An ear swab and gastric aspirate will show if a baby has been exposed to a certain bacteria and (where I worked at least) was not routine unless the were any risk factors or bubs had to be admitted to the NICU/SCN where it was part of a routine infection screen. The swabs only show what could be the potential cause of infection. Even if a baby had these done after birth (they have to be done soon after birth and definately before the first feed in the case of the gastric aspirate), and they show signs of infection they will strongly recommend a full blood workup looking for bacteria in the blood and other biochemical signs of infection and possibly antibiotics as well. The swabs will also take up to 48 hours to grow anything and if bub has an infection from birth it will have shown itself before then. The reason they like to do the vaginal swabs is because GBS is a highly dangerous bacteria for babies, it causes babies to become critically ill very very quickly.. We are very lucky that GBS is one of the only bacteria that is still highly sensitive to penicillin.
Instead of having bub swabbed you can just keep a close watch for signs of sepsis in the first 48 - 72 hours. Things like unstable temperature (newborns are more likely to drop thier body temperature when they are sick but they can swing between high and low temps), lethargy, poor feeding etc