Background: Due to its diverse and non‐specific clinical presentations, malaria has been associated with most infections causing febrile illnesses. Despite being non-specific, clinical diagnosis is still the main method of malaria diagnosis in most health facilities in sub-Saharan Africa. This study aimed to establish the probable diagnoses among fever cases admitted at Bombo Hospital in north-eastern Tanzania.

Methods: This study involved patients admitted in Medical and Paediatric wards with a clinical diagnosis of severe malaria but having negative blood smears (BS) for malaria parasites. Finger prick blood specimens were collected for blood smear microscopy and rapid diagnostic test. Blood and urine cultures were done for all specimens collected. Some patients were also screened for HIV infection.

Results: A total of 227 patients were recruited and the majority (62.1%) were under-five children. Out of the 227 blood specimens cultured, 25 (11.0%) grew different bacteria species. Staphylococcus aureus was the most frequent pathogen (68.0%), followed by S. pneumoniae (24.0%), Salmonella species (4.0%) and Streptococcus pyogenes (4.0%). Only 7 (3.2%) out of 219 urine specimens cultured showed growth of Escherichia coli, Pseudomonas aeruginosa, S. aureus and Klebsiella pneumoniae . Of the 215 patients screened for HIV, 17 (7.9%) had positive reaction.

Conclusion: The findings indicate that S. aureus and S. pneumoniae as the commonest bacteria isolates from blood and P. aeruginosa, S. aureus and K. pneumoniae from urine cultures. These bacteria and HIV should be considered as important contributors to febrile illness cases among patients found with negative BS for malaria parasites.