It is horrible to see small children go though medical tests - they are painful, and the child can't understand. Not pleasant.
However, meningococcal sepsis and other serious infections can go from looking like a standard viral infection to a fulminant disease in a very short period of time, and babies can't tell you symptoms, so without investigations it is often very difficult to diagonse until it is close to being too late.
As you say, only a very small percentage of children will have something "serious". But I would hate for it to be my child that was the "unlucky" one and have the diagnosis missed.
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