Molecular Evaluation of Pediatric Joint Fluid

Principal Investigator: Kwabena Ampofo
Keywords: pneumonia , influenza , infection , sequencing , generation Department: Pediatric Administration
IRB Number: 00086496 Co Investigator:  
Specialty: Pediatric Infectious Diseases
Sub Specialties:
Recruitment Status: Recruiting

Contact Information

Priscilla  Cowan

Brief Summary

Community Acquired pneumonia (CAP) is a major cause of morbidity and mortality worldwide. Young children and older adults are particularly vulnerable. According to the World Health Organization (WHO) CAP is one of the leading cause of death in young children and older adults. In the United States, pneumonia and influenza are among the eighth leading causes of death. In the recent Etiology of Pneumonia in the Community (EPIC) study, the annual incidence of CAP was 15.7 cases per 10,000 children, with the highest rate among children younger than 2 years of age (62.2 cases per 10,000 children).  In adults, the annual incidence of CAP was 24.8 cases per 10,000 adults, with the highest rates among adults 65 to 79 years of age (63.0 cases per 10,000 adults) and those 80 years of age or older (164.3 cases per 10,000 adults).

Vaccines administered to children and adults have changed the etiologic profile of CAP, with respiratory viruses detected more common than bacteria. However despite the advances in microbiologic diagnostics, no pathogen were detected in 25% of children and 75% of adults with CAP in the EPIC study. The limitations of present diagnostics result in empirical clinical management of children and adults with CAP. Greater knowledge about the etiology of pediatric and adult CAP will improve clinical care and better prepare the nation for pandemic influenza. Newer investigational technology (e.g. next-generation sequencing (NGS)) now available have the potential to improve diagnostics in medicine. The NGS technology, makes it attractive to detect novel pathogens in patients with CAP. Such high throughput sequencing permits the identification of all nucleic acid sequences (viruses, bacteria and human) in a respiratory sample, provides the opportunity for identifying a broader spectrum of organism regardless of priori sequence knowledge, and is therefore ideal for application in novel virus and bacteria discovery.

In the absence of the detection of a pathogen, it is further challenging to differentiate viral from bacterial pneumonia due to their similar signs and symptoms. Even when a respiratory pathogen (e.g.  human rhinovirus,) is identified, it is often difficult to determine whether it is causing disease, as many respiratory pathogens are shed by asymptomatic children and adults.

Children and adults respond to viral and bacterial infection through a unique combination of pathogen-associated molecular patterns that interact with specific pattern-recognition receptors expressed on immune cells. This interaction result in unique transcriptional signatures expressed of ribonucleic acid (RNA) in immune cells (e.g. white blood cells). Thus far, in a number of studies RNA signatures in white blood cells have been used to discriminate pathogen specific viral from bacterial infection. A study by Zaas et al. have shown that RNA can reliably evaluate expression profiles and discriminate between multiple respiratory viruses among patients with acute respiratory tract infections. As part of the EPIC study, we evaluated the expression of 35 transcriptional RNA signatures in respiratory samples from children with CAP and healthy controls and were able to differentiate viral from bacterial causes of CAP when compared to healthy controls. Some of the blood collected during this study will be used to look RNA expression profiles. RNA is NOT DNA and contains no information about the genes themselves. The RNA can help determine what infection is present based on their body’s immune responses.

The objectives of the proposed study is to identify respiratory pathogens not currently detected by a panel of diagnostic tests in hospitalized children and adults with radiologically-confirmed CAP and compare them to samples from healthy individuals using state of the art diagnostic methods (e.g. NGS technology). These include

  1. Characterize the viral and bacterial microbiome in endotracheal samples from children and adults with and without CAP (healthy controls).
  2. Identify variant strains, unexpected pathogens, or previously unrecognized viruses in samples of children and adults with CAP and healthy controls.
  3. Evaluate and compare host RNA transcriptional profiling in the respiratory tract and blood in patients with CAP and healthy controls.

Inclusion Criteria

Cases are defined as patients who demonstrate 1) evidence of acute infection on presentation, 2) signs or symptoms of respiratory illness on presentation and 3) new radiologic evidence of pneumonia.  For enrollment purposes, cases must meet ALL eight inclusion criteria:

  1. Hospitalized at a study hospital.
  2. Enrollment within 72 hours of admission.
  3. Patient is intubated.
  4. Evidence of acute infection on presentation is defined as at least one of the following:
    1. Fever with documented temperature 38°C.
    2. Hypothermia with documented temperature < 35.5°C.
    3. Reported fever, chills, or feeling feverish without documentation.
    4. Initiation of antibacterial antibiotics.
    5. Abnormal white blood cell count (leukocytosis or leukopenia) compared to baseline, if available.
      1. for patients <5 years: >15,000/mm3 or <5,500/mm3
      2. for patients 5 years: >11,000/mm3 or <3,000/mm3
    6. For adults only: Altered mental status (change from baseline).
  5. Signs or symptoms of respiratory illness on presentation is defined as at least one of the following:
    1. New or different cough.
    2. New or different sputum production.
    3. Chest pain.
    4. Dyspnea or shortness of breath.
    5. Documented tachypnea (age <2 mons: >60 breaths/minute; age 2 months to <12 mons: >50 breaths/minute; age 12 months to 5 yrs: >40 breaths/minute; age >5 yrs: >25 breaths/minute).
    6. Abnormal findings consistent with a diagnosis of pneumonia on physical examination of the chest (e.g. rales, rhonchi, wheezing, dullness).
    7. Acute respiratory failure requiring mechanical ventilation
  6. Radiologic evidence of pneumonia is defined as an abnormal chest radiograph that indicates a new pulmonary infiltrate, opacity, or consolidation at admission or within the first 48 hours of admission (standard of care radiograph obtained as part of routine care in the ICU).  Any radiographic study, including chest CT scans, can be used to confirm presence of a radiographic abnormality; however, all patients are required to have a chest radiograph within 48 hours of enrollment.  At the time of enrollment, patients may be enrolled based on either the treating clinician"s or an on-call radiologist's initial interpretation of the radiograph.
  7. Any patient with parapneumonic empyema, regardless of prior hospital encounters or time since current admission.
  8. Primary Children's Medical Center enrollment is limited to children who are > 1 week old and < 18 years old.
  9. University of Utah Medical Center is limited to adults who are > 18 years old.

Controls are defined as patients who are evaluated 1) at Primary Children's Hospital or the University of Utah Medical Center; 2) for reasons unrelated to acute respiratory illness (e.g. same-day surgery or outpatient lab draw); 3) do not exhibit any signs/symptoms of respiratory illness.

For enrollment purposes, controls must meet BOTH inclusion criteria:

  1. Visiting Primary Children's Hospital or University of Utah Medical Center for a reason unrelated to acute respiratory illness.
  2. No signs/symptoms of acute respiratory illness within 7 days preceding screening.


Exclusion Criteria

The following criteria will be used to exclude patients as cases and controls from the study:
1. Recent hospitalization in relation to potential enrollment
• Children: <7 days for immunocompetent OR <90 days for immunosuppressed OR newborns who never left the hospital
• Adults: <28 days for immunocompetent OR <90 days for immunosuppressed
2. Enrollment in this pneumonia study <28 days prior to potential re-enrollment
3. Adult nursing home patients who are not independently functioning or children who reside in a chronic care facility regardless of functional status.
4. HIV positive patients with CD4 cell count <200 cells/mm3 or CD4 per cent <14%. If CD4 cell count information not available at enrollment, okay to enroll patient.
5. Any solid organ or hematopoietic stem cell transplant patient within 90 days of most recent transplant, or with documented graft versus host disease (GVHD) or bronchiolitis obliterans (BOOP)
6. Adults with tracheostomy or percutaneous endoscopic gastrostomy tube. For children, only those with tracheostomy will be excluded. Children with percutaneous endoscopic gastrostomy tubes will be excluded if they were hospitalized <7 days from potential enrollment.
7. Cystic Fibrosis
8. Patients who have a clear alternate diagnosis