Computational protocol: Molecular epidemiology of Klebsiella pneumoniae invasive infections over a decade at Kilifi County Hospital in Kenya

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Protocol publication

[…] A phylogeny was drawn for K. pneumoniae using RAxML v7.8.6 () to estimate the trees (100 bootstrap replicates) for the core genome and the General Time Reversal model with gamma correction.Average divergence within a lineage was calculated on the core genes by comparing the number of base differences per site from averaging over all sequence pairs within each lineage. Gaps were disregarded from the calculation. Divergence between lineages was calculated using the same method. MEGA v6.06 was used for the calculations. [...] The resfinder database of bacterial antimicrobial genes () was manually curated in-house to remove redundancy and partial genes, creating the resistome. Ariba ( was used to search de novo assembled contigs against the non-redundant resistome, which comprised of 1777 resistance genes. Search hits with >90% nucleotide identity over >80% of the resistance gene, were considered a match. […]

Pipeline specifications

Software tools RAxML, MEGA-V, ARIBA
Databases ResFinder The Resistome
Applications Phylogenetics, WGS analysis, GWAS
Organisms Klebsiella pneumoniae
Chemicals Cephalosporins, Carbapenems