Doxycycline after accutane

Started accutane 7 weeks ago. I was on 40mg daily except for week 5 I tried 80mg daily for the entire week but side effects were too much so I went back to 40. I now was told by my doctor I have a bacterial infection called ureaplasma (probably had it for a year now). The first line of treatment is doxycycline. My doctor told me to stop accutane for 1 week then begin doxycycline for 1 week. I know the drugs interact with one another. Maybe I should stop accutane for 2 weeks then begin the doxycycline? Has anybody been through a similar experience?