The first 3 are parasites that MAY be transmitted cross species, but I agree with TLC in thinking that it most likely came from the breeder and your baby just didn't show signs of it until he got stressed. UTI's are usually caused by bacteria that has traveled up the urinary tract, so it's not directly related.
Puppies, like human babies, are immune compromised. Until they build up a natural resistance, you need to keep their areas extra clean. For your little guy, that means keeping him out of harms way by keeping him on a lead while he goes out to do his business to keep him from eating the poo. Clean it up right after he goes. I'd also do a through clean up of his crate/kennel area to prevent reinfection. I like steam cleaners for that, just because I want to avoid chemicals.
My vet has always encouraged us to feed a good quality, PLAIN, NON-FAT yogurt. In addition to the probiotics, something about it makes the poo distasteful to them (who would have thought you would need to make poo taste even worse?!)
Is Yogurt Good For Dogs?