How can a medicine that kills germs help one germ take over?

Antibiotics can help a germ like Clostridioides difficile take over because they do not only kill the bacteria they are aimed at. Antibiotics are the most important agents for fighting bacterial infections, and they are widely used to treat and prevent them. But your gut is already full of bacteria. The gut flora defends against pathogens by fully colonising the space and making use of all available nutrients. When a course of antibiotics kills off competing bacteria in the intestine, whatever bacteria remain face less competition for space and nutrients. Disruption of the gut flora lets competitors such as C. difficile become established that are otherwise kept in check.

C. difficile is an unlikely villain. It was discovered in 1935 and found to be disease-causing only in 1978. It may live quietly in the colon without symptoms; about 2 to 5 percent of adults are carriers. When the crowd thins out, it multiplies and produces toxins. The result is watery diarrhoea, fever, nausea and abdominal pain, and C. difficile makes up about 20 percent of antibiotic-associated diarrhoea. Antibiotics also decrease short-chain fatty acid absorption, which adds to the watery diarrhoea.

It is hard to remove because of spores. When stressed, the bacteria produce spores that tolerate conditions that active bacteria cannot. The spores are heat-resistant and are not killed by alcohol-based hand cleansers or routine surface cleaning. Swallowed spores survive stomach acid, then germinate on exposure to bile acids and multiply in the colon.

None of this means antibiotics are a poor idea: they remain the most important agents against bacterial infections. It is a description of an ecosystem effect. In the gut, the microbes you do not notice are doing a job, and when they go, something else can take their place.