What could cause a chipmunk’s side to swell and produce a hole in the middle of the spot?
The chipmunk is likely infected with a parasitic warble, a bot fly in its larval stage. The larvae of bot flies (of the family Oestridae) are parasites on a wide range of mammals. The various species of bot fly are host-specific, so a rodent bot fly (genus Cuterebra) cannot infect humans. (There is a species of bot fly that infects humans in the tropics, but you won’t encounter it in cottage country.)
This fly’s life cycle is interesting, if a bit unpleasant from the chipmunk’s perspective. The female typically lays her eggs along runways or at entrances to a rodent’s burrow. The eggs hatch in response to the sudden increase in temperature and moisture that happens when a rodent passes by, and the larvae enter their victims through the nose, mouth, or a small cut in the skin. Eventually they migrate to locations under the skin, where they develop into “warbles” that contain a breathing hole. When they mature, 20 to 40 days after the original infection, they emerge as leathery, black larvae. They then pupate in the soil, emerge as adult bot flies, and mate.
Compared with other parasites, fully grown bot fly larvae are huge in proportion to their host – 20–42 millimetres long by 7–10 millimetres wide. Though the swelling is undoubtedly uncomfortable and may even prevent the chipmunk from moving around freely, it’s not necessarily a major health risk. Once the larva crawls out, the animal will be relieved of its burden. The hole the larva leaves behind can, however, become infected and cause more problems than the warble itself. There’s no easy way to remove a warble, though, so we can’t do much more than cheer on the chipmunk and hope for the best.