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Table 1 Sequencing metrics for the 1mL and 5mL CMg pipelines

From: Development and proof-of-concept demonstration of a clinical metagenomics method for the rapid detection of bloodstream infection

 

Total number of reads matching reference

Bacteria population relative abundance (%)

Average bp length of mapped reads to reference (average read coverage(%))

Average coverage to reference (X)

 

1 mL protocol

5 mL protocol

1 mL protocol

5 mL protocol

1 mL protocol

5 mL

protocol

1 mL protocol

5 mL protocol

Escherichia coli

 50–100 CFU/mL

6306.7 ± 3238.1

22,516.3 ± 1677.5

95.2 ± 0.9

96.9 ± 0.2

1878.8.3 ± 129.4

(91.0 ± 0.6)

1132.3 ± 54.5

(92.1 ± 4.0)

2.4 ± 1.25

4.7 ± 0.5

 5–10 CFU/mL

1662.3 ± 811.9

5384.7 ± 2655.6

90.5 ± 4.4

95.9 ± 1.4

2221.4 ± 108.9

(92.2 ± 0.4)

1197.1 ± 26.6

(88.2 ± 0.2)

0.7 ± 0.4

1.1 ± 0.6

 1–5 CFU/mL

392.7 ± 306.8

4521.3 ± 1701.9

94.9 ± 1.2

96.9 ± 0.2

2519.2 ± 71.8

(89.1 ± 3.6)

1148.9 ± 12.2

(87.8 ± 0.1)

0.2 ± 0.1

0.9 ± 0.3

Staphylococcus aureus

 50–100 CFU/mL

1224.7 ± 320.6

2963.0 ± 1279.6

98.9 ± 3.6

99.7 ± 0.1

1947.7 ± 117.3

(90.6 ± 0.4)

1336.5 ± 12.6

(89.0 ± 0.2)

0.8 ± 0.21

0.9 ± 0.4

 5–10 CFU/mL

98.0 ± 64.4

96.0 ± 42.8

96.2 ± 3.1

95.1 ± 1.8

2496.2 ± 390.1

(85.7 ± 6.0)

687.2 ± 21.2

(93.6 ± 2.3)

0.06 ± 0.04

0.02 ± 0.01

 1–5 CFU/mL

4.0 ± 2.6

34.0 ± 18.6

17.4 ± 3.2

98.6 ± 1.4

1892.7 ± 17.9

(91.6 ± 0.7)

797.1 ± 83.8

(94.7 ± 1.7)

0.002 ± 0.001

0.005 ± 0.002

Klebsiella pneumoniae

 50–100 CFU/mL

377.7 ± 192.4

4268.7 ± 1452.8

94.6 ± 1.6

99.3 ± 0.6

2481.8 ± 587.2

(92.0 ± 1.3)

1379.9 ± 55.6

(89.5 ± 0.4)

0.06 ± 0.02

2.7 ± 1.5

 5–10 CFU/mL

39.3 ± 31.1

479.3 ± 213.7

21.4 ± 6.7

98.9 ± 1.1

2219.5 ± 263.7

(92.5 ± 1.6)

1262.6 ± 50.3

(88.7 ± 0.2)

0.003 ± 0.002

0.1 ± 0.05

 1–5 CFU/mL

4.7 ± 3.3

382.3 ± 152.7

5.5 ± 4.1

95.3 ± 4.6

2345.9 ± 31.8

(93.9 ± 0.1)

1216.5 ± 49.6

(88.5 ± 0.4)

0.0007 ± 0.0

0.07 ± 0.03

Enterococcus faecalis

 50–100 CFU/mL

393.7 ± 125.4

268.0 ± 29.3

97.2 ± 0.8

97.9 ± 1.0

2350.3 ± 138.9

(91.3 ± 0.6)

1161.3 ± 66.7

(92.1 ± 4.0)

0.26 ± 0.07

0.04 ± 0.02

 5–10 CFU/mL

5.4 ± 4.8

78.0 ± 38.0

44.5 ± 29.4

98.2 ± 1.4

2474.4 ± 181.7

(90.6 ± 0.6)

1091.0 ± 109.9

(97.6 ± 0.3)

0.006 ± 0.005

0.008 ± 0.004

 1–5 CFU/mL

0.0 ± 0

7 ± 1.7

0.0 ± 0

100 ± 0

-

1107.7 ± 377.4

(96.3 ± 1.1)

-

0.002 ± 0.001

  1. Sequencing results obtained in experiments on 1mL and 5mL of blood spiked with 50–100, 10–50 and 1–5 CFU/mL of E. coli, S. aureus, K. pneumoniae and E. faecalis. Total number of reads matching reference = number of reads matching species reference species spiked. Bacteria population relative abundance (%) = abundance of targeted species reads over the total number of taxonomically classified reads obtained. Average bp length of mapped reads to reference (average read coverage (%)) = average length of the reads that matched the reference and percentage of identical nucleotides per read between template and consensus (spiked species). Average coverage to reference (X) = estimated depth of coverage taking into account the number of reads matching the reference and their average length. Data are means ± SD. n = 3 are biological replicates
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BMC Medical Genomics

ISSN: 1755-8794

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