The acetylation of pknH is linked to the ethambutol resistance of Mycobacterium tuberculosis

Interred mechanisms of resistance and host immune evasion revealed through network-connectivity analysis of M. tuberculosis complex graph pangenome

Mycobacterium tuberculosis complex successfully adapts to environmental pressures through mechanisms of rapid adaptation which remain poorly understood despite knowledge gained through decades of research. In this study, we used 110 reference-quality, complete de novo assembled, long-read sequenced clinical genomes to study patterns of structural adaptation through a graph-based pangenome analysis, elucidating rarely studied mechanisms that enable enhanced clinical phenotypes offering a novel perspective to the species' adaptation. Across isolates, we identified a pangenome of 4,325 genes (3,767 core and 558 accessory), revealing 290 novel genes, and a substantially more complete account of difficult-to-sequence esx/pe/pgrs/ppe genes. Seventy-four percent of core genes were deemed non-essential in vitro, 38% of which support the pathogen's survival in vivo, suggesting a need to broaden current perspectives on essentiality. Through information-theoretic analysis, we reveal the ppe genes that contribute most to the species' diversity-several with known consequences for antigenic variation and immune evasion. Construction of a graph pangenome revealed topological variations that implicate genes known to modulate host immunity (Rv0071-73, Rv2817c, cas2), defense against phages/viruses (cas2, csm6, and Rv2817c-2821c), and others associated with host tissue colonization. Here, the prominent trehalose transport pathway stands out for its involvement in caseous granuloma catabolism and the development of post-primary disease. We show paralogous duplications of genes implicated in bedaquiline (mmpL5 in all L1 isolates) and ethambutol (embC-A) resistance, with a paralogous duplication of its regulator (embR) in 96 isolates. We provide hypotheses for novel mechanisms of immune evasion and antibiotic resistance through gene dosing that can escape detection by molecular diagnostics.IMPORTANCEM. tuberculosis complex (MTBC) has killed over a billion people in the past 200 years alone and continues to kill nearly 1.5 million annually. The pathogen has a versatile ability to diversify under immune and drug pressure and survive, even becoming antibiotic persistent or resistant in the face of harsh chemotherapy. For proper diagnosis and design of an appropriate treatment regimen, a full understanding of this diversification and its clinical consequences is desperately needed. A mechanism of diversification that is rarely studied systematically is MTBC's ability to structurally change its genome. In this article, we have de novo assembled 110 clinical genomes (the largest de novo assembled set to date) and performed a pangenomic analysis. Our pangenome provides structural variation-based hypotheses for novel mechanisms of immune evasion and antibiotic resistance through gene dosing that can compromise molecular diagnostics and lead to further emergence of antibiotic resistance.

The implications of mutations in multiple genes associated with ethambutol resistance among multidrug-resistant tuberculosis isolates from China

OBJECTIVES

To assess the mutation effects of ethambutol (EMB) resistance-associated genes, including embCAB operon, ubiA, embR, and aftA, on the EMB resistance levels among multidrug-resistant tuberculosis (MDR-TB) isolates from China.

METHODS

A total of 159 MDR-TB from China had their EMB MICs quantified, and the sequences of the four ethambutol resistance-associated regions were analyzed. A multivariate regression model was established to evaluate the effects of mutations on EMB resistance.

RESULTS

Our results showed that overall 95.6% (109/114 isolates) of EMB-resistant isolates harbored at least one mutation within the regions associated with EMB resistance. Most mutations were in embB, particularly in the embB300-500, and the embC-embA intergenic regions. Mutations in other genes were seldom seen and mainly occurred along with mutations in the embB or the embC-embA among the EMB-resistant isolates. DNA sequencing of the embB300-500 and the embC-embA was the most effective approach for detecting EMB resistance, with an accuracy of 91.2%. Nevertheless, some EMB-susceptible isolates still had a single mutation in the gene related to EMB resistance. Moreover, there was a significant correlation between EMB high-level resistance and multiple mutations.

CONCLUSION

Distinct individual mutations, as well as multiple concurrent mutations, within EMB resistance-associated genes, contributed to variable levels of EMB resistance. These results have broadened our understanding of the molecular characteristics of EMB resistance in China.

Potential of the Novel Slot Blot Method with a PVDF Membrane for Protein Identification and Quantification in Kampo Medicines

Kampo is a Japanese traditional medicine modified from traditional Chinese medicine. Kampo medicines contain various traditional crude drugs with unknown compositions due to the presence of low-molecular-weight compounds and proteins. However, the proteins are generally rare and extracted with high-polarity solvents such as water, making their identification and quantification difficult. To develop methods for identifying and quantifying the proteins in Kampo medicines, in the current study we employ previous technology (e.g., column chromatography, electrophoresis, and membrane chromatography), focusing on membrane chromatography with a polyvinylidene difluoride (PVDF) membrane. Moreover, we consider slot blot analysis based on the principle of membrane chromatography, which is beneficial for analyzing the proteins in Kampo medicines as the volume of the samples is not limited. In this article, we assess a novel slot blot method developed in 2017 and using a PVDF membrane and special lysis buffer to quantify advanced glycation end products-modified proteins against other slot blots. We consider our slot blot analysis superior for identifying and quantifying proteins in Kampo medicines compared with other methods as the data obtained with our novel slot blot can be shown with both error bars and the statistically significant difference, and our operation step is simpler than those of other methods.