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In a population based study in New Dehli, where all children with fever received a blood culture, 14% of patients did not recover clinically with a 10 day course of ciprofloxacin, despite in vitro sensitivity of the organism (Sinha, Lancet 1999 354:734-7)
So even a well trained and clear thinking physician would conclude, I thought this was typhoid, but I gave the patient the best anti-typhoid drug available, and they did not recover.  So this must not have been typhoid.