Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7011490.fastq.gz | Fastqsanger.gz | |||
| SRR7011500.fastq.gz | Fastqsanger.gz | |||
| SRR7011491.fastq.gz | Fastqsanger.gz | |||
| SRR7011501.fastq.gz | Fastqsanger.gz | |||
| SRR7011492.fastq.gz | Fastqsanger.gz |
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Similar Datasets
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: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:Antibiotic resistance genes (ARGs) transmission in wastewater, seriously threaten the ecological safety and human health, which attracted increasing attention throughout the world. However, the correlations between bacterial interaction and environmental stress in photo-inactivation are rarely studied. In this study, the efficient ARGs photo-inactivation of ZIF@CF QDs-Fe were explored. The experimental results revealed that leaked e-ARGs and mobile genetic elements (MGEs) were immediately captured and attacked by the extracellular ROS, which blocking the antibiotic-resistance dissemination. Meanwhile, ZIF@CF QDs-Fe photo-treatment further neutralized the negative effect of ROS (·OH, ·O2–) induced oxidative stress, benefiting for the controlling of ARGs conjugative transfer. Combined with bacterial interactions, both bacterial density and abundance of ARGs host was synergically reduced when photo-treatment progressed, thus alleviating the natural dissemination risk of ARGs. Meanwhile, the downregulation of transporter proteins and antibiotic target proteins elucidated that ARGs transcription and bacterial reproduction were significantly suppressed under photo-inactivation. Interestingly, partial of antibiotic bacterial sensitivity would be recovered through the regulations of bacterial functional expressions and further alleviated potential ecological risk. Overall, these findings shed light on the inactivation mechanism of nanomaterial mediated photo-treatment in blocking the resistance transfer pathways, giving valuable guidance for mitigating the antibiotic resistance dissemination in wastewater treatments.
| PXD067488 |
Project description:Nanometric revolution is underway, promising technical innovations in a wide range of applications, leading to a potential boost in environmental discharges. Nanoparticle propensity to be transferred throughout trophic chains and to generate toxicity was mainly assessed in primary consumers while a lack of knowledge for higher trophic levels persists. This study focused on a predatory fish, the European eel Anguilla anguilla exposed to gold nanoparticles (AuNP, 10 nm, PEG-coated) for 21 days at three concentration levels in food: 0 (NP0), 1 (NP1) and 10 (NP10) mg Au.kg-1 . Transfer was assessed by gold quantification in eel tissues and transcriptomic responses in the liver and brain were revealed by a high-throughput RNA-sequencing approach. Eels fed at NP10 presented an erratic feeding behaviour while gold quantification only indicated transfer to intestine and kidney of NP1 exposed eels. RNA-Sequencing was performed in NP0 and NP1 eels. A total of 258 genes and 156 genes were significantly differentially transcribed in response to AuNP trophic exposure in the liver and brain, respectively. Enrichment analysis highlighted modifications in the immune system-related processes in the liver. In addition, results pointed out a shared response of both organs regarding 13 genes, most of them being involved in immune functions. This finding may shed light into the mode of action and toxicity of AuNP in fish.
2019-09-01 | GSE110011 | GEO
Project description:The cerebral cortex is a highly organized structure whose development depends on different progenitor cell types. These give rise to post-mitotic neurons that migrate across the developing cortical wall to their final positions in the cortical plate. Apical radial glia cells (aRGs) are the main progenitor type in early corticogenesis, responsible for the production of other progenitors, and regulating the final neuronal output. Abnormal behavior of aRG can severely impact corticogenesis resulting in cortical malformations. Mutations in the microtubule associated protein Eml1 lead to severe subcortical heterotopia, characterized by the presence of aberrantly located neurons beneath the normotopic cortex. Mutations in EML1/Eml1 have been reported in three families presenting severe atypical heterotopia, as well as in the Heterotopic cortex ‘HeCo’ spontaneous mouse mutant. In the latter, ectopically cycling aRGs were found cycling outside their normal proliferative ventricular zone (VZ) from early stages of corticogenesis (Croquelois et al., 2009, Kielar et al., 2014, Shaheen et al., 2017). Ectopic aRGs are likely to be responsible for the formation of the heterotopia. It is thus crucial to understand the role of Eml1 in aRGs to elucidate the physiological and pathological mechanisms causing aRGs to leave the VZ. The role of Eml1 in aRGs remains vastly unexplored. We have thus performed mass spectrometry with embryonic cortex lysates (E13.5) to shed light on the intracellular pathways and molecular mechanisms in which Eml1 could be involved. This data combined with other cell biology and biochemistry approaches will contribute to understand the role of this heterotopia protein at early stages of development.
2019-06-20 | PXD012714 | 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