Table 1 Characteristics of commonly used pathogen identification strategies
From: Metagenomic Sequencing in the ICU for Precision Diagnosis of Critical Infectious Illnesses
Identification method | Principle | Cost | Microbial detection | Additional considerations | Turnaround |
|---|---|---|---|---|---|
Culture | Growth and isolation of species present in a sample | Low-moderate | Some species are difficult to culture or cannot be cultured (e.g., atypical organisms, viral, fungal pathogens) | • Medium-dependent • Prior use of antimicrobial agents will affect sensitivity | Days to weeks |
Immunological methods | Detection via antibodies | Low-moderate | Determined by the choice of antibody/ antigen | • Antibody testing may not be useful during acute disease | Minutes to days |
Detection via antigens | • Limited by sensitivity/ specificity | ||||
PCR | Targeted amplification of specific pathogens | Moderate | Limited by PCR primer panel | • Detects only a few pre-selected microbes • Some species might be preferentially amplified | Minutes to days |
Metagenomics | Nucleotide sequences capture and amplification | High | Unbiased | • Host background will be dominant • Contamination will greatly affect utility | Hours to days |