Table 2.
Prevalence (%) of bacteria and viruses detected by quantitative PCR
| Respiratory pathogen | Positive carriage |
|||
|---|---|---|---|---|
| Nasal specimen, n (%) | Pharyngeal specimen, n (%) | p-value | Nasal or pharyngeal, n (%) | |
| Total | 476 (100)a | 474 (100)a | 477 (100)a | |
| Bacteria | 105 (22.1) | 280 (59.1) | <0.0001 | 313 (65.6) |
| Haemophilus influenzae | 46 (9.8) | 266 (56.4) | <0.0001 | 280 (58.7) |
| Klebsiella pneumoniae | 17 (3.5) | 20 (4.2) | 0.61 | 35 (7.3) |
| Staphylococcus aureus | 28 (5.9) | 12 (2.5) | <0.001 | 35 (7.3) |
| Streptococcus pneumoniae | 33 (7.0) | 36 (7.6) | 0.69 | 59 (12.4) |
| Virus | 34 (7.1) | 24 (5.1) | 0.18 | 51 (10.8) |
| Influenza A virus | 4 (0.8) | 4 (1.0) | – | 7 (1.5) |
| Influenza B virus | 4 (0.8) | 6 (1.3) | – | 7 (1.5) |
| Human rhinovirus | 20 (4.3) | 7 (1.5) | <0.001 | 25 (5.3) |
| Human respiratory syncytial virus | 1 (0.2) | 2 (0.4) | – | 3 (0.6) |
| Human metapneumovirus | 0 (0) | 0 (0) | – | 0 (0) |
| Human coronavirus | 5 (1.1) | 5 (1.1) | 0.99 | 10 (2.1) |
| HCoV-HKU1 | 0 (0) | 1 (0.2) | – | 1 (0.2) |
| HCoV-E229 | 3 (0.6) | 1 (0.2) | – | 4 (0.8) |
| HCoV-NL63 | 1 (0.2) | 0 (0) | – | 1 (0.2) |
| HCoV-OC43 | 1 (0.2) | 3 (0.6) | – | 4 (0.8) |
| Human para-influenza virus | 0 (0) | 1 (0.2) | – | 1 (0.2) |
a
A total of 473 participants had both nasal and pharyngeal sampling; three participants had only nasal swabs and one had only pharyngeal swabs. Participants having at least one nasal or pharyngeal positive sample were considered positive cases.