Research expertise and methodologies

• DNA extractions from bacterial isolates as well as environmental and clinical samples.
• Preparing bacterial DNA for examination in nanochannels.
• Whole genome sequencing of bacterial isolates.
• Competition experiments with fluorescently labelled bacteria.
• Genetic manipulation of bacteria such as conjugation, transformation, transduction.
  

Ongoing research projects

Monitoring antibiotic resistance in wastewater treatment plants.

Can we use wastewater to monitor the AMR situation in the society?

We have developed a method that combines cultivation and selection of the bacteria of interest with metagenomic sequencing. Our collaboration partners are setting up a bioinformatics pipeline to identify the AMR patterns in the samples.

Our pilot study is looking at ESBL producing E. coli. We are collaborating with two universities in South Africa to compare countries with widely different antibiotic use.

Legionella pneumophila in the paper industry

We are sampling the wastewater from factories producing paper mass in Sweden. We want to know why there are a lot of Legionella in some plants, and some part of the plants, whereas others have very few. Our goal is recommendations to reduce the number of bacteria in the plants as well easy methods for testing.

Rapid diagnostics of bacterial infections

We are developing a method that can identify bacterial species in a clinical sample, fast and accurate. We extract the bacterial DNA from the patient samples and enclose the DNA in an agarose plug to protect it from shearing. Our collaboration partners identify the sequence of the bacteria by a microscopy-based method combined with stretching the DNA in nanochannels. A bioinformatics pipeline analyses the result to identify the bacteria in the sample.

Key publications

1. Kunnath RN, Abbaspour Z, Johnning A, Frykholm K, Wrande M, Dvirnas A, Kk S, Giske CG, Ambjörnsson T, Sandegren L, Kristiansson E, Westerlund F. Strain-Level Typing of Streptococcus pyogenes Using Optical DNA Mapping. ACS Infect Dis. 2025 Nov14;11(11):3085-3092. PMID: 41091517 https://doi.org/10.1021/acsinfecdis.5c00430
2. Nyblom M, Johnning A, Frykholm K, Wrande M, Müller V, Goyal G, Robertsson M, Dvirnas A, Sewunet T, Kk S, Ambjörnsson T, Giske CG, Sandegren L, Kristiansson E, Westerlund F. Strain-level bacterial typing directly from patient samples using optical DNA mapping. ACS Commun Med (Lond). 2023 Feb 23;3(1):31. PMID: 36823379 https://doi.org/10.1038/s43856-023-00259-z