@article{fdi:010048500,
  title = {{M}ultispacer sequence typing for {M}ycobacterium tuberculosis genotyping},
  author = {{D}jelouadji, {Z}. and {A}rnold, {C}. and {G}harbia, {S}. and {R}aoult, {D}idier and {D}rancourt, {M}.},
  editor = {},
  language = {{ENG}},
  abstract = {{B}ackground: {G}enotyping methods developed to survey the transmission dynamics of {M}ycobacterium tuberculosis currently rely on the interpretation of restriction and amplification profiles. {M}ultispacer sequence typing ({MST}) genotyping is based on the sequencing of several intergenic regions selected after complete genome sequence analysis. {I}t has been applied to various pathogens, but not to {M}. tuberculosis. {M}ethods and {F}indings: {I}n {M}. tuberculosis, the {MST} approach yielded eight variable intergenic spacers which included four previously described variable number tandem repeat loci, one single nucleotide polymorphism locus and three newly evaluated spacers. {S}pacer sequence stability was evaluated by serial subculture. {T}he eight spacers were sequenced in a collection of 101 {M}. tuberculosis strains from five phylogeographical lineages, and yielded 29 genetic events including 13 tandem repeat number variations (44.82%), 11 single nucleotide mutations (37.93%) and 5 deletions (17.24%). {T}hese 29 genetic events yielded 32 spacer alleles or spacer-types ({ST}) with an index of discrimination of 0.95. {T}he distribution of {M}. tuberculosis isolates into {ST} profiles correlated with their assignment into phylogeographical lineages. {B}lind comparison of a further 93 {M}. tuberculosis strains by {MST} and restriction fragment length polymorphism-{IS}6110 fingerprinting and mycobacterial interspersed repetitive units typing, yielded an index of discrimination of 0.961 and 0.992, respectively. {MST} yielded 41 different profiles delineating 16 related groups and proved to be more discriminatory than {IS}6110-based typing for isolates containing {M}<8 {IS}6110 copies ({P}<0.0003). {MST} was successfully applied to 7/10 clinical specimens exhibiting a {C}ts <= 42 cycles in internal transcribed spacer-real time {PCR}. {C}onclusions: {T}hese results support {MST} as an alternative, sequencing-based method for genotyping low {IS}6110 copy-number {M}. tuberculosis strains. {T}he {M}. tuberculosis {MST} database is freely available (http://ifr48.timone.univ-mrs.fr/{MST}_{MT}uberculosis/mst).},
  keywords = {},
  booktitle = {},
  journal = {{P}los {O}ne},
  volume = {3},
  numero = {6},
  pages = {e2433},
  ISSN = {1932-6203},
  year = {2008},
  DOI = {10.1371/journal.pone.0002433},
  URL = {https://www.documentation.ird.fr/hor/fdi:010048500},
}