Detection of Pneumocystis jirovecii Pneumonia in Infants with Non-Human Immunodeficiency Virus Admitted to Pediatric Intensive Care Using Metagenomics Next-Generation Sequencing

Figures & data

Table 1 Comparison of Clinical Data and Pathogenic Microorganisms Between the Two Groups

Item	PCP Group (n=16 Cases)	Control Group (33 Cases)	T/z/χ^2	p
Gender
Age (month)	3.69±1.25	2.30±1.16	3.741	0.001
Weight (kg)	4.75±1.43	4.35±1.04	0.939	0.359
Malnutrition	7(43.8%)	6(18.2%)	3.614	0.086
Preterm infants	4(25.0%)	10(30.3%)	0.148	0.926
SGA	2(12.5%)	1(3.0%)	1.681	0.245
Fever	7(43.8%)	17(51.5%)	0.260	0.762
Cough	4(25%)	26(78.8%)	13.132	0.000
Wheezing	4(25%)	8(24.2%)	0.003	1.000
Lung rales	13(81.3%)	29(87.9%)	0.387	0.668
Operation History	8(50.0%)	3(39.1%)	10.358	0.003
Background disease	11(68.8%)	26(78.8%)	0.587	0.491
Breathing machine	9(56.3%)	9(27.3%)	3.893	0.048
Ground glass opacity in chest films	2(12.5%)	7(21.2%)	0.545	0.698
Elevation of ALT	4(25.0%)	9(27.3%)	0.029	1.000
Elevation of AST	7(43.8%)	11(33.3%)	0.503	0.537
Elevation of CK-MB	6(37.5%)	10(30.3%)	0.254	0.748
Elevation of Cr or/and BUN	0	3(9.0%)	/	/
Time of antibiotic use before examination	4(3, 17)	4(3, 10)	0.187	0.851
Use of triple antibiotics	5(31.1%)	4(12.1%)	2.630	0.13
Use of glucocorticoids throughout the body	5(31.3%)	10(30.3%)	0.005	1.000
White blood cells	13.31±7.26	10.04±3.99	1.954	0.057
Neutrophils	47.99±15.80	46.47±16.52	0.295	0.770
Lymphocytes	41.59±15.58	39.83±15.67	0.350	0.728
Increase of E counts	3(18.8%)	8(24.2%)	0.187	1
Increases of E ratio	3(18.8%)	6(18.2%)	0.002	1
High IgG	3(3/7, 42.9%)	5(5/12, 41.7%)	0.003	1
Low IgA	2(2/7, 28.6%)	2(2/12, 16.7%)	0.377	0.603
High C3	5(5/7, 71.4%)	3(3/12, 25%)	3.909	0.048
Low C4	5(71.4%)	1(1/12, 8.3%)	8.146	0.01
Decrease of total T lymphocytes	3(3/7, 42.9%)	1(1/12, 8.3%)	3.170	1.117
Increase of total B lymphocytes	4(4/7, 57.1%)	6(6/12, 50.0%)	0.090	1.000
Decrease of NK	5(5/7, 71.4%)	4(4/12, 33.3%)	2.574	0.17
Decrease of CD4^+T	3(3/7, 42.9%)	2(2/12, 16.7%)	1.564	0.305
Decrease of CD4^+/CD8^+T	5(5/7, 71.4%)	2(2/12, 16.7%)	5.698	0.045
CMV	7(43.8%)	5(15.2%)	4.766	0.04
RSV	4(25%)	12(36.4%)	0.663	0.526
EV	4(25%)	2(6.1%)	3.597	0.08
Staphylococcus aureus	4(25)	5(15.2%)	0.697	0.449
Klebsiella pneumoniae	0	6(18.2%)	/	/
Escherichia coli	1(6.3%)	6(18.2%)	1.253	0.402
Tiny Ureaplasma	2(12.5%)	2(6.1%)	0.596	0.588
Ureaplasma Urealyticum	2(12.5%)	0	/	/
Candida albicans	2(12.5%)	2(6.1%)	0.596	0.588
Virus dominated	10(62.5%)	14(42.2%)	4.332	0.037
Bacteria dominated	3(18.8%)	12(36.4%)	1.574	0.324
Multiple infection	6(37.5%)	6(18.2%)	2.175	0.169

Note: /: There is no need to compare the two groups because one of them is “0”.

Abbreviations: SGA, small for gestational age; CMV, cytomegalovirus; RSV, respiratory syncytial virus; EV, rhinovirus; ALT, glutamic pyruvic transaminase; AS, glutamic oxalacetic transaminase; CK-MB, creatine kinase -MB; Cr, creatinine; BUN, blood urea nitrogen; E, eosinophilic granulocyte; NK, natural killer cell.

Figure 1 Distribution of pathogens detected by mNGS in BALF of two groups pathogens.

Table 2 Detection of Pneumocystis and Other Pathogenic Microorganisms in 16 Children with PCP

Cases	Pneumocystis				Virus					Bacteria					Others
	Relative Abundance of DNA (%)	DNA Sequence Number	Relative Abundance of RNA (%)	RNA Sequence Number	CMV	RSV	EV	Torque Teno Virus	Human Respiratory Virus Type 3	Pseudomonas aeruginosa	Parainfluenza Virus	Staphylococcus aureus	Pseudomonas aeruginosa	Tropheryma whipplei	Candida albicans	Ureaplasma urealyticum
1	97.4	49	83	210	+
2	99	14,285	100	144,369	+		+								+
3	53.1	13	97.9	1539		+		+								+
4	0	0	41.9	16		+	+
5	0	0	21.6	13		+	+
6	22.2	2	0	0				+
7	0	0	7.2	19			+				+					+
8	0	0	36.2	42									+			+
9	3.4	6	0	0
10	89.5	13	45.4	75	+				+		+
11	99.9	2921	99.5	17,932	+				+
12	97.6	86	92.5	816						+		+
13	95.5	153	93.7	1320								+				+
14	99.8	23,518	0	0	+									+
15	38.1	9	10.4	7	+	+						+	+
16	99.8	8680	100	200,402	+										+

Note: “+”Indicates other pathogenic microorganisms in addition to pneumocystis in this case.

Table 3 Distribution of Symbiotic Microorganisms in the Two Groups

Category	Genus of Symbiotic Bacteria	Species of Symbiotic Bacteria	PCP Group (n=16)	Control Group (n=33)	Total (n=49)
G^+ bacteria	Streptococcus		16(100%)	30(90.9%)	46(93.9%)
		S. peroris	1	2	3
		S. mitis	9	26	35
		S. vestibularis	1	3	4
		S. pseudopneumoniae	7	12	19
		S. parasanguinis	3	11	14
		S. salivarius	3	6	9
		S. dysgalactiae	0	1	1
		S. sanguinis	0	1	1
	Propionibacterium		8(50.0%)	23(69.7%)	31(63.3%)
		P. acnes	4	20	24
	Rothia		9(56.3%)	21(63.6%)	30(61.2%)
		R. mucilaginosa	8	22	30
		R. aeria	1	1	2
	Staphylococcus		9(56.3%)	20(60.6%)	29(59.2%)
		S. epidermidis	5	16	21
		S. hominis	3	5	8
		S. capitis	2	4	6
		S. cohnii	1	3	4
		S. pettenkoferi	0	1	1
	Corynebacterium		4(25.0%)	5(15.2%)	9(18.4%)
		C. aurimucosum	0	2	2
		C. propinquum	4	1	5
		C. pseudodiphtheriticum	0	1	1
		C. jeikeium	1	1	2
		C. striatum	0	2	2
		C. accolens	0	1	1
	Gemella		1(6.3%)	7(21.2%)	8(16.3%)
		G. haemolysans	1	7	8
	Granulicatella		1(6.3%)	2(6.1%)	3(6.1%)
		G. elegans	1	1	2
		G. adiacens	0	1	1
	Actinomyces		1(6.3%)	0(0.0%)	1(2.0%)
		A. massiliensis	1	0
	Atopobium		0	1	1
		A. parvulum	0	1	1
	Peptostreptococcus		1(6.3%)	0(0.0%)	1(2.0%)
		P. stomatis	1	0	1
G^− bacteria	Moraxella		7(43.8)	15(45.5%)	22(44.9%)
		Moraxella osloensis	7	13	21
	Haemophilus		2(12.5%)	4(12.1%)	6(12.2%)
		H. haemolyticus	2	5	7
	Veillonella		1(6.3%)	4(12.1%)	5(10.2%)
		V. dispar	0	1	1
		V. atypica	1	2	3
		V. parvula	0	1	1
	Prevotella		2(12.5%)	2(6.1%)	4(8.2%)
		P. melaninogenica	1	2	3
		P. nigrescens	1	0	1
		P. bivia	0	1	1
	Fusobacterium		2(12.5%)	1(3.0%)	3(6.1%)
		F. nucleatum	1	1	2
		F. hwasookii	1	0	1
		F. periodonticum	1	0	1
	Porphyromonas		0(0.0%)	2(6.1%)	2(4.1%)
		P. catoniae	0	1	1
		P. somerae	0	2	2
	Campylobacter		1(6.3%)	0(0.0%)	1(2.0%)
		C. concisus	1	0	1
	Capnocytophaga		1(6.3%)	0(0.0%)	1(2.0%)
		C. sputigena	1	0	1
Fungi	Malassezia		5(3.1%)	11(33.3%)	16(32.7%)
		M. restricta	1	6	7
		M. globosa	1	4	5
		M. japonica	1	5	6
		M. furfur	4	0	4
	Candida		2(12.5%)	2(6.1%)	4(8.2%)
		C. parapsilosis	2	1	3
		C. metapsilosis	1	0	1
	Saccharomyces		1(6.3%)	2(6.1%)	3(6.1%)
		S. cerevisiae	1	0	1
	Meyerozyma		0(0.0%)	1(3.0%)	1(2.0%)
		M. guilliermondii	0	1	1

Abbreviations: G⁺ bacteria, Gram-positive bacteria; G⁻ bacteria, Gram-negative bacteria.

Figure 2 Distribution of human symbiotic microorganism detected by MNGs in BALF of the two groups.