Table 1 Comparison of Mykrobe predictor S. aureus resistance prediction results with consensus phenotype for validation set (St_B1).

From: Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis

Drug

FN(R)

FP(S)

VME (95% CI)

ME (95% CI)

PPV (95% CI)

NPV (95% CI)

PEN

1 (377)

11 (94)

0.3% (0.0–1.5%)

11.7% (6.0–20.0%)

97.2% (95.0–98.6%)

98.8% (93.5–100%)

ERY

1 (79)

0 (392)

1.3% (0.0–6.9%)

0.0% (0–0.9%)

100% (95.4–100%)

99.7% (98.6–100%)

CIP

3 (65)

1 (406)

4.6% (1.0–12.9%)

0.2% (0.0–1.4%)

98.4% (91.5–100%)

99.3% (97.9–99.8%)

METH

0 (54)

0 (417)

0.0% (0–6.6%)

0.0% (0–0.9%)

100% (93.4–100%)

100% (99.1–100%)

FUS

0 (41)

4 (430)

0.0% (0–8.6%)

0.9% (0.3–2.4%)

91.1% (78.8–97.5%)

100% (99.1–100%)

CLIN

0 (25)

1 (97)

0.0% (0–13.7%)

1.0% (0.0–5.6%)

96.2% (80.4–99.9%)

100% (96.2–100%)

TET

0 (17)

1 (454)

0.0% (0–19.5%)

0.2% (0.0–1.2%)

94.4% (72.7–99.9%)

100% (99.2–100%)

RIF

0 (5)

0 (466)

N/A

0.0% (0–0.8%)

N/A

100% (99.2–100%)

GEN

1 (3)

0 (468)

N/A

0.0% (0–0.8%)

N/A

99.8% (98.8–100%)

MUP

0 (2)

0 (348)

N/A

0.0% (0–1.1%)

N/A

100% (98.9–100%)

TRIM

0 (1)

1 (188)

N/A

0.5% (0.0–2.9%)

N/A

100% (98.0–100%)

VAN

0 (0)

0 (471)

N/A

0.0% (0–0.8%)

N/A

100% (99.2–100%)

  1. CI, confidence interval; CIP, ciprofloxacin; CLIN, clindamycin; ERY, erythromycin; FDA, food and drug administration; FN, false-negative calls; FP, false positives; FUS, fusidic acid; GEN, gentamicin; ME, major error rate (false-positive rate); METH, methicillin; MUP, mupirocin; N/A, not applicable; NPV, negative predictive value; PEN, penicillin; PPV, positive predictive value; R, total number of resistant samples; RIF, rifampicin; S, total number of susceptible samples; TET, tetracycline; TRIM, trimethoprim; VAN, vancomycin; VME, very major error rate (false-negative rate).
  2. Resistance prediction results for Mykrobe predictor on the S. aureus validation set (St_B1), treating the consensus phenotype as gold standard except for trimethoprim (which Phoenix does not test) where the disc test was used as truth. VME only shown where R>10. ME only shown where S>10. Error rates shown with 95% CI calculated by Clopper–Pearson. Error rates meeting the FDA requirements are in bold.
Back to article page