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Salmonella enterica serovar Typhimurium T000240

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close this sectionAbout this Microorganism


Photo by Department of Bacteriology I, National Institute of Infectious Diseases

Salmonella enterica serovar Typhimurium is one of the most important causative agents of acute human Salmonella gastroenteritis. The emergence of multidrug-resistant strains of S. enterica serovar Typhimurium have been reported in various countries, raising concerns about the difficulty in the treatment of infections. S. enterica serovar Typhimurium T000240 was isolated from a human source in 2000 as the first isolated strain displaying a high-level fluoroquinolone resistance in Japan.

The complete genome of S. enterica serovar Typhimurium T000240 consisted of a chromosome (4,954,814 bp; G+C content 52.2 %) and two circular plasmids (pSTMDT12_L: 106,510 bp; and pSTMDT12_S: 8,670 bp). An 82-kb genomic island, designated as GI-DT12, related to its highly resistant phenotype was identified on the chromosome. As GI-DT12 was revealed to be flanked by IS1-derivatives, IS1-mediated recombination likely played a role in the acquisition of this genomic island through horizontal transfer. Furthermore, the gene cassette responsible for gentamicin and trimethoprim resistance was identified on plasmid pSTMDT12_L, and appeared to have been acquired through homologous recombination with IS26.) Such ISs may represent potential landmarks to obtain variety of genetic elements present on the plasmids and chromosomes of pathogenic bacteria.

close this sectionProject history

close this date 2010-11-26 ..... 1
2010-11-26 Release of the Salmonella enterica serovar Typhimurium T000240 genomic data
imageWe published the genomic data of Salmonella enterica serovar Typhimurium T000240.

close this sectionSummary of the genomic data

SE1
Genomic size 5,069,994 bp
G+C content 52.25 %
Number of ORFs assigned 4,871
Percentage of the coding regions 88.11 %
Percentage of the intronic regions 0.00 %
Number of rRNA genes 22
5S16S23S
877
Number of tRNA genes 84
AlaArgAsnAspCysGln
494314
GluGlyHisIleLeuLys
461385
MetPheProSeCSerThr
623154
TrpTyrUndetVal
1316
Number of other features
(misc_RNA,misc_feature,repeat)
0

close this sectionGeneral Procedure

  • Short-read DNA sequencing and assembly
    An approximately 500-bp length shotgun library of S. enterica serovar Typhimurium T000240 strain was prepared using a genomic DNA Sample Prep Kit, and DNA clusters were generated on a slide using a Cluster Generation Kit (Illumina). All sequencing runs for 80-mers were performed using an Illumina Genome Analyzer using an Illumina Sequencing Kit. Fluorescent images were analyzed using an Illumina base-calling pipeline 1.4.0 to obtain FASTQ-formatted sequence data. Obtained 80-mer reads were trimmed based on the phred quality value (cutoff = 14) using the Euler-SR qualitytrimmer command. These sequences were then assembled using Euler-SR v1.0 with the default parameters.

  • Gap closing and data validation
    de novo assembly of short reads were ordered and oriented based on S. enterica serovar Typhimurium LT2 chromosomal DNA sequence (NC_003197.fna) as a reference. Homologous regions with the LT2 chromosome DNA were identified by BLASTN searched with 1E-10 as a cutoff value. Predicted gaps in supercontigs were amplified with a specific PCR primer pair, followed by Sanger DNA sequencing using BigDye Terminator v3.1 Cycle sequencing Kit (ABI). Resulted complete chromosome DNA sequence were validated by aligning of 40-mer short reads.

  • Annotation
    Annotation was performed using NCBI Prokaryotic Genomes Automatic Annotation Pipeline (PGAAP). Several of the suggested errors were inspected and revised manually. Finally, fluctuation of description was conformed throughout the genome.

  • Read Archive
    The short read archive for strain T000240 have been deposited in the DDBJ Sequence Read Archive (DRA000195).

close this sectionRelated links to external databases