(A) Microbes grown from patient samples provide microbial DNA for WGS in which millions of fragments are read in parallel and assembled to reconstruct the microbial genome. WGS is especially useful for the identification of pathogens associated with hospital outbreaks and detection of AMR genes. (B) tNGS directly amplifies genes from a clinical specimen prior to sequencing. This technique often focuses on genes that are shared among all members of a microbial kingdom, such as the 16S rRNA gene for bacteria. The sequencing of amplified products allows for detection and identification of the composition of the targeted microorganisms in the specimen. Expanded applications can assess thousands of genes in parallel, covering pathogens and AMR targets. (C) mNGS involves sequencing all nucleic acids contained within a sample (e.g. CSF), including those derived from the host, microbes, and even contaminating nucleic acid. mNGS shows promise in detecting rare pathogens in which diagnostics are unavailable, unsuspected pathogens based on the patients’ symptoms with conditions that affect routine testing results, and in situations with insidious organisms.