Mycobacterium tuberculosis--heterogeneity revealed through whole genome sequencing.
The emergence of whole genome sequencing (WGS) technologies as primary research tools has allowed for the detection of genetic diversity in Mycobacterium tuberculosis (Mtb) with unprecedented resolution. WGS has been used to address a broad range of topics, including the dynamics of evolution, transmission and treatment. Here, we have analyzed 55 publically available genomes to reconstruct the phylogeny of Mtb, and we have addressed complications that arise during the analysis of publically available WGS data. Additionally, we have reviewed the application of WGS to the study of Mtb and discuss those areas still to be addressed, moving from global (phylogeography), to local (transmission chains and circulating strain diversity), to the single patient (clonal heterogeneity) and to the bacterium itself (evolutionary studies). Finally, we discuss the current WGS approaches, their strengths and limitations.
Department of Immunology and Infectious Diseases, Harvard School of Public Health, 665 Huntington Avenue, Building 1, Boston, MA 02115, USA.
Chris
C
Ford
Karina
K
Yusim
Tom
T
Ioerger
Shihai
S
Feng
Michael
M
Chase
Mary
M
Greene
Bette
B
Korber
Sarah
S
Fortune
D015373:Bacterial Typing Techniques / Q000379:methods; D030561:Databases, Nucleic Acid; D014644:Genetic Variation; D016680:Genome, Bacterial; D006801:Humans; D009169:Mycobacterium tuberculosis / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA / Q000379:methods; D014376:Tuberculosis / Q000382:microbiology