Non-malarial etiology of acute febrile episodes in children attending five healthcare facilities in Mwanza, Tanzania years 2020–2021

Acute febrile illness (AFI) is a common cause of pediatric hospital visits in developing countries. Identifying the broad range of pathogens that can cause fever is critical to: improving AFI management, preventing unnecessary prescriptions, and guiding public health interventions. Between March 2020 and December 2021, 436 children in Mwanza, Tanzania were enrolled with acute fever lasting < 7 days. Malaria MRDT and microscopy, dengue rapid NSI antigen, dengue serology, chikungunya serology, urinalysis, blood and urine cultures were conducted. Multiplex reverse-transcriptase-polymerase-chain-reaction-ELISAs (m-RT-PCR-ELISA) were also performed for malaria, dengue virus type 1–4, Zika virus, chikungunya virus, yellow fever virus, Rift Valley fever virus, and West Nile virus. Nasopharyngeal swabs obtained from 77 children were used to identify respiratory pathogens using a multiplex PCR panel. Bacteria or viruses in the bloodstream, urinary and upper respiratory tracts were identified in 26/436 (6%), 47/436 (10.8%), and 33/77 (43%) of the participants, respectively. Pneumonia was diagnosed in 59/436 cases and confirmed in 8 by chest X-ray. The majority of isolates recovered from the bloodstream and upper respiratory tract were resistant to antibiotics commonly used clinically. Those organisms were most commonly found in cases of AFI. To conclude, there is an urgent need for point-of-care diagnostic assays for AFI that strengthen existing infection prevention interventions and evidence-based antimicrobial stewardship programs.