New technique offers high-resolution surveillance information about various common antibiotic-resistant bacteria simultaneously, which may assist in controlling infection spread.
Scientists have introduced an advanced genomic method capable of monitoring the spread of several superbugs within a hospital at the same time. This could significantly enhance the prevention and management of prevalent hospital infections more swiftly and effectively than previously possible.
This proof-of-concept study, conducted by the Wellcome Sanger Institute, the University of Oslo, Fondazione IRCCS Policlinico San Matteo in Italy, and other partners, describes a novel deep sequencing method that simultaneously detects all common infectious bacteria in a hospital. Traditional approaches require culturing and sequencing pathogens individually, which is more time-consuming and labor-intensive.
Published today (20 August) in the Lancet Microbe, the research captured a complete range of pathogenic bacteria from various hospital intensive care units (ICUs) and general wards during the first wave of the COVID-19 pandemic in 2020. The researchers identified the types of bacteria present in patients, including well-known antibiotic-resistant strains typically found in hospitals.
The findings revealed that every ICU patient in the study was carrying at least one antibiotic-resistant bacterium, with many harboring several at the same time.
The researchers believe that their new methodology could be incorporated into existing hospital clinical monitoring systems. Given that antibiotic resistance is a pervasive challenge in healthcare settings, this system could effectively identify, track, and curtail the proliferation of various treatment-resistant bacteria concurrently.
Bacteria often exist harmlessly in or on the body, termed colonization. However, if certain strains enter the bloodstream due to a weakened immune system, they can trigger severe, potentially life-threatening infections unless treated effectively with antibiotics.
An additional challenge for healthcare professionals arises from some of these bacteria being antibiotic-resistant (AMR). Infections caused by AMR bacteria are a significant concern in healthcare facilities, with projections suggesting these resistant strains could result in more deaths than cancer by 20501. Some hospitals do screen for AMR bacteria upon patient admission, but no current framework efficiently monitors all multi-drug resistant bacteria throughout a hospital.
Over the past 15 years, genomic surveillance has emerged as a vital tool for monitoring pathogen evolution and transmission, providing critical insights to help control disease spread.
Nonetheless, existing methods involve culturing individual strains of bacteria from samples and then sequencing each one separately. This labor-intensive process can take several days and often yields only a limited view of all clinically relevant bacteria present in a sample.
In this new study from the Wellcome Sanger Institute, the University of Oslo, Fondazione IRCCS Policlinico San Matteo in Italy, and their collaborators, the team devised an innovative approach that captures whole genome sequencing information across multiple pathogens simultaneously. This ‘pan-pathogen’ deep sequencing method can provide genomic data as quickly as hospitals can process the samples.
The researchers collected samples from 256 patients in an Italian hospital, analyzing bacteria found in the gut, upper respiratory tract, and lungs. A total of 2,418 DNA samples were linked to 52 species of bacteria, with 66 percent (2,148) representing various strains of the seven most prevalent bacterial infections2 seen in healthcare facilities.
They discovered that ICU patients were colonized by at least one bacterium capable of causing serious illness at any given time, with clinically significant AMR genes present in at least 40 percent of these cases.
The team successfully tracked the distribution of hospital bacteria over a five-week sampling period, enabling them to predict which bacteria were likely to result in hospital-acquired infections.
Professor Jukka Corander, co-senior author from the Wellcome Sanger Institute and the University of Oslo, noted: “Our method, which captures genetic data on various bacterial strains simultaneously, has the potential to revolutionize genomic surveillance of pathogens. It allows us to acquire crucial information more efficiently and comprehensively than ever before, without sacrificing detail. Our proof-of-concept study now provides a solid foundation for future research to fully capture high-risk bacteria within specific areas and potentially assist hospitals in tracking and curbing the spread of resistant bacteria.”
Dr. Harry Thorpe, first author from the University of Oslo and visiting researcher at the Wellcome Sanger Institute, said: “Our study demonstrates how we can leverage genomic advancements to obtain a complete perspective on antibiotic-resistant bacteria throughout ICUs and elsewhere in hospitals. Since antibiotic-resistant bacteria evolve swiftly, our tracking methodologies must adapt quickly as well. By understanding the genetic composition of all bacteria in a sample, we gain a more comprehensive view of diversity in a location, which is critical for assessing risk and understanding the factors that contribute to the spread of specific strains.”
Professor Fausto Baldanti, Director of the Microbiology and Virology Unit at Fondazione IRCCS Policlinico San Matteo, added: “Our unit identified the very first COVID-19 case in the Western world, witnessing the onset of the pandemic and the enormous global scientific effort on SARS-COV2. However, our research illustrates that superbugs did not vanish; the simultaneous presence of multiple drug-resistant bacteria in ICUs treating COVID-19 patients could have significantly influenced the clinical characteristics of those early cases.”
Professor Nicholas Thomson, co-senior author from the Wellcome Sanger Institute, stated: “Infections resistant to antibiotics pose a continual challenge in hospitals. Although healthcare professionals strive diligently to minimize these risks, it remains challenging to combat an unseen threat. By integrating a deep genomic sequencing approach into healthcare systems, hospital staff can enhance their ability to identify and track these bacteria, facilitating the diagnosis of infections and enabling the control of outbreaks. Adopting this approach could lead to improved guidelines for assessing and managing the risks posed by treatment-resistant infections across all hospital patients, especially those in intensive care units.”
