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Table 2 Real-time PCR using the cycle threshold (Ct) levels < 40 and Ct < 30, respectively, for pathogen detection in nasopharyngeal secretions from hospitalised children 2 to 59 months of age with severe or non-severe radiologically confirmed pneumonia

From: Bacteria and viruses in the upper respiratory tract of Congolese children with radiologically confirmed pneumonia

Pathogens Number of cases (%)
Real-time PCR detection level Ct < 30 Real-time PCR detection level Ct < 40
All pneumonia cases
n = 116
Severe pneumonia
n = 85
Non-severe pneumonia n = 31 p-value All pneumonia cases
n = 116
Severe pneumonia
n = 85
Non-severe pneumonia n = 31 p-value Ct value, median (severe/non-severe pneumonia)
Bacteria          
Streptococcus pneumoniae 61 (53) 44 (52) 17 (55) 0.76 111 (96) 81 (95) 30 (97) 0.72 30.8/30.4
Haemophilus influenzae 23 (20) 18 (21) 5 (16) 0.54 63 (54) 50 (59) 13 (42) 0.10 32.2/30.7
Bordetella pertussis 1 (1) 1 (1) 0 (0) 12 (10) 9 (11) 3 (9) 0.88 37.8/39.1
Chlamydia pneumoniae 0 (0) 0 (0) 0 (0) 5 (4) 3 (4) 2 (6) 0.49 34.7/34.9
Mycoplasma pneumoniae 0 (0) 0 (0) 0 (0) 4 (3) 3 (4) 1 (3) 0.93 31.5/36.2
 Any bacteria 72 (62) 59 (69) 13 (42) 0.008 112 (96) 81 (95) 30 (97) 0.72
Viruses          
 Rhinovirus 34 (29) 27 (32) 7 (23) 0.33 85(73) 64(75) 21(78) 0.41 31.8/32.9
 Enterovirus 2 (2) 1 (1) 1 (3) 0.47 20 (17) 16 (19) 4 (13) 0.45 36.8/34.7
 Adenovirus 5 (4) 4 (5) 1 (3) 0.72 13 (11) 9 (11) 4 (13) 0.72 34.0/–
 Bocavirus 5 (4) 4 (5) 1 (3.2) 0.72 12 (10) 8 (9) 4 (12.9) 0.58 31.1/37.2
 Parainfluenza virus 3 (3) 3 (4) 0 (0) 9 (8) 9 (11) 0 (0) 31.5/–
 RSV 5 (4) 4 (5) 1 (3) 0.72 8 (7) 7 (8) 1 (3) 0.36 27.9/28.2
 Coronavirus 1 (1) 1 (1) 0 (0) 8 (7) 6 (7) 2 (6) 0.90 33.6/34.2
 Influenza A virus 1 (1) 1 (1) 0 (0) 3 (3) 1 (1) 2 (6) 0.15
 Influenza B virus 0 (0) 0 (0) 0 (0) 1 (1) 1 (1) 0 (0)
 Human metapneumovirus 0 (0) 0 (0) 0 (0) 1 (1) 1 (1) 0 (0)
 Any virus 53 (47) 44 (52) 9 (29) 0.032 106 (91) 78 (92) 28 (90) 0.80
 Any bacteria and virus 29 (25) 24 (28) 5 (16) 0.18 104 (90) 76 (89) 28 (90) 0.88
  1. Bold indicates result with p-value < 0.05 that was considered statistically significant