Objective: The Illinois Data Bank provides Illinois researchers with the infrastructure to publish research data publicly. During a five-year review of the Research Data Service at the University of Illinois at Urbana-Champaign, it was recognized as the most useful service offering in the unit. Internal metrics are captured and used to monitor the growth, document curation workflows, and surface technical challenges faced as we assist our researchers. Here we present examples of these curation challenges and the solutions chosen to address them.
Methods: Some Illinois Data Bank metrics are collected internally by within the system, but most of the curation metrics reported here are tracked separately in a Google spreadsheet. The curator logs required information after curation is complete for each dataset. While the data is sometimes ambiguous (e.g., depending on researcher uptake of suggested actions), our curation data provide a general understanding about our data repository and have been useful in assessing our workflows and services. These metrics also help prioritize development needs for the Illinois Data Bank.
Results and Conclusions: The curatorial services polish and improve the datasets, which contributes to the spirit of data reuse. Although we continue to see challenges in our processes, curation makes a positive impact on datasets. Continued development and adaptation of the technical infrastructure allows for an ever-better experience for the curators and users. These improvements have helped our repository more effectively support the data sharing process by successfully fostering depositor engagement with curators to improve datasets and facilitating easy transfer of very large files.
BackgroundInfections with Carbapenem-resistant Enterobacteriaceae (CRE) and vancomycin-resistant Enterococci (VRE) can result in a 50% mortality rate in compromised hosts. A major risk factor for clinical infection is intestinal colonization with CRE or VRE. There are currently no FDA-approved compounds to decolonize these organisms from the gastrointestinal tract (gut). Commensal microbes offer protection from pathogen infection; however, in immunocompromised hosts or with antibiotic treatment, the protective properties of the microbial community are compromised, leaving the gut susceptible to pathogen colonization. Higher concentrations of pathogens within the gut correlate with an increased risk of infection with MDROs. Our hypothesis is that reducing colonization of the gut with MDROs would reduce the likelihood of a clinical infection.MethodsKaleido built a platform that emulates the gut environment and allows for high throughput screening of Kaleido’s Microbiome Metabolic Therapies (MMT™) in human gut microbiomes ex vivo. Over 500 compounds were screened for their ability to reduce the levels of CRE and VRE in fecal microbial communities from both healthy subjects and critically ill patients receiving broad-spectrum antibiotics.ResultsKaleido’s lead MMTs selectively favor the growth of the commensal microbiota at the expense of pathogens, resulting in a decrease of CRE and VRE from 80% of the initial community to 5% in a single batch culture, as measured by 16S rRNA gene and shotgun metagenomic sequencing. Lead MMTs do not support growth of CRE and VRE strains in culture, nor of other pathogens frequently encountered in critically ill and immunocompromised patients, such as Clostridium difficile and common fungal pathogens.ConclusionThese results suggest that intervention with MMTs may reduce CRE and VRE colonization and support further evaluation in patients colonized with CRE or VRE pathogens.
Disclosures
All authors: No reported disclosures.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.