title: Ecotypes of the Mycobacterium tuberculosis complex.
abstract: A phylogeny of the Mycobacterium tuberculosis complex has recently shown that the animal-adapted strains are found in a single lineage marked by the deletion of chromosomal region 9 (RD9) [Brosch et al., 2002. A new evolutionary scenario for the Mycobacterium tuberculosis complex. Proc. Natl Acad. Sci. USA 99 (6), 3684-3689]. We have obtained the spoligotype patterns of the RD9 deleted strains used to generate this new evolutionary scenario and we show that the presence of spoligotype spacers 3, 9, 16, 39, and 40-43 is phylogenetically informative in this lineage. We have used the phylogenetically informative spoligotype spacers to screen a database of spoligotype patterns and have identified further members of a group of strains apparently host-adapted to antelopes. The presence of the spoligotype spacers is congruent with the phylogeny generated by chromosomal deletions, suggesting that recombination is rare or absent between strains of this lineage. The phylogenetically informative spacers, in concert with the previously identified single nucleotide mutations and chromosomal deletions, can be used to identify a series of clades in the RD9 deleted lineage each with a separate host preference. Finally, we discuss the application of the ecotype concept to this series of clades and suggest that the M. tuberculosis complex may best be described as a series of host-adapted ecotypes.
authors.affiliation: TB Research Group, Veterinary Laboratories Agency, VLA, Addlestone, Surrey KT15 3NB, UK. Noel@Sussex.ac.uk
authors.forename: Noel H
authors.initials: NH
authors.lastname: Smith
authors.forename: Kristin
authors.initials: K
authors.lastname: Kremer
authors.forename: Jacqueline
authors.initials: J
authors.lastname: Inwald
authors.forename: James
authors.initials: J
authors.lastname: Dale
authors.forename: Jeffrey R
authors.initials: JR
authors.lastname: Driscoll
authors.forename: Stephen V
authors.initials: SV
authors.lastname: Gordon
authors.forename: Dick
authors.initials: D
authors.lastname: van Soolingen
authors.forename: R Glyn
authors.initials: RG
authors.lastname: Hewinson
authors.forename: John Maynard
authors.initials: JM
authors.lastname: Smith
mesh_terms: D000818:Animals; D000866:Antelopes / Q000382:microbiology; D015373:Bacterial Typing Techniques; D005075:Biological Evolution; D005798:Genes, Bacterial; D009169:Mycobacterium tuberculosis / Q000145:classification / Q000235:genetics*; D010802:Phylogeny