Infectious diseases

In Sweden, 65,000 patients are diagnosed annually with care-related infections and approximately 1,500 die as a result of an infectious disease. It is believed that nearly half of these deaths could be prevented through earlier detection and treatment.

NGS improves clinical diagnostics

Methods in which whole or parts of microbial genomes (genetic material) are examined with the use of NGS have significant potential for clinical diagnostics and treatment of infectious diseases. With the help of these techniques, certain microorganisms can be correctly identified, and antibiotic resistance can be determined, within a much shorter space of time. With NGS the amount of information from the same sequence has increased and the fastest analyses take just a few hours. Currently, the most successful use of NGS is on cultivated bacteria, however the goal is to find refined solutions in the foreseeable future, which may identify a pathogen directly from the patient’s sample (such as a blood test) in order to speed up diagnostics. This is especially important in cases of serious infection, such as sepsis and meningitis.

Sequencing has also become an important tool for tracking mutations, such as in the SARS-CoV-2 pandemic where the findings were of great importance for infection tracking and strategic efforts to reduce the spread of infection. The number of clinical samples analysed in Sweden with NGS is steadily increasing with >30,000 whole genome sequencing of bacteria and viruses as well as >9,500 16S sequencing in 2023.

Technology development makes it possible to reduce the spread of infectious diseases

By implementing NGS in healthcare, we can reduce the risk of infectious diseases spreading and thereby the occurrence of healthcare associated infections that often involve the problem of resistance.

With the help of this technology, we have been able to follow transmission routes of mutated virus strains in real time and thus implement measures to reduce the spread of infection during the Covid-19 pandemic. This requires new technical solutions, an IT infrastructure for data storage and data processing at hospitals. The SARS-CoV-2 pandemic has accelerated this work, where we now have been setting up technical solutions and a joint automated workflow for bioinformatics analysis not only for SARS-CoV-2 but also for typing of other microorganisms, metagenomic analysis both for shotgun sequencing (everything in the samples) and also target 16S long-read sequencing for fast sequencing of pathogens on the National genomics platform (NGP) within GMS. The NGP will be the basis for methods and results to be easily shared in real time between regions affected by outbreaks where the source of infection needs to be mapped out with the use of one single method and also to be able to identify new pandemic threats. International comparisons can thus be facilitated, which has clearly been shown to be of great importance during the pandemic.

Microbiology and infectious diseases are a focus for GMS

Our goal is to achieve fast and reliable identification of microorganisms that cause infectious diseases. Quality assured methods and results should be easily shared between regions in Sweden with the use of national technical solutions. This is necessary in order to, for example, identify pathways of infection in the case of outbreaks and achieve a national consensus on the characterisation of pathogenic microorganisms.

We develop improved analytical methods for diagnostics such as NGS-based sequencing, clinical metagenomics including prediction of antibiotic resistance directly from patient samples and rapid sequencing of disease-causing microorganisms. To streamline national and international monitoring in real time, we develop joint workflows, such as laboratory protocols and bioinformatics analysis pipelines, for gene sequencing of a number of microorganisms that cause infectious diseases. These joint workflows thus provide healthcare with better prerequisites for quality-assured NGS-based diagnostics throughout the country.

Co-chairs and coordinators Infectious diseases

Christian Giske (co-chair)
Paula Mölling (co-chair)
Per Sikora (co-chair)
Erika Tång Hallbäck (coordinator)
Isak Sylvin (coordinator, bioinformatics)