LRTI was defined by clinical signs or symptoms of respiratory tract infection and pulmonary infiltrate on radiographic imaging compatible with a bacterial or viral pneumonia (eg, consolidation, interstitial infiltrate, or ground-glass opacities). Healthcare visits and hospitalizations were classified as URI-related if URI symptoms were addressed in the encounter, regardless of the primary reason for the encounter. Peak flu season was defined as December through March [21 ]. Nasal swabs were submitted for respiratory viral testing at the clinicians’ discretion. Testing was generally performed using a laboratory-developed multiplex polymerase chain reaction (PCR) test that can detect 12 respiratory viruses [22–24 (link)]. Additional tests, including the Biofire FilmArray Respiratory Panel or Influenza-specific tests (Cepheid Xpert Flu), were also captured. Clostridioides difficile testing was performed using PCR (Xpert C. difficile; Cepheid).
Protocol detail
Respiratory Illness Diagnosis and Characterization
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Bacterial
Clostridioides
Hospitalizations
Multiplex polymerase chain reaction
Nasal
Polymerase chain reaction
Pulmonary
Radiographic
Respiratory
Respiratory tract infection
Viral pneumonia
Viruses
Corresponding Organization : Cape Town HVTN Immunology Laboratory / Hutchinson Centre Research Institute of South Africa
Other organizations : University of Nebraska Medical Center, Seattle Children's Hospital
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Variable analysis
independent variables
- Peak flu season (defined as December through March)
- Healthcare visits and hospitalizations
- Respiratory viral testing results
- Presence of URI symptoms during healthcare visits
- Clinicians' discretion in submitting nasal swabs for respiratory viral testing
- Use of laboratory-developed multiplex PCR test or other respiratory virus tests (Biofire FilmArray Respiratory Panel or Influenza-specific tests)
- PCR testing for Clostridioides difficile
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