Key resources table.
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| gene (Salmonella enterica serotype Typhi – S. Typhi) | Wild type | This study | PRJEB19289 | ENA sequence accession bank |
| Strain, strain background (S. Typhi)Wild type | Wild type | This study | Supplementary file 1 | |
| Strain, strain background (Escherichia coli) | ATCC | ATCC25922 | https://www.atcc.org/ › products › 25,922 | |
| Sequence-based reagent | Primer vi-F | This paper | PCR primers | GTTATTCAGC ATAAGGAG |
| Sequence-based reagent | Primer Vi-R | This paper | PCR Primers | CTTCCATACCA CTTTCCG |
| Sequence-based reagent | Primer prt-F | This paper | PCR Primers | CTTGCTATGGA AGACATAACGAACC |
| Sequence-based reagent | Primer prt-R | This paper | PCR Primers | CGTCTCCATCA AAAGCTCCATAGA |
| Commercial assay or kit | Bactec Media | Becton-Dickinson | BACTEC 9050 Blood Culture System | Blood culture media |
| Commercial assay or kit | Selenite F/MacConkey | Oxoid Ltd http://www.oxoid.com | CM0395/ CM0007 | Selective enrichment/ selective media |
| Commercial assay or kit | Salmonella-Shigella agar | Oxoid Ltd http://www.oxoid.com | CM0099 | Selective agar |
| Commercial assay or kit | Salmonella antisera | Murex Diagnostics, Dartford, UK https://www.dnb.com |
Salmonella typing antisera | |
| Commercial assay or kit | Wizard Genomic DNA Extraction Kit | https://worldwide.promega.com | Whole Genome DNA extraction | Cat#A1120 |
| Chemical compound, drug | Antimicrobial susceptibility test discs in cartridges | Oxoid Ltd http://www.oxoid.com |
Assorted antimicrobial discs for susceptibility testing | |
| Software, algorithm | Kraken |
Genome Biol
2014; 15: R46–12. |
ultrafast metagenomic sequence classification using exact alignment | |
| Software, algorithm | Multi-locus sequence typing (MLST) |
Genome Med
2014; 6: 90. |
Rapid genomic surveillance for public health and hospital microbiology labs. | |
| Software, algorithm | BIGSdb software |
BMC Bioinformatics
2010; 11: 595. |
Scalable analysis of bacterial genome variation at the population level. | Genomic analysis software |
| Software, algorithm | Pathogen-watch for AMR prediction. |
Nat Commun
2021; 12: 2879–12. |
AMR prediction software analysis | |
| Software, algorithm | Maximum Likelihood Analytical Tool |
Bioinformatics
2014; 30: 1312–3. |
RAxML (v8.2.9) version 8 | A tool for phylogenetic analysis and post- analysis of large phylogenies |
| Software, algorithm | MicroReact Tool | (https://microreact.org/project/wViqmaRdZuFVEb6yk4i1jU) | Interactive global H58 phylogeny | |
| Software, algorithm | Bandage assay | Bioinformatics 2015; 31: 3350–2. | Interactive visualisation of de novo genome assemblies. | |
| Software, algorithm | ISMapper | BMC Genomics 2015; 16: 667. | Genomics tool for phylogenetics |