Antibiotic resistance can probably be considered the problem of the century. As infectious diseases evolve the ability to evade or disable more of our drugs, we're struggling to come up with alternative approaches to get them under control. Bacterial infections can often persist despite repeated antibiotic treatments, like the C. difficile that inspired one of the first fecal transplants in 1999.

But antibiotic resistance isn't always to blame for persistent infections. Antibiotic resistant bacteria arise from heritable mutations in classic Darwinian fashion. If a bacterial population is exposed to an antibiotic and one cell has a genetic mutation that allows it to survive, all of its fellow cells will be killed, but the survivor will grow and divide. All of its progeny will inherit the mutation and therefore the resistance.

By contrast, some persistent infections can arise from special cells—persisters—that slow down their metabolism and cell division. Persisters aren't killed by antibiotics, but these cells leave behind progeny that can actually be susceptible to the drugs. How do bacterial cells become persisters? In one case, by getting eaten by immune cells.

In 2010, Sophie Helaine and her colleagues demonstrated that when mice are infected with Salmonella, a certain percentage of bacterial cells become non-dividing persisters. To track these cells, she used a technique she called fluorescent dilution. She engineered Salmonella cells to express a fluorescent protein upon exposure to a given chemical. Once the chemical is removed, as the cells divide, each daughter cell gets only half the amount of fluorescent protein, so the total fluorescence of the population keeps going down.

Or at least most of the population. The bacteria within immune cells called macrophages maintained their bright fluorescence during the infection, indicating that these cells were not dividing and growing. Now, Helaine has gone on to show that some of these nongrowing cells become the persisters that may seed subsequent infections.

Within minutes of infection, some percentage of bacteria gets eaten by macrophages, a process that is part of the body's normal response to pathogens. Some of the bacteria that get engulfed replicate and some do not. (Those that do not retain their fluorescence in these experiments.) Even after being stuck in a digestive organelle for 72 hours, 20 percent of the nonreplicators were fully able to grow once they were liberated "and may thus be a source of relapsing infection."

What is it about the macrophages that induces persistence? When eaten, bacteria are phagocytosed (subsumed) into the highly acidic digestive vacuole within macrophages. The conditions there—acid and with very few nutrients—also happen to induce Salmonella persistence. In addition to these external conditions, about 14 Salmonella genetic elements were also found to be necessary for persister formation. Oddly, nonpathogenic E. coli forms persisters by a different mechanism: it uses different genes and does not require passage through macrophages.

Getting eaten by vacuoles pushes Salmonella cells to enter one of a number of quiescent states. Some continue replicating; some die; some stay dormant; but some remain metabolically active and can start to grow again once released. The authors speculate that this heterogeneity may help the bugs survive antibiotic exposures as well as the immune system's attempt to clear the infection.

Science, 2014. DOI: 10.1126/science.1244705 (About DOIs).