By Tim Fitzsimons

Earlier this month, health officials reported the sixth confirmed failure of PrEP globally. The latest instance involved a San Francisco man who was consistently taking the HIV-prevention medicine during the time he contracted the virus.

PrEP, or pre-exposure prophylaxis, involves taking a Truvada pill once daily to stop HIV infection, and it is estimated to be nearly 100 percent effective.

Despite these six failures since Truvada was first approved as an HIV-prevention medication back in 2012, Dr. Stephanie Cohen, the medical director at the San Francisco City Clinic, said — unequivocally — that PreP is working as expected.

"Nothing is 100 percent effective, unfortunately," Cohen told NBC News.

“There’s a part of you that starts to think, ‘Maybe this is 100 percent effective, because this is so amazing,'" she added. But despite not being fail-proof, Truvada is still incredibly effective, especially considering that there are millions of new HIV cases globally each year, with tens of thousands in the U.S. alone.

Cohen’s clinic has been on the forefront of a nationwide effort to promote and distribute PrEP to at-risk people. The clinic operates one of San Francisco’s largest PrEP programs.

Cohen said the latest patient to contract HIV while on PrEP came to the clinic consistently for regular sexually transmitted infection (STI) testing and, after months with no issues, tested positive for HIV. But the patient insisted he had taken a Truvada tablet every day, as instructed. So Cohen and her team decided to dig in.

“Just scientifically, we wanted to understand,” Cohen said, “how can this have occurred.”

Using hair and blood samples, they determined the patient had indeed been adherent to the PrEP regiment and had taken Truvada consistently for at least three months. Testing of the man’s HIV strain revealed that he had contracted a rare strain that is simultaneously resistant to both ingredients in Truvada. Including his case, four of the six confirmed PrEP failures have involved rare, resistant HIV strains.

There is only one confirmed PrEP failure, involving a man from Amsterdam, in which the HIV strain contracted was not resistant to any drugs. One of the six cases is disputed — the patient may have had a very recent HIV infection before starting Truvada.

In all cases of PrEP failures thus far, the patients responded quickly to HIV treatment and became HIV-undetectable shortly after switching from Truvada to new medication.

The bottom line is that even with six failures since 2012, the estimated efficacy of PrEP is going up, according to Cohen.

Dr. Anthony Fauci, director of the National Institutes of Allergy and Infectious Diseases (NIAID), is the country’s leading infectious-disease prevention official, and has led America’s response to AIDS and Ebola. When asked about the latest PrEP failure in San Francisco, he said it did not change his opinion about the HIV-prevention medication.

“It’s notable because it’s such a rare event,” Fauci said of the man's HIV contraction. “You don’t tell people, ‘Don’t use condoms anymore,’ because there are failures with condoms, but there are likely more failures with condoms than with PrEP."

Condoms, according to the Centers for Disease Control and Prevention (CDC), are effective at stopping about 80 percent of HIV infections, so PrEP is more effective.

The public hears of PrEP failures, because clinicians actually know about PrEP failure. People taking PrEP in the U.S. receive quarterly HIV and STI checkups, and doctors frequently monitor patients for signs that their PrEP defenses failed. Unlike condom failure, PrEP failure makes the news.

“It doesn't lessen in any respect my strong feeling that PrEP is a very strong tool to prevent the acquisition of HIV infection,” Fauci said.

But there is a long way to go, Fauci said. Of the estimated 1.1 million Americans who would benefit from PrEP, just about 250,000 are taking or have taken the medication.

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