Antimicrobial susceptibility profile of <i>S</i>. Paratyphi A tested in the present study.

Antimicrobial susceptibility profile of S. Paratyphi A tested in the present study.</p

List of functional gene inactivation mutations identified between phylogenetic lineages.

List of functional gene inactivation mutations identified between phylogenetic lineages.</p

List of whole genome sequenced isolates collected from the participating sites of the SEFI network.

List of whole genome sequenced isolates collected from the participating sites of the SEFI network.</p

Lineage-defining missense mutations in <i>S</i>. Paratyphi A genomes.

Lineage-defining missense mutations in S. Paratyphi A genomes.</p

Rooted maximum likelihood phylogenetic tree of <i>rfb</i> loci of <i>S</i>. Paratyphi A isolates derived from the whole genome alignment by mapping against the reference genome of <i>S</i>. Paratyphi ATCC 9150 (Accession No: CP000026.1) using Snippy.

Lineages and genotypes are labelled as colour strips. Amino acid substitutions in the rfb loci are represented by heat maps. (TIF)</p

Distribution of <i>S</i>. Typhi and <i>S</i>. Paratyphi A isolates collected across the participating sites of the SEFI network.

Distribution of S. Typhi and S. Paratyphi A isolates collected across the participating sites of the SEFI network.</p

List of <i>S</i>. Paratyphi A genomes used in this study with accession IDs and metadata.

List of S. Paratyphi A genomes used in this study with accession IDs and metadata.</p

<i>Phylogenetic distribution of contemporary Indian S</i>. <i>Paratyphi A isolates in a global context</i>: Rooted maximum likelihood phylogenetic tree of contemporary Indian <i>S</i>. Paratyphi A (<i>n = 152)</i>, combined with global genome collection (<i>n = 400</i>) representing the current global distribution.

The tree was derived from 4286 SNPs mapped against the reference genome of S. Paratyphi ATCC 9150 (Accession No: CP000026.1) using Snippy and rooted to the outgroup strain (ERR028986: Lineage G). Red-colored dots at the tip of the branches indicates the position of this study isolates. Contemporary Indian S. Paratyphi A isolates of this study were found distributed across the global tree with both lineages A, C and F. Genomes with their respective metadata are labeled as color strips and key for each variable were mentioned. Strip 1 and 2 indicate the location and 3 represent MLST of each isolate. Heatmap represents the QRDR mutations that confer resistance to fluoroquinolone and the presence of plasmids. The scale bar indicates substitutions per site. Color keys for all the variables are given in the inset legend. The tree was visualized and labeled using iTOL (https://itol.embl.de/).</p

Time-calibrated Bayesian phylogeny phylogenetic tree showing the evolutionary events (HDCS forming mutations, insertions and deletions) that define the seven modern lineages and sub-lineages of <i>S</i>. Paratyphi A.

Major lineages/ genotypes were simplified as colored cartoon triangles using FigTree (http://tree.bio.ed.ac.uk/software/figtree/). Red arrow represents frameshift mutation/ gene degradation, Black arrow represent acquisition/ gene gain. Grey arrows demarcate nodes of interest, and the accompanying data indicate 95% HPD of node heights.</p

List of lineage-defining mutations in the O-antigen biosynthesis genes (<i>rfb</i> region) of <i>S</i>. Paratyphi A and their predicted impact on protein structures.

List of lineage-defining mutations in the O-antigen biosynthesis genes (rfb region) of S. Paratyphi A and their predicted impact on protein structures.</p