What is the recommended diagnostic approach using Nucleic Acid Amplification Test (NAAT)?

Recommended Diagnostic Approach Using Nucleic Acid Amplification Test (NAAT)

Nucleic Acid Amplification Tests (NAATs) should be used as the primary diagnostic tool for infectious disease detection due to their high sensitivity and specificity, with specific testing algorithms tailored to the suspected pathogen.

General NAAT Principles and Benefits

• NAATs detect genetic material (DNA or RNA) of pathogens with high sensitivity (88.5-100%) and specificity (>97%) 1
• Provide faster results than traditional culture methods, enabling earlier treatment decisions 2
• Can detect pathogens that are difficult to culture or present in low quantities

Pathogen-Specific NAAT Recommendations

For Tuberculosis Diagnosis

1. Initial Testing Approach:

   • NAAT should be performed on respiratory specimens from patients with suspected TB, especially when there is intermediate to high clinical suspicion 3
   • A positive NAAT can be used as presumptive evidence of TB and guide therapeutic decisions 3

2. Drug Susceptibility Testing:

   • Rapid molecular drug susceptibility testing (DST) for rifampin with/without isoniazid is strongly recommended for patients who are AFB smear positive or Hologic Amplified MTD positive and meet any of these criteria 3:
     • Previous TB treatment
     • Born in or lived for ≥1 year in a country with moderate TB incidence (≥20/100,000) or high primary MDR-TB prevalence (≥2%)
     • Contacts of MDR-TB patients
     • HIV infected

3. Specimen Collection:

   • For pulmonary TB, respiratory specimens should be collected
   • For TB lymphadenitis, NAAT results can be variable (sensitivity 2-100%, specificity 28-100%) and should be interpreted with caution 4

For Clostridioides difficile Infection

1. Recommended Testing Algorithms 3, 1:

   a) NAAT-only approach:

   • High sensitivity (95%) and specificity (98%)
   • Positive likelihood ratio: 46.0, negative likelihood ratio: 0.05
   • Excellent for ruling out infection

   b) GDH/NAAT algorithm (preferred):

   • Initial screening with glutamate dehydrogenase (GDH) test
   • Confirmation of positive GDH samples with NAAT
   • Positive likelihood ratio: 113.5, negative likelihood ratio: 0.09

   c) GDH/Toxin/NAAT algorithm:

   • Initial screening with GDH
   • Testing for toxins A/B
   • Confirmation with NAAT for discordant results
   • Positive likelihood ratio: 155.8, negative likelihood ratio: 0.11

2. Important Considerations:

   • Test only unformed stool specimens from symptomatic patients 1
   • Repeat testing within 7 days is not recommended (minimal diagnostic yield of only 3%) 3
   • NAAT detects the toxin gene but cannot distinguish between active infection and colonization 1

For SARS-CoV-2 Diagnosis

1. Testing Approach 3:

   • For symptomatic individuals: NAAT is strongly recommended over antigen testing
   • For asymptomatic exposed individuals: NAAT is conditionally recommended in specific situations

2. Specimen Collection 3:

   • For symptomatic individuals, the following specimens are acceptable:
     • Nasopharyngeal swab
     • Midturbinate swab
     • Combined anterior nares plus oropharyngeal swab
     • Saliva
     • Mouth gargle
   • Anterior nares and midturbinate specimens can be self-collected or collected by healthcare providers
   • Saliva NAAT has similar diagnostic accuracy to nasopharyngeal swab NAAT (sensitivity 83.2%, specificity 99.2%) 5

Implementation Considerations

1. Quality Control:

   • Commercial NAAT kits are preferred over in-house tests due to standardization 3
   • If in-house tests are used, they should be validated to have performance comparable to commercial tests 3

2. Limitations and Cautions:

   • False-negative results can occur due to:
     • Presence of inhibitors in the sample 3
     • Low pathogen load
     • Improper specimen collection
   • False-positive results can occur in low-prevalence settings 3
   • Laboratory-based diagnostic tests are not a replacement for clinical judgment 3

3. Turnaround Time:

   • Rapid NAATs (≤60-minute in-laboratory turnaround time) are preferred when available 3
   • Median time from specimen collection to NAAT result can vary significantly by health jurisdiction (1-11 days) 2

Special Situations

1. Blood Testing:

   • For suspected TB bacteremia, NAAT on blood samples has limited sensitivity (36%) 6
   • Point-of-care NAATs for blood samples are being developed but require further validation 7

2. Extrapulmonary TB:

   • NAAT performance for extrapulmonary TB is more variable than for pulmonary TB 4
   • Results should be interpreted in conjunction with clinical findings and other diagnostic tests

By following these pathogen-specific NAAT approaches, clinicians can maximize diagnostic accuracy and improve patient outcomes through earlier appropriate treatment.