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Optical genetic mapping defines regions of chromosomal variation in serovars of S. enterica subsp. enterica of concern for human and animal health

  • M. P. SAUNDERS (a1) (a2), G. WU (a1), M. ABUOUN (a1), Z. PAN (a1) (a2), M. ANJUM (a1) and M. J. WOODWARD (a1)...

Infections involving Salmonella enterica subsp. enterica serovars have serious animal and human health implications; causing gastroenteritis in humans and clinical symptoms, such as diarrhoea and abortion, in livestock. In this study an optical genetic mapping technique was used to screen 20 field isolate strains from four serovars implicated in disease outbreaks. The technique was able to distinguish between the serovars and the available sequenced strains and group them in agreement with similar data from microarrays and PFGE. The optical maps revealed variation in genome maps associated with antimicrobial resistance and prophage content in S. Typhimurium, and separated the S. Newport strains into two clear geographical lineages defined by the presence of prophage sequences. The technique was also able to detect novel insertions that may have had effects on the central metabolism of some strains. Overall optical mapping allowed a greater level of differentiation of genomic content and spatial information than more traditional typing methods.

Corresponding author
*Author for correspondence: Dr M. J. Woodward, Department of Food and Environmental Safety (FES), Veterinary Laboratories Agency (Weybridge), Addlestone, Surrey, KT15 3NB, UK. (Email:
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1.Plym Forshell L, Wierup M. Salmonella contamination: a significant challenge to the global marketing of animal food products. Revue Scientifique et Technique 2006; 25: 541554.
2.Mead PS, et al. Food related illness and death in the United States. Emerging Infectious Diseases 1999; 5: 607625.
3.Voetsch AC, et al. FoodNet estimate of the burden of illness caused by nontyphoidal Salmonella infections in the United States. Clinical Infectious Diseases 2004; 38: 127134.
4.Lahuerta A, Helwigh B, Makela P. Zoonoses in Europe: distribution and trends – the EFSA-ECDC Community Summary Report 2008. European Surveillance; 15: 19476.
5.Popoff MY, Bockemühl J, Gheesling LL.Antigenic formulas of the Salmonella serovars, World Health Organisation Collaborating Centre for Reference and Research on Salmonella, Pasteur Institute, 2001.
6.HPA.Salmonella in humans (excluding S. Typhi and S. Paratyphi), 2008 ( ?p=1191942172078). Accessed 2 February 2010.
7.Rodrigue DC, Tauxe RV, Rowe B. International increase in Salmonella enteritidis: a new pandemic? Epidemiology and Infection 1990; 105: 2127.
8.Gupta A, et al. Emergence of multidrug-resistant Salmonella enterica serotype Newport infections resistant to expanded-spectrum cephalosporins in the United States. Journal of Infectious Diseases 2003; 188: 17071716.
9.CDC. Preliminary FoodNet Data on the incidence of infection with pathogens transmitted commonly through food – 10 States, 2008. Morbidity and Mortality Weekly Report 2009; 58: 333337.
10.Defra.Salmonella in livestock production in GB, 2007. Veterinary Laboratories Agency, Department of Environment, Food and Rural Affairs.
11.Karama M, Gyles CL.Methods for genotyping verotoxin-producing Escherichia coli. Zoonoses and Public Health. Published online: 13 November 2009. doi:10.1111/j.1863-2378.2009.01259.x
12.Ribot EM, et al. Standardization of pulsed-field gel electrophoresis protocols for the subtyping of Escherichia coli O157:H7, Salmonella, and Shigella for PulseNet. Foodborne Pathogens and Disease 2006; 3: 5967.
13.Porwollik S, et al. Characterization of Salmonella enterica subspecies I genovars by use of microarray. Journal of Bacteriology 2004; 186: 58835898.
14.Chan K, et al. Genomic comparison of Salmonella enterica serovars and Salmonella bongori by use of an S. enterica serovar Typhimurium DNA microarray. Journal of Bacteriology 2003; 185: 553563.
15.Anjum MF, et al. Identification of core and variable components of the Salmonella enterica subspecies I genome by microarray. Infection and Immunity 2005; 73: 78947905.
16.Lim A, et al. Shotgun optical maps of the whole Escherichia coli O157:H7 genome. Genome Research 2001; 11: 15841593.
17.Dougan G, Barrow P, Achtman M.S. enterica Typhimurium DT104 NCTC 13348 ( Accessed 30 January 2010.
18.Zhou S, et al. Single-molecule approach to bacterial genomic comparisons via optical mapping. Journal of Bacteriology 2004; 186: 77737782.
19.Hermans APHM, et al. Identification of novel Salmonella enterica serovar Typhimurium DT104 specific prophage and nonprophage chromosomal sequences among serovar Typhimurium Isolates by genomic subtractive hybridization. Applied and Environmental Microbiology 2005; 71: 49794985.
20.Cooke FJ, et al. Prophage sequences defining hot spots of genome variation in Salmonella enterica serovar Typhimurium can be used to discriminate between field isolates. Journal of Clinical Microbiology 2007; 45: 25902598.
21.Boyd D, et al. Complete nucleotide sequence of a 43-kilobase genomic island associated with the multidrug resistance region of Salmonella enterica serovar Typhimurium DT104 and its identification in phage type DT120 and serovar Agona. Journal of Bacteriology 2001; 183: 57255732.
22.Brüssow H, Canchaya C, Hardt WD. Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion. Microbiology and Molecular Biology Reviews 2004; 68: 560602.
23.Ravel J, et al. Salmonella enterica subsp. enterica serovar Newport str. SL254. Direct Submission, NCBI Genome Project, 2008.
24.Pan Z, et al. Identification of genetic and phenotypic differences associated with prevalent and non-prevalent Salmonella Enteritidis phage types: analysis of variation in amino acid transport. Microbiology 2009; 155: 32003213.
25.Boyd DA, et al. Salmonella genomic island 1 (SGI1), variant SGI1-I, and new variant SGI1-O in Proteus mirabilis clinical and food isolates from China. Antimicrobial Agents and Chemotherapy 2008; 52: 340344.
26.Levings RS, et al. SGI2, a relative of Salmonella genomic island SGI1 with an independent origin. Antimicrobial Agents and Chemotherapy 2008; 52: 25292537.
27.Mulvey MR, et al. The genetics of Salmonella genomic island 1. Microbes and Infection 2006; 8: 19151922.
28.Doublet B, et al. Secondary chromosomal attachment site and tandem integration of the mobilizable Salmonella genomic island 1. PLoS ONE 2008; 3: e2060c.
29.Brown MR, Kornberg A. Inorganic polyphosphate in the origin and survival of species. Proceedings of the National Academy of Sciences USA 2004; 101: 1608516087.
30.Price-Carter M, et al. Polyphosphate kinase protects Salmonella enterica from weak organic acid stress. Journal of Bacteriology 2005; 187: 30883099.
31.Kuroda A, et al. Inorganic polyphosphate kinase is required to stimulate protein degradation and for adaptation to amino acid starvation in Escherichia coli. Proceedings of the National Academy of Sciences USA 1999; 96: 1426414269.
32.Jermyn WS, Boyd EF. Characterization of a novel Vibrio pathogenicity island (VPI-2) encoding neuraminidase (nanH) among toxigenic Vibrio cholerae isolates. Microbiology 2002; 148: 36813693.
33.Figueroa-Bossi N, et al. Variable assortment of prophages provides a transferable repertoire of pathogenic determinants in Salmonella. Molecular Microbiology 2001; 39: 260271.
34.Wu G, et al. Epidemic multidrug-resistant (MDR-AmpC) Salmonella enterica serovar Newport strains contain three phage regions and a MDR resistance plasmid. Environmental Microbiology Reports 2009; 2: 228235.
35.Figueroa-Bossi N, Bossi L. Inducible prophages contribute to Salmonella virulence in mice. Molecular Microbiology 1999; 33: 167176.
36.Jubelin G, et al. CpxR/OmpR interplay regulates curli gene expression in response to osmolarity in Escherichia coli. Journal of Bacteriology 2005; 187: 20382049.
37.Sun S, et al. Contribution of gene amplification to evolution of increased antibiotic resistance in Salmonella Typhimurium. Genetics 2009; 182: 11831195.
38.Humphreys S, et al. Role of the two-component regulator CpxAR in the virulence of Salmonella enterica serotype Typhimurium. Infection and Immunity 2004; 72: 46544661.
39.Carlin A, et al. The ars operon of Escherichia coli confers arsenical and antimonial resistance. Journal of Bacteriology 1995; 177: 981986.
40.Lan R, Reeves PR, Octavia S. Population structure, origins and evolution of major Salmonella enterica clones. Infection, Genetics and Evolution 2009; 9: 996–1005.
41.Ravel J, et al. Complete genome of Salmonella Dublin strain CT_02021853. Direct Submission, NCBI Genome Project, 2008.
42.Thomson NR, et al. Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways. Genome Research 2008; 18: 16241637.
43.McClelland M, et al. Complete genome sequence of Salmonella enterica serovar Typhimurium LT2. Nature 2001; 413: 852856.
44.Ravel J, et al. Complete genome of Salmonella Agona strain SL483. Direct Submission, NCBI Genome Project, 2008.
45.McClelland M, et al. Salmonella enterica subsp. enterica serovar Paratyphi B str. SPB7. Direct Submission, NCBI Genome Project, 2007.
46.Ravel J, et al. Complete genome of Salmonella Schwarzengrund strain CVM19633. Direct Submission, NCBI Genome Project, 2008.
47.Chiu CH, et al. The genome sequence of Salmonella enterica serovar Choleraesuis, a highly invasive and resistant zoonotic pathogen. Nucleic Acids Research 2005; 33: 16901698.
48.Ravel J, et al. Complete genome of Salmonella Heidelberg strain SL476. Direct Submission, NCBI Genome Project, 2008.
49.Holt KE, et al. Multidrug-resistant Salmonella enterica serovar Paratyphi A harbors IncHI1 plasmids similar to those found in serovar Typhi. Journal of Bacteriology 2007; 189: 42574264.
50.McClelland M, et al. Comparison of genome degradation in Paratyphi A and Typhi, human-restricted serovars of Salmonella enterica that cause typhoid. Nature Genetics 2004; 36: 12681274.
51.Deng W, et al. Comparative genomics of Salmonella enterica serovar Typhi strains Ty2 and CT18. Journal of Bacteriology 2003; 185: 23302337.
52.Parkhill J, et al. Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18. Nature 2001; 413: 848852.
53.McClelland M, et al. Salmonella enterica subsp. Arizonae serovar 62:z4,z23:--. Direct Submission, NCBI Genome Project, 2007.
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