DanielSano/Kpneumoniae_genomic_secondary_reanalysis

Supplementary materials for the secondary genomic reanalysis of South African Klebsiella pneumoniae genomes # Supplementary Materials for: Secondary Genomic Reanalysis of Publicly Available South African Klebsiella pneumoniae Genomes: A Pilot Workflow for Integrated Antimicrobial Resistance Surveillance and Vaccine-Relevant Genomic Insights Authors: Daniel Sano, Davison Anotida Muzondo, Aaron Sadindi, Blessed Kudakwashe Madana, Branham Kwaramba, Prosper Ndhlela, Convinience Chikwenya, Lyn Zihumo, Salody Sandra Shumba, Cecily Nkomo, Elliot Nyagumbo, Fanuel Songwe, Gerald Mboowa Corresponding authors: - Dr. Fanuel Songwe – songwef@staff.msu.ac.zw - Dr. Gerald Mboowa – gmboowa@gmail.com --- ## Contents This repository contains all supplementary material (Tables S1–S9 and Figures S1-S3 ) associated with the manuscript. ### Supplementary Tables | File | Description | |------|-------------| | `Supplementary_Table_S1_Metadata.xlsx` | Complete metadata and raw data accession numbers for the five analysed genomes | | `Supplementary_Table_S2_Assembly_Quality.xlsx` | QUAST assembly quality metrics (contig counts, N50, L50, total lengths, GC%, etc.) | | `Supplementary_Table_S3_AMR_Profiles.xlsx` | Antimicrobial resistance genes identified using AMRFinderPlus (Sheet 1) and ResFinder (Sheet 2) | | `Supplementary_Table_S4_Virulence_Profiles.xlsx` | Virulence determinants (Kleborate/ABRicate) including yersiniabactin, colibactin, aerobactin, salmochelin, RmpADC, and virulence scores | | `Supplementary_Table_S5_Plasmids_Mobility.xlsx` | MOB‑suite plasmid replicon and mobility reconstruction outputs | | `Supplementary_Table_S6_ISEScan_MGEs.xlsx` | Insertion sequence / mobile genetic element summaries (ISEScan) | | `Supplementary_Table_S7_Antigen_Loci.xlsx` | Kaptive K‑locus (Sheet 1) and O‑locus (Sheet 2) typing results | | `Supplementary_Table_S8_Core_SNPs.xlsx` | Core‑genome SNP alignment and phylogenetic tree data (Snippy) | | `Supplementary_Table_S9_Pangenome_Matrix.xlsx` | Panaroo gene presence/absence matrix (Sheet 1) and pangenome distribution statistics (Sheet 2) | ### Supp …