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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