For months, officials at Baylor St. Luke’s Medical Center have declined to specify the factors behind a rash of patient deaths in the hospital’s heart transplant program three years ago.

But a newly released federal document describes program leaders as more blunt in their assessment when regulators questioned them privately in December.

In an interview with the Centers for Medicare and Medicaid Services, one of the hospital’s top heart transplant physicians blamed the program’s struggles, at least in part, on “a retiring surgeon” — a “legend” — who “wouldn’t stop performing transplants,” according to typed notes prepared for CMS.

The notes, obtained by ProPublica and the Houston Chronicle under the Freedom of Information Act, do not identify anyone by name, but the descriptions make clear that the physician being interviewed could only be Dr. Andrew Civitello, the program’s top cardiologist. And there was only one retirement-age transplant surgeon at St. Luke’s in 2015 who could be described as a legend in the field of heart surgery: Dr. O.H. “Bud” Frazier, who is one of the world’s most prolific heart transplant surgeons.

Civitello acknowledged through a hospital spokeswoman that he spoke with CMS about changes in staffing at the transplant program but said the notes did not accurately reflect his remarks. Frazier did not respond to messages seeking comment for this story.

A spokesman for CMS said the agency stands behind the findings documented in its inspection reports and the notes that support them.

The inspector’s notes shed new light on how doctors at the hospital accounted for poor transplant outcomes that triggered federal scrutiny and led to the loss of Medicare funding. Combined with other details made public in recent months, the notes suggest a tense and dysfunctional transition more than two years ago as the heart transplant program, long known as one of the best in the nation, made staffing changes aimed at improving care.

Additional records reviewed by ProPublica and the Chronicle reveal this was not the first time the renowned transplant program has had an unusually high rate of patient deaths and considered changes.

According to the CMS inspector’s notes, the unnamed physician whose job description matches that of Civitello explained that a “very good” surgeon was hired to replace an aging surgeon, but the replacement “eventually left in frustration.” Dr. Hari Mallidi joined St. Luke’s as a top transplant surgeon in 2012 and left in mid-2015 for a job at a Harvard-affiliated teaching hospital.

“That left the program with an old surgeon and an inexperienced surgeon. Had many deaths in a short period of time,” the notes said of Civitello’s commentary, apparently referring to Frazier, 78, and Dr. Steve Singh, a junior surgeon at the program until 2016 and the only St. Luke’s physician from that time who matches that description. Singh did not respond to requests for comment.

In a statement provided by St. Luke’s, Civitello said: “The notes you provided are not my words and do not accurately reflect my comments. My conversation with the surveyor focused on the new policies and procedures we put in place to strengthen the heart transplant program, including the addition of intensivists in the ICU, internal lab analysis for consistency, and other measures.”

In response to questions for this story, CMS said inspectors take handwritten notes during hospital visits and that it has the “highest confidence” that they accurately reflect what they see and hear.

In 2015, seven out of 21 heart transplant recipients at St. Luke’s died within a year of their surgeries, significantly more than would have been expected. During a meeting with reporters in January about what led to the deaths, hospital leaders said only that the program slowed down that year and identified subtle ways to improve care. At the start of 2016, the hospital brought in a new surgeon, Dr. Jeffrey Morgan, to lead the program.

The CMS notes were written in December when at least one inspector visited the hospital to evaluate its poor transplant outcomes. The resulting report, obtained early this year by ProPublica and the Chronicle, referred to a St. Luke’s physician who “explained that issues were identified with the major issue being surgical technique with one of the heart transplant surgeons, who was no longer practicing.” The document did not provide any additional details, but the newly released notes suggest that the statement referred to Frazier.

In April, a St. Luke’s spokeswoman told reporters that “we did not discuss the technique of any individual surgeon with CMS” and that it would be “presumptuous to infer that the surgeon CMS referenced is Dr. Frazier.”

Civitello was not the only St. Luke’s physician interviewed by CMS in December who discussed the program’s surgical staffing.

The inspector also interviewed a St. Luke’s heart transplant surgeon, according to the newly released notes, who “explained that one surgeon had bad outcomes” in 2015 and that the deaths that year were due in part to the way in which the hospital was selecting patients eligible for transplants as well as the donor hearts it accepted for them. The unnamed doctor told the inspector that he was hired after the rash of poor outcomes in 2015 and that he reviews all organ offers; only Morgan matches that description.

It is not clear, based on the details provided, which surgeon Morgan was blaming for the poor outcomes that occurred prior to his arrival at the program. Morgan did not respond to a request for comment and the hospital did not provide one on his behalf.

In the January interview, Morgan, 44, spoke glowingly of his predecessor, saying that it had been “very, very special” to work with him and learn from him on a daily basis. During that same interview, Civitello told reporters that Frazier “is the heart and the soul of our organization.”

In the written statement this week, Civitello said, “We are grateful for Dr. Frazier’s decades of service, innovation and sacrifice to our patients, our community and the advancement of treatments for those who are critically ill facing heart failure.”

Frazier, who started the heart transplant program in 1982, stopped operating as its lead surgeon sometime in 2015. In a previous interview, Frazier said that he merely consulted on heart transplants during the period in question and that he personally made the decision to stop operating that year because of his age.

“I told them I was getting tired of being up all night,” Frazier said in April of his exit from the operating room three years ago. “I was 75, and I just told them I wasn’t going to do that anymore.”

ProPublica and the Chronicle sent the hospital and its affiliated Baylor College of Medicine a list of questions about its interactions with Frazier and his outcomes, but the hospital declined to answer them “given the pending litigation between Dr. Frazier and the two of you, the Houston Chronicle, and ProPublica.” Frazer is suing the news organizations and its reporters following an article published about him in May.

That article detailed, among other things, below-average one-year survival among Medicare patients who received an implantable heart pump from Frazier between 2010 to 2015, his final years operating. ProPublica and the Chronicle did not assess Frazier’s transplant outcomes.

In previous interviews, as well as in the legal complaint, Frazier has emphasized his willingness to operate on “mortally ill” patients who have been turned away by other surgeons and are often at a higher risk of dying after surgery.

Frazier has remained active in the heart program after 2015, conducting research and sometimes advising surgeons during complex operations.

A newly published book, “Ticker,” which details Frazier’s decades-long quest to develop an artificial heart, touches on the hospital’s concerns about his surgical outcomes prior to Morgan’s arrival.

“Depending on who you ask,” the book’s author, Mimi Swartz, wrote, “Bud either asked to operate less because of his back or his knees, or the hospital tried to ease him out of the operating room. Baylor brought in a much younger man from the Northeast who was supposed to take control; at least now he had most of the titles Bud had always been so proud of.”

Swartz, who reported spending many hours interviewing Frazier for the book over the course of several years, describes the relationship between Frazier and Morgan.

“(He) was exceedingly deferential to Bud, treading lightly, as if he were almost embarrassed to be nearby,” Swartz wrote, without identifying Morgan by name. “It was like sending in the waterboy to give instructions to the star quarterback.”

St. Luke’s leaders say the hospital’s heart transplant survival rate improved significantly after Morgan took over, though some of his colleagues raised concerns about his surgical performance.

In an interview in April, Frazier made clear that he was not asked to play a role in selecting his replacement: “I didn’t hire Jeff. He was hired by the people at Baylor without even consulting me. And the people that hired him never did a transplant. … But he’s, you know, he’s a hard worker academically.”

Some St. Luke’s physicians have blamed the heart transplant program’s issues in recent years on administrative changes that came after the hospital was purchased by Catholic Health Initiatives in 2013 and, a year later, entered into a joint-operating agreement with Baylor College of Medicine.

But documents reviewed by ProPublica and the Chronicle show that St. Luke’s has had poor heart transplant outcomes in the past.

Between 2000 and 2003, when the hospital was known as St. Luke’s Episcopal and the heart transplant program was still run by Frazier, only about 77 percent of the hospital’s heart transplant recipients survived at least a year, according to reports published in 2003, 2004 and 2005. Based on an analysis by the Scientific Registry of Transplant Recipients that took into account the severity of patient conditions and the quality of donor organs, about 86 percent of St. Luke’s heart recipients should have survived at least a year over that period.

St. Luke’s was one of a small number of hospitals nationally to be singled out for statistically worse-than-expected heart transplant outcomes at that time — the same finding that landed the program in trouble with regulators this year. But that was a couple of years before the Centers for Medicare and Medicaid Services began taking punitive action against centers based on their performance, and the hospital faced no public consequences.

The hospital did not respond to questions about its performance in those years, citing Frazier’s lawsuit against the news organizations.

In 2007, Dr. James Young, a prominent Cleveland Clinic cardiologist, was hired to review the hospital’s heart transplant and mechanical heart pump program. Young’s report, which primarily focused on compliance with federal research protocols, concluded that the transplant and mechanical pump program “was rather autocratic with a leader who is opinionated and commanding in authority, but also an incredibly skilled surgeon and driving force.” Those issues, along with a willingness to operate on “futile patients,” likely contributed to “less than stellar” outcomes after heart transplantation, Young wrote.

Young’s confidential report was made public in July when it was filed in Harris County District Court as part of the lawsuit against ProPublica and the Chronicle.

“These issues seem related to an appearance of ‘chaos and confusion’ that emerged,” Young wrote in his 2007 report. “Though leadership of the effort has been well meaning, with the interests of saving the lives of horribly ill patients, the program is in a vulnerable position.”

Young identified problems with research practices and documentation, but said “it does not appear that any egregious professional misconduct has occurred.”

It’s not clear what changes were made at that time.

Mallidi — referred to in the CMS inspector notes as the “replacement surgeon” — was hired five years later, in 2012, around the same time the program’s longtime No. 2 surgeon, Igor Gregoric, left St. Luke’s to start a heart transplant program at neighboring Memorial Hermann hospital. Frazier continued to serve as the surgical director of heart transplants at St. Luke’s, and Mallidi was put in charge of lung transplants.

Mallidi said recently that his relationship with Frazier did not factor in his decision to leave in 2015.

Morgan joined the hospital six months later, in January 2016, and Frazier formally transitioned to a non-surgical leadership post focused on research.

In their communication with federal regulators since then, St. Luke’s leaders have said the heart transplant program’s outcomes improved in 2016 and 2017, posting one-year survival rates at or above 94 percent, better than the national average.

In June, however, CMS concluded that the hospital had not corrected issues St. Luke’s had previously identified, and two months later, on Aug. 17, the agency formally terminated the program’s participation in the federal insurance program.

As a result, St. Luke’s can no longer bill Medicare or Medicaid for heart transplants, a move that could lead private insurance companies to follow suit. Experts say the losses could threaten the program’s long-term viability and force the hospital to restart the historic program from the ground up.

Administrators say the program remains open and continues to treat the 83 patients on its heart waiting list, but the program — which historically has performed about 45 heart transplants each year — did not perform any in June or July, the latest months for which public data is available.

Hospital officials did not answer Thursday when asked if the program had performed any heart transplants since then.