Salmonella
Salmonella classification
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.
[Genome Research Limited]
The Wellcome Trust Sanger Insitute is involved in several Salmonella sequencing projects.
The Wellcome Trust Sanger Insitute pathogen genomics group was funded to sequence Salmonella Typhi strain CT18
in collaboration with . 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.
The Wellcome Trust Sanger Insitute pathogen genomivs group was funded to sequence Salmonella Paratyphi A
strain AKU_12601 in collaboration with .
The Sanger Institute extended its program of comparative Salmonella sequencing to include further serovars of
S. enterica in collaboration with , 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
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 . In addition, there are two
plasmids: pHCM1 (218,150 bp, 249 CDS) with the accession number
and pHCM2 (106,516 bp, 131
CDS) with the accession number .
Shotgun and assembly data from this project are available from our .
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 . Similarly,
the plasmid is available from EMBL/GenBank with accession number .
Shotgun and assembly data from this project are available from our .
Nine serovars have thus far been sequenced:
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%
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%
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%
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:
Plasmids: ,
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%
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%
prediction) in Artemis format and
in fasta format. Please
Note: The preliminary annotation of the chromosome is based on the reverse complement of the original finished
genome sequence.
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 .
SampleStrainRun Accession
SampleStrainRun Accession
SampleStrainRun Accession
SampleStrainRun Accession
SampleStrainRun Accession
BL, , C1468, ATCC9150/SARB42.
ATCC9150/SARB42
SampleStrainRun Accession
CDC-2703-76
CEIM 24450
CEIM 44833
CEIM 46049
CEIM 24682
CEIM 44992
CEIM 44847
CEIM 46082
CEIM 24682
CEIM 44992
SV: 6,14:e,n,z15:-
SampleStrainRun Accession
Salmonella Typhi WT174
Salmonella Typhi WT174
SampleStrainRun Accession
SampleStrainRun Accession
SampleStrainRun Accession
SampleStrainRun Accession
ty2 quails
ty2 quails
ty2 quails
SampleStrainRun Accession
SampleStrainRun Accession
SampleStrainRun Accession
SampleStrainRun Accession
IP33K / RKS4587 (SARB48)
IP2/88 / RKS4594 (SARB49)
NVSL6321 (SARB4)
CDC3327/54 (SARB6)
CDC3327/54 (SARB6)
CDC3327/54 (SARB6)
CDC277/68 (SARB69)
SampleStrainRun Accession
SampleStrainRun Accession
SampleStrainRun Accession
SampleStrainRun Accession
SampleStrainRun Accession
SampleStrainRun Accession
SampleStrainRun Accession
SampleStrainRun Accession
S paratyphi B
S paratyphi B
S paratyphi B
SampleStrainRun Accession
SampleStrainRun Accession
CDC 129-73
556-59/192
CDC 6117-70
ST 73/21 Ew
SampleStrainRun Accession
SampleStrainRun Accession
STM3246/94
MEXSALYUHS03-31
MEXSALMIPUS03-21
SampleStrainRun Accession
SampleStrainRun Accession
SampleStrainRun Accession
SampleStrainRun Accession
SampleStrainRun Accession
SampleStrainRun Accession
SampleStrainRun Accession
GBO1GB 125
GBO1GB 169
SampleStrainRun Accession
Banker type1
Banker type1
Banker type3
Banker type3
Banker Type6
Banker Type6
A103(ParaA)
A103(ParaA)
Banker Type4
Banker Type4
Banker type5
Banker type5
JW-BL13440
JW-BL14275
JW-BL23318
SampleStrainRun Accession
01-00493-2
SARB14_FB_1
99-02017-2
02-02908-2
SampleStrainRun Accession
09:0008951R
09:0009241R
09:MF0017524R
08:MF0017271R
08:MF0017711R
08:MF0018567
09:MF0002762R
09:MF0001707R
09:MF0008371R
09:MF0001194R
09:MF0009245R
09:MF0009695R
09:MF0010690R
09:MF17524R
09:MF0012014R
09:MF17642
01-00493-2
08:MF0013950
08:MF0010405
08:MF0010337R
08:MF0010724R
08:MF0016603
08:MF0017270R
08:MF0011083
08:0012690R
09:MF0013408R
09:MF17767
09:MF0014001R
09:MF0016552R
SampleStrainRun Accession
SampleStrainRun Accession
SampleStrainRun Accession
SampleStrainRun Accession
H07 016 0417
H07 166 0082
H07 182 0182
H07 230 0280
H07 234 0179
H07 246 0338
H07 276 0382
H07 338 0264
H07 394 0379
H07 246 0339
H07 362 0321
H07 474 0455
09CEB7133SAL
SampleStrainRun Accession
SampleStrainRun Accession
SampleStrainRun Accession
SampleStrainRun Accession
05: MB7981
08: MB3817
08: MB15580
08: MB16115
08:MF0010464R
08:MF0010697R
08:MF0011943R
08:MF0016491R
08:MF0018323R
09:MF0000575R
09:MF0005148R
09:MF0010306R
09:MF0011240R
09:MF0012323S
09:MF0018182R
09:MF0019755R
09:MF0021482R
09:MF0017735R
SampleStrainRun Accession
SampleStrainRun Accession
SampleStrainRun Accession
SampleStrainRun Accession
SampleStrainRun Accession
SampleStrainRun Accession
SampleStrainRun Accession
UI 21054/2
SampleStrainRun Accession
SampleStrainRun Accession
SampleStrainRun Accession
SampleStrainRun Accession
SampleStrainRun Accession
MM_SW824_14_2
MM_SW824_14_1
MM_SW824_14
MM_SW824_10
MM_SW824_7
MM_SW824_4
MM_SW824_1
MM_SW824_0
MM_PT4_14_2
MM_PT4_14_1
LB_B20062_14
LB_B20062_13
LB_B20062_10
LB_B20062_7
LB_B20062_4
LB_B20062_1
LB_B20062_0
LB_SW824_14_2
LB_SW824_14_1
LB_SW824_14
LB_SW824_13
LB_SW824_10
LB_SW824_7
LB_SW824_4
LB_SW824_1
LB_SW824_0
LB_PT4_14_2
LB_PT4_14_1
SampleStrainRun Accession
129-0238-M
129-0254-M
129-0230-K
129-0257-M
129-0303-M
129-0339-M
129-0268-M
129-0177-M
129-0327-M
129-0289-M
129-0242-M
01-10-004247
01-10-004247
SampleStrainRun Accession
Salmonella Typhi WT174
Salmonella Typhi WT174
Salmonella Typhi WT174
Salmonella Typhi WT174
Salmonella Typhi WT174
Salmonella Typhi WT174
Salmonella Typhi WT174
Salmonella Typhi WT174
Salmonella Typhi WT174
Salmonella Typhi WT174
Salmonella Typhi WT174
Salmonella Typhi WT174
Salmonella Typhi WT174
Salmonella Typhi WT174
Salmonella Typhi WT174
Salmonella Typhi WT174
Salmonella Typhi WT174
Salmonella Typhi WT174
Salmonella Typhi WT174
Salmonella Typhi WT174
Salmonella Typhi WT174
Salmonella Typhi WT174
Salmonella Typhi WT174
Salmonella Typhi WT174
Salmonella Typhi WT174
Salmonella Typhi WT174
Salmonella Typhi WT174
Salmonella Typhi WT174
Salmonella Typhi WT174
Salmonella Typhi WT174
Salmonella Typhi WT174
Salmonella Typhi WT174
Salmonella Typhi WT174
Salmonella Typhi WT174
Salmonella Typhi WT174
Salmonella Typhi WT174
Salmonella Typhi WT174
Salmonella Typhi WT174
Salmonella Typhi WT174
Salmonella Typhi WT174
Salmonella Typhi WT174
Salmonella Typhi WT174
Salmonella Typhi WT174
Salmonella Typhi WT174
Salmonella Typhi WT174
Salmonella Typhi WT174
Salmonella enterica serovar Typhi Ty2
Salmonella enterica serovar Typhi Ty2
Salmonella enterica serovar Typhi Ty2
Salmonella enterica serovar Typhi Ty2
Salmonella enterica serovar Typhi Ty2
Salmonella enterica serovar Typhi Ty2
Salmonella enterica serovar Typhi Ty2
Salmonella enterica serovar Typhi Ty2
Salmonella enterica serovar Typhi Ty2
Salmonella enterica serovar Typhi Ty2
Salmonella enterica serovar Typhi Ty2
Salmonella enterica serovar Typhi Ty2
Salmonella enterica serovar Typhi Ty2
Salmonella enterica serovar Typhi Ty2
Salmonella enterica serovar Typhi Ty2
Salmonella enterica serovar Typhi Ty2
Salmonella enterica serovar Typhi Ty2
Salmonella enterica serovar Typhi Ty2
Salmonella enterica serovar Typhi Ty2
Salmonella enterica serovar Typhi Ty2
Salmonella enterica serovar Typhi Ty2
Salmonella enterica serovar Typhi Ty2
Salmonella enterica serovar Typhi Ty2
Salmonella enterica serovar Typhi Ty2
Salmonella enterica serovar Typhi Ty2
Salmonella enterica serovar Typhi Ty2
Salmonella enterica serovar Typhi Ty2
Salmonella enterica serovar Typhi Ty2
Salmonella enterica serovar Typhi Ty2
Salmonella enterica serovar Typhi Ty2
Salmonella enterica serovar Typhi Ty2
Salmonella enterica serovar Typhi Ty2
Salmonella enterica serovar Typhi Ty2
Salmonella enterica serovar Typhi Ty2
Salmonella enterica serovar Typhi Ty2
Salmonella enterica serovar Typhi Ty2
Salmonella enterica serovar Typhimurium SL1344
Salmonella enterica serovar Typhimurium SL1344
Salmonella enterica serovar Typhimurium SL1344
Salmonella enterica serovar Typhimurium SL1344
SampleStrainRun Accession
SampleStrainRun Accession
SampleStrainRun Accession
SampleStrainRun Accession
SampleStrainRun Accession
SampleStrainRun Accession
SampleStrainRun Accession
UI 25522_2
SampleStrainRun Accession
SampleStrainRun Accession
SampleStrainRun Accession
SampleStrainRun Accession
SampleStrainRun Accession
SampleStrainRun Accession
SampleStrainRun Accession
SampleStrainRun Accession
SampleStrainRun Accession
SampleStrainRun Accession
SampleStrainRun Accession
SampleStrainRun Accession
SampleStrainRun Accession
Typhimurium
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Typhimurium
Typhimurium
SampleStrainRun Accession
SampleStrainRun Accession
Distinguishable epidemics of multidrug-resistant Salmonella Typhimurium DT104 in different hosts.
Mather AE, Reid SW, Maskell DJ, Parkhill J, Fookes MC, Harris SR, Brown DJ, Coia JE, Mulvey MR, Gilmour MW, Petrovska L, de Pinna E, Kuroda M, Akiba M, Izumiya H, Connor TR, Suchard MA, Lemey P, Mellor DJ, Haydon DT and Thomson NR
Science (New York, N.Y.)&2013;341;6153;1514-7
PUBMED: ; PMC: ; DOI:
A comparison of dense transposon insertion libraries in the Salmonella serovars Typhi and Typhimurium.
Barquist L, Langridge GC, Turner DJ, Phan MD, Turner AK, Bateman A, Parkhill J, Wain J and Gardner PP
Nucleic acids research&2013;41;8;4549-64
PUBMED: ; PMC: ; DOI:
Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa.
Okoro CK, Kingsley RA, Connor TR, Harris SR, Parry CM, Al-Mashhadani MN, Kariuki S, Msefula CL, Gordon MA, de Pinna E, Wain J, Heyderman RS, Obaro S, Alonso PL, Mandomando I, MacLennan CA, Tapia MD, Levine MM, Tennant SM, Parkhill J and Dougan G
Nature genetics&2012;44;11;1215-21
PUBMED: ; PMC: ; DOI:
The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium.
Kr&ger C, Dillon SC, Cameron AD, Papenfort K, Sivasankaran SK, Hokamp K, Chao Y, Sittka A, H&brard M, H&ndler K, Colgan A, Leekitcharoenphon P, Langridge GC, Lohan AJ, Loftus B, Lucchini S, Ussery DW, Dorman CJ, Thomson NR, Vogel J and Hinton JC
Proceedings of the National Academy of Sciences of the United States of America&2012;109;20;E1277-86
PUBMED: ; PMC: ; DOI:
Salmonella bongori provides insights into the evolution of the Salmonellae.
Fookes M, Schroeder GN, Langridge GC, Blondel CJ, Mammina C, Connor TR, Seth-Smith H, Vernikos GS, Robinson KS, Sanders M, Petty NK, Kingsley RA, B&umler AJ, Nuccio SP, Contreras I, Santiviago CA, Maskell D, Barrow P, Humphrey T, Nastasi A, Roberts M, Frankel G, Parkhill J, Dougan G and Thomson NR
PLoS pathogens&2011;7;8;e1002191
PUBMED: ; PMC: ; DOI:
Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype.
Kingsley RA, Msefula CL, Thomson NR, Kariuki S, Holt KE, Gordon MA, Harris D, Clarke L, Whitehead S, Sangal V, Marsh K, Achtman M, Molyneux ME, Cormican M, Parkhill J, MacLennan CA, Heyderman RS and Dougan G
Genome research&2009;19;12;2279-87
PUBMED: ; PMC: ; DOI:
Pseudogene accumulation in the evolutionary histories of Salmonella enterica serovars Paratyphi A and Typhi.
Holt KE, Thomson NR, Wain J, Langridge GC, Hasan R, Bhutta ZA, Quail MA, Norbertczak H, Walker D, Simmonds M, White B, Bason N, Mungall K, Dougan G and Parkhill J
BMC genomics&2009;10;36
PUBMED: ; PMC: ; DOI:
Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways.
Thomson NR, Clayton DJ, Windhorst D, Vernikos G, Davidson S, Churcher C, Quail MA, Stevens M, Jones MA, Watson M, Barron A, Layton A, Pickard D, Kingsley RA, Bignell A, Clark L, Harris B, Ormond D, Abdellah Z, Brooks K, Cherevach I, Chillingworth T, Woodward J, Norberczak H, Lord A, Arrowsmith C, Jagels K, Moule S, Mungall K, Sanders M, Whitehead S, Chabalgoity JA, Maskell D, Humphrey T, Roberts M, Barrow PA, Dougan G and Parkhill J
Genome research&2008;18;10;1624-37
PUBMED: ; PMC: ; DOI:
High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi.
Holt KE, Parkhill J, Mazzoni CJ, Roumagnac P, Weill FX, Goodhead I, Rance R, Baker S, Maskell DJ, Wain J, Dolecek C, Achtman M and Dougan G
Nature genetics&2008;40;8;987-93
PUBMED: ; PMC: ; DOI:
Multidrug-resistant Salmonella enterica serovar paratyphi A harbors IncHI1 plasmids similar to those found in serovar typhi.
Holt KE, Thomson NR, Wain J, Phan MD, Nair S, Hasan R, Bhutta ZA, Quail MA, Norbertczak H, Walker D, Dougan G and Parkhill J
Journal of bacteriology&2007;189;11;4257-64
PUBMED: ; PMC: ; DOI:
Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18.
Parkhill J, Dougan G, James KD, Thomson NR, Pickard D, Wain J, Churcher C, Mungall KL, Bentley SD, Holden MT, Sebaihia M, Baker S, Basham D, Brooks K, Chillingworth T, Connerton P, Cronin A, Davis P, Davies RM, Dowd L, White N, Farrar J, Feltwell T, Hamlin N, Haque A, Hien TT, Holroyd S, Jagels K, Krogh A, Larsen TS, Leather S, Moule S, O'Gaora P, Parry C, Quail M, Rutherford K, Simmonds M, Skelton J, Stevens K, Whitehead S and Barrell BG
Nature&2001;413;6858;848-52
PUBMED: ; DOI:
454 Sequencing
Related links
Data Use Statement
This sequencing centre plans on publishing the completed and annotated sequences in a
peer-reviewed journal as soon as possible. Permission of the principal investigator should be
obtained before publishing analyses of the sequence/open reading frames/genes on a chromosome or
genome scale. See our .
Sequencing enquiries
Please address all sequencing enquiries to:
Wellcome Trust Sanger Institute, Genome Research Limited (reg no. 2742969) is a charity registered in England with number 1021457
Last modified: Tue, 11 Nov :40 GMT}