Molecular diagnosis of multiple bacterial zoonoses in febrile outpatients in north-eastern Kenya

Abstract Bacterial zoonoses are important causes of non-malarial fevers in Kenya, yet their epidemiology remains unclear. We investigated brucellosis, Q-fever and leptospirosis in 216 malaria-negative febrile patients recruited in two health centres in Garissa County in north-eastern Kenya. We determined exposure to the three zoonoses using serological and molecular testing and identified risk factors for exposure. We also used metagenomic sequencing on nine selected patients to assess the presence of other possible bacterial causes of non-malarial fevers. High PCR positivity was found for Brucella and Leptospira spp., and high endpoint titres were observed against leptospiral serovar Grippotyphosa from the serological testing. Patients aged 5-17 years old had 4.02 (95% CI: 1.18-13.70, p-value = 0.03) and 2.42 (95% CI: 1.09- 5.34, p-value = 0.03) times higher odds of infection with Brucella spp. and C. burnetii than those of ages 35-80. The source of water was also a significant predictor for exposure to C. burnetii . Other bacterial infections including those caused by Streptococcus spp. were determined using metagenomic sequencing. The substantial evidence for non-malarial fevers in healthcare centres in Garissa County calls for their inclusion in routine diagnosis to lower the human disease burden and ensure better health outcomes, especially in younger populations.