The flu is viral, not bacteria so antibiotics are not effective. Changing the airfilters will help people who suffer from allergies and asthma, but it will not reduce the spread of the flu since who knows how many people might be walking around, hacking on the merchandise. Your best bet is to get a flu shot and practice good handwashing protocol (and dont touch your face in public places).
To add to what Jessica wrote, nothing short of a hospital-grade HEPA filter (VERY expensive!) would be effective against a virus; they're simply too small to be captured by most filters.
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