Genome dynamics and evolution of Salmonella Typhi strains from the typhoid-endemic zones

Abstract

Typhoid fever poses significant burden on healthcare systems in Southeast Asia and other endemic countries. Several epidemiological and genomic studies have attributed pseudogenisation to be the major driving force for the evolution of Salmonella Typhi although its real potential remains elusive. In the present study, we analyzed genomes of S. Typhi from different parts of Southeast Asia and Oceania, comprising of isolates from outbreak, sporadic and carrier cases. The genomes showed high genetic relatedness with limited opportunity for gene acquisition as evident from pan-genome structure. Given that pseudogenisation is an active process in S. Typhi, we further investigated core and pan-genome profiles of functional and pseudogenes separately. We observed a decline in core functional gene content and a significant increase in accessory pseudogene content. Upon functional classification, genes encoding metabolic functions formed a major constituent of pseudogenes as well as core functional gene clusters with SNPs. Further, an in-depth analysis of accessory pseudogene content revealed the existence of heterogeneous complements of functional and pseudogenes among the strains. In addition, these polymorphic genes were also enriched in metabolism related functions. Thus, the study highlights the existence of heterogeneous strains in a population with varying metabolic potential and that S. Typhi possibly resorts to metabolic fine tuning for its adaptation.

Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits

“…Typhi known to be involved in the catabolic pathways for 7 of the 27 falsely predicted growth-supporting carbon sources, namely: citrate, l -glutamine, l -rhamnose, 1,2-propanediol, d -tagatose, ethanolamine and 4-hydroxyphenylacetic acid 24 . Pseudogene accumulation has been widely observed amongst Typhi strains 25 as well as other host-restricted strains of Salmonella 24 , 26 . We hypothesize that there could be additional disrupted genes involved in the utilization of some of the 20 remaining carbon sources.…”

Towards plant pangenomics

“…() who described the production of the first ever pangenome, for a bacterial species Streptococcus agalactiae . Since then, the concept of the pangenome has become increasingly popular with numerous examples available for bacteria (Baddam et al ., ; Donati et al ., ; Liu et al ., ; Zhou et al ., ) and other micro‐organisms (Read et al ., ). Recently, pangenomic studies of higher organisms have emerged including in maize (Hirsch et al ., ), soybean (Li et al ., ), Brassica rapa (Lin et al ., ) and rice (Schatz et al ., ).…”

SNP Discovery Using a Pangenome: Has the Single Reference Approach Become Obsolete?

“…This has led to a series of similar studies in other micro-organisms [4,5,6,7] as well as higher organisms including maize [8,9], soybean [10,11], rice [12,13], and Brassicas [14,15]. The pangenome can be thought of as the full complement of genes in a given species.…”