The Performance of Metagenomic Next-Generation Sequence in the Diagnosis of Suspected Opportunistic Infections in Patients with Acquired Immunodeficiency Syndrome

Figures & data

Table 1 The Detailed Information Related to 86 Patients of AIDS Patients with Suspected Opportunistic Infections

n=86
	Age, Years (Range)	Female/Male	Pneumonia	Blood Stream Infection	Central Nervous System Infection
Hunan Provincial People’s Hospital	45.75 (28–55)	0/4	2	0	2
The Central Hospital of Yueyang	41.5 (27–71)	6/28	16	12	6
Second Hospital of Nanjing	43.5 (32–77)	11/35	37	6	3
Hengshui People’s Hospital	36.5 (28–45)	0/2	1	0	1

Figure 1 The proportion of samples in this study.

Table 2 Clinical Characteristics of AIDS Patients with Suspected Opportunistic Infections

n = 86
Demographics
Age, median (range, years)	42.8 (range: 27–77)
Female/male	17/69
Clinical feature
Increased WBC (×109 /L)	18/86 (20.9%)
Increased CRP (mg/L)	26/86 (30.2%)
Increased PCT (ng/mL)	21/86 (24.4%)
Median CD4 count, cells/mm3	56.9 cells/mm^3
Anti-retroviral therapy	54/86 (62.8%)

Abbreviations: WBC, white blood cells; CRP, C-reactive protein; PCT, procalcitonin.

Figure 2 Breakdown of organisms identified by both metagenomics next-generation sequencing (mNGS) and conventional microbiological tests (CMTs), mNGS only, and CMTs only.

Table 3 Pathogens Missed by mNGS

Microbe	Count	Culture	Smear	Serology	Cilnical Diagnosis
Nontuberculosis mycobacteria	5	2			3
Mycobacterium tuberculosis	4	1	1		2
Syphilis	4			4
Toxoplasma Gondii	1			1

Table 4 Comparison of the Use Proportion of Antimicrobials Between Pre-mNGS and After-mNGS in Patients

Antimicrobials	Pre-mNGS	After-mNGS	P value
Moxifloxacin	30/86(34.9%)	9/86 (10.5%)	0.0001
Meropenem	8/86 (9.3%)	3/86 (3.5%)	00.119
Piperacillin Sodium and Tazobactam Sodium	20/86 (23.3%)	16/86 (11.6%)	00.453
Foscarnet	45/86 (52.3%)	20/86 (23.26%)	<0.0001
Cefoperazone Sodium and Sulbactam Sodium	18/86(20.9%)	9/86(10.5%)	00.059
Levofloxacin	28/86 (32.6%)	12/86 (14%)	00.003
Imipenem-Cilastatin sodium hydrate	12/86 (14%)	7/86 (8.1%)	00.223
Fluconazole	6/86 (7%)	3/86 (3.5%)	00.304
Itraconazole	5/86 (5.8%)	5/86(5.8%)	1
Voriconazole	6/86 (7%)	6/86(7%)	1
Amphotericin B	8/86 (9.3%)	16/86 (18.6%)	00.078
Caspofungin	10/86 (11.6%)	20/86(31.4and)	00.001
Acyclovir	6/86 (7%)	14/86 (16.3%)	0.057