As any rRNA gene based test, this assay has limitations. The test only detects and analyzes a short, specific genomic region, and taxonomic resolution or functional inference is therefore limited. For example, this assay cannot recognize the different serovars within S. enterica, or detect toxin genes that could distinguish pathogenic C. difficile or Escherichia strains from nonpathogenic strains, or resolve species within some of the genus-level targets. The correlation—or lack thereof—of 16S rRNA-based phylogenetic sequence identities with taxonomic levels such as genus or species has been extensively discussed elsewhere [51–54].