Table 1. Species combinations with significant prognostic value.
| Pretreatment | Posttreatment | ||||||
|---|---|---|---|---|---|---|---|
| Group 1 | Ref1 | RefRec1 | Ref Hi1 | Ref2 | Rec2 | ||
| Group 2 | RecRem | Rem | Ref Lo | RecRem | Rem | ||
| Species 1 | Mageeibacillus indolicus(BVAB3) (0.003) | Finegoldia magna (0) | Atopobium vaginae (2.3) | Mageeibacillus indolicus(BVAB3) (3.49) | Mageeibacillus indolicus(BVAB3) (3.49) | Dialister sp (1.4) | Aerococcus christensenii (0.092) |
| Species 2 | Mobiluncus curtisii* 0.228) | Gardnerella Gsp07 (0.007) | Megasphaera 1 (0.009) | Anaerococcus mediterraneensis (2.51) | Prevotella timonensis (5.63) | Gardnerella (9.2) | Atopobium vaginae (0.460) |
| Species 3 | Mycoplasma hominis (0.003) | Megasphaera1 (8.3) | Prevotella timonensis (4.6) | Gemella asaccharolytica* (0.276) | Gardnerella (6.9) | ||
| Species 4 | Sneathia sanguinegens (0.921) | Lactobacillus iners (27.6) | Lactobacillus jensenii* (0.092) | ||||
| Species 5 | Mobiluncus curtisii* (0.138) | Megasphaera 1 (0.018) | |||||
| Species 6 | Megasphaera 2 (0) | ||||||
| ROC AUC | 0.759 | 0.964 | 0.689 | 0.93 | 0.887 | 0.947 | 0.86 |
| 95% CI | 0.553–0.94 | 0.816–1 | 0.327–1 | 0.492–1 | 0.333–1 | 0.833–1 | 0.561–1 |
| Sensitivity | 0.824 | 0.882 | 1 | 1 | 0.833 | 0.938 | 1 |
| 95% CI | 0.566–0.962 | 0.636–0.985 | 0.715–1 | 0.541–1 | 0.359–0.996 | 0.698–0.998 | 0.715–1 |
| Specificity | 0.789 | 0.833 | 0.833 | 1 | 1 | 1 | 0.9 |
| 95% CI | 0.544–0.939 | .359-.996 | 0.359–0.996 | 0.398–1 | 0.398–1 | 0.839–1 | 0.555–0.997 |
| PPV | 0.778 | 0.938 | 0.917 | 1 | 1 | 1 | 0.917 |
| 95% CI | 0.524–0.936 | 0.698–0.998 | 0.615–0.998 | 0.541–1 | 0.478–1 | 0.782–1 | 0.615–0.998 |
| NPV | 0.833 | 0.714 | 1 | 1 | 0.8 | 0.955 | 1 |
| 95% CI | 0.586–0.964 | 0.290–0.963 | 0.478–1 | 0.398–1 | 0.284–0.995 | 0.772–0.999 | 0.664–1 |
| Odds Ratio | 17.5 | 37.5 | 84.3 | 117 | 33 | 444 | 146 |
| 95% CI | 0.31–92.5 | 2.77–508 | 2.93–2425 | 1.94–7067 | 1.06–1024 | 16.9–11660 | 5.29–4008 |
| Accuracy | 0.806 | 0.870 | 0.941 | 1.00 | 0.9 | 0.973 | 0.952 |
| 95% CI | 0.640–0.918 | 0.664–0.972 | 0.713–0.999 | 0.69–1 | 0.55–1.00 | 0.858–0.999 | 0.762–0.999 |
| p-value | 0.0006 | 0.0034 | 0.001 | 0.0048 | 0.0476 | <0.0001 | <0.0001 |
Thresholds in () after each species is the % abundance value from ROC analysis used to count patient samples; normal font of species indicates that Group 1 abundance is ≥ the threshold and bold font indicates that group 1 abundance is < the threshold. ROC analysis performed in Metaboanalyst.ca. Accuracies were calculated at MedCalc. Fisher tests and statistics were performed with GraphPad Prism. 1 Combination of two out of total number of key species identified to give best predictive values. 2 Combination of three out of total number of key species identified to give best predictive values. Three alternative sets of biomarker species were determined for the Ref Hi versus Ref Lo groups. Abbreviations: Ref: refractory; Rec: recurrent; Rem: remission; RefRec: patients from both refractory and recurrent outcome groups; RecRem: patients from both recurrent and remission outcome groups; Ref Hi: subset of refractory patients with high abundance (>1%) of Gardnerella Gsp07; Ref Lo: subset of refractory patients with low abundance (≤1%) of Gardnerella Gsp07; CI: confidence interval. Three alternative sets of biomarker species were determined for the Ref Hi versus Ref Lo groups.