Any disease fit the following criteria:
-
Can only be treated by certain antibiotics (i.e. Vancomycin),
-
Not too obscure or rare;
-
Can happen to the youngest of the young and oldest of the old (and also healthy people,)
-
Not a biological weapon,
-
Requires several consecutive weeks of continuous antibiotics to treat (it’s critical that treatment not be interrupted - this is an important plot point,)
-
Is often deadly if untreated,
-
Not usually the result of injury?
One I thought of was MRSA, but any other candidates?
Probably not deadly enough, but have you considered Lupus?
c.difficile? I had to take 3 courses of antibiotics for this, which would normally be 30 days (my case was slightly different because I developed an allergy). This was 3 different antibiotics, which are listed on the wiki page as the most common course of treatment. It re-occurs after treatment fairly often (20%). If you don’t take your meds, it will come back. It’s nasty - I had a fever of 104 and I was so sick within 4 hours or so that I couldn’t walk without smashing into walls or falling over.
I was exposed at a hospital where I had been for a medical procedure, but there are other scenarios that would work.
It’s not glamorous, but it’s real. 
I’ll see if anything else comes to mind.
Would XDR TB (drug resistant tuberculosis) fit?
It is resistant to most of the antibiotics normally used to treat TB. Most people have heard of tuberculosis, so while the drug resistant version is fairly rare, it’s not going to come off as obscure to your readers. It’s not super-contagious, but anyone can catch it. It’s not a biological weapon. If you fail to follow the antibiotic treatment, you’ll end up with an even more drug resistant TB which may be very difficult, if not impossible, to treat. It is not usually a result of injury.
I don’t know how long the treatment for it lasts, but several rounds of antibiotics may be necessary if they can’t find one that the disease responds to.
This was my first thought. And despite its reputation as a “disease of antiquity”, tuberculosis is not rare – it’s still one of the leading causes of death worldwide, with 1,700,000 deaths per year, mostly in low-income, poverty-ridden countries such as India.
What about Lyme disease? Or peritonitis from a burst appendix?
Multi-drug resistant necrotizing *Pseudomonas aeruginosa. *OMG - had it about a year ago when it hit my pancreas. I was on ‘life support’ (but able to pull many various tubes unwittingly) for about two months (zero memory of any ventilator, thankfully). Came with bilat DVT’s and bilat PE’s as well. Produced a fistula between colon and stomach, so I now sport an ileostomy (shit-bag on mid-belly). Took two major surgeries (removing all the abcesses and ‘rot’) and then another smaller belly opening for yet another abscess removal. Benzo/opiate withdrawal was easy after all that (and lots more).
Hard for me to imagine a worse infection - would’ve rather have lost an arm or leg. A year later, I’m still weak as hell, and getting to walk again was near-traumatic.
Good to be home for last three months…I so love my wife!
Is that close, Velocity? 
Bacterial endocarditis checks all your boxes. CRE bacterial infections - particularly with a liver abscess primary or somesuch - could also work well.
Like you (and buddha_david) I went to various resistant TB types too. I initially passed it over as not meeting #5 - when I see “continuous antibiotic treatment” I immediately assumed IV antibiotic therapy - but, re-reading the requirements, it doesn’t actually says that…
Only remaining issue might be exposure route (presuming a US-based story…not much XDR here…yet).
Lupus is an autoimmune disease. Antibiotics don’t work for them. In fact, there is no treatment that actually cures it.
5 is debatable for TB … it depends on what you mean by “critical”. critical for the patient to live, or critical for the TB to be wiped out ? Well they wipe out TB over many months, but thats a TB which kills over 10 years perhaps.
Consumption … I was reading where Alan Turing’s colledge friend died from bovine TB, and another friends mother also died from it. They had sufferred from it for a decade or more.
Here’s a list of bacterial infections.
Any of them could easily evolve into a form that is quite deadly and so are critical that antibiotics are not interrupted.
The thing with TB is that is most cases, persons infected with TB never suffer, 90%, and in the remaining cases, 90% will suffer consumption ,which is just general malaise and coughing, without the symptoms of serious disease such as fever.
There are the rare case of the patient having first signs of TB soon after contracting it, and getting it as lethal fever …
and its possible that TB, and any of the bacteria, could evolve to change from a lesser threat to a serious one.
Thanks for the suggestions everyone.
What about meningitis, does it sound like a suitable candidate?
Hansen’s Disease?
Of course, a story about a leper is a different kind of story because of the considerable cultural baggage that illness comes with.
It’s the bit about continuous antibiotics for weeks/months that makes it tougher.
I’d suggest candidates like osteomyelitis or endocarditis. TB disease is good too. NOT latent TB infection, though.
Meningitis B. The scary thing is this can easily be spread by sharing food.
I would think bacterial meningitis would fit. Spreads easily, antibiotics are the only way to treat it.
In college, a guy in my dorm was diagnosed with bacterial meningitis, and pretty much everyone who lived on campus got antibiotics as a preventative. One fun thing: the antibiotic of choice was Rifampin, which causes your body fluids to turn red or pink, so they cautioned everyone that, no, that’s not blood in your urine, and you’ll probably not want to wear soft contacts for a little while, because they’ll get discolored.
Does it have to be bacterial? I had a nasty bout of CMV (cytomegalovirus) a few months ago and I needed over a month of daily anti-viral IV medication. Could be that someone could need the treatment for longer.