An investigator swabbed high-traffic areas, including countertops and the handles on the self-serve milk dispensers. Specimens were sent to Philip Tierno, director of Clinical Microbiology and Immunology at New York University Langone Medical Center. About half were contaminated with “fecal organisms.” One specimen taken from a countertop at a Starbucks near Times Square was teeming with bacteria, including E. coli and a host of other organisms indicating “that fecal matter was placed on the counter at some point.”While the unfortunate business here is Starbucks, this could just as well be Dunkin Donuts or your friendly neighborhood coffee shop.
A swab from a countertop at Hell’s Kitchen Starbucks revealed a colony of yeast, which the doctor identified as either gastrointestinal or vaginal in origin.
Samples taken from milk containers in three separate Starbucks stores tested positive for traces of Enterococcus, fecal strep, E. coli, and Klebsiella.
I'm not sure how one can be 100% protected against this kind of stuff without turning into some kind of germophobe. It seems to me that, unfortunately, it a game of chance balanced by some sensible procedures like regularly washing your hands and using anti-bacterial wipes and lotion when it's feasible.