To, H. | bioRxiv Science

bioRxiv2019

Effects of a rifampicin pre-treatment on linezolid pharmacokinetics

Linezolid is an oxazolidinone antibiotic that effectively treats methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococci (VRE). Since rifampicin induces other antibiotic effects, it is combined with linezolid in therapeutic regimes. However, linezolid blood concentrations are reduced by this combination, which increases the risk of the emergence of antibiotic-resistant bacteria. We herein demonstrated that the combination of linezolid with rifampicin inhibited its absorption and promoted its elimination, but not through microsomal enzymes. Our results indicate that the combination of linezolid with rifampicin reduces linezolid blood concentrations via metabolic enzymes.

molecular biology↗

bioRxiv2018

ngsReports: An R Package for managing FastQC reports and other NGS related log files.

MotivationHigh throughput next generation sequencing (NGS) has become exceedingly cheap facilitating studies to be undertaken containing large sample numbers. Quality control (QC) is an essential stage during analytic pipelines and can be found in the outputs of popular bioinformatics tools such as FastQC and Picard. Although these tools provide considerable power when carrying out QC, large sample numbers can make identification of systemic bias a challenge.\n\nResultsWe present ngsReports, an R package designed for the management and visualization of NGS reports from within an R environment. The available methods allow direct import into R of FastQC output as well as that from aligners such as HISAT2, STAR and Bowtie2. Visualization can be carried out across many samples using heatmaps rendered using ggplot2 and plotly. Moreover, these can be displayed in an interactive shiny app or a HTML report. We also provide methods to assess observed GC content in an organism dependent manner for both transcriptomic and genomic datasets. Importantly, hierarchical clustering can be carried out on heatmaps with large sample sizes to quickly identify outliers and batch effects.\n\nAvailability and ImplementationngsReports is available at https://github.com/UofABioinformaticsHub/ngsReports.

bioinformatics↗