Journal article
Genomic epidemiology of a major Mycobacterium tuberculosis outbreak: Retrospective cohort study in a low incidence setting using sparse time-series sampling
Statens Serum Institut1
Department of Systems Biology, Technical University of Denmark2
University of Southern Denmark3
Department of Biotechnology and Biomedicine, Technical University of Denmark4
Infection Microbiology, Section for Microbial and Chemical Ecology, Department of Biotechnology and Biomedicine, Technical University of Denmark5
Since 1992, Denmark has documented the largest outbreak of tuberculosis in Scandinavia ascribed to a single genotype, termed 'C2/1112-15'. As of spring 2017, the International Reference Laboratory of Mycobacteriology in Copenhagen has collected and identified isolates from more than a thousand cases belonging to this outbreak via routine MIRU-VNTR typing.
Here, we present a retrospective analysis of the C2/1112-15 dataset, based on whole-genome data from a sparse time-series consisting of five randomly selected isolates from each of the 23 years. Even if these data are derived from only 12% of the collected isolates, we have been able to extract important key information, such as mutation rate, conserved single-nucleotide polymorphisms to identify discrete transmission chains, as well as the possible historical origins of the outbreak.
Language: | English |
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Publisher: | Oxford University Press |
Year: | 2017 |
Pages: | 366-374 |
ISSN: | 15376613 and 00221899 |
Types: | Journal article |
DOI: | 10.1093/infdis/jix298 |
ORCIDs: | Norman, Anders and Jelsbak, Lars |
Bacterial Typing Techniques DNA, Bacterial DNA, Bacterial/genetics Denmark Denmark/epidemiology Genotype Humans Incidence Linear Models M. tuberculosis Molecular Epidemiology Mutation Rate Mycobacterium tuberculosis Mycobacterium tuberculosis/genetics Polymorphism, Single Nucleotide Retrospective Studies Sequence Analysis, DNA Tuberculosis Tuberculosis/epidemiology WGS evolution outbreak transmission