I'm with Raryn. I'd say there's a 99.9% chance that the residency program is NOT going to allow something like this to prevent you from doing your residency there.
There will be hoops and perhaps even starting late (depends, from what I remember the injunction to not be around anyone is not for all that many days into your antibiotics (just what I remember vaguely writing on some dc paperwork for a coughing-up-blood TB'er after talking to the state health department)). But what's OK for gen pop is not always OK for docs.
Those antibiotics suck.
Take them correctly. I know of a med student who goofed up their doses like twice and it resulted in them having to take them for like 2x as long, like 10 months. Don't ask me. This is hearsay aside from the fact that you need to take taking any antibiotic regimen they give you very seriously.