Genomic analysis unveils genome degradation events and gene flux in the emergence and persistence of S. Paratyphi A lineages

Abstract

Paratyphoid fever caused by S. Paratyphi A is endemic in parts of South Asia and Southeast Asia. The proportion of enteric fever cases caused by S. Paratyphi A has substantially increased, yet only limited data is available on the population structure and genetic diversity of this serovar. We examined the phylogenetic distribution and evolutionary trajectory of S. Paratyphi A isolates collected as part of the Indian enteric fever surveillance study "Surveillance of Enteric Fever in India (SEFI)." In the study period (2017-2020), S. Paratyphi A comprised 17.6% (441/2503) of total enteric fever cases in India, with the isolates highly susceptible to all the major antibiotics used for treatment except fluoroquinolones. Phylogenetic analysis clustered the global S. Paratyphi A collection into seven lineages (A-G), and the present study isolates were distributed in lineages A, C and F. Our analysis highlights that the genome degradation events and gene acquisitions or losses are key molecular events in the evolution of new S. Paratyphi A lineages/sub-lineages. A total of 10 hypothetically disrupted coding sequences (HDCS) or pseudogenes-forming mutations possibly associated with the emergence of lineages were identified. The pan-genome analysis identified the insertion of P2/PSP3 phage and acquisition of IncX1 plasmid during the selection in 2.3.2/2.3.3 and 1.2.2 genotypes, respectively. We have identified six characteristic missense mutations associated with lipopolysaccharide (LPS) biosynthesis genes of S. Paratyphi A, however, these mutations confer only a low structural impact and possibly have minimal impact on vaccine effectiveness. Since S. Paratyphi A is human-restricted, high levels of genetic drift are not expected unless these bacteria transmit to naive hosts. However, public-health investigation and monitoring by means of genomic surveillance would be constantly needed to avoid S. Paratyphi A serovar becoming a public health threat similar to the S. Typhi of today.

Fig 1. Phylogenetic distribution of contemporary Indian S. Paratyphi A isolates in a global context: Rooted maximum likelihood phylogenetic tree of contemporary Indian S. Paratyphi A (n = 152), combined with global genome collection (n = 400) 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/).

Fig 2. 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 S. 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.