v2.1

Filename changes

• renamed AMR marker list to AMR_genes_mutations_plasmids.csv
• renamed Genotype_specification.csv to GenoTyphi_specification.csv

Changes to AMR/plasmid marker probeset

• corrected OXA-7 to ampicillin resistance not ESBL
• added probes for carbapenemase genes
• added probes for plasmids IncX1, p0111

Changes to parse_typhi_mykrobe.py

• changed output column header from 'species' to 'serovar'
• changed drug column name from 'sulfamethoxazole' to 'trimethoprim-sulfamethoxazole'

GenoTyphi v2.0

This version includes:

• five new genotypes (4.3.1.2.1, 4.3.1.2.1.1, 3.5.4.1, 3.5.4.2, 3.5.4.3)
• validated Mykrobe panels for genotyping (v20221207) and AMR
• updated genotyphi.py (v2.0) including the above new genotypes

GenoTyphi v1.9.1

Updated to include:

• Table of alleles for calling AMR mutations
• Table of alleles for calling genotypes (including suggested colours)

GenoTyphi v1.9.0

Updated to include:

• Genotype 4.3.1.3.Bdq
• gyrB-S464F/Y mutations

GenoTyphi v1.8.0

Updated to include:

• Genotype 2.1.7.1
• Genotype 2.1.7.2

GenoTyphi v1.7.1

Licence updated.

GenoTyphi v1.7.0

New release includes calling of the following H58 sublineages:

• 4.3.1.1.EA1 (H58 lineage I, East Africa 1)
• 4.3.1.2.EA2 (H58 lineage II, East Africa 2)
• 4.3.1.2.EA3 (H58 lineage II, East Africa 3)

GenoTyphi v1.6.0

This release of GenoTyphi includes the original S. Typhi genotyping scheme defined in Wong et al. 2016, and subsequent updates for:

• 4.3.1.1 (H58 lineage I)
• 4.3.1.2 (H58 lineage II)
• 4.3.1.3 (H58 lineage III)
• 4.3.1.1.P1 (XDR outbreak clade)
• 3.3.2 and sublineages 3.3.2.Bd1, 3.3.2.Bd2
• 2.5.2
• QRDR mutation calling
• acrB R717 mutation calling