Dr. Bennet Omalu, best known for his discovery of a concussion-related disease in football players, had served as the county’s chief forensic pathologist for a decade when he resigned in early December, citing a handful of cases in which Moore ignored his opinion that a death at the hands of law enforcement officers was a homicide.

KQED News has verified three cases, two in 2016 and one in 2008, in which the sheriff-coroner certified an in-custody death as an accident after Omalu found that it was a homicide.

Another former San Joaquin County forensic pathologist, Dr. Susan Parson, resigned about a week before Omalu and made similar allegations about Moore interfering with her work.

The doctors' resignations, and their reasons, have apparently made it hard to replace them. A recruiter was initially contacted by 20 candidates, according to a county administrator's report, but many of them later withdrew their interest.

"[M]any of the candidates have declined to pursue employment with San Joaquin County due to on-line searches revealing the media presence reporting on this issue, as well as the negative reaction to the location," the report says.

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Mitchell’s audit included a review of 130 investigatory and autopsy reports from 2016, or about 10 percent of the year’s coroner cases. Of the five cases where people died in custody, both in jail and during arrest, the audit found a discrepancy between the forensic pathologists’ opinion and the coroner's opinion. which determined the ultimate certification in the manner of death.

“The manner of death recorded by the forensic pathologist on the data sheet was not the manner of death certified by the coroner in several of the cases reviewed," the audit says. "In cases where there was a direct physical altercation with law enforcement, the forensic pathologist indicated the manner as homicide. The ultimate coroner manner of death was certified as accident for the aforementioned cases.”

Mitchell’s audit also included interviews of key staff in the coroner's office, including the two forensic pathologists -- Omalu and Parson -- Sheriff Moore and the district attorney, which is conducting a separate investigation into the doctors' allegations.

“The office must be and appear to be independent of law enforcement particularly when investigating deaths in the custody of law enforcement or while in jail/prison," Mitchell wrote. "This requires a complete shift towards a Medical Examiner System."

Mitchell wrote that the medical examiner system -- run by a physician certified in pathology -- offers the best tools to improve standards and service and to “maintain independent objectivity, and rebuild the public trust.”

“The organizational structure must ensure that the individuals with the most knowledge and experience in conducting medicolegal death investigations provide the ultimate management and leadership for the office,” Mitchell wrote.

San Joaquin County District Attorney Tori Verber Salazar, who called for the creation of an independent medical examiner’s office after the doctors' allegations against Moore surfaced, agrees with Mitchell's recommendation.

“Having a chief medical examiner, additional medical examiners and a highly skilled board-certified investigative team would address these issues and ensure those loved ones in our community who are no longer with us are receiving the best practices and procedures and the best investigation that we can provide them,” Verber Salazar said. “We owe them that.”

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She wants to set up an interim coroner for roughly a year while the medical examiner's office is being created, but in the meantime, she said, all deputies who conduct coroner work should receive robust training and certification in death investigations.

Mitchell's report found that while the five sheriff's deputies who are responsible for death investigations for the entire county receive 80 hours in death investigation training when they start on the job, they receive little-to-no ongoing education. Patrol deputies who respond to many of the coroner calls have even less formal education in death investigations and, according to the audit, there's no evidence that they consult physicians when the encounter complex death investigation scenes. Forensic pathologists are neither required nor encouraged to go to the scene themselves, the audit says.

“It's incumbent upon us to provide the best possible services that we can, with the best trained individuals, and do so in a manner that is respectful to them and to their family," Verber Salazar said.

She declined to comment on her ongoing investigation into the doctors’ allegations.

A separate report by San Joaquin County Counsel Mark Myles found some evidence of disruptive delays in getting medical records and detective reports, which in turn delayed the completion of autopsy reports. And he noted that none of the sheriff's deputies handling coroner cases were certified by an independent credentialing organization, such as the American Board of Medicolegal Death Investigators.

Only three of the coroner deputies had received in-depth training in death investigations, the county counsel found.

Aside from the need for more training, Myles concluded that most of the issues the doctors raised could have been “avoided, addressed, or remedied in an atmosphere of mutual respect and effective communication.”

Myles said last week that he found no evidence the sheriff broke any laws or violated standards supported by the National Association of Medical Examiners.

“The law grants great discretion to the coroner in the exercise of their duties,” Myles said. He said national standards note “room for a difference of opinion on determination of the manner of death.”

Myles’ review of allegations concluded: “Counsel has not found any facts to support nefarious or callous motives ascribed to the Chief Deputy Coroner or the Coroner.”

The San Joaquin Board of Supervisors will hear both reports at a meeting on April 24.

Read the audit and county counsel's report below: