Abundance Of Antibiotic Resistance Genes Research Articles

Effect of biochar on the fate of antibiotic resistant genes and integrons in compost amended agricultural soil.

The persistence and transmission of emerging pollutants such as antibiotic resistance genes (ARGs) via mobile genetic elements (MGEs) have caused concern to scientific community. Composting practises are often adapted for the reduction of organic waste or to enhance fertility in agriculture soil but its continuous usage has posed a potential risk of increased abundance of ARGs in soil. Thus, the present study scrutinises the emerging risk of ARGs and MGEs in agriculture soil and its potential mitigation using biochar owing to its proven environmental sustainability and performance. After 30days incubation, ARG distribution of SulI, SulII, dfrA1, dfrA12, tetA, flor, and ErmA was 50, 37.5, 37.5, 62.5, 42.11, 62.5, and 52.63% in control samples whereas it was 5, 15.78, 21.05, 15.79, 10.53, 21.05, and 31.58%, respectively, for biochar amended samples. Similarly, IntI1 and IntI2 in control and biochar amended samples were 18.75 and 6.25% and 10.53 and 5.26%, respectively. Principal component analysis (PCA) factor suggests that biochar amendment samples showed enhanced value for pH, organic matter, and organic carbon over control samples. Furthermore, Pearson's correlation analysis performed between detected ARGs and MGEs demonstrated the positive and significant correlation at p < 0.05 for both control and biochar amended samples.

Long-term beneficial effect of faecal microbiota transplantation on colonisation of multidrug-resistant bacteria and resistome abundance in patients with recurrent Clostridioides difficile infection

BackgroundMultidrug-resistant (MDR) bacteria are a growing global threat, especially in healthcare facilities. Faecal microbiota transplantation (FMT) is an effective prevention strategy for recurrences of Clostridioides difficile infections and can also be useful for other microbiota-related diseases.MethodsWe study the effect of FMT in patients with multiple recurrent C. difficile infections on colonisation with MDR bacteria and antibiotic resistance genes (ARG) on the short (3 weeks) and long term (1–3 years), combining culture methods and faecal metagenomics.ResultsBased on MDR culture (n = 87 patients), we notice a decrease of 11.5% in the colonisation rate of MDR bacteria after FMT (20/87 before FMT = 23%, 10/87 3 weeks after FMT). Metagenomic sequencing of patient stool samples (n = 63) shows a reduction in relative abundances of ARGs in faeces, while the number of different resistance genes in patients remained higher compared to stools of their corresponding healthy donors (n = 11). Furthermore, plasmid predictions in metagenomic data indicate that patients harboured increased levels of resistance plasmids, which appear unaffected by FMT. In the long term (n = 22 patients), the recipients’ resistomes are still donor-like, suggesting the effect of FMT may last for years.ConclusionsTaken together, we hypothesise that FMT restores the gut microbiota to a composition that is closer to the composition of healthy donors, and potential pathogens are either lost or decreased to very low abundances. This process, however, does not end in the days following FMT. It may take months for the gut microbiome to re-establish a balanced state. Even though a reservoir of resistance genes remains, a notable part of which on plasmids, FMT decreases the total load of resistance genes.

Effects of environmentally relevant concentrations of oxytetracycline and sulfadiazine on the bacterial communities, antibiotic resistance genes, and functional genes are different between maize rhizosphere and bulk soil.

Antibiotic contamination in soil has become a major concern worldwide. At present, it is not clear how two co-existed antibiotics with environmentally relevant concentrations would affect soil bacterial community structure, the abundances of antibiotic resistance genes (ARGs) and functional genes, and whether the effects of antibiotics would differ between rhizosphere and bulk soil. We conducted a greenhouse pot experiment to grow maize in a loess soil treated with oxytetracycline (OTC) or sulfadiazine (SDZ) or both at an environmentally relevant concentration (1 mg kg-1) to investigate the effects of OTC and SDZ on the rhizosphere and bulk soil bacterial communities, abundances of ARGs and carbon (C)-, nitrogen (N)-, and phosphorus (P)-cycling functional genes, and on plant growth and plant N and P nutrition. The results show that the effects of environmentally relevant concentrations of OTC and SDZ on bacterial communities and abundances of ARGs and functional genes differ between maize rhizosphere and bulk soil. The effects of two antibiotics resulted in a higher absolute abundances of accA, tet(34), tnpA-04, and sul2 in the rhizosphere soil than in the bulk soil and different bacterial community compositions and biomarkers in the rhizosphere soil and the bulk soil. However, OTC had a stronger inhibitory effect on the abundances of a few functional genes in the bulk soil than SDZ did, and their combination had no synergistic effect on plant growth, ARGs, and functional genes. The role of co-existed OTC and SDZ decreased shoot height and increased root N concentration. The results demonstrate that environmentally relevant concentrations of antibiotics shift soil microbial community structure, increase the abundances of ARGs, and reduce the abundances of functional genes. Furthermore, soil contamination with antibiotics can diminish agricultural production via phytotoxic effects on crops, and combined effects of antibiotics on plant growth and nutrient uptake should be considered.

A database on the abundance of environmental antibiotic resistance genes

Antimicrobial resistance (AMR) poses a severe threat to global health. The wide distribution of environmental antibiotic resistance genes (ARGs), which can be transferred between microbiota, especially clinical pathogens and human commensals, contributed significantly to AMR. However, few databases on the spatiotemporal distribution, abundance, and health risk of ARGs from multiple environments have been developed, especially on the absolute level. In this study, we compiled the ARG occurrence data generated by a high-throughput quantitative PCR platform from 1,403 samples in 653 sampling sites across 18 provinces in China. The database possessed 291,870 records from five types of habitats on the abundance of 290 ARGs, as well as 8,057 records on the abundance of 30 mobile genetic elements (MGEs) from 2013 to 2020. These ARGs conferred resistance to major common types of antibiotics (a total of 15 types) and represented five major resistance mechanisms, as well as four risk ranks. The database can provide information for studies on the dynamics of ARGs and is useful for the health risk assessment of AMR.

Microplastics provide new hotspots for frequent transmission of antibiotic resistance genes during anaerobic digestion of sludge containing antibiotics

Antibiotics and microplastics are emerging contaminants of widespread concern. Individual exposure to either antibiotics or microplastics may facilitate the dissemination of antibiotic resistance genes (ARGs). However, little is known about how the co-exposure of antibiotics and microplastics drives the dissemination of ARGs during sludge anaerobic digestion. This study established a series of long-term operational anaerobic digesters and found that 20 mg/L ofloxacin facilitated the dissemination of ARGs, whereas 200 mg/L ofloxacin led to a decrease in the absolute abundance of ARGs. However, the coexistence of polyamide and ofloxacin further increased the abundance of five ARGs by 4.4–359.1 % compare to singular ofloxacin exposure. The presence of polyamide not only complicated the microbial community structure but also increased the abundance of ARGs hosts by 12.2–108.7 %. Metagenome-assembled genomes indicated that 42 out of 53 ARGs hosts were functional microorganisms, and their enrichment under polyamide exposure facilitated the conversion of substrates into methane. Further mechanism exploration found that ofloxacin and polyamide promoted the formation of biofilm and enhanced the adhesion and communication among microorganisms. The upregulation of functional genes related to antioxidant, DNA repair, and type IV secretion systems provided evidence for the stimulated horizontal transfer of ARGs under the co-exposure of ofloxacin and polyamide. Partial least squares path modeling analysis identified that mobile genetic elements predominantly determined the variation of ARGs in this study. These findings emphasized that the coexistence of microplastics and antibiotics in sludge may further exacerbate the risk of antibiotic resistance transmission.

Lipid Metabolites as Potential Regulators of the Antibiotic Resistome in Tetramorium caespitum.

Antibiotic resistance genes (ARGs) are ancient but have become a modern critical threat to health. Gut microbiota, a dynamic reservoir for ARGs, transfer resistance between individuals. Surveillance of the antibiotic resistome in the gut during different host growth phases is critical to understanding the dynamics of the resistome in this ecosystem. Herein, we disentangled the ARG profiles and the dynamic mechanism of ARGs in the egg and adult phases of Tetramorium caespitum. Experimental results showed a remarkable difference in both gut microbiota and gut resistome with the development of T. caespitum. Meta-based metagenomic results of gut microbiota indicated the generalizability of gut antibiotic resistome dynamics during host development. By using Raman spectroscopy and metabolomics, the metabolic phenotype and metabolites indicated that the biotic phase significantly changed lipid metabolism as T. caespitum aged. Lipid metabolites were demonstrated as the main factor driving the enrichment of ARGs in T. caespitum. Cuminaldehyde, the antibacterial lipid metabolite that displayed a remarkable increase in the adult phase, was demonstrated to strongly induce ARG abundance. Our findings show that the gut resistome is host developmental stage-dependent and likely modulated by metabolites, offering novel insights into possible steps to reduce ARG dissemination in the soil food chain.

Can low-temperature thermal hydrolysis mitigate the oxidative stress of polystyrene nanoplastics on anaerobic digestion?

The presence of micro/nanoplastics (MPs/NPs) in sewage sludge has sparked considerable apprehensions over their potential negative effects on anaerobic digestion (AD) performance. The occurrence of MPs/NPs can trigger oxidative stress on the anaerobic microbiome, leading to potential inhibition of the AD process. While the thermal hydrolysis process (THP) is an extensively utilized sludge pretreatment method for AD, its impact on stress induced by MPs/NPs during AD remains poorly understood. In this study, we assessed the impacts of low-temperature THP (90 °C, 90 min) on AD of sewage sludge in the presence of 150 μg/L of polystyrene nanoplastics (PsNPs) under different solid retention times (SRTs) of 20, 15, and 10 d. The presence of PsNPs resulted in a higher reactive oxygen species (ROS) production and a higher abundance of antibiotic resistance genes (ARGs). Additionally, their presence caused a significant inhibition of methane production by 28.2%, 29.3%, and 38.8% for SRTs of 20, 15, and 10 d, respectively. Introducing low-temperature THP prior to the AD could partially recover methane production by mitigating ROS-induced stress and curbing the propagation of ARGs during the AD process. These results shed light on the potential benefits of THP and further optimization opportunities in alleviating the adverse effects of MPs/NPs-induced stress during sewage sludge AD.

Gamma-ray irradiation as an effective method for mitigating antibiotic resistant bacteria and antibiotic resistance genes in aquatic environments

The prevalence of antibiotic resistance genes (ARGs) in municipal wastewater treatment plants (MWTPs) has emerged as a significant environmental concern. Despite advanced treatment processes, high levels of ARGs persist in the secondary effluent from MWTPs, posing ongoing environmental risks. This study explores the potential of gamma-ray irradiation as a novel approach for sterilizing antibiotic-resistant bacteria (ARB) and reducing ARGs in MWTP secondary effluent. Our findings reveal that gamma-ray irradiation at an absorbed dose of 1.6 kGy effectively deactivates all culturable bacteria, with no subsequent revival observed after exposure to 6.4 kGy and a 96-h incubation in darkness at room temperature. The removal efficiencies for a range of ARGs, including tetO, tetA, blaTEM-1, sulI, sulII, and tetW, were up to 90.5% with a 25.6 kGy absorbed dose. No resurgence of ARGs was detected after irradiation. Additionally, this study demonstrates a considerable reduction in the abundances of extracellular ARGs, with the transformation efficiencies of extracellular tetracycline and sulfadiazine resistance genes decreasing by 56.3–81.8% after 25.6 kGy irradiation. These results highlight the effectiveness of gamma-ray irradiation as an advanced and promising method for ARB sterilization and ARG reduction in the secondary effluent of MWTPs, offering a potential pathway to mitigate environmental risks associated with antibiotic resistance.

Spatiotemporal Changes of Antibiotic Resistance, Potential Pathogens, and Health Risk in Kindergarten Dust.

The microorganisms present in kindergartens are extremely important for children's health during their three-year preschool education. To assess the risk of outdoor dust in kindergartens, the antibiotic resistome and potential pathogens were investigated in dust samples collected from 59 kindergartens in Xiamen, southeast China in both the winter and summer. Both high-throughput quantitative PCR and metagenome analysis revealed a higher richness and abundance of antibiotic resistance genes (ARGs) in winter (P < 0.05). Besides, the bloom of ARGs and potential pathogens was evident in the urban kindergartens. The co-occurrence patterns among ARGs, mobile genetic elements (MGEs), and potential pathogens suggested some bacterial pathogens were potential hosts of ARGs and MGEs. We found a large number of high-risk ARGs in the dust; the richness and abundance of high-risk ARGs were higher in winter and urban kindergartens compared to in summer and peri-urban kindergartens, respectively. The results of the co-occurrence patterns and high-risk ARGs jointly reveal that urbanization will significantly increase the threat of urban dust to human beings and their risks will be higher in winter. This study unveils the close association between ARGs/mobile ARGs and potential pathogens and emphasizes that we should pay more attention to the health risks induced by their combination.

Deciphering soil resistance and virulence gene risks in conventional and organic farming systems

Organic farming is a sustainable agricultural practice emphasizing natural inputs and ecological balance, and has garnered significant attention for its potential health and environmental benefits. However, a comprehensive evaluation of the emergent contaminants, particularly resistance and virulence genes within organic farming system, remains elusive. Here, a total of 36 soil samples from paired conventional and organic vegetable farms were collected from Jiangsu province, China. A systematic metagenomic approach was employed to investigate the prevalence, dispersal capability, pathogenic potential, and drivers of resistance and virulence genes across both organic and conventional systems. Our findings revealed a higher abundance of antibiotic resistance genes (ARGs), biocide resistance genes (BRGs), and virulence factor genes (VFGs) in organic farming system, with ARGs exhibiting a particularly notable increase of 10.76% compared to the conventional one. Pathogens such as Pseudomonas aeruginosa, Escherichia coli, and Mycobacterium tuberculosis were hosts carrying all four gene categories, highlighting their potential health implications. The neutral community model captured 77.1% and 71.9% of the variance in community dynamics within the conventional and organic farming systems, respectively, indicating that stochastic process was the predominant factor shaping gene communities. The relative smaller m value calculated in organic farming system (0.021 vs 0.023) indicated diminished gene exchange with external sources. Moreover, farming practices were observed to influence the resistance and virulence gene landscape by modifying soil properties, managing heavy metal stress, and steering mobile genetic elements (MGEs) dynamics. The study offers insights that can guide agricultural strategies to address potential health and ecological concerns.

Insights into the microbiological mechanism of antibiotic removal in an aerobic-microaerobic process treating manure-free piggery wastewater

A process integrating the sequencing batch reactor (SBR) and up-flow microaerobic sludge reactor (UMSR) has been innovatively developed to effectively remove antibiotics from manure-free piggery wastewater. This study provides a comprehensive analysis of bacteria, genes, and enzymes crucial for antibiotic biodegradation to reveal the underlying microbiological mechanism of antibiotic removal. During the 230-day operational period, a significant succession of microbial communities was observed in the SBR-UMSR system. Intriguingly, microbial interactions were pivotal in dominating the community succession, accounting for a substantial contribution of 69.12%, while abiotic factors only accounted for 30.88%. The analysis of the microbial community and network revealed that the predominant mechanism for antibiotic biodegradation in the SBR-UMSR system was driven by the metabolic activities of heterotrophic bacteria. More denitrifying bacteria were involved in antibiotic biodegradation than ammonia-oxidizing bacteria. In SBR, most of the potential antibiotic-degrading bacteria (PADB) were Gram-positive and facultatively anaerobic, whereas in UMSR, they were Gram-negative and aerobic. Propioniciclava and Norank_f__AKYH767 were the dominant PADB in the SBR and UMSR, respectively. Network analysis pinpointed redox reactions, transfer processes, and hydrolysis reactions as the core processes facilitating antibiotic biodegradation. Despite a general decrease in the abundance of most antibiotic resistance genes (ARGs) in the activated sludge of both SBR and UMSR over the 230-day operation, there was a notable enrichment in multidrug resistance genes. This underlines the necessity for proper sludge management to prevent secondary contamination by ARGs. This research provides deep insights into the mechanisms of antibiotic removal in intricate microbial ecosystems.

Performance of public drinking water purifiers in control of trihalomethanes, antibiotics and antibiotic resistance genes

Point-of-use water purifiers are widely applied as a terminal treatment device to produce drinking water with high quality. However, concerns are raised regarding low efficiency in eliminating emerging organic pollutants. To enhance our understanding of the reliability and potential risks of water purifiers, the removal of trihalomethanes, antibiotics, and antibiotic resistance genes (ARGs) in four public water purifiers was investigated. In the four public water purifiers in October and November, the removal efficiencies of trichloromethane (TCM) and bromodichloromethane (BDCM) were 15%–69% (averagely 37%) and 6%–44% (averagely 23%). The levels of TCM and BDCM were lowered by all water purifiers in October and November, but accelerated in effluent compared to the influent in one public water purifier in December. The removal efficiencies of twelve antibiotics greatly varied with species and time. Out of twelve sampling cases, the removal efficiencies of total antibiotics were 25%–75% in ten cases. In the other two cases, very low removal efficiency (6%) or higher levels of antibiotics present in effluent compared to the influent were observed. Two public water purifiers effectively remove ARGs from water, with log removal rates of 0.45 log–3.89 log. However, in the other two public water purifiers, the ARG abundance accidently increased in the effluents. Overall, public water purifiers were more effective in removing antibiotics and ARGs compared to household water purifiers, but less or equally effective in removing trihalomethanes. Both public and household water purifiers could be contaminated and release the accumulated micro-pollutants or biofilm-related pollutants into effluent. The production frequency and standing time of water within water purifiers can impact the internal contamination and purification efficacy.

Effect of wheat crops on the persistence and attenuation of antibiotic resistance genes in soil after swine wastewater application

Swine wastewater (SW) application introduces antibiotic resistance genes (ARGs) into farmland soils. However, ARG attenuation in SW-fertigated soils, especially those influenced by staple crops and soil type, remains unclear. This study investigated twelve soil ARGs and one mobile genetic element (MGE) in sandy loam, loam, and silt loam soils before and after SW application in wheat-planted and unplanted soils. The results revealed an immediate increase in the abundance of ARGs in soil by two orders of magnitude above background levels following SW application. After SW application, the soil total ARG abundance was attenuated, reaching background levels at 54 days; However, more individual ARGs were detected above the detection limit than pre-application. Among the 13 genes, acc(6′)-lb, tetM, and tetO tended to persist in the soil during wheat harvest. ARG half-lives were up to four times longer in wheat-planted soils than in bare soils. Wheat planting decreased the persistence of acc(6′)-lb, ermB, ermF, and intI2 but increased the persistence of others such as sul1 and sul2. Soil type had no significant impact on ARG and MGE fates. Our findings emphasize the need for strategic SW application and the consideration of crop cultivation effects to mitigate ARG accumulation in farmland soils.

Effects of reductive soil disinfestation on potential pathogens and antibiotic resistance genes in soil

Reductive soil disinfestation (RSD) is commonly employed for soil remediation in greenhouse cultivation. However, its influence on antibiotic resistance genes (ARGs) in soil remains uncertain. This study investigated the dynamic changes in soil communities, potential bacterial pathogens, and ARG profiles under various organic material treatments during RSD, including distillers’ grains, potato peel, peanut vine, and peanut vine combined with charcoal. Results revealed that applying diverse organic materials in RSD significantly altered bacterial community composition and diminished the relative abundance of potential bacterial pathogens (P < 0.05). The relative abundance of high-risk ARGs decreased by 10.7%-30.6% after RSD treatments, the main decreased ARG subtypes were AAC(3)_Via, dfrA1, ErmB, lnuB, aadA. Actinobacteria was the primary host of ARGs and was suppressed by RSD. Soil physicochemical properties, such as total nitrogen, soil pH, total carbon, were crucial factors affecting ARG profiles. Our findings demonstrated that RSD treatment inhibited pathogenic bacteria and could be an option for reducing high-risk ARG proliferation in soil.

Metagenomics reveals the resistance patterns of electrochemically treated erythromycin fermentation residue

Erythromycin fermentation residue (EFR) represents a typical hazardous waste produced by the microbial pharmaceutical industry. Although electrolysis is promising for EFR disposal, its microbial threats remain unclear. Herein, metagenomics was coupled with the random forest technique to decipher the antibiotic resistance patterns of electrochemically treated EFR. Results showed that 95.75% of erythromycin could be removed in 2 hr. Electrolysis temporarily influenced EFR microbiota, where the relative abundances of Proteobacteria and Actinobacteria increased, while those of Fusobacteria, Firmicutes, and Bacteroidetes decreased. A total of 505 antibiotic resistance gene (ARG) subtypes encoding resistance to 21 antibiotic types and 150 mobile genetic elements (MGEs), mainly including plasmid (72) and transposase (52) were assembled in EFR. Significant linear regression models were identified among microbial richness, ARG subtypes, and MGE numbers (r2=0.50–0.81, p< 0.001). Physicochemical factors of EFR (Total nitrogen, total organic carbon, protein, and humus) regulated ARG and MGE assembly (%IncMSE value = 5.14-14.85). The core ARG, MGE, and microbe sets (93.08%-99.85%) successfully explained 89.71%–92.92% of total ARG and MGE abundances. Specifically, gene aph(3′)-I, transposase tnpA, and Mycolicibacterium were the primary drivers of the resistance dissemination system. This study also proposes efficient resistance mitigation measures, and provides recommendations for future management of antibiotic fermentation residue.

Size effects of microplastics on antibiotic resistome and core microbiome in an urban river

Microplastics (MPs) in aquatic environments provide a new ecological niche that facilitates the attachment of antibiotic-resistance genes (ARGs) and pathogens. However, the effect of particle size on the colonization of antibiotic resistomes and pathogens remains poorly understood. To address this knowledge gap, this study explored the antibiotic resistome and core microbiome on three distinct types of MPs including polyethylene, polypropylene, and polystyrene (PS), with varying sizes of 30, 200, and 3000 μm by metagenomic sequencing. Our finding showed that the ARG abundances of the PS type increased by 4-folds with increasing particle size from 30 to 3000 μm, and significant differences in ARG profiles were found across the three MP types. In addition, the concentrations of ARGs and mobile genetic elements (MGEs) were markedly higher in the MPs than in the surrounding water, indicating their enrichment at these artificial interfaces. Notably, several pathogens such as Pseudomonas aeruginosa, Mycobacterium tuberculosis, and Legionella pneumophila were enriched in MP biofilms, and the co-occurrence of ARGs and virulence factor genes (VFGs)/MGEs suggested the presence of pathogenic antibiotic-resistant microbes with potential mobility. Both redundancy analysis (RDA) and structural equation modeling (SEM) demonstrated that physicochemical properties such as zeta potential, MP size, and contact angle were the most significant contributors to the antibiotic resistome. Strikingly, no significant differences were observed in the health risk scores of the ARG profiles among different sizes and types of MPs. This study expands our knowledge on the impact of MP size on microbial risks, thus enhancing our understanding of the potential health hazards they pose.

Longitudinal profiling of the intestinal microbiome in children with cystic fibrosis treated with elexacaftor-tezacaftor-ivacaftor.

The intestinal microbiome influences growth and disease progression in children with cystic fibrosis (CF). Elexacaftor-tezacaftor-ivacaftor (ELX/TEZ/IVA), the newest pharmaceutical modulator for CF, restores the function of the pathogenic mutated CF transmembrane conductance regulator (CFTR) channel. We performed a single-center longitudinal analysis of the effect of ELX/TEZ/IVA on the intestinal microbiome, intestinal inflammation, and clinical parameters in children with CF. Following ELX/TEZ/IVA, children with CF had significant improvements in body mass index and percent predicted forced expiratory volume in one second, and required fewer antibiotics for respiratory infections. Intestinal microbiome diversity increased following ELX/TEZ/IVA coupled with a decrease in the intestinal carriage of Staphylococcus aureus, the predominant respiratory pathogen in children with CF. There was a reduced abundance of microbiome-encoded antibiotic resistance genes. Microbial pathways for aerobic respiration were reduced after ELX/TEZ/IVA. The abundance of microbial acid tolerance genes was reduced, indicating microbial adaptation to increased CFTR function. In all, this study represents the first comprehensive analysis of the intestinal microbiome in children with CF receiving ELX/TEZ/IVA.IMPORTANCECystic fibrosis (CF) is an autosomal recessive disease with significant gastrointestinal symptoms in addition to pulmonary complications. Recently approved treatments for CF, CF transmembrane conductance regulator (CFTR) modulators, are anticipated to substantially improve the care of people with CF and extend their lifespans. Prior work has shown that the intestinal microbiome correlates with health outcomes in CF, particularly in children. Here, we study the intestinal microbiome of children with CF before and after the CFTR modulator, ELX/TEZ/IVA. We identify promising improvements in microbiome diversity, reduced measures of intestinal inflammation, and reduced antibiotic resistance genes. We present specific bacterial taxa and protein groups which change following ELX/TEZ/IVA. These results will inform future mechanistic studies to understand the microbial improvements associated with CFTR modulator treatment. This study demonstrates how the microbiome can change in response to a targeted medication that corrects a genetic disease.

Environmental factors dominate microbial community puppet-like driving the distribution of antibiotic resistance genes in different utilization lands

Excessive use of antibiotics has caused the accumulation of antibiotic resistance genes (ARGs) in the soil environment, posing a great challenge to environmental safety and public health. However, there is a lack of comprehensive investigations of soil ARGs profiles under different land utilization patterns, and the drivers that affect the distribution of ARGs remain poorly defined. Herein, we investigated the ARGs profiles of eight different land uses and explored the critical factors influencing the distribution of ARGs. The results showed that ARGs abundance in soil of parks, residential areas, farmland, and vegetable cultivation was significantly higher than that in other lands, with an average of 2.08 × 103 copies/g dry soil. The structural equation model demonstrated that the environmental variables were the pivotal drivers that dominated the differences in ARG distribution across land utilization types (path coefficient=0.934), in which the physicochemical factors exhibited the greatest contribution with an explanatory rate of 20.27%, which was markedly higher than that of antibiotics and heavy metal residues. Importantly, these physicochemical factors manipulate the succession of microbial communities by altering the connections between microorganisms, which in turn indirectly affects the distribution of ARGs. Moreover, ARG exposure was strongly correlated with fertilizer application, precipitation, and per capita water resources (p < 0.01). Overall, this study provides a well-rounded understanding of ARG exposure under different land-use patterns, which helps to develop management strategies for curbing ARGs dissemination in the environment.

Impact of Anthropogenic Activities on Microbial Community Structure in Riverbed Sediments of East Kazakhstan.

Heavy metal (HMe) pollution in regions with mining and metallurgy activities is known to be a serious environmental problem worldwide. Hydrological processes contribute to the dissemination of HMes (drainage, precipitation, flow rate). The aim of the present study is to investigate the microbial community structure in ten river sediments sampled in different regions of East Kazakhstan, which are contaminated with HMes. The overall degree of sediment contamination with HMes (Cr, Cu, Zn, Pb, and Cd) was assessed using the pollution index Zc, which ranged from 0.43 to 21.6, with the highest in Ridder City (Zc = 21.6) and Ust-Kamenogorsk City, 0.8 km below the dam of the hydroelectric power station (Zc = 19.6). The tested samples considerably differed in organic matter, total carbon, nitrogen, and phosphorus content, as well as in the abundance of HMe-related functional gene families and antibiotic resistance genes. Metagenomic analysis of benthic microorganisms showed the prevalence of Proteobacteria (88.84-97.61%) and Actinobacteria (1.21-5.98%) at the phylum level in all samples. At the class level, Actinobacteria (21.68-57.48%), Betaproteobacteria (19.38-41.17%), and Alphaproteobacteria (10.0-39.78%) were the most common among the classified reads. To the best of our knowledge, this is the first study on the metagenomic characteristics of benthic microbial communities exposed to chronic HMe pressure in different regions of East Kazakhstan.

NO3− as an electron acceptor elevates antibiotic resistance gene and human bacterial pathogen risks in managed aquifer recharge (MAR): A comparison with O2

Managed aquifer recharge (MAR) stands out as a promising strategy for ensuring water resource sustainability. This study delves into the comparative impact of nitrate (NO3−) and oxygen (O2) as electron acceptors in MAR on water quality and safety. Notably, NO3−, acting as an electron acceptor, has the potential to enrich denitrifying bacteria, serving as hosts for antibiotic resistance genes (ARGs) and enriching human bacterial pathogens (HBPs) compared to O2. However, a direct comparison between NO3− and O2 remains unexplored. This study assessed risks in MAR effluent induced by NO3− and O2, alongside the presence of the typical refractory antibiotic sulfamethoxazole. Key findings reveal that NO3− as an electron acceptor resulted in a 2 times reduction in dissolved organic carbon content compared to O2, primarily due to a decrease in soluble microbial product production. Furthermore, NO3− significantly enriched denitrifying bacteria, the primary hosts of major ARGs, by 747%, resulting in a 66% increase in the overall abundance of ARGs in the effluent of NO3− MAR compared to O2. This escalation was predominantly attributed to horizontal gene transfer mechanisms, as evidenced by a notable 78% increase in the relative abundance of mobile ARGs, alongside a minor 27% rise in chromosomal ARGs. Additionally, the numerous denitrifying bacteria enriched under NO3− influence also belong to the HBP category, resulting in a significant 114% increase in the abundance of all HBPs. The co-occurrence of ARGs and HBPs was also observed to intensify under NO3− influence. Thus, NO3− as an electron acceptor in MAR elevates ARG and HBP risks compared to O2, potentially compromising groundwater quality and safety.