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

Abstract

Background.: 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.

Methods.: 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.

Results.: 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).

Conclusions.: 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.

Keywords: children; colonization; etiology; pneumococcus; pneumonia.

Figure 1.

Pneumococcal colonization density by case and control group and Pneumonia Etiology Research for Child Health (PERCH) site; density was calculated by means of polymerase chain reaction (PCR) for the lytA gene performed on nasopharyngeal/oropharyngeal specimens from PCR-positive children. Diamonds represent group means; horizontal lines through boxes, group medians; dashed lines, areas outside the linear range of the assay for calculation of pneumococcal density from cycle threshold values, where there is a greater degree of uncertainty in density calculations. Boxes extend to the 25th and 75th percentiles and whiskers to minimum and maximum values. MCPP, microbiologically confirmed pneumococcal pneumonia; non-RTI, without respiratory tract illness.

Figure 2.

Pneumococcal colonization density distribution among cases with microbiologically confirmed pneumococcal pneumonia (MCPP) and controls (left) and among cases with MCPP by prior antibiotic use (right); density was calculated by means of polymerase chain reaction for the lytA gene performed on nasopharyngeal/oropharyngeal specimens. Dashed lines (densities less than 4 log₁₀ copies/ml and greater than 8 log₁₀ copies/ml) represent areas outside the linear range of the assay for calculation of pneumococcal density from cycle threshold values, where there is a greater degree of uncertainty in density calculations.

Figure 3.

Percentage of children with nasopharyngeal/oropharyngeal pneumococcal colonization density >6.9 log₁₀ copies/mL among positives, by site and case and control group; density was calculated by means of polymerase chain reaction for the lytA gene performed on nasopharyngeal/oropharyngeal specimens. Numbers above bars represent the number of microbiologically confirmed pneumococcal pneumonia (MCPP) cases at the site. RTI, respiratory tract illness.

Figure 4.

Pneumococcal colonization density by serotype of the invasive isolate among cases with microbiologically confirmed pneumococcal pneumonia (MCPP) or the colonizing isolate among all controls; density calculated by means of polymerase chain reaction for the lytA gene (copies/mL) performed on nasopharyngeal/oropharyngeal specimens. MCPP cases are limited to those for which the serotype of the invasive isolate was the same as that of the colonizing isolate. Shaded areas indicate areas outside the linear range of the assay for calculation of pneumococcal density from cycle threshold values, where there is a greater degree of uncertainty in density calculations.