Table 2 Patient and mNGS test characteristics associated with 1,164 samples from 1,053 patients in UCSF cohort

From: Seven-year performance of a clinical metagenomic next-generation sequencing test for diagnosis of central nervous system infections

Patient or mNGS test characteristic

 

Number (%) of patients (n = 1,053 patients)

Number (%) of cases or samples (n = 1,164 cases or samples)

Number (%) of infections (n = 220 infections)

Number (%) of patients or infections assigned to a specific category with positive mNGS testing

Median length of stay in days [IQR] (n = 1,164 cases or samples)

Sex

 

Male

579 (55.0%)

    
 

Female

474 (45.0%)

    

Age

 

<18

160 (15.2%)

    
 

18–65

630 (59.8%)

    
 

>65

263 (25.0%)

    

Immunosuppression

 

No immunosuppression

676 (64.2%)

  

48 (7.1%)a

 
 

Any immunosuppression

377 (35.8%)

  

63 (16.7%)a

 
 

HIV

48 (4.6%)

  

20 (41.7%)

 
 

Solid organ transplant

56 (5.3%)

  

12 (21.4%)

 
 

Hematopoietic stem cell transplant

45 (4.3%)

  

8 (17.8%)

 
 

Chemotherapy

40 (3.8%)

  

4 (10.0%)

 
 

Immunomodulatory agents

55 (8.1%)

  

4 (4.7%)

 
 

Primary immunodeficiency

16 (1.5%)

  

1 (6.3%)

 
 

Other immunosuppression

87 (8.3%)

  

14 (16.1%)

 

Primary clinical syndrome

 

Encephalitis

 

293 (25.2%)

 

29 (9.9%)b

 
 

Meningitis

 

293 (25.2%)

 

45 (15.4%)b

 
 

Meningoencephalitis

 

202 (17.4%)

 

36 (17.8%)b

 
 

Myelitis

 

69 (5.9%)

 

1 (1.4%)

 
 

Other

 

307 (26.3%)

 

16 (5.2%)

 

Clinical setting and outcomes

 

Inpatient

 

1,021 (87.7%)

   
 

ICU

 

450 (38.7%)

   
 

Length of stay

    

12 [5, 25]

 

Death at 60 days

 

119 (10.2%)

   

mNGS resultsc

 

Samples with at least one positive result

 

180 (15.5%)

   
 

Total number of organisms detectedd

 

227

   
 

Organisms considered incidental (excluded)

 

85

   
 

Organisms considered of unclear importance (excluded)

 

3

   
 

Organisms considered as positive detection

 

139

   
 

Negative detection (no organism detected)

 

907 (77.9%)

   
 

Negative detection (single organism, possible contaminant)

 

27 (2.3%)

   
 

Negative detection (multiple bacterial/fungal taxa, probable contaminant)

 

65 (5.6%)

   

Final adjudicated diagnosise

 

Noninfectious

 

432 (37.1%)

   
 

Prion

 

1 (0.1%)

   
 

Unknown

 

522 (44.8%)

   
 

Infectious

 

209 (18.0%)

   

Infectious diagnosis categoryf

      
 

Bacterial

  

55 (25%)

26 (47.3%)

 
 

DNA virus

  

71 (32.3%)

53 (74.6%)

 
 

RNA virus

  

30 (13.6%)

21 (70.0%)

 
 

Fungal

  

46 (20.9%)

23 (50.0%)

 
 

Parasitic

  

18 (8.1%)

12 (66.7%)

 
  1. aThe difference in mNGS positivity rate between no immunosuppression and any immunosuppression is statistically significant (P < 0.0001) using the two-tailed chi-squared test without adjustment for multiple comparisons.
  2. bThe difference in mNGS positivity rate between encephalitis and meningitis (P = 0.0466) or meningoencephalitis (P = 0.0103) is statistically significant using the two-tailed chi-squared test without adjustment for multiple comparisons.
  3. cSamples can fit in more than one category (for example, detection of multiple bacterial/fungal taxa suggesting contamination and positive detection of relevant RNA virus). Samples with multiple taxa detected for bacteria/fungi or single detected taxa corresponding to a commensal and/or environmental microorganism and reported with a comment about potential contamination were considered negative, as they represent likely contamination unless clearly related to the final adjudicated diagnosis. See Methods for a description of the result classification.
  4. dThis number includes three organisms initially reported as possible contamination and reclassified as positive detection given the clinical context.
  5. eClinical adjudication was performed to determine the etiology of the clinical syndrome by chart review. For the syndrome to be considered infectious, at least one microbiological test had to be positive, and consistent with the clinical adjudication.
  6. fFinal diagnoses included more than one causative organism for seven samples and were analyzed as separate infections.
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