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

18 whole-genome sequenced isolates of ESBL- and/or AmpC-producing Escherichia coli from backyard poultry in southern India. The dataset includes resistome, virulome, plasmidome, and CRISPR-Cas profiles, along with multilocus sequence typing and phylogenetic analysis. It was authored by Pavan Kalyan Nagaraja and last updated on 2026-05-29.

Use Cases

• Analyzing the prevalence of specific antimicrobial resistance genes (e.g., blaCTX-M-15, qnrS) based on resistome profiling.
• Studying plasmid-mediated resistance structuring based on reported strong plasmid-ARG associations (Cramér’s V > 0.5).
• Investigating genetic diversity and clonal heterogeneity based on 12 sequence types and a Simpson’s diversity index of 0.94.
• Profiling virulence-associated traits based on conserved genes for adhesion, iron acquisition, and stress response.

Strengths

• Includes whole-genome sequencing data for 18 confirmed ESBL/AmpC-positive E. coli isolates.
• Provides multi-faceted genomic analysis covering resistome, virulome, plasmidome, and CRISPR-Cas systems.
• Reports specific statistical findings, such as significant β-lactam resistance enrichment (Z=3.46, p<0.001).

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 very small (26.2 KB), indicating limited scope.

Provenance

Source

figshare, author Pavan Kalyan Nagaraja.

Collection Method

Isolates were obtained from 48 cloacal samples using a 30-cluster sampling strategy, with 18 selected for whole-genome sequencing.

Freshness

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

Geography

Southern India (rural households).