Teemu Kallonen
PhD, MSc
teemu.kallonen@utu.fi ORCID identifier: https://orcid.org/0000-0003-1741-6486 |
Microbiology, Genomics, Bioinformatics
Clinical Microbiome Bank, Institue of Biomedicine, Faculty of Medicine, University of Turku and Clinical Microbiology, Turku University Hospital
I did my PhD at the University of Turku and the Pertussis reference laboratory, Finnish institute for health and welfare and defended my thesis in 2011. The topic of my research was the evolution and adaptation of Bordetella pertussis, the causative agent of whooping couch, after the initiation of vaccinations.
I did a postdoc (2012-2013) with Prof. Olli Lassila on B cell and plasma cell differentiation after which I changed bact to studying bacteria. I did a postdocs wiht Prof. Julian Parkhill and Prof. Sharon Peacock at the Wellcome Sanger Institute, UK (2014-2016), and Prof. Jukka Corander at the University of Oslo, Norway (2017-2019), using bioinformatic analyses to study whole-genome sequenced bacteria and antibiotic resistance.
A the moment my reseach is still concentrated on WGS analyses and antibiotic resistance as well as microbiome studies.
Main focus of my research is in bacterial genomics, including bioinformatic analyses of population structure, antibiotic resistance and other factors affecting the success of different clones. Recently I have increasingly been involved with several research project investigating the role of the gut microbiome in human diseases e.g. acute appendicitis and prostate cancer.
- Altered oral microbiome, but normal human papilloma virus prevalence in cartilage-hair hypoplasia patients (2024)
- Orphanet Journal of Rare Diseases
(A1 Refereed original research article in a scientific journal) - Bioinformatiikka bakteriologiassa - lupauksia ja haasteita (2024)
- Duodecim
(A2 Refereed review article in a scientific journal ) - Comparative Metabolomics and Microbiome Analysis of Ethanol versus OMNImet/gene•GUT Fecal Stabilization (2024)
- Analytical Chemistry
(A1 Refereed original research article in a scientific journal) - Deep sequencing of Escherichia coli exposes colonisation diversity and impact of antibiotics in Punjab, Pakistan (2024)
- Nature Communications
(A1 Refereed original research article in a scientific journal) - Differences in Gut Microbiota Profiles and Microbiota Steroid Hormone Biosynthesis in Men with and Without Prostate Cancer (2024)
- European Urology Open Science
(A1 Refereed original research article in a scientific journal) - Exploring the pediatric nasopharyngeal bacterial microbiota with culture-based MALDI-TOF mass spectrometry and targeted metagenomic sequencing (2024)
- mBio
(A1 Refereed original research article in a scientific journal) - High-throughput DNA extraction strategy for fecal microbiome studies (2024)
- Microbiology spectrum
(A1 Refereed original research article in a scientific journal) - Modulation of multidrug-resistant clone success in Escherichia coli populations: a longitudinal, multi-country, genomic and antibiotic usage cohort study (2024)
- Lancet microbe
(A1 Refereed original research article in a scientific journal) - Pan-pathogen deep sequencing of nosocomial bacterial pathogens in Italy in spring 2020 : a prospective cohort study (2024)
- Lancet microbe
(A1 Refereed original research article in a scientific journal) - Optimal sampling and analysis methods for clinical diagnostics of vaginal microbiome (2023)
- European Journal of Clinical Microbiology and Infectious Diseases
(A1 Refereed original research article in a scientific journal) - A large-scale genomic snapshot of Klebsiella spp. isolates in Northern Italy reveals limited transmission between clinical and non-clinical settings (2022)
- Nature Microbiology
(A1 Refereed original research article in a scientific journal) - Appendiceal microbiome in uncomplicated and complicated acute appendicitis: A prospective cohort study (2022)
- PLoS ONE
(A1 Refereed original research article in a scientific journal) - External quality assessment of SARS-CoV-2-sequencing: An ESGMD-SSM pilot trial across 15 European laboratories (2022)
- Journal of Clinical Microbiology
(A1 Refereed original research article in a scientific journal) - Gut Microbiota and Serum Metabolome in Elite Cross-Country Skiers: A Controlled Study (2022)
- Metabolites
(A1 Refereed original research article in a scientific journal) - Bacterial genomic epidemiology with mixed samples (2021)
- Microbial genomics
(A1 Refereed original research article in a scientific journal) - Dynamics of intestinal multidrug-resistant bacteria colonisation contracted by visitors to a high-endemic setting: a prospective, daily, real-time sampling study (2021)
- Lancet microbe
(A1 Refereed original research article in a scientific journal) - Genetic evolution of invasive emm28 Streptococcus pyogenes strains and significant association with puerperal infections in young women in Finland (2021)
- Clinical Microbiology and Infection
(A1 Refereed original research article in a scientific journal) - Genome of Superficieibacter maynardsmithii, a novel, antibiotic susceptible representative of Enterobacteriaceae (2021)
- G3: genes, genomes, genetics
(A1 Refereed original research article in a scientific journal) - Real-time sampling of travelers shows intestinal colonization by multidrug-resistant bacteria to be a dynamic process with multiple transient acquisitions (2021)
- bioRxiv
(B1 Non-refereed article in a scientific journal) - High-resolution sweep metagenomics using fast probabilistic inference (2020)
- Wellcome Open Research
(A1 Refereed original research article in a scientific journal)