Welcome to the repository housing the dataset and associated code for the study on the respiratory microbiome and its role in Ventilator-Associated Pneumonia (VAP). This prospective observational study was conducted in an Intensive Care Unit (ICU) in Chía, Colombia, and involved 141 adult patients requiring mechanical ventilation. The dataset provides a comprehensive collection of clinical data, microbiome analysis, and inflammatory marker quantifications, offering valuable insights into the microbial ecology of VAP and its relationship with immune dysregulation.
The dataset contains:
Clinical Data: Collected at multiple time points during ICU admission. Microbiome Analysis: Involves DNA extraction and 16S ribosomal gene sequencing to analyze the respiratory microbiome. Inflammatory Markers: Quantification of pulmonary and systemic inflammatory markers using ELISA. This dataset is ideal for researchers interested in studying the interplay between the respiratory microbiome, immune responses, and disease progression in critically ill patients.
This repository is organized to provide easy access to the dataset and the tools necessary for its analysis:
R Code: Contains scripts and notebooks demonstrating how to perform descriptive statistics and microbiome analysis on the dataset. These resources are designed to help users understand the dataset structure, access data points, and start their analysis. Dataset Documentation: Provides detailed descriptions of the variables, the data collection process, and the methods used in microbiome analysis and inflammatory marker quantification. Getting Started
To begin working with the dataset and code in this repository, follow these steps:
Familiarize Yourself with the Dataset: Review the dataset documentation to understand the structure, types of data included, and the scope of the study. Explore the R Code: Use the provided R scripts and notebooks to conduct basic data analysis, microbiome profiling, and statistical evaluations. These resources will guide you through data manipulation, performing descriptive statistics, and interpreting key findings. Engage with the Research Community: If you have questions, suggestions, or contributions, feel free to reach out. Collaborative efforts are crucial for advancing research in respiratory microbiology and improving ICU outcomes. Acknowledgement
If you use the dataset or code in your research, please acknowledge the contribution by citing the dataset and the study as appropriate. Proper attribution supports the continued development and dissemination of valuable research resources.
This repository is licensed under the MIT License, allowing you the freedom to use, modify, and distribute the software, provided that the license and copyright notice are included with any substantial portions of the software. For more details, please refer to the LICENSE file in this repository.
Thank you for your interest in the Respiratory Microbiome and VAP Dataset Repository. We are excited to see how this resource contributes to the understanding and treatment of Ventilator-Associated Pneumonia and related conditions in critically ill patients.