The focus of our research is on Epidemiology, Taxonomy and Evolution of microorganisms. We are coordinating the Infectious diseases work package within Genomic Medicine Sweden in Region Uppsala and lead the work package “Microbiology” in Clinical Genomics Uppsala.
Our own ongoing projects are:
* Development, evaluation and implementation of molecular epidemiological source tracing methods and variant surveillance (Gullstrand fellow): In this project, we develop and adjust methods and workflows for the use in clinical laboratories in close collaboration or for the laboratory of clinical microbiology at the Uppsala University hospital. We developed the SARS-CoV-2 sequencing and bioinformatics pipeline that is used at the laboratory for clinical microbiology. The acquired data from this method are mainly for national surveillance at the public health institute.
* High throughput SARS-CoV-2 variant surveillance: In this project we optimize the clinical analysis workflow for SARS-CoV-2 sequencing regarding TAT and economy. At the beginning of the project, the library preparation with a 24 sample-multiplexing limit and bioinformatics analysis were done manually. An automated bioinformatics workflow for 96-sample processing was developed and implemented in the hospital. Pangolin and Nextclade was added to the pipeline to improve the efficiency and to minimize the hands on time as well as the human error rate in clinical analysis. The library preparation was upgraded to a semi-automated pipeline and in winter 2022, a fully automated library preparation for 96 samples multiplexing will be implemented.
* Genomic Pandemic Preparedness Portfolio: The role of our group in this GMS initiative is the coordination of the national ONT user network for dissemination of knowledge and collaborative method development. We are also involved in the development of a metagenomics approach for antibiotic- resistance- analysis.
* Symptom Genome (PI Mats Martinell): Our group is a collaboration partner in this project in which specific Covid symptoms shall be assigned to mutations in the SARS-CoV-2 genome.
* Campylobacter Taxonomy and Epidemiology: In this project, we aim to clarify the phylogenetic position of Campylobacter species and investigate outbreak scenarios.
* Phage ImmunoPrecipitation Sequencing: The method can be used for the investigation of SARS-CoV-2 antibody epitopes for the proof of asymptomatic Covid as well as the SARS-CoV-2 lineage, which a patient was infected with.
We also help other researches with high throughput long-read sequencing with optional automated library preparation to improve productivity, quality, and economy. The group owns a Hamilton NGSStar 2ODT, which allows multiplexed library preparation for up to 96 samples.
Furthermore, we support other groups with bioinformatics analysis or coding of user specific pipelines.
Rene Kaden, Assoc. Prof. (principal investigator)
Hilpi Rautelin, Prof. emerita, MD PhD (affiliated researcher)
Maria Rosengren, PhD (researcher)
Claes Ladenvall (bioinformatician CGU)
Ida Karlsson, PhD (bioinformatician)
Tomas Cumlin, MSc (bioinformatician)
Maryna Pimushyna, MSc (lab technician)
Paraskevi Saridaki, MSc (lab technician)
Badrul Hasan, PhD (affiliated researcher)