A One-Health Genomic Analysis of Clinical, Animal and Environmental Enterobac-terales Reveals Cross-Sector Transmission of Antibiotic-Resistance Genes

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.