Ontology highlight
ABSTRACT:
PROVIDER: PRJNA877232 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21440865_1.fastq.gz | Fastqsanger.gz | |||
| SRR21440865_2.fastq.gz | Fastqsanger.gz | |||
| SRR21440866_1.fastq.gz | Fastqsanger.gz | |||
| SRR21440866_2.fastq.gz | Fastqsanger.gz | |||
| SRR21440867_1.fastq.gz | Fastqsanger.gz |
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Project description:Incomplete antibiotic removal in pharmaceutical wastewater treatment plants (PWWTPs) could lead to the development and spread of antibiotic-resistant bacteria (ARBs) and genes (ARGs) in the environment, posing a growing public health threat. In this study, two multiantibiotic-resistant bacteria, Ochrobactrum intermedium (N1) and Stenotrophomonas acidaminiphila (N2), were isolated from the sludge of a PWWTP in Guangzhou, China. The N1 strain was highly resistant to ampicillin, cefazolin, chloramphenicol, tetracycline, and norfloxacin, while the N2 strain exhibited high resistance to ampicillin, chloramphenicol, and cefazolin. Whole-genome sequencing revealed that N1 and N2 had genome sizes of 0.52 Mb and 0.37 Mb, respectively, and harbored 33 and 24 ARGs, respectively. The main resistance mechanism in the identified ARGs included efflux pumps, enzymatic degradation, and target bypass, with the N1 strain possessing more multidrug-resistant efflux pumps than the N2 strain (22 vs 12). This also accounts for the broader resistance spectrum of N1 than of N2 in antimicrobial susceptibility tests. Additionally, both genomes contain numerous mobile genetic elements (89 and 21 genes, respectively) and virulence factors (276 and 250 factors, respectively), suggesting their potential for horizontal transfer and pathogenicity. Overall, this research provides insights into the potential risks posed by ARBs in pharmaceutical wastewater and emphasizes the need for further studies on their impact and mitigation strategies.
2024-10-20 | E-MTAB-14497 | biostudies-arrayexpress
Project description:Antibiotic resistance is exacerbated by the exchange of antibiotic resistance genes (ARGs) between microbes from diverse habitats. Plasmids are important ARGs mobile elements and are spread by horizontal gene transfer (HGT). In this study, we demonstrated the presence of multi-resistant plasmids from inhalable particulate matter (PM) and its effect on gene horizontal transfer. Three transferable multi-resistant plasmids were identified from PM in a hospital, using conjugative mating assays and nanopore sequencing. pTAir-3 contained 26 horizontal transfer elements and 10 ARGs. Importantly pTAir-5 harbored carbapenem resistance gene (blaOXA) which shows homology to plasmids from human and pig commensal bacteria, thus indicating that PM is a media for antibiotic resistant plasmid spread. In addition, 125 μg/mL PM2.5 and PM10 significantly increased the conjugative transfer rate by 110% and 30%, respectively, and augmented reactive oxygen species (ROS) levels. Underlying mechanisms were revealed by identifying the upregulated expressional levels of genes related to ROS, SOS, cell membranes, pilus generation, and transposition via genome-wide RNA sequencing. The study highlights the airborne spread of multi-resistant plasmids and the impact of inhalable PM on the horizontal transfer of antibiotic resistance.
2022-10-31 | GSE159850 | GEO
Project description:Recently it was discovered that the perfluorooctane sulfonate (PFOS) detected in wildlife, such as fish-eating birds, had a greater proportion of linear PFOS (L-PFOS) than the manufactured technical product (T-PFOS), which contains linear and branched isomers. This suggests toxicological studies based on T-PFOS data may inaccurately assess exposure risk to wildlife. To determine if PFOS effects were influenced by isomer content we compared the transcriptional profiles of cultured chicken embryonic hepatocytes (CEH) exposed to either L-PFOS or T-PFOS using Agilent microarrays. At equal concentrations (10 μM), T-PFOS altered the expression of more transcripts (340, >1.5 fold change, p<0.05) compared to L-PFOS (130 transcripts). Higher concentrations of L-PFOS (40 μM) were also less transcriptionally disruptive (217 transcripts) than T-PFOS at 10 μM. Functional analysis showed that L-PFOS and T-PFOS affected genes involved in lipid metabolism, hepatic system development and cellular growth and proliferation. Pathway and interactome analysis suggested that genes may be affected through the RXR receptor, oxidative stress response, TP53 signaling, MYC signaling, Wnt/β-catenin signaling and PPARγ and SREBP receptors. In all functional categories and pathways examined, the response elicited by T-PFOS was greater than L-PFOS. These data show that T-PFOS elicits a greater transcriptional response in CEH than L-PFOS alone and demonstrates the importance of considering the isomer-specific toxicological properties of PFOS when assessing exposure risk. Reference Design. Reference = pool of equal parts of all control and treated samples. Control groups and 5 treatment groups. Control samples were CEH exposed DMSO only (vehicle solvent). Treatments were: CEH exposed to 10 uM L-PFOS, 40 uM L-PFOS, 10 uM T-PFOS, 0.03 nM TCDD and 1 nM TCDD.
2011-10-28 | E-GEOD-33291 | biostudies-arrayexpress
Project description:Perfluorooctanesulfonate (PFOS) has been widely used in a variety of industrial and commercial applications as a surfactant and stain repellent. PFOS causes liver damage (including liver tumors) in experimental animals, primarily via interaction with PPARa and CAR/PXR. We investigated the involvement of microRNAs (miRNAs) in PFOS-induced hepatotoxicity, and mechanisms involved in abnormal TH homeostasis, in the livers of adult male rats exposed in feed to 50 mg PFOS/kg diet for 28 days. PFOS-treated rats exhibited expected histopathological and clinical chemistry changes. Global gene expression changes were consistent with the involvement of PPARα and CAR/PXR in PFOS-induced effects. Thirty-eight miRNAs were significantly altered. Three members of the miR-200 family were the most increased, while miR-122 and miR-21 were the most decreased, in PFOS-treated relative to control rats. Expression of the miR-23b/27b/24 cluster also decreased in PFOS-treated animals. Pathway analysis of miRNAs and associated gene expression changes demonstrated enrichment of transcripts involved in epithelial to mesenchymal transition (EMT), which is a primary process involved in tumor cell motility and cancer metastasis. Liver expression analysis revealed transcripts that may mediate PFOS effects on thyroid hormone (TH) homeostasis including: activation of the CAR/PXR pathway, phase II/III enzymes, and deiodinase. These changes are consistent with low serum TH due to enhanced metabolic clearance of TH. However, most TH hepatic target genes were not altered in a manner consistent with reduced TH signalling; suggesting that PFOS exposure did not induce functional hypothyroidism. Collectively, PFOS-induced miRNA perturbations were strongly associated with EMT suggesting an important role for miRNAs in PFOS-induced hepatotoxicity. The work also provides novel insights into the effects of PFOS on TH homeostasis.
2015-08-01 | GSE69521 | GEO
Project description:In this study, two multiantibiotic-resistant bacteria, Ochrobactrum intermedium (N1) and Stenotrophomonas acidaminiphila (N2), were isolated from the sludge of a PWWTP in Guangzhou, China. Whole-genome sequencing revealed that N1 and N2 had genome sizes of 0.52 Mb and 0.37 Mb, respectively, and harbored 33 and 24 ARGs, respectively. The main resistance mechanism in the identified ARGs included efflux pumps, enzymatic degradation, and target bypass, with the N1 strain possessing more multidrug-resistant efflux pumps than the N2 strain (22 vs 12). This also accounts for the broader resistance spectrum of N1 than of N2 in antimicrobial susceptibility tests. Additionally, both genomes contain numerous mobile genetic elements (89 and 21 genes, respectively) and virulence factors (276 and 250 factors, respectively), suggesting their potential for horizontal transfer and pathogenicity.
2024-10-20 | E-MTAB-14496 | biostudies-arrayexpress
Project description:Perfluorooctanesulfonic acid (PFOS) is a persistent, bio-accumulative pollutant that has been used for the last 60+ years in numerous industrial and commercial applications. In mice, PFOS administration is known to induce hepatomegaly and hepatic steatosis. The aim of the present study was to evaluate potential PFOS and diet interactions and explore the mechanism of PFOS induced liver lipid accumulation. Prior to PFOS administration, mice were fed either a standard chow diet (SD) or 60% kCal high fat diet (HFD) for 4 weeks to establish significant body weight increase. After 4 weeks of diet acclimation, the treatment groups received 0.0003% PFOS in diet for an additional 10 weeks. In addition, a subset of the mice fed HFD were switched to a SD (H-SD) to mimic weight-loss induced improvement of hepatic steatosis. A total of six treatment groups: i) SD, ii) HSD, iii) HFD (H), iv) SD +PFOS(SDP), v) H-SD +PFOS (HSDP), and vi) HFD +PFOS (HP) were included. PFOS and lipid concentrations were measured in both serum and liver. Relative liver mRNA expression was determined by targeted bead array and proteins were quantified using untargeted mass spectrometry. PFOS exposure increased liver weight, and in the HFD increased liver triglycerides and liver cholesterol content. Gene and protein expression in the liver demonstrated that PFOS exposure induced lipid utilization and xenobiotic metabolism pathways, and in a HFD, induced lipid synthesis. The data suggests that PFOS exposure acts on lipid utilization genes and exacerbates hepatic steatosis in mice fed a HFD.
2020-09-30 | PXD016161 | Pride
Project description:This series was used for two studies: Study 1: Recently it was discovered that the perfluorooctane sulfonate (PFOS) detected in wildlife, such as fish-eating birds, had a greater proportion of linear PFOS (L-PFOS) than the manufactured technical product (T-PFOS), which contains linear and branched isomers. This suggests toxicological studies based on T-PFOS data may inaccurately assess exposure risk to wildlife. To determine if PFOS effects were influenced by isomer content we compared the transcriptional profiles of cultured chicken embryonic hepatocytes (CEH) exposed to either L-PFOS or T-PFOS using Agilent microarrays. At equal concentrations (10 ?M), T-PFOS altered the expression of more transcripts (340, >1.5 fold change, p<0.05) compared to L-PFOS (130 transcripts). Higher concentrations of L-PFOS (40 ?M) were also less transcriptionally disruptive (217 transcripts) than T-PFOS at 10 ?M. Functional analysis showed that L-PFOS and T-PFOS affected genes involved in lipid metabolism, hepatic system development and cellular growth and proliferation. Pathway and interactome analysis suggested that genes may be affected through the RXR receptor, oxidative stress response, TP53 signaling, MYC signaling, Wnt/?-catenin signaling and PPAR? and SREBP receptors. In all functional categories and pathways examined, the response elicited by T-PFOS was greater than L-PFOS. These data show that T-PFOS elicits a greater transcriptional response in CEH than L-PFOS alone and demonstrates the importance of considering the isomer-specific toxicological properties of PFOS when assessing exposure risk. Study 2: In many bird populations, concentrations of perfluoroundanoic acid (PFUdA) are second only to perfluorooctane sulfonate (PFOS) among perfluoroalkyl compounds. Here, we used microarrays to characterize the transcriptional response of cultured chicken embryonic hepatocytes (CEH) to PFUdA and compared it to the response induced by PFOS. At non-cytotoxic doses, PFUdA (1 or 10 ?M) disrupted the expression of more genes (854) than PFOS (447, at 10 or 40 ?M) in CEH. Using functional, pathway and interactome analysis we identified several potentially important modes-of-action (MoAs) for PFUdA and some associated key events, including the suppression of the acute-phase response (APR) through peroxisome proliferator activated receptor activation. We then measured the expression of five APR genes, fibrinogen alpha (fga), fibrinogen gamma (fgg), thrombin (f2), plasminogen (plg), and protein C (proC), in the liver of chicken embryos exposed in ovo to PFUdA. The expression of fga, f2, and proC were down-regulated in embryo livers (100 or 1000 ng/g, p<0.1) as predicted from microarray analysis, whereas fibrinogen gamma (fgg) was up-regulated and plg was not significantly affected. Our results demonstrate PFUdA is more transcriptionally disruptive than PFOS in CEH. Additionally, we identified APR suppression as a potentially important and environmentally relevant MoA. These findings suggest in ovo exposure of birds to PFUdA could lead to post-hatch developmental deficiencies, such as impaired immune response.
2011-10-29 | GSE33291 | GEO
Project description:Perfluoroalkyl substances (PFASs) are a family of toxicants universally detected in human serum and known to cause dyslipidemia in animals and humans. Non-alcoholic fatty liver disease (NAFLD) is most prevalent form of liver disease in the United States and has been rising in global prevalence over recent years. This study explored diet-PFAS interactions and their potential role in the increasing global incidence of NAFLD. Male C57BL/6 mice were fed with either a low-fat diet (10% kcal from fat) or a moderately high fat diet (45% kcal from fat) with or without perfluorooctanesulfonic acid (PFOS) or perfluorononanoic acid (PFNA) at a low dose of 0.0003% w/w in feed for 12 weeks. Livers were excised for histology and quantification of PFASs and lipids. Proteomics and transcriptomics were utilized to conduct mechanistic pathway exploration. In a high fat diet, PFOS and PFNA protected against the onset of hepatic lipid accumulation and inflammatory progression. Genes and proteins related to lipid metabolism, synthesis, transport, and storage were modulated by PFAS exposure and further impacted by the presence of dietary fat. When combined with a high fat diet, low dose PFOS and PFNA are protective against the onset of NAFLD suggesting that dietary fat impacts the behavior of PFASs in vivo. Furthermore, both dietary fat content and the chemical functional head group exerted significant influence on tissue partitioning and the resulting hepatic biochemical signature.
2021-02-18 | PXD015977 | Pride
Project description:We identified ARGs in a genome-wide manner, in fly brains as well as in sorted neurons; they included dopaminergic neurons (DA) and a subset of circadian-related neurons (PDF+ neurons).
2016-12-12 | GSE83975 | GEO