This repository contains the R scripts used to generate some of the supporting information for ourpaper looking at porine defects in Klebsiella pneumoniae, as well some additional figures that were not used but which can provide useful additional insights (manuscript under review, soon available on BioRXiv) .
Briefly, we collected a total of 1,557 draft and complete K. pneumoniae genomes publicly available in Genbank (Feb 2017) to investigate the significance of mutations affecting major porines OmpK35 and OmpK36 in the context of a wider population.
data/ contains screening data stored in KP_screening_data.csv, with the following descriptors:
| Identifier | Description |
|---|---|
| Id | Isolate assembly identifier |
| genome_size | Genome size in bp |
| contigs | Number of contigs |
| n50 | N50 in bp |
| ST | Multi-locus sequence type |
| Insertion | Di-nucleotide insertion of GD or TD in OmpK36 loop L3 |
| ompK36 | Presence or absence (1 or 0) |
| ompK35 | Presence or absence (1 or 0) |
| Source | Source of isolates as described in original record |
| Source_edited | Source of isolates as described in original record - cleaned up (typo, font case, etc.) |
| Source_summarised | Source of isolates summarised in 3 major categories (blood, urine and other) |
| Host | Host origin (about half of the isolates don't have this information) |
| Country | Country of Origin |
| Year | Date of isolation simplified as year only |
| resistance_genes | Resistance profile as predicted by ResFinder |
| plasmids | Plasmids replicons identified by PlasmidFinder (not used in present analysis) |
| Organism | Organism name |
| Strain | Strain name |
scripts/ contains the following scripts:
- KP_associations_EDA.md
- KP_population_EDA.md
- KP_resistance_determinants_EDA.md
images/ contains images generated:
- Fig S7 KP_unnamed-chunk-2-1.png
- Fig S8 KPassoc_unnamed-chunk-8-1.png
- Fig S9 KPassoc_unnamed-chunk-9-1.png & KPassoc_unnamed-chunk-9-2.png
- Fig S10 KPassoc_unnamed-chunk-10-1.png & KPassoc_unnamed-chunk-10-2.png
- Fig S11 KPres_unnamed-chunk-7-1.png