Genomic diversity among drug sensitive and multidrug resistant isolates of Mycobacterium tuberculosis with identical DNA fingerprints.
BACKGROUND
Mycobacterium tuberculosis 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.


RESULTS
Here 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. We 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.


CONCLUSIONS
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 anti-tuberculosis drugs.
Niemann
Stefan
S
Molecular Mycobacteriology, Research Center Borstel, Borstel, Germany. sniemann@fz-borstel.de
Köser
Claudio U
CU
Gagneux
Sebastien
S
Plinke
Claudia
C
Homolka
Susanne
S
Bignell
Helen
H
Carter
Richard J
RJ
Cheetham
R Keira
RK
Cox
Anthony
A
Gormley
Niall A
NA
Kokko-Gonzales
Paula
P
Murray
Lisa J
LJ
Rigatti
Roberto
R
Smith
Vincent P
VP
Arends
Felix P M
FP
Cox
Helen S
HS
Smith
Geoff
G
Archer
John A C
JA
D000995:Antitubercular Agents / Q000627:therapeutic use; D015373:Bacterial Typing Techniques / Q000379:methods; D019295:Computational Biology / Q000379:methods; D004247:DNA / Q000235:genetics*; D016172:DNA Fingerprinting / Q000379:methods; D030541:Databases, Genetic; D024881:Drug Resistance, Bacterial; D018432:Drug Resistance, Multiple; D017353:Gene Deletion; D005821:Genetic Techniques; D014644:Genetic Variation; D016680:Genome, Bacterial; D005838:Genotype; D006801:Humans; D009169:Mycobacterium tuberculosis / Q000235:genetics* / Q000378:metabolism*; D014376:Tuberculosis / Q000235:genetics / Q000382:microbiology
D000995:Antitubercular Agents; D004247:DNA