Both in that discussion, here, and in the article I can find no mention of actual rates of suspected infections from this vector. You have a doctor who thinks that this is risky behavior by putting together the microbiome of the human face, and the nature of a neonate's immune status. This is the perceived risk, but the real risk can only be revealed by studying whether or not that risk is ever realized.

This isn't just academic, the public and media have limited ability to communicate important issues, and if this is a purely (or even mostly) hypothetical risk then that limited attention should be directed to issues that take or damage more lives.