DNA fingerprinting of Mycobacterium tuberculosis : From phage typing to whole-genome sequencing

DNA fingerprinting of Mycobacterium tuberculosis : From phage typing to whole-genome sequencing Current typing methods for Mycobacterium tuberculosis complex evolved from simple phenotypic approaches like phage typing and drug susceptibility profiling to DNA-based strain typing methods, such as IS 6110 -restriction fragment length polymorphisms (RFLP) and variable number of tandem repeats (VNTR) typing. Examples of the usefulness of molecular typing are source case finding and epidemiological linkage of tuberculosis (TB) cases, international transmission of MDR/XDR-TB, the discrimination between endogenous reactivation and exogenous re-infection as a cause of relapses after curative treatment of tuberculosis, the evidence of multiple M. tuberculosis infections, and the disclosure of laboratory cross-contaminations. 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. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Infection, Genetics and Evolution Elsevier

DNA fingerprinting of Mycobacterium tuberculosis : From phage typing to whole-genome sequencing

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Publisher
Elsevier
Copyright
Copyright © 2011 Elsevier B.V.
ISSN
1567-1348
D.O.I.
10.1016/j.meegid.2011.08.032
Publisher site
See Article on Publisher Site

Abstract

Current typing methods for Mycobacterium tuberculosis complex evolved from simple phenotypic approaches like phage typing and drug susceptibility profiling to DNA-based strain typing methods, such as IS 6110 -restriction fragment length polymorphisms (RFLP) and variable number of tandem repeats (VNTR) typing. Examples of the usefulness of molecular typing are source case finding and epidemiological linkage of tuberculosis (TB) cases, international transmission of MDR/XDR-TB, the discrimination between endogenous reactivation and exogenous re-infection as a cause of relapses after curative treatment of tuberculosis, the evidence of multiple M. tuberculosis infections, and the disclosure of laboratory cross-contaminations. 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.

Journal

Infection, Genetics and EvolutionElsevier

Published: Jun 1, 2012

References

  • Resolving lineage assignation on Mycobacterium tuberculosis clinical isolates classified by spoligotyping with a new high-throughput 3R SNPs based method
    Abadia, E.; Zhang, J.; dos Vultos, T.; Ritacco, V.; Kremer, K.; Aktas, E.; Matsumoto, T.; Refregier, G.; van Soolingen, D.; Gicquel, B.; Sola, C.
  • Evolution, population structure, and phylogeography of genetically monomorphic bacterial pathogens
    Achtman, M.
  • Genome-wide analysis of synonymous single nucleotide polymorphisms in Mycobacterium tuberculosis complex organisms: resolution of genetic relationships among closely related microbial strains
    Gutacker, M.M.; Smoot, J.C.; Migliaccio, C.A.L.; Ricklefs, S.M.; Hua, S.; Cousins, D.V.; Graviss, E.A.; Shashkina, E.; Kreiswirth, B.N.; Musser, J.M.
  • Multilocus sequence typing of bacteria
    Maiden, M.C.
  • Characterization of a Mycobacterium tuberculosis insertion sequence belonging to the IS3 family
    McAdam, R.A.; Hermans, P.W.; van Soolingen, D.; Zainuddin, Z.F.; Catty, D.; van Embden, J.D.; Dale, J.W.
  • The role of IS 6110 in the evolution of Mycobacterium tuberculosis
    McEvoy, C.R.; Falmer, A.A.; Gey van Pittius, N.C.; Victor, T.C.; van Helden, P.D.; Warren, R.M.
  • Characterization of the major formamidopyrimidine-DNA glycosylase homolog in Mycobacterium tuberculosis and its linkage to variable tandem repeats
    Olsen, I.; Balasingham, S.V.; Davidsen, T.; Debebe, E.; Rodland, E.A.; van Soolingen, D.; Kremer, K.; Alseth, I.; Tonjum, T.
  • High-throughput sequencing and clinical microbiology: progress, opportunities and challenges
    Pallen, M.J.; Loman, N.J.; Penn, C.W.
  • Phylogenetic understanding of clonal populations in an era of whole genome sequencing
    Pearson, T.; Okinaka, R.T.; Foster, J.T.; Keim, P.
  • Characterization of the highly abundant polymorphic GC-rich-repetitive sequence (PGRS) present in Mycobacterium tuberculosis
    Poulet, S.; Cole, S.T.
  • In silico simulation of fingerprinting techniques based on double endonuclease digestion of genomic DNA
    San Millan, R.; Garaizar, J.; Bikandi, J.
  • Mutations in the regulatory network that underlie the recent clonal expansion of a dominant subclone of the Mycobacterium tuberculosis Beijing genotype
    Schürch, A.C.; Kremer, K.; Warren, R.M.; Hung, N.V.; Zhao, Y.; Wan, K.; Boeree, M.J.; Siezen, R.; Smith, N.H.; van Soolingen, D.
  • Identification of novel intergenic repetitive units in a mycobacterial two-component system operon
    Supply, P.; Magdalena, J.; Himpens, S.; Locht, C.
  • Variable human minisatellite-like regions in the Mycobacterium tuberculosis genome
    Supply, P.; Mazars, E.; Lesjean, S.; Vincent, V.; Gicquel, B.; Locht, C.
  • Linkage disequilibrium between minisatellite loci supports clonal evolution of Mycobacterium tuberculosis in a high tuberculosis incidence area
    Supply, P.; Warren, R.M.; Banuls, A.L.; Lesjean, S.; Van Der Spuy, G.D.; Lewis, L.A.; Tibayrenc, M.; Van Helden, P.D.; Locht, C.
  • Short sequence repeats in microbial pathogenesis and evolution
    van Belkum, A.
  • Improved differentiation of Mycobacterium tuberculosis strains, including many Beijing genotype strains, using a new combination of variable number of tandem repeats loci
    Yokoyama, E.; Kishida, K.; Uchimura, M.; Ichinohe, S.
  • Concordance of variable-number tandem repeat (VNTR) and large sequence polymorphism (LSP) analyses of Mycobacterium tuberculosis strains
    Yokoyama, E.; Hachisu, Y.; Hashimoto, R.; Kishida, K.

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