A One-Health Genomic Analysis of Clinical, Animal and Environmental Enterobac-terales Reveals Cross-Sector Transmission of Antibiotic-Resistance Genes
Description
This dataset accompanies a One Health genomics study investigating the multisectoral spread, resistome architecture, and evolutionary dynamics of carbapenemase-producing Enterobacterales (CPE) across clinical, veterinary, and environmental sectors in South Africa. The work involved 1,530 presumptive CRE isolates collected from humans, pigs, abattoir wastewater, and rivers, from which 122 carbapenemase-positive strains were confirmed. Whole-genome sequencing (WGS) using Oxford Nanopore MinIon was performed on 26 representative isolates, providing insights into resistance mechanisms, mobile genetic elements (MGEs), and population structure. The dataset includes: Annotated draft genome assemblies for 26 CPE isolates Antibiotic resistance gene (ARG) profiles across 11 antimicrobial classes IncL/M and IncX3 plasmid maps showing bla_OXA-48, bla_NDM, bla_VIM contexts Maximum-likelihood phylogenies for Klebsiella pneumoniae, Proteus mirabilis, Serratia marcescens, and Providencia rettgeri Multiplex PCR results confirming carbapenemase gene presence Metadata including isolate ID, sample type, sector source, resistance profiles, and ARG counts WGS data were processed using state-of-the-art tools including SPAdes for de novo assembly, Prokka for annotation, ResFinder/CARD for ARG detection, PlasmidFinder and MOB-suite for plasmid typing and reconstruction, and ISFinder/IntegronFinder for MGE mapping. Phylogenomic inference was performed with RAxML on core genome alignments produced via Roary. The dataset underscores the ecological complexity of carbapenem resistance dissemination, the evolutionary convergence of ARGs across hosts and environments, and the urgent need for integrated surveillance. It enables comparative genomics, resistance tracking, plasmid evolution research, and development of diagnostic targets or control strategies.
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Steps to reproduce
To replicate the genomic, resistome, and phylogenetic analyses reported in this study: 1. Sample Processing and Bacterial Isolation Culture human, animal, and environmental samples on MacConkey agar with meropenem (10 µg) and incubate at 37 °C for 24 h. Confirm presumptive carbapenem-resistant isolates using VITEK 2 Compact. Preserve confirmed isolates in 20% glycerol broth at −80 °C. 2. DNA Extraction and Sequencing Extract genomic DNA using the Quick-DNA Miniprep kit (Zymo Research). Quantify and assess purity using Qubit 3.0 fluorometer and Nanodrop 2000. Prepare libraries with the Nextera DNA Flex kit and sequence on Oxford Nanopore's MinIon 3. Genome Assembly and Annotation Trim adapters with Trimmomatic v0.36. Assemble genomes using SPAdes v3.14.1. Annotate contigs with Prokka v1.14.6. 4. Resistance and Plasmid Gene Detection Identify ARGs using ABRicate with ResFinder and CARD databases. Detect plasmid replicons using PlasmidFinder and reconstruct with MOB-suite v3.0.1. Annotate insertion sequences and integrons with ISFinder and IntegronFinder. 5. Plasmid Mapping Extract and visualize plasmid fragments carrying bla_OXA-48, bla_NDM, and bla_VIM using SnapGene. Analyze genetic environments for integrons, transposons, ISs, and resistance cassettes. 6. Phylogenetic Analyses Align core genomes using Roary v3.13.0. Construct maximum-likelihood phylogenetic trees with RAxML-NG (GTR+Γ, 1000 bootstraps). Visualize trees and annotate clades with iTOL/Figtree. 7. PCR Confirmation of Resistance Genes Conduct multiplex PCR for bla_OXA-48 (~782 bp), bla_NDM (~782 bp), and bla_VIM (~438 bp). Visualize products on 1.5% agarose gels using 1 kb DNA ladder for size estimation. 8. Visualization and Statistics Create bar plots, pie charts, and heatmaps using GraphPad Prism, R (ggplot2), and Python (matplotlib). Generate ARG vs. phylogeny overlays using iTOL. All code, image files, annotated plasmid maps, and metadata spreadsheets are included or referenced in this dataset. The above tools and pipeline versions match those used in the published article. Detailed figure-generation scripts are available upon request.
Institutions
- University of Pretoria School of Medicine