To expand a bit on @Mohamed's answer, there are several mechanisms by which virulence gene products can be up- or down-regulated without changes to mRNA expression.
Adenylate cyclase-hemolysin (AC-Hly) is a toxin produced by the Bordetella pertussis, the causal agent of whooping cough. There are very few amino acid ...
Gene expression means making mRNA and then translated to protein. Their might be many steps unders regulation in this path where a gene makes mRNA but then that mRNA is not translated (like degraded or inactivated).