Table 4 Eligibility criteria of the study population

Recruitment

Prospective, recruited from 2010 to 2012

Retrospective, recruited from 2005 to 2006.

Prospective, recruited from 2011 to 2012

Prospective, recruited from 2011 to 2012

Inclusion Criteria

1. Adults ≥18 years

2. Hospitalized with CAP, with radiologic evidence

3. Agreed to participate in the study

4. Available NPS, urine, and blood samples

1. Patients ≥18 years

2. Hospitalized with CAP, with radiologic evidence

3. Agreed to participate in the study

1. Children between 1 month and 17 years

2. Hospitalized with CAP, with radiologic evidence

3. Agreed to participate in the study

4. Under 15 days of symptoms

1. Adults ≥18 years

2. Agreed to participate in the study

3. Completely healthy, recruited from blood banks, or individuals with rheumatic conditions, without respiratory infection, who could be receiving tumor necrosis factor antagonists (anti-TNF)

Exclusion Criteria

1. Hospitalization during the 2 weeks prior to recruitment

2. Obstructive pneumonia due to lung cancer

3. Had received antibiotics for over 72 continuous hours at the time of admission

4. Severely immunocompromised by:

 • Steroid treatment (prednisone ≥0.3 mg/kg/day for 3 weeks or more or ≥1 mg/kg/day for ≥7 days; if using other steroids, an equivalent dose was considered)

 • Treatment with cytostatics (except low doses of methotrexate: ≤15 mg/week),

5. AIDS diagnosis, lymphocyte count CD4+ <200/mm³ in patients over 5 years of age or less than 15 % of patients under 5 granulocytopenia <500/mm³, or hematologic neoplasia.

1. Hospitalization during the 2 weeks prior to recruitment

2. Obstructive pneumonia due to lung cancer

3. Severely immunocompromised by:

 • Steroid treatment (prednisone ≥0.3 mg/kg/day for 3 weeks or more or ≥1 mg/kg/day for ≥7 days; if using other steroids, an equivalent dose was considered)

 • Treatment with cytostatics (except low doses of methotrexate: ≤15 mg/week),

 • AIDS diagnosis, lymphocyte count CD4+ <200/mm³ in patients over 5 years or less than 15 % patients under 5

 • granulocytopenia <500/mm³ or hematologic neoplasia.

1. Hospitalization during the 2 weeks prior to recruitment

2. Primary immunodeficiency or severe acquired immunodeficiency

3. Cystic fibrosis

4. Neurological alterations (cerebral palsy or neuromuscular disorders) or psychiatric alterations that kept the individual from signing the consent form,

5. Inborn errors of metabolism,

6. Bronchiolitis in children under 2

7. Hematologic neoplasia,

8. Granulocytopenia <500 cell/mm3

9. Non-infectious chronic neumopathy

10. Had AIDS or lymphocyte count CD4 < 15 % in children under 5 years

11. Individuals currently being treated with:

 • High-dose steroids (prednisone ≥0.3 mg/kg/day for 3 weeks or more, or ≥1 mg/kg/day for ≥7 days; if using other steroids, an equivalent dose was considered)

 • Treatment with cytostatics

12. Had received antibiotics for over 72 continuous hours at time of admission

1. Respiratory infections in the last month

2. Hospitalization during the 2 weeks prior to recruitment

3. Healthcare workers

4. Heart disease or chronic lung diseases

5. Cancer, granulocytopenia, or infection by HIV/AIDS

6. Individuals currently being treated with:

 • High-dose steroids (prednisone ≥0.3 mg/kg/day for 3 weeks or more or ≥1 mg/kg/day for ≥7 days; if using other steroids, an equivalent dose was considered)

 • Treatment with cytostatics

 • methotrexate with doses >15 mg/week

7. Had received antibiotics for over 72 continuous hours at time of admission

Sample Type

NPS

NPA stored at −80 °C

NPS and IS

NPS

Commercial PCR used

Speed-Oligo®

Speed-oligo®

Seeplex® Pneumobacter

Speed-Oligo®