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Table 5 Confusion matrix to compare the performance of mNGS against microbial culture for the detection of species of interest (SOI)

From: Metagenomics for the microbiological diagnosis of hospital-acquired pneumonia and ventilator-associated pneumonia (HAP/VAP) in intensive care unit (ICU): a proof-of-concept study

 

Predicted condition by mNGS

 
 

Predicted positive

CSOI ≥ MT

PP = 38

Predicted negative

CSOI < MT or no detection

PN = 570

 

Microbial culture condition

 Positive

 Detection ≥ CT

 P = 26

True positive

TP = 25

False negative

FN = 0 (1 without SPC detection)

Sensitivity

\(\mathrm{Sensitivity}=\frac{\mathrm{TP}}{\mathrm{P}}\)

96.2%

 Negative (N)

 Detection < CT or no detection

 N = 582

False positive

FP = 13

True negative

TN = 269

(300 without SPC detection)

Specificity

\(\mathrm{Specificity}=\frac{\mathrm{TN}}{\mathrm{N}}\)

97.8%

 

Positive predictive value

\(\mathrm{PPV}=\frac{\mathrm{TP}}{\mathrm{PP}}\)

65.8%

Negative predictive value

\(\mathrm{NPV}=\frac{\mathrm{TN}}{\mathrm{PN}}\)

99.8%

 
  1. 19 SOI were assessed in 32 BALF representing a total data population equal to 608. Microbial cultures are classified as positive (P) when the SOI is quantified above or equal to the culture threshold (CT) and negative (N) when the SOI is quantified below the CT or when the SOI was not detected. Metagenomics predicts the result as positive (PP) when the concentration of SOI (CSOI) is calculated as equal to or greater than MT. Metagenomics predicts the result as negative (PN) when the CSOI is calculated to be lower than MT. Results that cannot be interpreted by mNGS, i.e. those in which neither SOI nor SPC has been detected (Fig. 1), are considered negative and the quantities are indicated separately in brackets. True positive (TP) and true negative (TN) correspond respectively to the concordant positive or negative results between the 2 methods. False negative (FN) corresponds to positive results in microbial culture but predicted as negative by mNGS. False positive (FP) corresponds to negative results in microbial culture but predicted as positive by mNGS. Sensitivity represents the culture positive detection of SOI classified as positive by mNGS to the total number of positive culture detection. Specificity expresses the ratio of correctly predicted negative by mNGS to the total number of negative detections of SOI by culture. Positive predictive value (PPV), also called precision, represents the proportion of positive detections by culture that were correctly classified to the total number of positive predicted detection by mNGS. Negative predictive value (NPV), or true negative accuracy, measures the proportion of negative detection by culture that were correctly predicted as negative by mNGS to the total number of negative prediction
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Respiratory Research

ISSN: 1465-993X

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