Table 1 Median cycle threshold (Ct) values and interquartile range (IQR) for microbes identified in throat and nasal swab samples. Non-acute samples were collected from Royal Thai Army barracks trainees at the start (R0) and at the end (RF) of each 10-week training period. Acute samples were collected from trainees who developed acute upper respiratory tract infection during follow-up. Percentages indicate the proportion of collected samples positive for each organism
|  | Non-acute (n = 312) | Acute (n = 145) | p-valuea | |||||||
|---|---|---|---|---|---|---|---|---|---|---|
R0 (n = 210) | RF (n = 102) | |||||||||
% (n) | Median Ct | IQR | % (n) | Median Ct | IQR | % (n) | Median Ct | IQR | ||
Bacteria | ||||||||||
 H. influenzae B | 83.8 (176) | 28.3 | 26.5–29.6 | 65.7 (67) | 29.7 | 28.6–31.4 | 64.8 (94) | 29.4 | 28.0–31.3 | 0.297 |
 H. influenzae non-B | 31.9 (67) | 30.2 | 28.4–31.1 | 73.5 (75) | 24.9 | 22.1–27.1 | 56.6 (82) | 26.7 | 22.0–29.0 | < 0.001 |
 S. pneumoniae | 8.1 (17) | 29.6 | 27.7–30.7 | 34.3 (35) | 28.0 | 26.1–31.0 | 15.2 (22) | 27.1 | 26.5–29.2 | 0.706 |
 K. pneumoniae | 14.3 (30) | 31.2 | 28.3–32.7 | 9.8 (10) | 29.0 | 26.8–32.0 | 15.9 (23) | 31.4 | 29.7–32.3 | 0.706 |
 S. aureus | 10.5 (22) | 31.3 | 30.4–32.5 | 9.8 (10) | 31.4 | 31.1–32.2 | 6.2 (9) | 31.1 | 30.6–31.6 | 0.739 |
 M. catarrhalis | 2.4 (5) | 30.6 | 27.7–31.5 | 3.9 (4) | 32.6 | 32.2–32.8 | 6.2 (9) | 29.7 | 29.5–31.5 | 0.564 |
 L. pneumophila | 2.4 (5) | 32.1 | 31.4–32.4 | 2.0 (2) | 31.3 | 30.3–32.4 | 2.8 (4) | 32.5 | 31.2–32.8 | 0.317 |
Viruses | ||||||||||
 Rhinovirus | 1.9 (4) | 30.6 | 28.6–31.8 | 15.7 (16) | 30.2 | 27.2–31.7 | 26.9 (39) | 28.9 | 26.9–31.4 | < 0.001 |
 Adenovirus | 0.5 (1) | 27.2 | 27.2–27.2 | 9.8 (10) | 30.5 | 29.6–31.4 | 2.8 (4) | 29.3 | 27.0–31.0 | 0.083 |
 Influenza B | 0 (0) | – | – | 0 (0) | – | – | 9.7 (14) | 25.4 | 23.6–31.2 | – |
 Coronavirus 229 | 1 (2) | 23.1 | 18.2–28.0 | 2.0 (2) | 29.3 | 27.2–31.5 | 4.8 (7) | 26.9 | 25.2–31.3 | 0.034 |
 Enterovirus | 0.5 (1) | 30.7 | 30.7–30.7 | 4.9 (5) | 30.2 | 30.1–30.3 | 0 (0) | – | – | – |
 Coronavirus 63 | 1 (2) | 28.5 | 24.5–32.4 | 1.0 (1) | 30.0 | 30.0–30.0 | 1.4 (2) | 22.6 | 21.9–23.3 | 0.157 |
 Coronavirus HKU | 0.5 (1) | 30.0 | 30.0–30.0 | 0 (0) | – | – | 2.1 (3) | 32.2 | 31.6–32.9 | – |
 Parainfluenza 2 | 0.5 (1) | 17.4 | 17.4–17.4 | 1.0 (1) | 25.3 | 25.3–25.3 | 1.4 (2) | 23.3 | 20.1–26.5 | 0.564 |
 Parainfluenza 4 | 0.5 (1) | 32.0 | 32.0–32.0 | 0 (0) | – | – | 1.4 (2) | 30.3 | 30.0–30.6 | 0.317 |
 Coronavirus 43 | 0.5 (1) | 28.1 | 28.1–28.1 | 0 (0) | – | – | 0.7 (1) | 32.6 | 32.6–32.6 | – |
 Bocavirus | 0.5 (1) | 17.4 | 17.4–17.4 | 0 (0) | – | – | 0 (0) | – | – | – |
 Influenza A | 0 (0) | – | – | 0 (0) | – | – | 0.7 (1) | 29.9 | 29.9–29.9 | – |