Genomic Profiles of ESBL/AmpC-Producing E. coli from Backyard Poultry in Southern India

Southern India is the source for this dataset of 18 whole-genome sequenced Escherichia coli isolates from backyard poultry. The data includes resistome, virulome, plasmidome, and CRISPR-Cas profiles, generated by Pavan Kalyan Nagaraja and last updated in May 2026. It captures 12 sequence types and multidrug resistance patterns from 45 confirmed isolates.

Use Cases

• Analyzing associations between plasmid replicons and antimicrobial resistance genes (ARGs) based on the strong plasmid-ARG associations mentioned.
• Studying the genetic diversity of E. coli strains based on the 12 identified sequence types and Simpson’s diversity index.
• Investigating CRISPR-Cas system prevalence and types based on the reported high prevalence of Type I-E arrays.
• Comparing virulence gene profiles for adhesion, iron acquisition, and stress response based on the listed virulome.
• Phylogenetic analysis of commensal E. coli strains based on SNP-based phylogeny and Clermont phylogrouping results.

Strengths

• Includes 18 whole-genome sequenced isolates with detailed genomic characterizations.
• Reports specific statistical results, including a β-lactam resistance enrichment Z-score of 3.46 and Simpson’s diversity index of 0.94.
• Profiles a wide range of genetic features: ARGs, virulence genes, plasmid replicons, and CRISPR-Cas arrays.

Limitations

• Row count is unknown, which may limit suitability assessment.
• Column-level documentation is absent; field semantics must be inferred after download.
• The dataset is small in scale (795.0 KB), representing a specific, localized sample.

Provenance

Source

Pavan Kalyan Nagaraja via figshare.

Collection Method

Isolates were obtained from 48 cloacal samples using a 30-cluster sampling strategy, with confirmation by multiplex PCR and whole-genome sequencing.

Freshness

Last updated 2026-05-29 05:50:56; freshness should be verified.

Geography

Backyard poultry in rural households in southern India.