What is a "strain" of bacteria? How is it possible that some strains of staphylococcus aureus can be harmless, but others can be deadly?

A strain is a low-level taxonomic rank used at the intraspecific level (within a species). While the majority of the members of the same species have very high similarity in their genomes, there occasionally is a proportion of the species that has a little different genome from the popular species group. This variability results in different strains on the species.

A harmless Staphylococcus aureus may have a muted virulence gene. However, either due to mutation of the gene or recombination with the harmful strain, a harmless Staphylococcus aureus could easily turn virulent (harmful).