BMC Infect Dis

BackgroundGlobally, 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.MethodsWe 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\uc2\ua0years 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 (BioM\uc3\ua9rieux, Luxemburg), which detects 23 respiratory pathogens including 18 viral and 5 bacterial agents.ResultsAmong the 160 samples tested, 138 (86\uc2\ua0%) tested positive for at least one viral or bacterial pathogen; in 22 (16\uc2\ua0%) sample, only one pathogen was detected. We detected at least one respiratory virus in 126 (78\uc2\ua0%) samples and at least one bacterium in 102 (64\uc2\ua0%) samples. Respiratory syncytial virus (56/160; 35\uc2\ua0%), rhinovirus (47/160; 29\uc2\ua0%) and parainfluenza virus (39/160; 24\uc2\ua0%) were the most common viral pathogens detected. Among bacterial pathogens, Streptococcus pneumoniae (90/160; 56\uc2\ua0%) and Haemophilus influenzae type b (20/160; 12\uc2\ua0%) predominated.ConclusionsThe high prevalence of certain viral and bacterial pathogens among children