Bayesian estimation of mixture models with prespecified elements to compare drug resistance in treatment-naïve and experienced tuberculosis cases

Isoniazid-resistant tuberculosis: a cause for concern?

The drug isoniazid (INH) is a key component of global tuberculosis (TB) control programmes. It is estimated, however, that 16.1% of TB disease cases in the former Soviet Union countries and 7.5% of cases outside of these settings have non-multidrug-resistant (MDR) INH resistance. Resistance has been linked to poorer treatment outcomes, post-treatment relapse and death, at least for specific sites of disease. Multiple genetic loci are associated with phenotypic resistance; however, the relationship between genotype and phenotype is complex, and restricts the use of rapid sequencing techniques as part of the diagnostic process to determine the most appropriate treatment regimens for patients. The burden of resistance also influences the usefulness of INH preventive therapy. Despite seven decades of INH use, our knowledge in key areas such as the epidemiology of resistant strains, their clinical consequences, whether tailored treatment regimens are required and the role of INH resistance in fuelling the MDR-TB epidemic is limited. The importance of non-MDR INH resistance needs to be re-evaluated both globally and by national TB control programmes.

Differences in rpoB, katG and inhA mutations between new and previously treated tuberculosis cases using the GenoType MTBDRplus assay

Drug resistance in new cases reflects primary transmission of resistant strains, while drug resistance in previously treated patients is more likely to reflect acquired resistance during previous tuberculosis (TB) treatment. In this study from a rural hospital in South India, we compared molecular differences between new and previously treated TB patients who had isoniazid or rifampicin resistance-conferring mutations using the GenoType MTBDRplus assay. Out of 2112 TB patients, 245 (11.6%) had rpoB mutations and 338 (16%) had isoniazid resistance-conferring mutations. Among patients with rpoB mutations, the proportion of new and previously treated cases with no isoniazid resistance-conferring mutations was 41.2% and 26% (P-value = 0.02; risk ratio [RR] 1.58, 95% confidence interval [CI] 1.09-2.31; risk difference [RD] 15.2%, 95% CI 18.2-28.6), respectively. Among patients with isoniazid resistance-conferring mutations, the proportion of new and previously treated cases with no rpoB mutations was 71.8% and 33.2% (P-value < 0.0001; RR 2.17, 95% CI 1.73-2.71; RD 38.7%, 95% CI 28.8-48.6), and the proportion with single inhA mutations (versus having katG mutations) was 33.1% and 20.9% (P-value = 0.012; RR 1.58, 95% CI 1.11-2.27; RD 12.2%, 95% CI 2.57-21.8), respectively. The most common resistance mutations were S531 L in the rpoB gene, S315T1 in the katG gene and C15T in the inhA gene, and there were no significant differences between new and previously treated patients. In conclusion, new TB cases were less likely to have combined isoniazid and rifampicin resistance-conferring mutations and, in cases with isoniazid resistance, they were more likely to have single inhA mutations than katG mutations. Taking into account that previous research has shown katG mutations precede mutations in the rpoB gene in most cases of rifampicin resistant TB, our results suggest a negative epistatic association between katG and rpoB mutations.

Genomic analysis of globally diverse Mycobacterium tuberculosis strains provides insights into the emergence and spread of multidrug resistance

Multidrug-resistant tuberculosis (MDR-TB), caused by drug resistant strains of Mycobacterium tuberculosis, is an increasingly serious problem worldwide. In this study, we examined a dataset of 5,310 M. tuberculosis whole genome sequences from five continents. Despite great diversity with respect to geographic point of isolation, genetic background and drug resistance, patterns of drug resistance emergence were conserved globally. We have identified harbinger mutations that often precede MDR. In particular, the katG S315T mutation, conferring resistance to isoniazid, overwhelmingly arose before rifampicin resistance across all lineages, geographic regions, and time periods. Molecular diagnostics that include markers for rifampicin resistance alone will be insufficient to identify pre-MDR strains. Incorporating knowledge of pre-MDR polymorphisms, particularly katG S315, into molecular diagnostics will enable targeted treatment of patients with pre-MDR-TB to prevent further development of MDR-TB.

Evolutionary Inference across Eukaryotes Identifies Specific Pressures Favoring Mitochondrial Gene Retention

Since their endosymbiotic origin, mitochondria have lost most of their genes. Although many selective mechanisms underlying the evolution of mitochondrial genomes have been proposed, a data-driven exploration of these hypotheses is lacking, and a quantitatively supported consensus remains absent. We developed HyperTraPS, a methodology coupling stochastic modeling with Bayesian inference, to identify the ordering of evolutionary events and suggest their causes. Using 2015 complete mitochondrial genomes, we inferred evolutionary trajectories of mtDNA gene loss across the eukaryotic tree of life. We find that proteins comprising the structural cores of the electron transport chain are preferentially encoded within mitochondrial genomes across eukaryotes. A combination of high GC content and high protein hydrophobicity is required to explain patterns of mtDNA gene retention; a model that accounts for these selective pressures can also predict the success of artificial gene transfer experiments in vivo. This work provides a general method for data-driven inference of the ordering of evolutionary and progressive events, here identifying the distinct features shaping mitochondrial genomes of present-day species.

Origin and proliferation of multiple-drug resistance in bacterial pathogens

SUMMARY

Many studies report the high prevalence of multiply drug-resistant (MDR) strains. Because MDR infections are often significantly harder and more expensive to treat, they represent a growing public health threat. However, for different pathogens, different underlying mechanisms are traditionally used to explain these observations, and it is unclear whether each bacterial taxon has its own mechanism(s) for multidrug resistance or whether there are common mechanisms between distantly related pathogens. In this review, we provide a systematic overview of the causes of the excess of MDR infections and define testable predictions made by each hypothetical mechanism, including experimental, epidemiological, population genomic, and other tests of these hypotheses. Better understanding the cause(s) of the excess of MDR is the first step to rational design of more effective interventions to prevent the origin and/or proliferation of MDR.