| Sumario: | Bacterial zoonoses are diseases caused by bacterial pathogens that can be naturally transmitted between humans and vertebrate animals. They are important causes of non-malarial fevers in Kenya, yet their epidemiology remains unclear. We investigated brucellosis, Q-fever and leptospirosis in the venous blood of 216 malaria-negative febrile patients recruited in two health centres (98 from Ijara and 118 from Sangailu health centres) in Garissa County in north-eastern Kenya. We determined exposure to the three zoonoses using serological (Rose Bengal test for <i>Brucella</i> spp., ELISA for <i>C. burnetti</i> and microscopic agglutination test for <i>Leptospira</i> spp.) and real-time PCR testing and identified risk factors for exposure. We also used non-targeted metagenomic sequencing on nine selected patients to assess the presence of other possible bacterial causes of non-malarial fevers. Considerable PCR positivity was found for <i>Brucella</i> (19.4%, 95% confidence intervals [CI] 14.2–25.5) and <i>Leptospira</i> spp. (1.7%, 95% CI 0.4–4.9), 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 <i>Brucella</i> spp. and <i>Coxiella burnetii</i> than those of ages 35–80. Additionally, patients who sourced water from dams/springs, and other sources (protected wells, boreholes, bottled water, and water pans) had 2.39 (95% CI 1.22–4.68, p-value = 0.01) and 2.24 (1.15–4.35, p-value = 0.02) times higher odds of exposure to <i>C. burnetii</i> than those who used unprotected wells. <i>Streptococcus</i> and <i>Moraxella</i> spp. were determined using metagenomic sequencing. Brucellosis, leptospirosis, <i>Streptococcus</i> and <i>Moraxella</i> infections are potentially important causes of non-malarial fevers in Garissa. This knowledge can guide routine diagnosis, thus helping lower the disease burden and ensure better health outcomes, especially in younger populations.
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