Table 3.
Number of samples in which each taxon was the most abundant by 16S rRNA read counts, separated by diagnostic group, with number of corresponding positive cultures in parentheses
| Predominant Taxon | No. Most Abundant by 16S rRNA Read Counts (No. identified by culture) |
||
|---|---|---|---|
| Cystic Fibrosis [n = 26] | Immunocompromised [n = 22] | Nonimmunocompromised [n = 29] | |
|
Routinely reported by microbiology laboratory | |||
| Staphylococcus sp. | 12 (12) | 9 (2) | 5 (0) |
| Delftia sp. | — | 1 (0) | — |
| Achromobacter sp. | 1 (1) | — | — |
| Stenotrophomonas sp. | 8 (8) | — | 1 (1) |
| Pseudomonas sp. | 1 (1) | 1 (0) | — |
| Proteus sp. | 1 (1) | — | — |
| Haemophilus sp. | 2 (1) | 3 (1) | 4 (2) |
| Streptococcus sp. | 0 | 2 (0) | 6 (1) |
|
Not routinely reported by microbiology laboratory | |||
| Neisseria subflava | — | 1 (0) | 3 (0) |
| Actinobacillus parahaemolyticus | — | — | 2 (0) |
| Corynebacterium sp. | — | 2 (0) | — |
| Prevotella spp. (2 OTUs) | 1 (0) | — | 1 (0) |
| Bacteroides sp. | — | — | 1 (0) |
| Pantoea agglomerans | — | — | 1 (0) |
| Granulicatella sp. | — | — | 1 (0) |
| Chryseobacterium sp. | — | — | 1 (0) |
| Acinetobacter rhizosphaerae | — | — | 1 (0) |
| Fusobacterium sp. | — | 1 (0) | — |
| Not identified to genus level | — | 2 (0) | 2 (0) |
Definition of abbreviation: OTU = operational taxonomic unit.
The total numbers of samples analyzed in each diagnostic group are listed in square brackets. Organisms “not routinely reported by microbiology laboratory” are those that are not reported in respiratory culture by our clinical laboratory.