Infections caused by rare micro-organisms are the subject of research, as researchers are encouraged to find the necessary health measures to prevent and treat the disease, as well as the search for new insights into human-microbial interactions. This report describes the case of a newborn boy diagnosed with hydrocephalus and myelomeningocele who developed ventriculitis and sepsis from resistant Empedobacter brevis. This case highlights the unexpected identification of this bacterium in the cerebrospinal fluid and its multi-resistant pattern, which was crucial for proper therapeutic management. This bacterium shows a mixture of different etiologies in the analysis of cerebrospinal fluid.