TABLE 2.
Bacterial species detected in clinical samples by 16S V1-V2 metagenomics and independently confirmed by secondary assaysd
| Confirmed identificationa (no. of isolates) | V1-V2 sufficient for species identification | MiniKraken taxonomic prediction | BLASTn taxonomic prediction (% identity) | Sequence in MiniKraken database | Tick borne | Previously associated with human illness | Mean read count | Median read count | Min read count | Max read count |
|---|---|---|---|---|---|---|---|---|---|---|
| Anaplasma phagocytophilum (498) | Yes | A. phagocytophilum | A. phagocytophilum (100) | Yes | Yes | Yes | 31,864.3 | 29,649.5 | 105 | 153,246 |
| Borrelia burgdorferi (87) | Yes | B. burgdorferi | B. burgdorferi (≥99.7) | Yes | Yes | Yes | 5,868.2c | 3,773.0 | 73 | 46,420 |
| Borrelia hermsii (3) | Yes | B. hermsii | B. hermsii (100) | Yes | Yes | Yes | 33,128.3 | 48,119.0 | 1,729 | 49,537 |
| Borrelia miyamotoi (24) | Yes | B. miyamotoi | B. miyamotoi (≥99.7) | Yes | Yes | Yes | 12,041.9 | 12,552.0 | 277 | 28,158 |
| Borrelia mayonii (15) | Yes | B. mayonii | B. mayonii (100) | Yes | Yes | Yes | 26,614.5 | 20,836.0 | 7,223 | 52,264 |
| Ehrlichia chaffeensis (209) | Yes | E. chaffeensis | E. chaffeensis (100) | Yes | Yes | Yes | 25,603.2 | 19,689.0 | 629 | 118,209 |
| Ehrlichia muris subsp. eauclairensis (6) | Yes | E. muris | E. muris (100) | Yes | Yes | Yes | 23,461.0 | 20,820.0 | 925 | 58,206 |
| Francisella tularensis (1) | Yes | F. tularensis | F. tularensis (100) | Yes | Yes | Yes | NA | NA | NA | 12,295 |
| Rickettsia rickettsii (3) | No | Rickettsia | R. rickettsii/R. peacockii/R. philipii/R. slovaca (100) | Yes | Yes | Yes | 19,474.7 | 27,178.0 | 1,216 | 30,030 |
| Ehrlichia ewingii (25) | Yes | E. chaffeensis | E. ewingii (100) | No | Yes | Yes | 37,312.0 | 35,024.0 | 4,827 | 118,405 |
| Anaplasma sp. (2) | Yes | Anaplasma centrale | Anaplasma sp. (98.2) | No | Yes | No | 24,911.0 | 24,911.0 | 16,295 | 33,527 |
| “Candidatus Borrelia johnsonii” (1) | Yes | Borrelia | Borrelia sp. strain EFL (99.7) | No | Yes | Nob | NA | NA | NA | 14,461 |
| Coxiella burnetii (2) | Yes | C. burnetii | C. burnetii (100) | Yes | No | Yes | 2,987.5 | 2,987.5 | 2,974 | 3,001 |
| Rickettsia typhi (1) | Yes | R. typhi | R. typhi (100) | Yes | No; flea borne | Yes | NA | NA | NA | 1,024 |
| Neorickettsia risticii (1) | Yes | N. risticii | N. risticii (99.7) | Yes | No | No | NA | NA | NA | 8,994 |
| Leptospira interrogans (2) | Yes | L. interrogans | L. interrogans (100) | Yes | No | Yes | 11,776.0 | 11,776 | 21,666 | 1,886 |
| Leptospira kirschneri (12) | Yes | L. interrogans | L. kirschneri (100) | No | No | Yes | 14,682.3 | 13,200.5 | 5,380 | 27,940 |
| Leptospira noguchii (1) | Yes | Leptospira | L. noguchii (100) | No | No | Yes | NA | NA | NA | 11,587 |
| Rickettsia-like (3) | Yes | Rickettsia | Rickettsia raoultii (97.9) | No | Unknown | No | 22,113.3 | 30,499.0 | 3,484 | 32,357 |
a
All species designations were independently validated by confirmatory assays.
b
Same specimen reported in reference 14.
c
The mean read counts for B. burgdorferi-positive blood (n = 64), synovial fluid (n = 22), and CSF (n = 1) were 5,523.9, 6,919.9, and 4,763.0, respectively.
d
NA, not applicable.