Salmonella

Salmonella classification is extremely complex; based on DNA-DNA hybridisation results the genus Salmonella is divided into two species: Salmonella enterica and Salmonella bongori. S. enterica is then further divided into six distinct subspecies (I, II, IIIa, IIIb, IV, and VI), based on biochemical differences. The genus Salmonella is further divided by serology into over 2,500 serovars using the Kauffman and White scheme (Popoff and LeMinor 2001). This classification scheme defines the serogroup according to expression of somatic lipopolysaccharide O antigens, and the serovar by expression of flagellar H antigens. Contained within the genus Salmonella are bacterial pathogens able to cause a spectrum of diseases in an array of different hosts and which are responsible for significant morbidity and mortality in both humans and animals. S. enterica subspecies I contains most species that cause disease in warm-blooded animals and includes examples of both promiscuous and host adapted pathotypes. We have generated reference whole genome sequences for the major human pathogenic serotypes of S. enterica and several that are important animal pathogens including S. Typhi, S. Typhimurium, S. Paratyphi A, S. Enteritidis, S. Gallinarum, S. Infantis, S. Hadar and S. Virchow. Within this collection we have defined the genomes of salmonellae able to infect a broad range of hosts including S. Typhimurium which causes self-limiting gastroenteritis in humans and a systemic infection in mice and those that are host restricted including S. Typhi which causes typhoid fever in humans. From these genomes we have shown patterns of evolution that have involved gene acquisition mediated by phage or other mobile genetic elements as well as functional gene loss (see above). We have also shown that some S. enterica serovars such as S. Gallinarum although restricted to chickens has only recently evolved, largely by genome degradation, from a broad host range serovar: S. Enteritidis. To extend our observations and understand the major themes that describe Salmonella evolution we are now sampling more broadly to look at more diverse serotypes and subspecies of S. enterica.

Data Downloads

• FTP site

• BLAST server

The Wellcome Trust Sanger Insitute is involved in several Salmonella sequencing projects.

Salmonella enterica Typhi Project

The Wellcome Trust Sanger Insitute pathogen genomics group was funded to sequence Salmonella Typhi strain CT18 in collaboration with Prof. Gordon Dougan. This strain is a highly pathogenic, multiple drug resistant strain isolated from a typhoid patient in Cho Quan Hospital, Ho Chi Minh City, Vietnam.

An additional 19 stains were then sequenced using both 454 and Illumina/Solexa rapid sequencing technologies.

Salmonella enterica Paratyphi A Project

The Wellcome Trust Sanger Insitute pathogen genomivs group was funded to sequence Salmonella Paratyphi A strain AKU_12601 in collaboration with Prof. Gordon Dougan.

Salmonella spp. comparative sequencing Project

The Sanger Institute extended its program of comparative Salmonella sequencing to include further serovars of S. enterica in collaboration with Prof. Gordon Dougan, Dr. Paul Barrow of the Institute for Animal Health, Compton, and Dr. Mark Achtman of the Max Planck Institute for Infection Biology, Berlin.

Published Genome Data

Salmonella enterica Typhi

The chromosome sequence is 4,809,037 bp in length with a G+C content of 52.09%, and was generated from 97,000 shotgun reads. There are 4,599 protein-coding genes (including 204 pseudogenes). Both the sequence and annotation have been deposited in the public databases with the accession number AL513382. In addition, there are two plasmids: pHCM1 (218,150 bp, 249 CDS) with the accession number AL513383 and pHCM2 (106,516 bp, 131 CDS) with the accession number AL513384.

Shotgun and assembly data from this project are available from our ftp site.

Salmonella enterica Paratyphi A

The genome is 4,581,797 bp in size and has a GC content of approximately 52.2%. There is also a plasmid of 212,711 bp. The completed chromosomal sequence and annotation is available from EMBL/GenBank with accession number FM200053. Similarly, the plasmid is available from EMBL/GenBank with accession number AM412236.

Shotgun and assembly data from this project are available from our ftp site.

Salmonella spp. comparative sequencing

Nine serovars have thus far been sequenced:

Published Serovars

S. enterica Enteritidis PT4 NCTC 13349

• Status: Published
• Assembly: 2 contigs >1kb (2 contigs >2kb); total size 4.686 Mb
• Shotgun: 68,660 reads totalling 48.605 Mb, theoretical genome coverage of 99.99%
• EMBL accession no.: AM933172

S. enterica Gallinarum 287/91 NCTC 13346

• Status: Published
• Assembly: 2 contigs >1kb (2 contigs >2kb); total size 4.747 Mb
• Shotgun: 80,266 reads totalling 58.710 Mb, theoretical genome coverage of 99.99%
• EMBL accession no.: AM933173

Salmonella bongori 12419 ATCC 43975

• Status: Finished
• Assembly: 1 contig >1kb (1 contig >2kb); total size 4.460 Mb
• Shotgun: 75,084 reads totalling 42.054 Mb, theoretical genome coverage of 99.99%
• EMBL accession no.: FR877557

S. enterica Typhimurium SL1344 NCTC 13347

• Status: Finished
• Assembly: 4 contigs >1kb (4 contigs >2kb); total size 5.067 Mb
• Shotgun: 81,802 reads totalling 38.198 Mb, theoretical genome coverage of 99.95%
• Chromosome: EMBL accession no.: FQ312003
• Plasmids: EMBL accession no.: HE654724, EMBL accession no.: HE654725, EMBL accession no.: HE654726

S. enterica Typhimurium D23580

• Status: Finished
• Assembly: 1 contigs >1kb (1 contigs >2kb); total size 4.879 Mb
• Shotgun: 89,080 reads totalling 56.194 Mb, theoretical genome coverage of 99.99%
• EMBL accession no.: FN424405

Finished Serovars

S. enterica Hadar

• Status: Finished
• Assembly: 3 contigs >1kb (3 contigs >2kb); total size 4.797 Mb
• Shotgun: 79,998 reads totalling 56.374 Mb, theoretical genome coverage of 99.99%

S. enterica Typhimurium DT104 NCTC 13348

• Status: Finished
• Assembly: 2 contigs >1kb (2 contigs >2kb); total size 5.028 Mb
• Shotgun: 76,534 reads totalling 54.807 Mb, theoretical genome coverage of 99.99%
• Preliminary annotation (gene prediction) in Artemis format and chromosome sequence in fasta format. Please Note: The preliminary annotation of the chromosome is based on the reverse complement of the original finished genome sequence.

Serovars In Progress

S. enterica Typhimurium DT2

• Status: Shotgun sequencing
• Assembly: 23 contigs >1kb (15 contigs >2kb); total size 4.983 Mb
• Shotgun: 76,073 reads totalling 50.381 Mb, theoretical genome coverage of 99.99%

Shotgun and assembly data from these projects are available from our ftp site.