Supporting material and code for: "Characterization of penicillin resistance in N. animaloris from bite wound samples"

This repository contains the supporting data and analysis code for a Master's thesis investigating reduced penicillin susceptibility in Neisseria animaloris, a commensal of the oral cavity of dogs and cats and an occasional cause of bite wound infection in humans. The study characterised β-lactam susceptibility and β-lactamase activity in clinical isolates, analysed variation in the penA gene (encoding penicillin-binding protein 2, PBP2) and its association with penicillin G MIC, and examined evidence for horizontal gene transfer of penA from related Neisseria species. Contents: Code PYMOL.txt — PyMOL script used for structural analysis of the AlphaFold 3 PBP2 model, including superimposition on gonococcal PBP2 crystal structures and visualisation of residues at positions associated with reduced penicillin susceptibility in pathogenic Neisseria. Project analysis in R.Rmd — RMarkdown script for data analysis and statistics, Mann-Whitney U tests and rank-biserial correlation for testing association between penA amino acid variants and penicillin G MIC, and summary of susceptibility testing results. Eurofins penA/ — Sanger sequencing chromatograms (.ab1 files) for the penA gene, generated by Eurofins Genomics. In-house penA/ — Sanger sequencing chromatograms (.ab1 files) for the penA gene, generated in-house. Sequencing files mrdA/ — Sanger sequencing chromatograms (.ab1 files) for the mrdA gene, generated in-house. FHI sequences/ — Nanopore sequencing data for two isolates, generated by the Norwegian Institute of Public Health (Folkehelseinstituttet, FHI).