Pneumonia [1] | Pleural Effusions alone [2] | ALRI with sequelae [3] | ALRI with normal CXR [4] | P values from comparisons between group [1], [2], [3] and [4] by Chi-squared or adjusted Chi-squared test | ||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
Grand total | Total | Cavitations [1a] | No cavitations[1b] | n (%) | n (%) | n (%) | [1a] vs. [1b] | [1] vs.[2] | [1] vs.[3] | [1] vs. [4] | [3] vs. [4] | |
1904 (%) | 959 (50.4) | 289 (30.1) | 670 (69.9) | 169 (8.9) | 455 (24.3) | 321 (17.1) | ||||||
Median age in years (IQR*) | 53 (38–65) | 51 | 50 | 52 (35–65) | 52 (40–66) | 60 (51–70) | 44 (17–59) | NS | NS | <0.001 | <0.001 | <0.001 |
Mean age in years | 50.0 | 48.6 | 49.3 | 48.3 | 51.0 | 59.0 | 40.5 | NS | NS | <0.001 | <0.001 | <0.001 |
Age groups in years | ||||||||||||
5-14 | 154 (8.1%) | 82 (8.6) | 0 (0.0) | 82 (12.2) | 3 (1.8) | 1 (0.2) | 68 (21.2) | <0.001 | <0.001 | <0.001 | <0.001 | <0.001 |
15 - 49 | 659 (34.6%) | 368 (38.4) | 144 (49.8) | 224 (33.4) | 72 (42.6) | 97 (21.3) | 122 (38.0) | <0.001 | NS | <0.001 | NS | <0.001 |
≥50 | 1091 (57.3) | 509 (53.1) | 145 (50.2) | 364 (54.3) | 94 (55.6) | 357 (78.5) | 131 (40.8) | 0.249 | NS | <0.001 | <0.001 | <0.001 |
Gender, male (%) | 941 (49.4) | 502 (52.3) | 157 (54.3) | 345 (51.5) | 90 (53.3) | 205 (45.1) | 144 (44.9) | NS | NS | 0.011 | 0.026 | NS |
Signs and symptoms on admission | ||||||||||||
Wheezing | 261 (13.9) | 105 (11.1) | 13 (4.5) | 92 (14.0) | 3 (1.8) | 50 (11.0) | 103 (32.8) | <0.001 | <0.001 | NS | <0.001 | <0.001 |
Dry cough | 519 (27.3) | 229 (23.9) | 39 (13.5) | 190 (28.4) | 111 (65.7) | 66 (14.5) | 113 (35.2) | <0.001 | <0.001 | <0.001 | <0.001 | <0.001 |
Time interval between presentation and symptoms onset in days (# of missing values = 112) | ||||||||||||
Median (IQR) | 6 (4–9) | 6 (4–9) | 7 (4–10) | 5 (4–9) | 6 (4–10) | 6 (4–10) | 4 (4–8) | <0.001 | NS | 0.032 | 0.004 | <0.001 |
Mean | 6.3 | 6.3 | 7.0 | 5.9 | 6. 6 | 6.7 | 5.6 | <0.002 | NS | 0.072 | 0.003 | <0.001 |
Duration of hospital stay in days | ||||||||||||
Median (IQR) | 7 (4–11) | 7 (4–10) | 6 (4–10) | 7 (4–10) | 5 (3–8) | 9 (6–14) | 7 (4–10) | NS | <0.001 | <0.001 | NS | <0.001 |
Mean | 8.4 | 7.9 | 7.8 | 8 | 6.5 | 10.7 | 7.7 | NS | <0.001 | <0.001 | NS | <0.001 |
Reports of medicine use prior to admission | ||||||||||||
No antibiotic used | 932 (48.9) | 455 (47.4) | 116 (40.1) | 339 (50.6) | 103 (60.9) | 211 (46.4) | 163 (50.8) | 0.004 | 0.002 | NS | NS | NS |
Intake of unknown origin | 776 (40.8) | 405 (42.2) | 143 (49.5) | 262 (39.1) | 43 (25.4) | 211 (46.4) | 117 (36.4) | 0.004 | <0.001 | NS | 0.078 | 0.013 |
Antibiotic used | 196 (10.3) | 99 (10.3) | 30 (10.4) | 69 (10.3) | 23 (13.6) | 33 (7.3) | 41 (12.8) | NS | NS | 0.087 | NS | 0.014 |
Patient outcomes | ||||||||||||
Deceased | 61 (3.2) | 43 (4.5) | 6 (2.1) | 37 (5.5) | 5 (3.0) | 11 (2.4) | 2 (0.6) | 0.021 | NS | 0.076 | 0.003 | NS |
Cured or improved | 1264 (66.4) | 572 (59.6) | 117 (40.5) | 455 (67.9) | 79 (46.7) | 321 (70.5) | 292 (91.0) | <0.001 | 0.002 | <0.001 | <0.001 | <0.001 |
Transferred | 482 (25.3) | 297 (31.0) | 154 (53.3) | 143 (21.3) | 82 (48.5) | 89 (19.6) | 14 (4.4) | <0.001 | <0.001 | <0.001 | <0.001 | <0.001 |
Escaped | 97 (5.1) | 47 (4.9) | 12 (4.2) | 35 (5.2) | 3 (1.8) | 34 (7.5) | 13 (4.0) | NS | NS | 0.066 | NS | 0.031 |
Reported co-morbid conditions | ||||||||||||
Cardiovascular disorder | 213 (11.2) | 129 (13.5) | 9 (3.1) | 120 (17.9) | 17 (10.1) | 28 (6.2) | 39 (12.1) | <0.001 | NS | <0.001 | NS | 0.003 |
Diabetes mellitus | 195 (10.2) | 111 (11.6) | 32 (11.1) | 79 (11.8) | 22 (13.0) | 40 (8.8) | 22 (6.9) | NS | NS | NS | 0.023 | NS |
Renal disorder | 136 (7.1) | 80 (8.3) | 25 (8.7) | 55 (8.2) | 8 (4.7) | 33 (7.3) | 15 (4.7) | NS | NS | NS | 0.044 | NS |
Liver disorder | 16 (0.8) | 10 (1.0) | 3 (1.0) | 7 (1.0) | 3 (1.8) | 1 (0.2) | 2 (0.6) | NS | NS | NS | NS | NFS |
Severe cases | 188 (9.9) | 121 (12.6) | 15 (5.2) | 106 (15.6) | 11 (6.5) | 14 (3.1) | 42 (13.1) | <0.001 | 0.032 | <0.001 | NS | <0.001 |
Laboratory results** | ||||||||||||
Leukocytosis (missing values = 12) | 663 (34.8) | 399 (41.9) | 120 (41.7) | 279 (42.2) | 42(25.3) | 133 (29.4) | 89 (27.8) | NS | <0.001 | <0.001 | <0.001 | NS |
Elevated neutrophils count (missing values = 65) | 629 (33.0) | 378 (40.9) | 114 (40.6) | 264 (41.1) | 40 (24.4) | 127 (28.9) | 84 (27.0) | NS | <0.001 | <0.001 | <0.001 | NS |
Lymphocytosis (missing values = 314) | 99 (5.2) | 46 (5.5) | 7 (3.0) | 39 (6.4) | 8 (5.0) | 22 (7.7) | 23 (7.5) | 0.004 | NS | NS | NS | NS |
Patients tested by microbiology method (excluding contaminated samples or cultures) | ||||||||||||
Blood culture | 1695 (89.0) | 862 (89.9) | 264 (91.3) | 598 (89.3) | 149 (88.2) | 412 (90.5) | 272 (84.7) | NS | NS | NS | 0.015 | 0.012 |
Sputum culture | 888 (46.6) | 464 (48.4) | 185 (64.0) | 279 (41.6) | 37 (21.9) | 270 (59.3) | 117 (36.4) | <0.001 | <0.001 | <0.001 | 0.002 | <0.001 |
Blood or sputum culture | 1789 (94.0) | 905 (94.4) | 280 (96.9) | 625 (93.3) | 152 (89.9) | 437 (96.0) | 295 (91.9) | NS | NS | NS | NS | 0.016 |
Sputum smear for acid-fast bacilli (AFB) | 1682 (88.3) | 850 (88.6) | 280 (96.9) | 570 (85.1) | 140 (82.8) | 434 (95.4) | 258 (80.4) | NS | NS | <0.001 | 0.001 | <0.001 |
Nasopharyngeal/throat swabs by PCR (a) | 1855 (97.4) | 935 (97.5) | 281 (97.2) | 654 (97.6) | 164 (97.0) | 442 (97.1) | 314 (97.8) | NS | NS | NS | NS | NS |
Samples collected for bacterial & AFB etiologies (b) | 1796 (94.3) | 911 (95.0) | 283 (97.9) | 628 (93.7) | 152 (89.9) | 438 (96.3) | 295 (91.9) | NS | NS | NS | NS | 0.008 |
Samples collected for bacterial & viral etiologies (c) | 1747 (91.8) | 887 (92.5) | 275 (95.2) | 612 (91.3) | 147 (87.0) | 425 (93.4) | 288 (89.7) | NS | NS | NS | NS | 0.064 |
Bacterial or viral yield ‡ | ||||||||||||
Positive blood culture | 33 (2.0) | 27 (3.1) | 5 (1.9) | 22 (3.7) | 4 (2.7) | 2 (0.5) | 0 (0.0) | NS | NS | 0.007 | 0.007 | NS |
Positive sputum culture | 272 (30.6) | 138 (29.7) | 44 (23.8) | 94 (33.7) | 8 (21.6) | 95 (35.2) | 31 (26.5) | 0.029 | NS | NS | NS | NS |
Positive blood or sputum culture (d) | 300 (16.8) | 161 (17.8) | 47 (16.8) | 114 (18.2) | 12 (7.9) | 96 (22.0) | 31 (10.5) | NS | 0.003 | 0.079 | 0.007 | <0.001 |
Positive AFB smear (e) | 264 (15.7) | 218 (25.7) | 153 (54.6) | 65 (11.4) | 2 (1.4) | 42 (9.7) | 2 (0.8) | <0.001 | <0.001 | <0.001 | <0.001 | <0.001 |
Positive PCR for viruses (f) | 305 (16.4) | 138 (14.8) | 22 (7.8) | 116 (17.7) | 17 (10.4) | 68 (15.4) | 82 (26.1) | <0.001 | NS | NS | <0.001 | 0.004 |
Bacterial etiologies† | ||||||||||||
H. influenzae | 114 (38.0) | 52 (32.3) | 13 (27.7) | 39 (34.2) | 0 (0.0) | 46 (47.9) | 16 (51.6) | NS | 0.005 | 0.002 | NS | 0.022 |
- In sputum 1 | 114 (41.9) | 52 (37.7) | 13 (29.5) | 39 (41.5) | 0 (0.0) | 46 (48.4) | 16 (51.6) | |||||
- In blood 2 | 1 (3.0) | 1 (3.7) | 1 (20.0) | 0 (0.0) | 0 (0.0) | 0 (0.0) | 0 (0.0) | |||||
S. pneumoniae | 53 (17.7) | 22 (13.7) | 6 (12.8) | 16 (14.0) | 1 (8.3) | 23 (24.0) | 7 (22.6) | NS | NS | 0.009 | NS | NS |
- In sputum 1 | 51 (18.8) | 20 (14.5) | 6 (13.6) | 14 (14.9) | 1 (12.5) | 23 (24.2) | 7 (22.6) | |||||
- In blood 2 | 2 (6.0) | 2 (7.4) | 0 (0.0) | 2 (9.1) | 0 (0.0) | 0 (0.0) | 0 (0.0) | |||||
B. pseudomallei | 28 (9.3) | 25 (15.5) | 10 (21.3) | 15 (13.2) | 1 (8.3) | 1 (1.0) | 1 (3.2) | NS | NS | <0.001 | 0.020 | NS |
- In sputum 1 | 16 (5.9) | 14 (10.1) | 7 (15.9) | 7 (7.4) | 1 (12.5) | 0 (0.0) | 1 (3.2) | |||||
- In blood 2 | 15 (45.5) | 14 (51.9) | 4 (9.0) | 10 (10.6) | 0 (0.0) | 1 (1.1) | 0 (0.0) | |||||
K. pneumoniae | 43 (14.3) | 28 (17.4) | 10 (21.3) | 18 (15.8) | 2 (16.7) | 8 (8.3) | 5 (16.1) | NS | NS | NS | NS | NS |
- In sputum 1 | 42 (15.4) | 27 (19.6) | 10 (22.7) | 17 (18.1) | 2 (25.0) | 8 (8.4) | 5 (16.1) | |||||
- In blood 2 | 1 (3.0) | 1 (3.7) | 0 (0.0) | 1 (4.6) | 0 (0.0) | 0 (0.0) | 0 (0.0) | |||||
P. aeruginosa | 37 (12.3) | 19 (11.8) | 6 (12.8) | 13 (11.4) | 1 (8.3) | 15 (15.6) | 2 (6.5) | NS | NS | NS | NS | 0.037 |
S. aureus | 11 (3.7) | 5 (3.1) | 2 (4.3) | 3 (2.6) | 1 (8.3) | 4 (4.2) | 1 (3.2) | NS | NS | NS | NS | NS |
Other bacteria | 39 (13.0) | 22 (13.7) | 4 (8.5) | 18 (15.8) | 7 (58.3) | 9 (9.4) | 1 (3.2) | NS | NS | NS | 0.040 | NS |
AFB-positive*** | 264 (15.7) | 218 (25.6) | 153 (54.6) | 65 (11.4) | 2 (1.4) | 42 (9.7) | 2 (0.8) | <0.001 | <0.001 | <0.001 | <0.001 | <0.001 |
Positive PCR results ^ | ||||||||||||
Rhinovirus | 151 (49.5) | 68 (49.3) | 10 (45.5) | 58 (50.0) | 8 (47.1) | 30 (44.1) | 45 (54.9) | 0.007 | NS | NS | <0.001 | 0.001 |
Respiratory syncytial virus | 54 (17.7) | 23 (16.7) | 5 (23.7) | 18 (15.5) | 5 (29.4) | 11 (16.2) | 15 (18.3) | NS | NS | NS | 0.064 | NS |
Influenza viruses | 37 (12.1) | 16 (11.6) | 3 (13.6) | 13 (11.2) | 0 (0.0) | 11 (16.2) | 10 (12.2) | NS | NS | NS | NS | NS |
Coronaviruses | 31 (10.2) | 18 (13.0) | 2 (9.9) | 16 (13.8) | 1 (5.9) | 11 (16.2) | 1 (1.2) | NS | NS | NS | 0.080 | 0.001 |
Human metapneumovirus | 14 (4.6) | 7 (5.1) | 0 (0.0) | 7 (6.0) | 2 (11.8) | 2 (2.9) | 3 (3.7) | NS | NS | NS | NS | NS |
Other viruses | 20 (6.6) | 6 (4.3) | 2 (9.1) | 4 (3.5) | 2 (11.8) | 5 (7.4) | 7 (8.5) | NS | NS | NS | NS | NS |
Mixed infections | ||||||||||||
>1 pathogen (AFB, bact. or virus) (% = n*100/d) | 63 (21.0) | 35 (21.7) | 16 (34.0) | 19 (16.7) | 2 (16.7) | 22 (22.9) | 4 (12.9) | NS | NS | NS | NS | NS |
>1 bacterium identified (% = n*100/d) | 24 (8.0) | 12 (7.5) | 4 (8.5) | 8 (7.0) | 0 (0.0) | 10 (10.4) | 2 (6.5) | NS | NS | NS | NS | NS |
AFB and ≥1 bacterium identified (% = n*100/d) | 30 (10.0) | 24 (14.9) | 16 (34.0) | 8 (7.0) | 0 (0.0) | 6 (6.3) | 0 (0.0) | NS | NS | NS | NS | NS |
AFB & virus (% = n*100/f) | 26 (8.5) | 18 (13.0) | 14 (63.6) | 4 (3.5) | 0 (0.0) | 8 (11.8) | 0 (0.0) | 0.005 | NS | NS | NS | NS |
>1 virus (% = n*100/f) | 9 (3.0) | 3 (2.2) | 1 (4.5) | 2 (1.7) | 2 (1.7) | 2 (2.9) | 2 (2.4) | NS | NS | NS | NS | NS |
Overall etiology results | ||||||||||||
Bacterial etiologies incl. AFB (% = n*100/b) | 520 (29.0) | 355 (39.0) | 184 (65.0) | 171 (27.2) | 0 (0.0) | 132 (30.1) | 33 (11.2) | <0.001 | <0.001 | 0.002 | <0.001 | <0.001 |
Viral detection (% = n*100/a) | 298 (16.1) | 135 (14.4) | 21 (7.5) | 114 (17.4) | 13 (7.9) | 68 (15.4) | 82 (26.1) | NS | 0.033 | NS | <0.001 | NS |
Identified etiologies (% = n*100/c) | 749 (42.9) | 449 (50.6) | 192 (69.8) | 257 (42.0) | 13 (8.8) | 178 (41.9) | 109 (37.8) | <0.001 | <0.001 | 0.004 | <0.001 | <0.001 |