Almost half of Alameda County hospitals will be penalized after being cited by the federal government for high rates of patient injuries, which for the first time includes the spread of antibiotic-resistant germs.

Of the 96 California hospitals cited, the six in Alameda County included three Kaiser facilities, in Oakland/Richmond, San Leandro and Fremont; Alta Bates Summit Medical Center in Berkeley; Eden Medical Center in Castro Valley; and St. Rose in Hayward.

Five Contra Costa County hospitals were cited: Contra Costa Regional Medical Center in Martinez; the John Muir Medical Center campuses in Concord and Walnut Creek; Kaiser in Walnut Creek; and San Ramon Regional Medical Center.

Nationally, 769 hospitals will be penalized 1 percent of their Medicare payments.

The federal Agency for Healthcare Research and Quality estimates there were 3.8 million hospital injuries last year, or 115 for every 1,000 patient hospital stays.

Among them were a quarter-million people infected in hospitals with bacteria resistant to antibiotics. The federal Centers for Disease Control and Prevention estimates that of a total of 2 million such cases last year, 23,000 people died.

The Hospital-Acquired Condition Reduction Program, run by the U.S. Department of Health and Human Services, emphasizes rates of infections from hysterectomies, colon surgeries, urinary tract catheters and central line tubes in ranking the hospitals on patient injuries. It also considers the frequency of bed sores, hip fractures, blood clots and four other complications.

Stephen Lockhart, chief medical officer for Sutter Health, which runs the Alta Bates and Eden Medical Center facilities, said in a statement, “We support the aim of the Hospital-Acquired Condition Reduction Program, as well as other quality surveys. They help us identify where we’re making the most strides in patient safety and where we need to improve.

“We have seen significant improvement in quality across our network over the past 10 years, and we always want to keep improving.”

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New to the survey this past year was the inclusion of two types of drug-resistant bacteria. There were 6,300 cases of infections from one, methicillin-resistant Staphylococcus aureus, last year, Agency for Healthcare Research and Quality estimates.

The other, Clostridium difficile, or C. difficile, was found in 100,000 cases last year, the agency reported.

Responding to the report, Barbara Crawford, a Kaiser Permanente Northern California vice president, said in a statement:

“We take hospital-acquired infections very seriously. Overall, Kaiser Permanente has had outstanding success in reducing C. Difficile infections in our Northern California hospitals, leading to significant learnings and best practices.

“We’ve seen our C. Difficile rate drop by 28 percent. We are continuing to focus on all hospital acquired conditions, and we see improvement as we look at recent numbers,” she said.

“Kaiser Permanente physicians and infectious disease experts always closely monitor infection cases.”

Specialized hospitals, such as those that treat psychiatric patients, veterans and children, are exempted from the penalties, as are those designated as the only provider in an area.

Under the terms of the Affordable Care Act, hospitals that fall to the lowest 25 percent of rankings in terms of patient injuries lose some of their Medicare funding.

Although the government does not specify the penalties for each hospital, the total national loss for the current fiscal year, which started in October, will be about $430 million, up 18 percent from last year, Kaiser Health News reported. Kaiser Health News is not associated with Kaiser Permanente.

Improvement over the previous year’s ratings does not spare a hospital from being cited if it still ranks in the lowest 25 percent, the report said.

None of the Alameda Health Systems hospitals, which includes Highland in Oakland, were cited this year. UCSF Benioff Children’s Hospital Oakland and Washington Hospital in Fremont also were not cited.

The penalties come as the Centers for Medicare & Medicaid Services begin new requirements that hospitals establish antibiotics protocols as a condition of receiving Medicare funding.

Infection experts fear that soon patients may face new strains of germs that are resistant to existing antibiotics. Studies have found that between 20 and 50 percent of all antibiotics prescribed in hospitals are either not needed or inappropriate, the Kaiser report said.

The proliferation of the drugs — inside the hospital, in doctor’s prescriptions and in farm animals sold for food — have hastened new strains of drug-resistant bacteria, according to the report.

Kaiser Health News is a national health policy news service that is part of the nonpartisan Henry J. Kaiser Family Foundation.