DNA from a pizza crust that was discarded earlier this year was used to link the suspect charged in the Gilgo murders case with one of the victims, prosecutors allege in court documents released Friday.

Rex Heuermann, 59, has been charged with three counts of first-degree murder and three counts of second-degree murder in the deaths of Melissa Barthelemy, Megan Waterman and Amber Costello, according to the indictment. Those three women, along with Maureen Brainard-Barnes, were all found in close proximity to one another in 2010 and have been called the "Gilgo Beach Four." 

In all, the bodies of at least 10 women were found in the area, believed to be the victims of a serial killer. Some of the victims had been wrapped in burlap.

In court Friday, Heuermann pleaded not guilty, and the judge ordered him held without bail. In the court filing, prosecutors outlined how investigators reexamined old clues that led to the suspect and developed new evidence to close in on him after so many years.

According to the newly released court documents, on or about Jan. 26, 2023, a surveillance team recovered a pizza box thrown by Heuermann into a garbage can on Fifth Avenue in Manhattan.

"This pizza box was sent to the Suffolk County Crime Laboratory for analysis, where a swab was taken from the leftover pizza crust," prosecutors wrote.

About three months later, on April 28, a detective hand-delivered a portion of male hair that was found on Megan Waterman that had been preserved as evidence to the same lab where the pizza crust had been tested.

On or about June 12, 2023, the forensic lab compared the mitochondrial DNA from the pizza and the hair and determined that the "DNA profile(s) are the same" — specifically that 99.96% of the North American population would be excluded as matches to the hair.

"It is significant that (Heuermann) cannot be excluded from the male hair recovered near the 'bottom of the burlap' utilized to restrain and transport Megan Waterman's naked and deceased body," prosecutors wrote.

Prosecutors said investigators were led to Heuermann initially after a witness reported seeing a pickup truck matching the model he owned when one of the victims disappeared in 2010. They also linked him to other evidence including burner phones used to arrange meetings with the victims.

Heuermann was arrested late Thursday and was charged Friday.

If convicted, he faces multiple life sentences without parole, authorities said.

CBS News senior investigative reporter Pat Milton contributed to this report.

In:
• Gilgo Beach Serial Killer
• Gilgo Beach Murders
• DNA
• Murder
• Long Island

Stephen Smith is a senior editor for CBSNews.com.