My Son Has Been Sick For About Three Days He

My son has been sick for about three days He was seen in the ER per his doctors request two days ago. His chief complaints where headache, sore neck and he had a fever. Every test under the sun was done on him , except one and that is meningitis . I refused the test just not feeling it was needed . yesterday his fever spiked to 104.5 , but immediately came down with meds. The fever has been staying around 99.8 ...but now he is complaining his eyes are hurting when he looks up. Should I be concerned about meningtis and could this be bacterial ?