With a swift swipe of his scalpel, Rabbi A Romi Cohn circumcises the baby boy, then leans down and sucks the blood from the wound as prayers in Hebrew fill the Brooklyn synagogue.

The Orthodox Jewish tradition known as oral suction circumcision reaches back to biblical times but it has created a modern-day dilemma for New York City health officials, who have linked it to 17 cases of infant herpes since 2000. Two infants died and two others suffered brain damage.

Mayor Bill de Blasio’s administration, which came into power a year ago with a promise to reconsider an existing regulation on the ritual, is now negotiating with a group of rabbis over how to protect children’s health while preserving religious freedom.

“The talks are ongoing but I cannot go into particulars,” said Avi Fink, the mayor’s deputy director of intergovernmental affairs who has been leading the talks. “Our goal is to achieve awareness of the risks.”

Such oral suction circumcisions are relatively rare, even in New York City, which is home to more than a million Jews – the largest Jewish population outside Israel. City health officials estimate more than 3,000 babies are circumcised each year using the oral suction method – formally called metzitzah b’peh in Hebrew.

A 2012 report by the federal Centers for Disease Control and Prevention (CDC) advised against the practice, saying it increases the risk of herpes infection in baby boys by 3.4 times that of other male newborns.

Oral suction circumcisions first came under scrutiny during Mayor Michael Bloomberg’s administration, and the city’s health board voted in 2012 to regulate the practice by asking a parent or guardian to sign a consent form indicating possible risks.

Health officials point to a number of factors they say have linked the known cases to the ritual. They look for lesions on the genitalia, indicating that is where the virus started. In addition, lab tests have showed that the timing of the infection coincides with the circumcision.

Two cases were recorded after oral suction in 2013 and four last year. In the most recent case, diagnosed in November, a baby boy was found to have lesions on his penis. But of those six cases, parents refused to identify the person who performed the circumcision – called a mohel – in four.

In the two cases in which the circumcisers were identified, both declined to be tested, the Health Department said. They were banned from performing the ritual.

The consent forms remain the regulatory standard for now, but most ultra-Orthodox rabbis have told their faithful not to comply, and the city acknowledges it does not collect them unless there is suspicion of herpes.

Cohn, an 85-year-old Holocaust survivor and native of what today is called Slovakia, is chairman of the American Board of Ritual Circumcision, which has certified 90 mohels, says he doubts the oral suction method had anything to do with spreading herpes. Cohn believes the infants may have been infected by the mother or another source.

“They’re wild accusations without any basis,” Cohn said. “I’ve done 35,000 circumcisions and never had an infection, of any kind.”

The rabbi does warn parents that circumcision, in general, has its risks, just like any medical procedure. His association mandates herpes testing and rinsing with mouthwash before the ceremony, in addition to scrubbing and sterilizing hands.

The rabbi followed those precautions one morning at Brooklyn’s Congregation Shaare Zion, where he circumcised week-old Yosef Sananas. Cohn first administered a topical anesthetic, wrapping gauze around the child’s legs to isolate the sterilized area. Then the baby, on a white pillow, was carried into the main worship space. Invited guests watched as Cohn did what he’s done thousands of other times.

“He’s the best mohel in New York,” says the boy’s mother, Becky Sananas. “We chose him because we trust him.”

While New York City wrestles with the issue, suburban Rockland County – itself home to thousands of Orthodox Jews – seems to have found a solution.

For any suspected case after circumcision, county health officials use DNA testing to try to link a baby with the source of infection. And members of the Jewish community participate voluntarily in the process, working with Dr Oscar Alleyne, Rockland’s director of epidemiology. No positive cases have been found there.

“That proves that they trust us,” Alleyne said. “We have cooperation, along with a scientific approach.”