Human Health Risk Assessment (HHRA) for environmental development and transfer of antibiotic resistance

Prevalence of Antimicrobial Resistant and Extended-Spectrum Beta-Lactamase-producing Escherichia coli in Dairy Cattle Farms in East Tennessee

Antimicrobials have been widely used in dairy farms to prevent and control dairy cattle diseases since 1960s. This led to the emergence of antimicrobial resistant bacteria (ARB) that, along with their antimicrobial resistance genes (ARGs), can spread from dairy farms to humans. Therefore, regular antimicrobial resistance (AMR) monitoring is important to implement proper mitigation measures. The objective of this study was to determine the prevalence of AMR and extended-spectrum beta-lactamases (ESBLs)-producing Escherichia coli in dairy cattle. A cross-sectional study was conducted in four dairy cattle farms (A-D) in East Tennessee. A total of 80 samples consisting of 20 samples each of bulk tank milk, feces, dairy cattle manure-amended soil, and prairie soil adjacent to the farms were collected and cultured for the isolation of E. coli. Tetracycline (TET^r)-, third-generation cephalosporin (TGC^r)- and nalidixic acid (NAL^r)-resistant E. coli (n = 88) were isolated and identified on agar media supplemented with TET, cefotaxime, and NAL, respectively. TGC^r E. coli were tested for ESBLs and other coselected ARGs. TET^r (74%, n = 88) was the most common, followed by TGC^r (20%) and NAL^r (8%). Farms had significant (p < 0.001) differences: the highest prevalence of TGC^r (55%) and TET^r (100%) were observed in farm D, while all NAL^r isolates were from farm C. Over 83% of TGC^r isolates (n = 18) harbored ESBL gene bla_CTX-M. Majority (78%) of the E. coli isolates were multidrug-resistant (MDR), being positive for beta-lactams (bla_CTX-M), TETs tet(A), tet(B), tet(M)), sulfonamides (sul2), aminoglycosides (strA), and phenicols (floR). This study indicated the widespread occurrence of MDR ESBLs-E. coli in dairy cattle farms. AMR surveillance of more dairy farms and identification of farm-level risk factors are important to mitigate the occurrence and spread of ARB of significant public health importance, such as ESBLs-E. coli.

Prevalence of enteric opportunistic pathogens and extended-spectrum cephalosporin- and carbapenem-resistant coliforms and genes in wastewater from municipal wastewater treatment plants in Croatia

Extended-spectrum β-lactamase (ESBL)- and carbapenemase-producing Enterobacterales are a critical global health problem and wastewater treatment plants (WWTPs) can promote their spread into the environment; yet their efficacy is not well characterized. Here, we have used conventional culturing to monitor coliform bacteria and quantitative PCR to monitor 2 ESBL and 5 carbapenemase (CP) genes and 4 enteric opportunistic pathogens (EOPs) in the influent and effluent of 7 Croatian WWTPs in two seasons. In general, levels of total, cefotaxime- and carbapenem-resistant coliforms were significantly reduced but not eliminated by conventional treatment in most WWTPs. Most WWTPs efficiently removed EOPs such as K. pneumoniae and A. baumannii, while E. coli and Enterococcus spp. were reduced but still present in relatively high concentrations in the effluent. ESBL genes (bla_TEM and bla_CTX-M-32) were only slightly reduced or enriched after treatment. CP genes, bla_KPC-3, bla_NDM and bla_OXA-48-like, were sporadically detected, while bla_IMP and bla_VIM were frequently enriched during treatment and correlated with plant size, number or size of hospitals in the catchment area, and COD effluent concentration. Our results suggest that improvements in wastewater treatment technologies are needed to minimize the risk of environmental contamination with top priority EOPs and ARGs and the resulting public health.

Multidrug resistance from a one health perspective in Ethiopia: A systematic review and meta-analysis of literature (2015–2020)

Purpose

The emergence of antimicrobial resistance is a major global health challenge and becoming an urgent priority for policymakers. There is a paucity of scientific studies presenting the multidrug resistance pattern from one health perspective in Ethiopia. Therefore, a systematic review and meta-analysis aimed to determine the pooled prevalence of multidrug resistance in bacteria from human, animal, food, and environmental sources.

Methods

In this systematic review and meta-analysis, an electronic search was made in PubMed & Google scholar using different keywords. The studies conducted in all areas of Ethiopia, published from 2015 to 2020 in peer-reviewed journals, English full-length papers were included. The meta-analysis was done on STATA version 14. The pooled prevalence of multidrug resistance for each bacterium was analysed using the random-effects model; Cochran Q statistics and the I² statistic was used to analyse heterogeneity and considered significant at p < 0.01.

Results

81 studies were included in the systematic review and meta-analysis; 53 human studies, eight animal studies, and 16 environments/food studies. The meta-analysis included six species from gram-positive bacteria and 13 from gram-negative bacteria. S. aureus 53% (95%CI: 42–64%), Coagulase negative Staphylococci 68%(95%CI:53–82), Pseudomonas spp. 73%(95%CI:48–93%), E. coli 70% (95%CI:61–78%), Citrobacter spp. 71%(95%CI:54–87%), Klebsiella spp. 68% (54–80%), Enterobacter spp. 67% (48–83%) and Salmonella spp. 65% (95%CI:48–81%) were the common multidrug-resistant species of bacteria from two or more sources.

Conclusion

In Ethiopia, the pooled prevalence of MDR is high in most bacterial species from humans, animals, food, and environmental sources. Staphylococcus, most members of the Enterobacteriaceae and Pseudomonas, are the standard MDR bacterial population involving all sources. Therefore, integrated policy and intervention measures should be implemented to reduce the emergence and spread of MDR bacteria for better animal and human health outcomes.

Gentamicin at sub-inhibitory concentrations selects for antibiotic resistance in the environment

Antibiotics released into the environment at low (sub-inhibitory) concentrations could select for antibiotic resistance that might disseminate to the human microbiome. In this case, low-level anthropogenic sources of antibiotics would have a significant impact on human health risk. In order to provide data necessary for the evaluation of this risk, we implemented river water microcosms at both sub-inhibitory and inhibitory concentrations of gentamicin as determined previously based on bacterial growth in enriched media. Using metagenomic sequencing and qPCR/RT-qPCR, we assessed the effects of gentamicin on water bacterial communities and their resistome. A change in the composition of total and active communities, as well as a gentamicin resistance gene selection identified via mobile genetic elements, was observed during a two-day exposure. We demonstrated the effects of sub-inhibitory concentrations of gentamicin on bacterial communities and their associated resistome in microcosms (simulating in situ conditions). In addition, we established relationships between antibiotic dose and the magnitude of the community response in the environment. The scope of resistance selection under sub-inhibitory concentrations of antibiotics and the mechanisms underlying this process might provide the basis for understanding resistance dispersion and associated risks in relatively low impacted ecosystems.

A Farm-to-Fork Quantitative Microbial Exposure Assessment of β-Lactam-Resistant Escherichia coli among U.S. Beef Consumers

Integrated quantitative descriptions of the transmission of β-lactam-resistant Escherichia coli (BR-EC) from commercial beef products to consumers are not available. Here, a quantitative microbial exposure assessment model was established to simulate the fate of BR-EC in a farm-to-fork continuum and provide an estimate of BR-EC exposure among beef consumers in the U.S. The model compared the per-serving exposures from the consumption of intact beef cuts, non-intact beef cuts, and ground beef. Additionally, scenario analysis was performed to evaluate the relative contribution of antibiotic use during beef cattle production to the level of human exposure to BR-EC. The model predicted mean numbers of BR-EC of 1.7 × 10-4, 8.7 × 10-4, and 6.9 × 10-1 CFU/serving for intact beef cuts, non-intact beef cuts, and ground beef, respectively, at the time of consumption. Sensitivity analyses using the baseline model suggested that factors related to sectors along the supply chain, i.e., feedlots, processing plants, retailers, and consumers, were all important for controlling human exposure to BR-EC. Interventions at the processing and post-processing stages are expected to be most effective. Simulation results showed that a decrease in antibiotic use among beef cattle might be associated with a reduction in exposure to BR-EC from beef consumption. However, the absolute reduction was moderate, indicating that the effectiveness of restricting antibiotic use as a standalone strategy for mitigating human exposure to BR-EC through beef consumption is still uncertain. Good cooking and hygiene practices at home and advanced safety management practices in the beef processing and post-processing continuum are more powerful approaches for reducing human exposure to antibiotic-resistant bacteria in beef products.

A roadmap for the generation of benchmarking resources for antimicrobial resistance detection using next generation sequencing

Next Generation Sequencing technologies significantly impact the field of Antimicrobial Resistance (AMR) detection and monitoring, with immediate uses in diagnosis and risk assessment. For this application and in general, considerable challenges remain in demonstrating sufficient trust to act upon the meaningful information produced from raw data, partly because of the reliance on bioinformatics pipelines, which can produce different results and therefore lead to different interpretations. With the constant evolution of the field, it is difficult to identify, harmonise and recommend specific methods for large-scale implementations over time. In this article, we propose to address this challenge through establishing a transparent, performance-based, evaluation approach to provide flexibility in the bioinformatics tools of choice, while demonstrating proficiency in meeting common performance standards. The approach is two-fold: first, a community-driven effort to establish and maintain “live” (dynamic) benchmarking platforms to provide relevant performance metrics, based on different use-cases, that would evolve together with the AMR field; second, agreed and defined datasets to allow the pipelines’ implementation, validation, and quality-control over time. Following previous discussions on the main challenges linked to this approach, we provide concrete recommendations and future steps, related to different aspects of the design of benchmarks, such as the selection and the characteristics of the datasets (quality, choice of pathogens and resistances, etc.), the evaluation criteria of the pipelines, and the way these resources should be deployed in the community.

Existing evidence on antibiotic resistance exposure and transmission to humans from the environment: a systematic map

BACKGROUND

Antimicrobial resistance (AMR) is predicted to become the leading cause of death by 2050 with antibiotic resistance being an important component. Anthropogenic pollution introduces antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) to the natural environment. Currently, there is limited empirical evidence demonstrating whether humans are exposed to environmental AMR and whether this exposure can result in measurable human health outcomes. In recent years there has been increasing interest in the role of the environment and disparate evidence on transmission of AMR to humans has been generated but there has been no systematic attempt to summarise this. We aim to create two systematic maps that will collate the evidence for (1) the transmission of antibiotic resistance from the natural environment to humans on a global scale and (2) the state of antibiotic resistance in the environment in the United Kingdom.

METHODS

Search strategies were developed for each map. Searches were undertaken in 13 bibliographic databases. Key websites were searched and experts consulted for grey literature. Search results were managed using EndNote X8. Titles and abstracts were screened, followed by the full texts. Articles were double screened at a minimum of 10% at both stages with consistency checking and discussion when disagreements arose. Data extraction occurred in Excel with bespoke forms designed. Data extracted from each selected study included: bibliographic information; study site location; exposure source; exposure route; human health outcome (Map 1); prevalence/percentage/abundance of ARB/antibiotic resistance elements (Map 2) and study design. EviAtlas was used to visualise outputs.

RESULTS

For Map 1, 40 articles were included, from 11,016 unique articles identified in searches, which investigated transmission of AMR from the environment to humans. Results from Map 1 showed that consumption/ingestion was the most studied transmission route. Exposure (n = 17), infection (n = 16) and colonisation (n = 11) being studied as an outcome a similar number of times, with mortality studied infrequently (n = 2). In addition, E. coli was the most highly studied bacterium (n = 16). For Map 2, we included 62 studies quantifying ARB or resistance elements in the environment in the UK, from 6874 unique articles were identified in the searches. The most highly researched species was mixed communities (n = 32). The most common methodology employed in this research question was phenotypic testing (n = 37). The most commonly reported outcome was the characterisation of ARBs (n = 40), followed by characterisation of ARGs (n = 35). Other genetic elements, such as screening for intI1 (n = 15) (which encodes a Class 1 integron which is used as a proxy for environmental ARGs) and point mutations (n = 1) were less frequently reported. Both maps showed that research was focused towards aquatic environments.

CONCLUSIONS

Both maps can be used by policy makers to show the global (Map 1) and UK (Map 2) research landscapes and provide an overview of the state of AMR in the environment and human health impacts of interacting with the environment. We have also identified (1) clusters of research which may be used to perform meta-analyses and (2) gaps in the evidence base where future primary research should focus.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1186/s13750-022-00262-2.

Sex differences in the pharmacokinetics and tissue residues of Macleaya cordata extracts in rats

Macleaya cordata extracts (MCE) are listed as feed additives in animal production by the European Food Authority. The core components of MCE are mainly sanguinarine (SA) and chelerythrine (CHE). This study aims to investigate sex differences in the pharmacokinetics and tissue residues of MCE in rats.Male and female rates were intragastrically administered MCE (1.25 mg·kg^-1 body weight and 12.5 mg·kg^-1 body weight dose for 28 days). SA and CHE concentrations were determined using high-performance liquid chromatography/tandem mass spectrometry.The peak plasma concentration (C_max) and area under the curve (AUC) of both CHE and SA were higher in female than in male rats (12.5 mg·kg^-1 body weight group), whereas their half-life (T_1/2) and apparent volume of distribution (V_d) was lower (p < 0.05). Tissue rfesidue analysis indicated that SA and CHE were more distributed in male than in female rats and were highly distributed in the cecum and liver. SA and CHE were completely eliminated from the liver, kidney, lung, heart, spleen, leg muscle, and cecum after 120 h, indicating they did not accumulate in rats for a long time.Overall, we found that the pharmacokinetics and tissue residues of SA and CHE of male and female rats showed sex differences.

Swine manure facilitates the spread of antibiotic resistome including tigecycline-resistant tet(X) variants to farm workers and receiving environment

The prevalence of antibiotic resistance genes (ARGs) in livestock and poultry manure is a severe threat to human health. However, the comprehensive characterization of antibiotic resistance in swine, workers, and the receiving environment is still lacking in the actual breeding environment. Hence, the ARG profile and the potential bacterial hosts producing among swine manure (including sows, piglets, finishing pigs, and nursery pigs), worker feces, and the receiving environment (including sediment and vegetable soil) were comprehensively analyzed based on the metagenomic method. The results showed that swine manure exhibited the high levels of richness and diversity of ARGs. Inactivating tetracycline resistance genes such as tet(X), tet(X1), and tet(X10) were prevalent on swine farms. Workers and the environment were the primary recipients of ARGs, and shared ARGs accounted for at least 90% of their ARG abundances. Network analysis revealed that Escherichia, Acinetobacter, and Erysipelothrix were the most dominant genera co-occurring with specific shared ARGs. The abundance of coexisting ARGs in swine at different developmental stages accounted for 76.4% to 90.8% of the shared ARGs in swine, workers, and environmental samples. The Mantel test revealed that Firmicutes and Proteobacteria had a significant correlation with the ARG profiles. In addition, variation partitioning analysis (VPA) showed that the joint effects of mobile genetic elements (MGEs) and bacterial communities accounted for 24.7% of the resistome variation and played a significant role in the ARG profiles. These results improve our understanding of the transmission and persistence of ARGs in the actual breeding environment.

Synchronous construction of a porous intramolecular D-A conjugated polymer via electron donors for superior photocatalytic decontamination

The development of conjugated polymers with intramolecular donor-acceptor (D-A) units has the capacity to enhance the photocatalytic performance of carbon nitride (g-C₃N₄) for the removal of antibiotics from ambient ecosystems. This strategy addresses the challenge of narrowing the band gap of g-C₃N₄ while maintaining its high LUMO position. For this study, we introduced the above donor units into g-C₃N₄ to construct intramolecular D-A structures through the copolymerization of dicyandiamide with creatinine, which strategically extended light absorption into the green region and expedited photoelectron separation. The introduction of electron donor blocks kept the LUMO distributed on the melem, which maintained the high LUMO energy level of the copolymer with the potential to generate oxygen radicals. The as-prepared porous D-A conjugated polymer enhanced the photocatalytic degradation of sulfisoxazole with kinetic constants 5.6 times higher than that of g-C₃N₄ under blue light and 15.3 times higher under green light. Furthermore, we surveyed the degradation mechanism including the effective active species and degradation pathways. This study offers a new perspective for the synchronous construction of a porous intramolecular D-A conjugated polymer to enhance water treatment and environmental remediation capacities.

A new modelling framework for assessing the relative burden of antimicrobial resistance in aquatic environments

The infections caused by antibiotic resistant bacteria (ARB) can lead to higher medical costs, prolonged hospital stays, and increased mortality compared to bacteria that are susceptible to antibiotics. Challenges exist in quantifying the potential risk/burden associated with antimicrobial resistance (AMR) as there is a lack of dose-response models available for pathogens which are resistant to antibiotics, in addition to the fact that very little is known regarding the health risks posed by antibiotic resistant genes (ARG). In this paper, we proposed a new modelling framework to evaluate the relative burden of AMR in natural aquatic environments. With this framework, an AMR burden score for each sample was calculated based on burden coefficients assigned for each ARB and ARG, as well as weighted burdens for the separate ARBs and ARGs components. The method developed in this study was applied to assess the relative burden of AMR in local aquatic environments with different land uses at different seasons. The collected filed data were used to verify the applicability of the proposed relative burden assessment method. Through the established method, the spatial and temporal hotspots of AMR were identified, which could provide useful information to agencies for better control and management of AMR emergence in natural aquatic environments.

Monitoring antibiotic resistance genes in wastewater environments: The challenges of filling a gap in the One-Health cycle

Antibiotic resistance (AR) is a global problem requiring international cooperation and coordinated action. Global monitoring must rely on methods available and comparable across nations to quantify AR occurrence and identify sources and reservoirs, as well as paths of AR dissemination. Numerous analytical tools that are gaining relevance in microbiology, have the potential to be applied to AR research. This review summarizes the state of the art of AR monitoring methods, considering distinct needs, objectives and available resources. Based on the overview of distinct approaches that are used or can be adapted to monitor AR, it is discussed the potential to establish reliable and useful monitoring schemes that can be implemented in distinct contexts. This discussion places the environmental monitoring within the One-Health approach, where two types of risk, dissemination across distinct environmental compartments, and transmission to humans, must be considered. The plethora of methodological approaches to monitor AR and the variable features of the monitored sites challenge the capacity of the scientific community and policy makers to reach a common understanding. However, the dialogue between different methods and the production of action-oriented data is a priority. The review aims to warm up this discussion.

Nitrate in Groundwater Resources of Hormozgan Province, Southern Iran: Concentration Estimation, Distribution and Probabilistic Health Risk Assessment Using Monte Carlo Simulation

High nitrate concentration in drinking water has the potential to cause a series of harmful effects on human health. This study aims to evaluate the health risk of nitrate in groundwater resources of Hormozgan province in four age groups, including infants, children, teenagers, and adults, based on the US EPA methodology and Monte Carlo technique to assess uncertainty and sensitivity analysis. A Geographic Information System (GIS) was used to investigate the spatial distribution of nitrate levels in the study area. The nitrate concentration ranged from 0.3 to 30 mg/L, with an average of 7.37 ± 5.61 mg/L. There was no significant difference between the average concentration of nitrate in all study areas (p > 0.05). The hazard quotient (HQ) was less than 1 for all age groups and counties, indicating a low-risk level. The HQ95 for infants and children in the Monte Carlo simulation was 1.34 and 1.22, respectively. The sensitivity analysis findings showed that the parameter with the most significant influence on the risk of toxicity in all age groups was the nitrate content. Therefore, implementing a water resources management program in the study area can reduce nitrate concentration and enhance water quality.

Human health and ecological risk assessment of 98 pharmaceuticals and personal care products (PPCPs) detected in Indian surface and wastewaters

The release of pharmaceuticals and personal care products (PPCPs) in environmental waters has become an urgent issue due to their pseudo-persistent traits. The present study was undertaken to conduct a screening-level risk assessment of 98 PPCPs, detected in different water matrices (treated wastewater, surface water, and groundwater) of India, for evaluating ecological risk (risk to fish, daphnia, and algae), human health risk, and antimicrobial resistance (AMR) selection risk by following risk quotient (RQ) based methodology. In the present study, 47% of the detected PPCPs in Indian waters were found to exert a possible risk (RQ > 1) to either aquatic species and human health, or cause AMR selection risk. 17 out of 25 antibiotics detected in the environmental waters were found to pose a threat of AMR selection. 11 out of 49 pharmaceuticals were found to exert human health risk from ingesting contaminated surface water, whereas only 2 pharmaceuticals out of 25 were found to exert risk from the intake of groundwater. Very high RQs (>1000) for few pharmaceuticals were obtained, signifying a great potential of the detected PPCPs in causing severe health concern, aquatic toxicity, and AMR spread. Within India, special attention needs to be given to the pharmaceutical hubs, as the environmental waters in these regions were found to be severely contaminated with drug residues resulting in extremely high RQs. The present study will be helpful in prioritizing the detected PPCPs in the environmental waters of India, for which immediate attention and enforceable guidelines are required.

Bacterial Genes Encoding Resistance Against Antibiotics and Metals in Well-Maintained Drinking Water Distribution Systems in Finland

Information on the co-occurrence of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) among bacterial communities in drinking water distribution systems (DWDSs) is scarce. This study characterized ARGs and MRGs in five well-maintained DWDSs in Finland. The studied DWDSs had different raw water sources and treatment methods. Two of the waterworks employed artificially recharged groundwater (ARGW) and used no disinfection in the treatment process. The other three waterworks (two surface and one groundwater source) used UV light and chlorine during the treatment process. Ten bulk water samples (two from each DWDS) were collected, and environmental DNA was extracted and then sequenced using the Illumina HiSeq platform for high-throughput shotgun metagenome sequencing. A total of 430 ARGs were characterized among all samples with the highest diversity of ARGs identified from samples collected from non-disinfected DWDSs. Furthermore, non-disinfected DWDSs contained the highest diversity of bacterial communities. However, samples from DWDSs using disinfectants contained over double the ratio of ARG reads to 16S rRNA gene reads and most of the MRG (namely mercury and arsenic resistance genes). The total reads and types of ARGs conferring genes associated with antibiotic groups namely multidrug resistance, and bacitracin, beta-lactam, and aminoglycoside and mercury resistance genes increased in waterworks treating surface water with disinfection. The findings of this study contribute toward a comprehensive understanding of ARGs and MRGs in DWDSs. The occurrence of bacteria carrying antibiotic or metal resistance genes in drinking water causes direct exposure to people, and thus, more systematic investigation is needed to decipher the potential effect of these resistomes on human health.

Playgrounds in City of Pushchino with Different Types of Coating as Reservoir of Antibiotic-Resistant Strains of Pseudomonas spp

In this study, we investigated antibiotic-resistant microorganisms isolated by the direct plating method from 6 playgrounds in the city of Pushchino, Moscow Region, with different types of coating: sand, soil with sand, grass and a modern playground coating made of pressed rubber crumb. According to the results of the study, sand is the cleanest type of coating, both in terms of the total count of cultivated microorganisms (8 × 10⁵/g of substrate) and in terms of the content of resistant strains. The most contaminated both in terms of the total count of cultivated microorganisms (1.2-1.9 × 10⁹/g of substrate) and in terms of the content of antibiotic-resistant strains was the coating of pressed rubber crumb. We isolated 65 antibiotic-resistant strains of fluorescent pseudomonads. Nine Pseudomonas strains were found to contain antibiotic resistance plasmids (one belongs to P-1 incompatibility group, seven to IncP-7 and one to unidentified incompatibility group). For the first time, we discovered a conjugative plasmid pD4A-46 conferring tetracycline resistance and belonging to the P-7 incompatibility group. Taking into account the results obtained under this study, it can be recommended to periodically treat the crumb rubber coating with non-toxic antiseptics, i.e. hydrogen peroxide or chlorhexidine.

Efficient, rapid and simple adsorption method by polydopamine polystyrene nanofibers mat for removal of multi-class antibiotic residues in environmental water

Polydopamine polystyrene nanofibers mat (PDA-PS NFsM) was prepared as an adsorbent for the simultaneous removal of multiple antibiotic residues in environmental water for the first time. PDA-PS NFsM can directly be used to adsorb 18 antibiotic residues belonging to 8 classes without any pretreatment of water samples. The adsorption process was completed within 5 min. All antibiotics could be removed at the same time, and the removal rate of each target was above 85%. Moreover, the used PDA-PS NFsM can be easily separated from the environmental water by taking out directly, and can be reused for 10 times after simple regeneration. The thermodynamic and kinetic properties of PDA-PS NFsM adsorption of antibiotic residues were further investigated consequently. It was found that the adsorptions of PDA-PS NFsM to the targets were spontaneous and endothermic process (ΔG<0, ΔH>0, ΔS>0). The results of adsorption kinetic experiments illustrated that the adsorption process was rapid, the adsorption equilibrium of which can be reached in 5 min. Adsorption isotherm experiments proved that the adsorption process of PDA-PS NFsM was consistent with Langmuir adsorption (R² > 0.994), and the maximum adsorption capacity of PDA-PS NFsM towards all targets were 123.76 mg g^-1. The developed method is rapid and simple, and can efficiently adsorb and remove a variety of antibiotics in environmental water, which has good practical application prospect.

Mucilaginibacter sp. Strain Metal(loid) and Antibiotic Resistance Isolated from Estuarine Soil Contaminated Mine Tailing from the Fundão Dam

In 2015 a mine dam with Mn-Fe-rich tailings collapsed releasing million tons of sediments over an estuary, in the Southwest of Brazil. The tailings have a high concentration of metals that contaminated soil until the present day. The high contaminant concentrations possibly caused a selection for microorganisms able to strive in such harsh conditions. Here, we isolated metal(loid) and anti-biotic resistance bacteria from the contaminated estuarine soil. After 16S rDNA sequencing to identify the strains, we selected the Mucilaginibacter sp. strain for a whole-genome sequence due to the bioprospective potential of the genus and the high resistance profile. We obtained a complete genome and a genome-guided characterization. Our finding suggests that the 21p strain is possibly a new species of the genus. The species presented genes for resistance for metals (i.e., As, Zn, Co, Cd, and Mn) beyond resistance and cross-resistance for antibiotics (i.e., quinolone, aminoglycoside, β-lactamase, sulphonamide, tetracycline). The Mucilaginibacter sp. 21p description as new species should be further explored, as their extracellular polymeric substances and the potential of this strain as bioremediation and as a growth promoter in high met-al(loid) contaminated soil.

A Risk-Based Approach for Managing Aquaculture Used Oxytetracycline-Induced TetR in Surface Water Across Taiwan Regions

Oxytetracycline (OTC), one of the most important antibiotics in aquaculture industry, has been linked to emergence of antibiotic resistant genes in the aquatic environment. Given rapid growth of the aquaculture industry and unregulated use of antibiotics, it is necessary to implement measures to mitigate the impact of antibiotic resistance risk on environmental and human health. However, there is a lack of quantitative models to properly assess risk of antibiotic resistance associated with environmentally relevant antibiotic residues. To address this issue, here we developed a computational framework to assess antibiotic resistance risk posed by low-concentration OTC in aquaculture ponds and rivers across Taiwan regions. To this end, estimated amount of aquaculture used OTC as a crucial input parameter was incorporated into a multimedia fugacity model to predict environmental concentrations of OTC in surface water/sediment. A pharmacodynamic-based dose–response model was used to characterize the OTC concentration–antibiotic resistance relationships. The risk of antibiotic resistance selection in an aquatic environment could be assessed based on a probabilistic risk model. We also established a control measure model to manage the risks of substantial OTC-induced antibiotic resistance impacts. We found that OTC residues were likely to pose a high risk of tetracycline resistance (tetR) genes selection in aquaculture ponds among all the study basins, whereas risk of tetR genes selection in rivers experienced a variably changing fashion. We also showed that it was extremely difficult to moderate the tetR genes selection rates to less than 10% increase in aquaculture ponds situated at northeastern river basins in that the minimum reductions on OTC emission rates during spring, summer, and autumn were greater than 90%. On the other hand, water concentrations of OTC during spring and summer in southwestern rivers should be prioritized to be severely limited by reducing 67 and 25% of OTC emission rate, respectively. Overall, incorporating a computational fugacity model into a risk assessment framework can identify relative higher risk regions to provide the risk-based control strategies for public health decision-making and development of robust quantitative methods to zero-in on environment with high risk of tetR genes selection in relation to aquaculture-used pharmaceutical residues.

Metagenomic evidence for co-occurrence of antibiotic, biocide and metal resistance genes in pigs

Antibiotic-resistant pathogens constitute an escalating public health concern. Hence a better understanding of the underlying processes responsible for this expansion is urgently needed. Co-selection of heavy metal/biocide and antibiotic resistance genes (ARGs) has been suggested as one potential mechanism promoting the proliferation of antimicrobial resistance (AMR). This paper aims to elucidate this interplay and exploit differences in antibiotic usage to infer patterns of co-selection by the non-antibiotic factors metals and biocides in the context of pig farming. We examined 278 gut metagenomes from pigs with continuous antibiotic exposure, only at weaning and at no exposure. Metals as growth promoters and biocides as disinfectants are currently used with little restrictions in stock farming. The pigs under continuous antibiotic exposure displayed the highest co-occurrence of ARGs and other genetic elements while the pigs under limited use of antibiotics still showed abundant co-occurrences. Pathogens belonging to Enterobacteriaceae displayed increased co-occurrence phenomena, suggesting that this maintenance is not a random selection process from a mobilized pool but pertains to specific phylogenetic clades. These results suggest that metals and biocides displayed strong selective pressures on ARGs exerted by intensive farming, regardless of the current use of antibiotics.

Investigation of the microbial community structure and diversity in the environment surrounding a veterinary antibiotic production factory

The ecological toxicity caused by antibiotic residues and resistance genes in the environment affects the community structures and activities of environmental microorganisms; the ecological toxicity effects of a long-term exposure to low doses antibiotic residues on microorganisms have not however been well-studied. In this work, sequence analysis and species annotation of the full-length 16S rRNA gene were carried out on the extracted whole genome by a 3-generation sequencing method to analyze the diversity of the microbial populations and the population differences among different sampling sites in the environment surrounding a veterinary antibiotic production factory. A total of 1720 OTUs (Operational Taxonomic Unit, OTU) were found, of which 1055 OTUs were in the river samples and 993 OTUs were in the soil samples. 643 and 438 bacterial strains were identified in the river water and soil samples respectively. The bacterial populations are classified into 29 phylum, 612 genus, and 849 species. The dominant phylum of bacteria was Proteobacteria, which was also the absolutely dominant phylum. Shannon diversity index of the bacteria showed that the bacterial abundance in downstream river was significantly higher than that in an upstream non-polluted area (P < 0.001), but the difference of bacterial abundance between soil samples was not significant. There were 61 biomarkers in the river water samples from different sampling points, and 14 biomarkers in soil samples. It was found by the difference statistics of the microbial community that there are multiple biomarkers between this veterinary drug production site and the upstream non-polluted area. Significant differences between multiple functional genes were also found in metabolic pathways of the microorganisms. A similar trend was found for the distribution of antibiotic resistance genes (ARGs). It is concluded that the population composition of microorganisms and diversity are likely related to antibiotic residues and to the distributions of ARGs in the environment surrounding the antibiotic production factory.

Treatment technologies to mitigate the harmful effects of recalcitrant fluoroquinolone antibiotics on the environ- ment and human health

Antibiotic proliferation in the environment and their persistent nature is an issue of global concern as they induce antibiotic resistance threatening both human health and the ecosystem. Antibiotics have therefore been categorized as emerging pollutants. Fluoroquinolone (FQs) antibiotics are an emerging class of contaminants that are used extensively in human and veterinary medicine. The recalcitrant nature of fluoroquinolones has led to their presence in wastewater, effluents and water bodies. Even at a low concentration, FQs can stimulate antibacterial resistance. The main sources of FQ contamination include waste from pharmaceutical manufacturing industries, hospitals and households that ultimately reaches the wastewater treatment plants (WWTPs). The conventional WWTPs are unable to completely remove FQs due to their chemical stability. Therefore, the development and implementation of more efficient, economical, convenient treatment and removal technologies are needed to adequately address the issue. This review provides an overview of the technologies available for the removal of fluoroquinolone antibiotics from wastewater including adsorptive removal, advanced oxidation processes, removal using non-carbon based nanomaterials, microbial degradation and enzymatic degradation. Each treatment technology is discussed on its merits and limitations and a comparative view is presented on the choice of an advanced treatment process for future studies and implementation. A discussion on the commercialization potential and eco-friendliness of each technology is also included in the review. The importance of metabolite identification and their residual toxicity determination has been emphasized. The last section of the review provides an overview of the policy interventions and regulatory frameworks that aid in retrofitting antibiotics as a central key focus contaminant and thereby defining the discharge limits for antibiotics and establishing safe manufacturing practices.

Responses of bacterial communities and antibiotic resistance genes to nano-cellulose addition during pig manure composting

Treatment with exogenous additives during composting can help to alleviate the accumulation of antibiotic resistance genes (ARGs) caused by the direct application of pig manure to farmland. In addition, nano-cellulose has an excellent capacity for adsorbing pollutants. Thus, the effects of adding 300, 600, and 900 mg/kg nano-cellulose to compost on the bacterial communities, mobile genetic elements (MGEs), and ARGs were determined in this study. After composting, treatment with nano-cellulose significantly reduced the relative abundance of ARGs, which was lowest in the compost product with 600 mg/kg added nano-cellulose. Nano-cellulose inhibited the rebound in ARGs from the cooling period to the maturity period, and weakened the selective pressure of heavy metals on microorganisms by passivating bio-Cu. The results also showed that MGEs explained most of the changes in the abundances of ARGs, and MGEs had direct effects on ARGs. The addition of 600 mg/kg nano-cellulose reduced the abundances of bacterial genera associated with ermQ, tetG, and other genes, and the number of links (16) between ARGs and MGEs was lowest in the treatment with 600 mg/kg added nano-cellulose. Therefore, adding 600 mg/kg nano-cellulose reduced the abundances of ARGs by affecting host bacteria and MGEs. The results obtained in this study demonstrate the positive effect of nano-cellulose on ARG pollution in poultry manure, where adding 600 mg/kg nano-cellulose was most effective at reducing the abundances of ARGs.

What Is the Role of the Environment in the Emergence of Novel Antibiotic Resistance Genes? A Modeling Approach

It is generally accepted that intervention strategies to curb antibiotic resistance cannot solely focus on human and veterinary medicine but must also consider environmental settings. While the environment clearly has a role in transmission of resistant bacteria, its role in the emergence of novel antibiotic resistance genes (ARGs) is less clear. It has been suggested that the environment constitutes an enormous recruitment ground for ARGs to pathogens, but its extent is practically unknown. We have constructed a model framework for resistance emergence and used available quantitative data on relevant processes to identify limiting steps in the appearance of ARGs in human pathogens. We found that in a majority of possible scenarios, the environment would only play a minor role in the emergence of novel ARGs. However, the uncertainty is enormous, highlighting an urgent need for more quantitative data. Specifically, more data is most needed on the fitness costs of ARG carriage, the degree of dispersal of resistant bacteria from the environment to humans, and the rates of mobilization and horizontal transfer of ARGs. This type of data is instrumental to determine which processes should be targeted for interventions to curb development and transmission of ARGs in the environment.

Impact of biosolids amendment and wastewater effluent irrigation on enteric antibiotic-resistant bacteria - a greenhouse study

Reuse of wastewater effluent and biosolids in agriculture is essential to sustainable water and nutrient resource management practices. Wastewater and biosolids, however, are reportedly the recipients, reservoirs, and sources of antibiotic-resistant enteric pathogens. While decay rates of fecal bacterial indicators in soil are frequently studied, very few studies have reported on the persistence of the antibiotic-resistant sub-populations. Little is known about how multi-drug resistance phenotypes of enteric bacteria in agricultural soil change over time. In this study, germinated carrot seeds were planted in soil that received biosolids amendment and/or wastewater effluent irrigation in a greenhouse setting. We quantified total and antibiotic-resistant fecal bacterial indicators (Escherichia coli and enterococci) weekly in soil and total E. coli at harvest (day 77) on carrots. Antibiotic susceptibility of 121 E. coli and 110 enterococci collected isolates were determined. E. coli or enterococci were not recovered from the soil without biosolids amendment regardless of the irrigation water source. After biosolids amendment, soil E. coli and enterococci concentrations increased more than 3 log₁₀ CFU/g-TS within the first week, declined slowly over time, but stayed above the detection limit (0.39 CFU/g-TS) over the entirety of the study. No statistical difference was found between effluent wastewater or water irrigation in soil total and antibiotic-resistant E. coli and enterococci concentrations or carrots E. coli levels. Soil antibiotic-resistant E. coli and enterococci decayed significantly faster than total E. coli and enterococci. Moreover, the prevalence of multi-drug resistant (resistance to three or more antibiotics) E. coli declined significantly over time, while almost all collected enterococci isolates showed multi-drug resistance phenotypes. At harvest, E. coli were present on carrots; the majority of which were resistant to ampicillin. The survival of antibiotic-resistant enteric bacteria in soil and on harvested carrots indicates there are transmission risks associated with biosolids amendment use in root crops.

Improved quantitative microbiome profiling for environmental antibiotic resistance surveillance

BACKGROUND

Understanding environmental microbiomes and antibiotic resistance (AR) is hindered by over reliance on relative abundance data from next-generation sequencing. Relative data limits our ability to quantify changes in microbiomes and resistomes over space and time because sequencing depth is not considered and makes data less suitable for Quantitative Microbial Risk Assessments (QMRA), critical in quantifying environmental AR exposure and transmission risks.

RESULTS

Here we combine quantitative microbiome profiling (QMP; parallelization of amplicon sequencing and 16S rRNA qPCR to estimate cell counts) and absolute resistome profiling (based on high-throughput qPCR) to quantify AR along an anthropogenically impacted river. We show QMP overcomes biases caused by relative taxa abundance data and show the benefits of using unified Hill number diversities to describe environmental microbial communities. Our approach overcomes weaknesses in previous methods and shows Hill numbers are better for QMP in diversity characterisation.

CONCLUSIONS

Methods here can be adapted for any microbiome and resistome research question, but especially providing more quantitative data for QMRA and other environmental applications.

Quantitative Microbial Risk Assessment of Antimicrobial Resistant and Susceptible Staphylococcus aureus in Reclaimed Wastewaters

The annual risks of colonization, skin infection, bloodstream infection (BSI), and disease burden from exposures to antibiotic-resistant and susceptible Staphylococcus aureus (S. aureus) were estimated using quantitative microbial risk assessment (QMRA). We estimated the probability of nasal colonization after immersion in wastewater (WW) or greywater (GW) treated across a range of treatment alternatives and subsequent infection. Horizontal gene transfer was incorporated into the treatment model but had little effect on the predicted risk. The cumulative annual probability of infection (resulting from self-inoculation) was most sensitive to the treatment log₁₀ reduction value (LRV), S. aureus concentration, and the newly calculated morbidity ratios and was below the health benchmark of 10^-4 infections per person per year (ppy) given a treatment LRV of roughly 3.0. The predicted annual disability-adjusted life years (DALYs), which were dominated by BSI, were below the health benchmark of 10^-6 DALYs ppy for resistant and susceptible S. aureus, given LRVs of 4.5 and 3.5, respectively. Thus, the estimated infection risks and disease burdens resulting from nasal colonization are below the relevant health benchmarks for risk-based, nonpotable, or potable reuse systems but possibly above for immersion in minimally treated GW or WW. Strain-specific data to characterize dose-response and concentration in WW are needed to substantiate the QMRA.

Metagenomic profiles and health risks of pathogens and antibiotic resistance genes in various industrial wastewaters and the associated receiving surface water

The aquatic environment may represent an essential route for transmission of antibiotic resistance to opportunistic human pathogens. Since industrial wastewater is discharged into the river after treatment, understanding the distribution of antibiotic resistance genes (ARGs) in river systems and the possibility of pathogens acquiring antibiotic resistance are challenges with far-reaching significance. This work mainly studied distribution profiles of pathogens and ARGs, and compared their health risk in various industrial wastewater with that of river water. Results showed that 166 pathogens were concurrently shared by the six water samples, with Salmonella enterica and Pseudomonas aeruginosa being the most abundant, followed by Fusarium graminearum and Magnaporthe oryzae. The similar composition of the pathogens suggests that pathogens in river water may mainly come from sewage discharge of slaughterhouses and that changes in water quality contribute significantly to the prevalence of these pathogens. Of the 57 ARG types detected, bacitracin was the most abundant, followed by sulfonamide, chloramphenicol, tetracycline, and aminoglycoside. Strikingly, the wastewater from a pharmaceutical factory producing Chinese medicine was also rich in bacA, sul1, mexW, mexB, mexF and oprn. It can be seen from the co-occurrence patterns that pathogens and the main ARGs have strong co-occurrence. Higher abundance of offensive virulence factors in industrial wastewater and their strong correlation with pathogens containing ARGs suggest higher microbiological risk. These findings highlight the need to assess ARG acquisition by pathogens in the surface water of human-impacted environments where pathogens and ARGs may co-thrive.

Does Irrigation with Treated and Untreated Wastewater Increase Antimicrobial Resistance in Soil and Water: A Systematic Review

Population growth and water scarcity necessitate alternative agriculture practices, such as reusing wastewater for irrigation. Domestic wastewater has been used for irrigation for centuries in many historically low-income and arid countries and is becoming more widely used by high-income countries to augment water resources in an increasingly dry climate. Wastewater treatment processes are not fully effective in removing all contaminants, such as antimicrobial resistant bacteria (ARB) and antimicrobial resistance genes (ARGs). Literature reviews on the impact of wastewater irrigation on antimicrobial resistance (AMR) in the environment have been inconclusive and mostly focused on treated wastewater. We conducted the first systematic review to assess the impact of irrigation with both treated or untreated domestic wastewater on ARB and ARGs in soil and adjacent water bodies. We screened titles/abstracts of 3002 articles, out of which 41 were screened in full text and 26 were included in this review. Of these, thirteen investigated irrigation with untreated wastewater, and nine found a positive association with ARB/ARGs in soil. Out of thirteen studies focused on treated wastewater, six found a positive association with ARB/ARGs while six found mixed/negative associations. Our findings demonstrate that irrigation with untreated wastewater increases AMR in soil and call for precautionary action by field workers, their families, and consumers when untreated wastewater is used to irrigate crops. The effect of irrigation with treated wastewater was more variable among the studies included in our review, highlighting the need to better understand to what extent AMR is disseminated through this practice. Future research should assess factors that modify the effect of wastewater irrigation on AMR in soil, such as the degree and type of wastewater treatment, and the duration and intensity of irrigation, to inform guidelines on the reuse of wastewater for irrigation.

Knowledge Gaps in the Understanding of Antimicrobial Resistance in Canada

Current limitations in the understanding and control of antimicrobial resistance (AMR) in Canada are described through a comprehensive review focusing on: (1) treatment optimization; (2) surveillance of antimicrobial use and AMR; and (3) prevention of transmission of AMR. Without addressing gaps in identified areas, sustained progress in AMR mitigation is unlikely. Expert opinions and perspectives contributed to prioritizing identified gaps. Using Canada as an example, this review emphasizes the importance and necessity of a One Health approach for understanding and mitigating AMR. Specifically, antimicrobial use in human, animal, crop, and environmental sectors cannot be regarded as independent; therefore, a One Health approach is needed in AMR research and understanding, current surveillance efforts, and policy. Discussions regarding addressing described knowledge gaps are separated into four categories: (1) further research; (2) increased capacity/resources; (3) increased prescriber/end-user knowledge; and (4) policy development/enforcement. This review highlights the research and increased capacity and resources to generate new knowledge and implement recommendations needed to address all identified gaps, including economic, social, and environmental considerations. More prescriber/end-user knowledge and policy development/enforcement are needed, but must be informed by realistic recommendations, with input from all relevant stakeholders. For most knowledge gaps, important next steps are uncertain. In conclusion, identified knowledge gaps underlined the need for AMR policy decisions to be considered in a One Health framework, while highlighting critical needs to achieve realistic and meaningful progress.

Influence of Legacy Mercury on Antibiotic Resistomes: Evidence from Agricultural Soils with Different Cropping Systems

Agricultural soils are important reservoirs for antibiotic resistance genes (ARGs), which have close linkage to human health via crop production. Metal stress in environments may function as a selection pressure for antibiotic resistomes. However, there is still a lack of field studies focusing on the effect of historical mercury (Hg) contamination on antibiotic resistomes in agricultural soils. Here, we explored the ARG profile in soils with different cropping systems (paddy and upland) and linked them to legacy Hg exposure. We found that ARG profiles were significantly different between paddy and upland soils. However, both paddy and upland soils with long-term field Hg contamination harbored higher diversity and abundance of ARGs than non-polluted soils. The co-occurrence network reveals significant associations among Hg, Hg resistance genes, mobile genetic elements (MGEs), and ARGs. Together with path analysis showing legacy Hg possibly affecting soil resistomes through the shifts of soil microbiota, Hg resistance genes, and MGEs, we suggest that legacy Hg-induced potential co-selection might elevate the ARG level. Redundancy analysis further supports that legacy Hg pollution had a significant association with ARG variations in the paddy and upland soils (P < 0.01). Collectively, our results highlight the underappreciated role of legacy Hg as a potential persistent selecting agent in contributing to soil ARGs in agroecosystems.

Seizing the moment: now is the time for integrated global surveillance of antimicrobial resistance in wastewater environments

Antimicrobial resistance (AMR) is a growing global health threat that requires coordinated action across One Health sectors (humans, animals, environment) to stem its spread. Environmental surveillance of AMR is largely behind the curve in current One Health surveillance programs, but recent momentum in the establishment of infrastructure for monitoring of the SARS-CoV-2 virus in sewage provides an impetus for analogous AMR monitoring. Simultaneous advances in research have identified striking trends in various AMR measures in wastewater and other impacted environments across global transects. Methodologies for tracking AMR, including metagenomics, are rapidly advancing, but need to be standardized and made modular for access by LMICs, while also developing systems for sample archiving and data sharing. Such efforts will help optimize effective global AMR policy.

Characterization of tetracycline-resistant microbiome in soil-plant systems by combination of H218O-based DNA-Stable isotope probing and metagenomics

The emergence and spread of antibiotic resistance have been considered as a global health threat. However, effective methods to identify antibiotic-resistant bacteria (ARB) in complex microbial community are lacking, and the potential transmission pathways of ARB and antibiotic resistance genes (ARGs) in the soil-plant system remain scarce. Here in this study, tetracycline was chosen as the target antibiotic due to its globally wide usage and clinical significance. DNA-based stable isotope probing with H₂¹⁸O was applied to identify the tetracycline-resistant bacteria from soil-plant systems. Eighteen-year organic fertilization significantly changed the composition of the tetracycline-resistant microbiome in the soil-wheat system and resulted in a higher relative abundance of ARGs in the wheat endophyte. Rhizosphere harboring the most diverse ARGs and mobile genetic elements was identified as a hot spot for horizontal gene transfer and an important bridge between bulk soil and wheat endophyte. Micrococcaceae and Sphingomonadaceae carrying ARGs associated with abundant mobile genetic elements, were identified as the core bacterial taxa in long-term manure-amended and untreated soil-wheat systems, respectively. This method contributes to a more precise track of ARB in the environment, and our work depicts the high potential of ARG transfer in the rhizosphere mediated by the core species.

Towards risk assessment for antibiotic resistant pathogens in recycled water: a systematic review and summary of research needs

Risk assessment is critical for identifying target concentrations of antibiotic resistant pathogens necessary for mitigating potential harmful exposures associated with water reuse. However, there is currently limited available data characterizing the concentrations of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in recycled water to support robust efforts at risk assessment. The objective of this systematic review was to identify and synthesize the existing literature documenting the presence and abundance of ARB and ARGs in recycled water. In addition, this review identifies best practices and explores monitoring targets for studying ARB and ARGs in recycled water to guide future work and identifies key research needs aimed at better supporting quantitative microbial risk assessment focused on recycled water and antibiotic resistance. Future efforts to collect data about ARB and ARG prevalence in recycled water should report concentration data per unit volume. Sample metadata should also be provided, including a description of treatment approach, a description of planned water uses (e.g., potable, irrigation), methods for conveyance to the point of use, and available physicochemical water quality data. Additional research is needed aimed at identifying recommended ARB and ARG monitoring targets and for developing approaches to incorporate metagenomic data into risk assessment.

Nanopore-based metagenomics analysis reveals prevalence of mobile antibiotic and heavy metal resistome in wastewater

In-depth studies of the microbiome and mobile resistome profile of different environments is central to understanding the role of the environment in antimicrobial resistance (AMR), which is one of the urgent threats to global public health. In this study, we demonstrated the use of a rapid (and easily portable) sequencing approach coupled with user-friendly bioinformatics tools, the MinION (Oxford Nanopore Technologies), on the evaluation of the microbial as well as mobile metal and antibiotic resistome profile of semi-rural wastewater. A total of 20 unique phyla, 43 classes, 227 genera, and 469 species were identified in samples collected from the Amherst Wastewater Treatment Plant, both from primary and secondary treated wastewater. Alpha diversity indices indicated that primary samples were significantly richer and more microbially diverse than secondary samples. A total of 1041 ARGs, 68 MRGs, and 17 MGEs were detected in this study. There were more classes of AMR genes in primary than secondary wastewater, but in both cases multidrug, beta-lactam and peptide AMR predominated. Of note, OXA β-lactamases, some of which are also carbapenemases, were enriched in secondary samples. Metal resistance genes against arsenic, copper, zinc and molybdenum were the dominant MRGs in the majority of the samples. A larger proportion of resistome genes were located in chromosome-derived sequences except for mobilome genes, which were predominantly located in plasmid-derived sequences. Genetic elements related to transposase were the most common MGEs in all samples. Mobile or MGE/plasmid-associated resistome genes that confer resistance to last resort antimicrobials such as carbapenems and colistin were detected in most samples. Worryingly, several of these potentially transferable genes were found to be carried by clinically-relevant hosts including pathogenic bacterial species in the orders Aeromonadales, Clostridiales, Enterobacterales and Pseudomonadales. This study demonstrated that the MinION can be used as a metagenomics approach to evaluate the microbiome, resistome, and mobilome profile of primary and secondary wastewater.

Microalgae-based technology for antibiotics removal: From mechanisms to application of innovational hybrid systems

Antibiotics contamination is an emerging environmental concern, owing to its potential risks to ecosystems and human health. Microalgae-based technology has been widely reported as a promising alternative to conventional wastewater treatment, since it is a solar-power driven, ecologically friendly, cost-effective, and sustainable reclamation strategy. This review provides fundamental insights into the major mechanisms underpinning microalgae-based antibiotics removal, including bioadsorption, bioaccumulation, and biodegradation. The critical role of extracellular polymeric substances on bioadsorption and extracellular biodegradation of antibiotics are also covered. Moreover, this review sheds light on the important factors affecting the removal of antibiotics by microalgae, and summarizes several novel approaches to improve the removal efficiency, including acclimation, co-metabolism and microbial consortium. Besides, hybrid systems (such as, microalgae-based technologies combined with the conventional activated sludge, advanced oxidation processes, constructed wetlands, and microbial fuel cells), and genetic engineering are also recommended, which will be feasible for enhanced removal of antibiotics. Finally, this review also highlights the need for further studies aimed at optimizing microalgae-based technology, with emphasis on improving performance and expanding its application in large-scale settings, especially in terms of technical, environmental-friendly and economically competitiveness. Overall, this review summarizes current understanding on microalgae-based technologies for removal of antibiotics and outlines future research directions.

Proliferation of antibiotic-resistant microorganisms and associated genes during composting: An overview of the potential impacts on public health, management and future

Antibiotic residues together with non-antibiotic drugs and heavy metals act as a selective pressure for the spread of antibiotic-resistant microorganisms (ARMs), antibiotic-resistant genes (ARGs), and mobile genetic elements (MGEs) during composting of livestock manure. ARMs, ARGs and MGEs have become emerging contaminants since they are regularly implicated in the majority of compost produced from livestock manure. The prevalence of these contaminants in agricultural soil receiving compost has drawn huge attention globally due to the risks they pose to the total environment. Although a large body of literature exists on the application of composting methods in minimizing the relative abundance of these contaminants, there is a paucity of information on the robustness, limitations and opportunities and threats of various composting protocols currently deployed. To address this knowledge gap, the current review compiled literature on the origin and mechanisms of the proliferation of ARMs, ARGs, and MGEs during composting of livestock manure. The effectiveness of current composting protocols in the reduction or removal of emerging contaminants was evaluated. Furthermore, the potential environmental impacts and human health risks of these contaminants following land application of compost were also presented. Finally, we propose some strategic approaches for the reduction of ARGs and MGEs during composting of livestock manure.

Environmental antimicrobial resistance and its drivers: a potential threat to public health

Imprudent and overuse of clinically relevant antibiotics in agriculture, veterinary and medical sectors contribute to the global epidemic increase in antimicrobial resistance (AMR). There is a growing concern among researchers and stakeholders that the environment acts as an AMR reservoir and plays a key role in the dissemination of antimicrobial resistance genes (ARGs). Various drivers are contributing factors to the spread of antibiotic-resistant bacteria and their ARGs either directly through antimicrobial drug use in health care, agriculture/livestock and the environment or antibiotic residues released from various domestic settings. Resistant micro-organisms and their resistance genes enter the soil, air, water and sediments through various routes or hotspots such as hospital wastewater, agricultural waste or wastewater treatment plants. Global mitigation strategies primarily involve the identification of high-risk environments that are responsible for the evolution and spread of resistance. Subsequently, AMR transmission is affected by the standards of infection control, sanitation, access to clean water, access to assured quality antimicrobials and diagnostics, travel and migration. This review provides a brief description of AMR as a global concern and the possible contribution of different environmental drivers to the transmission of antibiotic-resistant bacteria or ARGs through various mechanisms. We also aim to highlight the key knowledge gaps that hinder environmental regulators and mitigation strategies in delivering environmental protection against AMR.

A Preliminary Study of Antibiotic Resistance Genes in Domestic Honey Produced in China

Antibiotic resistance genes (ARGs) are emerging contaminants that pose a health risk to humans worldwide. Little information on ARGs in bee honey is available. This study profiles ARGs in bee honey samples produced in China, the biggest producer in the world. Of 317 known ARGs encoding resistance to 8 classes of antibiotics, 212 were found in collected honey samples by a real-time quantitative polymerase chain reaction approach. Occurrence frequencies of genes providing resistance to FCA (fluoroquinolone, quinolone, florfenicol, chloramphenicol, and amphenicol) and aminoglycosides were 21.0% and 18.5%, respectively. Frequencies of genes encoding efflux pumps were 42.5% and those of destructase genes 36.6%, indicating that these two mechanisms were predominant for resistance. Nine plasmid-mediated quinolone resistance genes were detected. Of the nine transposase genes known to be involved in antibiotic resistance, eight were found in the samples examined, with tnpA-4, tnpA-5, and tnpA-6 being more abundant. The abundance of the transposase genes was associated with genes conferring resistance to tetracyclines (r = 0.648, p < 0.01), macrolide-lincosamide-streptogramin B (r = 0.642, p < 0.01), FCA (r = 0.517, p < 0.01), and aminoglycosides (r = 0.401, 0.01 < p < 0.05). This is the first study on the abundance and diversity of ARGs in Chinese bee honey products. These findings suggest that bee honey may be a significant source of ARGs that might pose threat to public health. Further research is required to collect more samples in diverse geographic regions in China to make a more comprehensive judgment of ARG in bee honey.

An omics-based framework for assessing the health risk of antimicrobial resistance genes

Antibiotic resistance genes (ARGs) are widespread among bacteria. However, not all ARGs pose serious threats to public health, highlighting the importance of identifying those that are high-risk. Here, we developed an ‘omics-based’ framework to evaluate ARG risk considering human-associated-enrichment, gene mobility, and host pathogenicity. Our framework classifies human-associated, mobile ARGs (3.6% of all ARGs) as the highest risk, which we further differentiate as ‘current threats’ (Rank I; 3%) - already present among pathogens - and ‘future threats’ (Rank II; 0.6%) - novel resistance emerging from non-pathogens. Our framework identified 73 ‘current threat’ ARG families. Of these, 35 were among the 37 high-risk ARGs proposed by the World Health Organization and other literature; the remaining 38 were significantly enriched in hospital plasmids. By evaluating all pathogen genomes released since framework construction, we confirmed that ARGs that recently transferred into pathogens were significantly enriched in Rank II (‘future threats’). Lastly, we applied the framework to gut microbiome genomes from fecal microbiota transplantation donors. We found that although ARGs were widespread (73% of genomes), only 8.9% of genomes contained high-risk ARGs. Our framework provides an easy-to-implement approach to identify current and future antimicrobial resistance threats, with potential clinical applications including reducing risk of microbiome-based interventions.

Antibiotic resistance genes are common but not all are of high risk to human health. Here, the authors develop an omics-based framework for ranking genes by risk that incorporates level of enrichment in human associated environments, gene mobility, and host pathogenicity.

Occurrence, effects and behaviour of the antibiotic lincomycin in the agricultural and aquatic environment - A review

Lincomycin, an antibiotic commonly used in veterinary medicine, is frequently detected within the agricultural environment. The active compound enters the aquatic environment after manure application via infiltration or surface run-off, where it may negatively affect non-target organisms and contribute to the development and spread of resistant genes. However, a review on the fate of lincomycin within the agricultural and aquatic environment is lacking. Hence, to provide an overview, the main part of this paper summarizes the current literature on the occurrence, effects and behaviour of lincomycin in all relevant environmental compartments, including manure, soil, surface water and groundwater. Lincomycin was regularly detected in all environmental compartments and even in the food chain, appeared to sorb temporarily and mainly in its cationic microspecies, and dissipated after time periods that could cover days, months, or years, depending on the compartment and conditions. As noticed during the literature research conducted, information on the attenuation of lincomycin in terms of biological degradation in the aquatic environment is widely lacking, although it seems that biodegradation is the major removal mechanism. Therefore, a laboratory study, implemented by means of batch experiments, was carried out in order to evaluate the biological degradation of lincomycin in the aquatic environment. First order degradation started after a start-up phase of 10-14 days with a degradation rate constant of 0.55 d^-1 and a half-life time of 30 h. Further, the degradation rate constant was found to be independent of initial concentrations as long as concentrations did not exceed a concentration level at which the bacteria were inhibited, as it was the case in this study at a concentration of 10 mg L^-1. Biodegradation was confirmed as an important degradation pathway for LIN in the aquatic environment.

Dawning of a new ERA: Environmental Risk Assessment of antibiotics and their potential to select for antimicrobial resistance

Antibiotics and antimicrobials are used, misused and overused in human and veterinary medicine, animal husbandry and aquaculture. These compounds can persist in both human and animal waste and then enter the environment through a variety of mechanisms. Though generally measured environmental concentrations (MECs) of antibiotics in aquatic systems are significantly lower than point of therapeutic use concentrations, there is increasing evidence that suggests these concentrations may still enrich antimicrobial resistant bacteria. In light of this evidence, a rigorous and standardised novel methodology needs to be developed which can perform environmental risk assessment (ERA) of antimicrobials in terms of their selective potential as well as their environmental impact, to ensure that diffuse and point source discharges are safe. This review summarises and critically appraises the current methodological approaches that study selection at below point of therapeutic use, or sub-inhibitory, concentrations of antibiotics. We collate and compare selective concentration data generated to date. We recommend how these data can be interpreted in line with current ERA guidelines; outlining and describing novel concepts unique to risk assessment of AMR (such as direct selection of AMR or increased persistence of AMR). We consolidate terminology used thus far into a single framework that could be adopted moving forward, by proposing predicted no effect concentrations for resistance (PNECRs) and predicted no effect concentrations for persistence (PNECPs) be determined in AMR risk assessment. Such a framework will contribute to antibiotic stewardship and by extension, protection of human health, food security and the global economy.

On-Farm Anaerobic Digestion of Dairy Manure Reduces the Abundance of Antibiotic Resistance-Associated Gene Targets and the Potential for Plasmid Transfer

The present study investigated the impact of on-farm anaerobic digestion on the abundance of enteric bacteria, antibiotic resistance-associated gene targets, and the horizontal transfer potential of extended-spectrum β-lactamase (ESBL) genes. Samples of raw and digested manure were obtained from six commercial dairy farms in Ontario, Canada. Digestion significantly abated populations of viable coliforms in all six farms. Conjugative transfer of plasmids carrying β-lactamase genes from manure bacteria enriched overnight with buffered peptone containing 4 mg/liter cefotaxime into a β-lactam-sensitive green fluorescent protein (GFP)-labeled Escherichia coli recipient strain was evaluated in patch matings. Digestion significantly decreased the frequency of the horizontal transfer of ESBL genes. Twenty-five transconjugants were sequenced, revealing six distinct plasmids, ranging in size from 40 to 180 kb. A variety of ESBL genes were identified: bla_CTX-M-1, bla_CTX-M-14, bla_CTX-M-15, bla_CTX-M-27, bla_CTX-M-55, and bla_PER-1. bla_CTX-M-15 was the most prevalent ESBL gene detected on plasmids harbored by transconjugants. Various mobile genetic elements were found located proximal to resistance genes. Ten gene targets, including sul1, str(A), str(B), erm(B), erm(F), intI1, aadA, incW, bla_PSE, and bla_OXA-20, were quantified by quantitative PCR on a subset of 18 raw and 18 digested samples. Most targets were significantly more abundant in raw manure; however, erm(B) and erm(F) targets were more abundant in digested samples. Overall, on-farm digestion of dairy manure abated coliform bacteria, a number of antibiotic resistance-associated gene targets, and the potential for in vitro conjugation of plasmids conferring resistance to extended-spectrum β-lactams and other classes of antibiotics into E. coli CV601. IMPORTANCE Using livestock manure for fertilization can entrain antibiotic-resistant bacteria into soil. Manure on some dairy farms is anaerobically digested before being land applied. Recommending the widespread implementation of the practice should be founded on understanding the impact of this treatment on various endpoints of human health concern. Although lab-scale anaerobic treatments have shown potential for reducing the abundance of antibiotic resistance genes, there are very few data from commercial farms. Anaerobic digestion of manure on six dairy farms efficiently abated coliform bacteria, E. coli, and a majority of antibiotic resistance-associated gene targets. In addition, the conjugation potential of plasmids carrying ESBL genes into introduced E. coli strain CV601 was reduced. Overall, anaerobic digestion abated coliform bacteria, the genes that they carry, and the potential for ESBL-carrying plasmid transfer.

Insights into enhanced biodegradation of sulfadimethoxine by catalyst: Transcriptomic responses and free radical interactions

The occurrence of sulfonamides in the environment is a severe global threat to public health due to the increasing prevalence of antibiotic selection pressure that may lead to the development of antibiotic resistance. We report an enhanced biodegradation of sulfadimethoxine (SDM) by Phanerochaete chrysosporium (Pc) with lignocellulosic biomass (Lb) using Fe₃O₄-ZSM-5 as a catalyst (Pc/Fe₃O₄-ZSM-5/Lb). SDM was completely degraded within 4 days at pH 7.0 in the Pc/Fe₃O₄-ZSM-5/Lb system. Transcriptomic, metabolites and free radical analyses were performed to explore the detailed molecular mechanisms of SDM degradation. A total of 246 genes of Pc in the Pc/Fe₃O₄-ZSM-5/Lb system exhibited significant upregulation compared to that in Pc alone. Upregulated genes encoding cellulases, cytochrome P450, cellobiose quinone oxidoreductase, and cellobiose dehydrogenase were involved in SDM degradation in the Pc/Fe₃O₄-ZSM-5/Lb system. In addition, genes encoding glutathione S-transferase and cytochrome P450 genes related to oxidative stress and detoxification were all significantly upregulated (P < 0.01). Electron paramagnetic resonance revealed the generation of OH suggesting a free radical pathway could be catalyzed by Fe₃O₄-ZSM-5 and the enzymes. These findings of catalyst-assisted SDM biodegradation will be valuable for remediation of antibiotics from contaminated wastewater.

Macleaya cordata extract, an antibiotic alternative, does not contribute to antibiotic resistance gene dissemination

The abuse of antibiotics and their associated health risks are receiving global attention. The use of antibiotic additives in fodder has been banned in the European Union since 2006 and in China since 2020. Antibiotic alternatives are being developed, but their risks to the soil ecosystem remain poorly understood. Here, we compared the effects of the antibiotic oxytetracycline (OTC10, 10 mg/kg) with those of a Macleaya cordata extract (MCE, 10 and 100 mg/kg), the major antibiotic substitute. All tested concentrations of MCE and OTC10 exerted slight effects on the soil microbiome, but OTC10 and MCE100 could interfere with the structures and functions of the gut microbiome and might thus affect the soil ecological functions of Enchytraeus crypticus. Furthermore, OTC10 exposure inevitably increased the antibiotic resistance gene (ARG) abundance by 213%, whereas MCE did not induce ARG dissemination, which explains why MCE is considered to be associated with a low ecological risk. Our research provides the first demonstration of the risks posed by antibiotic alternatives to soil animals from the perspective of environmental toxicology and explores the potential development of antibiotic alternatives associated with a low ecological risk from a new perspective.

Heavy metal could drive co-selection of antibiotic resistance in terrestrial subsurface soils

Terrestrial surface ecosystems are important sinks for antibiotic resistance genes (ARGs) due to the continuous discharge of contaminants from human-impacted ecosystems. However, the abundance and resistance types of ARGs and their influencing factors in terrestrial subsurface soils are not well known. In this study, we investigated the abundance and diversity of ARGs, and their correlations with metal resistance genes (MRGs), mobile genetic elements (MGEs), bacteria, and heavy metals in subsurface soils using high throughput quantitative PCR and metagenomic sequencing approaches. Abundant and diverse ARGs were detected with high spatial heterogeneity among sampling sites. Vertically, there was no significant difference in ARG profiles between the aquifer and non-aquifer soils. Heavy metals were key factors shaping ARG profiles in soils with high heavy metal contents, while they showed no significant effect in low contents. Moreover, heavy metals could trigger the proliferation of antibiotic resistance by increasing MGE abundance or influencing bacterial communities. Metagenomic analysis also revealed the widespread co-occurrence of ARGs and MRGs, with heavy metals possibly enhancing the co-selection of ARGs and MRGs in soils with high heavy metal contents. This study highlighted the heavy metal-driven co-selection of ARGs and revealed the occurrence of ARG pollution in terrestrial subsurface soils.

Technologies towards antibiotic resistance genes (ARGs) removal from aquatic environment: A critical review

Antibiotic resistance genes (ARGs) have been recognized as emerging pollutants that are widely distributed and accumulated in most of aquatic environment. Although many ARGs-removal technologies are employed, a corresponding discussion of merits and limitations of known technologies is still currently lacking. More importantly, the removal mechanisms of ARGs remain unclear, hindering their ecological feasibility. Thus, further in-depth studies are highly required. In this review, the occurrence and risk of ARGs in aquatic environment are introduced, and the main routes and potential impacts of ARGs dissemination are enumerated. In addition, several novel ARGs detection methods are critically reviewed. Notably, to ensure greater applicability of these technologies, systematic information on how recent technologies impact the ARGs removal and control are comprehensively compared and summarized. Finally, future research directions to alleviate the risk of ARGs in aquatic environment are briefly introduced. Taken together, this review provides useful information to facilitate the development of innovative and feasible ARGs removal technologies and increase their economic viability and ecological sustainability.

Can heavy metal pollution induce bacterial resistance to heavy metals and antibiotics in soils from an ancient land-mine?

Microbial resistance to antibiotics is a growing challenge to human health. Recent evidence has indicated that antibiotic resistance can be co-selected for by exposure to heavy metals in agricultural soils. It remains unknown if this is a concern in other environments contaminated by metals. We here investigated soil microbial activities, composition and tolerance to heavy metals and antibiotics in a mining soil survey. We found that microbial respiration, growth, and biomass were affected by available metal concentrations. Most of the variation in microbial PLFA composition was explained by differences in heavy metal and pH. Additionally, pollution-induced bacterial community tolerance to toxicants including Cu, Pb, Zn, tetracycline and vancomycin was determined. Although only bacterial tolerance to Pb increased with higher levels of metals, the links between bacterial metal tolerance and soil metal concentrations were clear when considered together with previously published reports, suggesting that bacterial metal tolerance were universally elevated in the surveyed soils. The induced levels of heavy metal tolerance coincided with elevated levels of tolerance to vancomycin, but not to tetracycline. Our study showed that heavy metals can co-select for resistance to clinically important antibiotics also in ecosystems without manure input or antibiotic pollution.