QECHospitalKlebs

The QECHKlebs R package is a repository for data generated and reproducible analysis scripts for the manuscripts arising from this study:

Longitudinal analysis within one hospital in sub-Saharan Africa over 20 years reveals repeated replacements of dominant clones of Klebsiella pneumoniae and stresses the importance to include temporal patterns for vaccine design considerations

Eva Heinz^1,2, Oliver Pearse^2,3, Allan Zuza³, Sithembile Bilima³, Chisomo Msefula⁴, Patrick Musicha^2,3, Patriciah Siyabu⁵, Edith Tewesa⁵, Fabrice E Graf², Rebecca Lester^3,6, Samantha Lissauer^3,7, Jennifer Cornick^3,7, Joseph M Lewis^2,3,7, Kondwani Kawaza^3,4, Nicholas R Thomson^8,9, Nicholas A Feasey^2,3,10

1. Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK
2. Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
3. Malawi Liverpool Wellcome Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
4. Kamuzu University of Health Sciences, Blantyre, Malawi
5. Queen Elizabeth Central Hospital, Blantyre, Malawi
6. Division of Infection & Immunity, University College London, UK
7. Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, UK
8. Parasites and Microbes Program, Wellcome Sanger Institute, Hinxton, UK
9. London School of Hygiene and Tropical Medicine, London, UK
10. School of Medicine, St Andrews University, UK

Paper currently available as pre-print here

Installation

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:

install.packages("devtools")
devtools::install_github("https://github.com/EvitaH/QECHospitalKlebs")

The various data objects are described in the pkgdown site for this package here, and available via R in the usual way. They are all lazy loaded so will be available for use immediately.

Whole genome sequence accession numbers and metadata

Reads from all isolates sequenced as part of this study have been deposited in the European Nucleotide Archive (ENA); accession numbers are available in the Table S1 from the publication.

Analysis scripts

The analysis scripts to reproduce tables and figures for each manuscript are available as package vignettes; these can be built when downloading the package by running:

devtools::install_github(
  "https://github.com/EvitaH/QECHospitalKlebs", 
  build_vignettes = TRUE, 
  dependencies = TRUE )

The dependencies = TRUE option will install all the packages necessary to run the vignette.

Most analyses performed for the manuscript are straightforward, but please note that running rPinecone might take a while on the larger data sets (especially the K. pneumoniae subsp. pneumoniae).