i was just using "city" as a placeholder since it was used in the article. most of the problems mentioned in the article are perfectly capable of surfacing at a much smaller settlement size.
I don't think that's the case with disease. Diseases need to have always have some living host in order to not die out completely. I don't think groups of several dozen are large enough to support that. Further, it's possible that some of our diseases are actually from the animals we domesticated as a part of agriculture.