Limited Utility of Polymerase Chain Reaction in Induced Sputum Specimens for Determining the Causes of Childhood Pneumonia in Resource-Poor Settings: Findings From the Pneumonia Etiology Research for Child Health (PERCH) Study

Abstract

Background.: Sputum examination can be useful in diagnosing the cause of pneumonia in adults but is less well established in children. We sought to assess the diagnostic utility of polymerase chain reaction (PCR) for detection of respiratory viruses and bacteria in induced sputum (IS) specimens from children hospitalized with severe or very severe pneumonia.

Methods.: Among children aged 1-59 months, we compared organism detection by multiplex PCR in IS and nasopharyngeal/oropharyngeal (NP/OP) specimens. To assess whether organism presence or density in IS specimens was associated with chest radiographic evidence of pneumonia (radiographic pneumonia), we compared prevalence and density in IS specimens from children with radiographic pneumonia and children with suspected pneumonia but without chest radiographic changes or clinical or laboratory findings suggestive of pneumonia (nonpneumonia group).

Results.: Among 4232 cases with World Health Organization-defined severe or very severe pneumonia, we identified 1935 (45.7%) with radiographic pneumonia and 573 (13.5%) with nonpneumonia. The organism detection yield was marginally improved with IS specimens (96.2% vs 92.4% for NP/OP specimens for all viruses combined [P = .41]; 96.9% vs 93.3% for all bacteria combined [P = .01]). After accounting for presence in NP/OP specimens, no organism was detected more frequently in the IS specimens from the radiographic pneumonia compared with the nonpneumonia cases. Among high-quality IS specimens, there were no statistically significant differences in organism density, except with cytomegalovirus, for which there was a higher quantity in the IS specimens from cases with radiographic pneumonia compared with the nonpneumonia cases (median cycle threshold value, 27.9 vs 28.5, respectively; P = .01).

Conclusions.: Using advanced molecular methods with IS specimens provided little additional diagnostic information beyond that obtained with NP/OP swab specimens.

Keywords: PCR; community-acquired pneumonia.; induced sputum; nasopharyngeal swab; pneumonia etiology.

Figure 1.

Multiplex polymerase chain reaction (PCR) pathogen detection in paired nasopharyngeal/oropharyngeal (NP/OP) swab and induced sputum (IS) specimens from 1114 children aged 1–59 months, hospitalized with radiographic evidence of pneumonia (consolidation and/or other infiltrates) and with a high-quality IS specimen available. Gray bars represent pathogen detected in both IS and NP/OP specimens; black bars, pathogen detected in NP/OP but not IS specimens; and hatched bars, pathogen detected in IS but not NP/OP specimens. High-quality IS specimens were defined as <10 squamous epithelial cells per low-power field; radiographic evidence of pneumonia was defined as consolidation and/or other infiltrates. Abbreviations: CMV, cytomegalovirus; HCoV, human coronavirus; HMPV, human metapneumovirus A/B; PV/EV, parechovirus/enterovirus; RSV, respiratory syncytial virus.

Figure 2.

Cycle threshold (Ct) values in induced sputum (IS) specimens of 28 pathogens among cases with radiographic evidence of pneumonia (n = 1166) and those in the nonpneumonia group (n = 398) who had a high-quality IS specimen available. Radiographic evidence of pneumonia was defined as consolidation and/or other infiltrates. Nonpneumonia was defined as a normal chest radiograph, blood culture negative for pathogens, and either (1) a normal respiratory rate or no hypoxemia in the absence of crackles or (2) a normal respiratory rate and no hypoxemia in the presence of crackles. Diamonds represent group means; boxes, interquartile ranges; vertical lines through boxes, group medians; whiskers, 95% confidence intervals; and numbers on right axis, cases with positive results. *Significant difference (P < .05) in density between radiographic pneumonia and nonpneumonia groups. Abbreviations: CMV, cytomegalovirus; HCoV, human coronavirus; HMPV, human metapneumovirus A/B; PV/EV, parechovirus/enterovirus; RSV, respiratory syncytial virus.