Metagenomic sequencing is transforming microbiology but remains limited for pathogen surveillance due to poor sensitivity for low-abundance organisms in complex samples. Here, we present metagenomic target-amplified genome (mTAG) sequencing, a culture-free workflow that combines algorithmically designed probe panels with long-read sequencing to selectively enrich whole pathogen genome DNA. When applied to complex biological samples such as clinicnal stool or food safety samples, mTAG  achieves >200-fold improvements in pathogen coverage over standard shotgun metagenomics at matched throughput. This contribution to culture-independent diagnostics enables real-time detection of genomes of clinical and public health importance, even in settings where traditional laboratory infrastructure may not be readily available. It has broad utility for microbiologists, epidemiologists, and public health agencies seeking scalable, sensitive, and rapid methods for pathogen monitoring across clinical, agricultural, and environmental contexts. Currently, work is ongoing to develop high sensitivity and specificity modifications that can discern granular differences in strain-level genetic characteristics of genomes, especially those poorly represented in publicly available databases.