Antibiotic Resistance Microbiology Dataset (ARMD): A De-identified Resource for Studying Antimicrobial Resistance Using Electronic Health Records

The Antibiotic Resistance Microbiology Dataset (ARMD) is a de-identified resource derived from electronic health records (EHR) that facilitates research into antimicrobial resistance (AMR). ARMD encompasses data from adult patients, focusing on microbiological cultures, antibiotic susceptibilities, and associated clinical and demographic features. Key attributes include organism identification, susceptibility patterns for 55 antibiotics, implied susceptibility rules, and de-identified patient information. This dataset supports studies on antimicrobial stewardship, causal inference, and clinical decision-making. ARMD is designed to be reusable and interoperable, promoting collaboration and innovation in combating AMR. This paper describes the dataset's acquisition, structure, and utility while detailing its de-identification process.

Rapid identification of pathogenic bacteria using Raman spectroscopy and deep learning

Rapid identification of bacteria is essential to prevent the spread of infectious disease, help combat antimicrobial resistance, and improve patient outcomes. Raman optical spectroscopy promises to combine bacterial detection, identification, and antibiotic susceptibility testing in a single step. However, achieving clinically relevant speeds and accuracies remains challenging due to the weak Raman signal from bacterial cells and the large number of bacterial species and phenotypes. By amassing the largest known dataset of bacterial Raman spectra, we are able to apply state-of-the-art deep learning approaches to identify 30 of the most common bacterial pathogens from noisy Raman spectra, achieving antibiotic treatment identification accuracies of 99.0$\pm$0.1%. This novel approach distinguishes between methicillin-resistant and -susceptible isolates of Staphylococcus aureus (MRSA and MSSA) as well as a pair of isogenic MRSA and MSSA that are genetically identical apart from deletion of the mecA resistance gene, indicating the potential for culture-free detection of antibiotic resistance. Results from initial clinical validation are promising: using just 10 bacterial spectra from each of 25 isolates, we achieve 99.0$\pm$1.9% species identification accuracy. Our combined Raman-deep learning system represents an important proof-of-concept for rapid, culture-free identification of bacterial isolates and antibiotic resistance and could be readily extended for diagnostics on blood, urine, and sputum.