If you ever worry that you're a bit too optimistic about the future, try reading Maryn McKenna's posts about the growing threat of antibiotic resistance. The primary tools we've had to combat microbial disease for the past century are failing, and it's largely our own fault. Antibiotic resistance genes (or ARGs) are spreading fast, and we're running out of tricks to get around them.

But the problem is not really that ARGs exist - they've been around for millions, perhaps billions of years. Most of the antibiotics we use weren't invented by people, they were invented by microbes that wanted to kill other microbes, and the arms-race between anti-microbial compounds and resistance to those compounds has been going on long before we came along and noticed it. The problem is that those ARGs can fairly easily make the jump from harmless bugs battling fungus in the soil to battling our pharmaceuticals in hospital beds.

Pathogens containing antibiotic resistance genes usually pop up within a few months or years of doctors starting to use it (this was even true of our first antibiotic, penicillin), but it's still an open question as to where and how this jump happens. Certainly, a patient that's harboring an antibiotic resistant bug that takes subclinical doses of that antibiotic is going to select for the resistant bug, but resistance doesn't appear out of nowhere. There must be a place where pathogens and non-pathogens harboring resistance genes are commingling under the selective pressure of that antibiotic. One potential source is agriculture, where animals are loaded up with antibiotics even when they're not sick (for more on this, McKenna is again an excellent resource). But agricultural misuse, though clearly a problem, can't be the only explanation.

But a new paper in the journal of the International Society for Microbial Ecology (ISME) identifies another, potentially more worrying source: wastewater from hospitals.

Nadine Czekalski and colleagues at the Swiss Federal Institute of Aquatic Science and Technology analyzed the sediment in a bay of Lake Geneva at different distances from a waste water pipe that feeds into the lake. Critically, this waste-water pipe is the terminus of wastewater from a major Swiss hospital, and many microbes manage to make it through the waste water treatment facility. Since many human pathogens are likely to be in hospital effluent, and since antibiotic levels in hospital waste water is likely to be high, they hypothesized that this interaction of hospital microbes and environmental microbes would be a potent swapping ground.

And indeed, that's what they saw. They analyzed microbes found in the sediment at multiple points surrounding the pipe opening for the presence of many known antibiotic resistance genes, and found that the sites closest to the pipe had the largest abundance. Further, levels decreased the further away from the pipe they sampled.

I'd love to see how this compares to similar pipes from residential neighborhoods, or in any event, those that don't come from hospitals. It makes conceptual sense that hospital waste would be a larger source of ARGs, but a direct comparison would be great. Antibiotic resistance is a crisis, and we need to know what we're dealing with before we can hope to get a handle on the problem.