Quantitative Campylobacter spp., antibiotic resistance genes, and veterinary antibiotics in surface and ground water following manure application: Influence of tile drainage control

Influence of surfactant molecular features on tetracycline transport in saturated porous media of varied surface heterogeneities

This study aims to understand how surfactants affect the mobility of tetracycline (TC), an antibiotic, through different aquifer media. Two anionic and cationic surfactants, sodium dodecylbenzene sulfonate (SDBS) and cetyltrimethyl ammonium bromide (CTAB), were used to study their influence on TC mobility through clean sand and humic acid (HA)-coated sand. HA coating inhibits TC mobility due to its strong interaction with TC. Both surfactants promoted TC mobility at pH 7.0 due to competitive deposition, steric effect, and increased hydrophilicity of TC. CTAB had a more substantial effect than SDBS, related to the surfactants' molecular properties. Each surfactant's promotion effects were greater in HA-coated sand than in quartz sand due to differences in surfactant retention. CTAB inhibited TC transport at pH 9.0 due to its significant hydrophobicity effect. Furthermore, in the presence of Ca2+, SDBS enhanced TC transport by forming deposited SDBS-Ca2+-TC complexes. On the other hand, CTAB increased TC mobility due to its inhibition of cation bridging between TC and porous media. The findings highlight surfactants' crucial role in influencing the environmental behaviors of tetracycline antibiotics in varied aquifers.

Fate of pharmaceuticals in the Ebro River Delta region: The combined evaluation of water, sediment, plastic litter, and biomonitoring

The increasing consumption of pharmaceuticals, alongside their limited removal in wastewater treatment plants (WWTPs), have led to their ubiquitous occurrence in receiving aquatic environments. This study addresses the occurrence of 68 pharmaceuticals (PhACs) in the Ebro River Delta region (NE Spain), as well as their distribution in different environmental compartments, including surface water, sediments, biota (river biofilm and fish tissues), and field-collected plastic litter. In addition, their concentrations in serving WWTPs, as possible sources of environmental contamination, were also determined. Our study confirmed the widespread occurrence of PhACs in riverine and, to a more limited extent, coastal environments. Most frequently detected PhACs belonged to analgesics/anti-inflammatories (e.g., ibuprofen) and psychiatric drugs (e.g., venlafaxine) therapeutic groups, followed by antihypertensives (e.g., valsartan) and antibiotics (e.g., azithromycin). Seasonal differences in cumulative levels of PhACs were reported for water and sediments (winter>summer). Despite spatial gradients were not clear along the river, a non-negligible contribution of upstream Ebro sites (reference area) was highlighted, which was unexpected based on the low anthropogenic pressure. Sediments represented a minor attenuation pathway for the selected PhACs, whereas they were more heavily accumulated in biota: fish liver (up to 166 ng/g dw), river biofilms (up to 108 ng/g dw), fish plasma (up to 63 ng/mL), and fish muscle (up to 31 ng/g dw). These findings highlight the importance of biomonitoring in the characterization of polluted areas and prioritization of hazardous substances (e.g., psychiatric drugs) in aquatic systems, and a particular interest of fish plasma as non-destructive biomonitoring matrix. PhACs were also detected on plastic litter, demonstrating their role as environmental sinks for certain PhACs (e.g., analgesics/anti-inflammatories, psychiatric drugs). Overall, the widespread detection of PhACs in a variety of biotic and abiotic matrices from the lower Ebro River and Delta warns about their possible environmental implications.

Particle-size stratification of airborne antibiotic resistant genes, mobile genetic elements, and bacterial pathogens within layer and broiler farms in Beijing, China

The particle-size distribution of antimicrobial resistant (AMR) elements is crucial in evaluating their environmental behavior and health risks, and exposure to the fecal microbiome via particle mass (PM) is an important route of transmission of AMR from livestock to humans. However, few studies have explored the association between air and fecal AMR in farm environments from the perspective of particle-size stratification. We collected feces and PMs of different sizes from layer and broiler farms, quantified antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and human pathogenic bacteria (HPB) using Droplet digital PCR (ddPCR), and analyzed the bacterial communities based on 16S rRNA sequencing. The particle-size distributions of 16S rRNA and AMR elements were similar and generally increased with larger particle sizes in chicken farms. In broiler farms, we observed a bimodal distribution with two peaks at 5.8-9.0 μm and 3.3-4.7 μm. The dominant airborne bacterial phyla were Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes. The dominant phyla in the feces were the same as those in the air, but the order of relative abundance varied. The particle-size distributions of specific bacterial genera differed between the animal-farm types. Overall, the degree of association between feces and different particulates increased with increasing particle size. The microbial communities in the coarse particles were similar to those in fecal samples. Escherichia coli, Staphylococcus spp., Campylobacter spp., and sul 2 (sulfonamide ARGs) tended to attach to small particles. We highlight the particle size-specific relationship between fecal and air microbes involving ARGs, MGEs, and HPB and provide valuable information for comprehensively assessing the transmission of fecal microorganisms through the airpath and its environmental and occupational health risks.

Antibiotics, antibiotic resistance and associated risk in natural springs from an agroecosystem environment

This study investigates the occurrence, transport, and risks associated to antibiotic residues, antibiotic resistance genes (ARGs) and antibiotic resistant Escherichia coli (AR-E. coli) in eleven natural springs in an agroecosystem environment with intense livestock production, where groundwater nitrate concentration usually sets above 50 mg L^-1. Out of 23 multiple-class antibiotics monitored, tetracycline and sulfonamide residues were the most ubiquitous, and they were detected at concentrations ranging from ng L^-1 to μg L^-1. Five ARGs were monitored, conferring resistance to the antibiotic classes of major use in livestock production. Thus, genes conferring resistance to sulfonamides (sul1 and sul2) and tetracyclines (tetW) as well as a gene proxy for anthropogenic pollution (intI1) were present in most springs. sul1 was the most abundant, with absolute concentrations ranging from 4 × 10² to 5.6 × 10⁶ gene copies L^-1 water. AR-E. coli showing resistance to sulfonamides and tetracyclines was also detected, with a prevalence up to approximately 40 % in some sites but with poor correlations with the concentration of antibiotic residues and ARGs. The occurrence of antibiotics, ARGs and AR-E. coli was characterized by large seasonal variations which were mostly associated to both hydrological factors and reactive transport processes. Finally, a risk assessment approach pointed out towards low risk for both the groundwater environment and human health, when spring water is used for direct human consumption, associated with the occurrence of antibiotics, ARGs and AR-E. coli. However, long-term effects cannot be neglected, and proper actions must be taken to preserve groundwater quality.

Insight into the effect of phosphate on ferrihydrite colloid-mediated transport of tetracycline in saturated porous media

Colloid-mediated contaminant mobility is absolutely critical for the environmental behavior of contaminants such as antibiotics in water resources. In this study, the influences of phosphate (a commonly inorganic ligand in the environment) on the ferrihydrite colloid-mediated transport of tetracycline (TC, a typical antibiotic) in porous media were investigated. In the absence of colloids, phosphate promoted TC mobility due to the competitive deposition of phosphate and TC on the sand surface as well as the electrostatic repulsion. Interestingly, ferrihydrite colloids could inhibit TC transport; however, the inhibitory effect of the colloids was weakened by the addition of phosphate. This phenomenon stemmed from colloid-associated TC mobility, the increased electrostatic repulsion induced by adsorbed phosphate, and deposition site competition effect. Another interesting finding was that the impacts of phosphate on the colloid-mediated mobility of TC were pH-dependent. That is, phosphate exhibited a weaker effect on the inhibitory role of ferrihydrite colloids in TC mobility at pH 5.0 than that at pH 7.0; specially, ferrihydrite colloids acted as possible carriers of TC and facilitated antibiotic transport at pH 9.0. The observations were ascribed to different influences of phosphate on the binding affinity of ferrihydrite toward TC and the mobility of free TC under different pH conditions. Therefore, the findings of this study provide useful information about the fate and co-transport of antibiotics and natural mineral colloids in the presence of inorganic ligands in the aquatic environment.

Transport of tetracycline in saturated porous media: combined functions of inorganic ligands and solution pH

To date, there is still very little knowledge about the combined effects of typical inorganic ligands and solution pH values on mobility characteristics of tetracycline (TC) through saturated aquifer media. In this work, three typical inorganic ligands (i.e., phosphate, silicate, and iodate) were employed in the transport experiments. Generally, all the ligands promoted TC mobility over the pH range of 5.0-9.0 owing to the enhanced electrostatic repulsion between sand grains and TC anionic forms (i.e., TC^- and TC^2-) as well as the competitive deposition between ligands and antibiotic molecules for attachment sites. Furthermore, the transport-enhancement effects of ligands on TC intensively depended on ligand type and followed the sequence of phosphate > silicate > iodate. This phenomenon was ascribed to their different molecular sizes and binding abilities to sand grains. Interestingly, the differences in extents of enhanced effects of various inorganic ligands on TC transport varied with background solution pH due to pH-induced different extents of deposition site competition effects. Moreover, the two-site nonequilibrium model (which accounts for an equilibrium site and a kinetic site) as well as adsorption and kinetic studies were performed to help interpret the controlling mechanisms for the synergistic effects of inorganic ligands and solution pH on TC transport in saturated quartz sand. The findings of our study clearly demonstrate that inorganic ligands may be critical factors in assessing the fate and transport of antibiotics in groundwater systems.

Insights into the molecular mechanism of tetracycline transport in saturated porous media affected by low-molecular-weight organic acids: Role of the functional groups and molecular size

The transport of tetracycline possessed a great challenge in its environmental applications. This study looked at how various low-molecular-weight organic acids (LMWOAs) affect the transport of tetracycline in environments. To that end, four LMWOAs were employed in experiments; acetic acid, malonic acid, malic acid, and citric acid. It was observed that LMWOAs promoted the tetracycline passage in presence of various experimental environments. The LMWOAs steric hindrance and deposition competition facilitated tetracycline transport at pH 5.0. The other deposition mechanism for tetracycline was the electrostatic repulsion between tetracycline and sand enhanced by deprotonated LMWOAs at pH 7.0. Moreover, the enhanced effects of LMWOAs on tetracycline mobility were intensively dependent on LMWOA type with more functional groups (e.g. carboxyl and hydroxyl groups) and larger molecular size supported stronger deposition competition, steric hindrance as well as electrostatic repulsion. Additionally, cation-bridging played a vital role for the enhanced effects of LMWOAs on tetracycline transport with divalent cations (e.g., Ca²⁺ and Pb²⁺). Interestingly, tetracycline exhibited a higher mobility in the presence of Ca²⁺ relative to Pb²⁺ regardless of LMWOAs-free or LMWOAs-addition. This phenomenon was attributed to the fact that Pb²⁺ has a greater affinity with tetracycline and LMWOAs than Ca²⁺. Furthermore, under the shadow of numerous LMWOAs, the non-equilibrium two site transportation model was employed to investigate the movement of tetracycline in porous saturated media. The present study suggests that LMWOAs may be important considerations in assessing the antibiotic passage in soil as well as groundwater.

Colloid-mediated transport of tetracycline in saturated porous media: Comparison between ferrihydrite and montmorillonite

Given the ubiquitous mineral (e.g., clays and iron oxides) playing critical roles in impacting the fate of antibiotics in the subsurface environment, the effects of two mineral colloids (i.e., ferrihydrite and montmorillonite) on tetracycline (TC, a representative of antibiotic) transport in sand columns were investigated in this study. Interestingly, the results clearly showed that ferrihydrite colloids inhibited TC transport, while montmorillonite colloids enhanced TC mobility under neutral conditions (pH 7.0). This phenomenon resulted from the positively charged ferrihydrite colloids with weak mobility, which assisted TC deposition; besides, providing additional deposition sites for TC by the deposited ferrihydrite colloids was another important mechanism. In contrast, the transport-enhancement effect of montmorillonite on TC was attributed to the strong binding affinity of TC to clay particles as well as the competition between colloids and TC for deposition sites on sand surfaces. Moreover, the transport-inhibition effect of ferrihydrite at pH 7.0 was greater than that at pH 5.0, mainly due to more colloid-associated TC under neutral conditions. Surprisingly, ferrihydrite colloids could act as carriers of antibiotics and enhanced TC transport at pH 9.0. Because the surface charge of colloids was altered to negative and could break through the column. Meanwhile, the transport-enhancement effect of montmorillonite decreased with increasing pH from 5.0 to 9.0, resulting from the decrease of colloid-adsorbed TC. Furthermore, colloid-mediated transport of TC was influenced by ionic strength, which affected the aggregation characteristics of colloids and the binding affinities of TC to minerals. These findings provide critical information for assessing the risks of antibiotics in aquatic ecosystems where abundant natural minerals are present.

Accumulation of sulfamethazine and ciprofloxacin on grain surface decreases the transport of biochar colloids in saturated porous media

The increasing amount of antibiotics entering the environment through manure usage and sludge application from wastewater treatment plants (WWTP) attracts much concern due to their potential threat to ecological security and human health. When biochar, a soil and water amendment, is introduced into the soil for remediation, the antibiotics are usually co-present with the biochar colloids (BC) or pre-accumulated in soils. However, little is known about the effect of antibiotics on the behavior of BC. Column experiments were conducted at three different pH values to study the effect of sulfamethazine (SMT) or ciprofloxacin (CIP) on BC transport. Under certain conditions (co-present in the influent and pre-sorbed on quartz sand), large numbers of cation and zwitterion forms of the less mobile CIP at pH 5 and 7 led to less negatively-charged surface of BC and quartz sand, resulted in higher BC retention compared to the highly mobile SMT. The decrease in BC transport became more significant with a higher amount of SMT or CIP pre-sorption. Therefore, when biochar is applied into soils polluted by antibiotics, the pH-dependency and the loading amount of antibiotics in soil matrix should be paid attention to as they might affect the transport of BC and the related facilitated-contaminants transport.

Spread of antibiotic resistance genes and microbiota in airborne particulate matter, dust, and human airways in the urban hospital

Antimicrobial resistance is an increasingly serious threat to public health worldwide. The presence of antibiotic resistance genes (ARGs) in human airways and relevant environments has not received significant attention. In this study, abundances of ARGs and microbes from airborne particulate matter, dust, and human airways in a hospital were profiled using high-throughput qPCR and 16S rRNA gene sequencing. More diverse ARGs and microbes in indoor dust and higher levels of ARGs in particulate matter PM₁₀ and PM_2.5 were observed. Macrolides and aminoglycoside resistance genes were the most abundant ARGs in the airway and environmental samples, respectively. Moreover, the co-occurrences of priority pathogens, ARGs, and mobile genetic elements (MGEs) were shown by the Network analysis. Campylobacter spp. and Staphylococcus spp. positively correlated with fluoroquinolone (vatC-02, mexD) and β-lactams (blaZ, mecA) resistance genes, respectively. In this regard, based on SourceTracker analysis, inhalable particles contributed to 4.0% to 5.5% of ARGs in human airway samples, suggesting an important exchange between airborne inhalable particles and human commensals. This study may advance knowledge about ARGs in airborne particulate matter and dust associated environments, reveal their potential link between environments and humans, and provide a new sight and fundamental data for ARG risk assessment.

Long-read sequencing revealed cooccurrence, host range, and potential mobility of antibiotic resistome in cow feces

While it is well recognized that the environmental resistome is global, diverse, and augmented by human activities, it has been difficult to assess risk because of the inability to culture many environmental organisms, and it is difficult to evaluate risk from current sequence-based environmental methods. The four most important criteria to determine risk are whether the antibiotic-resistance genes (ARGs) are a complete, potentially functional complement; if they are linked with other resistances; whether they are mobile; and the identity of their host. Long-read sequencing fills this important gap between culture and short sequence-based methods. To address these criteria, we collected feces from a ceftiofur-treated cow, enriched the samples in the presence of antibiotics to favor ARG functionality, and sequenced long reads using Nanopore and PacBio technologies. Multidrug-resistance genes comprised 58% of resistome abundance, but only 0.8% of them were plasmid associated; fluroquinolone-, aminoglycoside-, macrolide-lincosamide-streptogramin (MLS)-, and β-lactam-resistance genes accounted for 2.7 to 12.3% of resistome abundance but with 19 to 78% located on plasmids. A variety of plasmid types were assembled, some of which share low similarity to plasmids in current databases. Enterobacteriaceae were dominant hosts of antibiotic-resistant plasmids; physical linkage of extended-spectrum β-lactamase genes (CTX-M, TEM, CMY, and CARB) was largely found with aminoglycoside-, MLS-, tetracycline-, trimethoprim-, phenicol-, sulfonamide-, and mercury-resistance genes. A draft circular chromosome of Vagococcus lutrae was assembled; it carries MLS-, tetracycline- (including tetM and tetL on an integrative conjugative element), and trimethoprim-resistance genes flanked by many transposase genes and insertion sequences, implying that they remain transferrable.

Distribution of genetic elements associated with antibiotic resistance in treated and untreated animal husbandry waste and wastewater

Animal breeding for meat production based on swine, cattle, poultry, and aquaculture is an activity that generates several impacts on the environment, among them the spread of antibiotic resistance. There is a worldwide concern related to the massive use of antibiotics, which causes selective pressure on the microbial community, triggering bacteria that contain "antibiotic resistance genes." According to the survey here presented, antibiotic resistance-related genes such as tetracyclines (tet), erythromycin (erm), and sulfonamides (sul), as well as the genetic mobile element interferon (int), are the most reported genetic elements in qualitative and quantitative studies of swine, cattle, poultry, and aquaculture manure/wastewater. It has been observed that biological treatments based on waste composting and anaerobic digestion are effective in ARG removal, particularly for tet, bla, erm, and qnr (quinolone) genes. On the other hand, sul and intI genes were more persistent in such treatments. Tertiary treatments, such advanced oxidative processes, are suitable strategies to improve ARG reduction. In general temperature, hydraulic retention time, and penetration of sunlight are the main operational parameters for ARG reduction in treatments applied to animal waste, and therefore attention should be addressed to optimize their efficacy regarding ARG removal. Despite being reduced, the presence of ARG in treated effluents and in biosolids indicates that there is a potential risk of antibiotic resistance spread in nature, especially through the release of treated livestock waste into the environment.

Sewage sludge in agriculture - the effects of selected chemical pollutants and emerging genetic resistance determinants on the quality of soil and crops - a review

In line with sustainable development principles and in order to combat climate change, which contributes to progressive soil depletion, various solutions are being sought to use treated sewage sludge as a soil amendment to improve soil quality and enrich arable soils with adequate amounts of biogenic compounds. This review article focuses on the effects of the agricultural use of biosolids on the environment. The article reviews the existing knowledge on selected emerging contaminants in treated sewage sludge and describes the impact of these pollutants on the environment and living organisms based on 183 publications selected from over 16,000 papers on related topics published over the last ten years. This study deals not only with chemical contaminants but also genetic determinants of resistance to these compounds. Current research has questioned the agricultural use of biosolids due to the presence of mutual interactions between antibiotics, heavy metals, the genetic determinants of resistance (antibiotic resistance genes - ARGs and heavy metal resistance genes - HMRGs) and non-steroidal anti-inflammatory drugs as well as the risks associated with their transfer to the environment. This study emphasizes the need for more extensive legal regulations that account for other pollutants of environmental concern (PEC), particularly in countries where sewage sludge is applied in agriculture most extensively. Future research should focus on more effective methods of eliminating PEC from sewage sludge, especially from the sludge that is used to fertilize agricultural land, because even small amounts of these micropollutants can have serious implications for the health and life of humans and animals.

Heavy metal pollution promotes antibiotic resistance potential in the aquatic environment

Water pollution is one of the main challenges and water crises, which has caused the existing water resources to be unusable due to contamination. To understand the determinants of the distribution and abundance of antibiotic resistance genes (ARGs), we examined the distribution of 22 ARGs in relation to habitat type, heavy metal pollution and antibiotics concentration across six lakes and wetlands of Iran. The concentration of 13 heavy metals was determined by inductively coupled plasma atomic emission spectroscopy (ICP-AES) by Thermo Electron Corporation, and five antibiotics by online enrichment and triple-quadrupole LC-MS/MS were investigated. We further performed a global meta-analysis to evaluate the distribution of ARGs across global lakes compared with our studied lakes. While habitat type effect was negligible, we found a strong correlation between waste discharge into the lakes and the abundance of ARGs. The ARGs abundance showed stronger correlation with the concentration of heavy metals, such as Vanadium, than with that of antibiotics. Our meta-analysis also confirmed that overuse of antibiotics and discharge of heavy metals in the studied lakes. These data point to an increase in the distribution of ARGs among bacteria and their increasing resistance to various antibiotics, implying the susceptibility of aquatic environment to industrial pollution.

Antibiotics and antibiotic resistant genes (ARGs) in groundwater: A global review on dissemination, sources, interactions, environmental and human health risks

The discovery and evolution of antibiotics for humans and animals are among the most significant milestones of the 20th century. However, antibiotics play a significant role in the induction and dissemination of antibiotic resistance genes (ARGs) in groundwater that has recently become the primary environmental concern. They are administrated to humans and animals on a large scale and are persistent in the environment. Long term impacts of antibiotics in the ecological environment are not still clearly understood, and their occurrence and consequences have become an important research topic worldwide. The hotspot reservoirs of antibiotics and ARGs include medical facilities, livestock farming, aquaculture, landfills, on-site sanitation systems, sewage, and wastewater treatment plants. Our meta-analysis demonstrated that antibiotics, including ciprofloxacin, sulfamethoxazole, erythromycin, and tetracycline were found at high concentrations while sulfonamide and tetracycline ARGs were more prevalent in groundwater. Moreover, the highest reported concentrations of targeted antibiotics were used to calculate hazard quotient (HQ) and risk quotient (RQ) in global groundwater bodies to estimate environmental and human health risks, respectively. Due to limited available ecotoxicity data, RQ and HQ can only be calculated for a few antibiotics in groundwater. The risk assessment of antibiotics demonstrated that antibiotics with their current groundwater levels pose no human health risks, whereas only ciprofloxacin, erythromycin, flumequine, and sulfamethoxazole revealed moderate to low risks to aquatic species. The occurrence of ARGs and antibiotic resistant bacteria (ARBs) in groundwater is also not likely to pose human health risk but consumption of groundwater contaminated with ARGs and ARBs might contribute to the development of antibiotic resistance in humans. The present review also sheds light on the relationship between ARGs, antibiotics, microbial communities, and environmental factors in groundwater, and reported a significant correlation between them. It also addresses prospects for future outlooks into further areas of relevant research.

Occurrence of antibiotic resistance genes and microbial source tracking markers in the water of a karst spring in Germany

The emergence of antimicrobial resistances causes serious public health concerns worldwide. In recent years, the aquatic ecosystem has been recognized as a reservoir for antibiotic-resistant bacteria and antibiotic resistance genes (ARGs). The prevalence of 11 ARGs, active against six antibiotic classes (β-lactams, aminoglycosides, tetracycline, macrolides, trimethoprim, and sulfonamides), was evaluated at a karst spring (Gallusquelle) in Germany, using molecular biological methods. In addition, fecal indicator bacteria (FIB), turbidity, electrical conductivity, spring discharge, and microbial source tracking markers specific for human, horse, chicken, and cow were determined. The ARGs most frequently detected were ermB (42.1%), tet(C) (40.8%), sul2 (39.5%), and sul1 (36.8%), which code for resistance to macrolides, tetracycline and sulfonamides, respectively. After a heavy rain event, the increase in FIB in the spring water was associated with the increase in ARGs and human-specific microbial source tracking (MST) markers. The determined correlations of the microbiological parameters, the observed overflow of a combined sewer overflow basin a few days before the increase of these parameters, and the findings of previous studies indicate that the overflow of this undersized basin located 9 km away from the spring could be a factor affecting the water quality of the karst spring. Our results provide a scientific basis for minimization of the input of fecal pollution and thus ARGs into the karst spring.

Tracing veterinary antibiotics in the subsurface - A long-term field experiment with spiked manure

The purpose of this long-term experiment was on gaining more insights into the environmental behaviour of veterinary antibiotics in the subsurface after application with manure. Therefore, manure spiked with a bromide tracer and eight antibiotics (enrofloxacin, lincomycin, sulfadiazine, sulfamethazine, tetracycline, tiamulin, tilmicosin and tylosin) in concentrations of milligrams per litre were applied at an experimental field site. Their pathway was tracked by continuous extraction of soil pore water at different depths and systematic sampling of groundwater for a period of two years. Seven target compounds were detected in soil pore water of which four leached into groundwater. Concentrations of the detected target compounds were, with few exceptions, in the range of nanograms per litre. It was concluded that a large fraction of the investigated antibiotics sorbed or degraded already within the first meter of the soil. Further, it was inferred from the data that long and warm dry periods cause attenuation of the target compounds through increased degradation or sorption occurring in the soil. In addition, the comprehensive data-set allowed to estimate a retardation factor between 1.1 and 2.0 for sulfamethazine in a Plaggic Anthrosol soil, and to classify the individual compounds by environmental relevance based on transport behaviour and persistence. According to the distribution of resistant genes in the environment, sulfamethazine was found to be the most mobile and persistent substance.

Impact of liquid hog manure applications on antibiotic resistance genes concentration in soil and drainage water in field crops

Agricultural practices such as manure applications could contribute to the spread of antibiotic resistance genes (ARGs) within the environment. Our objective was to assess the impact of certain fertilization methods (mineral or manure) and tillage practices (reduced or conventional) on the presence of ARGs and bacteria in soil and drainage water under wheat and grain corn crops. Targeted ARGs tet(T), sul1, and bla_CTX-M-1 in liquid hog manure, soil, and water samples were quantified by qPCR. Conventional PCR was used to detect mcr-1 and mcr-2. ARGs in control plots were detected despite the absence of manure, representing an environmental reservoir of resistant microorganisms. The manure application rate higher than 39 m³/ha increased tet(T) and sul1 gene concentrations in soil for more than 180 days. Tillage practices had no impact on ARG concentrations in soil and water samples. The bla_CTX-M-1 gene was only detected in seven water samples in 2016, but no link was established with the treatments. The mcr-1 and mcr-2 genes were not detected in all tested samples. This study demonstrated that tet(T) and sul1 gene concentrations increased in soil after liquid hog manure application as well as in drainage water in the next weeks.

Coupled effect of colloids and surface chemical heterogeneity on the transport of antibiotics in porous media

Release of antibiotics into the environment has caused ecological and human health concerns in recent years. However, little is known about their transport behaviors in chemically heterogeneous porous media. In this study, we investigated the coupled effects of surface chemistry and soil colloids on the transport of ciprofloxacin and tetracycline through sand under steady state saturated flow conditions. Both antibiotics had a much higher capacity of adsorption on soil colloids (17,500 mg/kg for ciprofloxacin and 8600 mg/kg for tetracycline) than on sand (5.11 mg/kg for ciprofloxacin and 2.80 mg/kg for tetracycline). However, ciprofloxacin adsorption increased to 8.91 mg/kg after the sand was coated with iron oxide and to 8.73 mg/kg after the sand was coated with humic acid. Tetracycline, adsorption increased to 7.99 mg/kg after sand was coated with iron oxide coated sand and to 8.35 mg/kg after the sand was coated with humic acid coated The high adsorption capacity of ciprofloxacin led to a recovery rate of <4% in the effluents of the columns containing 0%, 20% and 50% of iron oxide/humic acid coated sand. The surface coating decreased the recovery rates of tetracycline from 35.4% (in uncoated sand) to 12.0% (in column containing 50% iron oxide coated sand) and 0.010% (in column containing 50% humic acid coated sand), respectively. Once adsorbed to soil colloids, the recovery rate of ciprofloxacin increased by 26.7% in uncoated sand column, 21.1% in iron oxide coated sand column, and 32.7% in humic acid coated sand column. Similarly, the presence of the colloids increased the recovery rate of tetracycline from 13.8% to 33.2% after the sand was coated with humic acid. Colloids did not significantly influence the transport and recovery of tetracycline in the uncoated sand and iron oxide coated sand due likely to its lower adsorption affinity.

A review of the occurrence of selected micropollutants and microorganisms in different raw and treated manure - Environmental risk due to antibiotics after application to soil

This study consists of a review based on 104 papers published between 1980 and 2019, which dealt with the occurrence of pharmaceuticals, hormones and a selection of microorganisms in raw and treated manure from different types of animal farms. The selected pharmaceuticals and hormones are those regularly administered to livestock for treating and preventing diseases. Worldwide, manure is commonly spread on soil as a fertilizer due to its nutrient content. However, this practice also represents a potential pathway for micropollutant release into the environment. In this context, this study evaluates the predicted concentrations of some antibiotics in soil after the application of swine slurry on soil and compares them with corresponding measured concentrations found in the literature. Enrofloxacin, oxytetracycline and chlortetracycline were the antibiotics with the highest concentrations that were found in raw and treated manure and that showed a high risk together with sulfamethazine. Future research should focus on monitoring other pathogens, parent compounds and their main metabolites in raw and treated manure, studying the spread and development of antibiotic resistance genes in the environment due to residues of antibiotics in manure applied to soil, and evaluating predicted no effect concentrations of pharmaceuticals and hormones commonly administered to livestock with regard to terrestrial organisms.

Fate of pharmaceuticals and antibiotic resistance genes in a full-scale on-farm livestock waste treatment plant

This study investigated, for the first time, the distribution and fate of 28 multiple-class veterinary pharmaceuticals and antibiotics (PhACs), and their corresponding antibiotic resistance genes (ARGs), in a full-scale on-farm livestock waste treatment plant. The plant relies on several technologies, including: anaerobic digestion (AD), solid-liquid separation, and two stages reverse osmosis (RO) of the liquid digestate. Tetracycline, fluoroquinolone, lincosamide and pleuromutilin antibiotics, together with anti-helmintic (flubendazole) and anti-inflammatory (flunixin) drugs were the most frequently detected compounds in livestock waste and in slaughterhouse sludge. This last fraction is used as co-substrate in the AD process and showed to be an important input source of PhACs and ARGs. In terms of treatment performance, AD exhibited moderate to low PhACs and ARGs reduction, while a large fraction (<50%) of the PhACs present in the digestate were distributed onto the solid fraction, after solid-liquid separation. Both solid and liquid digestates had relatively high copy numbers of ARGs. Finally, RO showed high rejection percentages for all PhACs (<90%), with concentrations in the low ng L^-1 range in permeates, for most target PhACs. Nevertheless, moderate copy numbers of ARGs were detected in permeates.

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.

A review of bacteriophage therapy for pathogenic bacteria inactivation in the soil environment

The emerging contamination of pathogenic bacteria in the soil has caused a serious threat to public health and environmental security. Therefore, effective methods to inactivate pathogenic bacteria and decrease the environmental risks are urgently required. As a century-old technique, bacteriophage (phage) therapy has a high efficiency in targeting and inactivating pathogenic bacteria in different environmental systems. This review provides an update on the status of bacteriophage therapy for the inactivation of pathogenic bacteria in the soil environment. Specifically, the applications of phage therapy in soil-plant and soil-groundwater systems are summarized. In addition, the impact of phage therapy on soil functioning is described, including soil function gene transmission, soil microbial community stability, and soil nutrient cycling. Soil factors, such as soil temperature, pH, clay mineral, water content, and nutrient components, influence the survival and activity of phages in the soil. Finally, the future research prospects of phage therapy in soil environments are described.

A method to study antibiotic emission and fate for data-scarce rural catchments

Estimations of antibiotic emission and fate and thereby ecological risk in rural catchments still lack feasible methods due to data scarcity. This study developed a new framework to evaluate the emission and fate of typical antibiotics for data-scarce catchments with uncertainty analysis. We estimated antibiotic discharge through questionnaire surveys; predicted antibiotic fate in air, water, soil, and sediment phases using a multimedia fugacity model; and analyzed the uncertainties of predicted environmental concentrations (PECs) and ecological risks of antibiotics. The developed method was tested in the Meijiang River catchment in China, and the uncertainty was systematically analyzed. Results showed that the discharge of tetracycline antibiotics (TCs) in the studied watershed was 8.56 t/a, with approximately 93% from veterinary medicine. TCs existed dominantly in the soil phase, accounting for 87.3% of total discharge. TC levels at the equilibrium states were the highest in sediment and soil, followed by water and air. The emission levels of TCs may cause slight risk to algae, daphniids, and fish in the receiving water based on the ecological risk evaluation of PECs. Despite of some uncertainties, the developed method provided an effective alternative to evaluate the ecological risks of antibiotics in catchments where sufficient monitored data are unavailable.

Do reductions in agricultural field drainage during the growing season impact bacterial densities and loads in small tile-fed watersheds?

Predicting bacterial levels in watersheds in response to agricultural beneficial management practices (BMPs) requires understanding the germane processes at both the watershed and field scale. Controlling subsurface tile drainage (CTD) is a highly effective BMP at reducing nutrient losses from fields, and watersheds when employed en masse, but little work has been conducted on CTD effects on bacterial loads and densities in a watershed context. This study compared fecal indicator bacteria (FIB) [E. coli, Enterococcus, Fecal coliform, Total coliform, Clostridium perfringens] densities and unit area loads (UAL) from a pair of flat tile-drained watersheds (∼250-467 ha catchment areas) during the growing season over a 10-year monitoring period, using a before-after-control-impact (BACI) design (i.e., test CTD watershed vs. reference uncontrolled tile drainage (UCTD) watershed during a pre CTD intervention period and a CTD-intervention period where the test CTD watershed had CTD deployed on over 80% of the fields). With no tile drainage management, upstream tile drainage to ditches comprised ∼90% of total ditch discharge. We also examined FIB loads from a subset of tile drained fields to determine field load contributions to the watershed drainage ditches. Statistical evidence of a CTD effect on FIB UAL in the surface water systems was not strong; however, there was statistical evidence of increased FIB densities [pronounced when E. coli >200 most probable number (MPN) 100 mL^-1] in the test CTD watershed during the CTD-intervention period. This was likely a result of reduced dilution/flushing in the test CTD watershed ditch due to CTD significantly decreasing the amount of tile drainage water entering the surface water system. Tile E. coli load contributions to the ditches were low; for example, during the 6-yr CTD-intervention period they amounted to on average only ∼3 and ∼9% of the ditch loads for the test CTD and reference UCTD watersheds, respectively. This suggests in-stream, or off-field FIB reservoirs and bacteria mobilization drivers, dominated ditch E. coli loads in the watersheds during the growing season. Overall, this study suggested that decision making regarding deployment of CTD en masse in tile-fed watersheds should consider drainage practice effects on bacterial densities and loads, as well as CTD's documented capacity to boost crop yields and reduce seasonal nutrient pollution.

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.

Biochar combined with polyvalent phage therapy to mitigate antibiotic resistance pathogenic bacteria vertical transfer risk in an undisturbed soil column system

The vertical migration of antibiotic resistance pathogenic bacteria (ARPB) and antibiotic resistance genes (ARGs) in the surface soil-vadose soil system has become a new threat to ecological safety and public health; there is an imperative need to develop an efficient technique for targeted control and inactivation of ARPB in these systems. In this work, undisturbed soil columns (0 ∼ -5 m) were constructed to investigate the impact of biochar amendment or/and polyvalent bacteriophage (ΦYSZ-KK) therapy on the vertical control and inactivation of tetracycline-resistant Escherichia coli K-12 and chloramphenicol-resistant Klebsiella pneumonia K-6. The simultaneous application of polyvalent phage and biochar impeded the vertical migration of ARPB from the top soil to lower soil layers and stimulated the ARPB dissipation in the soil column. After 60-day incubation, levels of ARPB and ARGs decreased significantly in the soil column by magnitudes of 2-6. Additionally, high throughput sequencing indicated that the simultaneous application of biochar and phage clearly maintained the structure and diversity of the soil microbial communities (p <  0.05). This work therefore demonstrates that the application of a biochar/phage combination is an environmentally friendly, efficacious measure for the control and inactivation of ARPB/ARGs in vertical soil column systems.

Veterinary pharmaceuticals and antibiotics in manure and slurry and their fate in amended agricultural soils: Findings from an experimental field site (Baix Empordà, NE Catalonia)

The fate and transport of 34 veterinary pharmaceuticals (PhACs) is investigated in swine slurry and dairy cattle manure-amended agricultural soils, from an experimental field site, by using both analytical and modelled data. Potential differences on PhACs fate, attributed to the application of distinct swine slurry fractions (total, solid, and liquid), are herein assessed for the first time. Surface and deep soil layers, up to a depth of 120 cm, were analyzed at different periods after an annual fertilization event. Using input data representing typical agricultural soil conditions and the PhACs concentration measured in organic fertilizers the transport of these pollutants was modelled for a period of 10 years, including the monitored annual fertilization event. Fluoroquinolone, tetracycline and pleuromutilin antibiotics, together with anti-helmintics and analgesic and anti-inflammatories, were detected in manure-amended soils, at average concentrations ranging from 0.078 to 150 μg/kg dw in surface layers, with the highest levels found in the fields fertilized with the swine slurry solid fraction. Even though severe disagreements were observed between experimental and simulated PhACs concentrations along the soil column, both approaches pointed out that target compounds strongly adsorb onto surface layers, showing limited mobility along the soil profile. Thus, repeated manure and slurry fertilizations will contribute in building up persistent PhACs residues in the uppermost layers of the soil, while leaching will be a minor process governing their fate towards the subsurface. The ecotoxicological risks posed by the occurrence of PhACs in soils were estimated to be low for terrestrial organisms. Nevertheless the antibiotic enrofloxacin showed some potential to induce negative effects to crops.

The prevalence of Campylobacter spp. in vegetables, fruits, and fresh produce: a systematic review and meta-analysis

There are a number of reports indicating correlation between outbreaks of campylobacteriosis and the consumption of raw vegetables. This study is a meta-analysis on the prevalence of Campylobacter in fresh vegetables and fruits without any location limitation, which was performed through a documented review of the available resources. Relevant literature was reviewed by trained reviewers, who examined the results for the inclusion of articles in the meta-analysis. The prevalence of Campylobacter in raw vegetables, the sample source, the Campylobacter species, and the method of detection were extracted. The prevalence of Campylobacter in vegetables, fruits, and fresh produce were estimated to be 0.53%. Analysis of the various sample groups initially showed that the bean and sprouts group was the vegetable with the highest prevalence of Campylobacter (11.08%). The rate of contamination was higher when both the molecular and conventional methods were employed. The highest prevalence of Campylobacter was found in Asia (33.4%). Despite the low prevalence, consumption of raw vegetables is inherently risky because no treatment is used to inactivate the pathogens. Therefore, proper sanitation methods are recommended to treat the raw products.

Dissemination of antibiotic resistance genes and human pathogenic bacteria from a pig feedlot to the surrounding stream and agricultural soils

The dissemination of antibiotic resistance genes (ARGs), human pathogenic bacteria (HPB), and antibiotic-resistant HPB (ARHPB) from animal feedlot to nearby environment poses a potentially high risk to environmental ecology and public health. Here, a metagenomic analysis was employed to explore the dissemination of ARGs, HPB, and ARHPB from a pig feedlot to surrounding stream and agricultural soils. In total, not detectable (ND)-1,628.4 μg/kg of antibiotic residues, 18 types of ARGs, 48 HPB species, and 216 ARB isolates were detected in all samples. Antibiotic residues from pig feedlot mainly migrated into stream sediments and greenhouse soil. The dominant ARGs and HPB species from pig feedlot spread into stream sediments (tetracycline resistance genes, Clostridium difficile, and Mycobacterium tuberculosis), stream water (multidrug resistance (MDR) genes, Shigella flexneri, and Bordetella pertussis), and greenhouse soil (MDR genes, Bacillus anthracis, and Brucella melitensis). It is concerning that 54.4% of 216 ARB isolates from all samples were potential ARHPB species, and genome sequencing and functional annotation of 4 MDR HPB isolates showed 9 ARG types. Our findings revealed the potential migration and dissemination of antibiotic residues, ARGs, HPB, and ARHPB from pig feedlot to surrounding stream and agricultural soils via pig sewage discharge and manure fertilization.

Quantitative real-time PCR-based assessment of tile drainage management influences on bacterial pathogens in tile drainage and groundwater

This study compared the impact of controlled tile drainage (CD) and freely draining (FD) systems on the prevalence and quantitative real-time PCR-based enumeration of four major pathogens including Arcobacter butzleri, Campylobacter jejuni, Campylobacter coli, and Helicobacter pylori in tile- and groundwater following a fall liquid swine manure (LSM) application on clay loam field plots. Although the prevalence of all target pathogens were detected in CD and FD systems, the loads of A. butzleri, C. jejuni, and C. coli were significantly lower in CD tile-water (p<0.05), in relation to FD tile-water. However, concentrations of A. butzleri were significantly greater in CD than FD tile-water (p<0.05). In shallow groundwater (1.2m depth), concentrations of A. butzleri, C. coli, and H. pylori showed no significant difference between CD and FD plots, while C. jejuni concentrations were significantly higher in FD plots (p<0.05). No impact of CD on the H. pylori was observed since quantitative detection in tile- and groundwater was scarce. Although speculative, H. pylori occurrence may have been related to the application of municipal biosolids four years prior to the LSM experiment. Overall, CD can be used to help minimize off-field export of pathogens into surface waters following manure applications to land, thereby reducing waterborne pathogen exposure risks to humans.

Monitoring tylosin and sulfamethazine in a tile-drained agricultural watershed using polar organic chemical integrative sampler (POCIS)

This study evaluated the influence of temporal variation on the occurrence, fate, and transport of tylosin (TYL) and sulfamethazine (SMZ); antibiotics commonly used in swine production. Atrazine (ATZ) was used as a reference analyte to indicate the agricultural origin of the antibiotics. We also assessed the impact of season and hydrology on antibiotic concentrations. A reconnaissance study of the South Fork watershed of the Iowa River (SFIR), was conducted from 2013 to 2015. Tile drain effluent and surface water were monitored using polar organic integrative sampler (POCIS) technology. Approximately 169 animal feeding operations (AFOs) exist in SFIR, with 153 of them being swine facilities. All analytes were detected, and detection frequencies ranged from 69 to 100% showing the persistence in the watershed. Antibiotics were detected at a higher frequency using POCIS compared to grab samples. We observed statistically significant seasonal trends for SMZ and ATZ concentrations during growing and harvest seasons. Time weighted average (TWA) concentrations quantified from the POCIS were 1.87ngL^-1 (SMZ), 0.30ngL^-1 (TYL), and 754.2ngL^-1 (ATZ) in the watershed. SMZ and TYL concentrations were lower than the minimum inhibitory concentrations (MIC) for E. coli. All analytes were detected in tile drain effluent, confirming tile drainage as a pathway for antibiotic transport. Our results identify the episodic occurrence of antibiotics, and highlights the importance identifying seasonal fate and occurrence of these analytes.

Towards the understanding of antibiotic occurrence and transport in groundwater: Findings from the Baix Fluvià alluvial aquifer (NE Catalonia, Spain)

Antibiotics are an increasing focus of interest due to their high detection frequency in the environment. However, their presence in water bodies is not regulated by environmental policies. This field study investigates, for the first time, the occurrence, behavior and fate of a selection of 53 antibiotics, including up to 10 chemical groups, in an alluvial aquifer originated from manure application in an agricultural region using hydrogeological, hydrochemical and isotopic approaches. Up to 11 antibiotics were found in groundwater corresponding to 4 different chemical groups: fluoroquinolones, macrolides, quinolones and sulfonamides. In surface water, only 5 different antibiotics from 2 chemical groups: fluoroquinolones and sulfonamides, were quantified. The most frequent antibiotics were sulfamethoxazole and ciprofloxacin. Concentrations of antibiotics were in the order of ng/L, with maximum concentrations of 300ng/L in groundwater. Hydrochemistry and isotopic data and geostatistics confirmed the spatial trend observed for nitrates, where nitrate concentrations tend to be higher in the margin areas of the study area, and lower concentrations are found nearby the river. On the other hand, no clear continuous spatial concentration trend of antibiotics was observed in the aquifer, supported by the short spatial correlation found in the variograms. This indicates that the physical-chemical properties and processes of each antibiotic (mainly, sorption and degradation), and other environmental issues, such as a patchy diffuse input and the manure antibiotic content itself, play an important role in their spatial distribution in groundwater. A discussion on the estimation of the antibiotic sorption parameter reveals the difficulties of describing such phenomena. Furthermore, retardation factors will extend over several orders of magnitude, which highly affects the movement of individual antibiotics within the aquifer. To summarize, this study points out the difficulties associated with antibiotic research in groundwater in order to define water resources quality management strategies and environmental regulations.

Adsorptive removal of antibiotics from water using peanut shells from agricultural waste

The residues of sulfonamides in the environment have received widespread attention because of their potential hazards. In this study, the potential of peanut shells for antibiotic removal from aqueous solutions was investigated for four antibiotics (sulfamerazine, sulfamethazine, sulfathiazole, and sulfamethoxazole). The properties of the peanut shells were characterized using Brunauer–Emmett–Teller method, X-ray photoelectron spectroscopy, scanning electron microscopy and Fourier-transform infrared spectroscopy analyses, and the results of the analyses showed that the significant properties of peanut shells were mainly attributed to the antibiotics' adsorption process. A batch adsorption experiment was conducted to study the effect of dosage, concentration, and water factors (Fe³⁺, Mn²⁺, and Ca²⁺) on antibiotic adsorption. Adsorption kinetics and isotherms were also studied. The kinetic data showed that a pseudo-second order kinetic model fitted the experimental data, the adsorption isotherm experimental data fitted the Henry linear adsorption model well, and methanol was found to be an effective eluent for desorption of the antibiotics. The results indicate that peanut shells are a promising material for the removal of antibiotics from contaminated water, when present at low initial concentrations.

The porous structure of the materials was determined using the surface area and pore size analyzer (JW-BK132F) by N₂ adsorption–desorption isotherms at 77 K.

Catalogue of antibiotic resistome and host-tracking in drinking water deciphered by a large scale survey

BACKGROUND

Excesses of antibiotic resistance genes (ARGs), which are regarded as emerging environmental pollutants, have been observed in various environments. The incidence of ARGs in drinking water causes potential risks to human health and receives more attention from the public. However, ARGs harbored in drinking water remain largely unexplored. In this study, we aimed at establishing an antibiotic resistome catalogue in drinking water samples from a wide range of regions and to explore the potential hosts of ARGs.

RESULTS

A catalogue of antibiotic resistome in drinking water was established, and the host-tracking of ARGs was conducted through a large-scale survey using metagenomic approach. The drinking water samples were collected at the point of use in 25 cities in mainland China, Hong Kong, Macau, Taiwan, South Africa, Singapore and the USA. In total, 181 ARG subtypes belonging to 16 ARG types were detected with an abundance range of 2.8 × 10^-2 to 4.2 × 10^-1 copies of ARG per cell. The highest abundance was found in northern China (Henan Province). Bacitracin, multidrug, aminoglycoside, sulfonamide, and beta-lactam resistance genes were dominant in drinking water. Of the drinking water samples tested, 84% had a higher ARG abundance than typical environmental ecosystems of sediment and soil. Metagenomic assembly-based host-tracking analysis identified Acidovorax, Acinetobacter, Aeromonas, Methylobacterium, Methyloversatilis, Mycobacterium, Polaromonas, and Pseudomonas as the hosts of ARGs. Moreover, potential horizontal transfer of ARGs in drinking water systems was proposed by network and Procrustes analyses.

CONCLUSIONS

The antibiotic resistome catalogue compiled using a large-scale survey provides a useful reference for future studies on the global surveillance and risk management of ARGs in drinking water. .

Identification of antibiotics in wastewater: current state of extraction protocol and future perspectives

The release and occurrence of antibiotics in the aquatic environment has generated increased attention in the past few decades. The residual antibiotic in wastewater is important in the selection for antimicrobial resistance among microorganisms and the possibility of forming toxic derivatives. This review presents an assessment of the advancement in methods for extraction of antibiotics with solid phase extraction and liquid-liquid extraction methods applied in different aquatic environmental media. These advanced methods do enhance specificity, and also exhibit high accuracy and recovery. The aim of this review is to assess the pros and cons of the methods of extraction towards identification of quinolones and sulphonamides as examples of relevant antibiotics in wastewater. The challenges associated with the improvements are also examined with a view of providing potential perspectives for better extraction and identification protocols in the near future. From the context of this review, magnetic molecular imprinted polymer is superior over the remaining extraction methods (with the availability of commercial templates and monomers), is based on less cumbersome extraction procedures, uses less solvent and has the advantage of its reusable magnetic phase.

Agricultural soil denitrifiers possess extensive nitrite reductase gene diversity

Denitrification transforms nitrogen applied as fertilizer and emits N₂ O, which is a potent greenhouse gas. Very little is known about the identities of abundant and active denitrifiers in agricultural soils. We coupled DNA stable-isotope probing (DNA-SIP) with flow-through reactors (FTRs) to detect active agricultural soil denitrifiers. The FTRs were incubated with nitrate and ¹³ C₆ -glucose under anoxic conditions and sampled at multiple time points. Labelled DNA from active microorganisms was analyzed by 16S rRNA gene fingerprinting, amplicon and shotgun metagenomic sequencing. Taxonomic representation of heavy fractions was consistent across sites and time points, including Betaproteobacteria (71%; Janthinobacterium, Acidovorax, Azoarcus and Dechloromonas), Alphaproteobacteria (8%; Rhizobium), Gammaproteobacteria (4%; Pseudomonas) and Actinobacteria (4%; Streptomycetaceae). Most nitrite-reductase reads from heavy DNA annotated to the copper-containing form (nirK). Assigned taxonomies of active denitrifiers based on reads matching the nirK gene were comparable to those obtained through nitric oxide (norB) and RNA polymerase (rpoB) annotations but not the nitrous oxide reductase gene (nosZ). Analysis of recovered metagenomes from heavy DNA demonstrated extensive nirK sequence family diversity, including novel taxonomic groups that are not captured by existing primers.

Antibiotic pollution in the Katari subcatchment of the Titicaca Lake: Major transformation products and occurrence of resistance genes

An increasing number of studies pointed out the ubiquitous presence of medical residues in surface and ground water as well as in soil compartments. Not only antibiotics can be found in the environment but also their transformation products about which little information is generally available. The development of bacterial resistance to antibiotics is particularly worrying as it can lead to sanitary and health problems. Studies about the dissemination of antibiotics and associated resistances in the Bolivian Altiplano are scarce. We provide baseline information on the occurrence of Sulfamethoxazole (SMX) and Trimethoprim (TMP) antibiotics as well as on the most common human SMX transformation products (TP) and on the occurrence of sulfonamide resistance genes. The studied water and soil compartments presented high levels of antibiotic pollution. This situation was shown to be mainly linked with uncontrolled discharges of treated and untreated wastewaters, resulting on the presence of antibiotics in the Titicaca Lake. SMX TPs were detected in surface waters and on soil sampled next to the wastewater treatment plant (WWTP). SMX resistance genes sulI and sulII were widely detected in the basin hydrological network, even in areas unpolluted with antibiotics. Mechanisms of co-selection of antibiotic- and metal- resistance may be involved in the prevalence of ARG's in pristine areas with no anthropogenic activity and free of antibiotic pollution.

Use of commercial organic fertilizer increases the abundance of antibiotic resistance genes and antibiotics in soil

The application of manure-based commercial organic fertilizers (COFs) is becoming increasingly extensive because of the expanding market for organic food. The present study examined the effects of repeated applications of chicken or swine manure-based COFs on the fate of antibiotics and antibiotic resistance genes (ARGs) in soil by conducting a soil microcosm experiment. Application of COFs significantly increased antibiotics residues, as well as the relative abundance of ARGs and the integrase gene of class 1 integrons (intΙ1) in soil. Two months after each application, antibiotics and ARGs dissipated in amended soils, but they still remained at an elevated level, compared with the control. And, the accumulation of antibiotics was found due to repeated COF applications. However, the relative abundance of ARGs in most COF-amended soils did not differ significantly between the first application and the repeated application. The results imply that 2 months are not sufficient for ARGs to approach background levels, and that animal manure must be treated more effectively prior to using it in agriculture ecosystems.

Effect of biochar amendment on the control of soil sulfonamides, antibiotic-resistant bacteria, and gene enrichment in lettuce tissues

Considering the potential threat of vegetables growing in antibiotic-polluted soil with high abundance of antibiotic-resistant genes (ARGs) against human health through the food chain, it is thus urgent to develop novel control technology to ensure vegetable safety. In the present work, pot experiments were conducted in lettuce cultivation to assess the impedance effect of biochar amendment on soil sulfonamides (SAs), antibiotic-resistant bacteria (ARB), and ARG enrichment in lettuce tissues. After 100 days of cultivation, lettuce cultivation with biochar amendment exhibited the greatest soil SA dissipation as well as the significant improvement of lettuce growth indices, with residual soil SAs mainly existing as the tightly bound fraction. Moreover, the SA contents in roots and new/old leaves were reduced by one to two orders of magnitude compared to those without biochar amendment. In addition, isolate counts for SA-resistant bacterial endophytes in old leaves and sul gene abundances in roots and old leaves also decreased significantly after biochar application. However, neither SA resistant bacteria nor sul genes were detected in new leaves. It was the first study to demonstrate that biochar amendment can be a practical strategy to protect lettuce safety growing in SA-polluted soil with rich ARB and ARGs.

Feasibility of lettuce cultivation in sophoroliplid-enhanced washed soil originally polluted with Cd, antibiotics, and antibiotic-resistant genes

Vegetable cultivation in soils polluted with heavy metals, antibiotics and a high abundance of antibiotic-resistance genes (ARGs) can seriously threaten human health through the food chain. Therefore, novel techniques that not only remediate soil, but also ensure food security are urgently required. In the present study, two successive washings with 20gL(-1) of sophoroliplid solution plus ultrasonication (35kHz) were effective in extracting 71.2% Cd, 88.2% tetracycline, 96.6% sulfadiazine, and 100% roxithromycin. Simultaneously, relative abundance of ARGs (tetM, tetX, sulI, and sulII) was decreased to 10(-7)-10(-8) (ARG copies/16S copies). Further, lettuce cultivation in the 2nd washed soil showed significant improvement in vegetable growth indices (fresh/dry weight, root surface area, chlorophyll content and soluble protein content) and a decrease in isolate counts for antibiotic-resistant bacterial endophytes and ARG abundance in lettuce tissues. This combined cleanup strategy provides an environmentally friendly technology for ensuring vegetable security in washed soils.