Table 2.

Comparison of Cell-Free Plasma mNGS versus Respiratory mNGS for Detection of Clinically Confirmed Pneumonia Pathogens, with Microbes Ranked by Abundance (Reads per Million)

Pneumonia-Positive, Blood Culture/PCR-Positive Cases
ID	Respiratory Culture, Day 0	Blood Culture or PCR, Day 0	Plasma mNGS Rank, Day 0	Respiratory mNGS Rank, Day 0
252	Streptococcus	Streptococcus	1	2
	Enterobacter		ND	3
	Staphylococcus		ND	>10
289	Staphylococcus	Staphylococcus	1	2
298	Enterobacter*	Cytomegalovirus†	ND*, 2†	1*, >10†
334	Streptococcus	Streptococcus	1	1
Pneumonia-Positive Cases
ID	Respiratory Culture, Day 0	Blood Culture or PCR, Day 0	Plasma mNGS Rank, Day 0	Respiratory mNGS Rank, Day 0
213‡	Klebsiella	—	4	4
	Escherichia	—	ND	7
239	Staphylococcus	—	2	4
	Pseudomonas	—	ND	1
257	Enterobacter	—	ND	1
268	Pseudomonas	—	ND	1
	Stenotrophomonas	—	ND	2
278	Moraxella	—	1	1
277	Enterococcus	—	4	1
288	Staphylococcus	—	2	2
297	Pseudomonas	—	2	2
	Enterobacter	—	ND	3
	Morganella	—	ND	4
	Klebsiella	—	ND	7
314	Staphylococcus	—	1	2
	Streptococcus	—	2	4
335	Histoplasma§	—	1	1
350	Serratia	—	ND	1
382	Serratia	—	ND	1
386	Staphylococcus	—	ND	2
VAP Cases
ID	VAP Respiratory Culture, Day 4	Plasma mNGS Rank, Day 0	Respiratory mNGS Rank, Day 0	Respiratory mNGS Rank, Day 2
203	Enterobacter	1	ND	1
	Staphylococcus	2	ND	2
213‡	Serratia	1	7	n/a

Definition of abbreviations: mNGS = metagenomic next-generation sequencing; n/a = respiratory mNGS data not available; ND = not detected; VAP = ventilator-associated pneumonia. Pathogen detection was performed using respiratory mNGS as previously described (4).

^*Culture-identified pneumonia pathogen.

^†Detected by clinical PCR of blood.

^‡Patient developed Serratia VAP 4 days after enrollment.

^§Detected by serum antigen testing.