TABLE 1.
Characteristics of data setsa
| Type of samples | Age |
N (individuals) |
N (samples) |
Sequencing information | Culture results | Disease | Origin | Reference |
|---|---|---|---|---|---|---|---|---|
| NP | 2 mo | 223 | 223 | 2 × 150 bp paired-end sequencing; Illumina HiSeq; 11.4 Gb (mean) | 119 of 221 (54%; SP), 69 of 222 (31%; HI), 75 of 222 (33%; MC) 92 of 222 (41; SA) |
H | BD | (18) |
| NP | 4 mo | 199 | 199 | 2 × 150 bp paired-end sequencing; Illumina HiSeq; 11.4 Gb (mean) | 129 of 198 (65%; SP), 93 of 198 (47%; HI), 75 of 198 (38%; MC) 30 of 198 (15%; SA) |
H | BD | (18) |
| OP | <4 yr | 15 | 96 | NovaSeq 6000 PE150; 10 G of raw data per sample | 26 (27%; HI), 38 (40%; SA), 5 (5%; PA) |
CF | CH | This study |
| OP | 4–6 yr | 15 | 87 | NovaSeq 6000 PE150; 10 G of raw data per sample | 31 (36%; HI), 36 (41%; SA), 5 (6 %; PA) |
CF | CH | This study |
| OP | 6–8 yr | 14 | 60 | NovaSeq 6000 PE150; 10 G of raw data per sample | 19 (32%; HI), 34 (57%; SA), 1 (2%; PA) |
CF | CH | This study |
| OP | >8 yr | 8 | 16 | NovaSeq 6000 PE150; 10 G of raw data per sample | 8 (50%; HI), 15 (94%; SA) |
CF | CH | This study |
a
The total number of samples with available cultures from the NP samples are: M. catarrhalis (MC) (N = 378), H. influenzae (HI) (N = 380), S. pneumoniae (SP) (N = 377), and S. aureus (SA) (N = 375). Pseudomonas aeruginosa (PA) was only cultured for OP samples. For 1 OP sample, age was not available. Healthy individuals (H) and individuals with cystic fibrosis (CF) were included from Bangladesh (BD) and Switzerland (CH), respectively. Individuals were aged from 2 mo up to 10 yr.