We have developed several software tools and resources that are used by the global research community.

mykrobeshig

Parser script supporting rapid genotyping for Shigella sonnei and Shigella flexneri. Genotyping schemes for both organisms (sonneityping and Flex-It) are implemented in Mykrobe. These schemes use a curated set of SNPs to assign genomes to genotypes and detects resistance mechanisms for fluoroquinolones. Utilised for genomic surveillance in Australia and internationally. The S. sonnei scheme is described in Hawkey et al. 2021, and the S. flexneri scheme in Hawkey et al. 2026.

AMRrules

The AMRrules engine includes the software and rules for interpreting genotypic antimicrobial resistance in multiple different organisms, using AMRFinderPlus genotype reports as input. The software engine was developed in collaboration with Kat Holt at the London School of Hygeine and Tropical Medicine, and the rules were curated and developed by the ESGEM-AMR consortium.

ISMapper

ISMapper is a tool for identifying the location of insertion sequences (IS) in bacterial genomes from short-read sequencing data, relative to a provided reference genome. It has been used to detect IS upstream of antibiotic or virulence genes where the IS may be influencing gene expression, as well as for discovering the impact of IS on the evolution of bacterial species. ISMapper is described in Hawkey et al. 2015.