The Value of Metagenomic Next-Generation Sequencing in Hematological Malignancy Patients with Febrile Neutropenia After Empiric Antibiotic Treatment Failure

Figures & data

Table 1 Characteristics of Patients

Characteristics	Total n (%)	FN n (%)	Non-FN n (%)	P
Gender	192	102	90	0.440
Male	132 (68.75)	68 (66.67)	64 (71.11)
Female	60 (31.25)	34 (33.33)	26 (28.89)
Age ()	42.88±18.42	42.37±19.00	43.39±17.07	0.082
Previous treatment				0.076
Chemotherapy	124 (64.58)	60 (58.82)	64 (71.11)	0.572
CAR-T	23 (11.98)	14 (13.73)	9 (10.00)
Transplantation	45 (23.44)	28 (27.45)	17 (18.89)
Empirical antibiotics
Anti- (bacteria + fungi + virus)	68 (35.42)	37 (36.27)	31 (34.44)
Anti- (bacteria + fungi)	44 (22.92)	24 (23.53)	20 (22.22)
Anti-(bacteria)	53 (27.60)	30 (29.41)	23 (25.56)
Anti- (bacteria + virus)	27 (14.06)	11 (10.78)	16 (17.78)
Sample				0.467
Blood	157 (81.77)	89 (87.25)	68 (64.44)
BALF	11 (5.73)	4 (3.92)	7 (7.78)
Tissue	9 (4.69)	3 (2.94)	6 (6.67)
Body fluid	8 (4.17)	3 (2.94)	5 (5.56)
Pus	5 (2.60)	2 (1.96)	3 (3.33)
Sputum	2 (1.04)	1 (0.98)	1 (1.11)
Underlying diseases				<0.001*
AML	53 (27.60)	34 (33.33)	19 (21.11)
ALL	53 (27.60)	36 (35.29)	17 (18.89)
MDS	27 (14.06)	13 (12.75)	14 (15.56)
NHL	28 (14.58)	6 (5.88)	22 (24.44)
Others	31 (16.15)	13 (12.75)	18 (20.00)
Infection				0.616
Yes	145 (75.52)	75 (73.53)	70 (77.78)
No	22 (11.46)	12 (11.76)	11 (12.22)
Uncertain	24 (12.50)	15 (14.71)	9 (10.00)

Note: *P value < 0.05.

Abbreviations: FN, febrile neutropenia; non-FN, non-febrile neutropenia; BALF, bronchoalveolar lavage fluid, AML, Acute myelocytic leukemia; ALL, Acute lymphocytic leukemia; MDS, Myelodysplastic syndromes; NHL, Non-Hodgkin’s Lymphoma; CAR-T, Chimeric Antigen Receptor T-Cell Immunotherapy.

Figure 1 Distribution of pathogenic detected by mNGS in FN patients.

Figure 2 Distribution of pathogenic detected by mNGS in non-FN patients.

Table 2 Detection Efficiency of mNGS and Comparison in FN and Non-FN Groups

	Total n (%)		P	FN (102) n (%)	Non-FN (90) n (%)	P^a
	mNGS	Traditional Method
Positive rate (Total)	154 (80.21)	48 (25.00)	<0.001*	85 (83.33)	69 (76.67)	0.247
Detection rate of the Bacteria	93 (48.44)	18 (9.38)	<0.001*	48 (47.06)	45 (50.00)	0.684
Detection rate of the Fungus	44 (22.92)	8 (4.17)	<0.001*	33 (32.35)	11 (12.22)	0.001*
Detection rate of the Virus	81 (42.19)	24 (12.50)	<0.001*	43 (42.16)	38 (42.22)	0.993
Mixed pathogens^b						0.440
Yes	61 (39.61)	2 (4.17)	<0.001*	36 (45.00)	25 (27.78)
No	93 (60.39)	46 (95.83)		49 (48.04)	44
Pathogen species	141	15		83	58
Bacteria	72 (51.06)	8 (53.33)		36 (43.37)	36 (62.07)	0.021*
Fungus	33 (23.40)	4 (26.67)	0.887	26 (31.33)	7 (12.07)
Virus	36 (25.53)	3 (20.00)		21 (25.30)	15 (25.86)

Notes: *P value < 0.05. ^aWhether mNGS is statistically different between FN group and non-FN group. ^bMixed infection was defined as a non-single pathogen infection, such as bacteria + fungi/bacteria + virus/fungi + virus/bacteria + fungi + virus.

Abbreviations: FN, febrile neutropenia; non-FN, non-febrile neutropenia; mNGS, Metagenomic next generation sequencing.

Figure 3 The difference between mNGS and traditional method.

Notes: Analyzed the consistency between mNGS and traditional method. The result of mNGS and traditional methods were both positive in 48 (25%) cases, of which 31/48 (64.58%) were partly matched, 10/48 (20.83%) were fully matched, and 7/48 (14.58%) were mismatched.

Table 3 Diagnostic Efficiency of Culture and mNGS Compared to Clinical Diagnosis

	FN (%)			Non-FN (%)
	Traditional Method	mNGS	P	Traditional Method	mNGS	P
Sensitivity	29.33	88.00	<0.001*	37.14	81.42	<0.001*
Specificity	100.00	58.33	0.063	100.00	63.64	0.125
PPV	100.00	92.96		100.00	93.44
NPV	18.46	56.25		20.00	35.00

Note: *P value < 0.05.

Abbreviations: FN, febrile neutropenia; non-FN, non-febrile neutropenia; mNGS, Metagenomic next generation sequencing; PPV, positive predictive value; NPV, negative predictive value.

Table 4 The mNGS Results That Led Discontinued Inappropriate Antibiotics

Sample No.	Grouping	mNGS Result	Antibiotic Adjustment
9	Infection	Staphylococcus	Stoped Cancidas, added Daptomycin
10	Infection	Klebsiella oxytoca, Entero-bacter kobei	Stoped Daptomycin, added tigecycline
34	Infection	Hortaea werneckii	Stoped tigecycline, added Amphotericin B
38	Infection	Human betaher-pesvirus 5 and Human polyom-avirus 1	Stoped voriconazole
40	Infection	Human betaher-pesvirus 5 and Human polyom-avirus 1	Stoped Minocycline, Imipenem

Abbreviation: mNGS, Metagenomic next generation sequencing.

Table 5 Diagnostic Value of mNGS in Fungal Infection in Patients with FN

No.	Age/Sex	Underlying Disease	Culture/Pathology	mNGS*	G	GM	Final Clinical Diagnosis
1	54/M	AML	Negative	Candida	Negative	Negative	Pulmonary fungal infection
2	49/M	AML	Negative	Aspergillus	Negative	Positive	Pulmonary fungal infection
3	14/F	ALL	Negative	Candida	Negative	Negative	Exclude
4	54/M	DLBCL	Negative	Archangium	Negative	Negative	Exclude
5	75/F	MDS	Negative	Aspergillus	Negative	Negative	Pulmonary fungal infection
6	37/M	HAL	MUCOR	Mucor	Positive	Negative	Pulmonary fungal infection
7	38/M	MPN	Negative	Aspergillus	Negative	Negative	Exclude
8	18/F	ALL	Negative	Aspergillus	Negative	Negative	Exclude
9	58/M	AML	Negative	Mucor	Negative	Negative	Pulmonary fungal infection
10	43/M	ALL	Mucor	Mucor	Negative	Negative	Pulmonary fungal infection
11	43/M	ALL	Negative	Mucor	Negative	Negative	Pulmonary fungal infection
12	74/M	AML	Negative	Candida	Negative	Negative	Pulmonary fungal infection
13	36/M	ALL	Negative	Aspergillus	Negative	Negative	Exclude
14	42/F	MDS	Negative	Mucor	Negative	Negative	Fungal infections of the central nervous system
15	39/M	AML	Negative	Exophiala	Negative	Negative	Pulmonary fungal infection
16	14/F	ALL	Negative	Mucor	Negative	Negative	Fungal infections of the central nervous system
17	73/M	ALL	Candida	Candida, and Aspergillus	Negative	Positive	Fungal infections of the central nervous system
18	26/F	AML	Negative	Coprinus sp.	Negative	Negative	Exclude
19	49/F	AML	Negative	Aspergillus	Negative	Positive	Pulmonary fungal infection
20	64/M	ALL	Negative	Mucor	Negative	Negative	Pulmonary fungal infection
21	19/F	ALL	Negative	Aspergillus	Negative	Negative	Exclude
22	64/M	ALL	Negative	Aspergillus	Negative	Negative	Pulmonary fungal infection
23	49/F	AML	Negative	Aspergillus	Negative	Negative	Pulmonary fungal infection
24	54/F	MDS	Negative	Candida	Negative	Negative	Exclude
25	26/F	ALL	Negative	Coprinus sp.	Negative	Negative	Exclude
26	59/F	AML	Negative	Mucor	Negative	Negative	Pulmonary fungal infection
27	73/M	MDS	Negative	Mucor	Negative	Negative	Pulmonary fungal infection
28	51/F	AML	Candida	Candida	Negative	Negative	Fungemia
29	48/M	IRP	Negative	Mucor Pneumocystis jirovecii	Positive	Negative	Pulmonary fungal infection
30	49/F	MDS	Negative	Aspergillus	Negative	Negative	Exclude
31	15/M	DLBCL	Negative	Corynespora	Negative	Negative	Exclude
32	48/M	ALL	Negative	Aspergillus	Negative	Negative	Exclude
33	64/M	ALL	Negative	Aspergillus	Negative	Negative	Pulmonary fungal infection

Note: *Only show fungal results in mNGS.

Abbreviations: mNGS, Metagenomic next generation sequencing; G,1,3-β-D glucan test; GM, Galactomannan; AML, acute myelocytic leukemia; ALL, acute lymphoblastic leukemia; DLBCL, diffuse large B cell lymphoma; MDS, myelodysplastic syndromes; HAL, hybrid acute leukemia; MPN, myeloproliferative neoplasm; IRP, immune related pancytopenia.