What is the difference between phenotypic and genotypic (genetic type) methods?

From the Guidelines

Genotypic methods are preferred over phenotypic methods for identifying and characterizing microorganisms, due to their higher specificity, faster results, and ability to detect non-viable organisms and antimicrobial resistance genes directly. This is supported by the most recent study 1, which recommends the use of genotypic tests where possible, and phenotypic tests only in settings where genotypic tests are unavailable.

Key Differences Between Phenotypic and Genotypic Methods

• Phenotypic methods rely on observable characteristics and behaviors of organisms, including morphology, growth patterns, biochemical reactions, and antimicrobial susceptibility
• Genotypic methods analyze genetic material (DNA or RNA) directly, using techniques such as PCR, DNA sequencing, microarrays, and whole genome sequencing
• Genotypic methods offer greater specificity, can detect non-viable organisms, provide faster results, and can identify antimicrobial resistance genes directly

Advantages and Disadvantages of Each Method

• Phenotypic methods: less expensive, more accessible, but may require viable organisms, can be time-consuming, and may lack specificity for certain organisms
• Genotypic methods: higher specificity, faster results, can detect non-viable organisms and antimicrobial resistance genes directly, but generally require more specialized equipment, technical expertise, and higher costs

Recommendations for Clinical Practice

• Use genotypic methods as the primary approach for identifying and characterizing microorganisms, due to their higher specificity and faster results
• Use phenotypic methods in settings where genotypic tests are unavailable, or as a complementary approach to genotypic methods to maximize diagnostic accuracy and efficiency, as recommended by 1 and supported by earlier studies 1

From the FDA Drug Label

Baseline Genotype/Phenotype and Virologic Outcome Analyses Genotypic and/or phenotypic analysis of baseline virus may aid in determining darunavir susceptibility before initiation of darunavir/ritonavir 600 mg/100 mg twice daily therapy The effect of baseline genotype and phenotype on virologic response at 96 weeks was analyzed in as-treated analyses using pooled data from the Phase 2b trials (Trials TMC114-C213, TMC114-C202, and TMC114-C215) (n=439).

Both genotypic and phenotypic methods can be used to determine darunavir susceptibility.

• Genotypic analysis involves examining the genetic material of the virus to identify specific mutations associated with resistance to darunavir.
• Phenotypic analysis measures the actual susceptibility of the virus to darunavir in a laboratory setting. The choice between these methods may depend on various factors, including the specific clinical context and the availability of resources 2.

From the Research

Phenotypic vs Genotypic Methods

• Phenotypic methods, such as smear microscopy, culture, and indirect drug susceptibility testing (DST), have been considered the 'gold standard' for diagnosing tuberculosis (TB) 3.
• However, genotypic methods, including nucleic acid amplification tests (NAATs) and next-generation sequencing, are becoming increasingly important for rapid detection of TB and drug resistance 3, 4.
• Genotypic detection is already the preferred method for detecting rifampicin and pyrazinamide resistance 3.
• NAATs have been shown to be more sensitive than smear microscopy, particularly in patients with paucibacillary disease and in people living with HIV 4, 5.
• The Xpert MTB/RIF assay, a type of NAAT, has been endorsed by the World Health Organization for investigating patients suspected of having TB 5.
• Molecular methods, such as the GeneXpert MTB/RIF assay, have been found to have high sensitivity and specificity for detecting TB, with sensitivity and specificity of 96.8% and 99.3%, respectively 6.
• Next-generation sequencing can provide rapid information about Mycobacterium tuberculosis mutations associated with resistance to anti-tuberculosis drugs, which can inform clinical management of patients with multidrug-resistant or rifampicin-resistant TB 7.

Comparison of Phenotypic and Genotypic Methods

• Phenotypic methods, such as culture, can take weeks to provide results, while genotypic methods can provide results within hours 3, 6.
• Genotypic methods can detect TB more accurately than phenotypic methods, particularly in patients with paucibacillary disease and in people living with HIV 4, 5.
• However, phenotypic methods are still considered the 'gold standard' for diagnosing TB, and genotypic methods are often used as supplementary tests 3.
• The choice between phenotypic and genotypic methods depends on the specific clinical setting and the resources available 3, 4.

Clinical Implications

• The use of genotypic methods, such as NAATs and next-generation sequencing, can improve the diagnosis and treatment of TB, particularly in patients with multidrug-resistant or rifampicin-resistant TB 3, 4, 7.
• Molecular drug resistance testing can provide rapid information about Mycobacterium tuberculosis mutations associated with resistance to anti-tuberculosis drugs, which can inform clinical management of patients with TB 7.
• The implementation of molecular testing for TB can increase access to diagnosis and treatment, particularly in low-income countries where TB is prevalent 3, 4.