"Persons, especially young children or immunocompromised persons, should be discouraged from sharing their bed with their pets or regularly kissing their pets…. Although uncommon with healthy pets, the risk for transmission of zoonotic agents by close contact between pets and their owners through bed sharing, kissing or licking is real and has even been documented for life-threatening infections."To justify this warning, they cite 12, one dozen, cases of people who got a horrible disease and had an animal that was infected with the same disease.
One example given is this:
"...A 48-year-old man with diabetes and his wife had recurrent MRSA infections. Culture of nares samples from the family dog grew mupirocin-resistant MRSA that had a PFGE chromosomal pattern identical to the MRSA isolated from the patient’s nares and his wife’s wound. The couple reported that the dog routinely slept in their bed and frequently licked their faces…."Poor dog. It caught MRSA from licking its infected owners' faces. That's right. From the above paragraph it's impossible to determine who acquired MRSA from whom. It's exactly as likely that the dog got it from the people as the other way around. Who could tell? Were the people and the dog both tested prior to the licking to see who was MRSA-free? Unlikely. (Given that MRSA is commonly acquired by immune-compromised people who visit our lovely healthcare system, I'd say it's most likely that the dog caught it from the people.)
"A 2008 matched case–control study surveyed 9 plague survivors, 12 household members of these survivors, and 30 age- and neighborhood-matched controls about household and individual exposures. Four (44%) survivors … reported sleeping in the same bed with a pet dog …."Some of those folks may have gotten plague from fleas they got from the dog, or may just as likely they and the dog got fleas from rodents in their house. That's the usual vector for getting plague. One imagines they weren't letting the rats sleep in their beds...
As far as the irrationally risk averse part goes, twelve bad outcomes out of the millions of folks who sleep with pets and don't get any horrible diseases yields incredibly low odds of something bad actually happening.
For the record: I grew up sleeping with a dog, and nothing bad ever happened to me. The dog, and us, did wind up with fleas for a spell. Not fun, but not the plague, either.
Now, in my tick-infested neighborhood the dog sleeps on the floor. We regularly find ticks on our floor: that's what you call a real risk.
So yes, you're better off not sleeping with your pet. But if you do, don't lose sleep over it.