FLINT, Mich. — By the time Robert Skidmore, an 85-year-old former auto industry worker, died in late 2015, officials had seen signs for months that Flint was wrestling with outbreaks of Legionnaires’ disease, prosecutors say. Yet despite a wave of such cases in 2014 and 2015, no public warning was issued until early 2016.

By then, it was too late for Mr. Skidmore and 11 others: a failing so egregious, prosecutors say, that it amounted to involuntary manslaughter.

Five officials in Michigan, including the head of the state’s health department, were charged on Wednesday. It is the closest investigators have come to directly blaming officials for the deaths and illnesses that occurred when a water contamination crisis enveloped this city.

The tainted water has been tied to lead poisoning in children and prompted officials to begin a costly, yearslong process of replacing pipes all over the city. Even now, officials recommend that only filtered tap water be consumed, and many residents say they can trust only bottled water, given false assurances they once received from state and local officials.