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26 Jan 2022

Researchers develop optimised framework to help stem the spread of deadly, antibiotic-resistant pathogen

Peer review: Nature Communications
Funding: Melbourne Genomic Health Alliance, (funded by the Victorian Government Department of Jobs, Precincts and Regions, and ten member organisations)
DOI: 10.1038/s41467-022-28156-4.

Researchers at the Doherty Institute have developed a standardised test for accurately determining the transmission of the deadly pathogen Vancomycin resistant Enterococcus faecium (VREfm).

VREfm is a bacterial pathogen that has been listed by the World Health Organization as a high priority pathogen due to its resistance to antibiotics.

The pathogen can be acquired during a patient’s stay in hospital and its highly resistant nature means there are few effective antibiotics that can be used to treat VREfm infections.

Although numbers have not been consistently reported in Australia, VRE caused an estimated 54,500 infections and 5,400 deaths in the United States in a single year back in 2017.

While various methods of genome sequencing and analysis have been used to track the spread of VREfm in hospitals, until now these tests have never been standardised or optimised for accuracy, meaning transmission links can be missed, potentially enabling the bacteria to spread undetected.

Published today in Nature Communications, this new framework will enable the rapid identification of potential outbreaks, allowing public health teams to intervene early and prevent further transmission of the deadly pathogen.

Lead author on the paper, University of Melbourne PhD Candidate at the Doherty Institute, Charlie Higgs, explained that finding transmission links involves whole genome sequencing samples of the bacteria and the use of computer programs fluent in the language of genetic code, which compare the bacterial genomes and determine the number of differences between them.

“If two genomes of bacteria are shown to be very similar to each other then we can infer that a transmission event has occurred and begin looking at interventions to stop further spread,” Higgs explained.

“The problem is that these tests aren’t standardised, and with so many tests being used globally it is difficult to know which one is the most reliable.

“It also makes it very difficult to compare rates of transmission between different hospital sites and over multiple time points, meaning you are never getting a full picture and it is very difficult to assess the effectiveness of infection control interventions.”

To address this, the team systematically compared five genomic approaches and identified which method was most reliable and reproducible, as well as requiring minimal time and computational resources.

From there they were able to develop a standardised genomic framework for inferring VRE transmission that can be used as the basis for global deployment of VREfm genomics into routine outbreak detection and investigation.

University of Melbourne Professor Ben Howden, Director of the Microbiological Diagnostic Unit Public Health Laboratory (MDU-PHL) at the Doherty Institute, explained that the use of this new standardised framework across institutions will allow greater comparability of studies.

“The framework will facilitate the use of VRE genomics as a true ‘precision public health’ tool to inform the control of this high-risk AMR pathogen,” Professor Howden said.

This work was supported by the Melbourne Genomic Health Alliance (funded by the State Government of Victoria’s Department of Jobs, Precincts and Regions, and the ten member organisations).