blood culture malaria thick blood smear prior antibiotics ... - PLOS

Supplemental table S1. Detailed results of survival, malaria diagnosis, use of prior antibiotics, blood volume used for DNA extraction, blood culture, and replicated (run 1 and run 2) 16S metagenomics for the 75 patients.

patient MCMA429 MCMA430 MCMA431 MCMA433 MCMA434 MCMA435 MCMA436 MCMA437 MCMA440 MCMA441 MCMA442 MCMA443 MCMA444 MCMA445 MCMA446 MCMA447 MCMA448 MCMA449 MCMA451 MCMA452 MCMA453 MCMA455 MCMA458 MCMA459 MCMA460 MCMA462 MCMA463 MCMA464 MCMA465 MCMA466 MCMA468 MCMA469 MCMA470 MCMA472 MCMA473 MCMA474 MCMA475 MCMA476 MCMA477 MCMA478 MCMA480 MCMA484 MCMA489 MCMA491 MCMA493 MCMA495 MCMA497 MCMA501 MCMA502 MCMA513 MCMA515 MCMA516 MCMA520 MCMA521 MCMA523 MCMA526 MCMA528 MCMA532 MCMA533 MCMA534 MCMA535 MCMA537 MCMA547 MCMA550 MCMA557 MCMA560 MCMA562 MCMA564 MCMA565 MCMA566 MURB082 MURB083 MURB085 MURB088 MURB095

survival no yes yes yes yes yes unknown yes yes yes yes yes no yes yes yes yes yes yes yes no no yes yes unknown yes no yes no yes yes yes yes yes yes yes yes yes yes yes yes no yes yes yes yes yes yes yes yes yes yes yes yes yes no no yes no yes yes no yes no no yes yes no yes no yes yes yes yes yes

malaria yes yes yes yes no yes no no no no yes yes yes no yes yes yes yes yes yes no no no no yes yes no yes yes yes no no no yes no yes no no yes yes no no yes yes yes yes yes yes yes yes no yes no yes yes yes no no yes yes no yes no yes no yes yes no no no yes no yes yes yes

malaria thick blood smear pos pos pos pos neg pos neg neg neg neg pos neg neg neg neg pos pos neg pos pos neg neg neg neg neg neg neg neg neg pos neg neg neg pos neg pos neg neg pos neg neg neg pos neg pos pos pos pos pos pos neg pos neg neg pos neg neg neg pos neg neg neg neg pos neg pos pos neg neg neg pos neg pos pos pos

malaria SD Bioline Pf RDT pos pos pos pos neg pos neg neg neg neg pos pos pos neg pos pos pos pos pos pos neg neg neg neg pos pos neg pos pos pos neg neg neg pos neg pos neg neg pos pos neg neg pos pos pos pos pos pos pos pos neg pos neg pos pos pos neg neg pos pos neg pos neg pos neg pos neg neg neg neg pos neg pos pos pos

prior antibiotics neg pos neg pos pos neg neg pos pos neg neg neg neg pos neg pos neg neg neg neg neg pos neg pos pos neg pos pos pos neg pos pos pos neg pos pos pos neg neg pos neg neg neg neg neg neg neg neg neg neg neg neg neg pos neg pos pos neg neg pos neg pos pos neg neg neg neg neg neg pos neg neg neg neg neg

µl blood extracted 400 600 750 200 200 700 1000 500 300 400 500 300 700 550 600 750 600 300 450 750 300 350 300 750 200 300 750 350 500 350 750 600 800 400 450 650 600 550 1000 1000 1000 400 250 700 350 300 650 650 350 500 700 450 900 250 1000 200 400 1000 500 800 650 650 500 400 350 350 250 350 600 450 350 250 250 500 550

bBSI based on culture and/or two 16S metagenomics runs no no no possible yes yes yes no no no no possible yes no yes no no yes possible yes no yes no no possible no no no yes yes no possible no no possible no no yes no no yes no no no yes no no no no possible yes no yes no no yes yes no no no yes no yes no yes no no no yes yes possible no possible no no

blood culture

16S metagenomics

bacterium

bacterium 1 Acinetobacter parvus

reads run1 2

reads run2 1

Haemophilus influenza

Prevotella spp Streptococcus pseudopneumoniae Escherichia coli Haemophilus influenzae

20 123 21942 7

Salmonella Enteritidis

Corynebacterium mycetoides Salmonella enterica

Escherichia coli

Salmonella enteritidis

Salmonella Typhimurium

Staphylococcus aureus

bacterium 2

reads run1

reads run2

bacterium 3

reads run1

reads run2

bacterium 4

reads run1

reads run2

7 2 0 2

Shigella flexneri Salmonella enterica

7977 2

0 1

1 17869

1 5716

Enterobacter aerogenes Enterobacter cloacae

1 37

1 148

Salmonella enterica

5

4

Escherichia coli

4

3

Salmonella enterica Aeromonas media Salmonella enterica

2 5 6

1 1 1

Morganella morganii

24

4

Salmonella enterica

77071

35902

Enterobacter cloacae

154

711

Klebsiella spp.

2

2

Pantoea agglomerans

2

9

Enterobacter aerogenes

4

4

Salmonella enterica Salmonella enterica

102 5

39 1

Aeromonas media

3

1

Enterobacter aerogenes

9

2

Corynebacterium segmentosum

2

5

Enterobacter aerogenes

3

6

Prevotella spp

1

7

Salmonella enterica

7

3

Staphylococcus aureus

2

2

Salmonella enterica

7

3

Yersinia enterocolitica

2

1

Bordetella pertussis

5

6

Escherichia coli Escherichia coli

38 166

18 115

Shigella flexneri Shigella flexneri

10 48

4 34

Shigella sonnei Shigella sonnei

1 23

1 11

Enterobacter aerogenes Shigella dysenteriae

7 5

1 2

Neisseria meningitidis

7

4

Neisseria polysaccharea

7

2

Streptococcus pneumoniae Enterobacter aerogenes

173 4

11 5

Enterobacter aerogenes

9

5

Streptococcus pseudopneumoniae

90

19

reads run1

reads run2

6

8

Salmonella

Escherichia coli Escherichia coli

Neisseria meningitidis

Neisseria meningitidis

Streptococcus pneumoniae

Rickettsia bellii