Dataset for 'Predominance of multidrug-resistant Salmonella Typhi genotype 4.3.1 with low-level ciprofloxacin resistance in Zanzibar'

The whole genome sequencing data for this study (fastq files of all short read sequencing analyzes and five of the long read assemblies of the nine selected strains) have been deposited in the European Nucleotide Archive (ENA) at EMBL-EBI under accession number PRJEB59168 (https://www.ebi.ac.uk/ena/browser/view/PRJEB59168). The remaining four long read assemblies have been deposited in GenBank, National Institutes of Health (NIH), BioProject number PRJNA982791 (GenBank Overview (nih.gov)), accession numbers SAMN35714885 (ZNZ13L78), SAMN35713968 (ZNZ17F60), SAMN35714917 (ZNZ55M142), and SAMN35714939 (ZNZ57M158).). All other relevant data are within the manuscript, with the accession numbers of the genomes and additional information listed in the Supplementary information (S1 Table).