It doesn’t take long for mold to grow on empty beer bottles. Considering beer bottles get returned for a refund, you have to assume that the brewery will make an effort to reuse as many as possible.
I toured a brewery once and they showed us the big industrial bottle washing machine. They said the bottles get scanned for cracks using a laser, and rejects obviously get tossed. The question is: what about mold, which adheres quite well to the corners of the glass? I wonder if the laser also detects bottles that didn’t get clean. Or if they just figure the temps would kill everything and just be considered safe enough from there.
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I am aware that that happened in Oregon once, and even though the parts per million after one person’s bladder is empted into a tank of thousands of gallons is negligible, they emptied the whole water tank which covered a whole city and refilled it, and sent the guy a water bill for that.
I suggest watching the “how beer saved the world” documentary. It shows how they used filthy stagnant pond water with duck shit in it to brew beer, which was safe after the brewing process. But note the beer container is not part of the brewing process.
The water is not much of a risk. But filled bottles sit in warehouses with rats. Rats urinate on the bottles. This is why Europeans don’t drink directly from the bottle. I’m not sure why Americans are content drinking direct from the bottles… maybe US warehouses are rat-free.