Using CSI-Type Technology to Unravel the Source of Bacteria

By Mayo Clinic Center for Individualized Medicine • June 12, 2018

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Mayo Clinic laboratory workers have a new tool to perform high-tech genetic sleuthing for the source of stubborn, sometimes life-threatening bacteria. Bacterial whole-genome sequencing can trace individual isolates of bacteria such as Staphylococcus aureus, also known as Staph aureus, to determine if an outbreak is occurring. This common bacterium that has plagued health care facilities, nursing homes, neonatal intensive care units, and even sports teams can lead to serious infections and can be resistant to some available antibiotics.

“If we have two or more people infected with the same type of bacterium, the question sometimes arises as to whether they got the organisms from one another or a shared source. The answer to this question can shape an approach to limit further spread,” says Robin Patel, M.D., a clinical microbiologist with Mayo Clinic's Department of Laboratory Medicine and Pathology. “Or, a patient might have a bacterial infection and later a second infection with the same type of bacterium. Whole-genome sequencing can determine whether the patient picked up a new ‘version’ of the bacterium or if the old one never went away. This can matter for management of that patient.”

Staph aureus bacteria are a leading cause of skin and underlying infections, such as boils, abscesses, and cellulitis. Often, this type of infection is not serious. However, the same organism-type can cause more serious infections, such as bone or joint infections. Sometimes Staph aureus can spread to the bloodstream and become life threatening.

In the past, getting to the source of outbreaks and transmission was tricky. Prior to bacterial whole-genome sequencing, lab workers had to rely on a type of molecular testing, called pulsed-field gel electrophoresis, which was tedious, difficult to analyze, and produced only a fraction of the information that DNA sequencing does.

“It is important to develop tests that can distinguish how individual bacteria are related to one another and to understand and control the spread of bacterial infections,” says Nicholas Chia, Ph.D., Assistant Director of the Center for Individualized Medicine Microbiome Program.

The Mayo Clinic Center for Individualized Medicine is working with the Mayo Clinic Department of Laboratory Medicine and Pathology to bring to the medical practice new testing methods that look at the entire genomes of human pathogenic bacteria.

“With microbial whole-genome sequencing, we can discover all there is to possibly know about an organism. It is cutting-edge technology that’s a little like CSI (crime scene investigation) in a way. We are providing information to assess relatedness, which will in turn direct interventions to interrupt transmission,” says Dr. Patel.

Research has shown that whole-genome sequencing can help track the source of the stubborn superbugs such as methicillin-resistant Staphylococcus aureus (or MRSA) outbreaks that have been reported in high school, college, and professional sports teams, in addition to in health care facilities. Many times, MRSA infection is spread via turf, locker room towels, or personal contact between athletes. Whole-genome sequencing can confirm the presence of an outbreak.

“Examining the entire bacterial genome, we will, in the near future, be able to identify resistance genes and mutations, therefore defining which antibiotics are going to be active. Our early research indicates that we can use whole-genome sequencing to inform drug selection and therefore how that patient should be treated. It is so new, we’ve elected to look at this application separately from the strain-relatedness testing approach we are currently performing,” says Dr. Patel.

Mayo Clinic is one of the first medical centers in the United States to routinely perform whole-genome sequencing of the Staph aureus bacteria in its clinical labs. The tests for this and other bacteria are available to other health care facilities through Mayo Clinic's global reference laboratory Mayo Medical Laboratories.

Additional research can be found here.

Mayo Clinic Center for Individualized Medicine

The Mayo Clinic Center for Individualized Medicine is all about solving the clinical challenges of today and tomorrow by bringing the latest discoveries from the research laboratory to physicians' fingertips in the form of new genomics-based tests and treatments.