Genome Sequence and Comparative Pathogenomics Analysis of a Salmonella enterica Serovar Typhi Strain Associated with a Typhoid Carrier in Malaysia

Abstract

Salmonella enterica serovar Typhi is a human pathogen that causes typhoid fever predominantly in developing countries. In this article, we describe the whole genome sequence of the S. Typhi strain CR0044 isolated from a typhoid fever carrier in Kelantan, Malaysia. These data will further enhance the understanding of its host persistence and adaptive mechanism.

GENOME ANNOUNCEMENT

Typhoid fever caused by human-specific Salmonella enterica serovar Typhi (S. Typhi) remains a major health problem that affects 21.7 million people, with 217,000 deaths worldwide annually (6). S. Typhi is transmitted through the oral-fecal route and sometimes persists in the body, establishing an asymptomatic chronic carrier (10, 12). The risk of developing gallbladder diseases, including carcinoma, is also higher among typhoid carriers (5, 10, 21).

Although typhoid fever is endemic in many countries, including Malaysia, little is known about the mechanism of survival and persistence of S. Typhi in the host. Therefore, the genome sequence and comparative pathogenomics analysis of carrier strain will provide in-depth understanding of its persistence and adaptive mechanism within its host.

S. Typhi CR0044 was isolated from stool sample of a typhoid carrier in Kelantan, Malaysia, in 2007. This strain was subtyped as ST1 by multilocus sequence typing (14) and was highly similar to the outbreak strain in 2005 by pulsed field gel electrophoresis (PFGE) (2). Genome sequencing of S. Typhi strain CR0044 was performed using the Ilumina Genome Analyzer (GA2x, pipeline version 1.60, insert size 300), which generated 1.0 gigabyte of data with a 90× depth coverage and a 73-bp read length. Genome assembly was constructed with Velvet (26) using the de novo approach, which generated 201 contigs with a minimum contig length of more than 200 bp and an average size of 23,367 bp. The open reading frames (ORFs) of the resultant contigs were predicted using RAST (1) and Prodigal (13) and subsequently annotated using Blast2GO (4), whereas tRNA and rRNA genes were identified with tRNAscan-SE (17) and RNAmmer (15), respectively. The predicted genome size is approximately 4,769,054 bp, with an average GC content of 52.1% and coding percentage of 85.8. The genome revealed approximately 4,884 coding sequences (CDS) with an average length of 825 bp. The genome also contains predicted 69 tRNA and 22 rRNA genes.

The genome revealed a type III secretion system and flagellum subsystem as reported in S. Typhi strains Ty2 and CT18 (7, 12). The genome contains genes reported in Ty2 and CT18, such as the gene coding for type 4 fimbrial assembly protein, the yjbEFGH locus, yhjD conserved clusters, and wca genes, which are related to cell wall and biofilm formation and host persistence (3, 8, 7, 12, 18, 25). It is noteworthy that the genome sequence also revealed the presence of the GGDEF family protein YeaJ, which is associated with cell surface adhesion and biofilm formation, which was not identified in Ty2 and CT18 (9, 19). The gene encoding the rhamnogalacturonide transporter RhiT for rhamnose utilization was also found adjacent to a transposase gene in CR0044 (20). Interestingly, the genome also revealed a zonular occludens toxin family protein that was not previously reported in Salmonella spp.

S. Typhi in Southeast Asia is genetically diverse, with genome variations and clonal expansion reported (2, 11, 15, 16, 21, 22, 23, 24). The dynamic nature of the S. Typhi chromosome greatly enhances its persistence and adaptation within the host, which allows the pathogen to survive and thrive in typhoid carriers. The genomic information obtained here could unveil the genome evolution and mechanism involved in carrier-state transformation.

Nucleotide sequence accession numbers.

This Whole Genome Shotgun project has been deposited in GenBank under accession no. AKZO00000000. The version described in this paper is the first version, AKZO01000000. The Bioproject designation for this project is PRJNA160187.