Introduction:

In Finland, the Finnish Institute for Health and Welfare (THL) is responsible for epidemiological monitoring of communicable diseases and all the clinical laboratories are obliged to send monitoring required microbes causing infectious diseases to THL for molecular typing. During the COVID-19 pandemic, we started NGS sequencing for local epidemiological surveillance of SARS-CoV-2 variants in the Department of Clinical microbiology. We also participated HERA project, coordinated by THL, where the aim was to strengthen the WGS capacity and infrastructure in national level and strengthen the genome-based surveillance on national and EU level. One important goal of the project was to increase NGS capacity in Finland, especially in the central hospital laboratories.

Materials and methods:

In the end of 2022, we got Illumina Miseq and Nextseq2000 sequencers in our department. We had previously old Miseq and we had used Miniseq for SARS-CoV-2 sequencing. As part of the HERA project, we first sequenced Campylobacter jejuni strains collected at our department during 2021-2022. Since then, we have used bacterial WGS to investigate various local infection clusters and samples from possible ward epidemics, including e.g. Streptococcus pyogenes, MRSA, ESBL strains.

Results:

With bacterial WGS, we have been able to detect local outbreaks caused by S. pyogenes and MRSA. On the other hand, we have also been able to rule out ward epidemics based on the WGS result. Antimicrobial susceptibility results from WGS have been in line with phenotypic antimicrobial susceptibility testing results, however in our clinical laboratory setting WGS data is not going to replace AST determination in a near future. On January 2024 we introduced ‘BaktWGS, bacterium, whole genome sequencing’ laboratory research, as a first clinical microbiology laboratory in Finland.

Discussion:

Bacterial WGS gives us information that cannot get only with culture techniques. Bacterial WGS is a superior tool for microbial epidemiology and the use of WGS locally is important for epidemiological surveillance. WGS helps to identify places and wards where strict infection control measures are needed. Thus smooth cooperation with infectious diseases specialists has been important in finding the right applications for the use of bacterial WGS.