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

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 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 genes.

Pyrazinamide-resistant Tuberculosis Obscured From Common Targeted Molecular Diagnostics.

Here, we describe a clinical case of pyrazinamide-resistant (PZA-R) tuberculosis (TB) reported as PZA-susceptible (PZA-S) by common molecular diagnostics. Phenotypic susceptibility testing (pDST) indicated PZA-R TB. Targeted Sanger sequencing reported wild-type PncA, indicating PZA-S TB.

Distribution of Common and Rare Genetic Markers of Second-Line-Injectable-Drug Resistance in Mycobacterium tuberculosis Revealed by a Genome-Wide Association Study.

Point mutations in the gene and the promoter are known to confer resistance to the second-line injectable drugs (SLIDs) amikacin (AMK), capreomycin (CAP), and kanamycin (KAN). While mutations in these canonical genes confer the majority of SLID resistance, alternative mechanisms of resistance are not uncommon and threaten effective treatment decisions when using conventional molecular diagnostics. In total, 1,184 clinical Mycobacterium tuberculosis isolates from 7 countries were studied for genomic markers associated with phenotypic resistance.

Pyrazinamide Susceptibility Is Driven by Activation of the SigE-Dependent Cell Envelope Stress Response in Mycobacterium tuberculosis.

Pyrazinamide (PZA) plays a crucial role in first-line tuberculosis drug therapy. Unlike other antimicrobial agents, PZA is active against Mycobacterium tuberculosis only at low pH. The basis for this conditional drug susceptibility remains undefined.

Structure-Aware Mycobacterium tuberculosis Functional Annotation Uncloaks Resistance, Metabolic, and Virulence Genes.

Accurate and timely functional genome annotation is essential for translating basic pathogen research into clinically impactful advances. Here, through literature curation and structure-function inference, we systematically update the functional genome annotation of Mycobacterium tuberculosis virulent type strain H37Rv. First, we systematically curated annotations for 589 genes from 662 publications, including 282 gene products absent from leading databases.

Atypical Genetic Basis of Pyrazinamide Resistance in Monoresistant Mycobacterium tuberculosis.

Pyrazinamide (PZA) is a widely used antitubercular chemotherapeutic. Typically, PZA resistance (PZA-R) emerges in strains with existing resistance to isoniazid and rifampin (i.e.

Exact mapping of Illumina blind spots in the genome reveals platform-wide and workflow-specific biases.

Whole-genome sequencing (WGS) is fundamental to basic research and many clinical applications. Coverage across Illumina-sequenced genomes is known to vary with sequence context, but this bias is poorly characterized. Here, through a novel application of phylogenomics that distinguishes genuine coverage bias from deletions, we discern Illumina 'blind spots' in the reference genome for seven sequencing workflows.

Drivers and sites of diversity in the DNA adenine methylomes of 93 complex clinical isolates.

This study assembles DNA adenine methylomes for 93 complex (MTBC) isolates from seven lineages paired with fully-annotated, finished, de novo assembled genomes. Integrative analysis yielded four key results. First, methyltransferase allele-methylome mapping corrected methyltransferase variant effects previously obscured by reference-based variant calling.

SMRT genome assembly corrects reference errors, resolving the genetic basis of virulence in Mycobacterium tuberculosis.

Background: The genetic basis of virulence in Mycobacterium tuberculosis has been investigated through genome comparisons of virulent (H37Rv) and attenuated (H37Ra) sister strains. Such analysis, however, relies heavily on the accuracy of the sequences. While the H37Rv reference genome has had several corrections to date, that of H37Ra is unmodified since its original publication.