Based on the inspections and subsequent hospital improvement plans, the commission awarded accreditation to Mass. General, the Brigham, Dana-Farber Cancer Institute and Children's Hospital Boston. Boston Medical Center said it has not received the commission's final report, but was told after its inspection that it could expect to be reaccredited.
When hospitals do not meet one of the commission's roughly 250 standards,
they are issued a "requirement for improvement" in that category. Mass. General received 10 requirements for improvement; the Brigham, nine, Dana-Farber, which does not have overnight patients, three; and Children's Hospital, three. Boston Medical Center initially received eight requirements for improvement but has disputed two as allowed by the commission's policy; in addition, the hospital's residential mental health program received three and is appealing one.
Neither hospitals nor the commission usually release detailed results for individual organizations. But Mass. General president Dr. Peter Slavin wrote an e-mail to employees in December, soon after inspectors left, indicating that he was disappointed with the hospital's results, describing them as a wake-up call and promising immediate improvements. The hospital promised to release the final report. Following that, the Globe requested the findings from other Boston teaching hospitals, which agreed to either release their reports or describe the commission's findings in detail. Mass. General and the Brigham plan to post similar information on their websites.
"We're not trying to hide the fact that we have things we need to fix," said Dr. Andy Whittemore, the Brigham's chief medical officer.
The Illinois-based Joint Commission evaluates more than 15,000 healthcare organizations and is the country's primary inspector of hospitals, nursing homes, and other medical institutions and programs. The organization has been criticized in the past for being too easy on hospitals, which financially support the commission by paying a fee for inspections. As a result, the organization has made several changes in the past few years.
Four years ago, the commission began requiring hospitals to comply with a set of national patient safety goals, which include tracking patients' medications, time outs before procedures, and communicating critical test results quickly. Three years ago, it began following patients through their hospital stay, rather than just reviewing hospital policies and meeting with executives, as it had done previously. Last year, the commission switched from scheduled visits to surprise visits.
Hospitals are still adjusting to the revised system. Many Massachusetts hospitals began tracking patients' medications during transitions in care -- an emergency room visit, admission to the ICU, transfer to a patient floor, or discharge -- far sooner than institutions in other parts of the country, and much of the research about the potential harm of not doing so originated in Boston.
At Mass. General, inspectors also found that caregivers did not always document at set intervals whether patients on pain medication had improved or that they had quickly assessed patients for pain -- one surgery patient had no record of pain assessment for 22 hours after admission. And several patient records lacked information about whether they had signed "advance directives," which indicate whether patients want aggressive medical care if they can not communicate their wishes.
Dr. Gregg Meyer, senior vice president for quality and patient safety at Mass. General, said that the hospital is monitoring all areas where the commission found problems and has improved. He said that when the hospital fully switches to computerized medical records, it will drive improvement in many areas, because the system has automatic reminders built in and because computers at patients' bedsides make it easier for caregivers to note their actions.
Among the Brigham's problems, inspectors found that caregivers did not always re-evaluate every 24 hours the reasons for putting patients in restraints; and some pharmacies did not check all physician medication orders to ensure they were safe for patients. The hospital has an improvement plan in place.
At Children's Hospital, the commission discovered incomplete or illegible medical records, among other findings.
At Boston Medical Center, the commission's findings included cases where doctors had used dangerous and prohibited abbreviations that can easily be misunderstood. The hospital has started an education campaign.
"That's like trying to beat back 200 years of indoctrinated language in health care," said Peter Healy, vice president of professional services. "It's really hard to do all of these things perfectly all the time."
Liz Kowalczyk can be reached at kowalczyk@globe.com. 
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