S. Niemann, C.U. Koser, S. Gagneux, C. Plinke, S. Homolka, H. Bignell, R.J. Carter, R.K. Cheetham, A. Cox, N.A. Gormley, P. Kokko-Gonzales, L.J. Murray, R. Rigatti, V.P. Smith, F.P. Arends, H.S. Cox, G. Smith, J.A. Archer
PLoS One, 4(10), e7407, (2009)
complex (MTBC), the causative agent of tuberculosis (TB), is
characterized by low sequence diversity making this bacterium one of the
classical examples of a genetically monomorphic pathogen. Because of
this limited DNA sequence variation, routine genotyping of clinical MTBC
isolates for epidemiological purposes relies on highly discriminatory
DNA fingerprinting methods based on mobile and repetitive genetic
elements. According to the standard view, isolates exhibiting the same
fingerprinting pattern are considered direct progeny of the same
bacterial clone, and most likely reflect ongoing transmission or disease
relapse within individual patients.
we further investigated this assumption and used massively parallel
whole-genome sequencing to compare one drug-susceptible (K-1) and one
multidrug resistant (MDR) isolate (K-2) of a rapidly spreading M. tuberculosis Beijing genotype clone from a high incidence region (Karakalpakstan, Uzbekistan). Both isolates shared the same IS6110 RFLP pattern and the same allele at 23 out of 24 MIRU-VNTR loci.
generated 23.9 million (K-1) and 33.0 million (K-2) paired 50 bp purity
filtered reads corresponding to a mean coverage of 483.5 fold and 656.1
fold respectively. Compared with the laboratory strain H37Rv both
Beijing isolates shared 1,209 SNPs. The two Beijing isolates differed by
130 SNPs and one large deletion. The susceptible isolate had 55
specific SNPs, while the MDR variant had 75 specific SNPs, including the
five known resistance-conferring mutations.
Our results suggest that M. tuberculosis
isolates exhibiting identical DNA fingerprinting patterns can harbour
substantial genomic diversity. Because this heterogeneity is not
captured by traditional genotyping of MTBC, some aspects of the
transmission dynamics of tuberculosis could be missed or misinterpreted.
Furthermore, a valid differentiation between disease relapse and
exogenous reinfection might be impossible using standard genotyping
tools if the overall diversity of circulating clones is limited. These
findings have important implications for clinical trials of new