Tierno sits behind an institutional desk in a small, cluttered office just down the corridor from the microbiology lab at Manhattan's New York University Medical Center, which he oversees. There are piles of paper obscuring windows, an old stereo playing classical violin music, a corkboard with notes tacked up, and a dispenser that spews disinfecting foam into his hands whenever he returns to his warren. "Where there are people, there are germs," he says. Hotels, of course, rely on high volume—the more, the merrier—and, it turns out, use their discretion in establishing housekeeping protocol.

In other words, there is no industry standard for sanitizing a room, and few hotel companies are eager to give room-cleaning and upkeep details. So we decided to do some research into the matter. Tierno went to a storage room to pull out some sample-gathering tubes and to demonstrate the proper swabbing technique. Thus armed and schooled, we set out to quietly inspect three representative hotels in New York City and find what germs lingered there.

We'll call the high-end property (five stars, with rates starting at $745) Hotel Luxe; the mid-level place (judged more on hip quotient than stars, with rates starting at $579) Hotel Trendy, and the economy accommodation (stars irrelevant, location everything, and rates starting at $169) Hotel Budget. Tempted to stop by the hazmat supply store, we arrived instead in Balenciaga and J. Crew and set about collecting evidence—from shower floors, remote controls, ice buckets, and so forth—without wearing paper booties or even latex gloves. Not to kill the suspense, but cleanliness corresponded to price by and large. However, no hotel came out smelling like a rose.

While we didn't discover anything that would, according to Tierno, "cause your demise," there was plenty to make even a steel gut queasy. Among the findings: At Hotel Luxe, the ice bucket, phones, and clock radio were loaded with Escherichia coli, the fecal-borne organism commonly known as E. coli, and Candida albicans, a fungus that causes yeast infections. The remote control had evidence of E. coli and Enterococci (another germ from feces), as did the shower floor. At Hotel Trendy, the doorknobs showed strong evidence of respiratory secretions. "That's how you can get rhinovirus [the cause of the common cold]," says Tierno. And a swab from the underside of the toilet seat turned up a heap of E. coli. "That means it wasn't cleaned," he says. At Hotel Budget, the desk chair had evidence of feces on it, as did the bedroom floor. Tierno says people have a habit of sitting on hotel furniture in the nude, but even he raised an eyebrow at the findings on the floor. "Maybe someone sat there," he says. "Or did God knows what." As at the other two hotels, the phone, the remote control, and the clock radio had plenty of fecal-borne organisms on them. The bottom line: "Those things were not cleaned."