Clin Infect Dis. 2017 Jun 15;64(suppl_3):S317-S327. doi: 10.1093/cid/cix100.

Density of Upper Respiratory Colonization With Streptococcus pneumoniae and Its Role in the Diagnosis of Pneumococcal Pneumonia Among Children Aged <5 Years in the PERCH Study.

Baggett HC1,2, Watson NL3, Deloria Knoll M4, Brooks WA5,6, Feikin DR4,7, Hammitt LL4,8, Howie SRC9,10,11, Kotloff KL12, Levine OS4,13, Madhi SA14,15, Murdoch DR16,17, Scott JAG8,18, Thea DM19, Antonio M9,20,21, Awori JO8, Baillie VL14,15, DeLuca AN4,22, Driscoll AJ4, Duncan J23, Ebruke BE9, Goswami D6, Higdon MM4, Karron RA24, Moore DP14,15,25, Morpeth SC8,18,26, Mulindwa JM23, Park DE4,27, Paveenkittiporn W28, Piralam B29, Prosperi C4, Sow SO30, Tapia MD12, Zaman K6, Zeger SL31, O'Brien KL4; PERCH Study Group.

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Previous studies suggested an association between upper airway pneumococcal colonization density and pneumococcal pneumonia, but data in children are limited. Using data from the Pneumonia Etiology Research for Child Health (PERCH) study, we assessed this potential association.


PERCH is a case-control study in 7 countries: Bangladesh, The Gambia, Kenya, Mali, South Africa, Thailand, and Zambia. Cases were children aged 1-59 months hospitalized with World Health Organization-defined severe or very severe pneumonia. Controls were randomly selected from the community. Microbiologically confirmed pneumococcal pneumonia (MCPP) was confirmed by detection of pneumococcus in a relevant normally sterile body fluid. Colonization density was calculated with quantitative polymerase chain reaction analysis of nasopharyngeal/oropharyngeal specimens.


Median colonization density among 56 cases with MCPP (MCPP cases; 17.28 × 106 copies/mL) exceeded that of cases without MCPP (non-MCPP cases; 0.75 × 106) and controls (0.60 × 106) (each P < .001). The optimal density for discriminating MCPP cases from controls using the Youden index was >6.9 log10 copies/mL; overall, the sensitivity was 64% and the specificity 92%, with variable performance by site. The threshold was lower (≥4.4 log10 copies/mL) when MCPP cases were distinguished from controls who received antibiotics before specimen collection. Among the 4035 non-MCPP cases, 500 (12%) had pneumococcal colonization density >6.9 log10 copies/mL; above this cutoff was associated with alveolar consolidation at chest radiography, very severe pneumonia, oxygen saturation <92%, C-reactive protein ≥40 mg/L, and lack of antibiotic pretreatment (all P< .001).


Pneumococcal colonization density >6.9 log10 copies/mL was strongly associated with MCPP and could be used to improve estimates of pneumococcal pneumonia prevalence in childhood pneumonia studies. Our findings do not support its use for individual diagnosis in a clinical setting.


children; colonization; etiology; pneumococcus; pneumonia

PMID: 28575365 DOI: 10.1093/cid/cix100