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14 Apr 2022

Ahead of the curve – identifying and controlling superbugs before they spread

Researchers are using DNA analysis to identify potential superbug outbreaks before they become a threat.

Published in The Lancet Regional Health Western Pacific, the comprehensive study conducted by the Doherty Institute through funding from the Melbourne Genomics Health Alliance focused on assessing whether genomics could track the transmission of antibiotic-resistant bacteria in real time across multiple hospitals.

“The aim of the project was to see if we could identify potential superbug outbreaks before they became a threat, and therefore prevent further infections,” explains Austin Health infectious diseases physician and University of Melbourne researcher, Dr Norelle Sherry, the lead clinician on the project.

“The hypothesis was that rapid genomic sequencing of superbugs would enable us to detect transmission in a matter of days, enabling real time action on reducing infection risk.

“Genomics has been used in research for a long time, so we knew we could use it to detect transmission.

“What hasn’t been done before is applying this across multiple hospitals and multiple superbugs, and looking ahead; getting all the isolates as they come in, rather than going back after an outbreak has already occurred.”

Between April 2017 and November 2018, the team sequenced over 2200 isolates from 1900 patients across four hospital networks in Melbourne.

“By combining genomic information with patient movement data from the hospitals, for the first time we were able to define the number of patients who seemed to have acquired a superbug in hospital,” explains Dr Sherry. “

Overall, we found that 648 patients who had a superbug detected while they were in hospital probably acquired it there, rather than in the community. Importantly, most of these transmissions would not have been detected through usual methods.

“We were also able to show that there was more transmission of two common superbugs – Methicillin-resistant Staphylococcus aureus (MRSA) and Extended Spectrum Beta-Lactamases Escherichia coli (E.coli) – than currently thought, really challenging the existing dogma in hospital infection control.”

The second phase of the project fed information back to the hospitals to see if they could intervene to stop further transmission.

“There were challenges in communicating really complicated genomic information back to clinicians, and in trying to help them work out how to integrate this genomic data into their infection control programs,” says Dr Sherry.

“Through focus groups, we found that infection control teams wanted quite simplified information because they’ve got so much data coming from different places. This helped us formulate a communications strategy.”

The Controlling Superbugs study was led by University of Melbourne Professor Benjamin Howden, Director of the Microbiological Diagnostic Unit Public Health Laboratory, and Professor Lindsay Grayson, Director, Department of Infectious Diseases & Microbiology, Austin Health.

Peer reviewed:

This article was first published in the Celebrating Five Years of the Doherty Institute Impact Report.