery rates of BB-COPMAN for gram-negative and gram-positive bacteria were 17 and 2.1-fold higher, respectively, compared to the method for DNA/RNA detection. Additionally, BB-COPMAN exhibited the highest extraction efficiency among the tested methods, achieving 1.2-5.7 times more DNA and 1.1-69 times more RNA yield on average. BB-COPMAN allowed the detection of SARS-CoV-2 from all nine samples and PMMoV at concentrations 39-97 times higher than other methods. Moreover, BB-COPMAN detected larger amounts of DNA for four out of six DNA targets than the previously reported DNA/RNA detection method. These results demonstrated that BB-COPMAN enables enhanced detection of multiple targets in a single flow of nucleic acid extraction, making the method well-suited for automated systems. In conclusion, BB-COPMAN is a promising method in wastewater surveillance for assessing the prevalence of wide range of pathogenic microorganisms.

Methionine influences the profile of intestinal antibiotic resistome through inhibiting the growth of Escherichia coli

Antibiotic resistance genes (ARGs) are a new type of environmental pollutant. However, studies have mainly focused on the distribution characteristics of ARGs in the livestock environment, lacking of studies on the composition of ARGs in the intestinal tract of animals and the effect of nutrients on intestinal ARGs and microbial communities. Reducing antimicrobial resistance and maintaining optimal animal health and performance are urgently needed. Methionine is an essential amino acid which plays a critical role in the growth and reproductive performance of animals. In this study, feeding experiment, in vitro fermentation and bacterial culture experiment were performed to explore the influence of methionine on the intestinal resistome of sows. We found that dietary 0.2 % methionine supplementation decreased the total abundance of intestinal ARGs, which was further confirmed by in vitro fecal microbial fermentation of sows. Metagenome binning analysis identified that Escherichia coli was the major ARG host, which carried 60-113 ARGs and 134-286 virulence factors, indicating that Escherichia coli in the pig intestine is not only a core ARG host, but also an important pathogen. In addition, we found that methionine supplementation inhibited the growth of Escherichia coli, indicating that dietary methionine may reduce the resistome risk in sow intestine by inhibiting core ARG hosts such as Escherichia coli. These findings reveal that dietary methionine application plays a critical role in intestinal antibiotic resistance, providing a new idea for preventing and controlling environmental pollution by antibiotic-resistant microbes.

The Antibiotic Resistome and Its Association with Bacterial Communities in Raw Camel Milk from Altay Xinjiang

Raw camel milk is generally contaminated with varied microbiota, including antibiotic-resistant bacteria (ARB), that can act as a potential pathway for the spread of antibiotic resistance genes (ARGs). In this study, high-throughput quantitative PCR and 16S rRNA gene-based Illumine sequencing data were used to establish a comprehensive understanding of the antibiotic resistome and its relationship with the bacterial community in Bactrian camel milk from Xinjiang. A total of 136 ARGs and up to 1.33 × 108 total ARG copies per gram were identified, which predominantly encode resistance to β-lactamas and multidrugs. The ARGs' profiles were mainly explained by interactions between the bacteria community and physicochemical indicators (77.9%). Network analysis suggested that most ARGs exhibited co-occurrence with Corynebacterium, Leuconostoc and MGEs. Overall, raw camel milk serves as a reservoir for ARGs, which may aggravate the spread of ARGs through vertical and horizontal gene transfer in the food chain.

Climate and nutrients regulate biographical patterns and health risks of antibiotic resistance genes in mangrove environment

Mangroves are prone to receive pollutants and act as a sink for antibiotic resistance genes (ARGs). However, knowledge of the human health risk of ARGs and its influencing factors in mangrove ecosystems is limited, particularly at large scales. Here, we applied a high-throughput sequencing technique combined with an ARG risk assessment framework to investigate the profiles of ARGs and their public health risks from mangrove wetlands across South China. We detected 456 ARG subtypes, and found 71 of them were identified as high-risk ARGs, accounting for 0.25 % of the total ARG abundance. Both ARGs and bacterial communities showed a distance-decay biogeography, but ARGs had a steeper slope. Linear regression analysis between features of co-occurrence network and high-risk ARG abundance implies that greater connections in the network would result in higher health risk. Structural equation models showed that geographic distance and MGEs were the most influential factors that affected ARG patterns, ARGs and MGEs contributed the most to the health risk profiles in mangrove ecosystems. This work provides a novel understanding of biogeographic patterns and health risk assessment of ARGs in mangrove ecosystems and can have profound significance for mangrove environment management with regard to ARG risk control.

Removal of antibiotic resistance genes during livestock wastewater treatment processes: Review and prospects

Antibiotic resistance genes (ARGs) are emerging pollutants that have received extensive attention. Many different types of ARGs exist in livestock wastewater. If not effectively treated, they can threaten animal production, public health and the ecological safety of the surrounding environment. To address the high risk of livestock wastewater contamination by ARGs, the effects of different wastewater treatment processes on ARGs and their influencing factors and mechanisms are reviewed herein. Additionally, the current problems associated with removal of ARGs are discussed, and future research is proposed.