Antibiotic Resistance Microbiology Dataset (ARMD): A resource for antimicrobial resistance from EHRs

The Antibiotic Resistance Microbiology Dataset (ARMD) is a structured and de-identified resource developed using electronic health records (EHR) from Stanford Healthcare. It provides a comprehensive overview of microbiological cultures including urine, respiratory, and blood cultures. This dataset includes 283,715 unique adult patients and features detailed information on culture results, identified organisms, antibiotic susceptibility, and associated demographic and clinical data. The dataset was meticulously constructed through a multi-step process designed to enhance data quality and relevance. By enabling the study of antimicrobial resistance patterns and supporting antimicrobial stewardship efforts, ARMD offers a valuable resource for researchers and clinicians seeking to improve the management of infectious diseases and combat the growing threat of antimicrobial resistance., Cohort Selection
The ARMD was created using de-identified EHR data from Stanford Healthcare to address this need. This dataset provides microbiological cultures from adult patients (≥18 years old) and includes key clinical data points relevant to studying antimicrobial resistance. The cohort construction involved the following features and processes:

Culture Types: Microbiological cultures were included, specifically urine, respiratory, and blood cultures.

Temporal Adjustment: The timing of culture orders was adjusted for data privacy through jittering, ensuring patient confidentiality while retaining meaningful temporal relationships.

Culture Positivity: Each culture is flagged as either positive or negative, indicating whether an organism was identified. Cultures flagged as negative are represented by a null value in the susceptibility field.

Organism Identification and Susceptibility: For positive cultures, the identified organism and its antibiotic susceptibility are recorde..., , # Antibiotic Resistance Microbiology Dataset (ARMD): A resource for antimicrobial resistance from EHRs

## Background

Antimicrobial resistance (AMR) represents a pressing global health challenge, exacerbated by the overuse and misuse of antibiotics. Efforts to mitigate AMR require high-quality datasets to analyze trends in microbial susceptibility, guide clinical decision-making, and inform stewardship programs. Electronic health records (EHR) are a rich source of real-world data that can be leveraged to study antimicrobial use and resistance patterns. However, constructing meaningful datasets from EHR data requires rigorous curation and preprocessing to ensure accuracy, relevance, and usability. ARMD aims to facilitate research in antimicrobial stewardship, with applications in identifying resistance patterns, evaluating treatment practices, and informing public health interventions. By leveraging de-identified EHR data from Stanford Healthcare, this dataset provides a unique opportun...,