An unbiased attitude is vital to exploring the Beijing genotype of Mycobacterium tuberculosis

Molecular characteristics of Mycobacterium tuberculosis drug-resistant isolates from HIV- and HIV+ tuberculosis patients in Russia

Background

High burden of drug-resistant (DR) tuberculosis (TB) is a significant threat to national TB control programs all over the world and in the Russian Federation. Different Mycobacterium tuberculosis (MTB) genotypes are hypothesized to have specific characteristics affecting TB control programs. For example, Beijing strains are supposed to have higher mutation rates compared to strains of other genotypes and subsequently higher capability to develop drug-resistance.

Results

Clinical MTB isolates from HIV- and HIV+ patients from four regions of Russia were analyzed for genotypes and mutations conferring resistance to Isoniazid, Rifampicin, Ethambutol, aminoglycosides, and fluoroquinolones. Analysis of genotypes and polymorphism of genomic loci according to the HIV status of the patients – sources of MTB isolates were performed. Studied MTB isolates from HIV- TB patients belonged to 15 genotypes and from HIV + TB patients – to 6 genotypes. Beijing clinical isolates dominated in HIV- (64,7%) and HIV+ (74,4%) groups. Other isolates were of LAM (including LAM1 and LAM9), Ural, and 4 minor groups of genotypes (including 5 subclones T). The spectrum of genotypes in the HIV- group was broader than in the HIV+ group. PR of B0/W148 Beijing was significantly lower than of other Beijing genotypes in susceptible and MDR-XDR isolates. Rates of isolates belonging to non-Beijing genotypes were higher than Beijing in susceptible isolates from HIV- patients.

Conclusions

Beijing genotype isolates prevailed in clinical isolates of all drug susceptibility profiles both from HIV- and HIV+ patients, although B0/W148 Beijing genotype did not dominate in this study. Genome loci and mutations polymorphisms were more pronounced in clinical isolates from HIV- patients, than from HIV+.

New approaches to mutation rate fold change in Luria-Delbrück fluctuation experiments

For nearly eight decades the Luria-Delbrück protocol remains the preferred method for experimentally determining microbial mutation rates. However, earnest development and rigorous applications of statistical methods for mutation rate comparison using fluctuation assay data are a relatively recent phenomenon. While likelihood ratio tests tailored for the fluctuation protocol give investigators appropriate tools, researchers sometimes may prefer to view the comparison of two mutation rates through the lens of the ratio of the two mutation rates. The idea of using the bootstrap technique to construct intervals for mutation rate fold change was proposed nearly a decade ago, but it failed to gain traction partly due to a failure to incorporate likelihood-based estimation. In addition to extending the bootstrap method, this paper proposes two new methods of constructing intervals for mutation rate fold change: a profile likelihood method and a Bayesian method utilizing Monte Carlo Markov chain. All three methods are assessed by large-scale simulations.