New Genomic Technique Tracks Superbugs in Hospitals Simultaneously

A team led by researchers from Wellcome Sanger Institute has developed a genomic technique that can track the spread of multiple superbugs in a hospital simultaneously, which could help prevent and manage common hospital infections quicker and more effectively than ever before.

The novel approach employs deep sequencing to capture all common infectious bacteria in a hospital environment at once. Unlike existing methods that require separate culturing and sequencing of each pathogen, this technique is faster and less labor-intensive, according to the team.

Published in the Lancet Microbe, the study was conducted during the first wave of the 2020 COVID-19 pandemic. It analyzed pathogenic bacteria populations in various hospital wards, including ICUs, revealing that every ICU patient was colonized by at least one antibiotic-resistant bacterium, with many hosting multiple strains. This new method could be integrated with hospital surveillance systems to better identify, track, and control the spread of treatment-resistant bacteria.

Colonization by bacteria, often harmless, can lead to severe infections if certain strains enter the bloodstream, especially in patients with weakened immune systems. The rise of antibiotic-resistant (AMR) bacteria poses a significant challenge, with predictions that they could cause more deaths than cancer by 2050. Despite some hospitals testing for AMR bacteria upon patient admission, a comprehensive system to track all multi-drug resistant bacteria is lacking.

The research team collected samples from 256 patients in an Italian hospital, identifying 52 bacterial species, with 66% of DNA samples comprising strains of the seven most common hospital infections. The presence of clinically significant AMR genes was noted in 40% of ICU patients. This approach allowed researchers to map bacterial spread over five weeks, predicting potential infection-causing strains. 

According to first author Harry Thorpe, “Our study is an example of how we can use the power of genomics to create a full picture of antibiotic-resistant bacteria across intensive care units and also elsewhere in hospitals. Antibiotic-resistant bacteria evolve and spread quickly, and therefore our tracking methods have to keep pace with them. Knowing the sequencing of all the bacteria in a sample gives a more complete picture of the diversity found in an area, which is crucial in predicting risk and understanding the external factors involved in the spread of a specific strain.”