AD 1348 - 1665, Plague transmission rates increased 4x. So David Earn (McMaster U, Canada) and others.
Yersinia is a bacillus. Bacilli mutate, but not as fast as viruses. Yersinia itself mutated: it's been recorded in Central Asian skeletons from Andronovo / Sintasha (Aryan) and Afanasyevo (Tocharian? paraTocharian?). Septicaemic by then. I had the idea it weakened the Balkan Cucuteni culture, as well. Probably not Indus; they seem to have taken sanitation seriously.
These researchers don't think Yersinia was primarily airbourne in AD 1348, when it transmitted quite a bit. Person-to-person is mainly pneumonic. It should have knocked out 15% given its virulence; but it knocked out 30%. So Dr Earn told UPI. I'm unsure about the maths here and not really up for tracing it all down, so do read the preprint.
As to why this bug became more transmissible as the population decreased and cities were (supposedly) improving: at a guess, after the initial shock, cities started crowding in again. Cholera wasn't licked until AD 1854. And then there those Confederate idiots who tried spreading yellow fever among the Union with... blankets. So I fully believe that sanitation was slapdash and ineffective over the three centuries in question. No real need to suggest an improvement in the Yersinia genome.
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