TABLE 3.
Diagnostic accuracies of the Sanger, Illumina, and Nanopore 16S rRNA sequencing methods
| Sequencing method | No. of samples analyzed | No. of samples with matched taxa | Diagnostic accuracy (%) | 95% CIc | P value (chi-square test)d |
|---|---|---|---|---|---|
| Sanger 16S | 165 | 159 | 96.36 | 92.25–98.65 | |
| Resolved Illumina 16Sa | 165 | 115 | 69.70 | 62.07–76.60 | <0.0001* |
| Analyzed by MSR | 165 | 59 | 35.76 | 28.46–43.58 | |
| Analyzed by Illumina_BLAST+ | 165 | 118 | 71.52 | 63.98–78.26 | |
| Resolved Nanopore 16Sb | 165 | 159 | 96.36 | 92.25–98.65 | 0.0291* |
| Analyzed by Epi2ME | 165 | 147 | 89.09 | 83.31–93.41 | |
| Analyzed by NanoBLAST+ | 165 | 148 | 89.70 | 84.02–93.88 |
a
Discordant samples between MSR and Illumina_BLAST+ were analyzed by nf-core/ampliseq; classified species in nf-core/ampliseq were considered resolved identities in Illumina workflow.
b
Discordant samples between Epi2me and NanoBLAST+ were analyzed by NanoCLUST; classified species in NanoCLUST were considered resolved identities in Nanopore workflow.
c
CI, confidence interval.
d
*, P < 0.05, statistically significantly different from Sanger 16S results.