Table 1 Metagenomic sequencing pipeline results.

From: Optimization of cerebrospinal fluid microbial DNA metagenomic sequencing diagnostics

Sample

Verified pathogen

Clinical method

qPCR (Geq/ml)

PaRCA (reads)

Kraken2 (reads)

Centrifuge (reads)

CosmosID (reads)

BLAST (reads)

Calculated reads

Range (ppm)

Leukocytes (× 106/l)

1

HSV1

qPCR

1.0 × 104

97

105

107

107

108

90

6.2–7.2

41

2

VZV

qPCR

3.9 × 105

213

219

223

211

213

365

14.9–16.0

272

3

VZV

qPCR

1.9 × 105

2196

2234

2251

2170

2197

3072

134.8–147.1

17

4

JCV

qPCR

1.9 × 105

23,766

24,018

24,190

22,318

23,847

N/A

1757–2096

N/A

5

JCV

qPCR

4.3 × 103

496

512

515

484

498

N/A

39.8–57.1

N/A

6

S. pneumoniae

Cultivation/16S rRNA

N/A

766,744

699,662

575,646

701,304

643,083

N/A

30,704–60,611

55

7

S. pneumoniae EBV

16S rRNA

qPCR

N/A

3.7 × 102

12,988

–

11,762

–

12,511

–

12,277

–

12,274

–

N/A

0.1

679–804

Undet.

1064

8

Enterovirus

qPCR

6.6 × 104

–

–

–

–

–

N/A

Undet.

95

9

Enterovirus EBV

qPCR

qPCR

5.8 × 104

4.1 × 102

–

–

–

–

–

–

–

–

–

–

N/A

0.1

Undet.

Undet.

814

10

EBV

VZV

qPCR

qPCR

1.9 × 103

4.7 × 103

10

7

9

7

9

7

8

7

9

7

2.5

4.5

0.8–1.1

0.7–0.8

181

11

EBV

VZV

qPCR

qPCR

5.0 × 101

2.9 × 103

–

15

–

15

–

15

–

12

–

15

0.1

5.5

Undet.

1.2–1.7

90

12

EBV

Yeast sp.

qPCR

Cultivation/filmarray

9.1 × 102

N/A

–

–

–

–

–

–

–

–

–

–

0.2

N/A

Undet.

Undet.

164

13

EBV

qPCR

1.9 × 103

81

85

82

79

82

20.5

6.7–7.5

26

14

EBV

qPCR

3.7 × 102

–

–

–

–

–

0.6

Undet.

253

15

EBV

qPCR

3.2 × 102

6

6

6

6

6

2.5

0.4–0.5

44

16

EBV

qPCR

2.7 × 102

232

228

225

213

223

18.5

21.2–22.8

4

17

EBV

qPCR

1.6 × 102

11

10

11

11

11

0.3

1.0–1.2

148

18

EBV

qPCR

1.6 × 102

–

–

–

–

–

N/A

Undet.

 < 4

19

EBV

qPCR

8.1 × 101

–

–

–

–

–

0.6

Undet.

31

20

EBV

qPCR

5.0 × 101

–

1

1

–

1

0.99

0–0.1

14

21

EBV

qPCR

5.0 × 101

8

8

8

8

9

1.5

0.7–0.8

9

  1. Reads from each classifier from verified pathogen. Calculated reads in accordance with the presented algorithm N/A: leukocyte count missing for sample 4 and 5, leukocyte count for sample 18 is below reference value, calculation is not applicable for bacteria, fungi and RNA virus.
  2. 16S rRNA 16S rRNA gene Sanger sequencing, HSV1 Herpes simplex virus 1, VZV Varicella Zoster virus, JCV JC polyomavirus, EBV Epstein-Barr virus.
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