Genotypic and Phenotypic Landscape of Carbapenem-Resistant Pseudomonas aeruginosa Isolated From Respiratory and Non-Respiratory Samples in a Tertiary Hospital

# Additional file 4 — Code & Data package (DOI-ready)

**Recommended deposition:** Zenodo (DataCite DOI) or OSF (DataCite/Crossref DOI).  **Title (Zenodo):** Code and data for “Genotypic and Phenotypic Landscape of Carbapenem-Resistant Pseudomonas aeruginosa Isolated From Respiratory and Non-Respiratory Samples in a Tertiary Hospital”  **Creators:** Hamiyet Büşra Gündoğdu, et al.  **Description:** Reproducible materials accompanying the manuscript. Includes Python script, machine-readable raw counts (Table 3 / Table 4), and a conda environment to reproduce the figures and statistics (Fisher’s exact tests, BH-FDR).  **Keywords:** Pseudomonas aeruginosa; CRPA; carbapenem resistance; exoT; exoY; PFGE; Fisher’s exact test; FDR; BH; EUCAST; reproducible research  **Version:** 1.0 (2025-08-26)**Funding:** [Recep Tayyip Erdoğan University] Scientific Research Projects Coordination Unit (BAP), grant [TTU-2020-1191]

## ContentsSee `Additional_file_4_manifest.csv` for file sizes and SHA256 checksums.

- `reproduce_analysis_corrected.py` — analysis/plot script- `table3_counts.csv` — gene-prevalence counts- `table4_counts_corrected.csv` — exoT/exoY vs antibiotic counts- `environment.yml` — conda environment spec

## How to reproduce```bashconda env create -f environment.ymlconda activate crpa_analysispython reproduce_analysis_corrected.py```Figures S1–S2 (q-value plots) will be generated as PNG/PDF.

## Licensing- **Data (CSV):** CC BY 4.0 recommended.  - **Code (Python):** MIT recommended.  If you prefer a single-license deposition on Zenodo, select **CC BY 4.0** and also include `LICENSE-MIT.txt` inside the archive for code-level permission. This README clarifies the dual intent.

## Suggested citation (will update after DOI is minted)Gündoğdu HB, Rakıcı E, Ejder N, Çopur Çiçek A, Özgümüş OB. (2025). Code and data for “Genotypic and Phenotypic Landscape of Carbapenem-Resistant Pseudomonas aeruginosa Isolated From Respiratory and Non-Respiratory Samples in a Tertiary Hospital” (Version 1.0) [Dataset]. Zenodo. https://doi.org/10.5281/zenodo.16029015

## ContactCorresponding author: Osman Birol Özgümüş — [[e-mail]]