Pan-Genomic Analysis Provides Insights into the Genomic Variation and Evolution of Salmonella Paratyphi A

Weili Liang,Jun Yu,Yongbing Zhao,Jingfa Xiao,Xiaoying Cui,Biao Kan,Chunxia Chen,Marc Robinson-Rechavi

doi:10.1371/journal.pone.0045346

Abstract

Salmonella Paratyphi A (S. Paratyphi A) is a highly adapted, human-specific pathogen that causes paratyphoid fever. Cases of paratyphoid fever have recently been increasing, and the disease is becoming a major public health concern, especially in Eastern and Southern Asia. To investigate the genomic variation and evolution of S. Paratyphi A, a pan-genomic analysis was performed on five newly sequenced S. Paratyphi A strains and two other reference strains. A whole genome comparison revealed that the seven genomes are collinear and that their organization is highly conserved. The high rate of substitutions in part of the core genome indicates that there are frequent homologous recombination events. Based on the changes in the pan-genome size and cluster number (both in the core functional genes and core pseudogenes), it can be inferred that the sharply increasing number of pseudogene clusters may have strong correlation with the inactivation of functional genes, and indicates that the S. Paratyphi A genome is being degraded.

Highlights

Salmonella are important human and animal pathogens and include two species, Salmonella bongori (S. bongori) and Salmonella enterica (S. enterica)
General Features of Sequenced Genomes After assembling the reads from the Solexa sequencer, 24 to 30 scaffolds were available for the five epidemic strains
To understand the features of the pseudogene population quantitatively, we examined the relationship between the pangenome sizes of pseudogenes or the number of core pseudogene clusters and the number of strains using the same method as was used for the functional genes (Figure 2B)

Summary

Introduction

Salmonella are important human and animal pathogens and include two species, Salmonella bongori (S. bongori) and Salmonella enterica (S. enterica). S. enterica are further classified into distinct subspecies, and include more than 2500 serovars [1]. Most serovars within S. enterica infect a broad range of host species and cause self-limiting gastroenteritis [2,3]. Paratyphi A, B and C, only infect humans and elicit typhoid, paratyphoid or enteric fever, which are severe infections of the reticuloendothelial system with high rates of complications and mortality [4,5]. The clinical features of paratyphoid fever resemble typhoid fever, but it is a relatively milder illness, and an accurate differential diagnosis relies on laboratory confirmation [6,7]

Methods

Results

Conclusion