MykrobeShig

June 15, 2026 ยท View on GitHub

This package parses Mykrobe predict results for Shigella sonnei and Shigella flexneri. It is adapted from the sonneityping tool originally developed for Shigella sonnei.

Mykrobe v0.9.0+ can identify input genomes and assign them to hierarchical genotypes based on detection of single nucleotide variants (SNVs), and report known mutations in the quinolone-resistance determining region (QRDR) of genes gyrA and parC.

This package parses the JSON files output by Mykrobe (one per genome) and tabulates the results in a single tab-delimited file.

Requirements

  • Python 3.7+ (has been tested on 3.12)
  • No external dependencies (uses only Python standard library)

Installation

git clone https://github.com/ShigellaGenomics/mykroshig.git
cd mykrobeshig
pip install .

Quickstart

mykrobeshig --jsons mykrobe_results/*.json --prefix results_mykrobe_parsed

Usage (including running Mykrobe)

Install Mykrobe

First, install Mykrobe (v0.9.0+) as per the instructions on the Mykrobe github.

Once Mykrobe is installed, make sure you run the following two commands to ensure you have the most up-to-date panels for genotyping:

mykrobe panels update_metadata
mykrobe panels update_species all

You can check what version of the scheme is currently loaded in your Mykrobe installation via:

mykrobe panels describe

Run mykrobe predict on each genome

Example command (using Illumina reads):

mykrobe predict --sample SAMPLE_NAME --species flexneri --format json --out SAMPLE_NAME.json --seq reads_1.fastq.gz reads_2.fastq.gz
  • For Oxford Nanopore reads, add the flag --ont to your command.
  • For full details on all Mykrobe options, please see the Mykrobe documentation.

Parse Mykrobe output with MykrobeShig

Once Mykrobe results are generated, use mykrobeshig to parse them. MykrobeShig automatically detects whether samples have been typed using the S. flexneri or S. sonnei schemes from the Mykrobe output.

Arguments

  • --jsons: JSON files output from mykrobe predict
  • --prefix: prefix for output file
  • --force: If you used --force with your Mykrobe call, to enforce a genotype call even when the species and phylogroup calls are not above the internal Mykrobe thresholds, you can force the parser to output this forced genotype for you. Otherwise, genomes with no phylogroup or no species Mykrobe calls will be skipped
mykrobeshig --jsons mykrobe_results/*.json --prefix results_mykrobe_parsed

Example data

We have provided two example Mykrobe output files inside the example_data directory in this repository. You can test your installation is working correctly by running the following command, and checking that the resulting file matches the one found in example_data/example_output_predictResults.tsv.

myrkboeshig --jsons example_data/ERR047239.json example_data/SRR7223147.json --prefix example_output

Output

The output table will be named prefix_predictResults.tsv, and will be in tab-delimited format.

Explanation of columns in the output:

  • genome: sample ID
  • species: species call, one of:
    • S. flexneri - if species coverage is >85.5
    • S. sonnei - if species coverage is >90
    • 'Unknown E. coli/Shigella' - if species coverage not met, but Mykrobe determines it belongs to Ecoli_Shigella genus, then it is likely an E. coli or Shigella genome but not one with a matching genotyping scheme
    • 'Not E. coli/Shigella' - Mykrobe was unable to detect the uidA gene, therefore this genome is unlikely to be E. coli or Shigella
    • 'forced call' - if --force provided, then no species is entered here and 'forced call' is used instead
  • final genotype: final genotype call from Mykrobe
  • name: human readable alias for genotype. Pulled from the data/alleles_*.txt files. Only used for S. sonnei.
  • scheme: scheme used for typing the genome in Mykrobe (one of sonnei or flexneri)
  • confidence: measure of confidence in the final genotype call, summarising read support across all levels in the hierarchy (lineage, clade, subclade, etc)
    • strong - high quality calls (quality of '1' reported by Mykrobe) for ALL levels;
    • moderate - reduced confidence for ONE node (Mykrobe quality of '0.5', but still with >50% read support for the marker allele), high quality calls for ALL OTHERS;
    • weak - low quality for one or more nodes (Mykrobe quality of '0.5' and <50% read support OR Mykrobe quality of '0').
  • num QRDR: Total number of mutations detected in the quinolone-resistance determining regions (QRDR) of genes gyrA and parC
  • parC_S80I, gyrA_S83L, gyrA_S83A, gyrA_D87G, gyrA_D87N, gyrA_D87Y: calls for each individual QRDR mutation. 0 indicates mutation is absent, 1 indicates mutation is present.
  • phylogroup_coverage: Percent coverage to the uidA marker for the E. coli/Shigella grouping, as detected by Mykrobe.
  • species_coverage: Percent coverage to the species markers for either S. sonnei or S. flexneri, as detected by Mykrobe. Determines the call in species column for the output, based on the thresholds outlined above.
  • lowest support for genotype marker: For any markers in the final genotype call that do not have a Mykrobe quality of '1', this column reports the percentage of reads supporting the marker allele at the most poorly supported marker
  • poorly supported markers: Lists any markers in the final genotype call that do not have Mykrobe quality of '1'. Markers are separated by ';', values in brackets represent the quality call from Mykrobe, followed by the read depth at the alternate / reference alleles.
  • max support for additional markers: For any markers detected that are incongruent with the final genotype call, this column reports the percentage of reads supporting the marker allele at the best supported additional marker.
  • additional markers: Lists any markers that are incongruent with the final genotype call. Markers are separated by ';', and the format is identical to column poorly supported markers.
  • node support: A list of all markers in the final genotype call with their Mykrobe quality calls (1, 0.5, or 0) and the read depths at the marker allele / reference allele.

Unexpected results

As recombination patterns may vary in either S. flexneri or S. sonnei, if you see anything reported in the "additional markers" column, it is worth investigating further whether you have contaminated sequence data (which would produce low-quality calls with low read support at additional markers) or genuine recombination/mixed infections. In such cases it may also be illuminating to investigate the original Mykrobe output file for further information.

License

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

Citation

If you use the sonnei scheme for typing, please cite: Hawkey, J. et al. Global population structure and genotyping framework for genomic surveillance of the major dysenteric pathogen, Shigella sonnei. Nat Commun 12, 2684 (2021). https://doi.org/10.1038/s41467-021-22700-4

If you use the flexneri scheme for typing, please cite: Hawkey, J. et al. Flex-It: A global standardised genotyping framework for Shigella flexneri. bioRxiv (2026). https://doi.org/10.64898/2026.04.17.719127