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ResTransfer: Predicting Horizontal Gene Transfer of Resistance Genes in Microbes

ResTransfer is a bioinformatics pipeline designed to predict the likelihood of horizontal gene transfer (HGT) of antibiotic resistance genes in microbial strains. This tool leverages BLAST for sequence alignment and a categorization system to assess gene transfer potential based on identity, query coverage, and other criteria. The results are scored and categorized into three levels of resistance transfer likelihood.

Features

  • BLAST Integration: Uses BLAST for sequence alignment between query genomes and reference databases.
  • Gene Categorization: Categorizes matches into predefined groups, including Resistance, T4SS, Integrative Conjugative Element (ICE), and Adherence.
  • Scoring System: Assigns scores to gene categories based on their contribution to resistance gene transfer likelihood.
  • Excel Output: Outputs results in a structured Excel file, including total scores and resistance transfer likelihood categories.

Prerequisites

Ensure the following software and packages are installed:

  1. BLAST: Download and configure from NCBI BLAST+.
  2. Python: Version 3.8 or higher.
  3. Python Libraries:
    • pandas
    • openpyxl

Install the required Python libraries using:

pip install pandas openpyxl

Installation

Clone the repository:

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git clone https://github.com/Umeshkumarku1/ResTransfer.git

cd ResTransfer

Ensure BLAST executables are added to your system PATH.

The reference_db.nsq file can be accessed from this link.

Here is the direct link to access the reference_db.nsq file: https://drive.google.com/file/d/1Tw67zxHtDQePQsi3ZtrZQoB9sqc9NFk-/view?usp=drive_link.

Usage

Step 1: Input Preparation

Prepare the input files:

Query genome in FASTA format (e.g., Query_Genome.fasta).

Reference database for BLAST (e.g., reference_db).

Step 2: Running the Pipeline

Run the pipeline using the script:

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python ResTransfer.py

Script Workflow

Run BLAST:

The script executes a blastn search against the reference database.

Results are saved in a TSV file (blast_output.tsv).

Parse BLAST Results:

Filters BLAST results based on identity, query coverage, and e-value thresholds.

Categorizes gene matches into predefined groups.

Score and Categorize:

Computes a total score for each query based on gene categories.

Classifies results into:

  • High chance for antibiotic resistance gene transfer.

  • Moderate chance for antibiotic resistance gene transfer.

  • Low chance for antibiotic resistance gene transfer.

Export Results:

Saves results, scores, and categories to an Excel file (Gene_Counts.xlsx).

Example Workflow

  • Prepare the Query Genome and Reference Database:

  • Place your genome FASTA file in the appropriate location.

  • Configure the reference database using makeblastdb:

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makeblastdb -in reference.fasta -dbtype nucl -out reference_db

Run the Script:

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python ResTransfer.py

View Results:

Check the generated Gene_Counts.xlsx for scores and resistance gene transfer categories.

Outputs

The pipeline generates the following outputs:

  • BLAST Output (blast_output.tsv): Tabular format of BLAST results.

  • Final Results (Gene_Counts.xlsx).

  • Gene counts for each category.

  • Total score for each query.

  • Resistance transfer likelihood category.

Troubleshooting

-BLAST Errors: Ensure BLAST is installed and added to the system PATH. -Missing Output File: Check input file paths and permissions. -Excel Not Generated: Verify input data meets filter criteria.

License

This project is licensed under the MIT License. See the LICENSE file for details.

Contact

For issues or feedback and the required documents, please reach out to:

Name: Umeshkumar KU

Email: Research.umeshkumarku@gmail.com

GitHub: https://github.com/Umeshkumarku1