Genomic Epidemiology and Resistome Analysis of Carbapenem-Resistant Enterobacterales Colonizing Pregnant Women at Delivery in South Africa: Implications for Maternal and Neonatal Health
Description
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.
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Steps to reproduce
Participant Recruitment and Sampling: Enroll pregnant women presenting in labour at a tertiary hospital, ensuring ethical approval and informed consent. Collect rectal swabs from each participant upon admission for delivery, label anonymized samples, and record relevant clinical metadata (e.g., age, gestational age, comorbidities, antibiotic exposure). Microbiological Screening and Isolation: Plate swabs onto selective CHROMagar™ and mSuperCARBA™ media according to the manufacturer’s protocols. Incubate plates at 37°C for 18–24 hours and examine for colonies morphologically consistent with Enterobacterales. Subculture positive colonies for pure isolates. Species Identification and Phenotypic Characterization: Identify isolates using Vitek 2 GN ID cards (or comparable automated system). Perform antimicrobial susceptibility testing by broth microdilution per CLSI guidelines, recording MICs for key antibiotics (carbapenems, aminoglycosides, colistin, tigecycline, etc.). Assess carbapenemase production using the modified carbapenem inactivation method (mCIM). Confirm presence of common carbapenemase genes (bla<sub>OXA-48</sub>-like, bla<sub>KPC</sub>, bla<sub>NDM</sub>, bla<sub>VIM</sub>, bla<sub>IMP</sub>) using multiplex PCR. DNA Extraction and Whole-Genome Sequencing: Extract genomic DNA from confirmed CRE isolates using a commercial kit (e.g., Qiagen DNeasy). Quantify and assess purity of DNA, then prepare SMRTbell libraries following PacBio Sequel II (or equivalent) protocols. Sequence DNA using the PacBio Sequel II platform to obtain long-read data. Genome Assembly and Annotation: Assemble reads de novo with HGAP4 or Canu. Polish assemblies and assess completeness; close genomes and plasmids where possible. Annotate genomes using Prokka or Bakta, and screen for AMR genes with ResFinder, plasmid replicons with PlasmidFinder, and mobile genetic elements using ISfinder and INTEGRALL. Identify methylation motifs using SMRT Link and REBASE databases. Detect CRISPR arrays and toxin-antitoxin systems with CRISPRCasFinder and TADB. Phylogenetic and Comparative Genomics: Assign sequence types with MLST 2.0. Construct core-genome alignments (e.g., with Roary or Panaroo). Build maximum-likelihood phylogenetic trees using IQ-TREE or RAxML, including >250 global reference genomes. Calculate SNP matrices and pairwise SNP distances with snippy or SNP-sites. Plasmid Analysis: Perform BLASTn comparisons of study plasmids to international references from NCBI. Generate comparative maps with Easyfig or BRIG, and synteny plots with progressiveMauve or clinker to assess gene order and structural variation. Data Availability and Documentation: Deposit raw reads, assembled genomes (chromosomes/plasmids), annotation files, MIC data, and clinical metadata as described. Ensure all data is anonymized and compliant with ethical approvals. All data are fully anonymized, and the study received institutional ethical approval.
Institutions
- University of Pretoria School of Medicine