Genomic annotations and supplemental analyses for bovine Salmonella enterica serovar Dublin clinical isolates from British Columbia, 2015–2022

Description

This dataset contains supplementary materials supporting genomic analyses of 51 bovine Salmonella enterica serovar Dublin isolates recovered from routine diagnostic submissions in British Columbia, Canada, during 2015–2022. Files include a de-identified isolate-level annotation table, a supplemental spatial-context figure, a supplemental temporal-signal evaluation, and a README describing file contents, variable definitions, coding conventions, abbreviations, and de-identification procedures. The files support analyses of antimicrobial resistance determinants, quinolone resistance-determining region mutations, virulence loci, plasmid replicons, FastBAPS clusters, and region-level metadata. Raw whole-genome sequencing reads are deposited separately in NCBI SRA.

Steps to reproduce

Raw whole-genome sequencing reads are deposited separately in NCBI SRA and are not duplicated in this Mendeley Data record. To reproduce the analyses summarized in the deposited supplemental files, start from the SRA paired-end reads for the 51 bovine Salmonella enterica serovar Dublin isolates. Reads were quality-checked with FastQC v0.12.1 and processed with fastp v1.0.1. Draft assemblies were generated with shovill v1.1.0 using SKESA v2.5.1, then assessed with QUAST v5.2.0, BUSCO v5.7.0, and CheckM v1.2.3. Assemblies were annotated with Prokka v1.14.6, typed with mlst v2.23.0, and serovar assignments were checked with SISTR v1.1.2 and SeqSero2 v1.3.1. AMR determinants were identified with AMRFinderPlus v4.0.19 using database version 2024-12-18.1 and summarized at the gene level. QRDR mutations were screened from Snippy-annotated VCFs at canonical gyrA and parC codons. Virulence-associated loci were summarized from AMRFinderPlus and Abricate VFDB results. Plasmid replicons and plasmid-associated contigs were characterized with PlasmidFinder v2.1.6 and MOB-suite v3.1.9. For phylogenetic analyses, reads were mapped to the Salmonella enterica serovar Dublin reference genome GCF_028893395.1_ASM2889339v1 with Snippy v4.6.0. The core-genome alignment was recombination-masked with Gubbins v3.4.3, and a maximum-likelihood tree was inferred with IQ-TREE v2.4.0 under the HKY model with 1,000 ultrafast bootstrap and SH-aLRT replicates. AMR, QRDR, virulence, plasmid, FastBAPS, and metadata annotations were aligned to the tree for figure generation in R. Temporal trends were evaluated using quasi-Poisson regression for AMR determinant counts and logistic regression for gyrA QRDR mutation status. Temporal signal was evaluated using midpoint-rooted root-to-tip regression, treedater, and 50 date-randomized treedater refits. In this Mendeley record, Table S1 contains the de-identified isolate-level annotation table used to support the phylogeny-linked genomic summaries; Figure S1 provides exploratory spatial context for the time-scaled phylogeny; Supplemental Text S1 reports the temporal-signal evaluation. The README provides file descriptions, variable definitions, coding conventions, and de-identification notes. Exact farm identifiers, owner information, diagnostic case identifiers, exact addresses, and exact coordinates are not included.

Institutions

• Kwantlen Polytechnic University

  British Columbia, Surrey

Categories

Licence