title: Etiology and Incidence of viral and bacterial acute respiratory illness among older children and adults in rural western Kenya, 2007-2010.
abstract: BACKGROUND
  Few comprehensive data exist on disease incidence for specific etiologies of acute respiratory illness (ARI) in older children and adults in Africa.
  
  
  RESULTS
  From March 1, 2007, to February 28, 2010, among a surveillance population of 21,420 persons >5 years old in rural western Kenya, we collected blood for culture and malaria smears, nasopharyngeal and oropharyngeal swabs for quantitative real-time PCR for ten viruses and three atypical bacteria, and urine for pneumococcal antigen testing on outpatients and inpatients meeting a ARI case definition (cough or difficulty breathing or chest pain and temperature >38.0 °C or oxygen saturation <90% or hospitalization). We also collected swabs from asymptomatic controls, from which we calculated pathogen-attributable fractions, adjusting for age, season, and HIV-status, in logistic regression. We calculated incidence by pathogen, adjusting for health-seeking for ARI and pathogen-attributable fractions. Among 3,406 ARI patients >5 years old (adjusted annual incidence 12.0 per 100 person-years), influenza A virus was the most common virus (22% overall; 11% inpatients, 27% outpatients) and Streptococcus pneumoniae was the most common bacteria (16% overall; 23% inpatients, 14% outpatients), yielding annual incidences of 2.6 and 1.7 episodes per 100 person-years, respectively. Influenza A virus, influenza B virus, respiratory syncytial virus (RSV) and human metapneumovirus were more prevalent in swabs among cases (22%, 6%, 8% and 5%, respectively) than controls. Adenovirus, parainfluenza viruses, rhinovirus/enterovirus, parechovirus, and Mycoplasma pneumoniae were not more prevalent among cases than controls. Pneumococcus and non-typhi Salmonella were more prevalent among HIV-infected adults, but prevalence of viruses was similar among HIV-infected and HIV-negative individuals. ARI incidence was highest during peak malaria season.
  
  
  CONCLUSIONS
  Vaccination against influenza and pneumococcus (by potential herd immunity from childhood vaccination or of HIV-infected adults) might prevent much of the substantial ARI incidence among persons >5 years old in similar rural African settings.
authors.affiliation: Global Disease Detection Division, Centers for Disease Control and Prevention, International Emerging Infections Program, Kisumu, Kenya. dfeikin@jhsph.edu
authors.forename: Daniel R
authors.initials: DR
authors.lastname: Feikin
authors.forename: M Kariuki
authors.initials: MK
authors.lastname: Njenga
authors.forename: Godfrey
authors.initials: G
authors.lastname: Bigogo
authors.forename: Barrack
authors.initials: B
authors.lastname: Aura
authors.forename: George
authors.initials: G
authors.lastname: Aol
authors.forename: Allan
authors.initials: A
authors.lastname: Audi
authors.forename: Geoffrey
authors.initials: G
authors.lastname: Jagero
authors.forename: Peter Ochieng
authors.initials: PO
authors.lastname: Muluare
authors.forename: Stella
authors.initials: S
authors.lastname: Gikunju
authors.forename: Leonard
authors.initials: L
authors.lastname: Nderitu
authors.forename: Amanda
authors.initials: A
authors.lastname: Balish
authors.forename: Jonas
authors.initials: J
authors.lastname: Winchell
authors.forename: Eileen
authors.initials: E
authors.lastname: Schneider
authors.forename: Dean
authors.initials: D
authors.lastname: Erdman
authors.forename: M Steven
authors.initials: MS
authors.lastname: Oberste
authors.forename: Mark A
authors.initials: MA
authors.lastname: Katz
authors.forename: Robert F
authors.initials: RF
authors.lastname: Breiman
mesh_terms: D000293:Adolescent; D000328:Adult; D016022:Case-Control Studies; D002648:Child; D002675:Child, Preschool; D005260:Female; D006801:Humans; D015994:Incidence; D009980:Influenza A virus / Q000302:isolation & purification*; D007251:Influenza, Human / Q000453:epidemiology* / Q000209:etiology* / Q000821:virology; D007630:Kenya / Q000453:epidemiology; D008297:Male; D008875:Middle Aged; D011159:Population Surveillance; D015995:Prevalence; D012141:Respiratory Tract Infections / Q000453:epidemiology* / Q000209:etiology* / Q000382:microbiology; D012424:Rural Population; D013296:Streptococcus pneumoniae / Q000302:isolation & purification*