Which technique lacks strain-level precision?
At subspecies resolution, 16S rRNA sequencing shows limited discriminatory capacity because closely related strains often exhibit greater than 99 percent identity across the conserved gene. Clinical epidemiologists require strain-level distinctions to track outbreaks, virulence variants, and antimicrobial resistance clones. High-resolution methods such as whole-genome SNP analysis, core-genome MLST, and average nucleotide identity detect genome-wide variation absent in ribosomal marker. Consequently, while valuable for broad community surveys, genus identification, and initial taxonomic screen
Ref: Nature Microbiology, 16S rRNA limitations species level resolution; QIAGEN, species strain identification 16S versus shotgun metagenomics comparison
