BACKGROUND: Childhood pneumonia in developing countries is the foremost cause of morbidity and death. Fresh information on etiology is needed, considering the changing epidemiology of pneumonia in the setting of greater availability of effective vaccines, changing antibiotic use and improved access to care. We report here the Zambia site results of the Pneumonia Etiology Research for Child Health study on the etiology of pneumonia among HIV-uninfected children in Lusaka, Zambia. METHODS: We conducted a case-control study of HIV-uninfected children age 1-59 months admitted with World Health Organization-defined severe or very severe pneumonia to a large tertiary care hospital in Lusaka. History, physical examination, chest radiographs (CXRs), blood cultures and nasopharyngeal/oropharyngeal swabs were obtained and tested by polymerase chain reaction and routine microbiology for the presence of 30 bacteria and viruses. From age and seasonally matched controls, we tested blood and nasopharyngeal/oropharyngeal samples. We used the Pneumonia Etiology Research for Child Health integrated analysis to determine the individual and population etiologic fraction for individual pathogens as the cause of pneumonia. RESULTS: Among the 514 HIV-uninfected case children, 208 (40.5%) had abnormal CXRs (61 of 514 children were missing CXR), 8 (3.8%) of which had positive blood cultures. The overall mortality was 16.0% (82 deaths). The etiologic fraction was highest for respiratory syncytial virus [26.1%, 95% credible interval (CrI): 17.0-37.7], Mycobacterium tuberculosis (12.8%, 95% CrI: 4.3-25.3) and human metapneumovirus (12.8%, CrI: 6.1-21.8). CONCLUSIONS: Childhood pneumonia in Zambia among HIV-uninfected children is most frequently caused by respiratory syncytial virus, M. tuberculosis and human metapneumovirus, and the mortality remains high.
Zambia is a landlocked middle-income country in Southern Africa with relatively high infant mortality (56 per 1000) and HIV prevalence (19.4% among Lusaka women of child-bearing age).8 Childhood vaccines are widely available and distributed, although pneumococcal conjugate vaccine (PCV) was not introduced until the end of the study. Detailed country characteristics are available in Supplemental Digital Content 1, http://links.lww.com/INF/D850. This study was conducted at the University Teaching Hospital (UTH) in Lusaka, the densely populated capital of Zambia.9 UTH is a 1500-bed academic and tertiary healthcare facility in Lusaka serving the greater Lusaka district, including the most impoverished segments of the population, and is a referral center for the entire country. Access to mechanical ventilation was limited and rarely used. Obtaining radiographs required taking children to the Radiology Department at some distance from the pediatric wards and at the caregivers’ expense, therefore, were not routinely performed (for nonstudy patients). Oxygen, however, was routinely available. Nearly all children presenting to UTH are initially seen and evaluated at surrounding Lusaka clinics, transported (mostly by private means) to UTH and have often received initial antibiotics (typically benzylpenicillin G) from the clinic, if clinically indicated. Study participants were children 1–59 months of age living within the Lusaka catchment area. Details of study methods have been published elsewhere, and are described in Supplemental Digital Content 1, http://links.lww.com/INF/D850.5,10 Briefly, cases were children hospitalized between November 2011 and October 2013 with WHO-defined11 severe or very severe pneumonia (pre-2013), including cough and/or difficulty in breathing plus danger signs (central cyanosis, difficulty breast-feeding/drinking, vomiting everything, multiple or prolonged convulsions, lethargy/unconsciousness, or head nodding) defined as “very severe pneumonia,” or lower chest wall in-drawing in the absence of danger signs defined as “severe pneumonia.” Due to constraints in processing samples on weekends and study staffing, enrolment occurred on weekdays from 07:30 to 18:00 hours. Nighttime admissions were eligible for participation the following morning. Controls were children without case-defining pneumonia who were randomly selected from the community and frequency matched on age and season (within 3 weeks) to cases. They were not excluded if they had evidence of upper respiratory tract infections. Cases and controls were excluded if they had been hospitalized within the previous 14 days or if they were a PERCH study participant within 30 days; cases were also excluded if lower chest wall in-drawing resolved with bronchodilator challenge (if applicable). Standardized study clinical examinations for cases occurred on admission and at 24 and 48 hours. One-month postdischarge, examinations occurred to determine clinical and vital status. Chest radiographs (CXR) were obtained at admission from cases and classified as normal, consolidation, other infiltrate, consolidation and other infiltrate or uninterpretable as defined by the WHO standardized interpretation of pediatric CXRs.12,13 For controls, clinical assessments only occurred at time of enrolment in PERCH. Specimen collection, microbiologic testing and laboratory methods were highly standardized (Supplemental Digital Content 1, http://links.lww.com/INF/D850).14–20 Blood and nasopharyngeal/oropharyngeal (NP/OP) specimens were collected from cases and controls. Induced sputum and pleural fluid specimens (where clinically indicated) were collected from cases only for culture and polymerase chain reaction (PCR) testing. Positivity was defined using quantitative PCR density thresholds for four pathogens where there was similar prevalence in cases and controls; these include Streptococcus pneumoniae (≥2.2 log10 copies/mL) from whole blood17 and S. pneumoniae (≥6.9 log10 copies/mL),21 Haemophilus influenzae (≥5.9 log10 copies/mL),19 cytomegalovirus (CMV, ≥4.9 log10 copies/mL) and Pj (≥4 log10 copies/mL),19 NP/OP (CMV threshold analysis available from authors). HIV exposure status of the child was obtained from the mother’s health antenatal card or by maternal recall if card not available. All exposed children had HIV testing performed by DNA PCR or serology, as per Zambian National HIV Guidelines. Odds ratios and 95% confidence intervals (CIs) of pathogens detected on NP/OP PCR in cases compared with controls were calculated using logistic regression adjusted for age in months and presence of all other pathogens detected on NP/OP PCR to account for associations between pathogens. Logistic regression adjusted for age in months was used to compare clinical characteristics by case–control status and, among cases, by vital status. Results were stratified by age, severity, CXR status and mortality. P values <0.05 were considered significant. The percent of pneumonia due to each pathogen was estimated using the PERCH integrated analysis (PIA) method, which is described in detail elsewhere.22–24 In brief, the PIA is a Bayesian nested partially latent class analysis that integrates the results for each case from blood culture, NP/OP PCR, whole blood PCR for pneumococcus and induced sputum culture for Mycobacterium tuberculosis. The PIA also integrates test results from controls to account for imperfect test specificity of NP/OP PCR and whole blood PCR. Blood culture results (excluding contaminants) and induced sputum or gastric aspirate results for M. tuberculosis were assumed to be 100% specific (ie, the etiology for a case was attributed 100% to the pathogen that was detected in their blood by culture). The PIA accounts for imperfect sensitivity of each test/pathogen measurement by using a priori estimates of their sensitivity (ie, estimates regarding the plausibility range of sensitivity which varied by laboratory test method and pathogen). Sensitivity of blood culture was reduced if blood volume was low (<1.5 mL) or if antibiotics were administered before specimen collection. Sensitivity of NP/OP PCR for S. pneumoniae and H. influenzae was reduced if antibiotics were administered before specimen collection (Supplemental Digital Content 2, http://links.lww.com/INF/D851). As a Bayesian analysis, both the list of pathogens and their initial “prior” etiologic fraction (EF) values were specified a priori, which favored no pathogen over another (ie, “uniform”). The pathogens selected for inclusion in the analysis included any noncontaminant bacteria detected by culture in blood at any of the 9 PERCH sites, regardless of whether it was observed at the Zambia site specifically, Mycobacterium tuberculosis, and all of the multiplex quantitative PCR pathogens except those considered invalid because of poor assay specificity (Klebsiella pneumoniae25 and Moraxella catarrhalis). A category called “Pathogens Not Otherwise Specified” was also included to estimate the fraction of pneumonia caused by pathogens not tested for or not observed. A child negative for all pathogens would still be assigned an etiology, which would be either one of the explicitly estimated pathogens (implying a “false negative,” accounting for imperfect sensitivity of certain measurements) or not otherwise specified. The model assumes that each child’s pneumonia was caused by a single pathogen. Analyses were adjusted for age (<1 vs. ≥1 year) to account for differences in pathogen prevalences by this factor; analyses stratified by pneumonia severity could not adjust for age due to small sample size. For results stratified by case clinical data (eg, to CXR+, very severe, vital status, etc.), the test results from all controls were used. However, for analyses stratified by age, only data from controls representative of that age group were used. A separate integrated etiology model was run with in-hospital vital status as a covariate, adjusting for the child’s age. The PIA estimated both the individual- and population-level etiology probability distributions, each summing to 100% across pathogens where each pathogen has a probability ranging from 0% to 100%. The population-level EF estimate for each pathogen was approximately the average of the individual case probabilities and was provided with a 95% credible interval (95% CrI), the Bayesian analogue of the CI. Statistical analyses were conducted using SAS 9.3 (SAS Institute, Cary, NC), R Statistical Software 3.3.1 (The R Development Core Team, Vienna, Austria) and Bayesian inference software JAGS 4.2.0 (http://mcmc-jags.sourceforge.net/). The R package used to perform the PIA, named the Bayesian Analysis Kit for Etiology Research, is publicly available at https://github.com/zhenkewu/baker. The study protocol was approved by the Institutional Review Boards at Boston University, the Johns Hopkins Bloomberg School of Public Health in the United States and by the ERES Converge Ethical Review Committee in Zambia. Parents or guardians of participants provided written informed consent.