How long does it take for the ceftriaxone injection and azythromycin to kill the bacterium in your system? I was recently diagnosed with gonorrhea and was given the single dose ceftriaxone injection and azythromycin. I'd imaging that the antibiotic would be out of your system in about 24-48 hours? So I'm guessing that the gonorrhea/chlamydia bacterium must be all killed within that time frame even though the symptom may last for a bit longer?