TABLE 3.
Comparison between genomic loads measured by lytA rtPCR from sputum and from nasopharyngeal swabs
| Performance | No. of lytA rtPCR results of >10,000/ml/total no. (%) in sputum ofa: |
No. of NP swab lytA rtPCR results of >8,000/ml/total no. (%) (n = 222) | ||
|---|---|---|---|---|
| Any quality (n = 222) | Good quality (n = 42) | Suboptimal quality (n = 180) | ||
| Sensitivity | 63/81 (77.8) | 22/28 (78.6) | 41/53 (77.4) | 64/81 (79.0) |
| Specificity | 94/141 (66.7) | 9/14 (64.3) | 85/127 (66.9) | 96/141 (68.1) |
| PPVb | 63/110 (57.3) | 22/27 (81.5) | 41/83 (49.4) | 64/109 (58.7) |
| NPV | 94/112 (83.9) | 9/15 (60.0) | 85/97 (87.6) | 96/113 (85.0) |
| Additional yield | 47/141 (33.3) | 5/14 (35.7) | 42/127 (32.3) | 45/141 (31.9) |
a
Composite diagnostic standard: positive blood culture, induced-sputum culture or Gram stain, urine antigen, or whole-blood lytA rtPCR; for this comparison, the cutoff value of >8,000 copies/ml for NP swab lytA rtPCR criterion was not included in the composite diagnostic.
b
PPV, positive predictive value; NPV, negative predictive value; additional yield, 1−specificity (i.e., patients with sputum lytA rtPCR cutoff value of >10,000/ml or NPS lytA rtPCR cutoff value of >8,000/ml and a negative composite diagnostic standard represent false positives).