Genomic analysis to assess the impact of an infection control bundle on K. pneumoniae populations causing sepsis in neonates in an ICU in Zambia. This paper uses data collected as part of the SPINZ study.
This repository includes data and code from the paper 'Transmission dynamics of Klebsiella pneumoniae in a neonatal intensive care unit in Zambia before and after an infection control bundle', Phillips LT et al, MedRxiv 2025.
Output phylogenetic trees are in output_trees/, single nucleotide variant distances are in output_snv_distances/ and cluster estimates in output_clusters/
Additional data needed to create figures or tables is in data/
The directories figures/ and tables/ contain all the figures and tables from the paper, including supplementary. The code to generate these is in the Data_analysis_SPINZ.Rmd R markdown file, and a knitR file showing the executed code is in Data_analysis_SPINZ.html.
If you use the data, code, figures or tables presented here please cite the below paper and this repository via DOI: 10.5281/zenodo.17589084.
Phillips LT et al, 'Transmission dynamics of Klebsiella pneumoniae in a neonatal intensive care unit in Zambia before and after an infection control bundle', 2025, MedRxiv. DOI: 10.1101/2025.11.12.25340082
