High throughput profiling of antibiotic resistance genes in urban park soils with reclaimed water irrigation

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

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

Soil biota, antimicrobial resistance and planetary health

The concept of planetary health acknowledges the links between ecosystems, biodiversity and human health and well-being. Soil, the critical component of the interconnected ecosystem, is the most biodiverse habitat on Earth, and soil microbiomes play a major role in human health and well-being through ecosystem services such as nutrient cycling, pollutant remediation and synthesis of bioactive compounds such as antimicrobials. Soil is also a natural source of antimicrobial resistance, which is often termed intrinsic resistance. However, increasing use and misuse of antimicrobials in humans and animals in recent decades has increased both the diversity and prevalence of antimicrobial resistance in soils, particularly in areas affected by human and animal wastes, such as organic manures and reclaimed wastewater, and also by air transmission. Antimicrobials and antimicrobial resistance are two sides of the sword, while antimicrobials are essential in health care; globally, antimicrobial resistance is jeopardizing the effectiveness of antimicrobial drugs, thus threatening human health. Soil is a crucial pathway through which humans are exposed to antimicrobial resistance determinants, including those harbored by human pathogens. In this review, we use the nexus of antimicrobials and antimicrobial resistance as a focus to discuss the role of soil in planetary health and illustrate the impacts of soil microbiomes on human health and well-being. This review examines the sources and dynamics of antimicrobial resistance in soils and uses the perspective of planetary health to track the movement of antimicrobial-resistance genes between environmental compartments, including soil, water, food and air.

Synergistic effects of key parameters on the fate of antibiotic resistance genes during swine manure composting

Livestock manure is a reservoir of antibiotic resistance genes (ARGs), posing a potential risk to environment and human health. However, there has been no optimization study about the comprehensive composting treatment for livestock manure ARGs based on multiple operation factors. In this study, anaerobic composting of swine manure in light was conducted under different combined conditions of composting time, temperature, water content, pH, heavy metal passivators and wheat straw. The diversity and relative abundance of ARGs in the compost were detected using high throughput quantitative real-time PCR, and the concentrations of antibiotics and heavy metals were determined. The results showed that under the optimized conditions (composting time, 30 d; temperature, 50 °C; water content, 50%; pH 9.0; heavy metal passivators and wheat straw), compared with the control, the detected number of ARGs and mobile genetic elements in the compost was reduced by 45% and 27.3%, and their relative abundance decreased by 33.9% and 36.9%, respectively. Moreover, the exchangeable heavy metal content of the compost declined by 34.7-57.1%, and the antibiotic level decreased by 28.8-77.8%. This study proposes that synergistic effects of key parameters can effectively mitigate the combined contamination of ARGs, antibiotics, and heavy metals in swine manure. MAIN FINDING: Optimized parameters (anaerobic composting time 30 d, temperature 50 °C, water content 50%, pH 9.0) effectively mitigated the combined pollution of ARGs, antibiotics, and heavy metals in swine manure.

Comparison of Microbiomes and Resistomes in Two Karst Groundwater Sites in Chongqing, China

Karst groundwater is an important water resource, as it accounts for about 15% of the total landscape of the earth and supplies 20% of potable water worldwide. The antibiotics resistance is an emerging global concern, and antibiotics residual and increase of antibiotic resistance genes represent serious global concerns and emerging pollutants. There is no report on the antibiotic resistance genes in groundwater. To survey resistome and microbiome in karst groundwater, two karst water samples were chosen for metagenome and metatranscriptome study, namely the 37^th spring (C) and Dongcao spring (R) in Beibei, Chongqing, China. The two sites differ significantly in sulfur content, geochemical parameters, community structure, antibiotic resistance genes, and mechanisms, and these results may be influenced by anthropogenic activities. Combining with the Antibiotic Resistance Genes Database, three types of resistance genes baca, sul2, sul1 are present in R and C, and ant3ia, ermc, tetpa are also present in R. The number of all resistance genes in R was more than C, and Proteobacteria, Bacteroidetes, Nitrospirae are the main sources of antibiotic resistance genes. In addition, a large number of genes related to antibiotic gene transmission and drug resistance were found in both samples. Karst groundwater is an important source of drinking water and a possible venue for the transmission of microbial antibiotic resistance genes. However, few studies addressed this issue in karst groundwater, despite its widespread and great importance to global ecosystem. Karst groundwater is a reservoir for antibiotic resistant genes, and measures to control these resistant genes are urgently needed.

Antimicrobial resistance genes present in the faecal microbiota of free-living Galapagos tortoises (Chelonoidis porteri)

Antimicrobial resistance (AMR), encoded by plasmid-mediated AMR genes (ARGs), is an increasing global public health threat. Wildlife play a fundamental role as sentinels, reservoirs and potential vectors of ARGs. For the first time in Galapagos, we have identified and quantified the presence of ARGs in free-living giant tortoises (Chelonoidis porteri). We performed ARG analyses by quantitative PCR of faeces collected from the cloaca of 30 tortoises widely distributed across Santa Cruz Island. Validated samples (n = 28) were analysed by a panel of up to 21 different ARGs and all 28 tortoise samples were positive to one or more genes encoding resistance. Thirteen of 21 tested ARGs were present in at least one sample, and 10 tortoises (35.7%) had a multi-resistant pattern. We recommend additional research so we may more fully understand resistance patterns across taxa and geographical locations throughout the Galapagos archipelago, and the implications of ARGs for the health of wildlife, domestic animals, and humans. In this study, we found 100% of sampled giant tortoises had ARGs present in their faeces, suggesting a large-scale distribution of these genes within the archipelago.

Abundance of antibiotic resistance genes and their association with bacterial communities in activated sludge of wastewater treatment plants: Geographical distribution and network analysis

Wastewater treatment plants (WWTPs) are deemed reservoirs of antibiotic resistance genes (ARGs). Bacterial phylogeny can shape the resistome in activated sludge. However, the co-occurrence and interaction of ARGs abundance and bacterial communities in different WWTPs located at continental scales are still not comprehensively understood. Here, we applied quantitative PCR and Miseq sequence approaches to unveil the changing profiles of ARGs (sul1, sul2, tetW, tetQ, tetX), intI1 gene, and bacterial communities in 18 geographically distributed WWTPs. The results showed that the average relative abundance of sul1and sul2 genes were 2.08 × 10^-1 and 1.32 × 10^-1 copies/16S rRNA copies, respectively. The abundance of tetW gene was positively correlated with the Shannon diversity index (H'), while both studied sul genes had significant positive relationship with the intI1gene. The highest average relative abundances of sul1, sul2, tetX, and intI1 genes were found in south region and oxidation ditch system. Network analysis found that 16 bacterial genera co-occurred with tetW gene. Co-occurrence patterns were revealed distinct community interactions between aerobic/anoxic/aerobic and oxidation ditch systems. The redundancy analysis model plot of the bacterial community composition clearly demonstrated that the sludge samples were significant differences among those from the different geographical areas, and the shifts in bacterial community composition were correlated with ARGs. Together, these findings from the present study will highlight the potential risks of ARGs and bacterial populations carrying these ARGs, and enable the development of suitable technique to control the dissemination of ARGs from WWTPs into aquatic environments.

High throughput quantification of the functional genes associated with RDX biodegradation using the SmartChip real-time PCR system

The explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) is a contaminant at many military sites. RDX bioremediation as a clean-up approach has been gaining popularity because of cost benefits compared to other methods. RDX biodegradation has primarily been linked to six functional genes (diaA, nfsI, pnrB, xenA, xenB, xplA). However, current methods for gene quantification have the risk of false negative results because of low theoretical primer coverage. To address this, the current study designed new primer sets using the EcoFunPrimer tool based on sequences collected by the Functional Gene Pipeline and Repository and these were verified based on residues and motifs. The primers were also designed to be compatible with the SmartChip Real-Time PCR system, a massively parallel singleplex PCR platform (high throughput qPCR), that enables quantitative gene analysis using 5,184 simultaneous reactions on a single chip with low volumes of reagents. This allows multiple genes and/or multiple primer sets for a single gene to be used with multiple samples. Following primer design, the six genes were quantified in RDX-contaminated groundwater (before and after biostimulation), RDX-contaminated sediment, and uncontaminated samples. The final 49 newly designed primer sets improved upon the theoretical coverage of published primer sets, and this corresponded to more detections in the environmental samples. All genes, except diaA, were detected in the environmental samples, with xenA and xenB being the most predominant. In the sediment samples, nfsI was the only gene detected. The new approach provides a more comprehensive tool for understanding RDX biodegradation potential at contaminated sites.

Use of synthesized double-stranded gene fragments as qPCR standards for the quantification of antibiotic resistance genes

Pollution of various environmental matrices by antibiotic resistance genes (ARGs) has become a growing threat to human health. For the quantitative analysis of the presence of ARGs, there is a need for sensitive and robust qPCR assays which can detect various genes from different types of DNA extracts. Fourteen ARGs were selected as target genes in this study including: bla_TEM, bla_OXA-1 and bla_CTX-M coded for resistance to β-lactams; ermB for macrolides; tetA, tetG, tetM, tetQ, tetW and tetX for tetracyclines; sul I and sul II for sulfonamides; drfA1 and drfA12 d for trimethoprim; and integron gene intI 1 and intI 2. Chemically synthesized double-stranded gene fragments were modified using molecular biology methods and used as real-time PCR standards as well as to establish in-house qPCR assays. The ermB gene from a naturally occurring plasmid was used to compare the performance of qPCR assay with the chemically synthesized ermB. Additionally, environmental water, soil and faeces samples were used to validate the established qPCR assays. Importantly, the study proves the usefulness of rapidly synthesized oligonucleotides serving as qPCR standards for ARG analysis and provides comparable sensitivity and reliability to a traditional amplicon standard.

Characterization of bacterial community changes and antibiotic resistance genes in lamb manure of different incidence

Bacterial enteritis is the most important disease in lamb for breeding greatly affects the growth of animals. Changes in the community of intestinal flora can cause the disorder of the colonic environment induced diarrhea. This study aimed to investigate the relationship between the incidence of bacterial enteritis and the number of intestinal microbiome, then the prevalence of drug-resistant genes was detected. Fecal samples were collected at five fattening sheep farms with different incidence of bacterial enteritis, pathogenic bacteria were isolated and identified, drug sensitivity tests were performed. Then, changes in number and structure of intestinal flora were compared by 16S rDNA V3-V4 region high-throughput sequencing, and the ARGs were detected using high-throughput real-time PCR. Our results revealed that the microbial communities were positively correlated with the incidence of bacterial enteritis in different farms. Bacterial communities were higher in YJ (with highest incidence of diarrhea) than any other farms. However, the ARGs seemed not to be more affected by the incidence of bacterial enteritis, but one of the significant findings to emerge from this study is that MCR-1 and NDM are detected in manure. This study has provided an insight of the changes occurring in intestinal flora and AGRs in fattening sheep farms with diverse incidence of bacterial enteritis.

ARGA, a pipeline for primer evaluation on antibiotic resistance genes

Molecular biology techniques have assisted in the investigation of antibiotic resistance genes (ARGs) from various environments. However, their accuracy relies on primer quality and data interpretation, both of which require a full-coverage sequence database for ARGs. Here, based upon the abandoned Antibiotic Resistance Genes Database (ARDB), we created an updated sequence database of antibiotic resistance genes (SDARG). A total of 1,260,069 protein sequences and 1,164,479 nucleotide sequences, 56 times more sequences than ARDB, from 448 types of ARGs (enabling resistance to 18 categories of antibiotics) were collected and integrated with different hierarchical credibility and full-scale taxonomic information. Based on this comprehensive sequence database, an online pipeline - ARG analyzer (ARGA, http://mem.rcees.ac.cn:8083/) was developed to assess current ARGs primers, as well as annotate ARGs from environmental metagenomes. Thereafter, a list of 658 published primer pairs, targeting 173 ARGs, was evaluated using ARGA and integrated in ARGA as ARGs primer database. The results showed that 65.05% primers are of high specificity (≥90%), while only 29.79% primers cover >50% of targeted sequences, indicating a divergence in the quality of current ARG primers. Hence, primer assessment or redesign is highly recommended to improve the accuracy of ARGs studies. ARGs primer database was attached in ARGA to provide researchers alternatives to better survey ARGs in the environment.

Biocides and health-care agents are more than just antibiotics: Inducing cross to co-resistance in microbes

Health-care chemicals are used worldwide as important components of different industries as consumer products, food industry, animal husbandry and agribusiness. There are innumerable reports on the effect of these chemicals (biocides) impacting the development of cross to co-resistance in pathogenic bacteria. However, reports are limited on the concurrent use of agricides (pesticides, herbicides, fungicides and insecticides) which influence the microbial activities in soils and contribute to the increase in incidences of co-resistance. Undoubtedly, indiscriminate use of biocides and agricides has contaminated both water and soil environments. This review describes the onset of cross and co-resistance to biocides and antibiotics which is increasingly being exhibited by specific bacteria under a persistent selective pressure. It also re-examines the significance of mobile genetic platforms and horizontal gene transfer from one to another bacterial species, for understanding the kinetics and efficiency of genetic exchange in stressed environments leading to natural selection of tolerant strains over susceptible ones. The investigation is much warranted, particularly with respect to agricides that commonly occur in recalcitrant states in soil and water ecosystem, livestock, etc and is transmitted either directly or via the food-chain to human beings, facilitating the switch from cross to co-resistance.

Antibiotic Resistomes in Plant Microbiomes

Microorganisms associated with plants may alter the traits of the human microbiome important for human health, but this alteration has largely been overlooked. The plant microbiome is an interface between plants and the environment, and provides many ecosystem functions such as improving nutrient uptake and protecting against biotic and abiotic stress. The plant microbiome also represents a major pathway by which humans are exposed to microbes and genes consumed with food, such as pathogenic bacteria, antibiotic-resistant bacteria, and antibiotic-resistance genes. In this review we highlight the main findings on the composition and function of the plant microbiome, and underline the potential of plant microbiomes in the dissemination of antibiotic resistance via food consumption or direct contact.

Exploration of antibiotic resistance risks in a veterinary teaching hospital with Oxford Nanopore long read sequencing

The Oxford Nanopore MinION DNA sequencing device can produce large amounts of long sequences, typically several kilobases, within a few hours. This long read capacity was exploited to detect antimicrobial resistance genes (ARGs) in a large veterinary teaching hospital environment, and to assess their taxonomic origin, genetic organisation and association with mobilisation markers concurrently. Samples were collected on eight occasions between November 2016 and May 2017 (inclusive) in a longitudinal study. Nanopore sequencing was performed on total DNA extracted from the samples after a minimal enrichment step in broth. Many ARGs present in the veterinary hospital environment could potentially confer resistance to antimicrobials widely used in treating infections of companion animals, including aminoglycosides, extended-spectrum beta-lactams, sulphonamides, macrolides, and tetracyclines. High-risk ARGs, defined here as single or multiple ARGs associated with pathogenic bacterial species or with mobile genetic elements, were shared between the intensive care unit (ICU) patient cages, a dedicated laundry trolley and a floor cleaning mop-bucket. By contrast, a floor surface from an office corridor without animal contact and located outside the veterinary hospital did not contain such high-risk ARGs. Relative abundances of high-risk ARGs and co-localisation of these genes on the same sequence read were higher in the laundry trolley and mop bucket samples, compared to the ICU cages, suggesting that amplification of ARGs is likely to occur in the collection points for hospital waste. These findings have prompted the implementation of targeted intervention measures in the veterinary hospital to mitigate the risks of transferring clinically important ARGs between sites and to improve biosecurity practices in the facility.

Spatial and seasonal variation of the airborne microbiome in a rapidly developing city of China

Exposure to airborne microbes (AM) can affect the human microbiome and has various consequences for human health. Investigating the profiles of AM and the potential bacterial pathogens within, along with the factors influencing their community, is pivotal for understanding the impact of AM on human health. In this study, we collected AM during spring and summer from 11 sites with various levels of urbanization in the city of Xiamen, China. Bacterial community compositions of the AM were determined based on 16S rRNA gene amplicon sequencing. Firmicutes and Proteobacteria were the predominating phyla in the airborne bacterial communities, and a higher (P < 0.05) diversity of AM was found during the summer as compared to the spring. Significant differences in the community structure of the AM and the potential bacterial pathogens within airborne microbes were observed among the seasons and the sites with different levels of urbanization. Increases and/or decreases in the abundance of Bacillus and Acinetobacter could explain a major part of the variations in the AM community compositions. The proportion of potential bacterial pathogens during the summer was significantly higher (P < 0.01) than in the spring, and the relative abundance of several bacterial pathogens (i.e. Burkholderia multivoran, Enterococcus faecium and Streptococcus thermophilus) related to human diseases (39.8% of total pathogens on average) increased with increasing urbanization levels, suggesting that urbanization can increase the AM-associated human health risk.

Assessment of extracellular antibiotic resistance genes (eARGs) in typical environmental samples and the transforming ability of eARG

The emergence and spread of antibiotic resistance has pose a huge threat to both human health and environmental ecosystem. However, little is known regarding the pool of ARGs in extracellular DNA (eDNA). In this study ten ARGs (sul1, sul2, tetW, tetX, ermA, ermB, bla_TEM, ampC, cat and cmr) and class I integron (intI1) in the sludge from hospital, pharmaceutical industry, wastewater treatment plant (WWTP), and swine manure, and sediment in urban lake in the form of both eDNA and intracellular DNA (iDNA) were evaluated by quantitative polymerase chain reaction (qPCR). The results showed that every gram of sludge dry weight contained from 7.31 × 10³ to 1.16 × 10¹⁰ copies of extracellular ARGs (eARGs) and from 1.04 × 10⁵ to 2.74 × 10¹² copies of intracellular ARGs (iARGs). The sludge from hospital with the highest ratio of eARGs to total ARGs (11.02-89.63%), followed by the sediment from urban lake, implying that most of the ARGs in these regions were contributed by eARGs. The relative abundance of eARGs were higher than iARGs in sludge from WWTP and pharmaceutical industry, moreover, 1/3 and 5/9 detected eARGs were higher than the ARGs in the iDNA extracted from sludge of hospital and sediment from urban lake, respectively. Furthermore, the transforming ability of eARGs suggesting that adsorbed eARG is more preferentially coupled to the competent cells than free eARG. These findings highlight the need to focus attention on the contribution of eARGs to the dissemination of antibiotic resistance into environment, and also future needs in mitigating the spread of eARGs in the environment.

Organic carbon: An overlooked factor that determines the antibiotic resistome in drinking water sand filter biofilm

Biofilter, an essential water treatment process, is reported to be the harbor of bacterial antibiotic resistance genes (ARGs). Due to the oligotrophic characteristic of source water, filter biofilm is largely influenced by the concentration of organic carbon. The objective of this study was to investigate the effect of organic carbon concentration on shaping bacterial antibiotic resistome in filter biofilm. Our study was based on pilot-scale sand filters, and we investigated the antibiotic resistome using high-throughput qPCR. A total of 180 resistance genes from eight categories of antibiotics were detected in 15 biofilm samples of three sand filters. The results indicated that higher concentration of influent organic carbon led to lower diversity of bacterial community and richness of antibiotic resistance genes (ARGs) in biofilm. We discovered a negative correlation (p ≤ 0.01) between the richness of ARGs and the corresponding TOC level. Moreover, the absolute abundance of ARGs was positively correlated (p ≤ 0.05) with the abundance of 16S rRNA gene and was determined by the organic carbon concentration. Sand filters with gradient influent organic carbon concentration led to the formation of different antibiotic resistomes and canonical correspondence analysis (CCA) indicated that difference in bacterial community composition was likely the main reason behind this difference. We also observed a similar trend in the relative abundance of ARGs, which increased with the depth of sand filters. However, this trend was more pronounced in filters with low organic carbon concentrations. Overall, this study revealed that the organic carbon concentration determined the absolute abundance of ARGs and also shaped the diversity and relative abundance of ARGs in drinking water sand filters. These results may provide new insights into the mechanism of persistent bacterial antibiotic resistance in drinking water treatment.

Importance of sludge conditioning in attenuating antibiotic resistance: Removal of antibiotic resistance genes by bioleaching and chemical conditioning with Fe[III]/CaO

Conditioning can drastically improve the dewaterability of sewage sludge and thus it is widely practiced in most wastewater treatment plants (WWTPs). In WWTPs, various antibiotic resistance genes (ARGs) present in sewage are concentrated in the sewage sludge, but the effect of sludge conditioning on ARGs in sewage sludge remains unclear. Here, we evaluated and compared the effectiveness of four sludge conditioning methods (namely chemical conditioning with polyacrylamide (PAM), chemical conditioning with Fe[III]/CaO, bioleaching conditioning, and chemical acidification conditioning) and an aerobic incubation control in removing 46 target ARGs and intI1 from a municipal sewage sludge. The damage of sludge microbial cells and the change in the sludge bacterial community during the various sludge conditioning treatments were also characterized. The results suggested that the chemical conditioning with PAM and aerobic incubation treatment did not remove ARGs and intI1 from the sewage sludge. The chemical acidification reduced the absolute abundances of most ARGs and intI1, but increased their relative abundances. However, the chemical conditioning with Fe[III]/CaO and bioleaching conditioning reduced both the absolute and relative abundances of most ARGs and removed a majority of extracellular ARGs in the sludge. During sludge conditioning treatments, the sludge microbial cells were severely damaged to decrease the total bacterial biomass in sludge, and accordingly the bacterial hosts carrying ARGs and intI were effectively damaged to reduce the absolute abundances of most ARGs and intI1. In addition, the sludge bacterial community in conditioned sludge determined the relative abundances of residual ARGs. Our findings suggest that sludge conditioning can be an important sludge treatment process in attenuating antibiotic resistance in sewage sludge, and bioleaching and chemical conditioning with Fe[III]/CaO can be employed as effective conditioning ways to reduce ARGs in sewage sludge, potentially limiting their release to the environment.

Higher Temperatures Do Not Always Achieve Better Antibiotic Resistance Gene Removal in Anaerobic Digestion of Swine Manure

This study employed high-throughput quantitative PCR and 16S rRNA sequencing to evaluate the effect of temperature and residual antibiotics on the dynamics of antibiotic resistance genes (ARGs) and microbial communities during anaerobic digestion of swine manure. The abundances of total ARGs and 16S rRNA genes significantly decreased in all of four treatments (25°C, 37°C, and 37°C with 50 mg of wet weight antibiotics of body weight, and 55°C). The abundances of most ARG types were significantly correlated with those of the 16S rRNA gene and transposase gene (P < 0.01). However, the abundances of total ARGs at 55°C were much higher than those of other treatments. Meanwhile, the microbial communities at 55°C, where the Streptococcus pathogen remained at a relatively high abundance and cellulose degraders and hydrogen producers, such as Ethanoligenens and Coprococcus bacteria, increased, were markedly different from those of other treatments. Redundancy analysis indicates that temperature, pH, and the genus Streptococcus had the highest explanation for ARG variation among experimental factors, chemical properties, and representative genera, respectively. Network analysis further showed that the genus Streptococcus contributed greatly to the higher ARG abundance at 55°C. The moderate antibiotic residue only caused a slight and transitory inhibition for microbially diverse populations and promotion for ARG abundance, probably due to the degradation of antibiotics and microbial adaptability. Our results clarify the cooperativity of gene transfer-related items on ARG variation and intensively prove that higher temperature cannot always achieve better ARG removal in anaerobic digestion unless pathogens and gene transfer elements are more efficiently inhibited.IMPORTANCE Antibiotic resistance genes (ARGs) are frequently detected with high abundance in manure-applied soils. Anaerobic digestion is one of widely used processes for animal waste treatment. Thus, it is critical to understand the potential of anaerobic digestion to attenuate ARGs. Although some previous studies recommended thermophilic digestion for ARG removal, they did not get sufficient evidence to support this view. The antibiotics applied to animals are mostly excreted through feces and urine because of incomplete metabolism. It is indispensable to know whether residual antibiotics in manure will hinder ARG attenuation in anaerobic digesters. The significance of our research is in comprehensively understanding the evolution and mechanism of ARGs in anaerobic digestion of swine manure affected by temperature and residual antibiotics, which will allow the development of an ARG elimination strategy before their release into the environment.

Evidence for co-selection of antibiotic resistance genes and mobile genetic elements in metal polluted urban soils

Antibiotic resistance genes (ARGs) constitute emerging environmental pollutants and pose risks to public health. Toxic metals are known to select for metal-resistant bacteria in metal-contaminated soils, but there is growing concern that metal contaminants can also act as co-selective agents thereby causing environmental proliferation of antibiotic resistance. In this study, we quantified ARGs and selected mobile genetic elements (MGEs) known to constitute potential ARG hosts in 50 archived urban and suburban soils from the Belfast metropolitan area using a high-throughput qPCR ARG chip. ARG prevalence was linked to concentrations of individual metals and a soil metal toxicity index calculated based on the relative toxicity of different metals to soil microbial processes. A total of 164 ARGs were detected across the 50 soils analyzed with an average absolute abundance of 3.4 × 10⁷ ARG gene copies per gram of soil. A significant correlation between abundance of ARGs and MGEs was observed, suggesting the importance of horizontal gene transfer for ARG dissemination. Network analysis revealed significant co-occurrence patterns between specific metals (As, Cd, Co, Cr, Cu. Hg, Ni and Zn) and associated ARGs. Path analysis further indicated that the soil metal toxicity index significantly affected the number of detected ARGs (λ = 0.32, P < 0.001) and the abundance of metal co-occurring ARGs (λ = 0.612, P < 0.001) via effects on MGEs. Collectively, our results indicate a role of soil metals in co-selection of ARGs and MGEs in urban and semi-urban soils and suggest a risk for environmental ARG dissemination via horizontal gene transfer.

Practical implications of erythromycin resistance gene diversity on surveillance and monitoring of resistance

Use of antibiotics in human and animal medicine has applied selective pressure for the global dissemination of antibiotic-resistant bacteria. Therefore, it is of interest to develop strategies to mitigate the continued amplification and transmission of resistance genes in environmental reservoirs such as farms, hospitals and watersheds. However, the efficacy of mitigation strategies is difficult to evaluate because it is unclear which resistance genes are important to monitor, and which primers to use to detect those genes. Here, we evaluated the diversity of one type of macrolide antibiotic resistance gene (erm) in one type of environment (manure) to determine which primers would be most informative to use in a mitigation study of that environment. We analyzed all known erm genes and assessed the ability of previously published erm primers to detect the diversity. The results showed that all known erm resistance genes group into 66 clusters, and 25 of these clusters (40%) can be targeted with primers found in the literature. These primers can target 74%–85% of the erm gene diversity in the manures analyzed.

Prevalence of Antibiotic Resistance Genes in Air-Conditioning Systems in Hospitals, Farms, and Residences

High-throughput quantitative PCR combined with Illumina sequencing and network analysis were used to characterize the antibiotic resistance gene (ARG) profiles in air-conditioning filters from different environments. In total, 177 ARGs comprising 10 ARG types were determined. The detectable numbers and the relative abundance of ARGs in hospitals and farms were significantly higher than those in city and village residences. Compared to hospitals, farms had a higher level of tetracycline, multidrug, integrase, and macrolide⁻lincosamide⁻streptogramin (MLS) B resistance genes but a lower level of beta-lactam resistance genes. The bl3_cpha gene was the most abundant resistance gene subtype in hospital samples with an abundance of 2.01 × 10^-4 copies/16S rRNA, while a level of only 5.08 × 10^-12 copies/16S rRNA was observed in farm samples. There was no significant difference in bacterial diversity among the hospitals, farms, and residences, and Proteobacteria was the most abundant phylum. Network analysis revealed that Proteobacteria and Actinobacteria were possible hosts of the beta-lactam, MLSB, aminoglycoside, multidrug, sulfonamide, and tetracycline resistance genes. The results demonstrate that ARGs exist in indoor environments and that farms and hospitals are important sources. This study provides a useful reference for understanding the distribution patterns and risk management of ARGs in indoor environments.

DirtyGenes: testing for significant changes in gene or bacterial population compositions from a small number of samples

High throughput genomics technologies are applied widely to microbiomes in humans, animals, soil and water, to detect changes in bacterial communities or the genes they carry, between different environments or treatments. We describe a method to test the statistical significance of differences in bacterial population or gene composition, applicable to metagenomic or quantitative polymerase chain reaction data. Our method goes beyond previous published work in being universally most powerful, thus better able to detect statistically significant differences, and through being more reliable for smaller sample sizes. It can also be used for experimental design, to estimate how many samples to use in future experiments, again with the advantage of being universally most powerful. We present three example analyses in the area of antimicrobial resistance. The first is to published data on bacterial communities and antimicrobial resistance genes (ARGs) in the environment; we show that there are significant changes in both ARG and community composition. The second is to new data on seasonality in bacterial communities and ARGs in hooves from four sheep. While the observed differences are not significant, we show that a minimum group size of eight sheep would provide sufficient power to observe significance of similar changes in further experiments. The third is to published data on bacterial communities surrounding rice crops. This is a much larger data set and is used to verify the new method. Our method has broad uses for statistical testing and experimental design in research on changing microbiomes, including studies on antimicrobial resistance.

Turning pig manure into biochar can effectively mitigate antibiotic resistance genes as organic fertilizer

The composting of fresh manure is an effective way to inactivate pathogens and reduce the levels of antibiotics and some antibiotic resistance genes (ARGs) prior to its application on agricultural land as organic fertilizer. However, some ARGs could still exist and even be enriched after composting. This study investigated whether converting composted pig manure into biochar could reduce the dissemination of ARGs into the soil in comparison with a compost amendment. We performed a pot experiment using pakchoi (Brassica chinensis), with two pig manure-based composts and the biochar derived from composted pig manure, as organic fertilizers. The distributions of the antibiotic resistome, mobile genetic elements (MGEs) and bacterial community composition in soils during cultivation were evaluated by high-throughput qPCR and Illumina sequencing. The total ARGs and MGEs abundance in the biochar-treated soils were significantly lower than those in the compost-amended soils during cultivation. The total ARGs abundance in the biochar-amended soils was similar to that in the control soils during cultivation. Thus, the dissemination of ARGs from animal waste to the environment can be effectively mitigated by converting manure into biochar.

High-throughput profiling of antibiotic resistance gene dynamic in a drinking water river-reservoir system

The rapid construction of reservoir in river basin generates a river-reservoir system containing an environmental gradient from river system to reservoir system in modern aquatic environment worldwide. Profiles of antibiotic resistance genes (ARGs) in river-reservoir system is essential to better understand their dynamic mechanisms in aquatic eco-environment. In this study, we investigated the diversity, abundance, distribution of ARGs and mobile genetic elements (MGEs) in a representative river-reservoir system using high-throughput quantitative PCR, as well as ranked the factors (e.g. antibiotics, bacterial biomass, bacteria communities, and MGEs) influencing the patterns of ARGs based on structural equation models (SEMs). Seasonal variations in absolute abundance of ARGs and MGEs exhibited similar trends with local rainfall, suggesting that seasonal runoff induced by the rainfall potentially promote the absolute abundance of ARGs and MGEs. In contrast, environmental gradient played more important roles in the detected number, relative abundance, distribution pattern of ARGs and MGEs in the river-reservoir system. Moreover, environmental gradient also made the co-occurrence patterns associated with ARGs subtypes, MGEs and bacteria genera in river system different from those in reservoir system. The SEMs revealed that MGEs contributed the most to shape the ARG profiles. Overall, our findings provide novel insights into the mechanisms of environmental gradient on ARGs dynamics in river-reservoir system, probably via influencing the MGEs, antibiotics, pathogenic bacteria community and nonpathogenic bacteria community.

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

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

Contributions and Challenges of High Throughput qPCR for Determining Antimicrobial Resistance in the Environment: A Critical Review

Expansion in whole genome sequencing and subsequent increase in antibiotic resistance targets have paved the way of high throughput qPCR (HT-qPCR) for analyzing hundreds of antimicrobial resistance genes (ARGs) in a single run. A meta-analysis of 51 selected studies is performed to evaluate ARGs abundance trends over the last 7 years. WaferGen^TM SmartChip is found to be the most widely used HT-qPCR platform among others for evaluating ARGs. Up till now around 1000 environmental samples (excluding biological replicates) from different parts of the world have been analyzed on HT-qPCR. Calculated detection frequency and normalized ARGs abundance (ARGs/16S rRNA gene) reported in gut microbiome studies have shown a trend of low ARGs as compared to other environmental matrices. Disparities in the HT-qPCR data analysis which are causing difficulties to researchers in precise interpretation of results have been highlighted and a possible way forward for resolving them is also suggested. The potential of other amplification technologies and point of care or field deployable devices for analyzing ARGs have also been discussed in the review. Our review has focused on updated information regarding the role, current status and future perspectives of HT-qPCR in the field of antimicrobial resistance.

Land Use Influences Antibiotic Resistance in the Microbiome of Soil Collembolans Orchesellides sinensis

Numerous studies have investigated the composition and diversity of antibiotic resistance genes (ARGs) in multiple environments but the pattern of ARGs in field-collected soil fauna remains poorly understood. In the present study soil collembolans were collected from six sites with three different land use types (parkway land, park land, and arable land) and 285 ARGs and 10 mobile genetic elements (MGEs) in the microbiome of these "wild" collembolans were quantified by high-throughput quantitative PCR. A total of 76 unique ARGs and 5 MGEs were detected. There were significant differences between collection sites in the antibiotic resistome in the collembolans. Land use significantly altered the distribution patterns of collembolan ARGs. Thirty shared ARGs and three shared MGEs were identified. The co-occurrences of shared resistomes were largely random, and more positive relationships were found in the coassociation network. Partial redundancy analysis confirms that the changes in bacterial communities explained 27.77% of the variation in ARGs. These findings suggest that resistance genes are pervasive in the microbiome associated with the field collembolan and the activity of the collembolans may contribute to the spread and dissemination of resistance genes in the environment, an aspect of ARGs that has until now been largely overlooked.

Rapid Detection of AGs using Microchip Capillary Electrophoresis Contactless Conductivity Detection

Background:

In order to realize current aminoglycosides supervision in food and environment, our team improved the sensitivity and separation efficiency of the portable ITO detector, based on the technology of microchip capillary electrophoresis and contactless conductivity detection.

Experiment:

Parameters (the separation voltage, buffer concentration, electrodes gap, elicitation frequency, elicitation voltage) were optimized for the detection of three aminoglycosides, gentamicin, kanamycin and streptomycin and the separation of their mixture in background electrolyte consists of 2-(N-Morpholino) ethanesulfonic acid (MES) and L-Histidine (His). The enhanced method was also applied to other types of aminoglycosides.

Results:

Under optimal conditions, the monitoring of three types of aminoglycosides obtained such a sensitive response that the limits of detection of gentamicin sulfate, kanamycin sulfate and streptomycin sulfate were calculated as 3.1 µg/ml, 0.89 µg/ml and 0.96 µg/ml, at signal-to-noise ratio 3, respectively. In addition they got separated completely from each other only in 40 s. The results of other varieties of aminoglycosides including tobramycin sulfate and amikacin sulfate also met the standard.

Conclusion:

We successfully proposed here an unprecedentedly portable, miniaturized and rapid microchip capillary electrophoresis contactless conductivity detection system to realize current aminoglycosides supervision in food and environment.

Long-Term Effect of Different Fertilization and Cropping Systems on the Soil Antibiotic Resistome

Different fertilization and cropping systems may influence short- and long-term residues of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in soil. Soils from dryland (peanut) and paddy (rice) fields, which originated from the same nonagricultural land (forested), were treated with either chemical fertilizer, composted manure, or no fertilizer for 26 years before sampling, which occurred one year after the last applications. ARGs and MGEs were investigated using highly parallel qPCR and high-throughput sequencing. Six of the 11 antibiotics measured by LC-MS/MS were detected in the manure applied soil, but not in the nonmanured soils, indicating their source was from previous manure applications. Compared to the unfertilized control, manure application did not show a large accumulation of ARGs in either cropping system but there were some minor effects of soil management on indigenous ARGs. Paddy soil showed higher accumulation of these ARGs, which corresponded to higher microbial biomass than the dryland soil. Chemical fertilizer increased relative abundance of these ARGs in dryland soil but decreased their relative abundance in paddy soil. These results show how long-term common soil management practices affect the abundance and type of ARGs and MGEs in two very different soil environments, one aerobic and the other primarily anaerobic.

Functional genera, potential pathogens and predicted antibiotic resistance genes in 16 full-scale wastewater treatment plants treating different types of wastewater

This study aimed to investigate the bacterial communities and antibiotic resistance genes (ARGs) in 16 wastewater treatment plants (WWTPs) treating municipal, industrial and mixed wastewater. Wastewater types showed obvious effects on bacterial communities and functions. Nitrosomonas, Nitrospira, Hyphomicrobium and Accumulibacter were the main functional genera. Mycobacterium was the dominant potential pathogens. A total of 69 ARGs were obtained, and the dominant ARGs subtypes were similar in different WWTPs. Efflux pumps were the most common resistance mechanisms. Copper and zinc resistance genes were the main metal resistance genes (MRGs). Wastewater types affected the distributions of ARGs and MRGs, and they were more similar in industrial and mixed wastewater. The co-occurrence of ARGs existed within or across ARG types, and they were also positively linked to MRGs, some functional and pathogenic genera or environmental factors. This study furthers the understanding of interactions between bacterial communities, ARGs and MRGs in different WWTPs.

Responses and successions of sulfonamides, tetracyclines and fluoroquinolones resistance genes and bacterial community during the short-term storage of biogas residue and organic manure under the incubator and natural conditions

Biogas residue and organic manure are frequently used for crop planting. However, the evaluation of antibiotic resistant bacteria (ARB), antibiotic resistance genes (ARGs) and bacterial community before their applications to fields is still lacking. This study monitored the variations of bacteria resistant to sulfadiazine, tetracycline and norfloxacin, 57 resistance genes for sulfonamides, tetracyclines and fluoroquinolones as well as the bacterial community during the 28-day aerobic storage of biogas residue and organic manure by using viable plate counts, high-throughput qPCR and Illumina MiSeq sequencing methods. Then two storage conditions, incubator (25 °C) and natural environment, were used to assess the responses of ARB and ARGs to the environmental factors. Results showed that a total of 35 and 21 ARGs were detected in biogas residue and organic manure, respectively. ARB and ARGs were enriched up to 8.01-fold in biogas residue after the 28-day storage, but varied in a narrow range during the storage of organic manure. Compared with the incubator condition, the proliferation of ARB and ARGs in biogas residue under the natural condition was relatively inhibited by the varied and complicated environmental factors. However, we found that there was no significant difference of ARB and ARGs in organic manure between the incubator and natural conditions. Bacterial community was also shifted during the storage of biogas residue, especially Bacteroidetes_VC2.1_Bac22, Aequorivita, Luteimonas and Arenimonas. Network analysis revealed that the relationship in biogas residue was much more complicated than that in organic manure, which ultimately resulted in large successions of ARB and ARGs during the short-term storage of biogas residue. Therefore, we suggest that further measures should be taken before the application of biogas residue to fields.

Microbial Community Composition and Antibiotic Resistance Genes within a North Carolina Urban Water System

Wastewater treatment plants (WWTPs) are thought to be potential incubators of antibiotic resistance. Persistence of commonly used antibiotics in wastewater may increase the potential for selection of resistance genes transferred between bacterial populations, some of which might pose a threat to human health. In this study, we measured the concentrations of ten antibiotics in wastewater plant influents and effluents, and in surface waters up- and downstream from two Charlotte area treatment facilities. We performed Illumina shotgun sequencing to assay the microbial community and resistome compositions at each site across four time points from late winter to mid-summer of 2016. Antibiotics are present throughout wastewater treatment, and elevated concentrations of multiple antibiotics are maintained in moving stream water downstream of effluent release. While some human gut and activated sludge associated taxa are detectable downstream, these seem to attenuate with distance while the core microbial community of the stream remains fairly consistent. We observe the slight suppression of functional pathways in the downstream microbial communities, including amino acid, carbohydrate, and nucleic acid metabolism, as well as nucleotide and amino acid scavenging. Nearly all antibiotic resistance genes (ARGs) and potentially pathogenic taxa are removed in the treatment process, though a few ARG markers are elevated downstream of effluent release. Taken together, these results represent baseline measurements that future studies can utilize to help to determine which factors control the movement of antibiotics and resistance genes through aquatic urban ecosystems before, during, and after wastewater treatment.

Assessing the safety of thermally processed penicillin mycelial dreg following the soil application: Organic matter's maturation and antibiotic resistance genes

To degrade the residual penicillin G in penicillin mycelial dreg (PMD), thermal treatment was used as a pretreatment for practical disposal. Given that the characteristics of treated-PMD aren't adequately clear, a lab-scale experiment was conducted to verify its safety assessment for land application under the following points: (i) variation of penicillin G residue (ii) maturity of organic matter (OM) (iii) phytotoxicity (iv) abundance of antibiotic resistance genes (ARGs). A high-throughput quantitative polymerase chain reaction (HT-qPCR) method was used to perform an overall investigation of soil ARGs. The results show that heat treatment effectively degrades 98% of penicillin in PMD within 120 min. After thermal treatment, the treated-PMD was applied to soil. The original penicillin level was considerably lower and completely degraded within 4 days. Variation of germination index (GI) implied that the created phytotoxicity was significantly reduced. Furthermore, compared with PMD, the addition of treated-PMD didn't cause enrichment of soil ARGs in diversity and abundance. Therefore, heat treatment can be considered as an effective pretreatment for PMD practical application.

Primer set 2.0 for highly parallel qPCR array targeting antibiotic resistance genes and mobile genetic elements

The high-throughput antibiotic resistance gene (ARG) qPCR array, initially published in 2012, is increasingly used to quantify resistance and mobile determinants in environmental matrices. Continued utility of the array; however, necessitates improvements such as removing or redesigning questionable primer sets, updating targeted genes and coverage of available sequences. Towards this goal, a new primer design tool (EcoFunPrimer) was used to aid in identification of conserved regions of diverse genes. The total number of assays used for diverse genes was reduced from 91 old primer sets to 52 new primer sets, with only a 10% loss in sequence coverage. While the old and new array both contain 384 primer sets, a reduction in old primer sets permitted 147 additional ARGs and mobile genetic elements to be targeted. Results of validating the updated array with a mock community of strains resulted in over 98% of tested instances incurring true positive/negative calls. Common queries related to sensitivity, quantification and conventional data analysis (e.g. Ct cutoff value, and estimated genomic copies without standard curves) were also explored. A combined list of new and previously used primer sets is provided with a recommended set based on redesign of primer sets and results of validation.

Amendment soil with biochar to control antibiotic resistance genes under unconventional water resources irrigation: Proceed with caution

The spread of antibiotic resistance genes (ARGs) has become a cause for serious concern because of its potential risk to public health. The use of unconventional water resources (e.g., reclaimed water or piggery wastewater) in agriculture to relieve groundwater shortages may result in an accumulation of ARGs in soil. Biochar addition has been proven to be a beneficial method to alleviate the pollution of ARGs in manure-amended soil. However, the role of biochar on ARGs in soil-plant systems repeatedly irrigated with unconventional water resources is unknown. Under reclaimed water or piggery wastewater irrigation, rhizobox experiments using maize plants in soil amended with biochar were conducted to investigate the variation of typical ARGs (tet and sul genes) in soil-plant systems during a 60-day cultivation, and ARGs was characterized by high-throughput qPCR with a 48 (assays) × 108 (samples) array. Only piggery wastewater irrigation significantly increased the abundance of ARGs in rhizosphere and bulk soils and root endophytes. Following 30-day cultivation, the abundance of ARGs in soil was significantly lower due to biochar addition. However, by day 60, the abundance of ARGs in soil supplemented with biochar was significantly higher than in the control soils. Antibiotics, bio-available heavy metals, nutrients, bacterial community, and mobile gene elements (MGEs) were detected and analyzed to find factors shaping ARGs dynamics. The behavior of ARGs were associated with antibiotics but not with bio-available heavy metals. The correlation between ARGs and available phosphorus was stronger than that of ARGs with total phosphorus. MGEs had good relationship with ARGs, and MGEs shifts contributed most to ARGs variation in soil and root samples. In summary, this study provides insights into potential options for biochar use in agricultural activities.

Dietary Withania sominefera root confers protective and immunotherapeutic effects against Aeromonas hydrophila infection in Nile tilapia (Oreochromis niloticus)

In the present study, effect of dietary Withania sominefera (W. sominefera) root powder was evaluated to modulate immune and antioxidant response against Aeromonas hydrophila (A. hydrophila) infection in Nile tilapia (Oreochromis niloticus). W. sominefera root powder supplemented diets at two concentrations 2.5% (W 2.5%) and 5% (W 5%); fed for 6 weeks prior to the A. hydrophila challenge and continued the same respective diets during the post challenge period (2 weeks). Results showed that fish fed W. sominefera at 5% enhanced immune response in both pre and post-challenge period. NBT level exhibited only significant increase (P < 0.05) in the pre-challenge period compared to control. Malondialdehyde (MDA) levels in liver and muscle revealed significant decrease in both Withania supplemented groups compared to the control in post challenge period. Antioxidant enzymes activities (catalase/CAT/, glutathione S-transferase/GST/, glutathione/GSH; and superoxide dismutase/SOD) were improved in liver and muscle in post challenge period. Glutathione peroxidase (GPx) level in muscle and serum total antioxidant capacity (TAC) showed a significant increase in both Withania supplemented groups compared to the control post challenge. Withania supplementation enhanced disease resistance against A. hydrophila and reduced mortalities (20%), especially at supplemented concentration of 5%. Our findings suggest that W. sominefera root powder may have protective and immunotherapeutic roles in Nile tilapia against A. hydrophila infection which may be useful in controlling important fish bacterial diseases.

Occurrence and Distribution of Tetracycline Antibiotics and Resistance Genes in Longshore Sediments of the Three Gorges Reservoir, China

The widespread use of antibiotics and the induced antibiotic resistance genes have attracted much attention in recent years. The longshore sediments in the water-level-fluctuating zone of the Three Gorges Reservoir were selected to investigate the spatial-temporal distribution of antibiotics and antibiotic resistance genes in two different operation stages (low-water level in summer and high-water level in winter). Three kinds of tetracycline antibiotics (tetracycline, oxytetracycline, and chlortetracycline) and three kinds of tetracycline resistance genes [tet(A), tet(C), and tet(M)] were analyzed and quantified. The results showed that the distribution of tetracyclines and resistance genes in riverine, transition and lacustrine zones showed a certain regularity, and the tetracycline antibiotics concentration and the total abundance of the tetracycline resistance genes were highest in the transition zone, and then the riverine zone. Meanwhile, there were significant seasonal variations of tetracycline and the resistance genes. The concentrations of the tetracycline and resistance genes were higher in summer than those in winter, while the relative abundance of resistance genes was higher in winter. It was suggested that the different seasonal distribution of antibiotics and resistance genes may be correlated with the reservoir operation in the Three Gorges Reservoir and the higher use of antibiotics in winter. In addition, Pearson correlation analysis showed that the concentrations of the tetracycline, class 1 integron and 16S rRNA were positively correlated with the abundance of the tetracycline resistance genes.

Antibiotic Resistome Associated with Small-Scale Poultry Production in Rural Ecuador

Small-scale poultry farming is common in rural communities across the developing world. To examine the extent to which small-scale poultry farming serves as a reservoir for resistance determinants, the resistome of fecal samples was compared between production chickens that received antibiotics and free-ranging household chickens that received no antibiotics from a rural village in northern Ecuador. A qPCR array was used to quantify antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) using 248 primer pairs; and the microbiome structure was analyzed via 16S rRNA gene sequencing. A large number of ARGs (148) and MGEs (29) were detected. The ARG richness in production chickens was significantly higher than that of household chickens with an average of 15 more genes detected ( p < 0.01). Moreover, ARGs and MGEs were much more abundant in production chickens than in household chickens (up to a 157-fold difference). Production chicken samples had significantly lower taxonomic diversity and were more abundant in Gammaproteobacteria, Betaproteobacteria, and Flavobacteria. The high abundance and diversity of ARGs and MGEs found in small-scale poultry farming was comparable to the levels previously found in large scale animal production, suggesting that these chickens could act as a local reservoir for spreading ARGs into rural communities.

Exploring abundance, diversity and variation of a widespread antibiotic resistance gene in wastewater treatment plants

An updated sul1 gene sequence database was constructed and new degenerate primers were designed to better investigate the abundance, diversity, and variation of a ubiquitous antibiotic resistance gene, sul1, with PCR-based methods in activated sludge from wastewater treatment plants (WWTPs). The newly designed degenerate primers showed high specificity and higher coverage in both in-silico evaluations and activated sludge samples compared to previous sul1 primers. Using the new primers, the abundance and diversity of sul1 gene, together with 16S rRNA gene, in activated sludge from five WWTPs in summer and winter were determined by quantitative PCR and MiSeq sequencing. The sul1 gene was found to be prevalent and displayed a comparable abundance (0.081 copies per bacterial cell in average) to the total bacteria across all samples. However, compared to the significant seasonal and geographical divergences in the quantity and diversity of bacterial communities in WWTPs, there were no significant seasonal or geographical variations of representative clusters of sul1 gene in most cases. Additionally, the representative sul1 clusters showed fairly close phylogeny and there was no obvious correlation between sul1 gene and the dominant bacterial genera, as well as the int1 gene, suggesting that bacterial hosts of sul1 gene is not stable, the sul1 gene may be carried by mobile genetic elements, sometimes integrated with class 1 integrons and sometimes not. Thus mobile genetic elements likely play a greater role than specific microbial taxa in determining the composition of sul1 gene in WWTPs.

The antibiotic resistome of free-living and particle-attached bacteria under a reservoir cyanobacterial bloom

In freshwater systems, both antibiotic resistance genes (ARGs) and cyanobacterial blooms attract global public health concern. Cyanobacterial blooms can greatly impact bacterial taxonomic communities, but very little is known about the influence of the blooms on antibiotic resistance functional community. In this study, the ARGs in both free-living (FL) and particle-attached (PA) bacteria under bloom and non-bloom conditions were simultaneously investigated in a subtropical reservoir using high-throughput approaches. In total, 145 ARGs and 9 mobile genetic elements (MGEs) were detected. The most diverse and dominant of which (68.93%) were multidrug resistance genes and efflux pump mechanism. The richness of ARGs in both FL and PA bacteria was significantly lower during the bloom period compared with non-bloom period. The abundance of ARGs in FL bacteria was significantly lower under bloom condition than in the non-bloom period, but the abundance of ARGs in PA bacteria stayed constant. More importantly, the resistant functional community in PA bacteria was more strongly influenced by the cyanobacterial bloom than in the FL bacteria, although >96% ARGs were shared in both FL and PA bacteria or both bloom and non-bloom periods. We also compared the community compositions between taxonomy and function, and found antibiotic resistant communities were highly variable and exhibited lower similarity between bloom and non-bloom periods than seen in the taxonomic composition, with an exception of FL bacteria. Altogether, cyanobacterial blooms appear to have stronger inhibitory effect on ARG abundance in FL bacteria, and stronger influence on antibiotic resistant community composition in PA bacteria. Our results further suggested that both neutral and selective processes interactively affected the ARG composition dynamics of the FL and PA bacteria. However, the antibiotic resistant community of FL bacteria exhibited a higher level of temporal stochasticity following the bloom event than PA bacteria. Therefore, we emphasized the bacterial lifestyles as an important mechanism, giving rise to different responses of antibiotic resistant community to the cyanobacterial bloom.

Tracking antibiotic resistome during wastewater treatment using high throughput quantitative PCR

Wastewater treatment plants (WWTPs) contain diverse antibiotic resistance genes (ARGs), and thus are considered as a major pathway for the dissemination of these genes into the environments. However, comprehensive evaluations of ARGs dynamic during wastewater treatment process lack extensive investigations on a broad spectrum of ARGs. Here, we investigated the dynamics of ARGs and bacterial community structures in 114 samples from eleven Chinese WWTPs using high-throughput quantitative PCR and 16S rRNA-based Illumina sequencing analysis. Significant shift of ARGs profiles was observed and wastewater treatment process could significantly reduce the abundance and diversity of ARGs, with the removal of ARGs concentration by 1-2 orders of magnitude. Whereas, a considerable number of ARGs were detected and enriched in effluents compared with influents. In particular, seven ARGs mainly conferring resistance to beta-lactams and aminoglycosides and three mobile genetic elements persisted in all WWTPs samples after wastewater treatment. ARGs profiles varied with wastewater treatment processes, seasons and regions. This study tracked the footprint of ARGs during wastewater treatment process, which would support the assessment on the spread of ARGs from WWTPs and provide data for identifying management options to improve ARG mitigation in WWTPs.

Chronic impacts of oxytetracycline on mesophilic anaerobic digestion of excess sludge: Inhibition of hydrolytic acidification and enrichment of antibiotic resistome

We evaluated the chronic impact of oxytetracycline (OTC) on performance and antibiotic resistance development during the mesophilic anaerobic digestion (AD) of antibiotic-containing biomass. Mesophilic AD was conducted in a completely stirred tank reactor by constantly feeding municipal excess sludge spiked with increasing concentrations of OTC (0-1000 mg L^-1) under a solid retention time of 20 days over a period of 265 days. Results showed that methane generation of mesophilic AD was inhibited when the OTC concentration in digested sludge was increased to around 18,000 mg kg^-1 (OTC dose, 1000 mg L^-1), due to the inhibition of fermenting and acidogenic bacteria. Metagenomic sequencing and high-throughput quantitative PCR analysis demonstrated that tetracycline resistance genes were the most dominant type (38.47-43.76%) in the resistome, with tetG, tetX, tetM, tetR, tetQ, tetO, and tetL as the dominant resistant subtypes throughout the whole experimental period. The relative abundance of these tet genes increased from 2.10 × 10^-1 before spiking OTC (OTC concentration in digested sludge, 8.97 mg kg^-1) to 2.83 × 10^-1 (p < 0.05) after spiking OTC at a dose of 40 mg L^-1 (OTC concentration in digested sludge, 528.52 mg kg^-1). Furthermore, mobile genetic elements, including integrons, transposons, and plasmids, were also enriched with the increase in OTC dose. Based on partial canonical correspondence analysis, the contributions of horizontal (mobile element alteration) and vertical (bacterial community shift) gene transfer to antibiotic resistome variation were 29.35% and 21.51%, respectively. Thus, considering the inhibition of hydrolytic acidification and enrichment of antibiotic resistome, mesophilic AD is not suggested to directly treat the biomass containing OTC concentration higher than 200 mg L^-1.

Metagenomic Characterization of Antibiotic Resistance Genes in Full-Scale Reclaimed Water Distribution Systems and Corresponding Potable Systems

Water reclamation provides a valuable resource for meeting nonpotable water demands. However, little is known about the potential for wastewater reuse to disseminate antibiotic resistance genes (ARGs). Here, samples were collected seasonally in 2014-2015 from four U.S. utilities' reclaimed and potable water distribution systems before treatment, after treatment, and at five points of use (POU). Shotgun metagenomic sequencing was used to profile the resistome (i.e., full contingent of ARGs) of a subset ( n = 38) of samples. Four ARGs ( qnrA, bla_TEM, vanA, sul1) were quantified by quantitative polymerase chain reaction. Bacterial community composition (via 16S rRNA gene amplicon sequencing), horizontal gene transfer (via quantification of intI1 integrase and plasmid genes), and selection pressure (via detection of metals and antibiotics) were investigated as potential factors governing the presence of ARGs. Certain ARGs were elevated in all ( sul1; p ≤ 0.0011) or some ( bla_TEM, qnrA; p ≤ 0.0145) reclaimed POU samples compared to corresponding potable samples. Bacterial community composition was weakly correlated with ARGs (Adonis, R² = 0.1424-0.1734) and associations were noted between 193 ARGs and plasmid-associated genes. This study establishes that reclaimed water could convey greater abundances of certain ARGs than potable waters and provides observations regarding factors that likely control ARG occurrence in reclaimed water systems.

High-throughput profiling of seasonal variations of antibiotic resistance gene transport in a peri-urban river

The rapid expansion of human activity in a region can exacerbate human health risks induced by antibiotic resistance genes (ARGs). Peri-urban ecosystems serve at the symbiotic interface between urban and rural ecosystems, and investigations into the dissemination of ARGs in peri-urban areas provide a basic framework for tracking the spread of ARGs and potential mitigations. In this study, through the use of high-throughput quantitative PCR and 16S rRNA gene high-throughput sequencing, seasonal and geographical distributions of ARGs and their host bacterial communities were characterized in a peri-urban river. The abundance of ARGs in downstream was 5.2-33.9 times higher than upstream, which indicated distinct antibiotic resistance pollution in the areas where human lives. With the comparison classified based on land use nearby, the abundance of ARGs in samples near farmland and villages was higher than in the background (3.47-5.58 times), pointing to the high load in the river caused by farming and other human activities in the peri-urban areas. With the co-occurrence pattern revealed by network analysis, blaVEB and tetM were proposed to be indicators of ARGs which get together in the same module. Furthermore, seasonal variations in ARGs and the transport of bacterial communities were observed. The effects of seasonal temperature on the dissemination of ARGs along the watershed was also evaluated. The highest absolute abundance of ARGs occurred in summer (2.81 × 10⁹ copies/L on average), the trends of ARG abundances in four seasons were similar with local air temperature. The Linear discriminant analysis effect size (LEfSe) suggested that nine bacterial genera were implicated as biomarkers for the corresponding season. Mobile genetic elements (MGEs) showed significant positive correlation with ARGs (P < 0.01) and MGEs were also identified as the key-contributing factor driving ARG alteration. This study provides an overview of seasonal and geographical variations in ARGs distribution in a peri-urban river and draws attention to controlling pollutants in peri-urban ecosystems.

Enrichment of antibiotic resistance genes in soil receiving composts derived from swine manure, yard wastes, or food wastes, and evidence for multiyear persistence of swine Clostridium spp

The impact of amendment with swine manure compost (SMC), yard waste compost (YWC), or food waste compost (FWC) on the abundance of antibiotic resistance genes in soil was evaluated. Following a commercial-scale application of the composts in a field experiment, soils were sampled periodically for a decade, and archived air-dried. Soil DNA was extracted and gene targets quantified by qPCR. Compared with untreated control soil, all 3 amendment types increased the abundance of gene targets for up to 4 years postapplication. The abundance of several gene targets was much higher in soil amended with SMC than in soil receiving either YWC or FWC. The gene target ermB remained higher in the SMC treatment for a decade postapplication. Clostridia were significantly more abundant in the SMC-amended soil throughout the decade following application. Eight percent of Clostridium spp. isolates from the SMC treatment carried ermB. Overall, addition of organic amendments to soils has the potential to increase the abundance of antibiotic resistance genes. Amendments of fecal origin, such as SMC, will in addition entrain bacteria carrying antibiotic resistance genes. Environmentally recalcitrant clostridia, and the antibiotic resistance genes that they carry, will persist for many years under field conditions following the application of SMC.

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.

Antibiotic resistome promotion in drinking water during biological activated carbon treatment: Is it influenced by quorum sensing?

The contamination of antibiotic resistance genes (ARGs) in drinking water may pose a direct threat to human health. This study applied high-throughput qPCR and sequencing to investigate the dynamics of ARGs and bacterial communities during the advanced treatment of drinking water using biological activated carbon. The promotion of ARGs was observed, and the normalized copy number of ARGs increased significantly after BAC treatment, raising the number of detected ARGs from 84 to 159. Twenty-nine ARGs were identified as biofilm-influencing sources in the BAC, and they persisted after chlorination. The shift of bacterial communities primarily had effects on the changes in resistome. Firmicutes, Cyanobacteria were related to persistent ARGs mostly in the BAC biofilm. Meanwhile, the Acyl-Homoserine Lactones (AHLs), quorum sensing molecules, and bacteria that produced AHLs were identified to understand the promotion of ARGs. The isolated AHL-producing bacteria belonged to the Proteobacteria, Firmicutes and Bacteroidetes phyla. Six detectable AHLs had an influence on plasmid-based horizontal gene transfer in the intragenus mating systems, indicating that the dynamics of ARGs were strongly affected by quorum sensing between specific bacteria in the biofilm. These results provide new insight into the mechanism of antibiotic resistome promotion in BAC biofilms.