A Paired Comparison of Plasma and Bronchoalveolar Lavage Fluid for Metagenomic Next-Generation Sequencing in Critically Ill Patients with Suspected Severe Pneumonia

Figures & data

Table 1 Characteristics of Patients with Suspected Severe Pneumonia Included in the Study

Characteristics	All Patients (n = 57)	Negative Plasma mNGS Group (n = 35)	Positive Plasma mNGS Group (n = 22	P value
Age, mean ± SD (years)	59.9 ± 14.4	64.7 ± 11.7	52.1 ± 15.2	0.001
Male, n (%)	40 (70.2)	25 (71.4)	15 (67.2)	0.794
Mechanical ventilation, n (%)	29 (50.9)	19 (54.3)	10 (45.5)	0.516
Septic shock, n (%)	17 (29.8)	12 (34.3)	5 (22.7)	0.353
Immunosuppression, n (%)	31 (54.4)	20 (57.1)	11 (50.0)	0.598
APACHE II score, mean ± SD	14.5 ± 4.4	15.3 ± 4.4	13.2 ± 4.3	0.097
SOFA score, median (Q1–Q3)	4.0 (3.0–7.0)	4.0 (3.0–7.0)	4.5 (3.0–6.8)	0.843
BALF culture positive, n (%)	19 (36)	8 (22.9)	11 (50.0)	0.033
Days of hospital stay at specimen acquisition, median (Q1–Q3)	7.0 (2.5–14.5)	11 (4.0–16.0)	4.5 (2.0–7.5)	0.028
Days of ICU stay at specimen acquisition, median (Q1–Q3)	2.0 (1.0–5.0)	2.0 (1.0–5.5)	1.0 (1.0–2.2)	0.388
Prior antibiotic exposure, n (%)	49 (86)	31 (88.6)	18 (81.8)	0.475
Total 28-day mortality, n (%)	14 (24.6)	11 (31.4)	3 (13.6)	0.400

Abbreviations: Q, quartile; mNGS, metagenomic next-generation sequencing; SD, standard deviation; BALF, bronchoalveolar lavage fluid; APACHE, acute physiology and chronic health evaluation scoring system; SOFA, sequential organ failure assessment; ICU, intensive care unit.

Figure 1 Pathogen spectrum of mNGS results in patients with severe pneumonia (n = 53).

Abbreviations: BALF, bronchoalveolar lavage fluid; mNGS, metagenomic next-generation sequencing.

Figure 2 Diagnostic performance of mNGS in patients with severe pneumonia (n = 53). (A) Comparison of positive rates (P < 0.001) between BALF and plasma mNGS. (B) Different spectra of bacteria, fungi, and viruses were detected using BALF and plasma mNGS. No differences in the detected proportions of bacteria, fungi, and viruses were observed between BALF and plasma mNGS (P > 0.05). (C) Cases with various numbers of detected pathogens via mNGS. (D) Distribution of different types of pathogens in panel C. Outer circle, pathogens identified by BALF mNGS (n = 53); inner circle, pathogens identified by plasma mNGS (n = 22).

Abbreviations: BALF, bronchoalveolar lavage fluid; mNGS, metagenomic next-generation sequencing.

Table 2 Diagnostic Performance of mNGS and CMTs in Patients with Suspected Severe Pneumonia (n = 57)

Clinical Composite Diagnosis
	Sensitivity	Specificity	PPV	NPV	Accuracy
	% (95% CI)	% (95% CI)	% (95% CI)	% (95% CI)	% (95% CI)
BALF mNGS	100 (93–100) ^a	50 (68–93)	96 (87–100)	100 (16–100)	96 (88–99)
Plasma mNGS	42 (28–56)	100 (40–100)	100 (85–100)	11 (3–27)	46 (32–59)
CMTs	53 (39–67)	100 (40–100)	100 (88–100)	14 (4–32)	56 (42–69)

Note: ^aBALF mNGS vs plasma mNGS, P < 0.001.

Abbreviations: mNGS, metagenomic next-generation sequencing; BALF, bronchoalveolar lavage fluid; CMTs, conventional microbiological tests; PPV, positive predictive value; NPV, negative predictive value.

Table 3 Impact of Microorganisms Detected Using Only Plasma mNGS in the Paired Sample (11 Cases)

Patient ID	Plasma mNGS Result (SDSMRN)	Clinical Composite Diagnosis	Change in Treatment
03	Torque teno virus (77)	Non-pathogenic microbe	No change
06	Aspergillus (8)	Definite pathogen	Change, add voriconazole
10	Human adenovirus (7)	Definite pathogen	No change ^a
25	Epstein-Barr virus (3)	Non-pathogenic microbe	No change
28	Epstein-Barr virus (3)	Non-pathogenic microbe	No change
41	Human alphaherpesvirus 3 (9)	Probable pathogen	Change, add acyclovir
43	Torque teno virus (14)	Non-pathogenic microbe	No change
	Cytomegalovirus (5)	Definite pathogen	Change, add ganciclovir
52	Epstein-Barr virus (4)	Non-pathogenic microbe	No change
53	Human alphaherpesvirus 3 (13)	Probable pathogen	Change, add acyclovir
54	Cytomegalovirus (3)	Definite pathogen	No change ^b
55	Cytomegalovirus (7)	Probable pathogen	Change, Add ganciclovir

Notes: ^aThis patient had been diagnosed with adenovirus pneumonia prior to this test. ^bThis patient had a suspected Pneumocystis jirovecii and cytomegalovirus co-infection and had received sulfamethoxazole and ganciclovir as empirical treatment.

Abbreviations: mNGS, metagenomic next-generation sequencing; SDSMRN, standardized strictly mapped reads number.