TABLE 2.

Current NGS approaches for infectious disease diagnostics^a

Sequencing approach	Target	Advantage(s)	Disadvantage(s)
16S rRNA gene	Bacteria	Lower cost, targets and amplifies most bacteria present, low-complexity bioinformatics	Specific to bacteria, can still miss some species due to primer mismatches, bacterial ID only
18S rRNA gene/ITS gene	Fungi and some parasites	Lower cost, targets and amplifies most fungi present and some parasites, low-complexity bioinformatics	Specific to fungi and a subset of parasites, can still miss some species due to primer mismatches
Whole genome	Cultured organism	Provides in-depth coverage of a single organism with associated virulence and antimicrobial genes	Requires a cultured organism, high-complexity bioinformatics
Metagenomic whole genome	Unbiased	Sequence any organism that is present, can analyze entire genomes, ID of virulence and AMR genes	High cost, high-complexity bioinformatics, host contamination

^aID, identification.