🧬 Comparative Pangenomics & AMR Gene Profiling of 50 Acinetobacter Genomes

An end-to-end bioinformatics pipeline analyzing 50 Acinetobacter genomes to explore their pangenome structure, core genome evolutionary relationships, and antimicrobial resistance (AMR) gene profiles.

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📌 Executive Summary

• Open Pangenome Dynamics: The accumulation curve displays a continuous, non-saturating trajectory across 50 strains, reaching over 14,000 total gene clusters, confirming an open pan-genome driven by active horizontal gene acquisition.
• Core Genome Conservation: Identified 2,189 core genes shared across all strains, serving as the foundation for high-resolution phylogenetic reconstruction.
• AMR Gene Burden: Comprehensive screening revealed widespread aminoglycoside resistance (ant(2'')-Ia), critical carbapenemases (blaOXA-23, blaOXA-66, blaNDM-1), and co-occurring multidrug resistance (MDR) blocks (sul2, tet(B), msr(E)).

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📊 Key Results & Visualizations

1. Pangenome Accumulation Curve (Open vs. Closed)

The accumulation plot confirms the open nature of the Acinetobacter pan-genome, highlighting continuous genetic diversification as new genomes are added.

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2. Core Genome Phylogenetic Tree

A Maximum Likelihood phylogenetic tree constructed with FastTree ($GTR+CAT$ model) on the 2,189 core gene alignments, resolving distinct clonal and divergent lineages.

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3. AMR Resistance Profile Heatmap

A binary presence/absence matrix generated using ABRicate (NCBI database), illustrating the distribution of key resistance markers across all 50 strains.

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🗂️ Project Workflow & Repository Structure

pangenomic_project/
├── 01_Data_Acquisition.ipynb      # Genome retrieval & NCBI assembly data checks
├── 02_Genome_Annotation.ipynb     # Automated annotation with Prokka (.gff generation)
├── 03_Pangenome_Analysis.ipynb    # Roary pipeline & Open vs Closed accumulation curve
├── 04_Phylogenetic_Analysis.ipynb # FastTree ML tree construction & Biopython plotting
├── 05_AMR_Gene_Profiling.ipynb    # ABRicate screening & Seaborn AMR Heatmap matrix
├── my_genomes/                    # Raw FASTA genome files (.fna)
├── gff_files/                     # Prokka output GFF files
├── roary_output/                  # Pangenome alignments & statistics
├── pangenome_curve.png            # Saved Pangenome plot
├── core_tree.png                  # Saved Phylogenetic Tree plot
├── amr_heatmap.png                # Saved AMR Heatmap plot
└── README.md                      # Project documentation