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I feel like there is some conflation between several things: bacteria, viruses, mold, yeast, microorganisms. I am willing to bet that the terms are more ambiguous in Japanese than in English. It is a nice attention to detail that they are trying to show germ theory in the same ways that it was supported in our world. That microscope is a huge leap forward compared to the earliest microscopes used on Earth.
You also have to consider what the prince was thinking about Serea, that she was a child in her previous world and that her understanding of medicine comes from her being a patient in her past life.
Or, in more simple terms, the author has no clue.
