Table 22.16.

Molecular Assays Commonly in Use for the Diagnosis of Respiratory Diseases

Molecular Assay	Principle	Main Use	Comment
Singleplex PCR	Single DNA or RNA target that is amplified	Can be designed for the detection of any known DNA or RNA sequence	Generally higher sensitivity than multiplex PCR as the targets are not competing
Multiplex PCR	Simultaneous amplification of several DNA or RNA targets	Respiratory pathogens; immunocompromised protocols; detection of various pathogens in blood cultures	Wide coverage of pathogens in a single test informs clinical management in a timely manner
16S rRNA sequencing	Amplification of 16S ribosomal RNA followed by sequencing of the product	Used to detect bacterial species in a clinical specimen that has failed to detect pathogens in culture.	Covers a wide range of pathogens listed in accessible sequence databases
Next-generation sequencing	Sequencing of a whole bacterial or viral genome or simultaneous sequencing of multiple bacterial or viral genes	Resistance testing and outbreak investigations	Can offer multiple gene sequences simultaneously or whole genome sequencing as well as de novo sequencing; currently, high cost prohibits routine use

PCR, Polymerase chain reaction.