this took place during the napoleonic wars (1803-15), but the doctor expresses guilt about people dying from his infections. i don't think medicine understood infections back then.
shareMedicine didn't understand infections *well* back then, but they understood that some wounds could get infected and that any little infection could turn deadly, and that women who gave birth were likely to die of "childbed fever" (infection caused by poor hygiene). There were no antibiotics back then and even sulfur-based anti-bacterial medications didn't come along until the 20th century, so in the early 19th century doctors like Maturin had absolutely nothing that worked against localized infections or infectious diseases... which wouldn't stop a caring doctor from feeling guilty when his pathetic medicines fail and he either had to amputate a limb for lack of alternatives, or watch another patient be buried at sea.
The books are really well-researched, BTW, they're written by a historian who decided to have some fun with his knowledge base. The medical stuff is accurate and interesting, and the books are just great fun.