joelewis101/blantyreESBL

Data and code repository for study aiming to understand ESBL carriage in Blantyre, Malawi # blantyreESBL The blantyreESBL R package is a repository for data generated as part of a study into carriage of resistant bacteria in Blantyre, Malawi. It also includes reproducible analysis script for three manuscripts arising from the study: **Colonization dynamics of extended-spectrum beta-lactamase-producing Enterobacterales in the gut of Malawian adults** Joseph M Lewis 1,2,3,4 , , Madalitso Mphasa 1 , Rachel Banda 1 , Matthew Beale 4 , Eva Heinz 2 , Jane Mallewa 5 , Christopher Jewell 6 , Nicholas R Thomson 4,7 , Nicholas A Feasey 1,2 Paper available at Nature Microbiology here **Genomic analysis of extended-spectrum beta-lactamase (ESBL) producing Escherichia coli colonising adults in Blantyre, Malawi reveals previously undescribed diversity** Joseph M Lewis 1,2,3,4 , , Madalitso Mphasa 1 , Rachel Banda 1 , Matthew Beale 4 , Jane Mallewa 5 , Catherine Anscombe 1,2 , Allan Zuza 1 , Adam P Roberts 2 , Eva Heinz* 2 , Nicholas Thomson* 4,7 , Nicholas A Feasey\* 1,2 - = contributed equally Paper available at Microbial Genomics here **Genomic and antigenic diversity of colonising *Klebsiella pneumoniae* isolates mirrors that of invasive isolates in Blantyre, Malawi** Joseph M Lewis 1,2,3,4 , , Madalitso Mphasa 1 , Rachel Banda 1 , Matthew Beale 4 , Jane Mallewa 5 , Eva Heinz 2 , Nicholas Thomson 4,7 , Nicholas A Feasey 1,2 Available at Microbial Genomics here ### Installing and accessing data If you just want the data, then all the data to replicate the analysis are bundled with the package. To install the package from GitHub: ``` r install.packages("devtools") devtools::install_github("github.com") ``` The various data objects are described in the pkgdown site for this package here, and available via R in the usual way (i.e. `?btESBL_participants` brings up the definitions for the `btESBL_participants` data. They are all lazy loaded so will be available for use immediately; they all start with `btESBL_` to make …