Fig. 4: Proposed genomic analysis pipeline for identifying potential vancomycin-resistant Enterococcus faecium transmission.
Outlined is each step in the analysis pipeline, the software used and the required whole genome sequencing data. 1 core genome multiloicus sequence type (cgMLST) allele scheme by de Been et al. 2 The COREugate pipeline was used to assign the allelic profiles and build a matrix of the pairwise allelic differences. 3 Split kmers were generated from short read data at k = 15. 4 The threshold for determining transmission events was determined based on within patient diversity. For this data set and split kmer analysis (SKA) this was found to be 7 single nucleotide polymorphisms (SNPs).
