E. coli Genomes with Colibactin Loci, Associated with Lineage and AMR Patterns

9,700 curated Escherichia coli genomes from BV-BRC were analyzed, identifying 498 genomes carrying complete or near-complete colibactin (pks) loci. The dataset, authored by Adel Azour and last updated in May 2026, shows pks-positive genomes are enriched in phylogroup B2, associated with fewer antimicrobial resistance genes and plasmid replicons compared to pks-negative genomes.

Use Cases

• Identify lineage-specific genomic markers based on the association of pks loci with phylogroup B2 and specific sequence types.
• Analyze the relationship between plasmid burden and secondary metabolite carriage based on the reported lower plasmid replicon count in pks-positive genomes.
• Investigate patterns of antimicrobial resistance gene distribution in relation to specific genomic islands like colibactin.
• Study pangenome structure and accessory genome architecture in defined bacterial subpopulations based on the reported differences in core and accessory genome sizes.

Strengths

• Analysis is based on 9,700 curated E. coli genomes, providing a population-scale perspective.
• Findings are specific, reporting 498 pks-positive genomes and their association with lineages like ST73, ST95, ST127, and ST12.
• Comparative analysis includes controlled comparisons within phylogroup B2 to isolate effects.

Limitations

• Column-level documentation is absent; field semantics must be inferred after download.
• Row count for the specific supplementary data file is unknown, which may limit suitability assessment.
• The primary data file is a 5.2 MB DOCX document, which may require extraction or conversion for computational analysis.

Provenance

Source

Genomes sourced from the BV-BRC database.

Collection Method

Computational analysis of curated genomes to identify pks loci and associated genomic features.

Freshness

Last updated 2026-05-26 06:01:58