Colibactin production and resistance in 1 991 hybrid assemblies from the NORM collection

Files used in generating a species-wide phylogeny from the panaroo core gene alignment for 1 991 Escherichia coli hybrid assemblies from the NORM collection. Data Isolation, sequencing, and assembly are described in the following two studies: [1] Gladstone et al. "Emergence and dissemination of antimicrobial resistance in Escherichia coli causing bloodstream infections in Norway in 2002–17: a nationwide, longitudinal, microbial population genomic study". The Lancet Microbe (2021). doi: 10.1016/S2666-5247(21)00031-8. [2] Arredondo-Alonso et al. "Plasmid-driven strategies for clone success in Escherichia coli". Nature communications (2025). doi: 10.1038/s41467-025-57940-1. Sequencing data is available from the European Nucleotide Archive under accession numbers PRJEB45354 and PRJEB57633. Pangenome inference Pangenome inference from the annotations was performed using panaroo v1.5.2 (GitHub: gtonkinhill/panaroo) with the “--clean-mode strict” and “--remove-invalid-genes” options: [3] Tonkin-Hill et al. "Producing polished prokaryotic pangenomes with the Panaroo pipeline." Genome Biology (2020). doi: 10.1186/s13059-020-02090-4. Output files from panaroo are available in a separate Zenodo upload: doi: 10.5281/zenodo.17521040. Phylogenetic inference The phylogenetic tree was constructed using VeryFastTree [4] v4.0.0 72,73 using a Gamma+GTR+CAT model with 20 categories, no bootstrap support values, the -fastest option, and 32-bit floating point precision. [4] Piñeiro, C., Abuín, J. M. & Pichel, J. C. "Very Fast Tree: speeding up the estimation of phylogenies for large alignments through parallelization and vectorization strategies." Bioinformatics (2020). doi: 10.1093/bioinformatics/btaa582.