Table 2.
Bacterial Identification Results for Twelve Bronchoalveolar Lavage (BAL) Samples by Standard Culture Methods and Culture-Independent Pyrosequencinga–c
| BAL sample no. | Culture results (cfu) | Species by 454 pyrosequencing (% sequences) | Phylum by 454 pyrosequencing(% sequences) | Antibiotic treatment |
|---|---|---|---|---|
| 1 | Klebsiella pneumoniae (1) |
Staphylococcus aureus (99.6) Streptococcus spp. (0.2) |
Firmicutes (99.94) | Ticarcillin–clavulanic acid and piperacillin–tazobactam |
| 2 |
Klebsiella oxytoca (100,000) Haemophilus influenzae (100,000) Respiratory tract flora (20,000) |
Streptococcus spp. (41.3) Streptococcus anginosus (15.5) |
Firmicutes (72.7) Proteobacteria (20.8) |
|
| 4 | Haemophilus influenzae (50,000) |
Haemophilus spp. (58.22) Haemophis influenza (36.7) |
Proteobacteria (97.7) | |
| 6 | None |
Mycoplasma spp. (89.6) Prevotella spp. (3.3) |
Tenericutes (89.8) | |
| 7 | Respiratory tract flora (25,000) |
Klebsiella spp. (35.2) Stenotrophomonas maltophilia (28.8) |
Proteobacteria (97.4) | |
| 8 |
Enterobacter cloacae (100,000) Pseudomonas aeruginosa (20,000) |
Methylomicrobium spp. (8.97) Staphylococcus aureus (7.6) |
Proteobacteria (46.1) Firmicutes (26.6) |
Piperacillin–tazobactam and vancomycin |
| 9 |
Klebsiella pneumoniae (100,000) Stenotrophomonas maltophilia (100,000) |
Haemophilus influenza (42.2) Haemophilus spp. (32.7) |
Proteobacteria (77.7) Firmicutes (9.3) |
Piperacillin–tazobactam and vancomycin |
| 10 | Staphylococcus aureus (7,000) | Haemophilus influenza (17.9) Haemophilus spp. (14.5) | Proteobacteria (48.3) Firmicutes (30.1) |
Sulfamethoxazole–trimethoprim |
| 11 |
Streptococcus pneumoniae (50,000) Haemophilus influenzae (100,000) |
Staphylococcus aureus (13.5) Ruminococcus spp. (7.5) |
Firmicutes (44.8) Proteobacteria (37.6) |
|
| 13 | Enterobacter aerogenes (100,000) | Haemophilus influenza (39.2) Haemophilus spp. (26.9) | Proteobacteria (76.3) Tenericutes (19.7) |
Vancomycin |
| 14 | None |
Mycoplasma spp. (69.0) Klebsiella spp. (9.5) |
Tenericutes (69.1) Proteobacteria (30.9) | Vancomycin, ticarcillin–clavulanic acid, and piperacillin–tazobactam |
| 15 | Staphylococcus aureus (50,000) |
Pseudomonas spp. (91.6) Pseudomonas aeruginosa (6.4) |
Proteobacteria (98.4) |
a
Estimated number of colony-forming units (cfu) is listed in parentheses for standard culture.
b
Percent of pyrosequences identified in each sample is denoted by the appropriate taxonomic designation.
c
Antibiotic column denotes type of antibiotic treatment (if any) that was given before BAL.