A genomic surveillance method monitors multiple superbugs in hospitals

Researchers have developed a new genomic technique that can track the spread of multiple superbugs in a hospital at the same time, which could help prevent and manage common hospital infections faster and more efficiently than ever before.

A proof-of-concept study by Wellcome Sanger Institute, University of Oslo, Fondazione IRCCS Policlinico San Matteo in Italy and collaborators details a new deep sequencing method that captures all common infectious bacteria in a hospital at once. With current methods, each pathogen is cultured and sequenced separately, which takes longer and requires more work.

Published on August 20 Lancet microbeDuring the first wave of the 2020 COVID-19 pandemic, the study included the entire population of pathogenic bacteria found in several hospital intensive care units (ICUs) and general wards. The researchers could see what types of bacteria the patients had, including all known antibiotic-resistant pathogens found in hospitals.

They found that every ICU patient tested in the study was colonized by at least one of these drug-resistant bacteria, while most were colonized by several of them simultaneously.

The researchers believe their approach can be integrated with existing hospital clinical monitoring systems. As drug resistance is a widespread problem in hospitals and other clinical settings, this system can simultaneously detect, track and limit the spread of common multidrug-resistant bacteria.

Bacteria are usually found in or on the body without damage, which is called colonization. However, when certain strains enter the bloodstream due to a weakened immune system, they can cause severe and life-threatening infections unless effectively treated with antibiotics.

As an additional challenge for healthcare providers, some of these bacteria are antibiotic resistant (AMR). Infections caused by AMR bacteria are a major problem in hospitals, as these treatment-resistant bacteria are projected to cause more deaths than cancer by 2050. Although some hospitals test for AMR bacteria on arrival, no system effectively monitors all multidrug-resistant bacteria throughout the period. to the hospital.

Over the past 15 years, genome surveillance has become a powerful tool for tracking the evolution and transmission of pathogens, providing critical insights for managing the spread of disease.

However, current methods involve growing one strain of bacteria in a sample at a time and then sequencing the entire genome for each of them separately. This is a laborious process that can easily take several days and provides only a partial view of all the clinically relevant bacteria found in a sample.

In this new study from the Wellcome Sanger Institute, the University of Oslo, Fondazione IRCCS Policlinico San Matteo in Italy and collaborators, the team developed a new approach that incorporated whole-genome sequencing data from multiple pathogens simultaneously. This is known as “pan-pathogen” deep sequencing and can provide genomic data as fast as hospitals can process samples.

The team sampled 256 patients at an Italian hospital, capturing bacteria found in the gut, upper respiratory tract and lungs. 2,418 DNA samples could be associated with 52 bacterial species. Of these, 66% (2148) were different strains of the seven most common bacterial infections seen in hospitals.

They found that ICU patients were colonized by at least one bacterium that can cause severe disease at any time, and that clinically relevant AMR genes were present in at least 40% of them.

The team effectively mapped the spread of nosocomial bacteria over a five-week sampling period, also allowing them to predict which bacteria were most likely to show up in infections acquired during hospital stays.

Professor Jukka Corander, co-author from the Wellcome Sanger Institute and the University of Oslo, said: “Our method, which collects genetic information from multiple bacterial strains simultaneously, could revolutionize the genomic surveillance of pathogens, allowing us to capture important information faster and more comprehensively than ever before, without losing resolution.

“With our proof-of-concept study, this approach can now be confidently used in future studies to capture the full breadth of high-risk bacteria in the region, and hopefully hospitals can help monitor and limit the spread of drug-resistant bacteria.”

Dr Harry Thorpe, first author from the University of Oslo and visiting fellow at the Wellcome Sanger Institute, said: “Our study is an example of how we can use the power of genomics to build a complete picture of antibiotic-resistant bacteria in intensive care units and also elsewhere in hospitals.

“Antibiotic-resistant bacteria evolve and spread rapidly, and therefore our surveillance methods must keep up with them. Knowing the sequence of all the bacteria in a sample provides a more complete picture of the diversity in an area, which is crucial for predicting risk and understanding the external factors associated with the spread of a particular strain.”

Professor Fausto Baldanti, Director of the Microbiology and Virology Unit at the Fondazione IRCCS Policlinico San Matteo, said: “Our unit identified the first case of COVID-19 in the Western world and we witnessed the dawn of a pandemic with huge scientific efforts worldwide. However, with SARS-COV2, our researchers’ study showed that superbugs do not gone.

“Indeed, the simultaneous presence of multiple drug-resistant bacterial species in intensive care units receiving patients with COVID-19 may have been an important component of the clinical manifestation of the new disease in those dramatic days.”

Co-author Professor Nicholas Thomson, from the Wellcome Sanger Institute, said: “Antibiotic-resistant infections are an ongoing problem in hospitals, and while healthcare professionals work hard to minimize them as much as possible, it’s hard to fight something you can’t fully see.

“Integrating a deep genomic sequencing approach into healthcare systems provides a new way for those working in hospitals to see and monitor these bacteria, helping to diagnose infections and allow outbreaks to be identified and controlled. Integrating this approach can help develop and improve guidelines for risk assessment and management of drug-resistant infections in all hospital patients for, especially in intensive care units.