I am a fairly new instructor of a Microbiology course at a small technical college.  I inherited purchased strains of several microorganisms for classroom use, including E. coli and S. aureus.    I am concerned about accumulated genetic changes that might make the bacteria more pathogenic, for example, the possibility a student might be colonized with MRSA and through contamination transform my stock culture.  How long is it safe to keep subculturing microbial strains over and over before I need to order new ones?

It is usually standard practice in molecular biology labs to keep bacterial strains on agar plates for a few weeks-months at 4 degrees C. Sterile technique in plating and opening plates helps minimize contamination, as does a tight seal (e.g., with clingfilm and tape) when the plates are stored. Even then you might end up with spurious growth (of different colours!!). Most of us keep glycerol or DMSO frozen stocks (ideally kept at -80 degrees C but -20 degrees C will suffice for shorter term (perhaps less than a year) storage) to replenish cultures as a safeguard against cross-contamination from other bugs used or present in the lab (yeast is often a culprit), or from mutations that may render bacteria antibiotic resistant. You can take scrapes for years from the frozen stocks to set up new cultures.

I do not routinely (or purposely!) grow Staph but here is an article on general culture techniques and antibiotic resistance testing - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4070006/