Provided herein are methods of amplifying and detecting pathogens and drug resistance markers (e.g., antibiotic resistance genes) in complex samples (e.g., blood), as well as related panels and compositions (e.g., primers, probes, magnetic particles, systems, cartridges, and kits). The methods, panels, and compositions can be used for comprehensive detection of pathogens and drug resistance markers for patient identification, patient selection, optimization of therapies, and antimicrobial stewardship.