Molecular Detection and Characterization of Infectious Agents
Quantitative assays
Viral load tests for HIV, HBV, HCV, and CMV report in IU/mL traceable to WHO standards. One log is a ten-fold change. Distinguish "target not detected" from "detected below limit of quantification"; neither equals cure. Interpret in context: baseline level, on-treatment response, and assay lower limit of detection all matter. Limit of detection (analytic sensitivity) differs from limit of quantification (precision) and from clinical sensitivity.
Qualitative detection
Common targets include Chlamydia trachomatis and Neisseria gonorrhoeae, MRSA (mecA), VRE (vanA/vanB), Clostridioides difficile toxin genes (tcdB), group B streptococcus, Mycobacterium tuberculosis complex with rpoB for rifampin resistance, and HPV with 16/18 genotyping. Syndromic panels cover respiratory, gastrointestinal, and central nervous system pathogens. 16S rRNA gene sequencing identifies bacteria; ITS regions identify fungi; MALDI-TOF identifies colonies.
Characterization and resistance
Sanger or NGS sequencing of HIV pol, HBV polymerase, or HCV NS5A/NS5B guides resistance decisions. gyrA sequencing predicts fluoroquinolone resistance in gonorrhea. Whole-genome sequencing with core-genome MLST or SNP typing supports outbreak investigation.
Traps
A frequent error is equating detectable nucleic acid with active disease: CMV and EBV DNA may reflect latent leukocyte carriage, and HSV can shed asymptomatically. Others include confusing copies with IU, ignoring PCR inhibitors (blood, heparin, urine), assuming a negative NAT excludes infection during the serologic window period, and forgetting contamination as a false-positive source.
Worked example
A change from 20,000 to 2,000 IU/mL is a ten-fold, one-log reduction, equivalent to a 90% decrease, not a 10% decrease.