Genomic Epidemiology and Resistome Analysis of Carbapenem-Resistant Enterobacterales Colonizing Pregnant Women at Delivery in South Africa: Implications for Maternal and Neonatal Health

This dataset comprises comprehensive genomic, epidemiological, phenotypic, and phylogenetic data generated from a prospective study of carbapenem-resistant Enterobacterales (CRE) carriage in pregnant women presenting in labour at a tertiary hospital in Pretoria, South Africa, between November 2020 and September 2021. The primary aim was to investigate the prevalence, genetic mechanisms, and transmission potential of CRE in an obstetric population—a setting rarely surveyed in Africa—using high-resolution whole-genome sequencing alongside detailed clinical metadata.
Clinical and Phenotypic Data:
Rectal swabs were collected from 150 women upon admission for delivery. Data include patient demographics (age, gestational age, comorbidities), delivery outcomes, and recent antimicrobial exposures (where available). CRE screening was performed using selective media (CHROMagar™ + mSuperCARBA™), with isolates subjected to identification via Vitek 2 and antimicrobial susceptibility profiling using broth microdilution according to CLSI standards. Phenotypic resistance profiles (including MICs for carbapenems, aminoglycosides, colistin, tigecycline, and others) are provided.
Genomic Data:
DNA from all confirmed CRE isolates (n=5) underwent long-read whole-genome sequencing on the PacBio Sequel II platform. Assembled genomes are provided in FASTA format (chromosome and plasmids), with accompanying annotation files (GenBank format), and raw read files (subsampled). The dataset includes assembled genomes for Klebsiella pneumoniae (ST39) and four Enterobacter cloacae complex isolates (various STs). Genomes are fully annotated for antimicrobial resistance genes (AMR), plasmid replicon types, mobile genetic elements (IS, transposons, integrons), methylation motifs, CRISPR arrays, and toxin–antitoxin systems.
Phylogenetic and Comparative Analyses:
Core-genome alignments, phylogenetic trees (Newick format), and SNP distance matrices are provided for both K. pneumoniae and Enterobacter spp. isolates, including comparison to over 250 global reference genomes. The dataset enables detailed exploration of clonal relationships, evolutionary context, and international transmission patterns.
Plasmid Comparative Analyses:
BLAST ring images, synteny dotplots, and gene order comparison files are included for all closed plasmids, demonstrating structural similarities and unique insertions/deletions relative to international references. These support analyses of modularity, horizontal gene transfer, and the dissemination of resistance determinants.
Re-use Value:
The dataset is designed for broad utility in antimicrobial resistance (AMR) genomics, One Health studies, epidemiological surveillance, and method development. Potential uses include benchmarking bioinformatic pipelines, training machine-learning models for AMR prediction, or expanding global studies of CRE transmission in maternal and neonatal settings.

No patient-identifiable information is included.