NYC hospital system reports rise in carbapenem-resistant Klebsiella infections

Carbapenem-resistant Enterobacterales

CDC / Stephanie Rossow


Analysis of data from a large public healthcare system in New York City shows concerning changes in the numbers and epidemiology of carbapenem-resistant Klebsiella pneumoniae (CRKP) infections since 2016.

The data, published yesterday in Emerging Infectious Diseases, show a notable increase in CRKP infections in the New York City Health and Hospitals Enterprise during the COVID-19 pandemic, more cases originating in the community, and the rise of newer resistance mechanisms that challenge first-line antibiotics.

Notable increase in late 2021, early 2022

For the study, researchers used National Healthcare Safety Network data to characterize laboratory-identified CRKP infections in the hospital system, which includes 11 acute care hospitals and serves more than 1.2 million people each year. They used patient medical records to determine where the patients were admitted from, and reviewed results of testing conducted by the New York State Department of Health to assess antibiotic susceptibility and identify the enzymes conferring carbapenem resistance.

The Centers for Disease Control and Prevention considers CRKP and other members of the carbapenem-resistant Enterobacterales (CRE) family to be an urgent public health threat. CRKP infections tend to originate in healthcare settings among severely ill patients who have been on antibiotics and are on ventilators or have indwelling devices. They're challenging to treat because carbapenem antibiotics are a last-resort treatment option for multidrug-resistant infections. In 2017, an estimated 1,100 US patients died from CRE infections.

The number of community-onset cases, the increasing overall numbers, and the emergence of NDM-possessing carbapenem-resistant K. pneumoniae identified in this study are concerning.

From January 1, 2016, to June 30, 2022, the researchers identified 509 CRKP patients. The major sources of positive cultures were the genitourinary tract (52%), respiratory tract (21%), bloodstream (12%), and skin or other soft tissue (11%). Of the 509 patients, more than half (262) were considered to have community-onset positive cultures, with 149 living at home, 108 coming from a long-term care facility, and 5 transferred from other acute-care facilities.

Although CRKP cases declined from 2016 to 2020, the data reveal a notable increase in cases in late 2021 and early 2022. The study authors say this likely reflects the national increases observed among several healthcare-associated infections during the pandemic, which were caused by multiple factors, including prolonged COVID hospitalizations and increased antibiotic use. Staff shortages and less attention to standard infection prevention and control methods also contributed.

About half of cases community-onset

In addition, the authors say they were surprised by the large number of community-onset CRKP cases that were identified. Previous studies have indicated that only 10% of CRE cases are community-onset.

"It is disconcerting that approximately half of the patients had community-onset cultures; 31% of patients with community-onset isolates lived at home, were not on hemodialysis, and had not been recently hospitalized," they wrote.

They also note that the percentage of cases coming from long-term care facilities rose from 36.3% during 2016-2020 to 59.1% over the next 18 months.

The authors say the increase in community-onset cases could be related to socioeconomic factors, including poverty and overcrowded living conditions—factors that have been implicated in community spread of other bacterial pathogens, like methicillin-resistant Staphylococcus aureus. But they add that further research is needed to assess the contribution of these factors.

Fewer treatment options

Finally, the analysis also revealed a marked shift in the type of carbapenemase enzymes identified in the CRKP isolates.

Prior to 2018, the primary mechanism of resistance to carbapenems in hospitals in New York City and around the country has been Klebsiella pneumoniae carbapenemase (KPC). But, of the 182 samples with carbapenemase identification or antibiotic susceptibility testing (which can be a proxy for carbapenemase identification), 39 had confirmed or suspected metallo-beta-lactamase enzymes, most notably the New Delhi metallo-beta-lactamase (NDM) enzyme. The proportion of cases with metallo-beta-lactamases rose from 11.8% during 2016-202 to 33.8% during 2021-2022.

While all carbapenemase-producing bacteria are a concern, NDM-producing strains are even more problematic, because NDM is impervious to ceftazidime-avibactam, a newer combination antibiotic that is used to treat carbapenem-resistant infections. That leaves even fewer treatment options for CRKP infections.

"The number of community-onset cases, the increasing overall numbers, and the emergence of NDM-possessing carbapenem-resistant K. pneumoniae identified in this study are concerning," the authors wrote. "Aggressive and universal surveillance and isolation measures involving both acute-care and long-term care facilities…will likely be needed to control further spread of these pathogens."

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