Then human overpopulation led to diseases like Cholera and Black Plague

Life is healthier out on the farm in the country or on a ranch with herding animals usually. 

So, when people gather in large cities this also draws rats and mice and other things and rats especially and mice carry all sorts of things including fleas that carry diseases to humans.

How would the humans get infected?

Likely their grain stores would be burrowed into by Rats especially because rats are known to gnaw through wood or even cement if there is some reason they want to get through this like under a house in the winter time to stay warmer so they don't freeze to death. So, likely rats and mice would get into the grains and when the people ate the grains in the Graneries the got the diseases from the rats and mice and fleas on both and millions died of things like Black Plague.

by the way a Granery is just where threshed Grain is Stored. So, people likely were infected in the large graneries but also wherever they stored it in their homes because rats can gnaw through anything wood or cement. So, unless it was some kind of metal thick enough to keep them out people were eventually going to get sick and die.

So, also this is where cooking food and boiling it came in too. Because cooking and boiling food kills most diseases.

In fact, the way we protected ourselves as a family as we traveled around from illness mostly was boiling any water we drank the night before we were going to use it. So, we carried army canteens on our hips (wife and I and three children) while traveling through India and Nepal especially.

When I saw someone filling the used water bottles with a hose in Thailand I realized that there is no real safe way to know when water is boiled or safe to drink at that time. So, we boiled it ourselves.

So, after that if we couldn't boil water to drink we bought Campos Orange sodas in India and Nepal especially because that had been cooked in the making which is a lot like Fanta Orange Soda sold here in the U.S.

We traveled across mostly Thailand, India and Nepal. We also went to Japan but then it was too expensive for a family of 5 to visit then when I was 37. But, Thailand India and Nepal were relatively inexpensive to visit then in 1985 and 1986 for us. The biggest expense is the air fare to fly there in the first place. At least this was true when we went. If you are going you need to check the exchange rates on the U.S. dollar. Also, I would recommend (if they still sell them) Lonely planet Travel Guide books to know what you are getting into going there now.