# | Rank | Similarity | Title + Abs. | Year | PMID |
|---|---|---|---|---|---|
| 0 | 1 | 2 | 3 | 4 | 5 |
| 3548 | 0 | 1.0000 | From flagellar assembly to DNA replication: CJSe's role in mitigating microbial antibiotic resistance genes. The emergence of Antibiotic Resistance Genes (ARGs) in Campylobacter jejuni (CJ) poses a severe threat to food safety and human health. However, the specific impact of CJ and its variants on ARGs and other related factors remains to be further elucidated. Herein, integrated metagenomic sequencing and co-occurrence network analysis approach were employed to investigate the impact of CJ and CJ incorporated with biogenic selenium (CJSe) on ARGs, flagellar assembly pathways, microbial communities, and DNA replication pathways in chicken manure. Compared to the Control (CON) and CJ groups, the CJSe group exhibited 2.4-fold increase selenium levels (P < 0.01) in chicken manure. Notable differences were also observed between the CJ and CJSe groups, with sequence results showing a CJ > CJSe > CON trend in total ARG copy numbers. Furthermore, the CJSe group showed 31.6 % fewer flagellar assembly genes compared to the CJ group. Additionally, compared to the CJ group, CJSe inhibited pathways such as basal body/hook (e.g., FliH, FliO, FliQ reduced by 25-52 %) and stator (MotB downregulated by 42.3 %), suppressing flagellar assembly. We also found that both CJ and CJSe influenced bacterial DNA replication pathways, with the former increasing ARG-carrying bacteria and the latter, under selenium-induced selective pressure, reducing ARG-carrying bacteria. Moreover, compared to the CJ group, the CJSe group showed a significantly lower 9.72 % copy number of total archaeal DNA replication genes. Furthermore, through intricate co-occurrence network analysis, we discovered the complex interplay between changes in ARGs and bacterial and archaeal DNA replication dynamics within the microbial community. These findings indicate that CJSe mitigates the threat posed by CJ and reduces ARG prevalence, while its dual functionality enables applications in biofortified crop production and soil remediation in selenium-deficient regions, thereby advancing circular economy systems. While the current study demonstrates CJSe's dual functionality under controlled conditions, future work will implement a dedicated ecological risk assessment framework encompassing Se speciation/leaching tests and non-target organism assays to confirm environmental safety under field-relevant scenarios. This approach aligns with sustainable strategies for food security and public health safeguarding. | 2025 | 41108960 |
| 7713 | 1 | 0.9990 | Metagenome analyses of corroded concrete wastewater pipe biofilms reveal a complex microbial system. BACKGROUND: Concrete corrosion of wastewater collection systems is a significant cause of deterioration and premature collapse. Failure to adequately address the deteriorating infrastructure networks threatens our environment, public health, and safety. Analysis of whole-metagenome pyrosequencing data and 16S rRNA gene clone libraries was used to determine microbial composition and functional genes associated with biomass harvested from crown (top) and invert (bottom) sections of a corroded wastewater pipe. RESULTS: Taxonomic and functional analysis demonstrated that approximately 90% of the total diversity was associated with the phyla Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. The top (TP) and bottom pipe (BP) communities were different in composition, with some of the differences attributed to the abundance of sulfide-oxidizing and sulfate-reducing bacteria. Additionally, human fecal bacteria were more abundant in the BP communities. Among the functional categories, proteins involved in sulfur and nitrogen metabolism showed the most significant differences between biofilms. There was also an enrichment of genes associated with heavy metal resistance, virulence (protein secretion systems) and stress response in the TP biofilm, while a higher number of genes related to motility and chemotaxis were identified in the BP biofilm. Both biofilms contain a high number of genes associated with resistance to antibiotics and toxic compounds subsystems. CONCLUSIONS: The function potential of wastewater biofilms was highly diverse with level of COG diversity similar to that described for soil. On the basis of the metagenomic data, some factors that may contribute to niche differentiation were pH, aerobic conditions and availability of substrate, such as nitrogen and sulfur. The results from this study will help us better understand the genetic network and functional capability of microbial members of wastewater concrete biofilms. | 2012 | 22727216 |
| 6834 | 2 | 0.9989 | Landscape of antibiotic resistance genes and bacterial communities in groundwater on the Tibetan Plateau, and distinguishing their difference with low-altitude counterparts. Groundwater is a vital source of drinking water for Tibetans. Antibiotic resistance genes (ARGs) and bacterial communities in groundwater on the Tibetan Plateau remain unclear. Furthermore, the characterization of their differences between high-altitude and low-altitude groundwater is still unrevealed. Herein, 32 groundwater samples were collected on the plateau, and intra- and extracellular ARGs (iARGs and eARGs), and bacterial communities were characterised through qPCR assays to 19 ARGs and 16S rRNA sequencing. It showed top four abundant intra- and extracellular last-resort ARGs (LARGs) were bla(OXA-48), mcr-1, vanA, and vanB, whereas dominant common ARGs (CARGs) were tetA and ermB, respectively. CARGs had higher abundances than LARGs, and iARGs were more frequently detected than eARGs. Proteobacteria, an invasive resident phylum, and Firmicutes dominated eDNA release. Network analysis revealed all observed LARGs co-occurred with pathogenic and non-pathogenic bacteria. Community diversity was significantly associated with longitude and elevation, while nitrate correlated with ARGs. Comparative analysis demonstrated eARG frequencies and abundances were higher at high altitudes than at low altitudes. Additionally, Acinetobacter and Pseudomonas specifically dominated at high altitudes. This study reveals the widespread prevalence of ARGs, particularly LARGs, in groundwater on the less-disturbed Tibetan Plateau and underlines the potential risks associated with the LARG-carrying bacteria. ENVIRONMENTAL IMPLICATION: Antibiotic resistance genes (ARGs), which are defined as emerging environmental contaminants, are becoming a global concern due to their ability to confer antibiotic resistance to pathogens. Our findings highlight the prevalence of ARGs, particularly LARGs, in groundwater on the Tibetan Plateau, and the possibility that naturally-occurring pathogenic and non-pathogenic bacteria carry multiple LARGs. In addition, we further reveal differences in the distribution of ARGs and bacterial community between high-altitude and low-altitude groundwater. Collectively, our findings offer an important insight into the potential public risks related to groundwater on the Tibetan Plateau. | 2023 | 37595466 |
| 7533 | 3 | 0.9989 | NO(3)(-) as an electron acceptor elevates antibiotic resistance gene and human bacterial pathogen risks in managed aquifer recharge (MAR): A comparison with O(2). Managed aquifer recharge (MAR) stands out as a promising strategy for ensuring water resource sustainability. This study delves into the comparative impact of nitrate (NO(3)(-)) and oxygen (O(2)) as electron acceptors in MAR on water quality and safety. Notably, NO(3)(-), 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 O(2). However, a direct comparison between NO(3)(-) and O(2) remains unexplored. This study assessed risks in MAR effluent induced by NO(3)(-) and O(2), alongside the presence of the typical refractory antibiotic sulfamethoxazole. Key findings reveal that NO(3)(-) as an electron acceptor resulted in a 2 times reduction in dissolved organic carbon content compared to O(2), primarily due to a decrease in soluble microbial product production. Furthermore, NO(3)(-) 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 NO(3)(-) MAR compared to O(2). 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 NO(3)(-) 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 NO(3)(-) influence. Thus, NO(3)(-) as an electron acceptor in MAR elevates ARG and HBP risks compared to O(2), potentially compromising groundwater quality and safety. | 2024 | 38266895 |
| 6987 | 4 | 0.9989 | Chemical fertilizers promote dissemination of ARGs in maize rhizosphere: An overlooked risk revealed after 37-year traditional agriculture practice. Bacterial communities in soil and rhizosphere maintain a large collection of antibiotic resistance genes (ARGs). However, few of these ARGs and antibiotic resistant bacteria (ARB) are well-characterized under traditional farming practices. Here we compared the ARG profiles of maize rhizosphere and their bulk soils using metagenomic analysis to identify the ARG dissemination and explored the potential impact of chemical fertilization on ARB. Results showed a relatively lower abundance but higher diversity of ARGs under fertilization than straw-return. Moreover, the abundance and diversity of MGEs were significantly promoted by chemical fertilizer inputs in the rhizosphere compared to bulk soil. Machine learning and bipartite networks identified three bacterial genera (Pseudomonas, Bacillus and Streptomyces) as biomarkers for ARG accumulation. Thus we cultured 509 isolates belonging to these three genera from the rhizosphere and tested their antimicrobial susceptibility, and found that multi-resistance was frequently observed among Pseudomonas isolates. Assembly-based tracking explained that ARGs and four class I integrons (LR134330, LS998783, CP065848, LT883143) were co-occurred among contigs from Pseudomonas sp. Chemical fertilizers may shape the resistomes of maize rhizosphere, highlighting that rhizosphere carried multidrug-resistant Pseudomonas isolates, which may pose a risk to animal and human health. This study adds knowledge of long-term chemical fertilization on ARG dissemination in farmland systems and provides information for decision-making in agricultural production and monitoring. | 2024 | 38844214 |
| 7451 | 5 | 0.9989 | Plant species influences the composition of root system microbiome and its antibiotic resistance profile in a constructed wetland receiving primary treated wastewater. INTRODUCTION: Constructed wetlands (CWs) are nature-based solutions for wastewater treatment where the root system microbiome plays a key role in terms of nutrient and pollutant removal. Nonetheless, little is known on plant-microbe interactions and bacterial population selection in CWs, which are mostly characterized in terms of engineering aspects. METHODS: Here, cultivation-independent and cultivation-based analyses were applied to study the bacterial communities associated to the root systems of Phragmites australis and Typha domingensis co-occurring in the same cell of a CW receiving primary treated wastewaters. RESULTS AND DISCUSSION: Two endophytic bacteria collections (n = 156) were established aiming to find novel strains for microbial-assisted phytodepuration, however basing on their taxonomy the possible use of these strains was limited by their low degrading potential and/or for risks related to the One-Health concept. A sharp differentiation arose between the P. australis and T. domingensis collections, mainly represented by lactic acid bacteria (98%) and Enterobacteriaceae (69%), respectively. Hence, 16S rRNA amplicon sequencing was used to disentangle the microbiome composition in the root system fractions collected at increasing distance from the root surface. Both the fraction type and the plant species were recognized as drivers of the bacterial community structure. Moreover, differential abundance analysis revealed that, in all fractions, several bacteria families were significantly and differentially enriched in P. australis or in T. domingensis. CWs have been also reported as interesting options for the removal of emerging contaminants (e.g, antibiotic resistance genes, ARGs). In this study, ARGs were mostly present in the rhizosphere of both plant species, compared to the other analyzed fractions. Notably, qPCR data showed that ARGs (i.e., ermB, bla (TEM), tetA) and intl1 gene (integrase gene of the class 1 integrons) were significantly higher in Phragmites than Typha rhizospheres, suggesting that macrophyte species growing in CWs can display a different ability to remove ARGs from wastewater. Overall, the results suggest the importance to consider the plant-microbiome interactions, besides engineering aspects, to select the most suitable species when designing phytodepuration systems. | 2024 | 39113842 |
| 6880 | 6 | 0.9989 | Co-occurrence and co-expression of antibiotic, biocide, and metal resistance genes with mobile genetic elements in microbial communities subjected to long-term antibiotic pressure: Novel insights from metagenomics and metatranscriptomics. The burgeoning of antibiotic resistance has emerged as a pressing global challenge. To gain a deeper understanding of the interactions between antibiotic resistance genes (ARGs), biocide and metal resistance genes (BRGs&MRGs), and mobile genetic elements (MGEs), this study utilized metagenomics and metatranscriptomics to investigate their co-occurrence and co-expression in two consortia subjected to long-term exposure to chloramphenicol and lincomycin. Long-term exposure to these antibiotics resulted in significant disparities in resistance profiles: Consortium(CAP) harbored 130 ARGs and 150 BRGs&MRGs, while Consortium(LIN) contained 57 ARGs and 32 BRGs&MRGs. Horizontal gene transfer (HGT) events were predicted at 125 and 300 instances in Consortium(CAP) and Consortium(LIN), respectively, facilitating the emergence of multidrug-resistant bacteria, such as Caballeronia (10 ARGs, 2 BRGs&MRGs), Cupriavidus (2 ARGs, 10 BRGs&MRGs), and Bacillus (14 ARGs, 21 BRGs&MRGs). Chloramphenicol exposure significantly enriched genes linked to phenicol resistance (floR, capO) and co-expressed ARGs and BRGs&MRGs, while lincomycin exerted narrower effects on resistance genes. Additionally, both antibiotics modulated the expression of degradation genes and virulence factors, highlighting their role in altering bacterial substrate utilization and pathogenic traits. This study provides quantitative insights into the impact of antibiotics on microbial resistance profiles and functions at both DNA and RNA levels, highlighting the importance of reducing antibiotic pollution and limiting the spread of resistance genes in the environment. | 2025 | 39965334 |
| 7726 | 7 | 0.9989 | Distribution and comparison of bacterial communities in HVAC systems of two university buildings: Implications for indoor air quality and public health. The installation of HVAC systems in building is meant to enhance indoor air quality as well as increase comfort to occupants. However, HVAC systems have also become a vehicle of contamination of indoor air with potentially pathogenic microorganisms. DNA was extracted from ten HVAC filter dust samples collected from two buildings and subjected to high throughput sequencing analysis to determine the bacterial community structure. Further, the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) software was used to predict the potential functional capabilities of the bacterial communities. Sequencing analysis led to the identification of five major bacterial phyla, including Proteobacteria, Cyanobacteria, Actinobacteria, Firmicutes and Bacteroidetes. At genus level, Mycobacterium, Bacillus, Cupriavidus, Hyphomicrobium and Mesorhizobium were the most dominant. With the exception of the later two bacterial genera, the first three are potential pathogens whose presence in HVAC systems poses a significant public health risk, especially among immunocompromised individuals. Nine pathways associated with antibiotics resistance and bacterial pathogenicity were identified, including polymyxin resistance and peptidoglycan biosynthesis pathways. Further, investigation of the relationship between the detected bacterial meta-communities and predicted potential virulence factors (antibiotic resistance and pathogenic genes) led to the detection of 350 positive associations among 43 core bacteria, 2 pathogenic genes (sitA and uidA) and 14 resistance genes. Overall, the heterogeneous nature of microorganisms found in HVAC systems observed in this study shows that HVAC systems are the origin of airborne infections in indoor environments, and must be periodically cleaned and disinfected to avoid the build-up of pathogens, and the subsequent exposure of human occupants of these pathogens. | 2021 | 33415530 |
| 6878 | 8 | 0.9989 | Reduction in antimicrobial resistance in a watershed after closure of livestock farms. Natural environments play a crucial role in transmission of antimicrobial resistance (AMR). Development of methods to manage antibiotic resistance genes (ARGs) in natural environments are usually limited to the laboratory or field scale, partially due to the complex dynamics of transmission between different environmental compartments. Here, we conducted a nine-year longitudinal profiling of ARGs at a watershed scale, and provide evidence that restrictions on livestock farms near water bodies significantly reduced riverine ARG abundance. Substantial reductions were revealed in the relative abundance of genes conferring resistance to aminoglycosides (42%), MLSB (36%), multidrug (55%), tetracyclines (53%), and other gene categories (59%). Additionally, improvements in water quality were observed, with distinct changes in concentrations of dissolved reactive phosphorus, ammonium, nitrite, pH, and dissolved oxygen. Antibiotic residues and other pharmaceuticals and personal care products (PPCPs) maintain at a similarly low level. Microbial source tracking demonstrates a significant decrease in swine fecal indicators, while human fecal pollution remains unchanged. These results suggest that the reduction in ARGs was due to a substantial reduction in input of antibiotic resistant bacteria and genes from animal excreta. Our findings highlight the watershed as a living laboratory for understanding the dynamics of AMR, and for evaluating the efficacy of environmental regulations, with implications for reducing environmental risks associated with AMR on a global scale. | 2024 | 38925006 |
| 7532 | 9 | 0.9989 | Underrated risk of antibiotic resistance genes dissemination mediated by bioaerosols released from anaerobic biological wastewater treatment system. Antibiotic resistance has been recognized as one of the most prevalent public health problems. The bioaerosol-mediated spread of antibiotic resistance genes (ARGs) is an important but underrated pathway. Therefore, this work investigated the comprehensive resistome and pathogen-induced risk in bioaerosols released from anaerobic ammonium oxidation (anammox) process under antibiotic stress. The results showed that the bioaerosol oxidation potential increased by 2.7 times after the addition of sulfamethoxazole (SMX) into the anammox system. Based on the metagenomic analyses, abundant ARGs were enriched in bioaerosols, especially novA, olec, msbA and patA. There were many antibiotic resistance contigs carrying at least two mobile genetic elements (MGEs) in bioaerosols. Compared to the control, SMX caused the significant increase in ARGs proportion in plasmids from 11.4 % to 19.4 %. Similarly, the abundance of the type IV secretion system protein encoding genes (mtrA and mtrB) increased by 30.2 % and 31.5 %, respectively, which was conducive to gene transfer between bacteria. In addition, SMX stress induced the reactive oxygen species (ROS) production and the upregulation of genes related to membrane protein and DNA replication, further facilitating ARGs transfer. The co-occurrence networks showed that Aquamicrobium and Microbacterium probably were the hosts of most ARGs. Notably, four abundant human pathogens were detected in bioaerosols from the anammox system, which raised concerns on the health risk of resistant bioaerosol diffusion. These findings reveal the potential of horizontal gene transfer through bioaerosols and provide a guidance for systematically assessing the risk of environmental antibiotic resistance and relevant pathogens. | 2025 | 40073489 |
| 7714 | 10 | 0.9989 | Functional traits and health implications of the global household drinking-water microbiome retrieved using an integrative genome-centric approach. The biological safety of drinking water plays a crucial role in public health protection. However, research on the drinking water microbiome remains in its infancy, especially little is known about the potentially pathogenic bacteria in and functional characteristics of the microbiome in household tap water that people are directly exposed to. In this study, we used a genomic-centric approach to construct a genetic catalogue of the drinking water microbiome by analysing 116 metagenomic datasets of household tap water worldwide, spanning nine countries/regions on five continents. We reconstructed 859 high-quality metagenome-assembled genomes (MAGs) spanning 27 bacterial and 2 archaeal phyla, and found that the core MAGs belonging to the phylum Proteobacteria encoded the highest metabolic functional diversity of the 33 key complete metabolic modules. In particular, we found that two core MAGs of Brevibacillus and Methylomona encoded genes for methane metabolism, which may support the growth of heterotrophic organisms observed in the oligotrophic ecosystem. Four MAGs of complete ammonia oxidation (comammox) Nitrospira were identified and functional metabolic analysis suggested these may enable mixotrophic growth and encode genes for reactive oxygen stress defence and arsenite reduction that could aid survival in the environment of oligotrophic drinking water systems. Four MAGs were annotated as potentially pathogenic bacteria (PPB) and thus represented a possible public health concern. They belonged to the genera Acinetobacter (n = 3) and Mycobacterium (n = 1), with a total relative abundance of 1.06 % in all samples. The genomes of PPB A. junii and A. ursingii were discovered to contain antibiotic resistance genes and mobile genetic elements that could contribute to antimicrobial dissemination in drinking water. Further network analysis suggested that symbiotic microbes which support the growth of pathogenic bacteria can be targets for future surveillance and removal. | 2024 | 38183799 |
| 7707 | 11 | 0.9988 | Exploring the dynamics of gut microbiota, antibiotic resistance, and chemotherapy impact in acute leukemia patients: A comprehensive metagenomic analysis. Leukemia poses significant challenges to its treatment, and understanding its complex pathogenesis is crucial. This study used metagenomic sequencing to investigate the interplay between chemotherapy, gut microbiota, and antibiotic resistance in patients with acute leukemia (AL). Pre- and post-chemotherapy stool samples from patients revealed alterations in microbial richness, taxa, and antibiotic resistance genes (ARGs). The analysis revealed a decreased alpha diversity, increased dispersion in post-chemotherapy samples, and changes in the abundance of specific bacteria. Key bacteria such as Enterococcus, Klebsiella, and Escherichia coli have been identified as prevalent ARG carriers. Correlation analysis between gut microbiota and blood indicators revealed potential links between microbial species and inflammatory biomarkers, including C-reactive protein (CRP) and adenosine deaminase (ADA). This study investigated the impact of antibiotic dosage on microbiota and ARGs, revealing networks connecting co-occurring ARGs with microbial species (179 nodes, 206 edges), and networks associated with ARGs and antibiotic dosages (50 nodes, 50 edges). Antibiotics such as cephamycin and sulfonamide led to multidrug-resistant Klebsiella colonization. Our analyses revealed distinct microbial profiles with Salmonella enterica elevated post-chemotherapy in NF patients and Akkermansia muciniphila elevated pre-chemotherapy. These microbial signatures could inform strategies to modulate the gut microbiome, potentially mitigating the risk of neutropenic fever in patients undergoing chemotherapy. Finally, a comprehensive analysis of KEGG modules shed light on disrupted metabolic pathways after chemotherapy, providing insights into potential targets for managing side effects. Overall, this study revealed intricate relationships between gut microbiota, chemotherapy, and antibiotic resistance, providing new insights into improving therapy and enhancing patient outcomes. | 2024 | 39620486 |
| 7445 | 12 | 0.9988 | Efficient removal of antibiotic resistance genes and of enteric bacteria from reclaimed wastewater by enhanced Soil Aquifer Treatments. Soil Aquifer Treatment (SAT) is a robust technology to increase groundwater recharge and to improve reclaimed water quality. SAT reduces dissolved organic carbon, contaminants of emerging concern, nutrients, and colloidal matter, including pathogen indicators, but little is known about its ability to reduce loads of antibiotic resistance genes (ARGs) from reclaimed waters. Here we test six pilot SAT systems to eliminate various biological hazards from the secondary effluents of a wastewater treatment plant (WWTP), equipped with reactive barriers (RBs) including different sorptive materials. Using flow cytometry, qPCR and 16S rRNA gene amplicon sequencing methods, we determined that all six SAT systems reduced total loads of bacteria by 80 to 95 % and of clinically relevant ARGs by 85 to 99.9 %. These efficiencies are similar to those reported for UV/oxidation or membrane-based tertiary treatments, which require much more energy and resources. The presence and composition of reactive barriers, the season of sampling (June 2020, October 2020, and September 2021), or the flow regime (continuous versus pulsating) did not affect ARG removal efficiency, although they did alter the microbial community composition. This suggests that an adequate design of the SAT reactive barriers may significantly increase their performance. Under a mechanistic point of view, we observed an ecological succession of bacterial groups, linked to the changing physical-chemical conditions along the SAT, and likely correlated to the removal of ARGs. We concluded that SAT is as cost-efficient technology able to dramatically reduce ARG loads and other biological hazards from WWTP secondary effluents. | 2024 | 39244046 |
| 7417 | 13 | 0.9988 | Limited impacts of high doses of dietary copper on the gut bacterial metal resistome explain negligible co-selection of antibiotic resistance. High dietary intake of Cu has previously been linked to the selection of Cu resistance and co-selection of antibiotic resistance in specific gut bacteria. Based on a novel HT-qPCR metal resistance gene chip as combined with 16S rRNA gene amplicon sequencing and phenotypic resistance typing of Escherichia coli isolates, we here report the impacts of two contrasting Cu-based feed additives on the swine gut bacterial metal resistome and community assembly. DNA was extracted from fecal samples (n = 80) collected at day 26 and 116 of the experiment from 200 pigs allotted to five dietary treatments: negative control (NC) diet with 20 μg CuSO(4) g(-1) and four diets added 125 or 250 μg CuSO(4) g(-1) feed or 125 or 250 μg Cu(2)O g(-1) feed to the NC diet. Dietary Cu supplementation reduced the relative abundance of Lactobacillus, but it had negligible impacts on bacterial community composition relative to the gut microbiome maturation effect (time). The relative importance of different bacterial community assembly processes was not markedly affected by the dietary Cu treatments, and differences in swine gut metal resistome composition could be explained primarily by differences in bacterial community composition rather than by dietary Cu treatments. High dietary Cu intake (250 μg Cu g(-1)) selected for phenotypic Cu resistance in E. coli isolates, but surprisingly it did not result in increased prevalence of the Cu resistance genes targeted by the HT-qPCR chip. In conclusion, the lacking impacts of dietary Cu on the gut bacterial metal resistome explain results from a previous study showing that even high therapeutic doses of dietary Cu did not cause co-selection of antibiotic resistance genes and mobile genetic elements known to harbor these genes. | 2023 | 37201857 |
| 7700 | 14 | 0.9988 | Rapid identification of antibiotic resistance gene hosts by prescreening ARG-like reads. Effective risk assessment and control of environmental antibiotic resistance depend on comprehensive information about antibiotic resistance genes (ARGs) and their microbial hosts. Advances in sequencing technologies and bioinformatics have enabled the identification of ARG hosts using metagenome-assembled contigs and genomes. However, these approaches often suffer from information loss and require extensive computational resources. Here we introduce a bioinformatic strategy that identifies ARG hosts by prescreening ARG-like reads (ALRs) directly from total metagenomic datasets. This ALR-based method offers several advantages: (1) it enables the detection of low-abundance ARG hosts with higher accuracy in complex environments; (2) it establishes a direct relationship between the abundance of ARGs and their hosts; and (3) it reduces computation time by approximately 44-96% compared to strategies relying on assembled contigs and genomes. We applied our ALR-based strategy alongside two traditional methods to investigate a typical human-impacted environment. The results were consistent across all methods, revealing that ARGs are predominantly carried by Gammaproteobacteria and Bacilli, and their distribution patterns may indicate the impact of wastewater discharge on coastal resistome. Our strategy provides rapid and accurate identification of antibiotic-resistant bacteria, offering valuable insights for the high-throughput surveillance of environmental antibiotic resistance. This study further expands our knowledge of ARG-related risk management in future. | 2025 | 40059905 |
| 6900 | 15 | 0.9988 | Tracking the extracellular and intracellular antibiotic resistance genes across whole year in wastewater of intensive dairy farm. Monitoring the annual variation of antibiotic resistance genes (ARGs) in livestock wastewater is important for determining the high-risk period of transfer and spread of animal-derived antibiotic resistance into the environment. However, the knowledge regarding the variation patterns of ARGs, especially intracellular ARGs (iARGs) and extracellular ARGs (eARGs), over time in livestock wastewater is still unclear. Herein, we conducted a year-round study to trace the profiles of ARGs at a Chinese-intensive dairy farm, focusing on the shifts observed in different months. The results showed significant differences in the composition and variation between iARGs and eARGs. Tetracycline, sulfonamide, and macrolide resistance genes were the major types of iARGs, while cfr was the major type of eARG. The environmental adaptations of the host bacteria determine whether ARGs appear as intracellular or extracellular forms. The total abundance of ARGs was higher from April to September, which can be attributed to the favorable climatic conditions for bacterial colonization and increased antibiotic administration during this period. Integron was found to be highly correlated with most iARGs, potentially playing a role in the presence of these genes within cells and their similar transmission patterns in wastewater. The intracellular and extracellular bacterial communities were significantly different, primarily because of variations in bacterial adaptability to the high salt and anaerobic environment. The intracellular co-occurrence network indicated that some dominant genera in wastewater, such as Turicibacter, Clostridium IV, Cloacibacillus, Subdivision5_genera_incertae_sedis, Saccharibacteria_genera_incertae_sedis and Halomonas, were potential hosts for many ARGs. To the best of our knowledge, this study demonstrates, for the first time, the annual variation of ARGs at critical points in the reuse of dairy farm wastewater. It also offers valuable insights into the prevention and control of ARGs derived from animals. | 2024 | 38039853 |
| 7031 | 16 | 0.9988 | Free-living lifestyle preferences drive the antibiotic resistance promotion during drinking water chlorination. The risk associated with antibiotic resistance genes (ARGs) in size-fractionated bacterial community during drinking water chlorination remains unclear, and is of paramount importance for risk mitigation through process selection and optimization. This study employed metagenomic approaches to reveal the alterations of ARGs, their potential functions and hosts within the free-living and particle-associated fractions. The total relative abundance of ARGs, mobile genetic elements (MGEs), and virulence factor genes (VFGs) significantly increased in the free-living fraction after chlorination. The contribution of the free-living fraction to the ARG relative abundance rose from 16.40 ± 1.31 % to 93.62 ± 0.47 % after chlorination. Multidrug resistance genes (e.g. mexF and mexW) were major contributors, and their co-occurrence with MGEs in the free-living fraction was enhanced after chlorination. Considering multiple perspectives, including presence, mobility, and pathogenicity, chlorination led to a significant risk of the antibiotic resistome in the free-living fraction. Moreover, potential functions of ARGs, such as cell wall/membrane/envelope biogenesis, defense mechanisms, and transcription in the free-living fraction, were intensified following chlorination. Potential pathogens, including Pseudomonas aeruginosa, Pseudomonas alcaligenes, and Acinetobacter junii, were identified as the predominant hosts of multidrug resistance genes, with their increased abundances primarily contributing to the rise of the corresponding ARGs. Overall, alterations of hosts as well as enhancing mobility and biological functions could collectively aid the proliferation and spread of ARGs in the free-living fraction after chlorination. This study provides novel insights into antibiotic resistance evolution in size-fractionated bacteria community and offers a management strategy for microbiological safety in drinking water. | 2024 | 38043346 |
| 8664 | 17 | 0.9988 | Genome-centric metagenomics reveals the host-driven dynamics and ecological role of CPR bacteria in an activated sludge system. BACKGROUND: Candidate phyla radiation (CPR) constitutes highly diverse bacteria with small cell sizes and are likely obligate intracellular symbionts. Given their distribution and complex associations with bacterial hosts, genetic and biological features of CPR bacteria in low-nutrient environments have received increasing attention. However, CPR bacteria in wastewater treatment systems remain poorly understood. We utilized genome-centric metagenomics to answer how CPR communities shift over 11 years and what kind of ecological roles they act in an activated sludge system. RESULTS: We found that approximately 9% (135) of the 1,526 non-redundant bacterial and archaeal metagenome-assembled genomes were affiliated with CPR. CPR bacteria were consistently abundant with a relative abundance of up to 7.5% in the studied activated sludge system. The observed striking fluctuations in CPR community compositions and the limited metabolic and biosynthetic capabilities in CPR bacteria collectively revealed the nature that CPR dynamics may be directly determined by the available hosts. Similarity-based network analysis further confirmed the broad bacterial hosts of CPR lineages. The proteome contents of activated sludge-associated CPR had a higher similarity to those of environmental-associated CPR than to those of human-associated ones. Comparative genomic analysis observed significant enrichment of genes for oxygen stress resistance in activated sludge-associated CPR bacteria. Furthermore, genes for carbon cycling and horizontal gene transfer were extensively identified in activated sludge-associated CPR genomes. CONCLUSIONS: These findings highlight the presence of specific host interactions among CPR lineages in activated sludge systems. Despite the lack of key metabolic pathways, these small, yet abundant bacteria may have significant involvements in biogeochemical cycling and bacterial evolution in activated sludge systems. Video Abstract. | 2023 | 36945052 |
| 7464 | 18 | 0.9988 | Antibiotic resistance at environmental multi-media interfaces through integrated genotype and phenotype analysis. Antibiotic resistance is currently an unfolding global crisis threatening human health worldwide. While antibiotic resistance genes (ARGs) are known to be pervasive in environmental media, the occurrence of antibiotic resistance at interfaces between two or more adjacent media is largely unknown. Here, we designed a microcosm study to simulate plastic pollution in paddy soil and used a novel method, stimulated Raman scattering coupled with deuterium oxide (D(2)O) labelling, to compare the antibiotic resistance in a single medium with that at the interface of multiple environmental media (plastic, soil, water). Results revealed that the involvement of more types of environmental media at interfaces led to a higher proportion of active resistant bacteria. Genotypic analysis showed that ARGs (especially high-risk ARGs) and mobile genetic elements (MGEs) were all highly enriched at the interfaces. This enrichment was further enhanced by the co-stress of heavy metal (arsenic) and antibiotic (ciprofloxacin). Our study is the first to apply stimulated Raman scattering to elucidate antibiotic resistance at environmental interfaces and reveals novel pathway of antibiotic resistance dissemination in the environment and overlooked risks to human health. | 2024 | 39413517 |
| 6879 | 19 | 0.9988 | Airborne antibiotic and metal resistance genes - A neglected potential risk at e-waste recycling facilities. Heavy metal-rich environments can promote the selection of metal-resistance genes (MRGs) in bacteria, often leading to the simultaneous selection of antibiotic-resistance genes (ARGs) through a process known as co-selection. To comprehensively evaluate the biological pollutants at electronic-waste (e-waste) recycling facilities, air, soil, and river samples were collected at four distinct Swiss e-waste recycling facilities and analyzed for ARGs, MRGs, mobile genetic elements (MGEs), endotoxins, and bacterial species, with correlations drawn to heavy metal occurrence. To our knowledge, the present work marks the first attempt to quantify these bio-pollutants in the air of e-waste recycling facilities, that might pose a significant health risk to workers. Although ARG and MRG's profiles varied among the different sample types, intl1 consistently exhibited high relative abundance rates, identifying it as the predominant MGE across all sample types and facilities. These findings underscore its pivol role in driving diverse bacterial adaptations to extreme heavy metal exposure by selection and dissemination of ARGs and MRGs. All air samples exhibited consistent profiles of ARGs and MRGs, with blaTEM emerging as the predominant ARG, alongside pbrT and nccA as the most prevalent MRGs. However, one facility, engaged in batteries recycling and characterized by exceptionally high concentrations of heavy metals, showcased a more diverse resistance gene profile, suggesting that bacteria in this environment required more complex resistance mechanisms to cope with extreme metal exposure. Furthermore, this study unveiled a strong association between gram-negative bacteria and ARGs and less with MRGs. Overall, this research emphasizes the critical importance of studying biological pollutants in the air of e-waste recycling facilities to inform robust safety measures and mitigate the risk of resistance gene dissemination among workers. These findings establish a solid foundation for further investigations into the complex interplay among heavy metal exposure, bacterial adaptation, and resistance patterns in such distinctive ecosystems. | 2024 | 38365028 |