Data and Code Supporting Typhi Mykrobe Development and Validation

This repository holds the tabulated data and code behind the paper of the Global Typhoid Genomics Consortium, "Typhi Mykrobe: fast and accurate lineage identification and antimicrobial resistance genotyping directly from sequence reads for the typhoid fever agent Salmonella Typhi" published in Genome Medicine, 2025 (preprint available in BioRxiv).

Note that Typhi Mykrobe is not a QC tool. It is recommended that users continue to undertake their own QC on short and long read data.

Licenses and and re-use:

• The code in this repository is shared under a GNU general public license v3.0.

• The data, figures and tables in this repository form part of the publication noted above, which is published under a Creative Commons 4.0 License. If you use material in this repository, you should cite both the paper and this repository as the source.

Main data files

Supplementary_Table_1.csv

• Tabulated Typhi Mykrobe output table, for all genomes included in validation analyses.

Supplementary_Table_2.csv

• Line list of all genomes used for validation, including sequence data accessions; plus genome-derived genotype, AMR and plasmid variables (where available) for mapping-based GenoTyphi lineage calls, and PathogenWatch.

Supplementary_Table_3.xlsx

• Details of AMR genotype calls comparison (in /AMRplasmid directory)

Supplementary_Table_4.csv

• csv file of all isolates with publicly availble antimicrobial susceptibility testing (AST) data sourced from three separate datasets used for validation of phenotype prediction. Includes minimum inhibitory concentration (MIC) data from the UK Health Security Agency (UKHSA) for n=852 isolates (following EUCAST standards), and the US Centres for Disease Control and Prevention (US CDC) for n=720 isolates (following CLSI standards), and disk diffusion data (following CLSI standards) for n=2,446 isolates collected and analysed from three countries as part of the Surveillance for Enteric Fever in Asia Project (SEAP).

Supplementary_Table_5.csv

• Comparison and error rates for AMR genotype and phenotype data (in /AST directory)

Supplementary_Table_6.csv

• Details of genomes used for validation of typing from nanopore reads (i.e. with matched Illumina and ONT data), including data accessions, ONT sequencing details and Mykrobe calls from both sequence data types.

Genotype analysis

/genotypes directory

• Mykrobe_genotypes.Rmd = R markdown file for validation of genotype calls (Typhi Mykrobe vs mapping-based)

• Mykrobe_genotypes.html = knitR output of Rmd file, including all figures and numbers included in manuscript text

AMR and plasmid analysis

/AMRplasmid directory

• Mykrobe_AMRplasmid.Rmd = R markdown file for validation of AMR and plasmid typing calls (Typhi Mykrobe vs Pathogenwatch)

• Mykrobe_AMRplasmid.html = knitR output of Rmd file, including all figures and numbers included in manuscript text

• figure files (PNG and PDF format; output from executing Rmd file)

• supplementary table files (CSV format; output from executing Rmd file)

AST AMR analysis

/AST directory

• Mykrobe_AMR_AST.Rmd = R markdown file for validation of AMR prediction (Typhi Mykrobe predictions vs lab phenotype)

• Mykrobe_AMR_AST.html = knitR output of Rmd file, including output figures

• figure files (PNG and PDF format; output from executing Rmd file)

• supplementary table files (CSV format; output from executing Rmd file)

Mykrobe on ONT data

/ONT directory

• Mykrobe_ONT.Rmd = R markdown file for validation of typing from ONT reads (Typhi Mykrobe results for Illumina vs ONT reads)

• Mykrobe_ONT.html = knitR output of Rmd file, including output figures

Benchmarking

/benchmarking directory

• The README file provides details of the benchmarking analyses.

• Supplementary figure file (PNG format) showing run time for Typhi Mykrobe.