Sequencing the mobilome of antimicrobial resistant bacterial isolates spanning a range of GC content: The potential of a sustainable low cost, low infrastructure approach for surveillance with Oxford Nanopore sequencing
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB47698 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR8007740.fastq.gz | Fastqsanger.gz | |||
| ERR8007750.fastq.gz | Fastqsanger.gz | |||
| ERR8007760.fastq.gz | Fastqsanger.gz | |||
| ERR8007770.fastq.gz | Fastqsanger.gz | |||
| ERR8007780.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 199 |
Similar Datasets
Project description:Long-read sequencing (LRS) can resolve repetitive regions, a limitation of short read (SR) data. Reduced cost and instrument size has led to a steady increase in LRS across diagnostics and research. Here, we re-basecalled FAST5 data sequenced between 2018 and 2021 and analyzed the data in relation to gDNA across a large dataset (n = 200) spanning a wide GC content (25-67%). We examined whether re-basecalled data would improve the hybrid assembly, and, for a smaller cohort, compared long read (LR) assemblies in the context of antimicrobial resistance (AMR) genes and mobile genetic elements. We included a cost analysis when comparing SR and LR instruments. We compared the R9 and R10 chemistries and reported not only a larger yield but increased read quality with R9 flow cells. There were often discrepancies with ARG presence/absence and/or variant detection in LR assemblies. Flye-based assemblies were generally efficient at detecting the presence of ARG on both the chromosome and plasmids. Raven performed more quickly but inconsistently recovered small plasmids, notably a ∼15-kb Col-like plasmid harboring bla KPC . Canu assemblies were the most fragmented, with genome sizes larger than expected. LR assemblies failed to consistently determine multiple copies of the same ARG as identified by the Unicycler reference. Even with improvements to ONT chemistry and basecalling, long-read assemblies can lead to misinterpretation of data. If LR data are currently being relied upon, it is necessary to perform multiple assemblies, although this is resource (computing) intensive and not yet readily available/useable.
| S-EPMC8928191 | biostudies-literature
Project description:Next-generation sequencing has evolved technically and economically into the method of choice for interrogating the genome in cancer and inherited disorders. The introduction of procedural code sets for whole-exome and genome sequencing is a milestone toward financially sustainable clinical implementation; however, achieving reimbursement is currently a major challenge. As part of a prospective quality-improvement initiative to implement the new code sets, we adopted Agile, a development methodology originally devised in software development. We implemented eight functionally distinct modules (request review, cost estimation, preauthorization, accessioning, prebilling, testing, reporting, and reimbursement consultation) and obtained feedback via an anonymous survey. We managed 50 clinical requests (January to June 2015). The fraction of pursued-to-requested cases (n = 15/50; utilization management fraction, 0.3) aimed for a high rate of preauthorizations. In 13 of 15 patients the insurance plan required preauthorization, which we obtained in 70% and ultimately achieved reimbursement in 50%. Interoperability enabled assessment of 12 different combinations of modules that underline the importance of an adaptive workflow and policy tailoring to achieve higher yields of reimbursement. The survey confirmed a positive attitude toward self-organizing teams. We acknowledge the individuals and their interactions and termed the infrastructure: human pipeline. Nontechnical barriers currently are limiting the scope and availability of clinical genomic sequencing. The presented human pipeline is one approach toward long-term financial sustainability of clinical genomics.
| S-EPMC5397703 | biostudies-other
Project description:A new low-cost material with a polymeric base formed from sodium silicate was developed. The material presents a nanostructured, highly rich iron surface with a large phosphorus retention capacity and potential reuse as a crop fertilizer. In the present study, we demonstrate that iron is the element that acts as an adsorbent for phosphate, while the polymeric base functions exclusively as a support for iron. The iron is uniformly adsorbed on the surface of the material, forming nanostructures, which ensure that iron works similarly to nanoparticles in solution but avoid other problems, such as particle agglomeration or the difficulty of separating them after the removal process. Materials were characterised by SEM, EDS, N2 sorption, and image processing, and the effect of pH, ionic strength, and temperature was studied. Sorption kinetics were analysed using Boyd's diffusion model, and adsorption equilibria were studied using several adsorption models. A maximum iron adsorption on the polymeric base of 23.9 ± 0.3 mg Fe∙g-1 was found, while maximum phosphorus adsorption was 366 ± 21 mg P∙g-1 Fe. Thus, phosphorus is recovered from the aqueous medium with an inexpensive material that has the potential to be used directly as a fertilizer.
| S-EPMC10097266 | biostudies-literature
Project description:Climate change and increasing natural disasters coupled with years of deferred maintenance have added pressure to infrastructure in urban areas. Thus, monitoring for failure of these systems is crucial to prevent future impacts to life and property. Participatory assessment technique for infrastructure provides a community-based approach to assess the capacity and physical condition of infrastructure. Furthermore, a participatory assessment technique for infrastructure can encourage grassroots activism that engages residents, researchers, and planners in the identification of sustainable development concerns and solutions. As climate change impacts disproportionately affect historically disenfranchised communities, assessment data can further inform planning, aiming to balance the distribution of public resources towards sustainability and justice. This paper explains the development of the participatory assessment technique for infrastructure that can provide empirical data about the condition of infrastructure at the neighborhood-level, using stormwater systems in a vulnerable neighborhood in Houston, Texas as a case study. This paper argues for the opportunity of participatory methods to address needs in infrastructure assessment and describes the ongoing project testing the best use of these methods.
| S-EPMC6200349 | biostudies-other
Project description:The repository Chemotion provides solutions for current challenges to store research data in a feasible manner. A main advantage of Chemotion is the comprehensive functionality, offering options to collect, prepare, and reuse data with discipline-specific methods and data-processing tools.
| S-EPMC7756630 | biostudies-literature
Project description:The island of New Guinea hosts the third largest expanse of tropical rainforest on the planet. Papua New Guinea-comprising the eastern half of the island-plans to nearly double its national road network (from 8,700 to 15,000 km) over the next three years, to spur economic growth. We assessed these plans using fine-scale biophysical and environmental data. We identified numerous environmental and socioeconomic risks associated with these projects, including the dissection of 54 critical biodiversity habitats and diminished forest connectivity across large expanses of the island. Key habitats of globally endangered species including Goodfellow's tree-kangaroo (Dendrolagus goodfellowi), Matchie's tree kangaroo (D. matschiei), and several birds of paradise would also be bisected by roads and opened up to logging, hunting, and habitat conversion. Many planned roads would traverse rainforests and carbon-rich peatlands, contradicting Papua New Guinea's international commitments to promote low-carbon development and forest conservation for climate-change mitigation. Planned roads would also create new deforestation hotspots via rapid expansion of logging, mining, and oil-palm plantations. Our study suggests that several planned road segments in steep and high-rainfall terrain would be extremely expensive in terms of construction and maintenance costs. This would create unanticipated economic challenges and public debt. The net environmental, social, and economic risks of several planned projects-such as the Epo-Kikori link, Madang-Baiyer link, Wau-Malalaua link, and some other planned projects in the Western and East Sepik Provinces-could easily outstrip their overall benefits. Such projects should be reconsidered under broader environmental, economic, and social grounds, rather than short-term economic considerations.
| S-EPMC6656346 | biostudies-literature
Project description:An evidence-based research mentor training (RMT) curricular series has been shown to improve the knowledge and skills of research mentors across disciplines and career stages. A train-the-trainer model was used in the context of several targeted approaches aimed at sustainability to support national dissemination of RMT and expand the network of facilitators prepared to implement the curricula. These infrastructure elements included 1) an expansion initiative to increase the number of trained facilitators able to deliver train-the-trainer workshops nationwide; 2) adaptation of RMT curricula for multiple audiences and career stages to increase accessibility; 3) implementation resources to support facilitators and help them overcome implementation barriers; and 4) standardized evaluation of training. This approach to dissemination and implementation has resulted in the preparation of nearly 600 trained facilitators, a large percentage of whom have implemented mentor training for more than 4000 graduate student, junior faculty, and senior faculty mentors. Implications for and challenges to building and sustaining the national dissemination of RMT are discussed.
| S-EPMC6234808 | biostudies-other
Project description:Wet coal beneficiation in Colombia is prohibitive due to the high cost and scarcity of commonly used dense media. The practical value of this study is that it demonstrates for the first time that a common fertilizer, calcium nitrate, can be used in the beneficiation of low-grade Colombian coals. Three high-ash low-grade Colombian coals (Valle, Cundinamarca, and Antioquia) commonly used in Colombian sugar mill stoker furnaces were tested. Coal mineralogy and prevalence were analyzed before and after washing using mineral liberation analysis. The swelling potential of the coals was assessed using a novel application of thermal mechanical analysis (TMA) and an ash fusion oven (AFO). Calcium nitrate reduced ash levels across all size fractions, even for high-ash coals like Valle (29% to below 7%) to acceptable levels for coke manufacturing or pulverized fuel combustion. The novel use of TMA and AFO to analyze coal swelling demonstrated that swelling varies under constrained and unconstrained conditions and the small sample size allows for rapid testing of coal swelling. This study has demonstrated that the use of common fertilizers can allow beneficiation to become a processing option for low-grade coals in Official Development Assistance countries where conventional dense media is prohibitively expensive.
| S-EPMC8811924 | biostudies-literature
Project description:ObjectiveSustainable diets are diets with low environmental impacts and high affordability which contribute to food and nutrition security. The present study aimed to develop a healthy, low-cost and environmental-friendly food basket for Iran based on current consumption.DesignThe Households Income and Expenditure Survey data were used. Linear Programming was utilised to obtain the optimal diets, separately, for each goal of the sustainable food basket: (1) Diet with maximum Nutrient Rich Food (NRF) index, (2) Diet with minimum cost, (3) Diet with the minimum water footprint and (4) Diet with the minimum carbon footprint. Goal Programming techniques were used to optimise the sustainable food basket by considering all goals simultaneously.SettingIran.ParticipantsHouseholds (n 100 500) in urban and rural areas of Iran, nationally representative.ResultsIn the 'optimal model', compared with the usual consumption, the amount of the 'bread, cereal, rice, and pasta', 'meat, poultry, fish, eggs, legumes, and nuts' and 'fats, oils, sugars, and sweets' groups was decreased. Inside those food groups, cereals, poultry and vegetable oil subgroups were increased. Also, dairy, fruits and vegetable groups were increased. In this model, there was a 14 % reduction in the total water footprint, a 14 % decrease in the total carbon footprint, a 23 % decrease in the cost and a 7 % increase in NRF of diet compared with the usual consumption.ConclusionsIncreasing the consumption of dairy, fruits and vegetables and reducing the consumption of bread, rice, pasta, meat, fish, eggs, legumes, nuts, hydrogenated fats and sugars are required to achieve a sustainable food basket.
| S-EPMC10195622 | biostudies-literature
Project description:The presence of Donor-Specific anti-HLA Antibodies (DSA) is associated with an increased risk of both acute and chronic antibody-mediated rejection (AMR) in kidney allografts. AMR has remained challenging in kidney transplantation and is the major cause of late allograft loss. However, not all patients with DSA develop AMR, leading to the question of whether this represents accommodation, if other protective mechanisms exist or if this is actually a state of pre-rejection. Clinical and histological features, and gene expression profiles of kidney biopsy and blood samples of donor-specific antibody (DSA)+ patients without rejection were compared to antibody-mediated rejection (AMR) patients to elucidate the mechanisms involved in prevention of AMR. Of the 71 DSA+ patients, 46 had diagnosis of AMR and 25 did not show rejection. 50 DSA- patients without rejection were used as control. A subgroup of patients with available biopsy (n=61) and blood samples (n=54) were analyzed by microarrays. Both, DSA+/AMR+ and DSA+/AMR- biopsies showed increased expression of gene transcripts associated with cytotoxic T, natural killer cells, macrophages, interferon-gamma and rejection compared to DSA- biopsies. Regulatory T cell transcripts were up-regulated in DSA+/AMR+ and B cell transcripts in DSA+/AMR- biopsies. Whole blood gene expression analysis showed increased immune activity in only DSA+/AMR+ patients. There were no differentially expressed tolerant genes studied (n=14) in the blood or biopsy specimens of DSA+/AMR- patients. During a median 36 months follow-up, 4 DSA+/AMR- patients developed AMR, 12 continued to have DSAs but 9 lost DSAs. Gene expression profiles did not predict the development of AMR or persistence of DSAs. These results indicate increased immune activity in DSA+/AMR- biopsies despite lack of histologic findings of rejection.
2013-08-23 | GSE50084 | GEO