Simultaneously, phylogenetic analyses were developed based on single nucleotide polymorphisms
(SNPs), genomic deletions usually referred to as regions of difference (RDs) and spoligotyping which
served both strain typing and phylogenetic analysis. National and international initiatives that rely on
the application of these typing methods have brought significant insight into the molecular epidemiology
of tuberculosis. However, current DNA fingerprinting methods have important limitations. They can often
not distinguish between genetically closely related strains and the turn-over of these markers is variable.
Moreover, the suitability of most DNA typing methods for phylogenetic reconstruction is limited as they
show a high propensity of convergent evolution or misinfer genetic distances. In order to fully explore the
possibilities of genotyping in the molecular epidemiology of tuberculosis and to study the phylogeny of
the causative bacteria reliably, the application of whole-genome sequencing (WGS) analysis for all M.
tuberculosis isolates is the optimal, although currently still a costly solution. In the last years WGS for typing
of pathogens has been explored and yielded important additional information on strain diversity in
comparison to the classical DNA typing methods. With the ongoing cost reduction of DNA sequencing
it is possible that WGS will become the sole diagnostic tool in the secondary laboratory diagnosis of
tuberculosis for identification, drug susceptibility testing and genetic characterization.
Simultaneously, phylogenetic analyses were developed based on single nucleotide polymorphisms(SNPs), genomic deletions usually referred to as regions of difference (RDs) and spoligotyping whichserved both strain typing and phylogenetic analysis. National and international initiatives that rely onthe application of these typing methods have brought significant insight into the molecular epidemiologyof tuberculosis. However, current DNA fingerprinting methods have important limitations. They can oftennot distinguish between genetically closely related strains and the turn-over of these markers is variable.Moreover, the suitability of most DNA typing methods for phylogenetic reconstruction is limited as theyshow a high propensity of convergent evolution or misinfer genetic distances. In order to fully explore thepossibilities of genotyping in the molecular epidemiology of tuberculosis and to study the phylogeny ofthe causative bacteria reliably, the application of whole-genome sequencing (WGS) analysis for all M.tuberculosis isolates is the optimal, although currently still a costly solution. In the last years WGS for typingof pathogens has been explored and yielded important additional information on strain diversity incomparison to the classical DNA typing methods. With the ongoing cost reduction of DNA sequencingit is possible that WGS will become the sole diagnostic tool in the secondary laboratory diagnosis oftuberculosis for identification, drug susceptibility testing and genetic characterization.
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