TABLE 3.
Pathogen Detection in Nasopharyngeal/Oropharyngeal Specimens Among Cases and Controls—PERCH, Thailand, 2012–2013
| All Cases (N = 223) | CXR+ Cases (N = 98) | Controls (N = 657) | Adjusted OR (95% CI)a | ||
|---|---|---|---|---|---|
| All Cases vs. Controls | CXR+ Cases vs. Controls | ||||
| Any pathogen | 215 (96.4) | 97 (99.0) | 634 (96.5) | 0.90 (0.34, 2.43) | 2.97 (0.38, 23.56) |
| Median (IQR) number of organisms | 3.0 (2.0, 4.0) | 3.0 (2.0, 4.0) | 3.0 (2.0, 4.0) | ||
| Bacteria | |||||
| Any bacteria | 191 (85.7) | 86 (87.8) | 587 (89.3) | ||
| Streptococcus pneumonia | |||||
| Any positivity | 121 (54.3) | 59 (60.2) | 406 (61.8) | 0.74 (0.51, 1.07) | 0.95 (0.56, 1.63) |
| ≥6.9 log10 copies/mL | 3 (1.3) | 2 (2.0) | 8 (1.2) | 0.71 (0.13, 3.84) | 1.19 (0.16, 9.01) |
| PCV13-typeb | 3 (1.3) | 2 (2.0) | 6 (0.9) | 1.15 (0.14, 9.30) | 2.60 (0.22, 31.20) |
| Non PCV13-typeb | 1 (0.4) | 1 (1.0) | 3 (0.5) | 0.36 (0.01, 9.36) | 0.22 (0.01, 9.38) |
| Haemophilus influenza | |||||
| Non-b | 74 (33.2) | 29 (29.6) | 262 (39.9) | 0.83 (0.58, 1.20) | 0.65 (0.38, 1.13) |
| Non-b ≥ 5.9 log10 copies/mL | 20 (9.0) | 7 (7.1) | 70 (10.7) | 1.21 (0.69, 2.13) | 1.01 (0.43, 2.41) |
| Type b | 5 (2.2) | 3 (3.1) | 15 (2.3) | 0.80 (0.23, 2.73) | 1.57 (0.35, 7.01) |
| Type b ≥ 5.9 log10 copies/mL | 0 (0) | 0 (0) | 0 (0) | — | — |
| Staphylococcus aureus | 27 (12.1) | 14 (14.3) | 107 (16.3) | 0.69 (0.41, 1.15) | 0.81 (0.41, 1.62) |
| Chlamydia pneumoniae | 0 (0) | 0 (0) | 1 (0.2) | 0.00 (0.00, >999) | 0.00 (0.00, >999) |
| Moraxella catarrhalis | 101 (45.3) | 44 (44.9) | 362 (55.1) | 0.71 (0.50, 1.01) | 0.72 (0.44, 1.19) |
| Mycoplasma pneumoniae | 10 (4.5) | 6 (6.1) | 20 (3.0) | 1.23 (0.51, 2.98) | 1.90 (0.64, 5.66) |
| Salmonella species | 0 (0) | 0 (0) | 2 (0.3) | 0.00 (0.00, >999) | 0.00 (0.00, >999) |
| Legionella | 0 (0) | 0 (0) | 0 (0) | — | — |
| Bordetella pertussis | 0 (0) | 0 (0) | 3 (0.5) | 0.00 (0.00, >999) | 0.00 (0.00, >999) |
| Fungi | |||||
| Pneumocystis jirovecii | 5 (2.2) | 3 (3.1) | 32 (4.9) | 0.52 (0.19, 1.44) | 0.73 (0.20, 2.66) |
| P. jirovecii ≥4 log10 copies/mL | 0 (0) | 0 (0) | 7 (1.1) | 0.00 (0.00, >999)c | 0.00 (0.00, >999)c |
| Viruses | |||||
| Any virus | 190 (85.2) | 88 (89.8) | 540 (82.2) | ||
| Adenovirus | 31 (13.9) | 13 (13.3) | 140 (21.3) | 0.72 (0.45, 1.15) | 0.68 (0.34, 1.34) |
| CMV | 103 (46.2) | 41 (41.8) | 402 (61.2) | 0.57 (0.39, 0.83) | 0.54 (0.32, 0.92) |
| CMV ≥4.9 log10 copies/mL | 30 (13.5) | 10 (10.2) | 110 (16.7) | 0.64 (0.38, 1.07) | 0.35 (0.16, 0.79) |
| Coronavirus 43 | 7 (3.1) | 3 (3.1) | 13 (2.0) | 2.71 (1.01, 7.26) | 2.26 (0.57, 9.02) |
| Coronavirus 63 | 3 (1.3) | 1 (1.0) | 12 (1.8) | 1.25 (0.33, 4.64) | 0.92 (0.11, 7.53) |
| Coronavirus HKU | 0 (0) | 0 (0) | 2 (0.3) | 0.00 (0.00, >999) | 0.00 (0.00, >999) |
| Coronavirus 229 | 0 (0) | 0 (0) | 2 (0.3) | 0.00 (0.00, >999) | 0.00 (0.00, >999) |
| HBOV | 40 (17.9) | 17 (17.3) | 123 (18.7) | 1.07 (0.68, 1.68) | 1.21 (0.64, 2.29) |
| HMPV A/B | 8 (3.6) | 4 (4.1) | 10 (1.5) | 3.67 (1.35, 9.92) | 4.08 (1.14, 14.56) |
| Influenza A | 4 (1.8) | 1 (1.0) | 0 (0) | >999 (0.00, >999)d | >999 (0.00, >999)d |
| Influenza B | 3 (1.3) | 1 (1.0) | 2 (0.3) | 9.54 (1.51, 60.18) | 7.57 (0.63, 91.10) |
| Influenza C | 0 (0) | 0 (0) | 0 (0) | — | — |
| Parainfluenza 1 | 5 (2.2) | 1 (1.0) | 2 (0.3) | 12.53 (2.28, 68.82) | 8.34 (0.70, 98.93) |
| Parainfluenza 2 | 0 (0) | 0 (0) | 1 (0.2) | 0.00 (0.00, >999) | 0.00 (0.00, >999) |
| Parainfluenza 3 | 6 (2.7) | 3 (3.1) | 15 (2.3) | 1.94 (0.71, 5.28) | 2.48 (0.67, 9.21) |
| Parainfluenza 4 | 2 (0.9) | 1 (1.0) | 9 (1.4) | 1.10 (0.22, 5.42) | 1.21 (0.15, 10.05) |
| PV/EV | 21 (9.4) | 7 (7.1) | 57 (8.7) | 1.47 (0.82, 2.64) | 0.94 (0.39, 2.27) |
| Rhinovirus | 43 (19.3) | 15 (15.3) | 93 (14.2) | 2.30 (1.48, 3.57) | 1.57 (0.82, 3.01) |
| RSV | 51 (22.9) | 30 (30.6) | 19 (2.9) | 13.91 (7.66, 25.25) | 20.48 (10.17, 41.26) |
aOR adjusted for age (months). ORs for individual pathogens also adjusted for all other pathogens.
bPneumococcal serotypes were determined by PCR deduction followed by Quellung reaction if the results were mixed or ambiguous.
cFisher exact test P value is 0.201 for all cases versus controls and 0.604 for CXR+ cases versus controls.
dFisher exact test P value is 0.004 for all cases versus controls and 0.253 for CXR+ cases versus controls.
PERCH indicates Pneumonia Etiology Research for Child Health; OR, odds ratio; CXR+, chest Radiograph positive; CMV, cytomegalovirus; HBOV, human bocavirus; HMPV, human metapneumovirus; PV/EV, parechovirus/enterovirus; RSV, respiratory syncytial virus.
Bold indicates significance of P < 0.05.