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/.