Targeted next-generation sequencing for pathogen and antimicrobial resistance detection

This repository contains primary data files and R analysis code supporting the study. Archived sputum samples from pneumonia inpatients were analysed using the Ion AmpliSeq Pan-Bacterial panel (targeted next-generation sequencing, tNGS) and results were compared to conventional microbiology (CM) - bacterial culture with MALDI-TOF MS identification and disk diffusion antimicrobial susceptibility testing (AST).