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It's your actions and intentions, so it's your karma.
Karma isn't a concept to tie you to your previous lives, it's a guide to further your future. Whatever hardships you face, the actions you choose will determine how close you can get to realizing the Beyond Within.
Though you are right, Hinduism/Jainism had no concept of microbes and/or modern biology. It is quite a struggle to judge 'how well' you are doing in this life with the realizations of sharing the world with soooooo many different lifeforms, but they themselves are causing you pain and accumulating 'bad' karma themselves, of which their consequences may be an antibiotic death.
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Think like a man of action, act like a man of thought. -H. Bergson
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