PorinPredict

In silico prediction of OprD porin-loss in Pseudomonas aeruginosa isolates from assembled genomes

Overview

PorinPredict is a command-line tool for the standardized detection of OprD-inactivating mutations in Pseudomonas aeruginosa genomes. OprD loss typically leads to carbapenem resistance.

The program and associated databases can be downloaded from https://github.com/MBiggel/PorinPredict.

For the complementary detection of carbapenemases consider using AMRFinderPlus, RGI, Resfinder or similar tools.

Installation

Requirements

• Linux or macOS
• Python3 and pandas
• DIAMOND >=v2.0.0
• BLAST+
• R and packages dplyr and Biostrings

PorinPredict expects DIAMOND, BLASTn, and Rscript to be available in $PATH.

Installation of dependencies via conda

To install required dependencies in a separate Conda environment, run the following commands:

git clone https://github.com/MBiggel/PorinPredict
cd PorinPredict
conda env create -n porinpredict --file porinpredict.yaml

conda activate porinpredict
/path/to/porinpredict.py --version

Run PorinPredict

conda activate porinpredict
/path/to/porinpredict.py -i /path/to/genome.fasta -o /path/to/output_directory/ --threads 8

To analyze multiple assemblies and create a summary table, you can use a for loop in combination with the "--summarize" flag:

for i in /path/to/input_directory/*.fasta; do /path/to/porinpredict.py -i $i -o /path/to/output_directory/ --summarize ; done

Assemblies for a test run are included in the repository folder PorinPredict/test_assemblies:

for i in ./test_assemblies/*.fasta; do ./porinpredict.py -i $i -o test_run --summarize -t 8; done

Output Files

Filename	Description
PREFIX_PA_PorinPredict.tsv	PorinPredict results and classification
PorinPredict_results_table.tsv	PorinPredict collated results (when run with the "--summarize" flag)

Considerations

• PorinPredict relies on high-quality genome assemblies. Before running PorinPredict, we recommend to confirm Pseudomonas aeruginosa species affiliation using e.g. rMLST and to assess the assembly quality using CheckM, QUAST, or similar tools. In low-quality assemblies, absence of oprD may be caused by technical reasons such as an insufficient coverage.

• In addition to inactivating mutations in OprD and promoter disruptions, PorinPredict reports missense mutations. Specific amino acid substitutions associated with carbapenem resistance are described in our publication

• 15 intact OprD variants are currently included in the database. With the increasing number of available genomes, the database will be supplemented with additional variants of carbapenem-susceptible isolates.

Citation

Biggel, M., Johler, S., Roloff, T., Tschudin-Sutter, S., Bassetti, S., Siegemund, M., Egli, A., Stephan, R., & Seth-Smith, H. M. B. (2023). PorinPredict: In Silico Identification of OprD Loss from WGS Data for Improved Genotype-Phenotype Predictions of P. aeruginosa Carbapenem Resistance. Microbiology spectrum, e0358822. https://doi.org/10.1128/spectrum.03588-22

License

GNU General Public License, version 3