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Table 1 Specific scoring algorithm for the detection of bacterial and fungal pathogens

From: Clinical evaluation of metagenomic next-generation sequencing in unbiased pathogen diagnosis of urinary tract infection

Gold standard or composite standard

mNGS

TP/FN score

TN/FP score

Positive for 1 organism

Positive for the identical organism

1 TP

 

Positive for different organism(s) or negative

1 FN

 

Positive for 2 organisms

Positive for the 2 identical organisms

1 TP

 

Positive for only 1 identical organism

0.5 TP and 0.5 FN

 

Positive for the different organism(s) or negative

1 FN

 

Positive for 3 organisms

Positive for the 3 identical organisms

1 TP

 

Positive for only 2 identical organisms

2/3 TP and 1/3 FN

 

Positive for only 1 identical organism

1/3 TP and 2/3 FN

 

Positive for the different organism(s) or negative

1 FN

 

Positive for 4 organisms

Positive for the 4 identical organisms

1 TP

 

Positive for only 3 identical organisms

3/4 TP and 1/4 FN

 

Positive for only 2 identical organisms

2/4 TP and 2/4 FN

 

Positive for only 1 identical organism

1/4 TP and 3/4 FN

 

Positive for the different organism(s) or negative

1 FN

 

Negative

Negative

 

1 TN

Positive for any organism(s)

 

1 FP

  1. TP, true positives; FN, false negatives; TN, true negatives; FP, false positives