Prolonged Transmission of a Resistant Bacterial Strain in a Northern California Hospital

June 23, 2019

How whole genome sequencing helped scientists demonstrate connections among bacterial strains identified over multiple years.

San Francisco, Calif. – June 23, 2019 –  Researchers have used whole genome sequencing (WGS) to demonstrate transmission of a single bacterial strain that possessed a carbapenem-resistance gene in a northern California hospital. The gene armed the bacteria with resistance to carbapenems, a type of antimicrobial drug reserved as a last-line treatment for serious infections. The research is presented on Sunday, June 23rd at ASM Microbe, the annual meeting of the American Society for Microbiology.

Epidemiologists from the local public health department and the California Department of Public Health (CDPH) collaborated with laboratory scientists from the CDPH Microbial Diseases Laboratory (MDL) to characterize the strain and identify potential transmission pathways in combination with epidemiologic information.

The bacterial strain persisted in the hospital for more than 3 years, potentially due to transmission from patient to patient combined with lengthy stays in the hospital intensive care unit (ICU). “Our investigation highlights the importance of regular epidemiological and microbiological monitoring of resistant strains in hospitals and the use of the advanced molecular technologies to track their spread,” said Varvara Kozyreva, Ph.D. Genotyping Unit Chief, Microbial Diseases Laboratory Program, California Department of Public Health.

Between 2013 and 2015, the hospital identified eight patients who were positive for a strain of Klebsiella pneumoniae bacteria that produced an enzyme conferring resistance to carbapenems. The initial four patients identified with the resistant strain had overlapping stays in the ICU over a one-month period. One of these initial patients remained in the ICU for two years, during which time an additional four patients with the resistant bacterial strain were found in the facility. WGS analyses of the bacteria from the eight different patients demonstrated they were all highly related genetically.

“WGS allowed us to understand and demonstrate connections among the patients over a multiple year time period, which would not have been possible using epidemiologic information alone,” said Dr. Kozyreva. WGS also showed that this particular bacterial strain’s carbapenem-resistance gene appeared to be located on the chromosome. Normally, such resistance genes are located on additional “mobile” DNA pieces called plasmids, that can be transferred between different strains (and even different species) of bacteria.

“Since this particular strain had less means to efficiently share its carbapenem-resistance genes with other bacteria in the hospital environment, it is all the more likely that this one antibiotic-resistant clone of bacteria persisted in the hospital over multiple years,” said Dr. Kozyreva. Using WGS to track resistant bacterial strains can help hospitals and public health officials target infection control interventions to halt transmission sooner.


ASM Microbe is the annual meeting of the American Society for Microbiology, held June 20th through 24th in San Francisco, California.

The American Society for Microbiology is the largest single life science society, composed of more than 30,000 scientists and health professionals. ASM's mission is to promote and advance the microbial sciences.

ASM advances the microbial sciences through conferences, publications, certifications and educational opportunities. It enhances laboratory capacity around the globe through training and resources. It provides a network for scientists in academia, industry and clinical settings. Additionally, ASM promotes a deeper understanding of the microbial sciences to diverse audiences.

Author: ASM Communications

ASM Communications
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