Specimen Collection and Laboratory Methods

Standardized specimen collection and laboratory procedures were followed in cases and controls, as previously described,^20–23 and are detailed in Supplemental Digital Content 1, http://links.lww.com/INF/D829. A blood culture and a chest radiograph was obtained from cases as part of the routine diagnostic work-up.²⁴ Study-specific specimens obtained from cases and controls included nasopharyngeal, oropharyngeal (NP/OP) swabs for multiplex real-time polymerase chain reaction (PCR) to detect 33 respiratory pathogens (Fast Track Diagnostics Respiratory Pathogens 33 test (FTD-33), Fast Track Diagnostics, Sliema, Malta), whole blood for detection of pneumococcal autolysin (lytA) by PCR,²⁵ and serum for antibiotic activity.²⁶ Age-appropriate HIV testing was also done, with consent, in all participants. HIV-exposure status was determined as detailed in Supplemental Digital Content 1, http://links.lww.com/INF/D829.