Abstract
Progress in the study of Salmonella survival, colonization, and virulence has increased rapidly with the advent of complete genome sequencing and higher capacity assays for transcriptomic and proteomic analysis. Although many of these techniques have yet to be used to directly assay Salmonella growth on foods, these assays are currently in use to determine Salmonella factors necessary for growth in animal models including livestock animals and in in vitro conditions that mimic many different environments. As sequencing of the Salmonella genome and microarray analysis have revolutionized genomics and transcriptomics of salmonellae over the last decade, so are new high-throughput sequencing technologies currently accelerating the pace of our studies and allowing us to approach complex problems that were not previously experimentally tractable.
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Adams P, Fowler R et al. (1999) Defining protease specificity with proteomics: a protease with a dibasic amino acid recognition motif is regulated by a two-component signal transduction system in Salmonella. Electrophoresis 20(11):2241–2247
Adams P, Fowler R et al. (2001) Proteomic detection of PhoPQ-and acid-mediated repression of Salmonella motility. Proteomics 1(4):597–607
Adkins JN, Mottaz HM et al. (2006) Analysis of the Salmonella typhimurium proteome through environmental response toward infectious conditions. Mol Cell Proteomics 5(8):1450–1461
Aebersold R, Mann M (2003) Mass spectrometry-based proteomics. Nature 422(6928):198–207
Agudo D, Mendoza MT et al. (2004) A proteomic approach to study Salmonella typhi periplasmic proteins altered by a lack of the DsbA thiol: disulfide isomerase. Proteomics 4(2):355–363
Alausa KO, Montefiore D et al. (1977) Septicaemia in the tropics. A prospective epidemiological study of 146 patients with a high case fatality rate. Scand J Infect Dis 9(3):181–185
Alpuche-Aranda CM, Racoosin EL et al. (1994) Salmonella stimulate macrophage macropinocytosis and persist within spacious phagosomes. J Exp Med 179:601–608
Alpuche Aranda CM, Swanson JA et al. (1992) Salmonella typhimurium activates virulence gene transcription within acidified macrophage phagosomes. Proc Natl Acad Sci USA 89(21):10079–10083
Althouse C, Patterson S et al. (2003) Type 1 fimbriae of Salmonella enterica serovar Typhimurium bind to enterocytes and contribute to colonization of swine in vivo. Infect Immun 71(11):6446–6452
Altier C, Suyemoto M (1999) A recombinase-based selection of differentially expressed bacterial genes. Gene 240(1):99–106
Altier C, Suyemoto M et al. (2000) Regulation of Salmonella enterica serovar typhimurium invasion genes by csrA. Infect Immun 68(12):6790–6797
Andrews-Polymenis HL, Rabsch W et al. (2004) Host restriction of Salmonella enterica serotype Typhimurium pigeon isolates does not correlate with loss of discrete genes. J Bacteriol 186(9):2619–2628
Andrews-Polymenis HL, Santiviago C et al. (2009) Novel genetic tools for studying food borne Salmonella. Curr Opin Biotechnol 20:1–9
Ansong C, Yoon H et al. (2008) Proteomics analysis of the causative agent of typhoid fever. J Proteome Res 7(2):546–557
Ansong C, Yoon H et al. (2009) Global systems-level analysis of Hfq and SmpB deletion mutants in Salmonella: implications for virulence and global protein translation. PLoS One 4(3):e4809
Ansorge WJ (2009) Next-generation DNA sequencing techniques. N Biotechnol 25(4):195–203
Baba T, Ara T et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2:2006.0008
Badarinarayana V, Estep PW 3rd et al. (2001) Selection analyses of insertional mutants using subgenic-resolution arrays. Nat Biotechnol 19(11):1060–1065
Bajaj V, Lucas RL et al. (1996) Co-ordinate regulation of Salmonella typhimurium invasion genes by environmental and regulatory factors is mediated by control of hilA expression. Mol Microbiol 22(4):703–714
Baldwin DN, Salama NR (2007) Using genomic microarrays to study insertional/transposon mutant libraries. Methods Enzymol 421:90–110
Bar-Meir M, Raveh D et al. (2005) Non-Typhi Salmonella gastroenteritis in children presenting to the emergency department: characteristics of patients with associated bacteraemia. Clin Microbiol Infect 11:651–655
Bauer-Garland J, Frye JG et al. (2006) Transmission of Salmonella enterica serotype Typhimurium in poultry with and without antimicrobial selective pressure. J Appl Microbiol 101(6):1301–1308
Bäumler AJ, Kusters JG et al. (1994) Salmonella typhimurium loci involved in survival within macrophages. Infect Immun 62:1623–1630
Bearson SM, Bearson BL et al. (2006) Identification of Salmonella enterica serovar Typhimurium genes important for survival in the swine gastric environment. Appl Environ Microbiol 72(4):2829–2836
Bearson BL, Wilson L et al. (1998) A low pH-inducible, PhoPQ-dependent acid tolerance response protects Salmonella typhimurium against inorganic acid stress. J Bacteriol 180(9):2409–2417
Becker D, Selbach M et al. (2006) Robust Salmonella metabolism limits possibilities for new antimicrobials. Nature 440(7082):303–307
Bispham J, Tripathi BN et al. (2001) Salmonella pathogenicity island 2 influences both systemic salmonellosis and Salmonella-induced enteritis in calves. Infect Immun 69(1):367–377
Boddicker JD, Ledeboer NA et al. (2002) Differential binding to and biofilm formation on, HEp-2 cells by Salmonella enterica serovar Typhimurium is dependent upon allelic variation in the fimH gene of the fim gene cluster. Mol Microbiol 45(5):1255–1265
Bogomolnaya LM, Santiviago CA et al. (2008) ‘Form variation’ of the O12 antigen is critical for persistence of Salmonella Typhimurium in the murine intestine. Mol Microbiol 70(5):1105–1119
Bowe F, Lipps CJ et al. (1998) At least four percent of the Salmonella typhimurium genome is required for fatal infection of mice. Infect Immun 66:3372–3377
Brawn LC, Hayward RD et al. (2007) Salmonella SPI1 effector SipA persists after entry and cooperates with a SPI2 effector to regulate phagosome maturation and intracellular replication. Cell Host Microbe 1(1):63–75
Brent A, Oundo J et al. (2006) Salmonella bacteremia in Kenyan children. Pediatr Infect Dis J 25(3):230–236
Brown NF, Vallance BA et al. (2005) Salmonella pathogenicity island 2 is expressed prior to penetrating the intestine. PLoS Pathog 1(3):e32
Bumann D (2002) Examination of Salmonella gene expression in an infected mammalian host using the green fluorescent protein and two-colour flow cytometry. Mol Microbiol 43(5):1269–1283
Camilli A, Mekalanos JJ (1995) Use of recombinase gene fusions to identify Vibrio cholerae genes induced during infection. Mol Microbiol 18(4):671–683
Carnell SC, Bowen AJ et al. (2007) Role in virulence and protective efficacy in pigs of Salmonella enterica serovar Typhimurium secreted components identified by signature-tagged mutagenesis. Microbiology 153:1940–1952
Carrol ME, Jackett PS et al. (1979) Phagolysosome formation, cyclic adenosine 3′:5′-monophosphate and the fate of Salmonella typhimurium within mouse peritoneal macrophages. J Gen Microbiol 110(2):421–429
CDC (2005) Salmonella annual summary 2005. Department of Health and Human Services, Centers for Disease Control and Prevention, National Institute of Infectious Diseases
CDC (2008) Division of Bacterial and Mycotic Diseases, Disease listing: Salmonellosis.http://www.cdc.gov/salmonella
Chan K, Baker S et al. (2003) Genomic comparison of Salmonella enterica serovars and Salmonella bongori by use of an S. enterica serovar typhimurium DNA microarray. J Bacteriol 185(2):553–563
Chan K, Kim CC et al. (2005) Microarray-based detection of Salmonella enterica serovar Typhimurium transposon mutants that cannot survive in macrophages and mice. Infect Immun 73(9):5438–5449
Charles IG, Maskell DJ (2001) Transposon mediated differential hybridisation. International Patent Number WO2001/007651
Chaudhuri RR, Peters SE et al. (2009) Comprehensive identification of Salmonella enterica serovar typhimurium genes required for infection of BALB/c mice. PLoS Pathog 5(7):e1000529
Cheesbrough JS, Taxman BC et al. (1997) Clinical definition for invasive Salmonella infection in African children. Pediatr Infect Dis J 16(3):277–283
Chiu CH, Tang P et al. (2005) The genome sequence of Salmonella enterica serovar Choleraesuis, a highly invasive and resistant zoonotic pathogen. Nucleic Acids Res 33(5):1690–1698
Chowdhury SM, Shi L et al. (2009) A method for investigating protein-protein interactions related to Salmonella typhimurium pathogenesis. J Proteome Res 8(3):1504–1514
Cirillo DM, Valdivia RH et al. (1998) Macrophage-dependent induction of the Salmonella pathogenicity island 2 type III secretion system and its role in intracellular survival. Mol Microbiol 30(1):175–188
Clark MA, Hirst BH et al. (1998) Inoculum composition and Salmonella pathogenicity island 1 regulate M-cell invasion and epithelial destruction by Salmonella typhimurium. Infect Immun 66(2):724–731
Coldham NG, Woodward MJ (2004) Characterization of the Salmonella typhimurium proteome by semi-automated two-dimensional HPLC-mass spectrometry: detection of proteins implicated in multiple antibiotic resistance. J Proteome Res 3(3):595–603
Crawford RW, Rosales-Reyes R et al. (2010) Gallstones play a significant role in Salmonella ssp. gallbladder colonization and carriage. Proc Natl Acad Sci USA 107(9):4353–4358
Croucher NJ, Fookes MC et al. (2009) A simple method for directional transcriptome sequencing using Illumina technology. Nucleic Acids Res 37(22):e148
Crump JA, Luby SP et al. (2004) The global burden of typhoid fever. Bull World Health Organ 82(5):346–353
Datsenko KA, Wanner BL (2000) One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci USA 97(12):6640–6645
Deiwick J, Rappl C et al. (2002) Proteomic approaches to Salmonella Pathogenicity island 2 encoded proteins and the SsrAB regulon. Proteomics 2(6):792–799
Deng W, Liou SR et al. (2003) Comparative genomics of Salmonella enterica serovar Typhi strains Ty2 and CT18. J Bacteriol 185(7):2330–2337
Drecktrah D, Knodler LA et al. (2005) The Salmonella SPI1 effector SopB stimulates nitric oxide production long after invasion. Cell Microbiol 7(1):105–113
Drecktrah D, Knodler LA et al. (2007) Salmonella trafficking is defined by continuous dynamic interactions with the endolysosomal system. Traffic 8(3):212–225
Ellis HM, Yu D et al. (2001) High efficiency mutagenesis, repair, and engineering of chromosomal DNA using single-stranded oligonucleotides. Proc Natl Acad Sci USA 98(12):6742–6746
Encheva V, Wait R et al. (2005) Proteome analysis of serovars Typhimurium and Pullorum of Salmonella enterica subspecies I. BMC Microbiol 5:42
Encheva V, Wait R et al. (2007) Protein expression diversity amongst serovars of Salmonella enterica. Microbiology 153(Pt 12):4183–4193
Eriksson S, Lucchini S et al. (2003) Unravelling the biology of macrophage infection by gene expression profiling of intracellular Salmonella enterica. Mol Microbiol 47(1):103–118
Faucher SP, Porwollik S et al. (2006) Transcriptome of Salmonella enterica serovar Typhi within macrophages revealed through the selective capture of transcribed sequences. Proc Natl Acad Sci USA 103(6):1906–1911
Fields PI, Swanson RV, Haidaris CG, Heffron F (1986) Mutants of Salmonella typhimurium that cannot survive within the macrophage are avirulent. Proc Natl Acad Sci USA 83:5189–5193
Fink RC, Evans MR et al. (2007) FNR is a global regulator of virulence and anaerobic metabolism in Salmonella enterica serovar Typhimurium (ATCC 14028s). J Bacteriol 189(6):2262–2273
Flierl MA, Rittirsch D et al. (2007) Phagocyte-derived catecholamines enhance acute inflammatory injury. Nature 449(7163):721–725
Frye J, Karlinsey JE et al. (2006) Identification of new flagellar genes of Salmonella enterica serovar Typhimurium. J Bacteriol 188(6):2233–2243
Galán JE, Curtiss R 3rd (1989) Cloning and molecular characterization of genes whose products allow Salmonella typhimurium to penetrate tissue culture cells. Proc Natl Acad Sci USA 86:6383–6387
Galán JE, Ginocchio C et al. (1992) Molecular and functional characterization of the Salmonella invasion gene invA: homology of InvA to members of a new protein family. J Bacteriol 174:4338–4349
Garcia-Calderon CB, Casadesus J et al. (2007) Rcs and PhoPQ regulatory overlap in the control of Salmonella enterica virulence. J Bacteriol 189(18):6635–6644
Garcia Vescovi E, Soncini FC et al. (1996) Mg2+ as an extracellular signal: environmental regulation of Salmonella virulence. Cell 84(1):165–174
Geddes K, Cruz F et al. (2007) Analysis of cells targeted by Salmonella type III secretion in vivo. PLoS Pathog 3(12):e196
Geddes K, Worley M et al. (2005) Identification of new secreted effectors in Salmonella enterica serovar Typhimurium. Infect Immun 73(10):6260–6271
Gordon MA, Banda HT et al. (2002) Non-typhoidal Salmonella bacteraemia among HIV-infected Malawian adults: high mortality and frequent recrudescence. AIDS 16(12):1633–1641
Gordon MA, Walsh AL et al. (2001) Bacteraemia and mortality among adult medical admissions in Malawi – predominance of non-typhi salmonellae and Streptococcus pneumoniae. J Infect 42(1):44–49
Guina T, Yi EC et al. (2000) A PhoP-regulated outer membrane protease of Salmonella enterica serovar typhimurium promotes resistance to alpha-helical antimicrobial peptides. J Bacteriol 182(14):4077–4086
Gulig PA, Curtiss R (1987) Plasmid-associated virulence of Salmonella typhimurium. Infect Immun 1987:2891–2901
Gulig PA, Curtiss R 3rd (1988) Cloning and transposon insertion mutagenesis of virulence genes of the 100-kilobase plasmid of Salmonella typhimurium. Infect Immun 56(12):3262–3271
Gulig PA, Caldwell AL, Chiodo VA (1992) Identification, genetic analysis and DNA sequence of a 7.8-kb virulence region of the Salmonella typhimurium virulence plasmid. Mol Microbiol 6:1395–1411
Gulig PA, Doyle TJ (1993) The Salmonella typhimurium virulence plasmid increases the growth rate of Salmonellae in mice. Infect Immun 61:504–511
Gunn JS, Miller SI (1996) PhoP-PhoQ activates transcription of pmrAB, encoding a two-component regulatory system involved in Salmonella typhimurium antimicrobial peptide resistance. J Bacteriol 178(23):6857–6864
Gupta PK (2008) Single-molecule DNA sequencing technologies for future genomics research. Trends Biotechnol 26(11):602–611
Haneda T, Ishii Y et al. (2009) Genome-wide identification of novel genomic islands that contribute to Salmonella virulence in mouse systemic infection. FEMS Microbiol Lett 297(2):241–249
Haraga A, Ohlson MB et al. (2008) Salmonellae interplay with host cells. Nat Rev Microbiol 6:53–66
Hardt WD, Chen LM et al. (1998) S. typhimurium encodes an activator of Rho GTPases that induces membrane ruffling and nuclear responses in host cells. Cell 93(5):815–826
Harshey RM (2003) Bacterial motility on a surface: many ways to a common goal. Annu Rev Microbiol 57:249–273
Harshey RM, Matsuyama T (1994) Dimorphic transition in Escherichia coli and Salmonella typhimurium: surface-induced differentiation into hyperflagellate swarmer cells. Proc Natl Acad Sci USA 91(18):8631–8635
Heithoff DM, Conner CP et al. (1997) Bacterial infection as assessed by in vivo gene expression. Proc Natl Acad Sci USA 94(3):934–939
Hensel M, Shea JE et al. (1995) Simultaneous identification of bacterial virulence genes by negative selection. Science 269:400–403
Hensel M, Shea JE et al. (1997) Analysis of the boundaries of Salmonella pathogenicity island 2 and the corresponding chromosomal region of Escherichia coli K-12. J Bacteriol 179:1105–1111
Hensel M, Shea JE et al. (1998) Genes encoding putative effector proteins of the type III secretion system of Salmonella pathogenicity island 2 are required for bacterial virulence and proliferation in macrophages. Mol Microbiol 30(1):163–174
Hernandez LD, Hueffer K et al. (2004) Salmonella modulates vesicular traffic by altering phosphoinositide metabolism. Science 304(5678):1805–1807
Hinton JC, Hautefort I et al. (2004) Benefits and pitfalls of using microarrays to monitor bacterial gene expression during infection. Curr Opin Microbiol 7(3):277–282
Hisert KB, MacCoss M et al. (2005) A glutamate-alanine-leucine (EAL) domain protein of Salmonella controls bacterial survival in mice, antioxidant defence and killing of macrophages: role of cyclic diGMP. Mol Microbiol 56(5):1234–1245
Holt KE, Parkhill J et al. (2008) High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi. Nat Genet 40(8):987–993
Holt KE, Thomson NR et al. (2009) Pseudogene accumulation in the evolutionary histories of Salmonella enterica serovars Paratyphi A and Typhi. BMC Genomics 10:36
Hornick RB, Greisman SE et al. (1970a) Typhoid fever: pathogenesis and immunologic control. N Engl J Med 283(13):686–691
Hornick RB, Greisman SE et al. (1970b) Typhoid fever: pathogenesis and immunologic control. 2. N Engl J Med 283(14):739–746
Huang Y, Leming CL et al. (2007) Genome-wide screen of Salmonella genes expressed during infection in pigs, using in vivo expression technology. Appl Environ Microbiol 73(23):7522–7530
Jarvik T, Smillie C et al. (2010) Short-term signatures of evolutionary change in the Salmonella enterica serovar typhimurium 14028 genome. J Bacteriol 192(2):560–567
Jiang X, Rossanese OW et al. (2004) The related effector proteins SopD and SopD2 from Salmonella enterica serovar Typhimurium contribute to virulence during systemic infection of mice. Mol Microbiol 54(5):1186–1198
Jones BD, Ghori N et al. (1994) Salmonella typhimurium initiates murine infection by penetrating and destroying the specialized epithelial M cells of the Peyer’s patches. J Exp Med 180:15–23
Joseph B, Otta SK et al. (2001) Biofilm formation by Salmonella spp. on food contact surfaces and their sensitivity to sanitizers. Int J Food Microbiol 64(3):367–372
Julio SM, Heithoff DM et al. (2000) ssrA (tmRNA) plays a role in Salmonella enterica serovar Typhimurium pathogenesis. J Bacteriol 182(6):1558–1563
Kang MS, Besser TE et al. (2006) Identification of specific gene sequences conserved in contemporary epidemic strains of Salmonella enterica. Appl Environ Microbiol 72(11):6938–6947
Kankwatira AM, Mwafulirwa GA et al. (2004) Non-typhoidal Salmonella bacteraemia – an under-recognized feature of AIDS in African adults. Trop Doct 34(4):198–200
Karatzas KA, Randall LP et al. (2008) Phenotypic and proteomic characterization of multiply antibiotic-resistant variants of Salmonella enterica serovar Typhimurium selected following exposure to disinfectants. Appl Environ Microbiol 74(5):1508–1516
Karavolos MH, Spencer H et al. (2008) Adrenaline modulates the global transcriptional profile of Salmonella revealing a role in the antimicrobial peptide and oxidative stress resistance responses. BMC Genomics 9:458
Kariuki S, Revathi G et al. (2006) Characterisation of community acquired non-typhoidal Salmonella from bacteraemia and diarrhoeal infections in children admitted to hospital in Nairobi, Kenya. BMC Microbiol 6:101
Karlinsey JE (2007) Lambda-red genetic engineering in Salmonella enterica serovar Typhimurium. Methods Enzymol 421:199–209
Karzai AW, Susskind MM et al. (1999) SmpB, a unique RNA-binding protein essential for the peptide-tagging activity of SsrA (tmRNA). Embo J 18(13):3793–3799
Kim W, Killam T et al. (2003) Swarm-cell differentiation in Salmonella enterica serovar typhimurium results in elevated resistance to multiple antibiotics. J Bacteriol 185(10):3111–3117
Kingsley RA, Msefula CL et al. (2009) Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype. Genome Res 19(12):2279–2287
Klein JR, Fahlen TF et al. (2000) Transcriptional organization and function of invasion genes within Salmonella enterica serovar Typhimurium pathogenicity island 1, including the prgH, prgI, prgJ, prgK, orgA, orgB, and orgC genes. Infect Immun 68(6):3368–3376
Klumpp J, Fuchs TM (2007) Identification of novel genes in genomic islands that contribute to Salmonella typhimurium replication in macrophages. Microbiology 153(Pt 4):1207–1220
Korbel JO, Doerks T et al. (2005) Systematic association of genes to phenotypes by genome and literature mining. PLoS Biol 3(5):e134
Ku YW, McDonough SP et al. (2005) Novel attenuated Salmonella enterica serovar Choleraesuis strains as live vaccine candidates generated by signature-tagged mutagenesis. Infect Immun 73(12):8194–8203
Kukral AM, Strauch KL et al. (1987) Genetic analysis in Salmonella typhimurium with a small collection of randomly spaced insertions of transposon Tn10 delta 16 delta 17. J Bacteriol 169(5):1787–1793
Langridge GC, Phan MD et al. (2009) Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants. Genome Res 19(12):2308–2316
Lawley TD, Chan K et al. (2006) Genome-wide screen for Salmonella genes required for long-term systemic infection of the mouse. PLoS Pathog 2(2):e11
Ledeboer NA, Frye JG et al. (2006) Salmonella enterica serovar Typhimurium requires the Lpf, Pef, and Tafi fimbriae for biofilm formation on HEp-2 tissue culture cells and chicken intestinal epithelium. Infect Immun 74(6):3156–3169
Ledeboer NA, Jones BD (2005) Exopolysaccharide sugars contribute to biofilm formation by Salmonella enterica serovar typhimurium on HEp-2 cells and chicken intestinal epithelium. J Bacteriol 187(9):3214–3226
Lewis C, Skovierova H et al. (2009) Salmonella enterica Serovar Typhimurium HtrA: regulation of expression and role of the chaperone and protease activities during infection. Microbiology 155(Pt 3):873–881
Lichtensteiger CA, Vimr ER (2003) Systemic and enteric colonization of pigs by a hilA signature-tagged mutant of Salmonella choleraesuis. Microb Pathog 34(3):149–154
Liu W-Q, Feng Y, Wang Y, Zou Q-H, Chen F, Guo J-T, Peng Y-H, Jin Y, Li Y-G, Hu S-N, Johnston RN, Liu G-R, Liu S-L (2009) Salmonella paratyphi C: Genetic Divergence from Salmonella choleraesuis and Pathogenic Convergence with Salmonella typhi. PLoS ONE 4(2):e4510
Lodge J, Douce GR et al. (1995) Biological and genetic characterization of TnphoA mutants of Salmonella typhimurium TML in the context of gastroenteritis. Infect Immun 63(3):762–769
MacLean D, Jones JD et al. (2009) Application of ‘next-generation’ sequencing technologies to microbial genetics. Nat Rev Microbiol 7(4):287–296
Mahan MJ, Slauch JM et al. (1993) Selection of bacterial virulence genes that are specifically induced in host tissues. Science 259(5095):686–688
Mahan MJ, Tobias JW et al. (1995) Antibiotic-based selection for bacterial genes that are specifically induced during infection of a host. Proc Natl Acad Sci USA 92(3):669–673
Manes NP, Gustin JK et al. (2007) Targeted protein degradation by Salmonella under phagosome-mimicking culture conditions investigated using comparative peptidomics. Mol Cell Proteomics 6(4):717–727
Mardis ER (2008) Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 9:387–402
Mariconda S, Wang Q et al. (2006) A mechanical role for the chemotaxis system in swarming motility. Mol Microbiol 60(6):1590–1602
McClelland M, Sanderson KE et al. (2001) Complete genome sequence of Salmonella enterica serovar Typhimurium LT2. Nature 413(6858):852–856
McClelland M, Sanderson KE et al. (2004) Comparison of genome degradation in Paratyphi A and Typhi, human-restricted serovars of Salmonella enterica that cause typhoid. Nat Genet 36:1268–1274
Mead PS, Slutsker L et al. (1999) Food-related illness and death in the United States. Emerg Infect Dis 5(5):607–625
Merighi M, Ellermeier CD et al. (2005) Resolvase-in vivo expression technology analysis of the Salmonella enterica serovar Typhimurium PhoP and PmrA regulons in BALB/c mice. J Bacteriol 187(21):7407–7416
Miao EA, Miller SI (2000) A conserved amino acid sequence directing intracellular type III secretion by Salmonella typhimurium. Proc Natl Acad Sci USA 97(13):7539–7544
Miller SI (1991) PhoP/PhoQ: macrophage-specific modulators of Salmonella virulence? Mol Microbiol 5(9):2073–2078
Miller SI, Kukral AM et al. (1989a) A two-component regulatory system (phoP phoQ) controls Salmonella typhimurium virulence. Proc Natl Acad Sci USA 86(13):5054–5058
Miller I, Maskell D et al. (1989b) Isolation of orally attenuated Salmonella typhimurium following TnphoA mutagenesis. Infect Immun 57(9):2758–2763
Molero C, Rodriguez-Escudero I et al. (2009) Addressing the effects of Salmonella internalization in host cell signaling on a reverse-phase protein array. Proteomics 9(14):3652–3665
Monack DM, Bouley DM et al. (2004) Salmonella typhimurium persists within macrophages in the mesenteric lymph nodes of chronically infected Nramp1+/+ mice and can be reactivated by IFNgamma neutralization. J Exp Med 199(2):231–241
Morgan E, Campbell JD et al. (2004) Identification of host-specific colonization factors of Salmonella enterica serovar Typhimurium. Mol Microbiol 54(6):994–1010
Morozova O, Marra MA (2008) Applications of next-generation sequencing technologies in functional genomics. Genomics 92(5):255–264
Mottaz-Brewer HM, Norbeck AD et al. (2008) Optimization of proteomic sample preparation procedures for comprehensive protein characterization of pathogenic systems. J Biomol Tech 19(5):285–295
Nagalakshmi U, Wang Z et al. (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320(5881):1344–1349
Navarre WW, Porwollik S et al. (2006) Selective silencing of foreign DNA with low GC content by the H-NS protein in Salmonella. Science 313(5784):236–238
Nunn BL, Shaffer SA et al. (2006) Comparison of a Salmonella typhimurium proteome defined by shotgun proteomics directly on an LTQ-FT and by proteome pre-fractionation on an LCQ-DUO. Brief Funct Genomic Proteomic 5(2):154–168
Osman KM, Ali MM et al. (2009) Comparative proteomic analysis on Salmonella Gallinarum and Salmonella Enteritidis exploring proteins that may incorporate host adaptation in poultry. J Proteomics 72(5):815–821
Padalon-Brauch G, Hershberg R et al. (2008) Small RNAs encoded within genetic islands of Salmonella typhimurium show host-induced expression and role in virulence. Nucleic Acids Res 36(6):1913–1927
Pang T, Bhutta ZA et al. (1995) Typhoid fever and other salmonellosis: a continuing challenge. Trends Microbiol 3(7):253–255
Parkhill J, Dougan G et al. (2001) Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18. Nature 413(6858):848–852
Patel JC, Galan JE (2006) Differential activation and function of Rho GTPases during Salmonella-host cell interactions. J Cell Biol 175(3):453–463
Patel JC, Galan JE (2008) Investigating the function of Rho family GTPases during Salmonella/host cell interactions. Methods Enzymol 439:145–158
Perkins TT, Kingsley RA et al. (2009) A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi. PLoS Genet 5(7):e1000569
Porwollik S, Boyd EF et al. (2004) Characterization of Salmonella enterica subspecies I genovars by use of microarrays. J Bacteriol 186(17):5883–5898
Porwollik S, Santiviago CA et al. (2005) Differences in gene content between Salmonella enterica serovar Enteritidis isolates and comparison to closely related serovars Gallinarum and Dublin. J Bacteriol 187(18):6545–6555
Prouty AM, Gunn JS (2003) Comparative analysis of Salmonella enterica serovar Typhimurium biofilm formation on gallstones and on glass. Infect Immun 71(12):7154–7158
Prouty AM, Schwesinger WH et al. (2002) Biofilm formation and interaction with the surfaces of gallstones by Salmonella spp. Infect Immun 70(5):2640–2649
Rabsch W, Tschape H et al. (2001) Non-typhoidal salmonellosis: emerging problems. Microbes Infect 3(3):237–247
Raffatellu M, Santos RL et al. (2008) Simian immunodeficiency virus-induced mucosal interleukin-17 deficiency promotes Salmonella dissemination from the gut. Nat Med 14:4
Raghunathan A, Reed J et al. (2009) Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction. BMC Syst Biol 3:38
Rappl C, Deiwick J et al. (2003) Acidic pH is required for the functional assembly of the type III secretion system encoded by Salmonella pathogenicity island 2. FEMS Microbiol Lett 226(2):363–372
Rathman M, Sjaastad MD et al. (1996) Acidification of phagosomes containing Salmonella typhimurium in murine macrophages. Infect Immun 64(7):2765–2773
Rech EL, De Bem AR et al. (1996) Biolistic-mediated gene expression in guinea pigs and cattle tissues in vivo. J Med Biol Res 29(10):1265–1267
Rediers H, Rainey PB et al. (2005) Unraveling the secret lives of bacteria: use of in vivo expression technology and differential fluorescence induction promoter traps as tools for exploring niche-specific gene expression. Microbiol Mol Biol Rev 69(2):217–261
Reen FJ, Boyd EF et al. (2005) Genomic comparisons of Salmonella enterica serovar Dublin, Agona, and Typhimurium strains recently isolated from milk filters and bovine samples from Ireland, using a Salmonella microarray. Appl Environ Microbiol 71(3):1616–1625
Richter-Dahlfors A, Buchan AMJ et al. (1997) Murine salmonellosis studied by confocal microscopy: Salmonella typhimurium resides intracellularly inside macrophages and exerts a cytotoxic effect on phagocytes in vivo. J Exp Med 186(4):569–580
Rodland KD, Adkins JN et al. (2008) Use of high-throughput mass spectrometry to elucidate host-pathogen interactions in Salmonella. Future Microbiol 3(6):625–634
Rogers LD, Kristensen AR et al. (2008) Identification of cognate host targets and specific ubiquitylation sites on the Salmonella SPI-1 effector SopB/SigD. J Proteomics 71(1):97–108
Roumagnac P, Weill FX et al. (2006) Evolutionary history of Salmonella typhi. Science 314(5803):1301–1304
Santiviago C, Reynolds MM et al. (2009) Array-based analysis of pools of Salmonella targeted deletion mutants identifies novel genes under selection during infection. PLoS Pathog 5(7):e1000477
Sassetti CM, Boyd DH et al. (2001) Comprehensive identification of conditionally essential genes in mycobacteria. Proc Natl Acad Sci USA 98(22):12712–12717
Sawitzke JA, Thomason LC et al. (2007) Recombineering: in vivo genetic engineering in E. coli, S. enterica, and beyond. Methods Enzymol 421:171–199
Schmidt F, Schmid M et al. (2009) Assembling proteomics data as a prerequisite for the analysis of large scale experiments. Chem Cent J 3(1):2
Shah DH, Lee MJ et al. (2005) Identification of Salmonella gallinarum virulence genes in a chicken infection model using PCR-based signature-tagged mutagenesis. Microbiology 151(Pt 12):3957–3968
Shea JE, Hensel M et al. (1996) Identification of a virulence locus encoding a second type III secretion system in Salmonella typhimurium. Proc Natl Acad Sci USA 93:2593–2597
Shelobolina ES, Sullivan SA et al. (2004) Isolation, characterization, and U(VI)-reducing potential of a facultatively anaerobic, acid-resistant bacterium from low-pH, nitrate- and U(VI)-contaminated subsurface sediment and description of Salmonella subterranea sp. nov. Appl Environ Microbiol 70(5):2959–2965
Shi L, Adkins JN et al. (2006) Proteomic analysis of Salmonella enterica serovar typhimurium isolated from RAW 264.7 macrophages: identification of a novel protein that contributes to the replication of serovar typhimurium inside macrophages. J Biol Chem 281(39):29131–29140
Shi L, Chowdhury SM et al. (2009) Proteomic investigation of the time course responses of RAW 264.7 macrophages to infection with Salmonella enterica. Infect Immun 77(8):3227–3233
Sittka A, Lucchini S et al. (2008) Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq. PLoS Genet 4(8):e1000163
Sittka A, Pfeiffer V et al. (2007) The RNA chaperone Hfq is essential for the virulence of Salmonella typhimurium. Mol Microbiol 63(1):193–217
Sonck KA, Kint G et al. (2009) The proteome of Salmonella Typhimurium grown under in vivo-mimicking conditions. Proteomics 9(3):565–579
Stanley TL, Ellermeier CD et al. (2000) Tissue-specific gene expression identifies a gene in the lysogenic phage Gifsy-1 that affects Salmonella enterica serovar typhimurium survival in Peyer’s patches. J Bacteriol 182(16):4406–4413
Steele-Mortimer O, Meresse S et al. (1999) Biogenesis of Salmonella typhimurium-containing vacuoles in epithelial cells involves interactions with the early endocytic pathway. Cell Microbiol 1(1):33–49
Surette MG, Miller MB et al. (1999) Quorum sensing in Escherichia coli, Salmonella typhimurium, and Vibrio harveyi: a new family of genes responsible for autoinducer production. Proc Natl Acad Sci USA 96(4):1639–1644
Swords WE, Cannon BM et al. (1997) Avirulence of LT2 strains of Salmonella typhimurium results from a defective rpoS gene. Infect Immun 65(6):2451–2453
Thompson A, Rolfe MD et al. (2006) The bacterial signal molecule, ppGpp, mediates the environmental regulation of both the invasion and intracellular virulence gene programs of Salmonella. J Biol Chem 281(40):30112–30121
Thomson NR, Clayton DJ et al. (2008) Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways. Genome Res 18(10):1624–1637
Toguchi A, Siano M et al. (2000) Genetics of swarming motility in Salmonella enterica serovar typhimurium: critical role for lipopolysaccharide. J Bacteriol 182(22):6308–6321
Tsolis RM, Townsend SM et al. (1999) Identification of a putative Salmonella enterica serotype typhimurium host range factor with homology to IpaH and YopM by signature-tagged mutagenesis. Infect Immun 67(12):6385–6393
Turner AK, Lovell A et al. (1998) Identification of Salmonella typhimurium genes required for colonization of the chicken alimentary tract and for virulence in newly hatched chicks. Infect Immun 66:2099–2106
Typas A, Nichols RJ et al. (2008) High-throughput, quantitative analyses of genetic interactions in E. coli. Nat Methods 5(9):781–787
Valdivia RH, Falkow S (1996) Bacterial genetics by flow cytometry: rapid isolation of Salmonella typhimurium acid-inducible promoters by differential fluorescence induction. Mol Microbiol 22(2):367–378
Valdivia RH, Falkow S (1997) Fluorescence-based isolation of bacterial genes expressed within host cells. Science 277(5334):2007–2011
Valentin-Hansen P, Eriksen M et al. (2004) The bacterial Sm-like protein Hfq: a key player in RNA transactions. Mol Microbiol 51(6):1525–1533
Vernikos GS, Parkhill J (2006) Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands. Bioinformatics 22(18):2196–2203
Voetsch AC, Van Gilder TJ et al. (2004) FoodNet estimate of the burden of illness caused by nontyphoidal Salmonella infections in the United States. Clin Infect Dis 38(Suppl 3):S127–S134
Wang Q, Frye JG et al. (2004) Gene expression patterns during swarming in Salmonella typhimurium: genes specific to surface growth and putative new motility and pathogenicity genes. Mol Microbiol 52(1):169–187
Wang Q, Mariconda S et al. (2006) Uncovering a large set of genes that affect surface motility in Salmonella enterica serovar Typhimurium. J Bacteriol 188(22):7981–7984
Waterman SR, Holden DW (2003) Functions and effectors of the Salmonella pathogenicity island 2 type III secretion system. Cell Microbiol 5(8):501–511
Wilhelm BT, Marguerat S et al. (2008) Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature 453(7199):1239–1243
Winterberg KM, Reznikoff WS (2007) Screening transposon mutant libraries using full-genome oligonucleotide microarrays. Methods Enzymol 421:110–125
Wolters DA, Washburn MP et al. (2001) An automated multidimensional protein identification technology for shotgun proteomics. Anal Chem 73(23):5683–5690
Worley MJ, Ching KH et al. (2000) Salmonella SsrB activates a global regulon of horizontally acquired genes. Mol Microbiol 36(3):749–761
Worley MJ, Nieman GS et al. (2006) Salmonella typhimurium disseminates within its host by manipulating the motility of infected cells. Proc Natl Acad Sci USA 103(47):17915–17920
Yu D, Ellis HM et al. (2000) An efficient recombination system for chromosome engineering in Escherichia coli. Proc Natl Acad Sci USA 97(11):5978–5983
Zhang S, Adams LG et al. (2003a) Secreted effector proteins of Salmonella enterica serotype Typhimurium elicit host-specific chemokine profiles in animal models of typhoid fever and enterocolitis. Infect Immun 71:4795–4803
Zhang CG, Chromy BA et al. (2005) Host-pathogen interactions: a proteomic view. Expert Rev Proteomics 2(2):187–202
Zhang S, Kingsley RA et al. (2003b) Molecular pathogenesis of Salmonella enterica serotype typhimurium-induced diarrhea. Infect Immun 71(1):1–12
Zhang A, Wassarman KM et al. (2003c) Global analysis of small RNA and mRNA targets of Hfq. Mol Microbiol 50(4):1111–1124
Zhou Z, Ribeiro AA et al. (2001) Lipid A modifications in polymyxin-resistant Salmonella typhimurium: PMRA-dependent 4-amino-4-deoxy-L-arabinose, and phosphoethanolamine incorporation. J Biol Chem 276(46):43111–43121
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Canals, R., McClelland, M., Santiviago, C.A., Andrews-Polymenis, H. (2011). Genomics of Salmonella Species. In: Wiedmann, M., Zhang, W. (eds) Genomics of Foodborne Bacterial Pathogens. Food Microbiology and Food Safety. Springer, New York, NY. https://doi.org/10.1007/978-1-4419-7686-4_7
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