Vock, I. | Search bioRxiv

bioRxiv2025

Phylodynamic estimation of the within-host mutation rate of extended-spectrum beta-lactamase-producing Enterobacterales

Despite their clinical relevance, the within-host evolution of extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-PE) is still poorly understood. To estimate the within-host mutation rates of ESBL-producing Escherichia coli and Klebsiella pneumoniae species complex, we fitted phylodynamic models to genomic sequence data of longitudinally collected rectal swabs from 64 colonized hospital patients. We estimated an average within-host mutation rate of 7.71e-07 [4.60e-07,1.10e-06] mutations/site/year for E. coli and 4.20e-07 [1.57e-07,7.14e-07] mutations/site/year for K. pneumoniae species complex, with limited variation observed across patients and sequence types. These estimates are presumably the most accurate reported so far and are useful for future epidemiological and evolutionary studies. Impact statementUnderstanding the within-patient mutation rates of extended-spectrum beta-lactamase (ESBL)-producing E. coli and K. pneumoniae species complex is critical for elucidating their evolutionary dynamics and transmission potential. In this study, we employed Bayesian phylodynamic models to analyze longitudinal isolates collected over a 10-year period from hospitalized patients. Our findings reveal limited variability in mutation rates across patients and sequence types, suggesting evolutionary stability within these pathogens in hospital settings. This work provides new insights into the persistence and evolutionary dynamics of ESBL-PE, offering valuable guidance for antimicrobial resistance surveillance and infection prevention strategies. Data summaryThe data used in this study are publicly available in the NCBI database under the BioProject number PRJNA910977. Supporting metadata are provided in Appendix 1. The code for the phylodynamic analyses, including the BEAST2 XML files, is available at https://github.com/EtthelWindels/esbl-pe_mutation. All supporting data, code and protocols have been provided within the article, supplementary data files or public repositories.

genomics↗

bioRxiv2024

Expanding and improving analyses of nucleotide recoding RNA-seq experiments with the EZbakR suite

Nucleotide recoding RNA sequencing methods (NR-seq; TimeLapse-seq, SLAM-seq, TUC-seq, etc.) are powerful approaches for assaying transcript population dynamics. In addition, these methods have been extended to probe a host of regulated steps in the RNA life cycle. Current bioinformatic tools significantly constrain analyses of NR-seq data. To address this limitation, we developed EZbakR, an R package to facilitate a more comprehensive set of NR-seq analyses, and fastq2EZbakR, a Snakemake pipeline for flexible preprocessing of NR-seq datasets, collectively referred to as the EZbakR suite. Together, these tools generalize many aspects of the NR-seq analysis workflow. The fastq2EZbakR pipeline can assign reads to a diverse set of genomic features (e.g., genes, exons, splice junctions, etc.), and EZbakR can perform analyses on any combination of these features. EZbakR extends standard NR-seq mutational modeling to support multi-label analyses (e.g., s4U and s6G dual labeling), and implements an improved hierarchical model to better account for transcript-to-transcript variance in metabolic label incorporation. EZbakR also generalizes dynamical systems modeling of NR-seq data to support analyses of premature mRNA processing and flow between subcellular compartments. Finally, EZbakR implements flexible and well-powered comparative analyses of all estimated parameters via design matrix-specified generalized linear modeling. The EZbakR suite will thus allow researchers to make full, effective use of NR-seq data.

bioinformatics↗