Table 2. Metagenomic sequencing results used for detection of bacterial zoonotic pathogens among febrile patients, Tanzania, 2007–2009*.
| Organism | V1–V2 sufficient for species ID | MiniKraken taxonomic prediction† | BLASTn taxonomic prediction (% identity)‡ | Sequence in database | Read count | % Abundance |
|---|---|---|---|---|---|---|
| Bartonella quintana | Y | B. quintana | B. quintana AP019773.1 (100) | Y | 4,730 | 98.21 |
|
B. quintana
|
Y |
B. quintana
|
B. quintana AP019773.1 (100) |
Y |
3,568 |
38.60 |
|
Coxiella burnetii
|
Y |
C. burnetii
|
C. burnetii CP014563.1 (100) |
Y |
1,795 |
47.97 |
|
Leptospira borgpetersenii
|
Y |
L. borgpetersenii
|
L. borgpetersenii CP047520.1 (100) |
Y |
18,903 |
94.41 |
|
L. kirschneri
|
Y |
Leptospira spp. |
L. kirschneri CP092660.1 (100) |
N |
28,008 |
99.32 |
|
Rickettsia conorii
|
Y |
Rickettsia spp. |
R. conorii MG564258.1 (100) |
N |
159 |
28.29 |
| R. typhi | Y | Rickettsia typhi | R. typhi LS992663.1 (100) | Y | 429 | 47.72 |
| R. typhi | Y | Rickettsia typhi | R. typhi LS992663.1 (100) | Y | 7,274 | 82.02 |
|
R. typhi
|
Y |
Rickettsia typhi
|
R. typhi LS992663.1 (100) |
Y |
9,527 |
83.16 |
| Candidatus Neoehrlichia spp. | Y | Anaplasmataceae, Ehrlichia ruminantium, Ehrlichia | Uncultured Candidatus Neoehrlichia sp. SA1 OP208838.1 (100) | N | 40,238 | 98.56 |
*ID, identification; V1–V2, variable regions 1 and 2. †Johns Hopkins University Center for Computational Biology (https://ccb.jhu.edu/software/kraken). ‡National Center for Biotechnology Information taxonomy and accession nos. from BLASTn (https://blast.ncbi.nlm.nih.gov).