I don't recall. But in old Europe, beer and wine were drunk instead of water, which was frequently contaminated. Maybe she got sick from the local water...? And isn't beer with its hops and yeast supposedly good for keeping the gut healthy? Just guessing here.
Sister Luke contracted TB, the doctor put her on something called "the gold treatment" and also called it "the gold dust cure", and said its rough on the kidneys; beer is great for running through your system fast, you can almost drink a beer and stand at the urinal at the same time. So, that's what I think, the beer helps cleanse her kidneys out, plus the added benefit from calories; beer is a healthy drink (in moderation), beer like wine is as much a food item as it is a beverage.
Dr. Fortunati being devilish by nature probably thought it would also do her spirit good getting a little beer drunk, I mean, what could be funnier than a drunken nun?