Viral and bacterial causes of severe acute respiratory illness among children aged less than 5 years in a high malaria prevalence area of Western Kenya, 2007-2010

Daniel R. Feikin, M. Kariuki Njenga, Godfrey Bigogo, Barrack Aura, George Aol, Allan Audi, Geoffrey Jagero, Peter O. Muluare, Stella Gikunju, Leonard Nderitu, Jonas M. Winchell, Eileen Schneider, Dean D. Erdman, M. Steven Oberste, Mark A. Katz, Robert F. Breiman

Research output: Contribution to journalReview articlepeer-review

53 Scopus citations


Background: Few comprehensive data exist on the etiology of severe acute respiratory illness (SARI) among African children. Methods: From March 1, 2007 to February 28, 2010, we collected blood for culture and nasopharyngeal and oropharyngeal swabs for real-time quantitative polymerase chain reaction for 10 viruses and 3 atypical bacteria among children aged <5 years with SARI, defined as World Health Organization-classified severe or very severe pneumonia or oxygen saturation <90%, who visited a clinic in rural western Kenya. We collected swabs from controls without febrile or respiratory symptoms. We calculated odds ratios for infection among cases, adjusting for age and season in logistic regression. We calculated SARI incidence, adjusting for healthcare seeking for SARI in the community. Results: Two thousand nine hundred seventy-three SARI cases were identified (54% inpatient, 46% outpatient), yielding an adjusted incidence of 56 cases per 100 person-years. A pathogen was detected in 3.3% of noncontaminated blood cultures; non-typhi Salmonella (1.9%) and Streptococcus pneumoniae (0.7%) predominated. A pathogen was detected in 84% of nasopharyngeal/oropharyngeal specimens, the most common being rhino/enterovirus (50%), respiratory syncytial virus (RSV, 22%), adenovirus (16%) and influenza viruses (8%). Only RSV and influenza viruses were found more commonly among cases than controls (odds ratio 2.9, 95% confidence interval: 1.3-6.7 and odds ratio 4.8, 95% confidence interval: 1.1-21, respectively). Incidence of RSV, influenza viruses and S. pneumoniae were 7.1, 5.8 and 0.04 cases per 100 person-years, respectively. Conclusions: Among Kenyan children with SARI, RSV and influenza virus are the most likely viral causes and pneumococcus the most likely bacterial cause. Contemporaneous controls are important for interpreting upper respiratory tract specimens.

Original languageEnglish (US)
Pages (from-to)e14-e19
JournalPediatric Infectious Disease Journal
Issue number1
StatePublished - Jan 2013
Externally publishedYes


  • Africa
  • Kenya
  • Streptococcus pneumoniae
  • pneumonia
  • respiratory viruses
  • severe acute respiratory illness

ASJC Scopus subject areas

  • Pediatrics, Perinatology, and Child Health
  • Microbiology (medical)
  • Infectious Diseases


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