Open Access

Impact of viral multiplex real-time PCR on management of respiratory tract infection: a retrospective cohort study

  • Lena M. Mayer1, 4,
  • Christian Kahlert2, 4,
  • Frank Rassouli3,
  • Pietro Vernazza4 and
  • Werner C. Albrich4Email author
Pneumonia20179:4

https://doi.org/10.1186/s41479-017-0028-z

Received: 4 October 2016

Accepted: 18 January 2017

Published: 25 February 2017

Abstract

Background

Significance and clinical utility of multiple virus detection by multiplex real-time polymerase chain reaction (rtPCR) in respiratory tract infection remain unclear.

Methods

This retrospective cohort study analyzed how virus detection affected clinical management. During a 27-month period, clinical and laboratory information was collected from all children and adults in two Swiss tertiary centres whose respiratory samples were tested for respiratory viruses with a 16-plex rtPCR test.

Results

Pathogens were identified in 140 of 254 patients (55%); of those patients, there was ≥1 virus in 91 (65%), ≥ 1 bacterium in 53 (38%), and ≥1 virus and bacterium in 11 (8%). Of 80 patients with viral infection, 59 (74%) received antibiotics. Virus detection was associated with discontinuation of antibiotics in 2 of 20 adults (10%) and 6 of 14 children (43%). Overall 12 adults (34%) and 18 children (67%) were managed correctly without antibiotics after virus detection (p = 0.01). When taking biomarkers, radiologic presentations, and antibiotic pre-treatment into account, the impact of rtPCR and appropriateness of therapy for clinically viral infections increased to 100% in children and 62% in adults.

Conclusions

A substantial reduction of unnecessary antibiotic prescriptions seems possible. Appropriate application of rtPCR results in respiratory tract infections should be encouraged.

Keywords

Multiplex real-time PCR Respiratory viruses Antibiotic management

Background

Establishing the etiology of respiratory tract infections (RTI) is often difficult due to the lack of a diagnostic gold standard and the inability to detect the causative pathogen. A large proportion of RTI is believed to be caused by respiratory viruses [16]. With widespread availability of molecular methods such as multiplex real-time polymerase chain reaction (rtPCR), clinical workflow has changed dramatically and the sensitivity of viral diagnostics has increased remarkably compared to conventional methods [3, 713]. However, the significance of virus detection remains unclear as the presence of a virus does not prove causality. Many respiratory viruses can be carried by asymptomatic children [4, 6, 14] and can be shed over prolonged periods, thus discrimination between carriage and infection is challenging [1315]. Viral infection was reported previously to predispose to bacterial super-infection and concerns about possible bacterial co-infection remain [3, 713, 1619]. Ruling out a bacterial infection with traditional microbiological techniques is frequently impossible [1, 5]. The predictive value of clinical signs to differentiate between viral and bacterial infection is also low [13, 17, 2022]. On these grounds, clinical management of patients after respiratory virus diagnosis is controversial and surprisingly poorly studied. Overall, extensive yet often unnecessary use of antibiotics in RTI is common [1, 5, 6]. This adult and pediatric retrospective cohort study analyzed whether identification of a virus by multiplex rtPCR was associated with changes in the antibiotic treatment.

Methods

Study design and population

This was a retrospective cohort study of all pediatric and adult in- and outpatients in whom a 16-plex rtPCR assay for respiratory viruses was performed for upper and lower RTI, from either the Kantonsspital St. Gallen or Children’s hospital of Eastern Switzerland. Both hospitals are tertiary-care Swiss teaching hospitals with active infectious diseases consult services and easily accessible web-based local guidelines (www.guidelines.ch) for the treatment of community-acquired or hospital-acquired pneumonia. The guidelines are strongly recommended for use but not strictly reinforced, and include use of rtPCR as optional diagnostic in hospitalized patients, particularly with immune suppression. The study period was from September 2012 (when this assay was introduced) to November 2014. The documented application dates of anti-infective medication were matched with the date of rtPCR analysis in order to determine whether treatment was changed in response to rtPCR results. The main outcome of interest was whether antibiotic therapy was modified according to results of multiplex rtPCR. Secondary outcomes were prevalence and distribution of positive results of rtPCR, complications, length of stay (LOS), and antibiotic therapy depending on identified pathogens.

Data collection

To identify patients, the database of the Centre for Laboratory Medicine was searched. Medical records were retrospectively analyzed to obtain basic demographic, clinical, laboratory and radiological parameters and data on clinical management. All chest radiographs (CXR) and computed tomographies (CT) for adults and children were reviewed by a pulmonologist and a pediatrician, respectively.

Clinical definitions

rtPCR results were available within 24 hours after testing. The application dates of anti-infective medication as documented in the medical records were correlated with the day of, or the day after, rtPCR analysis in order to define whether treatment initiation or discontinuation was associated with the results of viral testing.

The identified pathogens were retrospectively determined as relevant by an infectious disease specialist who integrated all available information. Etiologies were divided in four mutually exclusive groups: (i) bacterial (≥1 bacteria); (ii) viral (≥1 respiratory viruses); (iii) mixed (≥1 bacteria and ≥1 respiratory viruses); or (iv) no pathogen (including fungi, non-respiratory virus, bacterial contaminant including coagulase-negative staphylococci, propionibacterium, corynebacterium, colonizing oral and respiratory flora). For some children, rapid detection tests (Alere BinaxNOW Influenza A&B, Quidel QuickVue RSV Test) for respiratory syncytial virus (RSV) and influenza A/B virus were available. These results were additionally considered in forming the different groups.

For each patient, changes of antibiotic management, i.e. either starting or stopping antibiotics, were determined. All other situations were defined as no change.

Management was considered correct for viral infections if there was no antibiotic treatment before and after rtPCR or antibiotics were stopped after positive rtPCR results became available; for bacterial or mixed infections, if antibiotics were given before and after rtPCR or were started after a negative rtPCR result. Patients with an indication other than RTI for antibiotic therapy were excluded. For patients with febrile neutropenia without a specific focus, the antibiotic indication was defined as “other” because antibiotics would usually not be stopped despite a viral detection. If a patient underwent repeated testing for respiratory viruses within 3 weeks, only the first positive result was counted. If the time interval was longer or the detected viruses diverged, a different episode was presumed and analyzed separately [23].

To reflect clinical decision making in real-life situations, sub-analyses were performed. Cases without detection of bacteria (i.e. patients with viral etiology or with no pathogen) were evaluated as clinically bacterial if they fulfilled one of the following criteria: unilobar or multilobar pulmonary infiltrate on CT or CXR; C-reactive protein (CRP) >100 mg/l; procalcitonin (PCT) >0.25 μg/l; antibiotic therapy before rtPCR and with indeterminate biomarkers (CRP >100 mg/l and PCT ≤0.25 μg/l or CRP 51–100 mg/l and PCT not available). These criteria were adapted from earlier publications [17, 21] regarding the diagnosis of bacterial lower RTI.

The subgroup of patients with a viral etiology who had no clinically bacterial infection was considered to have a clinically viral infection. Children (<18 years) and adults (≥18 years) were analyzed separately. Sepsis was defined according to standard criteria at the time [24]. Systemic inflammatory response syndrome (SIRS) criteria for children were defined as age-specific [25].

For the imaging, if patients had interstitial infiltrates or ground glass opacities in the absence of unilobar or multilobar infiltrates, only therapy against “atypical” pathogens (macrolide, quinolone, tetracycline; but not antibiotics for coverage of “typical” bacterial pathogens) was considered appropriate. If both CXR and CT were available, only CT readings were used for further analyses. An infiltrate was required for the diagnosis of pneumonia but no radiography was needed to diagnose a RTI in general.

Laboratory procedures

The multiplex rtPCR was performed according to the manufacturer’s instruction (Seegene, Korea). The Anyplex™ II RV16 detection kit (Seegene, Korea) detects the following viruses: adenovirus, influenza A virus, influenza B virus, parainfluenza virus 1, parainfluenza virus 2, parainfluenza virus 3, parainfluenza virus 4, rhinovirus A/B/C, RSV A, RSV B, bocavirus 1/2/3/4, human metapneumovirus, coronavirus 229E, coronavirus NL63, coronavirus OC43, and enterovirus. Specimens that arrived before mid-morning from Monday to Friday were processed daily and results were provided by mid-afternoon. Specimens that arrived afterwards were processed on the following workday and reported by mid-afternoon. Dates of specimen collection and testing were available, but not date and time of reporting of results. For CRP, white blood cell count (WBC) and platelets, the most pathologic values within 3 days before and after rtPCR results were documented.

Statistical analyses

Quantitative variables are described as means ± standard deviations or median and interquartile range (IQR), as appropriate. Qualitative variables are presented as absolute counts and relative percentages. χ2-test or Fisher’s exact test were used to compare proportions, as appropriate. For continuous variables, the 2-sample independent t-test or the Mann-Whitney-U-test were used. P-values ≤0.05 (2-sided) were considered statistically significant. Multivariate logistic regression was used to examine whether different predictors were associated with virus detection. Variables with a p-value ≤0.05 in the univariate logistic regression were included. SPSS version 20.0 for Windows software, OpenEpi (www.openepi.com) and Microsoft Excel 2010 were used for statistical analyses.

Results

rtPCR for respiratory viruses was performed on 328 respiratory specimens, of which 74 samples were excluded due to insufficient clinical information or repeated testing of separate specimens for respiratory viruses in the same patient within 3 weeks. Data on 254 patients were analyzed, including 11 sputa, 47 nasopharyngeal swabs, 63 nasopharyngeal aspirates, 123 bronchoalveolar lavages, 9 tracheal aspirates and 1 pleural effusion.

Clinical characteristics

Baseline characteristics are presented in Tables 1, 2 and 3. One hundred and seven patients (42%) were female, and 72 were children (28%). Mean age in the group with viral infections was lower than in the remaining patients (29 vs. 47 years; p < 0.001) but the difference was not significant if children and adults were analyzed separately (children 4.3 vs. 5.7 years; p = 0.28; adults 53.6 vs. 56.6 years; p = 0.31). There were more patients with neutropenia, hematological malignancy or collagen vascular disease/vasculitis in the viral group (p < 0.001; p = 0.04; p = 0.01). Diagnosis of bronchitis and upper RTI were more common in the viral group (p = 0.02; p = 0.004).
Table 1

Baseline characteristics for adult patients

 

Missing

Total

Viral a

Any virus b

Other c

p-value d

values

(n = 182)

(n = 40)

(n = 46)

(n = 142)

Viral vs. any virus

Viral vs. other

Demographics

 Age, mean years ± SD (range)

 

55.9 ± 16.1 (18–88)

53.6 ± 16.1 (18–83)

53.9 ± 15.9 (18–83)

56.6 ± 16.1 (18–88)

0.93

0.30

 Female sex, n (%)

 

76 (41.8)

14 (35.0)

19 (41.3)

62 (43.7)

0.55

0.33

 Outpatients, n (%)

 

20 (11.0)

5 (12.5)

5 (10.9)

15 (10.6)

1.00

0.92

Comorbidities, n (%)

  

 Asthma

 

13 (7.1)

2 (5.0)

4 (8.7)

11 (7.7)

0.81

0.85

 COPD

 

27 (10.6)

5 (12.5)

7 (15.2)

22 (15.5)

0.72

0.64

 Other chronic lung diseasee

 

26 (14.3)

2 (5.0)

2 (4.3)

24 (16.9)

1.00

0.06

 Solid cancerf

 

25 (13.7)

3 (7.5)

3 (6.5)

22 (15.5)

1.00

0.20

 Hematologic malignancy

 

38 (20.9)

13 (32.5)

15 (32.6)

25 (17.6)

0.99

0.04

 Organ transplantation

 

13 (7.1)

3 (7.5)

3 (6.5)

10 (7.0)

1.00

1.00

 Neutropenia

 

20 (11.0)

9 (22.5)

9 (19.6)

11 (7.7)

0.74

0.03

 HIV infection

 

6 (3.3)

1 (2.5)

2 (4.3)

5 (3.5)

1.00

1.00

 Diabetes mellitus

 

27 (14.8)

6 (15.0)

7 (15.2)

21 (14.8)

0.98

0.97

 Collagen vascular disease/Vasculitis

 

33 (18.1)

4 (10.0)

5 (10.9)

29 (20.4)

1.00

0.13

 Systemic steroids

 

49 (26.9)

11 (27.5)

14 (30.4)

38 (26.8)

0.77

0.93

 Other Immunosuppressiong

 

21 (11.5)

5 (12.5)

6 (13.0)

16 (11.3)

0.94

1.00

 Chronic renal failure

 

45 (24.7)

11 (27.5)

13 (28.3)

34 (23.9)

0.94

0.65

Clinical findings

 Systolic blood pressure, mmHg, mean ± SD (range)

9

125 ± 24 (63–207)

129 ± 27 (63–207)

128 ± 28 (63–207)

123 ± 22 (67–197)

0.87

0.17

 Heart rate, beats/min, mean ± SD (range)

8

94 ± 20 (51–155)

91 ± 19 (51–150)

94 ± 19 (51–150)

94 ± 20 (56–155)

0.47

0.40

 Respiratory rate, breaths/min, mean ± SD (range)

130

26 ± 9 (10–60)

23 ± 8 (12–36)

27 ± 13 (12–60)

27 ± 10 (10–60)

0.39

0.23

 Body temperature, °C, mean ± SD (range)

20

37.6 ± 1.0 (35.4–42.0)

37.5 ± 0.9 (35.6–39.6)

37.5 ± 0.9 (35.6–39.6)

37.6 ± 1.0 (35.4–42.0)

1.00

0.59

Laboratory findingsh, mean ± SD (range)

 C-reactive protein (maximum), mg/l

13

151 ± 127 (1–500)

159 ± 148 (1–500)

166 ± 152 (1–500)

148 ± 121 (1–499)

0.83

0.64

 White blood cells (maximum), G/l

11

11.5 ± 10.2 (0.0–97.0)

12.2 ± 16.8 (1.8–97.0)

12.6 ± 16.3 (1.8–97.0)

11.3 ± 7.3 (0.0–41.1)

0.91

0.75

 Platelets (minimum), G/l

11

202 ± 128 (4–713)

159 ± 117 (5–513)

165 ± 117 (5–513)

215 ± 129 (4–713)

0.82

0.02

Discharge diagnosis, n (%)

 Bronchitis

 

22 (12.1)

7 (17.5)

7 (15.2)

15 (10.6)

0.78

0.36

 Acute exacerbation of COPD

 

5 (2.7)

1 (2.5)

1 (2.2)

4 (2.8)

1.00

1.00

 Upper respiratory tract infection

 

8 (4.4)

4 (10.0)

4 (8.7)

4 (2.8)

1.00

0.14

 Respiratory tract infection, unspecified

 

7 (3.8)

2 (5.0)

4 (8.7)

5 (3.5)

0.81

0.96

 Community-acquired pneumonia

 

65 (35.7)

21 (52.5)

25 (54.3)

44 (31.0)

0.86

0.01

 Hospital-acquired pneumonia

 

12 (6.6)

0 (0.0)

0 (0.0)

12 (8.5)

n/a

0.09

 Aspiration pneumonia

 

1 (0.5)

0 (0.0)

0 (0.0)

1 (0.7)

n/a

1.00

 Tuberculosis

 

3 (1.6)

0 (0.0)

0 (0.0)

3 (2.1)

n/a

0.95

 Otheri

 

59 (32.4)

5 (12.5)

5 (10.9)

54 (38.0)

1.00

0.002

°C, degree Celsius, COPD chronic obstructive pulmonary disease, HIV human immunodeficiency virus, n number, SD standard deviation

aCases in which only one or more respiratory viruses were detected

bCases in which one or more respiratory viruses were detected (as single or mixed infection)

cIncludes bacterial etiology, mixed etiology, no pathogen

dFor continuous variables, 2-sample independent t-test was used. For categorical variables, Mantel-Haenszel chi square or Fisher exact test were used

eOther chronic lung diseases, e.g. cystic fibrosis, pulmonary sarcoidosis, pulmonary hypertension

fAll solid tumors including bronchial carcinoma

gPatients with one of the following conditions: primary or secondary antibody deficiency, congenital immunodeficiency, immunosuppressive therapy other than steroids, severe malnutrition with cachexia

hHighest/lowest value within a time period of 3 days before and 3 days after date of rtPCR

iOther infections (n = 10); neoplastic diseases (n =6); collagen vascular; other rheumatologic or autoimmune (n = 14); sarcoidosis (n = 3); non-infectious non-neoplastic pulmonary diseases (n = 23); cardiovascular diseases (n = 3)

Table 2

Baseline characteristics for pediatric patients

 

Missing

Total

Viral a

Any virus b

Other c

p-value d

values

(n = 72)

(n = 40)

(n = 45)

(n = 32)

Viral vs. any virus

Viral vs. other

Demographics

 Age, mean years ± SD (range)

 

4.9 ± 5.7 (0–17)

4.3 ± 5.4 (0–16)

4.7 ± 5.5 (0–16)

5.7 ± 6.0 (0–17)

0.74

0.30

 Female sex, n (%)

 

31 (43.1)

14 (35.0)

18 (40.0)

17 (53.1)

0.64

0.13

 Outpatients, n (%)

 

3 (4.2)

2 (5.0)

2 (4.4)

1 (3.1)

1.00

1.00

Comorbidities, n (%)

 Asthma

 

1 (1.4)

1 (2.5)

1 (2.2)

0 (0.0)

1.00

1.00

 Other chronic lung diseasee

 

13 (18.1)

7 (17.5)

8 (17.8)

6 (18.8)

0.97

0.89

 Solid cancerf

 

1 (1.4)

0 (0.0)

0 (0.0)

1 (3.1)

n/a

0.89

 Haematologic malignancy

 

10 (13.9)

8 (20.0)

9 (20.0)

2 (6.3)

1.00

0.18

 Organ transplantation

 

1 (1.4)

1 (2.5)

1 (2.2)

0 (0.0)

1.00

1.00

 Neutropenia

 

9 (12.5)

8 (20.0)

8 (17.8)

1 (3.1)

0.79

0.06

 Systemic steroids

 

8 (11.1)

5 (12.5)

6 (13.3)

3 (9.4)

0.91

0.98

 Other Immunosuppressiong

 

3 (4.2)

3 (7.5)

3 (6.7)

0 (0.0)

1.00

0.33

Clinical findings

 Systolic blood pressure, mmHg, mean ± SD (range)

29

100 ± 18 (59–140)

106 ± 15 (71–140)

105 ± 14 (71–140)

95 ± 18 (59–120)

0.82

0.04

 Heart rate, beats/min, mean ± SD (range)

3

136 ± 33 (60–234)

138 ± 32 (60–186)

134 ± 32 (60–186)

135 ± 35 (72–234)

0.58

0.71

 Respiratory rate, breaths/min, mean ± SD (range)

15

41 ± 20 (16–103)

41 ± 21 (18–103)

40 ± 21 (16–103)

40 ± 19 (16–88)

0.84

0.86

 Body temperature, °C, mean ± SD (range)

3

37.6 ± 1.1 (35.0–40.1)

37.5 ± 1.1 (35.0–39.5)

37.5 ± 1.1 (35.0–39.5)

37.7 ± 1.1 (35.1–40.1)

1.00

0.46

Laboratory findingsh, mean ± SD (range)

 C-reactive protein (maximum), mg/l

2

85 ± 141 (5–999)

62 ± 77 (5–291)

67 ± 81 (5–293)

113 ± 191 (7–999)

0.78

0.16

 White blood cells (maximum), G/l

2

16.0 ± 12.1 (0.2–63.1)

12.6 ± 10.0 (0.2–57.0)

13.6 ± 11.3 (0.2–57.0)

20.1 ± 13.3 (1.8–63.1)

0.68

0.01

 Platelets (minimum), G/l

2

246 ± 144 (15–674)

257 ± 175 (15–674)

244 ± 169 (15–674)

234 ± 96 (16–488)

0.73

0.49

Discharge diagnosis, n (%)

 Bronchitis

 

10 (13.9)

9 (22.5)

9 (20.0)

1 (3.1)

0.78

0.04

 Upper respiratory tract infection

 

14 (19.4)

9 (22.5)

10 (22.2)

5 (15.6)

0.98

0.47

 Respiratory tract infection, unspecified

 

4 (5.6)

4 (10.0)

4 (8.9)

0 (0.0)

1.00

0.18

 Community-acquired pneumonia

 

15 (20.8)

6 (15.0)

8 (17.8)

9 (28.1)

0.73

0.18

 Hospital-acquired pneumonia

 

10 (13.9)

5 (12.5)

6 (13.3)

5 (15.6)

0.91

0.96

 Aspiration pneumonia

 

2 (2.8)

1 (2.5)

2 (4.4)

1 (3.1)

1.00

1.00

 Otheri

 

17 (23.6)

6 (15.0)

6 (13.3)

11 (34.4)

0.83

0.06

°C, degree Celsius, COPD chronic obstructive pulmonary disease, HIV human immunodeficiency virus, n number, SD standard deviation

aCases in which only one or more respiratory viruses were detected

bCases in which one or more respiratory viruses were detected (as single or mixed infection)

cIncludes bacterial etiology, mixed etiology, no pathogen

dFor continuous variables, 2-sample independent t-test was used. For categorical variables, Mantel-Haenszel chi square or Fisher exact test were used

eOther chronic lung diseases, e.g. cystic fibrosis, pulmonary sarcoidosis, pulmonary hypertension

fAll solid tumors including bronchial carcinoma

gPatients with one of the following conditions: primary or secondary antibody deficiency, congenital immunodeficiency, immunosuppressive therapy other than steroids, severe malnutrition with cachexia

hHighest/lowest value within a time period of 3 days before and 3 days after date of rtPCR

iOther infections (n = 14); neoplastic diseases (n = 1); collagen vascular; other rheumatologic or autoimmune (n = 1); gastroesophageal diseases (n = 1)

Table 3

Baseline characteristics for all patients

 

Missing

Total

Viral a

Any virus b

Other c

p-value d

values

(n = 254)

(n = 80)

(n = 91)

(n = 174)

Viral vs. any virus

Viral vs. other

Demographics

 Age, mean years ± SD (range)

 

41.5 ± 26.9 (0–88)

29.0 ± 27.5 (0–83)

29.6 ± 27.4 (0–83)

47.2 ± 24.7 (0–88)

0.89

<0.001

 Female sex, n (%)

 

107 (42.1)

28 (35.0)

37 (40.7)

79 (45.4)

0.45

0.12

 Children, n (%)

 

72 (28.3)

40 (50.0)

45 (49.5)

32 (18.4)

0.94

<0.001

 Outpatients, n (%)

 

23 (9.1)

7 (8.8)

7 (7.7)

16 (9.2)

0.80

0.91

Comorbidities, n (%)

 Asthma

 

14 (5.5)

3 (3.8)

5 (5.5)

11 (6.3)

0.87

0.61

 COPD

 

27 (10.6)

5 (6.3)

7 (7.7)

22 (12.6)

0.71

0.13

 Other chronic lung diseasee

 

39 (15.4)

9 (11.3)

10 (11.0)

30 (17.2)

0.96

0.22

 Solid cancerf

 

26 (10.2)

3 (3.8)

3 (3.3)

23 (13.2)

1.00

0.02

 Haematologic malignancy

 

48 (18.9)

21 (26.3)

24 (26.4)

27 (15.5)

0.99

0.04

 Organ transplantation

 

14 (5.5)

4 (5.0)

4 (4.4)

10 (5.7)

1.00

1.00

 Neutropenia

 

29 (11.4)

17 (21.3)

17 (18.7)

12 (6.9)

0.68

<0.001

 HIV infection

 

6 (2.4)

1 (1.3)

2 (2.2)

5 (2.9)

1.00

0.77

 Diabetes mellitus

 

27 (10.6)

6 (7.5)

7 (7.7)

21 (12.1)

0.96

0.28

 Collagen vascular disease/Vasculitis

 

33 (13.0)

4 (5.0)

5 (5.5)

29 (16.7)

1.00

0.01

 Systemic steroids

 

57 (22.4)

16 (20.0)

20 (22.0)

41 (23.6)

0.75

0.53

 Other Immunosuppressiong

 

24 (9.4)

8 (10.0)

9 (9.9)

16 (9.2)

0.98

0.84

 Chronic renal failure

 

45 (17.7)

11 (13.8)

13 (14.3)

34 (19.5)

0.92

0.26

Clinical findings

 Systolic blood pressure, mmHg, mean ± SD (range)

38

120 ± 25 (59–207)

121 ± 26 (63–207)

119 ± 26 (63–207)

119 ± 24 (59–197)

0.67

0.60

 Heart rate, beats/min, mean ± SD (range)

11

106 ± 31 (51–234)

114 ± 35 (51–186)

114 ± 33 (51–186)

102 ± 28 (56–234)

1.00

0.01

 Respiratory rate, breaths/min, mean ± SD (range)

145

34 ± 18 (10–103)

37 ± 21 (12–103)

37 ± 20 (12–103)

32 ± 15 (10–88)

1.00

0.17

 Body temperature, °C, mean ± SD (range)

23

37.6 ± 1.0 (35.0–42.0)

37.5 ± 1.0 (35.0–39.6)

37.5 ± 1.0 (35.0–39.6)

37.6 ± 1.0 (35.1–42.0)

1.00

0.48

Laboratory findingsh, mean ± SD (range)

 C-reactive protein (maximum), mg/l

15

132 ± 134 (1–999)

111 ± 127 (1–500)

117 ± 132 (1–500)

141 ± 137 (1–999)

0.77

0.11

 White blood cells (maximum), G/l

13

12.8 ± 11.0 (0.0–97.0)

12.4 ± 13.8 (0.2–97.0)

13.1 ± 14.0 (0.2–97.0)

13.1 ± 9.4 (0.0–63.1)

0.75

0.69

 Platelets (minimum), G/l

13

215 ± 134 (4–713)

208 ± 156 (5–674)

204 ± 149 (5–674)

218 ± 123 (4–713)

0.87

0.62

Discharge diagnosis, n (%)

 Bronchitis

 

32 (12.6)

16 (20.0)

16 (17.6)

16 (9.2)

0.69

0.02

 Acute exacerbation of COPD

 

5 (2.0)

1 (1.3)

1 (1.1)

4 (2.3)

1.00

0.99

 Upper respiratory tract infection

 

22 (8.7)

13 (16.3)

14 (15.4)

9 (5.2)

0.88

0.004

 Respiratory tract infection, unspecified

 

11 (4.3)

6 (7.5)

8 (8.8)

5 (2.9)

0.76

0.18

 Community-acquired pneumonia

 

80 (31.5)

27 (33.8)

33 (36.3)

53 (30.5)

0.73

0.60

 Hospital-acquired pneumonia

 

22 (8.7)

5 (6.3)

6 (6.6)

17 (9.8)

0.93

0.36

 Aspiration pneumonia

 

3 (1.2)

1 (1.3)

2 (2.2)

2 (1.1)

1.00

1.00

 Tuberculosis

 

3 (1.2)

0 (0.0)

0 (0.0)

3 (1.7)

n/a

0.64

 Otheri

 

76 (29.9)

11 (13.8)

11 (12.1)

65 (37.4)

0.75

<0.001

°C, degree Celsius, COPD chronic obstructive pulmonary disease, HIV human immunodeficiency virus, n number, SD standard deviation

aCases in which only one or more respiratory viruses were detected

bCases in which one or more respiratory viruses were detected (as single or mixed infection)

cIncludes bacterial etiology, mixed etiology, no pathogen

dFor continuous variables, 2-sample independent t-test was used. For categorical variables, Mantel-Haenszel chi square or Fisher exact test were used

eOther chronic lung diseases, e.g. cystic fibrosis, pulmonary sarcoidosis, pulmonary hypertension

fAll solid tumors including bronchial carcinoma

gPatients with one of the following conditions: primary or secondary antibody deficiency, congenital immunodeficiency, immunosuppressive therapy other than steroids, severe malnutrition with cachexia

hHighest/lowest value within a time period of 3 days before and 3 days after date of rtPCR

iOther infections (n = 24); neoplastic diseases (n = 7); collagen vascular; other rheumatologic or autoimmune (n = 15); sarcoidosis (n = 3); non-infectious non-neoplastic pulmonary diseases (n = 23); cardiovascular diseases (n = 3); gastroesophageal diseases (n = 1)

Pathogen identification

Any pathogen was identified in 140 patients (55%), in 89 of 182 adults (49%) and in 51 of 72 children (71%). Among these patients, one or more respiratory virus was detected in 91 (65%), one or more bacteria in 53 (38%) and a mixed viral-bacterial infection in 11 (8%) patients. 45 of 72 children (63%) were infected with one or more respiratory viruses. Compared to children, viral detection in adults was less frequent (25%, n = 46; p < 0.001). A single pathogen was identified in 99 patients (39%); multiple pathogens were detected in 41 patients (16%). Distribution of detected pathogens and the differences between children and adults are shown in Table 4, and Figs. 1, 2a and b.
Table 4

Relevant pathogens identified from respiratory specimens

 

Total (n = 254)

Adults (n = 182)

Children (n = 72)

Bacteria, n (%)

66 (26.0)

54 (29.7)

12 (16.7)

Haemophilus influenzae

12 (4.7)

11 (6.0)

1 (1.4)

Klebsiella pneumoniae

8 (3.1)

6 (3.3)

2 (2.8)

Staphylococcus aureus

4 (1.6)

1 (0.5)

3 (4.2)

Escherichia coli

4 (1.6)

3 (1.6)

1 (1.4)

Pseudomonas aeruginosa

4 (1.6)

4 (2.2)

0 (0.0)

Streptococcus pneumoniae

3 (1.2)

2 (1.1)

1 (1.4)

Streptococcus pyogenes

3 (1.2)

2 (1.1)

1 (1.4)

Legionella pneumophila

3 (1.2)

3 (1.6)

0 (0.0)

Mycobacterium tuberculosis

3 (1.2)

3 (1.6)

0 (0.0)

Mycoplasma pneumoniae

1 (0.4)

0 (0.0)

1 (1.4)

 Other bacteria

21 (8.3)

19 (10.4)

2 (2.8)

Viruses, n (%)

119 (46.9)

54 (29.7)

65 (90.3)

 Rhinovirus A/B/C

33 (13.0)

16 (8.8)

17 (23.6)

 Influenza A virus

17 (6.7)

11 (6.0)

6 (8.3)

 Influenza B virus

4 (1.6)

0 (0.0)

4 (5.6)

 Adenovirus

14 (5.5)

4 (2.2)

10 (13.9)

 Bocavirus 1/2/3/4

9 (3.5)

0 (0.0)

9 (12.5)

 Respiratory syncytial virus A

8 (3.1)

4 (2.2)

4 (5.6)

 Respiratory syncytial virus B

6 (2.4)

5 (2.7)

1 (1.4)

 Parainfluenza virus 1

1 (0.4)

1 (0.5)

0 (0.0)

 Parainfluenza virus 2

1 (0.4)

0 (0.0)

1 (1.4)

 Parainfluenza virus 3

6 (2.4)

3 (1.6)

3 (4.2)

 Parainfluenza virus 4

5 (2.0)

2 (1.1)

3 (4.2)

 Human Metapneumovirus

5 (2.0)

2 (1.1)

3 (4.2)

 Enterovirus

3 (1.2)

0 (0.0)

3 (4.2)

 Coronavirus 229E

1 (0.4)

1 (0.5)

0 (0.0)

 Coronavirus NL63

2 (0.8)

1 (0.5)

1 (1.4)

 Coronavirus OC43

1 (0.4)

1 (0.5)

0 (0.0)

 Non respiratory viruses

3 (1.2)

3 (1.6)

0 (0.0)

Fungi, n (%)

10 (3.9)

9 (4.9)

1 (1.4)

 Pneumocystis jirovecii

6 (2.4)

6 (3.3)

0 (0.0)

 Other fungi

4 (1.6)

3 (1.6)

1 (1.4)

Pathogens associated with mixed infections were counted individually

Fig. 1

Distribution of respiratory viruses detected as single or mixed pathogen

Fig. 2

a Distribution of identified pathogens for adults. b Distribution of identified pathogens for children

Antibiotic therapy

Of the 254 patients in the cohort, 61 (24%) received antibiotics before hospitalization, and 149 (59%) of all in- and outpatients received antibiotics at the time of rtPCR testing. Of 80 patients with a viral etiology, 59 (74%) received antibiotics at any time point, 28 of 40 children (70%) and 31 of 40 adults (78%). Inpatients with a bacterial etiology were treated with antibiotics in 92% (p = 0.09) and longer than those with a viral etiology or no pathogen (p = 0.02; p = 0.01). If children and adults were analyzed individually, similar but non-significant trends were observed (Tables 5, 6 and 7).
Table 5

Outcome depending on relevant detected pathogen for adult patients

 

Viral

Bacterial

Mixed

No pathogen

p-value a

(n = 40)

(n = 36)

(n = 6)

(n = 100)

Viral vs. bacterial

Viral vs. mixed

Viral vs. no pathogen

LOS inpatients, median days (IQR)

8 (6–21)

21 (13–35)

11.5 (5–44.25)

15 (8–23.5)

<0.001

0.67

0.03

 Complications, n (%)

  ICU admission

11 (27.5)

13 (36.1)

3 (50.0)

24 (24.0)

0.42

0.51

0.67

  Mechanical ventilation

6 (15.0)

11 (30.6)

3 (50.0)

19 (19.0)

0.11

0.16

0.58

  ARDS

3 (7.5)

5 (13.9)

2 (33.3)

6 (6.0)

0.60

0.24

1.00

  Sepsis

24 (60.0)

24 (66.7)

5 (83.3)

6 (6.0)b

0.55

0.53

n/a

  Mortality (all cause)

4 (10.0)

4 (11.1)

1 (16.7)

6 (6.0)

1.00

1.00

0.62

 Antibiotic use (any indication)

  Any inpatient antibiotics, n (%)

30/35 (85.7)

29/32 (90.6)

4/6 (66.7)

72/89 (80.9)

0.81

0.54

0.53

  Duration of inpatient use, mean days ± SD (range)

12.5 ± 14.3 (0–63)

18.1 ± 16.0 (0–72)

10.3 ± 12.1 (0–31)

10.8 ± 11.4 (0–63)

0.14

0.73

0.49

  Discharged receiving oral antibiotics, n (%)

11 (30.6)c

17 (53.1)d

1 (20.0)e

23 (24.5)f

0.06

1.00

0.48

ARDS acute respiratory distress syndrome, ICU intensive care unit, IQR interquartile range, LOS length of stay, n number, SD standard deviation

aFor continuous variables, 2-sample independent t-test or Mann-Whitney-U-test were used. For categorical variables, Mantel-Haenszel chi square or Fisher exact test were used

bSepsis requires a pathogen per definition. In these six cases sepsis was exceptionally defined according to discharge papers

Missing values due to death or ongoing hospitalisation at time of analysis (number): c4; d4; e1; f6. For calculation of percentage and p-value missing values were excluded

Table 6

Outcome depending on relevant detected pathogen for pediatric patients

 

Viral

Bacterial

Mixed

No pathogen

p-value a

(n = 40)

(n = 6)

(n = 5)

(n = 21)

Viral vs. bacterial

Viral vs. mixed

Viral vs. no pathogen

LOS inpatients, median days (IQR)

18.5 (6–48.75)

47.5 (14–95.75)

34 (17.5–201.5)

37 (8–70)

0.19

0.10

0.45

 Complications, n (%)

  ICU admission

18 (45.0)

4 (66.7)

5 (100.0)

12 (57.1)

0.58

0.06

0.37

  Mechanical ventilation

8 (20.0)

4 (66.7)

4 (80.0)

11 (52.4)

0.07

0.03

0.01

  ARDS

1 (2.5)

0 (0.0)

1 (20.0)

0 (0.0)

1.00

0.42

1.00

  Sepsis

17 (42.5)

4 (66.7)

2 (40.0)

0 (0.0)

0.50

1.00

n/a

  Mortality (all cause)

2 (5.0)

0 (0.0)

0 (0.0)

0 (0.0)

1.00

1.00

0.85

 Antibiotic use (any indication)

  Any inpatient antibiotics, n (%)

28/38 (73.7)

6/6 (100.0)

5/5 (100.0)

18/20 (90.0)

0.38

0.49

0.26

  Duration of inpatient use, mean days ± SD (range)

8.6 ± 13.4 (0–73)

14.2 ± 11.0 (0–34)

13.8 ± 7.8 (7–24)

6.2 ± 4.8 (0–18)

0.34

0.40

0.33

  Discharged receiving oral antibiotics, n (%)

6 (15.8)b

0 (0.0)

1 (20.0)

3 (15.0)c

0.78

1.00

1.00

ARDS acute respiratory distress syndrome, ICU intensive care unit, IQR interquartile range, LOS length of stay, n number, SD standard deviation

aFor continuous variables, 2-sample independent t-test or Mann-Whitney-U-test were used. For categorical variables, Mantel-Haenszel chi square or Fisher exact test were used

Missing values due to death or ongoing hospitalisation at time of analysis (number): b2; c1. For calculation of percentage and p-value missing values were excluded

Table 7

Outcome depending on relevant detected pathogen for all patients

 

Viral

Bacterial

Mixed

No pathogen

p-value a

(n = 80)

(n = 42)

(n = 11)

(n = 121)

Viral vs. bacterial

Viral vs. mixed

Viral vs. no pathogen

LOS inpatients, median days (IQR)

12 (6–25.5)

22 (13–42.5)

27 (8–72)

16 (8–29.25)

0.004

0.20

0.20

 Complications, n (%)

  ICU admission

29 (36.3)

17 (40.5)

8 (72.7)

36 (29.8)

0.65

0.05

0.34

  Mechanical ventilation

14 (17.5)

15 (35.7)

7 (63.6)

30 (24.8)

0.03

0.01

0.22

  ARDS

4 (5.0)

5 (11.9)

3 (27.3)

6 (5.0)

0.31

0.07

1.00

  Sepsis

41 (51.3)

28 (66.7)

7 (63.6)

6 (5.0)b

0.10

0.44

n/a

  Mortality (all cause)

6 (7.5)

4 (9.5)

1 (9.1)

6 (5.0)

0.94

1.00

0.65

 Antibiotic use (any indication)

  Any inpatient antibiotics, n (%)

58/73 (79.5)

35/38 (92.1)

9/11 (81.8)

90/109 (82.6)

0.09

1.00

0.60

  Duration of inpatient use, mean days ± SD (range)

10.5 ± 13.9 (0-73)

17.5 ± 15.3 (0–72)

11.9 ± 10.0 (0–31)

10.0 ± 10.6 (0–63)

0.02

0.75

0.80

  Discharged receiving oral antibiotics, n (%)

17 (23.0)c

17 (44.7)d

2 (20.0)e

26 (22.8)f

0.02

1.00

0.98

ARDS acute respiratory distress syndrome, ICU intensive care unit, IQR interquartile range, LOS length of stay, n number, SD standard deviation

aFor continuous variables, 2-sample independent t-test or Mann-Whitney-U-test were used. For categorical variables, Mantel-Haenszel chi square or Fisher exact test were used

bSepsis requires a pathogen per definition. In these six cases sepsis was exceptionally defined according to discharge papers

Missing values due to death or ongoing hospitalisation at time of analysis (number): c6; d4; e1; f7. For calculation of percentage and p-value missing values were excluded

Influence of rtPCR testing on management

The effect of rtPCR analysis on antibiotic management is presented in Tables 8, 9 and 10. After exclusion of patients who received antibiotics for other indications virus detection was temporally associated with discontinuation of antibiotics in 2 of 20 adults (10%) and 6 of 14 children (43%). In patients with viral etiology, management was more frequently judged correct in children (18/27, 67%) than in adults (12/35, 34%; p = 0.01) after rtPCR results became available. In adults, management of viral etiology was less often judged correct compared to adults with bacterial etiology (p = 0.002). Among patients with clinically viral etiology, children were more frequently managed correctly (15/15, 100%) than adults (8/13, 62%; p = 0.03).
Table 8

Change of antibiotic therapy after rtPCR, adult patients with another indication for antibiotics were excluded

 

Viral

Bacterial

Mixed

No pathogen

Clinically

Clinically

p-value c

(n = 35)

(n = 33)

(n = 6)

(n = 84)

bacterial a (n = 84)

viral b (n = 13)

Viral vs. bacterial

Viral vs. mixed

Viral vs. no pathogen

No antibiotic treatment before and after rtPCR, n (%)

10 (28.6)

7 (21.2)

2 (33.3)

32 (38.1)

18 (21.4)

8 (61.5)

0.49

1.00

0.32

Antibiotic treatment stopped after rtPCR, n (%)

2 (5.7)

2 (6.1)

0 (0.0)

2 (2.4)

4 (4.8)

0 (0.0)

1.00

1.00

0.67

Antibiotic treatment started after rtPCR, n (%)

5 (14.3)

4 (12.1)

2 (33.3)

8 (9.5)

7 (8.3)

3 (23.1)

1.00

0.54

0.64

Antibiotic treatment before and after rtPCR, n (%)

18 (51.4)

20 (60.6)

2 (33.3)

42 (50.0)

55 (65.5)

2 (15.4)

0.45

0.71

0.89

Correct management, n (%)

12 (34.3)

24 (72.7)

4 (66.7)

 

62 (73.8)

8 (61.5)

0.002

0.30

n/a

n number; rtPCR, real-time polymerase chain reaction

aCases without detection of bacteria were evaluated as clinically bacterial if they fulfilled one of the following criteria: unilobular or multilobular pulmonary infiltrate or CRP >100 mg/l or PCT >0.25 μg/l or antibiotic therapy before rtPCR and no bacterium detection and biomarkers indeterminate (CRP >100 mg/l and PCT ≤0.25 μg/l or CRP between 51 and 100 mg/l and PCT not available)

bCases with a detected viral pathogen excluding those patients with a clinically bacterial co-infection (as described above)

cMantel-Haenszel chi square test or Fisher exact test were used

Table 9

Change of antibiotic therapy after rtPCR, pediatric patients with another indication for antibiotics were excluded

 

Viral

Bacterial

Mixed

No pathogen

Clinically

Clinically

p-value c

(n = 27)

(n = 4)

(n = 3)

(n = 18)

bacterial a (n = 22)

viral b (n = 15)

Viral vs. bacterial

Viral vs. mixed

Viral vs. no pathogen

No antibiotic treatment before and after rtPCR, n (%)

12 (44.4)

1 (25.0)

0 (0.0)

6 (33.3)

6 (27.3)

11 (73.3)

0.87

0.40

0.46

Antibiotic treatment stopped after rtPCR, n (%)

6 (22.2)

0 (0.0)

0 (0.0)

1 (5.6)

2 (9.1)

4 (26.7)

0.80

1.00

0.27

Antibiotic treatment started after rtPCR, n (%)

1 (3.7)

0 (0.0)

1 (33.3)

3 (16.7)

3 (13.6)

0 (0.0)

1.00

0.39

0.34

Antibiotic treatment before and after rtPCR, n (%)

8 (29.6)

3 (75.0)

2 (66.7)

8 (44.4)

11 (50.0)

0 (0.0)

0.23

0.50

0.32

Correct management, n (%)

18 (66.7)

3 (75.0)

3 (100.0)

 

14 (63.6)

15 (100.0)

1.00

0.66

n/a

n number; rtPCR, real-time polymerase chain reaction

aCases without detection of bacteria were evaluated as clinically bacterial if they fulfilled one of the following criteria: unilobular or multilobular pulmonary infiltrate or CRP >100 mg/l or PCT >0.25 μg/l or antibiotic therapy before rtPCR and no bacterium detection and biomarkers indeterminate (CRP >100 mg/l and PCT ≤0.25 μg/l or CRP between 51 and 100 mg/l and PCT not available)

bCases with a detected viral pathogen excluding those patients with a clinically bacterial co-infection (as described above)

cMantel-Haenszel chi square test or Fisher exact test were used

Table 10

Change of antibiotic therapy after rtPCR, all patients with another indication for antibiotics were excluded

 

Viral

Bacterial

Mixed

No pathogen

Clinically

Clinically

p-value c

(n = 62)

(n = 37)

(n = 9)

(n = 102)

bacterial a (n = 106)

viral b (n = 28)

Viral vs. bacterial

Viral vs. mixed

Viral vs. no pathogen

No antibiotic treatment before and after rtPCR, n (%)

22 (35.5)

8 (21.6)

2 (22.2)

38 (37.3)

24 (22.6)

19 (67.9)

0.15

0.71

0.82

Antibiotic treatment stopped after rtPCR, n (%)

8 (12.9)

2 (5.4)

0 (0.0)

3 (2.9)

6 (5.7)

4 (14.3)

0.40

0.64

0.03

Antibiotic treatment started after rtPCR, n (%)

6 (9.7)

4 (10.8)

3 (33.3)

11 (10.8)

10 (9.4)

3 (10.7)

1.00

0.16

0.82

Antibiotic treatment before and after rtPCR, n (%)

26 (41.9)

23 (62.2)

4 (44.4)

50 (49.0)

66 (62.3)

2 (7.1)

0.05

1.00

0.38

Correct management, n (%)

30 (48.4)

27 (73.0)

7 (77.7)

 

76 (71.7)

23 (82.1)

0.02

0.19

n/a

n number; rtPCR, real-time polymerase chain reaction

aCases without detection of bacteria were evaluated as clinically bacterial if they fulfilled one of the following criteria: unilobular or multilobular pulmonary infiltrate or CRP >100 mg/l or PCT >0.25 μg/l or antibiotic therapy before rtPCR and no bacterium detection and biomarkers indeterminate (CRP >100 mg/l and PCT ≤0.25 μg/l or CRP between 51 and 100 mg/l and PCT not available)

bCases with a detected viral pathogen excluding those patients with a clinically bacterial co-infection (as described above)

cMantel-Haenszel chi square test or Fisher exact test were used

Eight adults and one child received oseltamivir. In four of five patients with proven influenza A virus infection, the antiviral medication was prescribed in response to the positive rtPCR analysis. In another child, oseltamivir was commenced after the third successive detection of influenza A virus within a month and stopped after 1 day. In two other patients, antiviral therapy was started or continued despite an rtPCR analysis negative for influenza and positive for other respiratory viruses. In another patient with identification of only bacterial pathogens, oseltamivir was stopped after negative rtPCR results were available. In an additional case with detection of bacteria only, antiviral medication was started 3 days after rtPCR analysis and it was stopped again on the next day.

Outcomes depending on etiology

Hospital length of stay (LOS) was longer in patients with bacterial etiology compared to patients with a viral etiology. For children, LOS did not significantly vary in the different groups between viral and bacterial etiologies (Tables 5, 6 and 7). Patients with a mixed infection were more frequently admitted to the intensive care unit (ICU) and mechanically ventilated compared to patients with a viral etiology (p = 0.05; p = 0.005; respectively). If children and adults were analyzed separately, the differences within the adult population were not significant; in children, more patients with a mixed infection were mechanically ventilated (p = 0.03). All-cause and RTI-associated mortality was comparable between pathogen groups.

In patients with viral etiology there was no difference in mortality between those who discontinued antibiotics compared to those who did not (1/8 [13%] vs. 3/26 [12%]; p = 1.00). LOS was shorter in inpatients who discontinued antibiotics (median days 5 [IQR 3–11.75] vs. 10.5 [IQR 6–19.25]; p = 0.05). Patients in whom antibiotics were continued despite a viral detection were as frequently admitted to ICU (11/26 [42%] vs. 5/8 [63%]; p = 0.55) or mechanically ventilated (6/26 [23%] vs. 1/8 [13%]; p = 0.93) as patients in whom antibiotics were discontinued. The proportion of patients with sepsis was comparable (16/26 [62%] vs. 6/8 [75%]; p = 0.80). These results were similar if adults and children were analyzed separately.

Radiological findings depending on etiology

Normal CXR findings were significantly more frequent in patients with viral infection compared to bacterial infections (30% vs. 9%; p = 0.03). Multilobar infiltrates and pleural effusion on CXR were observed less often among subjects with viral infection (Tables 11, 12 and 13).
Table 11

Radiological findings for adult patients

 

Viral

Bacterial

Mixed

No pathogen

 

p-value a

 

(n = 40)

(n = 36)

(n = 6)

(n = 100)

Viral vs. bacterial

Viral vs. mixed

Viral vs. no pathogen

X-ray, (n)

33

26

5

81

   

 Unilobar infiltrate, n (%)

9 (27.3)

5 (19.2)

0 (0.0)

14 (17.3)

0.48

0.47

0.23

 Multilobar infiltrates, n (%)

6 (18.2)

10 (38.5)

2 (40.0)

30 (37.0)

0.09

0.56

0.05

 Interstitial infiltrates, n (%)

3 (9.1)

7 (26.9)

1 (20.0)

17 (21.0)

0.14

0.89

0.13

 Pleural effusion, n (%)

5 (15.2)

11 (42.3)

0 (0.0)

24 (29.6)

0.02

0.95

0.11

 Normal, n (%)

8 (24.2)

2 (7.7)

1 (20.0)

14 (17.3)

0.18

1.00

0.40

Computer tomography, (n)

23

29

5

71

   

 Unilobar infiltrate, n (%)

5 (21.7)

4 (13.8)

0 (0.0)

7 (9.9)

0.70

0.69

0.26

 Multilobar infiltrates, n (%)

11 (47.8)

16 (55.2)

4 (80.0)

32 (45.1)

0.60

0.42

0.82

 Ground glass opacity, n (%)

4 (17.4)

6 (20.7)

2 (40.0)

29 (40.8)

1.00

0.57

0.04

 Pleural effusion, n (%)

5 (21.7)

13 (44.8)

1 (20.0)

25 (35.2)

0.09

1.00

0.23

 Normal, n (%)

2 (8.7)

0 (0.0)

0 (0.0)

0 (0.0)

0.38

1.00

0.12

n number. Multiple findings were counted individually

aMantel-Haenszel chi square test or Fisher exact test were used

Table 12

Radiological findings for pediatric patients

 

Viral

Bacterial

Mixed

No pathogen

 

p-value a

 

(n = 40)

(n = 6)

(n = 5)

(n = 21)

Viral vs. bacterial

Viral vs. mixed

Viral vs. no pathogen

X-ray, (n)

28

6

5

16

   

 Unilobar infiltrate, n (%)

6 (21.4)

0 (0.0)

1 (20.0)

2 (12.5)

0.56

1.00

0.76

 Multilobar infiltrates, n (%)

6 (21.4)

2 (33.3)

4 (80.0)

6 (37.5)

0.88

0.04

0.42

 Interstitial infiltrates, n (%)

2 (7.1)

1 (16.7)

1 (20.0)

2 (12.5)

0.91

0.80

0.93

 Pleural effusion, n (%)

4 (14.3)

2 (33.3)

1 (20.0)

2 (12.5)

0.56

1.00

1.00

 Normal, n (%)

10 (35.7)

1 (16.7)

0 (0.0)

3 (18.8)

0.70

0.28

0.40

Computer tomography, (n)

5

1

2

3

   

 Unilobar infiltrate, n (%)

2 (40.0)

0 (0.0)

0 (0.0)

0 (0.0)

1.00

0.95

0.71

 Multilobar infiltrates, n (%)

2 (40.0)

1 (100.0)

2 (100.0)

3 (100.0)

1.00

0.57

0.36

 Ground glass opacity, n (%)

0 (0.0)

0 (0.0)

1 (50.0)

0 (0.0)

n/a

0.57

n/a

 Pleural effusion, n (%)

2 (40.0)

1 (100.0)

1 (50.0)

2 (66.7)

1.00

1.00

1.00

 Normal, n (%)

1 (20.0)

0 (0.0)

0 (0.0)

0 (0.0)

1.00

1.00

1.00

n number. Multiple findings were counted individually

aMantel-Haenszel chi square test or Fisher exact test were used

Table 13

Radiological findings for all patients

 

Viral

Bacterial

Mixed

No pathogen

 

p-value a

 

(n = 80)

(n = 42)

(n = 11)

(n = 121)

Viral vs. bacterial

Viral vs. mixed

Viral vs. no pathogen

X-ray, (n)

61

32

10

97

   

 Unilobar infiltrate, n (%)

15 (24.6)

5 (15.6)

1 (10.0)

16 (16.5)

0.32

0.57

0.21

 Multilobar infiltrates, n (%)

12 (19.7)

12 (37.5)

6 (60.0)

36 (37.1)

0.06

0.03

0.02

 Interstitial infiltrates, n (%)

5 (8.2)

8 (25.0)

2 (20.0)

19 (19.6)

0.06

0.51

0.05

 Pleural effusion, n (%)

9 (14.8)

13 (40.6)

1 (10.0)

26 (26.8)

0.01

1.00

0.08

 Normal, n (%)

18 (29.5)

3 (9.4)

1 (10.0)

17 (17.5)

0.03

0.37

0.08

Computer tomography, (n)

28

30

7

74

   

 Unilobar infiltrate, n (%)

7 (25.0)

4 (13.3)

0 (0.0)

7 (9.5)

0.26

0.35

0.10

 Multilobar infiltrates, n (%)

13 (46.4)

17 (56.7)

6 (85.7)

35 (47.3)

0.44

0.14

0.94

 Ground glass opacity, n (%)

4 (14.3)

6 (20.0)

3 (42.9)

29 (39.2)

0.82

0.25

0.02

 Pleural effusion, n (%)

7 (25.0)

14 (46.7)

2 (28.6)

27 (36.5)

0.09

1.00

0.28

n number. Multiple findings were counted individually

aMantel-Haenszel chi square test or Fisher exact test were used

Predictors of viral etiology

In multivariate logistic regression (Tables 14 and 15), the absence of pleural effusion in adults was associated with detection of respiratory viruses (odds ratio [OR] 0.31, 95% confidence interval [CI] 0.12–0.80). For children, the lack of multilobar infiltrates was a significant predictor of respiratory virus detection (OR 0.22, 95% CI 0.06–0.81).
Table 14

Prediction of respiratory virus detection for adult patients

 

Univariable analysis

Multivariable analysis

Predictor

p-value

OR (95% CI)

p-value

OR (95% CI)

 Neutropenia

0.01

3.46 (1.32–9.07)

0.27

2.11 (0.56–7.89)

 Hematologic malignancy

0.04

2.25 (1.02–4.97)

0.59

1.35 (0.45–4.01)

 Pleural effusion

0.02

0.36 (0.15–0.86)

0.02

0.31 (0.12–0.80)

 Platelets (minimum), G/l

0.02

1.00 (0.99–1.00)

0.20

1.00 (0.99–1.00)

Table 15

Prediction of respiratory virus detection for pediatric patients

 

Univariable analysis

Multivariable analysis

Predictor

p-value

OR (95% CI)

p-value

OR (95% CI)

 Neutropenia

0.06

7.75 (0.92–65.66)

0.10

7.44 (0.69–80.42)

 Multilobular infiltrates

0.03

0.31 (0.11–0.91)

0.02

0.22 (0.06–0.81)

 White blood cells (maximum), G/l

0.02

0.94 (0.89–0.99)

0.10

0.95 (0.90–1.01)

OR odds ratio, CI confidence interval

Discussion

There are three main findings in this retrospective cohort study of the impact of viral multiplex rtPCR. First, the majority of patients with viral RTI received antibiotics and antibiotics were discontinued after viral detection in only a minority of patients. Second, when biomarkers, radiologic presentations and antibiotic pre-treatment were taken into account and categories of clinically bacterial and clinically viral infections were created (which more closely reflect clinical decision making), the multiplex rtPCR showed a greater impact and considerably improved correct management of clinically viral infections, from 67 to 100% among children and from 34 to 62% among adults. Third, the impact of rtPCR testing seemed to be more accentuated in children than in adults. More children than adults had an appropriate discontinuation of antibiotics, and the overall management of viral infections was superior in children compared to adults. Importantly, but with the caveat of small numbers, there was no evidence that outcome was worse in those with viral etiology who discontinued antibiotics compared to those who did not.

Several previous studies analyzed the impact of rapid availability of rtPCR results on antibiotic use. In a randomized controlled trial (RCT) of 107 adults with lower RTI, antibiotics were partially or totally discontinued in 6 (11%) of 55 patients for whom rtPCR results were available, albeit without overall reduction in antibiotic treatment duration [7]. In a controlled clinical trial enrolling 583 children with acute RTI, Wishaupt et al. [4] evaluated the diagnostic yield and effect of rapid communication of rtPCR results (within 12–36 h vs. 4 weeks after testing) and failed to show a significant influence on the duration of antibiotic treatment. In contrast, Brittain-Long et al. [20] demonstrated in a RCT with 406 adults that patients randomized to rapid rtPCR results received antibiotics less frequently for acute RTI in a primary care setting during their initial visit (4.5% vs. 12.3%; p = 0.01). However, at the 10-day follow-up the prescription rates were similar again (13.9% vs. 17.2%; p = 0.36) [20]. Contrary to these findings, a retrospective pre-post study of 1136 children showed that the introduction of an expanded multiplex rtPCR had a shorter turnaround time and decreased the duration of antibiotic use (2.8 vs. 3.2 days; p = 0.003) without reducing the proportion of antibiotic prescriptions [26].

As in most previous studies, typical respiratory bacteria were not included in the test panel. Due to this technical limitation, missing a treatable pathogen is of concern in light of potential bacterial-viral co-infections [3, 713, 1619]. It was shown that clinical suspicion of a bacterial super-infection was one reason for physicians to not stop antibiotics in rtPCR-positive patients [3]. We tried to partially overcome this by creating categories of clinically bacterial and clinically viral infections. This definition, aided by providing a biomarker criterion, accounted for the possibility of a viral infection in the setting of bacterial carriage. One of the major differences and advantages of the current study compared to previous publications is that it not only assessed the impact of the rtPCR results, which themselves had a limited impact on appropriate therapy, but it also integrated other ‘real-world’ clinical and radiologic parameters into the decision process.

Advanced molecular diagnostic tests have to be interpreted in the context of available clinical and diagnostic information in order to improve clinical management. The results confirmed the important role of clinical judgement for appropriate antibiotic prescriptions, with rtPCR providing additional information rather than being solely responsible for treatment decisions.

Quantification of genomic viral load might improve specificity of virus detection, with higher organism burden being associated with higher risk of complications and severe disease in adults and children [27, 28]. Unfortunately, quantitative results were not available with the applied assay. Similarly, optimal timing of molecular testing in relation to symptom onset and inclusion of an ever-expanding number of respiratory viruses might be important to further increase sensitivity [27]. However, to the authors’ knowledge, it has not yet been studied whether either of these two factors would improve clinical management.

A pathogen was identified in 140 (55%) patients in this study, in accordance with detection rates in other studies ranging from 38 to 82% [4, 12, 17, 19, 20, 22, 2935]. A mixed bacterial-viral etiology was found in 11 (8%) patients. Previously described rates varied between 2 and 23% [17, 19, 22, 2935]. Some studies suggested that mixed bacterial-viral infections result in more severe clinical diseases (as measured by the CURB-65 score or the pneumonia severity index) [17, 34], a higher rate of mechanical ventilation, longer duration of ICU care [36, 37], longer hospital stays [22, 36], or higher mortality [37, 38], while other studies did not [29, 39, 40]. In this study, mixed bacterial-viral infections were associated with a higher rate of ICU admission and mechanical ventilation compared to pure viral (p = 0.05; p = 0.005) and pure bacterial (p = 0.06; p = 0.19) infections if all patients were considered. However, these results should not be viewed as representative of the etiology of lower RTI in East Switzerland as these hospitals presented a preselected group of patients.

In agreement with the findings of some studies [20, 22, 34] and in contrast to others [7, 29, 39], this study failed to identify specific predictors of viral detection in multivariate logistic regression. Advancing age was previously described as more common in viral infections [19, 22, 29, 35] but the evidence is inconclusive [31, 32]. In this study, younger age was a significant predictor of virus detection in univariable logistic regression if all patients were considered, but not in stratified analyses in children and adults. The mean age in the group with respiratory viral infections was lower than in the remaining patients (29 vs. 47 years; p < 0.001) but the differences were not significant if stratified for children and adults.

There are some limitations to the study. First, the change of anti-infective management was retrospectively matched with the date of the rtPCR analysis. Exact time specifications were not available, leaving room for potential inaccuracies. It is not known whether and to what extent these or other factors contributed to the clinical decisions in starting, stopping, or continuing antibiotic therapy. Due to the retrospective nature of the study, it was not possible to consider the clinical presentation in the analysis. Therefore, it was difficult to reproduce the decision-making process and the primary indication for antibiotic therapy. This is an important limitation because clinical judgement remains essential concerning the use of antibiotics [41]. Furthermore, data on the consequences of rtPCR results on antibiotic treatment are difficult to obtain in the ambulatory setting, which explains the relatively small number of enrolled outpatients. Prospective studies or ideally RCTs will be necessary to confirm the findings.

Second, creating categories of clinically bacterial and clinically viral etiology by means of biomarker, radiologic presentations and antibiotic pre-treatment was done arbitrarily to reflect real-life decision-making. These theoretical reflections were important to better understand the findings; however, and as noted above, retrospectively the actual decision-making process remained unclear.

Third, the study included patients with upper and lower respiratory tract infections and did not exclude patients with antibiotic pre-treatment or significant underlying pathologic conditions, which may have biased the results but reflects clinical routine. Not having algorithms in place when to perform rtPCR testing or how to apply the results likewise mirrors the real-world scenario.

Fourth, the study’s multiplex rtPCR only included respiratory viruses. Newer generation assays additionally cover atypical and typical bacteria and increase the detection of potential respiratory pathogens, albeit with yet unresolved specificity issues as these typical bacterial pathogens might also represent carriage in the absence of disease [42].

Fifth, the prevalence of RSV was underestimated in this study. In the population of hospitalized children, rapid detection tests for RSV were performed initially and, if positive, no additional rtPCR was performed. Because the study included only patients in whom an rtPCR assay for respiratory viruses was performed, the number of RSV infections was lower than expected from epidemiological data.

Conclusion

This study reveals the real-life impact of viral multiplex rtPCR in both children and adults, which was more limited in adults but improved when results were seen in the context of biomarkers, radiology, and antibiotic pre-treatment. As substantial reduction of unnecessary antibiotic prescriptions seems possible, it will be necessary to develop more structured management algorithms incorporating molecular diagnostics including bacterial pathogens, which need to be prospectively tested in their efficacy and safety in RTI.

Abbreviations

CRP: 

C-reactive protein

CT: 

Computer tomography

CXR: 

Chest radiograph

ICU: 

Intensive care unit

IQR: 

Interquartile range

LOS: 

Length of stay

PCT: 

Procalcitonin

RCT: 

Randomized controlled trial

RSV: 

Respiratory syncytial virus

RTI: 

Respiratory tract infection

rtPCR: 

Real-time polymerase chain reaction

SIRS: 

Systemic inflammatory response syndrome

WBC: 

White blood cells count

Declarations

Acknowledgements

We are grateful to the laboratory team and the archive staff of Kantonsspital St. Gallen and Children’s hospital of Eastern Switzerland for providing the necessary data. We thank Michael Mayer for input in statistics.

Funding

The study was funded by the Department of Infectious Diseases and Hospital Epidemiology, Kantonsspital St. Gallen and Children’s Hospital of Eastern Switzerland.

Availability of data and materials

The dataset supporting the conclusions of this article can be obtained from the authors upon request.

Authors’ contributions

All the authors met authorship criteria. LMM, WCA, CK conceived the study, generated and designed the research plan. Data collection was performed by LMM. Data analysis was conducted by LMM and supervised by WCA. CK, FR and PV assisted with the clinical interpretation of the data. LMM and WCA wrote the first draft of the manuscript. All authors critically reviewed the manuscript for important intellectual content and agreed with the manuscript results and conclusions. All read and approved the final manuscript.

Competing interests

The authors declare that they have no competing interests.

Ethics approval and consent to participate

The study was approved by the cantonal ethics review board (EKSG 14/140). Due to the retrospective nature of the study, informed consent was waived.

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

Authors’ Affiliations

(1)
School of Medicine, University of Basel
(2)
Children’s Hospital of Eastern Switzerland
(3)
Clinic for Pulmonology & Sleep Medicine, Kantonsspital St. Gallen
(4)
Division of Infectious Diseases & Hospital Epidemiology, Kantonsspital St. Gallen

References

  1. Musher DM, Roig IL, Cazares G, Stager CE, Logan N, Safar H. Can an etiologic agent be identified in adults who are hospitalized for community-acquired pneumonia: results of a 1-year study. J Infect. 2013;67:11–8. doi:https://doi.org/10.1016/j.jinf.2013.03.003.View ArticlePubMedGoogle Scholar
  2. Lieberman D, Korsonsky I, Ben-Yaakov M, Lazarovich Z, Friedman MG, Dvoskin B, et al. A comparative study of the etiology of adult upper and lower respiratory tract infections in the community. Diagn Microbiol Infect Dis. 2002;42:21–8.View ArticlePubMedGoogle Scholar
  3. van de Pol AC, Wolfs TF, Tacke CE, Uiterwaal CS, Forster J, Van Loon AM, et al. Impact of PCR for respiratory viruses on antibiotic use: theory and practice. Pediatr Pulmonol. 2011;46:428–34. doi:https://doi.org/10.1002/ppul.21385.PubMedGoogle Scholar
  4. Wishaupt JO, Russcher A, Smeets LC, Versteegh FG, Hartwig NG. Clinical impact of RT-PCR for pediatric acute respiratory infections: a controlled clinical trial. Pediatrics. 2011;128:e1113–20. doi:https://doi.org/10.1542/peds.2010-2779.View ArticlePubMedGoogle Scholar
  5. Creer DD, Dilworth JW, Gillespie SH, Johnston AR, Ling C, Patel S, et al. Aetiological role of viral and bacterial infections in acute adult lower respiratory tract infection (LRTI) in primary care. Thorax. 2006;61:75–9.View ArticlePubMedGoogle Scholar
  6. Rhedin S, Lindstrand A, Rotzén-Östlund M, Tolfvenstam T, Ohrmalm L, Rinder MR, et al. Clinical utility of PCR for common viruses in acute respiratory illness. Pediatrics. 2014;133:e538–45. doi:https://doi.org/10.1542/peds.2013-3042.View ArticlePubMedGoogle Scholar
  7. Oosterheert JJ, Van Loon AM, Schuurman R, Hoepelman AI, Hak E, Thijsen S, et al. Impact of rapid detection of viral and atypical bacterial pathogens by real-time polymerase chain reaction for patients with lower respiratory tract infection. Clin Infect Dis. 2005;41:1438–44.View ArticlePubMedGoogle Scholar
  8. van de Pol AC, Wolfs TF, Jansen NJ, Van Loon AM, Rossen JW. Diagnostic value of real-time polymerase chain reaction to detect viruses in young children admitted to the pediatric intensive care unit with lower respiratory tract infection. Crit Care. 2006;10:R61.View ArticlePubMedPubMed CentralGoogle Scholar
  9. Nolte FS. Molecular diagnostics for detection of bacterial and viral pathogens in community-acquired pneumonia. Clin Infect Dis. 2008;47:S123–6. doi:https://doi.org/10.1086/591392.View ArticlePubMedGoogle Scholar
  10. Templeton KE, Scheltinga SA, van den Eeden WC, Graffelman AW, van den Broek PJ, Claas EC. Improved diagnosis of the etiology of community-acquired pneumonia with real-time polymerase chain reaction. Clin Infect Dis. 2005;41:345–51.View ArticlePubMedGoogle Scholar
  11. Sanghavi SK, Bullotta A, Husain S, Rinaldo CR. Clinical evaluation of multiplex real-time PCR panels for rapid detection of respiratory viral infections. J Med Virol. 2012;84:162–9. doi:https://doi.org/10.1002/jmv.22186.View ArticlePubMedGoogle Scholar
  12. Johansson N, Kalin M, Tiveljung-Lindell A, Giske CG, Hedlund J. Etiology of community-acquired pneumonia: increased microbiological yield with new diagnostic methods. Clin Infect Dis. 2010;50:202–9. doi:https://doi.org/10.1086/648678.View ArticlePubMedGoogle Scholar
  13. Ruuskanen O, Lahti E, Jennings LC, Murdoch DR. Viral pneumonia. Lancet. 2011;377:1264–75. doi:https://doi.org/10.1016/S0140-6736(10)61459-6.View ArticlePubMedGoogle Scholar
  14. Martin ET, Fairchok MP, Stednick ZJ, Kuypers J, Englund JA. Epidemiology of multiple respiratory viruses in childcare attendees. J Infect Dis. 2013;207:982–9. doi:https://doi.org/10.1093/infdis/jis934.View ArticlePubMedGoogle Scholar
  15. Walsh EE, Peterson DR, Kalkanoglu AE, Lee FE, Falsey AR. Viral shedding and immune response to respiratory syncytial virus infection in older adults. J Infect Dis. 2013;207:1424–32. doi:https://doi.org/10.1093/infdis/jit038.View ArticlePubMedPubMed CentralGoogle Scholar
  16. Bakaletz LO. Viral potentiation of bacterial superinfection of the respiratory tract. Trends Microbiol. 1995;3:110–4.View ArticlePubMedGoogle Scholar
  17. Falsey AR, Becker KL, Swinburne AJ, Nylen ES, Formica MA, Hennessey PA, et al. Bacterial complications of respiratory tract viral illness: a comprehensive evaluation. J Infect Dis. 2013;208:432–41. doi:https://doi.org/10.1093/infdis/jit190.View ArticlePubMedPubMed CentralGoogle Scholar
  18. De Roux A, Ewig S, García E, Marcos MA, Mensa J, Lode H, et al. Mixed community-acquired pneumonia in hospitalised patients. Eur Respir J. 2006;27:795–800.View ArticlePubMedGoogle Scholar
  19. Van Gageldonk-Lafeber AB, Wever PC, van der Lubben IM, De Jager CP, Meijer A, De Vries MC, et al. The etiology of community-acquired pneumonia and implications for patient management. Neth J Med. 2013;71:418–25.PubMedGoogle Scholar
  20. Brittain-Long R, Westin J, Olofsson S, Lindh M, Andersson LM. Access to a polymerase chain reaction assay method targeting 13 respiratory viruses can reduce antibiotics: a randomised, controlled trial. BMC Med. 2011;9:44. doi:https://doi.org/10.1186/1741-7015-9-44.View ArticlePubMedPubMed CentralGoogle Scholar
  21. Stolz D, Christ-Crain M, Gencay MM, Bingisser R, Huber PR, Müller B, et al. Diagnostic value of signs, symptoms and laboratory values in lower respiratory tract infection. Swiss Med Wkly. 2006;136:434–40.PubMedGoogle Scholar
  22. Huijskens EG, Koopmans M, Palmen FM, Van Erkel AJ, Mulder PG, Rossen JW. The value of signs and symptoms in differentiating between bacterial, viral and mixed etiology in patients with community-acquired pneumonia. J Med Microbiol. 2014;63:441–52. doi:https://doi.org/10.1099/jmm.0.067108-0.View ArticlePubMedGoogle Scholar
  23. Ambrosioni J, Bridevaux PO, Wagner G, Mamin A, Kaiser L. Epidemiology of viral respiratory infections in a tertiary care centre in the era of molecular diagnosis, Geneva, Switzerland, 2011–2012. Clin Microbiol Infect. 2014;20:O578–84. doi:https://doi.org/10.1111/1469-0691.12525.View ArticlePubMedGoogle Scholar
  24. Bone RC, Balk RA, Cerra FB, Dellinger RP, Fein AM, Knaus WA, et al. Definitions for sepsis and organ failure and guidelines for the use of innovative therapies in sepsis. The ACCP/SCCM Consensus Conference Committee. American College of Chest Physicians/Society of Critical Care Medicine. Chest. 1992;101:1644–55.View ArticlePubMedGoogle Scholar
  25. Goldstein B, Giroir B, Randolph A. International pediatric sepsis consensus conference: definitions for sepsis and organ dysfunction in pediatrics. Pediatr Crit Care Med. 2005;6:2–8.View ArticlePubMedGoogle Scholar
  26. Rogers BB, Shankar P, Jerris RC, Kotzbauer D, Anderson EJ, Watson JR, et al. Impact of a rapid respiratory panel test on patient outcomes. Arch Pathol Lab Med. 2015;139:636–41. doi:https://doi.org/10.5858/arpa.2014-0257-OA.View ArticlePubMedGoogle Scholar
  27. Lee N, Chan MCW, Lui GCY, Li R, Wong RYK, Yung IMH, et al. High viral load and respiratory failure in adults hospitalized for respiratory syncytial virus infections. J Infect Dis. 2015;212(8):1237–40. doi:https://doi.org/10.1093/infdis/jiv248.View ArticlePubMedGoogle Scholar
  28. Hasegawa K, Jartti T, Mansbach JM, Laham FR, Jewell AM, Espinola JA, et al. Respiratory syncytial virus genomic load and disease severity among children hospitalized with bronchiolitis: Multicenter cohort studies in the United States and Finland. J Infect Dis. 2015;211(10):1550–9. doi:https://doi.org/10.1093/infdis/jiu658.View ArticlePubMedGoogle Scholar
  29. Johnstone J, Majumdar SR, Fox JD, Marrie TJ. Viral infection in adults hospitalized with community-acquired pneumonia: prevalence, pathogens, and presentation. Chest. 2008;134:1141–8. doi:https://doi.org/10.1378/chest.08-0888.View ArticlePubMedGoogle Scholar
  30. Cillóniz C, Ewig S, Polverino E, Marcos MA, Esquinas C, Gabarrús A, et al. Microbial etiology of community-acquired pneumonia and its relation to severity. Thorax 2011; 66: 340–346. Thorax. 2011;66:340–6. doi:https://doi.org/10.1136/thx.2010.143982.View ArticlePubMedGoogle Scholar
  31. Viasus D, Marinescu C, Villoslada A, Cordero E, Gálvez-Acebal J, Fariñas MC, et al. Community-acquired pneumonia during the first post-pandemic influenza season: a prospective, multicentre cohort study. J Infect. 2013;67:185–93. doi:https://doi.org/10.1016/j.jinf.2013.05.006.View ArticlePubMedGoogle Scholar
  32. Michelow IC, Olsen K, Lozano J, Rollins NK, Duffy LB, Ziegler T, et al. Epidemiology and clinical characteristics of community-acquired pneumonia in hospitalized children. Pediatrics. 2004;113:701–7.View ArticlePubMedGoogle Scholar
  33. Choi SH, Hong SB, Ko GB, Lee Y, Park HJ, Park SY, et al. Viral infection in patients with severe pneumonia requiring intensive care unit admission. Am J Respir Crit Care Med. 2012;186:325–32. doi:https://doi.org/10.1164/rccm.201112-2240OC.View ArticlePubMedGoogle Scholar
  34. Jennings LC, Anderson TP, Beynon KA, Chua A, Laing RT, Werno AM, et al. Incidence and characteristics of viral community-acquired pneumonia in adults. Thorax. 2008;63:42–8.View ArticlePubMedGoogle Scholar
  35. Jain S, Self WH, Wunderink RG, Fakhran S, Balk R, Bramley AM, et al. Community-Acquired Pneumonia Requiring Hospitalization among U.S. Adults. N Engl J Med. 2015;373:415–27. doi:https://doi.org/10.1056/NEJMoa1500245.View ArticlePubMedPubMed CentralGoogle Scholar
  36. Ghani AS, Morrow BM, Hardie DR, Argent AC. An investigation into the prevalence and outcome of patients admitted to a pediatric intensive care unit with viral respiratory tract infections in Cape Town, South Africa. Pediatr Crit Care Med. 2012;13:e275–81. doi:https://doi.org/10.1097/PCC.0b013e3182417848.View ArticlePubMedGoogle Scholar
  37. Rice TW, Rubinson L, Uyeki TM, Vaughn FL, John BB, Miller 3rd RR, et al. Critical illness from 2009 pandemic influenza A virus and bacterial coinfection in the United States. Crit Care Med. 2012;40:1487–98. doi:https://doi.org/10.1097/CCM.0b013e3182416f23.View ArticlePubMedPubMed CentralGoogle Scholar
  38. Diederen BM, Van Der Eerden MM, Vlaspolder F, Boersma WG, Kluytmans JA, Peeters MF. Detection of respiratory viruses and Legionella spp. by real-time polymerase chain reaction in patients with community acquired pneumonia. Scand J Infect Dis. 2009;41:45–50. doi:https://doi.org/10.1080/00365540802448799.View ArticlePubMedGoogle Scholar
  39. Bello S, Mincholé E, Fandos S, Lasierra AB, Ruiz MA, Simon AL, et al. Inflammatory response in mixed viral-bacterial community-acquired pneumonia. BMC Pulm Med. 2014;14:123. doi:https://doi.org/10.1186/1471-2466-14-123.View ArticlePubMedPubMed CentralGoogle Scholar
  40. Marcos MA, Camps M, Pumarola T, Martinez JA, Martinez E, Mensa J, et al. The role of viruses in the etiology of community-acquired pneumonia in adults. Antivir Ther. 2006;11(3):351–9.Google Scholar
  41. Filice GA, Drekonja DM, Thurn JR, Hamann GM, Masoud BT, Johnson JR. Diagnostic Errors that Lead to Inappropriate Antimicrobial Use. Infect Control Hosp Epidemiol. 2015;36:949–56. doi:https://doi.org/10.1017/ice.2015.View ArticlePubMedGoogle Scholar
  42. Gadsby NJ, Russell CD, Mchugh MP, Mark H, Conway Morris A, Laurenson IF, et al. Comprehensive molecular testing for respiratory pathogens in community-acquired pneumonia. Clin Infect Dis. 2016;62(7):817–23. doi:https://doi.org/10.1093/cid/civ1214.View ArticlePubMedPubMed CentralGoogle Scholar

Copyright

© The Author(s) 2017

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