Diagnosis of Neonatal Bacterial Meningitis Cerebrospinal fluid (CSF) cell counts, glucose and protein levels, Gram stain, and culture Polymerase chain reaction (PCR) testing Sometimes ultrasonography or CT or MRI of the brain Definitive diagnosis of neonatal bacterial meningitis is made by CSF examination via lumbar puncture (LP), which should be done in any neonate suspected of having sepsis or meningitis.