Dataset Information

Consensus assessment of the contamination level of publicly available cyanobacterial genomes.

ABSTRACT: Publicly available genomes are crucial for phylogenetic and metagenomic studies, in which contaminating sequences can be the cause of major problems. This issue is expected to be especially important for Cyanobacteria because axenic strains are notoriously difficult to obtain and keep in culture. Yet, despite their great scientific interest, no data are currently available concerning the quality of publicly available cyanobacterial genomes. As reliably detecting contaminants is a complex task, we designed a pipeline combining six methods in a consensus strategy to assess the contamination level of 440 genome assemblies of Cyanobacteria. Two methods are based on published reference databases of ribosomal genes (SSU rRNA 16S and ribosomal proteins), one is indirectly based on a reference database of marker genes (CheckM), and three are based on complete genome analysis. Among those genome-wide methods, Kraken and DIAMOND blastx share the same reference database that we derived from Ensembl Bacteria, whereas CONCOCT does not require any reference database, instead relying on differences in DNA tetramer frequencies. Given that all the six methods appear to have their own strengths and limitations, we used the consensus of their rankings to infer that >5% of cyanobacterial genome assemblies are highly contaminated by foreign DNA (i.e., contaminants were detected by 5 or 6 methods). Our results will help researchers to check the quality of publicly available genomic data before use in their own analyses. Moreover, we argue that journals should make mandatory the submission of raw read data along with genome assemblies in order to facilitate the detection of contaminants in sequence databases.

SUBMITTER: Cornet L

PROVIDER: S-EPMC6059444 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Consensus assessment of the contamination level of publicly available cyanobacterial genomes.

Cornet Luc L Meunier Loïc L Van Vlierberghe Mick M Léonard Raphaël R RR Durieu Benoit B Lara Yannick Y Misztak Agnieszka A Sirjacobs Damien D Javaux Emmanuelle J EJ Philippe Hervé H Wilmotte Annick A Baurain Denis D

PloS one 20180725 7

Publicly available genomes are crucial for phylogenetic and metagenomic studies, in which contaminating sequences can be the cause of major problems. This issue is expected to be especially important for Cyanobacteria because axenic strains are notoriously difficult to obtain and keep in culture. Yet, despite their great scientific interest, no data are currently available concerning the quality of publicly available cyanobacterial genomes. As reliably detecting contaminants is a complex task, w ...[more]

PMID: 30044797

Similar Datasets

Project description:Background: Antibiotics are often prescribed empirically to treat infection syndromes before causative bacteria and their susceptibility to antibiotics are identified. Guidelines on empiric antibiotic prescribing are key to effective treatment of infection syndromes, and need to be informed by likely bacterial aetiology and antibiotic resistance patterns. We aimed to create a clinically-relevant composite index of antibiotic resistance for common infection syndromes to inform recommendations at the national level. Methods: To create our index, we used open-access antimicrobial resistance (AMR) surveillance datasets, including the ECDC Surveillance Atlas, CDDEP ResistanceMap, WHO GLASS and the newly-available Pfizer ATLAS dataset. We integrated these with data on aetiology of common infection syndromes, existing empiric prescribing guidelines, and pricing and availability of antibiotics. Results: The ATLAS dataset covered many more bacterial species (287) and antibiotics (52) than other datasets (ranges = 8-11 and 16-32 respectively), but had a similar number of samples per country per year. Using these data, we were able to make empiric prescribing recommendations for bloodstream infection, pneumonia and cellulitis/skin abscess in up to 44 countries. There was insufficient data to make national-level recommendations for the other six syndromes investigated. Results are presented in an interactive web app, where users can visualise underlying resistance proportions to first-line empiric antibiotics for infection syndromes and countries of interest. Conclusions: We found that whilst the creation of a composite resistance index for empiric antibiotic therapy was technically feasible, the ATLAS dataset in its current form can only inform on a limited number of infection syndromes. Other open-access AMR surveillance datasets are largely limited to bloodstream infection specimens and cannot directly inform treatment of other syndromes. With improving availability of international AMR data and better understanding of infection aetiology, this approach may prove useful for informing empiric prescribing decisions in settings with limited local AMR surveillance data.

Project description:ImportanceThere are limited resources providing postdonation conditions that can occur in living donors (LDs) of solid-organ transplant. Consequently, it is difficult to visualize and understand possible postdonation outcomes in LDs.ObjectiveTo assemble an open access resource that is representative of the demographic characteristics in the US national registry, maintained by the Organ Procurement and Transplantation Network and administered by the United Network for Organ Sharing, but contains more follow-up information to help to examine postdonation outcomes in LDs.Design, setting, and participantsCohort study in which the data for the resource and analyses stemmed from the transplant data set derived from 27 clinical studies from the ImmPort database, which is an open access repository for clinical studies. The studies included data collected from 1963 to 2016. Data from the United Network for Organ Sharing Organ Procurement and Transplantation Network national registry collected from October 1987 to March 2016 were used to determine representativeness. Data analysis took place from June 2016 to May 2018. Data from 20 ImmPort clinical studies (including clinical trials and observational studies) were curated, and a cohort of 11?263 LDs was studied, excluding deceased donors, LDs with 95% or more missing data, and studies without a complete data dictionary. The harmonization process involved the extraction of common features from each clinical study based on categories that included demographic characteristics as well as predonation and postdonation data.Main outcomes and measuresThirty-six postdonation events were identified, represented, and analyzed via a trajectory network analysis.ResultsThe curated data contained 10?869 living kidney donors (median [interquartile range] age, 39 [31-48] years; 6175 [56.8%] women; and 9133 [86.6%] of European descent). A total of 9558 living kidney donors with postdonation data were analyzed. Overall, 1406 LDs (14.7%) had postdonation events. The 4 most common events were hypertension (806 [8.4%]), diabetes (190 [2.0%]), proteinuria (171 [1.8%]), and postoperative ileus (147 [1.5%]). Relatively few events (n?=?269) occurred before the 2-year postdonation mark. Of the 1746 events that took place 2 years or more after donation, 1575 (90.2%) were nonsurgical; nonsurgical conditions tended to occur in the wide range of 2 to 40 years after donation (odds ratio, 38.3; 95% CI, 4.12-1956.9).Conclusions and relevanceMost events that occurred more than 2 years after donation were nonsurgical and could occur up to 40 years after donation. Findings support the construction of a national registry for long-term monitoring of LDs and confirm the value of secondary reanalysis of clinical studies.

Project description:Background: Health technology assessment (HTA) provides a globally-accepted and structured approach to synthesising evidence for cost and clinical effectiveness alongside ethical and equity considerations to inform evidence-based priorities. India is one of the most recent countries to formally commit to institutionalising HTA as an integral component of the heath resource allocation decision-making process. The effective conduct of HTA depends on the availability of reliable data. Methods: We draw from our experience of collecting, synthesizing, and analysing health-related datasets in India and internationally, to highlight the complex requirements for undertaking HTA, and explore the availability of such data in India. We first outlined each of the core data components required for the conduct of HTA, and their availability in India, drawing attention to where data can be accessed, and different ways in which researchers can overcome the challenges of missing or low quality data. Results: We grouped data into the following categories: clinical efficacy; cost; epidemiology; quality of life; service use/consumption; and equity. We identified numerous large local data sources containing epidemiological information. There was a marked absence of other locally-collected data necessary for informing HTA, particularly data relating to cost, service use, and quality of life. Conclusions: The introduction of HTA into the health policy space in India provides an opportunity to comprehensively assess the availability and quality of health data capture across the country. While epidemiological information is routinely collected across India, other data inputs necessary for HTA are not readily available. This poses a significant bottleneck to the efficient generation and deployment of HTA into the health decision space. Overcoming these data gaps by strengthening the routine collection of comprehensive and verifiable health data will have important implications not only for embedding economic analyses into the priority setting process, but for strengthening the health system as a whole.

Dataset Information

Consensus assessment of the contamination level of publicly available cyanobacterial genomes.

Publications

Consensus assessment of the contamination level of publicly available cyanobacterial genomes.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets