Modeling the fate of antibiotic resistance genes and class 1 integrons during thermophilic anaerobic digestion of municipal wastewater solids

Combined virome analysis and metagenomic sequencing to reveal the viral communities and risk of virus-associated antibiotic resistance genes during composting

The issue of antibiotic resistance genes (ARGs) pollution in manure has garnered significant attention, with viruses now being recognized as crucial carriers and disseminators of ARGs. However, the virus-associated ARG profiles and potential health risks in composts are still unclear. In this study, the viral communities and associated ARGs in biogas residue and pig faeces composts were profiled by virome analysis. The viral communities were dominated by Caudovirales, and non-thermophilic viruses were inactivated during composting. The diversity and abundance of ARGs were lower in virome than in metagenome, while ARGs' risk was greater in virome than in metagenome. There were six bacterial genera identified as viral hosts at the genomic level, Pseudomonas and Clostridium carried high-risk ARGs. Virus-associated ARGs in viral hosts had a higher risk rank than non-virus-associated ARGs. Composting reduced the diversity, abundance and risk of viral ARGs. The risk of ARGs in biogas residues was significantly lower than that of pig faeces in the initial period of composting, and the two different substracts equally less harmful after composting. These results revealed that viruses play a non-negligible role in spreading ARGs, posing high risk to environmental and human health.

Risk control of antibiotics, antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB) during sewage sludge treatment and disposal: A review

Sewage sludge is an important reservoir of antibiotics, antibiotic resistance genes (ARGs), and antibiotic resistant bacteria (ARB) in wastewater treatment plants (WWTPs), and the reclamation of sewage sludge potentially threats human health and environmental safety. Sludge treatment and disposal are expected to control these risks, and this review summarizes the fate and controlling efficiency of antibiotics, ARGs, and ARB in sludge involved in different processes, i.e., disintegration, anaerobic digestion, aerobic composting, drying, pyrolysis, constructed wetland, and land application. Additionally, the analysis and characterization methods of antibiotics, ARGs, and ARB in complicate sludge are reviewed, and the quantitative risk assessment approaches involved in land application are comprehensively discussed. This review benefits process optimization of sludge treatment and disposal, with regard to environmental risks control of antibiotics, ARGs, and ARB in sludge. Furthermore, current research limitations and gaps, e.g., the antibiotic resistance risk assessment in sludge-amended soil, are proposed to advance the future studies.

A review on antibiotics removal: Leveraging the combination of grey and green techniques

Antibiotics are currently a major source of concern around the world due to the serious risks posed to human health and the environment. The performance of the secondary wastewater treatment processes/technologies (representing grey process) and constructed wetlands (CWs) (typical green process) in removing antibiotics and antibiotic resistance genes (ARG) was reviewed. The result showed that the grey process mainly removes antibiotics, but does not significantly remove ARG, and some processes may even cause ARG enrichment. The overall treatment in CWs is better than WWTPs, especially for ARG. Vertical subsurface flow CWs (VFCWs) are more conductive to antibiotics removal, while horizontal subsurface flow CWs (HFCWs) have a better ARG removal. More importantly, this review admits and suggests that the combination of grey process with green process is an effective strategy to remove antibiotics and ARG. The most advantage of the combination lies in realizing complementary advantages, i.e. the grey process as the primary treatment while CWs as the polishing stage. The efficiency of such the hybrid system is much higher than either single treatment process.

Tracking antibiotic resistance through the environment near a biosolid spreading ground: Resistome changes, distribution, and metal(loid) co-selection

The application of urban wastewater treatment plants (WWTPs) products to agricultural lands has contributed to the rising level of antibiotic resistance and drawn a critical public health concern. It has not been thoroughly investigated at which spatial scales a biosolid applied area as a potentially predominant source affects surrounding soil resistomes. This study investigated distribution and impact of WWTP biosolids treated with anaerobic digestion on an agricultural area. Heterotrophic plate counts (HPCs) and quantitative polymerase chain reaction (qPCR) were performed for detection of selected antibiotic-resistant bacteria (ARB), selected antibiotic resistance genes (ARGs), intI1 genes, and 16S rRNA genes. Biosolid samples contained significantly higher levels of selected ARGs than the raw agricultural soils (p < 0.05). The average relative abundances of intI1, sul1, bla_SHV, and ermB genes were significantly higher in biosolid-amended soils than nearby agricultural soils (p < 0.05). Spatial interpolation analysis of relative gene abundances of intI1, sul1, sul2, and tetW across the studied area further indicated directional trends towards the northwest and southeast directions, highlighting possible airborne spread. Concentrations of Co, Cu, Ni, and Fe were found to be significantly and positively correlated with relative abundances of intI1, sul1, and tetW genes (p < 0.05). The resistance ratios of culturable antibiotic-resistant bacteria in agricultural soils with biosolid amendments were generally identical to those without biosolid amendments. This study will advance the understanding of the antibiotic resistome in agricultural soils impacted by long-term waste reuse and inform the evaluation strategies for future biosolids application and management.

Identification of factors affecting removal of antibiotic resistance genes in full-scale anaerobic digesters treating organic solid wastes

Efficiencies of removing antibiotic resistance genes (ARGs) and intI1 were explored using eight full-scale anaerobic digesters. The digesters demonstrated different characteristics on the basis of substrate types (food waste, manure or sludge); configuration (single or two-stage); temperature (psychrophilic, mesophilic or thermophilic); hydraulic retention time (HRT) (9.7-44 days); and operation mode (continuous stirred tank reactor or plug flow reactor). Digesters' configuration or operating parameters showed a greater effect on abundance of ARGs than the type of input substrate. Redundancy analysis (RDA) accounted for 85.2% of the total variances and digesters with the same configuration and operational conditions showed similar performance for removal of ARGs. The highest efficiencies of removing ARGs (99.99%) were observed in two-stage thermophilic digesters with relatively long HRTs (32 days). The lowest removal efficiency (97.93%) was observed in single-stage mesophilic with relatively short HRTs (9.7 days), likely due to vertical and horizontal gene transfer.

Quantification of antibiotic resistance genes and mobile genetic in dairy manure

Background

Antibiotic resistance genes (ARGs) are considered to be emerging environmental contaminants of concern potentially posing risks to human and animal health, and this research studied the prevalence of antimicrobial resistance in dairy manure.

Methods

This study is focused on investigating prevalence of ARGs in California dairy farm manure under current common different manure management. A total of 33 manure samples were collected from multiple manure treatment conditions: (1) flushed manure (FM), (2) fresh pile (FP), (3) compost pile (CP), (4) primary lagoon (PL), and (5) secondary lagoon (SL). After DNA extraction, all fecal samples were screened by PCR for the presence of eight ARGs: four sulfonamide ARGs (sulI, sulII, sulIII, sulA), two tetracycline ARGs (tetW, tetO), two macrolide-lincosamide-streptogramin B (MLS_B) ARGs (ermB, ermF). Samples were also screened for two mobile genetic elements (MGEs) (intI1, tnpA), which are responsible for dissemination of ARGs. Quantitative PCR was then used to screen all samples for five ARGs (sulII, tetW, ermF, tnpA and intI1).

Results

Prevalence of genes varied among sample types, but all genes were detectable in different manure types. Results showed that liquid-solid separation, piling, and lagoon conditions had limited effects on reducing ARGs and MGEs, and the effect was only found significant on tetW (p = 0.01). Besides, network analysis indicated that sulII was associated with tnpA (p < 0.05), and Psychrobacter and Pseudomonas as opportunistic human pathogens, were potential ARG/MGE hosts (p < 0.05). This research indicated current different manure management practices in California dairy farms has limited effects on reducing ARGs and MGEs. Improvement of different manure management in dairy farms is thus important to mitigate dissemination of ARGs into the environment.

Distribution of antibiotic resistance genes in the environment

The prevalence of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in the microbiome is a major public health concern globally. Many habitats in the environment are under threat due to excessive use of antibiotics and evolutionary changes occurring in the resistome. ARB and ARGs from farms, cities and hospitals, wastewater treatment plants (WWTPs) or as water runoffs, may accumulate in water, soil, and air. We present a global picture of the resistome by examining ARG-related papers retrieved from PubMed and published in the last 30 years (1990-2020). Natural Language Processing (NLP) was used to retrieve 496,640 papers, out of which 9374 passed the filtering test and were further analyzed to determine the distribution and diversity of ARG subtypes. The papers revealed seven major antibiotic families together with their respective ARG subtypes in different habitats on six continents. Asia, especially China, had the highest number of ARGs related papers compared to other countries/regions/continents. ARGs belonging to multidrug, glycopeptide, and β-lactam families were the most common in reports from hospitals and sulfonamide and tetracycline families were common in reports from farms, WWTPs, water and soil. We also highlight the 'omics' tools used in resistome research, describe some factors that shape the development of resistome, and suggest future work needed to better understand the resistome. The goal was to show the global nature of ARB and ARGs in order to encourage collaborate research efforts aimed at reducing the negative impacts of antibiotic resistance on the One Health concept.

Degradation of antibiotic resistance genes and mobile gene elements in dairy manure anerobic digestion

Antibiotic resistance genes (ARGs) are emerging contaminants causing serious global health concern. Interventions to address this concern include improving our understanding of methods for treating waste material of human and animal origin that are known to harbor ARGs. Anaerobic digestion is a commonly used process for treating dairy manure, and although effective in reducing ARGs, its mechanism of action is not clear. In this study, we used three ARGs to conducted a longitudinal bench scale anaerobic digestion experiment with various temperatures (28, 36, 44, and 52°C) in triplicate using fresh dairy manure for 30 days to evaluate the reduction of gene abundance. Three ARGs and two mobile genetic elements (MGEs) were studied: sulfonamide resistance gene (sulII), tetracycline resistance genes (tetW), macrolide-lincosamide-streptogramin B (MLSB) superfamily resistance genes (ermF), class 1 integrase gene (intI1), and transposase gene (tnpA). Genes were quantified by real-time quantitative PCR. Results show that the thermophilic anaerobic digestion (52°C) significantly reduced (p < 0.05) the absolute abundance of sulII (95%), intI1 (95%), tnpA (77%) and 16S rRNA gene (76%) after 30 days of digestion. A modified Collins–Selleck model was used to fit the decay curve, and results suggest that the gene reduction during the startup phase of anaerobic digestion (first 5 days) was faster than the later stage, and reductions in the first five days were more than 50% for most genes.

The impact of antimicrobials on the efficiency of methane fermentation of sewage sludge, changes in microbial biodiversity and the spread of antibiotic resistance

The study was designed to simultaneously evaluate the influence of high doses (512-1024 µg/g) the most commonly prescribed antimicrobials on the efficiency of anaerobic digestion of sewage sludge, qualitative and quantitative changes in microbial consortia responsible for the fermentation process, the presence of methanogenic microorganisms, and the fate of antibiotic resistance genes (ARGs). The efficiency of antibiotic degradation during anaerobic treatment was also determined. Metronidazole, amoxicillin and ciprofloxacin exerted the greatest effect on methane fermentation by decreasing its efficiency. Metronidazole, amoxicillin, cefuroxime and sulfamethoxazole were degraded in 100%, whereas ciprofloxacin and nalidixic acid were least susceptible to degradation. The most extensive changes in the structure of digestate microbiota were observed in sewage sludge exposed to metronidazole, where a decrease in the percentage of bacteria of the phylum Bacteroidetes led to an increase in the proportions of bacteria of the phyla Firmicutes and Proteobacteria. The results of the analysis examining changes in the concentration of the functional methanogen gene (mcrA) did not reflect the actual efficiency of methane fermentation. In sewage sludge exposed to antimicrobials, a significant increase was noted in the concentrations of β-lactam, tetracycline and fluoroquinolone ARGs and integrase genes, but selective pressure was not specific to the corresponding ARGs.

Antibiotic resistance gene dissipation in soil microcosms amended with antibiotics and swine manure

The use of antibiotics in animal agriculture has exacerbated the presence of both antibiotic resistance genes (ARGs) and residual antibiotics excreted in animal manure. Field application of this manure is a common practice because its nutrient rich material can benefit crop growth. However, this practice can also introduce antibiotics and ARGs into nonagricultural settings. The integration of prairie buffer strips within and at the edge of crop fields is a potential management solution to reduce concentrations of ARGs commonly transported via water runoff and infiltration. An incubation experiment was conducted to investigate the fate of ARGs in directly manured crop field soils and the surrounding affected prairie strip soils. Row crop and prairie strip soils sampled from three sites received either an antibiotic spike and swine manure addition or a control water addition. The concentrations of select ARGs were then monitored over a 72-d period. Although soil vegetation and site location were not observed to influence ARG dissipation, the select genes did display different half-lives from one another. For example, tetM demonstrated the fastest dissipation of the genes quantified (average half-life, 5.18 d). Conversely, sul1 did not conform to the first-order linear regression kinetics used to describe the other investigated genes and was highly abundant in control prairie strip soils. The quantified half-lives of these select ARGs are comparable to previous studies and can inform monitoring and mitigative efforts aimed at reducing the spread of ARGs in the environment.

Metagenomic Quantification of Genes with Internal Standards

qPCR and metagenomics are central molecular techniques that have offered insights into biological processes for decades, from monitoring spatial and temporal gene dynamics to tracking ARGs or pathogens. Still needed is a tool that can quantify thousands of relevant genes in a sample as gene copies per sample mass or volume.

We demonstrate that an assembly-independent and spike-in facilitated metagenomic quantification approach can be used to screen and quantify over 2,000 genes simultaneously, while delivering absolute gene concentrations comparable to those for quantitative PCR (qPCR). DNA extracted from dairy manure slurry, digestate, and compost was spiked with genomic DNA from a marine bacterium and sequenced using the Illumina HiSeq4000. We compared gene copy concentrations, in gene copies per mass of sample, of five antimicrobial resistance genes (ARGs) generated with (i) our quantitative metagenomic approach, (ii) targeted qPCR, and (iii) a hybrid quantification approach involving metagenomics and qPCR-based 16S rRNA gene quantification. Although qPCR achieved lower quantification limits, the metagenomic method avoided biases caused by primer specificity inherent to qPCR-based methods and was able to detect orders of magnitude more genes than is possible with qPCR assays. We used the approach to simultaneously quantify ARGs in the Comprehensive Antimicrobial Resistance Database (CARD). We observed that the total abundance of tetracycline resistance genes was consistent across different stages of manure treatment on three farms, but different samples were dominated by different tetracycline resistance gene families.

Prevalence and characterization of oxazolidinone and phenicol cross-resistance gene optrA in enterococci obtained from anaerobic digestion systems treating swine manure

The use of the phenicol antibiotic florfenicol in livestock can select for the optrA gene, which also confers resistance to the critically important oxazolidinone antibiotic linezolid. However, the occurrence and dissemination of florfenicol and linezolid cross-resistance genes in anaerobic treatment systems for livestock waste are unknown. Herein, the phenotypes and genotypes (optrA, fexA, fexB, and cfr) of florfenicol and linezolid cross-resistance were investigated in 339 enterococci strains isolated from lab- and full-scale mesophilic anaerobic digestion systems treating swine waste. It was found that optrA, fexA, and fexB were frequently detected in isolated enterococci in both systems by PCR screening, whereas cfr was not detected. The most abundant gene was optrA, which was detected in 73.5% (n = 50) and 38.9% (n = 23) of enterococci isolates in the full-scale influent and effluent, respectively. Most strains carried more than two resistance genes, and the average percentage of co-occurrence of optrA/fexA was 16.6%. Based on minimum inhibitory concentrations of the enterococci strain phenotypes, 85.7%, 77.5%, and 77.5% of strains in influent were resistant to chloramphenicol, florfenicol, and linezolid, respectively, while 56.3%, 65.2%, and 13% in the effluent isolates were found, respectively, which was consistent with the genotype results. The phenotypes and genotypes of florfenicol and linezolid resistance were relative stable in the enterococci isolated from the influent and effluent in lab-scale anaerobic digestion system. The findings signify the enterococci isolates harboring the optrA gene remained in effluents of both full- and lab-scale swine waste anaerobic digestion system; hence, effective management strategies should be implemented to prevent the discharge of antibiotic resistance from the livestock waste treatment systems.

Increased (Antibiotic-Resistant) Pathogen Indicator Organism Removal during (Hyper-)Thermophilic Anaerobic Digestion of Concentrated Black Water for Safe Nutrient Recovery

Source separated toilet water is a valuable resource for energy and fertilizers as it has a high concentration of organics and nutrients, which can be reused in agriculture. Recovery of nutrients such as nitrogen, phosphorous, and potassium (NPK) decreases the dependency on energy-intensive processes or processes that rely on depleting natural resources. In new sanitation systems, concentrated black water (BW) is obtained by source-separated collection of toilet water. BW-derived products are often associated with safety issues, amongst which pathogens and antibiotic-resistant pathogens. This study presents results showing that thermophilic (55–60 °C) and hyperthermophilic (70 °C) anaerobic treatments had higher (antibiotic-resistant) culturable pathogen indicators removal than mesophilic anaerobic treatment. Hyperthermophilic and thermophilic anaerobic treatment successfully removed Escherichia coli and extended-spectrum β-lactamases producing E. coli from source-separated vacuum collected BW at retention times of 6–11 days and reached significantly higher removal rates than mesophilic (35 °C) anaerobic treatment (p < 0.05). The difference between thermophilic and hyperthermophilic treatment was insignificant, which justifies operation at 55 °C rather than 70 °C. This study is the first to quantify (antibiotic-resistant) E. coli in concentrated BW (10–40 gCOD/L) and to show that both thermophilic and hyperthermophilic anaerobic treatment can adequately remove these pathogen indicators.

Comparing the fate of antibiotic resistance genes in two full-scale thermophilic anaerobic digestion plants treating food wastewater

This study focus on the fate of ARGs in the full-scale AD of food wastewater (FWW). Residue was collected from two different full-scale thermophilic AD treating FWW. Ten selected ARGs, including tetracycline resistance genes (tetM, tetX, tetQ, tetH and tetG), sulfonamide resistance genes (sul1 and sul2), quinolone resistance genes (qnrD) and macrolide resistance genes (ermB and ermC), were amplified using quantitative polymerase chain reaction (qPCR). Furthermore, the class 1 integron-integrase gene (intI1) was selected as a representative mobile gene element. Remarkable reduction in the ARGs and intI1 was observed in two-stage (acidogenic-methanogenic) AD, particularly, tetG, tetH, tetM, tetQ, tetX and intI1 not detected. Additionally, significant positive correlation (p < 0.01) between ARGs and intI1 suggested a strong likelihood of horizontal gene transfer (HGT). Furthermore, stepwise multiple linear regression analysis revealed significant factors related to the fate of individual ARGs and intI1 during AD.

Determining the composition of bacterial community and relative abundance of specific antibiotics resistance genes via thermophilic anaerobic digestion of sewage sludge

In this study, the effects of different temperature transitions on the dynamics of antibiotic resistance genes (ARGs) and bacterial community were investigated during start-up of thermophilic anaerobic digestion (AD) of sewage sludge. Although two thermophilic reactors showed dissimilar removal efficiencies of ARGs in batch mode, both the removal efficiency and reduction patterns of ARGs were similar in continuous stirred tank reactor (CSTR) mode, resulting in significant reduction of the total sum of the relative abundance of ARGs. Using network analysis to explore the correlation between bacterial community and some specific ARGs revealed that composition of the bacterial community played a vital role in the fluctuations in the relative abundance of the antibiotic resistome, demonstrating that shaping the development of ARGs was facilitated by vertical gene transfer. To facilitate eliminating ARGs, minimizing their hosts which persist even under long-term operations is vital in thermophilic AD.

Effect of nutritional energy regulation on the fate of antibiotic resistance genes during composting of sewage sludge

Sludge composting is increasingly adopted due to its end product for application as a soil nourishment amendment. Although the ratio of C/N is significant in the quality and process of composting, little information has been obtained from the effects of nutritional energy (carbon and nitrogen) on the fate of antibiotic resistance genes (ARGs) during sludge composting. Dynamic variations of ARGs, microbial community as well as functional characteristics during composting of sludge were investigated in this study. Three levels of carbon to nitrogen (20:1, 25:1 and 30:1) were developed for the composting of sludge with fermented straw plus a control which was just sewage sludge (C/N = 9.5:1). A novel finding of this work is that the highest initial C/N ratio (30:1) could prolong the thermophilic period, which was helpful to reduce some target ARGs. Some ARGs (sul1, sul2, and aadA1) had negative correlation with multiple metabolic pathways, which were difficult to remove.

Degradation of antibiotics and antibiotic resistance genes in erythromycin fermentation residues using radiation coupled with peroxymonosulfate oxidation

Ionizing radiation coupled with peroxymonosulfate (PMS) oxidation was developed to degrade antibiotics and antibiotic resistance genes (ARGs) from the erythromycin fermentation (EryF) residual wastes. The experimental results showed that the ERY content and ARGs abundance decreased with increase of the absorbed dose and PMS dosage and gamma irradiation was more effective to abate ARGs from the EryF wastes. The removal efficiency of ERY reached 49-55% and more than 96-99% of ARGs (1.32-2.55 log) was eliminated with the absorbed dose of 25-50 kGy and PMS dosage of 50-100 mM. Illumina pyrosequencing revealed that 3 bacterial phyla, Proteobacteria, Firmicutes and Fusobacteria were highly enriched and the ARGs-linked hosts were affiliated to the genera Aeromonas, Enterobacteriaceae and Enterobacter in the phylum Proteobacteria. The abundance of the ARGs-linked bacteria decreased by gamma/PMS treatment. Ionizing radiation/PMS treatment with the doses of 25 kGy and 50 mM PMS is proposed for potential practical application.

Additional reduction of antibiotic resistance genes and human bacterial pathogens via thermophilic aerobic digestion of anaerobically digested sludge

Thermophilic aerobic digestion (TAD) was applied to further reduce ARGs and heavy metal resistance genes (HMRGs) as well as class 1 integrons (intI1) in sludge from anaerobic digestion (AnD). Unlike after AnD, there was no enrichment of ARGs, HMRGs and intI1 after TAD. Residual gene fractions of intI1 and total ARGs (sum of targeted ARGs) were 0.03 and 0.08, respectively. Two kinetic models (Collins-Selleck and first-order) described the decay patterns of targeted genes, revealing rapid removal of intI1 during TAD. After TAD, the relative abundance of human bacterial pathogens (HBPs) and the numbers of HBPs species decreased to approximately 68% and 64% compared to anaerobically digested sludge, respectively. Thus, TAD, subsequent to AnD, may possess high potential for reducing biological risks resulting from ARGs, HMRGs, intI1 and HBPs in sewage sludge.

Fate of antibiotic resistance genes and antibiotic-resistant bacteria in water resource recovery facilities

Many important diseases are showing resistance to commonly used antibiotics, and the resistance is potentially caused by widespread use of antibiotics for maintaining human health and improving food production. Antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) are associated with this increase, and their fate in water resource recovery facilities is an important, emerging area of research. This literature review summarizes current findings of worldwide research on the fate of ARB and ARGs in various types of treatment plants. Twenty-five published studies were reviewed which contained 215 observations in activated sludge, membrane bioreactors, anaerobic digestion, constructed wetlands, coagulation-filtration, and three types of disinfection. We found 70% decreased observations, 18% increased observations, and 12% unchanged observations of all observations in all treatment processes. Resistance genes to tetracycline were most often observed, but more studies are needed in other antibiotic resistance genes. The causes for increased abundance of ARGs and ARB are not well understood, and further studies are warranted. PRACTITIONER POINTS: Antibiotic resistance is increasing with concern that treatment plants may acclimate bacteria to antibiotics. A literature survey found 215 resistance observations with 70% decreased, 18% increased, 12% unchanged after treatment. The type of treatment process is important with activated sludge showing the greatest reductions.

Factors influencing the fate of antibiotic resistance genes during thermochemical pretreatment and anaerobic digestion of pharmaceutical waste sludge

The prevalence of antibiotic resistance genes (ARGs) in waste sludge, especially for the pharmaceutical waste sludge, presents great potential risks to human health. Although ARGs and factors affecting their spreading are of major importance for human health, the factors influencing the fate of ARGs during sludge treatment, especially for pharmaceutical sludge treatment are not yet well understood. In order to be able to minimize ARGs spreading, it is important to find what is influencing their spreading. Therefore, certain factors, such as the sludge characteristics, bacterial diversity and community composition, and mobile genetic elements (MGEs) during the advanced AD of pharmaceutical sludge with different pretreatments were studied, and their affinity with ARGs was elucidated by Spearman correlation analysis. Furthermore, multiple linear regression was introduced to evaluate the importance of the various factors. Results showed that 59.7%-88.3% of the variations in individual ARGs and total ARGs can be explained by the corresponding factors. Bacterial diversity rather than specific bacterial community composition affected the fate of ARGs, whereas alkalinity was the most important factor on ARGs among all sludge characteristics investigated in this study. Besides, 66.4% of variation of total ARGs was driven by the changes of MGEs. Multiple linear regression models also reveal the collective effect of these factors on ARGs, and the contributions of each factor impact on ARGs. This study provides more comprehension about the factors impact on the fate of ARGs during pharmaceutical sludge treatment, and offers an approach to evaluate the importance of each factor, which method could be introduced for evaluation of factors influencing ARGs during other types of sludge or wastewater treatment.

Response of antibiotic and heavy metal resistance genes to two different temperature sequences in anaerobic digestion of waste activated sludge

Response of antibiotic resistance genes (ARGs) and heavy metal resistance genes (HMRGs) to two different temperature sequences (i.e., mesophilic-thermophilic and thermophilic-mesophilic) were investigated. Higher removal of total ARGs (twenty-one targeted subtypes) and HMRGs (three targeted subtypes) was achieved by the mesophilic-thermophilic sequence than by the thermophilic-mesophilic sequence. The sequence of mesophilic-thermophilic showed the highest removal of total ARGs, but the sequence of thermophilic-mesophilic proved more suitable for removal of class 1 integrons (intI1). Correlation analysis indicated that intI1 correlated significantly with tetG, tetQ, tetX, sul2, aac(6')-lb-cr, bla_TEM, ermB and floR. High-throughput sequencing revealed that the mesophilic-thermophilic sequence TPAD removed more human bacterial pathogens (HBPs) than did the thermophilic-mesophilic sequence. Also, significantly positive correlation was observed between ARGs and HBPs. For instance, Mycoplasma pneumonia showed significantly positive correlation with several ARGs including tetE, tetQ, tetX, tetZ, sul1, sul2, aac(6')-lb-cr and floR.

Impact of direct application of biogas slurry and residue in fields: In situ analysis of antibiotic resistance genes from pig manure to fields

Biogas slurry and residue contaminated with antibiotics are widely used as fertilizers in vegetable crop planting. However, their impact on the spreading of antibiotic resistance genes (ARGs) in vegetable fields is still largely unknown. In the present study, antibiotic resistant bacteria (ARB), ARGs and bacterial communities from pig manure to fields were monitored by using viable plate counts, high-throughput fluorescent quantitative PCR (HT-qPCR) and Illumina MiSeq sequencing. Eighty-three ARGs and 3 transposons genes were detected. Anaerobic digestion reduced relative abundance of tetracycline and Macrolide-Lincosamide-Streptogramin (MLSB) resistance genes. However, the number of ARB and the relative abundance of sulfa, aminoglycoside and florfenicol, chloramphenicol, and amphenicol (FCA) resistance genes, respectively, enriched up to 270 times and 52 times in biogas residue. Long-term application of biogas slurry and residue contaminated with antibiotics in fields increased the rate of ARB as well as relative abundance of ARGs and transposons genes. Additionally, bacterial communities significantly differed between the soil treated with biogas slurry and residue and the control sample, especially the phyla Bacteroidetes and Actinobacteria. Based on network analysis, 19 genera were identified as possible hosts of the detected ARGs. Our results provide an important significance for reasonable application of biogas slurry and residue.

Fate of antibiotic resistance genes and metal resistance genes during thermophilic aerobic digestion of sewage sludge

This study examines the fate of twenty-three representative antibiotic resistance genes (ARGs) encoding tetracyclines, sulfonamides, quinolones, β-lactam antibiotics, macrolides, florfenicol and multidrug resistance during thermophilic aerobic digestion (TAD) of sewage sludge. The bacterial community, class 1 integrons (intI1) and four metal resistance genes (MRGs) were also quantified to determine the key drivers of changes in ARGs during TAD. At the end of digestion, significant decreases in the quantities of ARGs, MRGs and intI1 as well as 16S rRNA genes were observed. Partial redundancy analysis (RDA) showed that shifts in temperature were the key factors affecting a decrease in ARGs. Shifts in temperature led to decreased amounts of ARGs by reducing resistome and bacterial diversity, rather than by lowering horizontal transfer potential via intI1 or co-resistance via MRGs.

Effect of Different Treatment Technologies on the Fate of Antibiotic Resistance Genes and Class 1 Integrons when Residual Municipal Wastewater Solids are Applied to Soil

Residual wastewater solids are a significant reservoir of antibiotic resistance genes (ARGs). While treatment technologies can reduce ARG levels in residual wastewater solids, the effects of these technologies on ARGs in soil during subsequent land-application are unknown. In this study we investigated the use of numerous treatment technologies (air drying, aerobic digestion, mesophilic anaerobic digestion, thermophilic anaerobic digestion, pasteurization, and alkaline stabilization) on the fate of ARGs and class 1 integrons in wastewater solids-amended soil microcosms. Six ARGs [erm(B), qnrA, sul1, tet(A), tet(W), and tet(X)], the integrase gene of class 1 integrons (intI1), and 16S rRNA genes were quantified using quantitative polymerase chain reaction. The quantities of ARGs and intI1 decreased in all microcosms, but thermophilic anaerobic digestion, alkaline stabilization, and pasteurization led to the most extensive decay of ARGs and intI1, often to levels similar to that of the control microcosms to which no wastewater solids had been applied. In contrast, the rates by which ARGs and intI1 declined using the other treatment technologies were generally similar, typically varying by less than 2 fold. These results demonstrate that wastewater solids treatment technologies can be used to decrease the persistence of ARGs and intI1 during their subsequent application to soil.

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.