Table 2.

Evaluation of the pathogen identification pipeline

	Thresholds					mNGS	Diagnosis
	SDSMRN	RAR	CF				+	−
Non-mycobacterium
All				NPV = 76%		+	26	26
				PPV = 50%		−	44	143
Sputum	4000	65	3	NPV = 66%		+	18	14
				PPV = 56%		−	26	50
BALF	4500	60	6	NPV = 80%		+	6	6
				PPV = 50%		−	11	45
Lung tissue	6000	55	4	NPV = 85%		+	1	5
				PPV = 17%		−	5	28
Pleural fluid	1000	35	8	NPV = 91%		+	1	1
				PPV = 50%		−	2	20
Mycobacterium
All				NPV = 76%		+	45	29
				PPV = 61%		−	51	166
Sputum	MRN = 3			NPV = 69%		+	14	11
				PPV = 56%		−	28	62
BALF	MRN = 3			NPV = 79%		+	17	11
				PPV = 61%		−	15	58
Lung tissue	MRN = 13			NPV = 81%		+	10	4
				PPV = 71%		−	4	23
Pleural fluid	MRN = 2			NPV = 85%		+	4	3
				PPV = 57%		−	4	23
Fungi
All				NPV = 85%		+	19	44
				PPV = 30%		−	37	212
Sputum	400	85	7.5	NPV = 87%		+	4	9
				PPV = 31%		−	20	131
BALF	100	90	9.5	NPV = 80%		+	3	5
				PPV = 38%		−	12	47
Lung tissue	600	80	8	NPV = 76%		+	2	6
				PPV = 25%		−	12	37
Pleural fluid	50	80	8.5	NPV = 91%		+	1	1
				PPV = 50%		−	2	20

BALF bronchoalveolar lavage fluid

SDSMRN StandarDized Strictly Mapping Read Numbers

RAR relative abundance rate

CF coverage fold

MRN mapped read number

Bold values are the results of the ‘All’s