The primary diagnostic technology used today is called nucleic acid amplification testing (NAAT). The most common variety is the tried and true polymerase chain reaction (PCR) technology. Though this has served as a powerful and important tool in infectious disease diagnostics over the past few decades, it does have its limitations. For some diagnostic purposes, NGS technology can overcome these limitations. Below is a table comparing the two technologies and where they should be used:

Diagnostic PurposeNAAT TechnologyNGS Technology
Point of Care Rapid DiagnosisYes – can be performed rapidly on small instruments in less than 1 hourNo – requires specialized equipment and time for sequencing and data analysis
Outpatient Clinic Routine DiagnosisYes – for mild to moderate illness, NAAT pathogen panels usually provide sufficient information for effective treatmentYes – in cases of mild to moderate chronic illness, more information (co-infection, rare infection, antimicrobial susceptibility) is often needed for effective treatment
Inpatient DiagnosisYes – in some cases, a rapid NAAT for targeted pathogens can be useful for inpatient managementYes – in cases of severe and/or chronic disease, more information (co-infection, rare infection, antimicrobial susceptibility) can be critical for the health of the patient and many times will lead to shorter hospital stays