title: Viral and bacterial etiology of severe acute respiratory illness among children < 5 years of age without influenza in Niger.
abstract: BACKGROUND
  Globally, pneumonia is the leading cause of morbidity and mortality in children, with the highest burden experienced in sub-Saharan Africa and Asia. However, there is a dearth of information on the etiology of severe acute respiratory illness (SARI) in Africa, including Niger.
  
  
  METHODS
  We implemented a retrospective study as part of national influenza sentinel surveillance in Niger. We randomly selected a sample of nasopharyngeal specimens collected from children <5 years of age hospitalized with SARI from January 2010 through December 2012 in Niger. The samples were selected from individuals that tested negative by real-time reverse transcription polymerase chain reaction (rRT-PCR) for influenza A and B virus. The samples were analyzed using the Fast Track Diagnostic Respiratory Pathogens 21plus Kit (BioMérieux, Luxemburg), which detects 23 respiratory pathogens including 18 viral and 5 bacterial agents.
  
  
  RESULTS
  Among the 160 samples tested, 138 (86%) tested positive for at least one viral or bacterial pathogen; in 22 (16%) sample, only one pathogen was detected. We detected at least one respiratory virus in 126 (78%) samples and at least one bacterium in 102 (64%) samples. Respiratory syncytial virus (56/160; 35%), rhinovirus (47/160; 29%) and parainfluenza virus (39/160; 24%) were the most common viral pathogens detected. Among bacterial pathogens, Streptococcus pneumoniae (90/160; 56%) and Haemophilus influenzae type b (20/160; 12%) predominated.
  
  
  CONCLUSIONS
  The high prevalence of certain viral and bacterial pathogens among children <5 years of age with SARI highlights the need for continued and expanded surveillance in Niger.
authors.affiliation: Centre de Recherche Médicale et Sanitaire (CERMES), 634 Bld de la Nation, BP:10887, YN034-, Niamey, Niger. adamsyn03@gmail.com.
authors.forename: Adamou
authors.initials: A
authors.lastname: Lagare
authors.affiliation: Centre de Recherche Médicale et Sanitaire (CERMES), 634 Bld de la Nation, BP:10887, YN034-, Niamey, Niger. halima@cermes.org.
authors.forename: Halima Boubacar
authors.initials: HB
authors.lastname: Maïnassara
authors.affiliation: Centre de Recherche Médicale et Sanitaire (CERMES), 634 Bld de la Nation, BP:10887, YN034-, Niamey, Niger. bassira@cermes.org.
authors.forename: Bassira
authors.initials: B
authors.lastname: Issaka
authors.affiliation: Centre de Recherche Médicale et Sanitaire (CERMES), 634 Bld de la Nation, BP:10887, YN034-, Niamey, Niger. sidiki@cermes.org.
authors.forename: Ali
authors.initials: A
authors.lastname: Sidiki
authors.affiliation: Influenza Division, Centers for Disease Control and Prevention, Georgia, Atlanta, USA. stefanot@nicd.ac.za.|Influenza Program, Centers for Disease Control and Prevention, Pretoria, South Africa. stefanot@nicd.ac.za.
authors.forename: Stefano
authors.initials: S
authors.lastname: Tempia
mesh_terms: D002675:Child, Preschool; D005260:Female; D006801:Humans; D007223:Infant; D008297:Male; D009305:Nasopharynx / Q000382:microbiology / Q000821:virology; D009548:Niger / Q000453:epidemiology; D011008:Pneumococcal Infections / Q000453:epidemiology / Q000382:microbiology; D018357:Respiratory Syncytial Virus Infections / Q000453:epidemiology / Q000821:virology; D012136:Respiratory Syncytial Viruses / Q000235:genetics / Q000302:isolation & purification / Q000472:pathogenicity; D012141:Respiratory Tract Infections / Q000453:epidemiology / Q000382:microbiology* / Q000821:virology*; D018108:Respirovirus / Q000302:isolation & purification / Q000472:pathogenicity; D010253:Respirovirus Infections / Q000453:epidemiology / Q000821:virology; D012189:Retrospective Studies; D012229:Rhinovirus / Q000302:isolation & purification / Q000472:pathogenicity; D013296:Streptococcus pneumoniae / Q000302:isolation & purification / Q000472:pathogenicity