Skip to main content
SpringerLink
Log in

Genomics of Escherichia and Shigella

  • Chapter
  • First Online:
Genomics of Foodborne Bacterial Pathogens

Part of the book series: Food Microbiology and Food Safety ((FMFS))

Abstract

The laboratory workhorse Escherichia coli K-12 is among the most intensively studied living organisms on earth, and this single strain serves as the model system behind much of our understanding of prokaryotic molecular biology. Dense genome sequencing and recent insightful comparative analyses are making the species E. coli, as a whole, an emerging system for studying prokaryotic population genetics and the relationship between system-scale, or genome-scale, molecular evolution and complex traits like host range and pathogenic potential. Genomic perspective has revealed a coherent but dynamic species united by intraspecific gene flow via homologous lateral or horizontal transfer and differentiated by content flux mediated by acquisition of DNA segments from interspecies transfers.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Bergthorsson U, Ochman H (1998) Distribution of chromosome length variation in natural isolates of Escherichia coli. Mol Biol Evol 15:6–16

    CAS  Google Scholar 

  • Bisercic M, Feutrier JY, Reeves PR (1991) Nucleotide sequences of the gnd genes from nine natural isolates of Escherichia coli: evidence of intragenic recombination as a contributing factor in the evolution of the polymorphic gnd locus. J Bacteriol 173:3894–3900

    CAS  Google Scholar 

  • Blattner FR, Burland V, Plunkett G 3rd, Sofia HJ, Daniels DL (1993) Analysis of the Escherichia coli genome. IV. DNA sequence of the region from 89.2 to 92.8 minutes. Nucleic Acids Res 21:5408–5417

    Article  CAS  Google Scholar 

  • Blattner FR, Plunkett G 3rd, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF et al (1997) The complete genome sequence of Escherichia coli K-12. Science 277:1453–1462

    Article  CAS  Google Scholar 

  • Brzuszkiewicz E, Bruggemann H, Liesegang H, Emmerth M, Olschlager T, Nagy G, Albermann K, Wagner C, Buchrieser C, Emody L et al (2006) How to become a uropathogen: comparative genomic analysis of extraintestinal pathogenic Escherichia coli strains. Proc Natl Acad Sci USA 103:12879–12884

    Article  Google Scholar 

  • Burland V, Plunkett G 3rd, Sofia HJ, Daniels DL, Blattner FR (1995) Analysis of the Escherichia coli genome VI: DNA sequence of the region from 92.8 through 100 minutes. Nucleic Acids Res 23:2105–2119

    Article  CAS  Google Scholar 

  • Burland V, Shao Y, Perna NT, Plunkett G, Sofia HJ, Blattner FR (1998) The complete DNA sequence and analysis of the large virulence plasmid of Escherichia coli O157:H7. Nucleic Acids Res 26:4196–4204

    Article  CAS  Google Scholar 

  • Chaudhuri RR, Sebaihia M, Hobman JL, Webber MA, Leyton DL, Goldberg MD, Cunningham AF, Scott-Tucker A, Ferguson PR, Thomas CM et al (2010) Complete genome sequence and comparative metabolic profiling of the prototypical enteroaggregative Escherichia coli strain 042. PLoS One 5:e8801

    Google Scholar 

  • Chen SL, Hung CS, Xu J, Reigstad CS, Magrini V, Sabo A, Blasiar D, Bieri T, Meyer RR, Ozersky P et al (2006) Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: a comparative genomics approach. Proc Natl Acad Sci USA 103:5977–5982

    Article  CAS  Google Scholar 

  • Daniels DL, Plunkett G 3rd, Burland V, Blattner FR (1992) Analysis of the Escherichia coli genome: DNA sequence of the region from 84.5 to 86.5 minutes. Science 257:771–778

    Article  CAS  Google Scholar 

  • Daubin V, Moran NA, Ochman H (2003) Phylogenetics and the cohesion of bacterial genomes. Science 301:829–832

    Article  CAS  Google Scholar 

  • Durfee T, Nelson R, Baldwin S, Plunkett G 3rd, Burland V, Mau B, Petrosino JF, Qin X, Muzny DM, Ayele M et al (2008) The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse. J Bacteriol 190:2597–2606

    Article  CAS  Google Scholar 

  • Dykhuizen DE, Green L (1991) Recombination in Escherichia coli and the definition of biological species. J Bacteriol 173:7257–7268

    CAS  Google Scholar 

  • Feng P, Lampel KA, Karch H, Whittam TS (1998) Genotypic and phenotypic changes in the emergence of Escherichia coli O157:H7. J Infect Dis 177:1750–1753

    Article  CAS  Google Scholar 

  • Ferenci T, Zhou Z, Betteridge T, Ren Y, Liu Y, Feng L, Reeves PR, Wang L (2009) Genomic sequencing reveals regulatory mutations and recombinational events in the widely used MC4100 lineage of Escherichia coli K-12. J Bacteriol 191:4025–4029

    Article  CAS  Google Scholar 

  • Fricke WF, Wright MS, Lindell AH, Harkins DM, Baker-Austin C, Ravel J, Stepanauskas R (2008) Insights into the environmental resistance gene pool from the genome sequence of the multidrug-resistant environmental isolate Escherichia coli SMS-3-5. J Bacteriol 190:6779–6794

    Article  CAS  Google Scholar 

  • Froehlich B, Parkhill J, Sanders M, Quail MA, Scott JR (2005) The pCoo plasmid of enterotoxigenic Escherichia coli is a mosaic cointegrate. J Bacteriol 187:6509–6516

    Article  CAS  Google Scholar 

  • Harris DR, Pollock SV, Wood EA, Goiffon RJ, Klingele AJ, Cabot EL, Schackwitz W, Martin J, Eggington J, Durfee TJ et al (2009) Directed evolution of ionizing radiation resistance in Escherichia coli. J Bacteriol 191:5240–5252

    Article  CAS  Google Scholar 

  • Hayashi T, Makino K, Ohnishi M, Kurokawa K, Ishii K, Yokoyama K, Han CG, Ohtsubo E, Nakayama K, Murata T et al (2001) Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12. DNA Res 8:11–22

    Article  CAS  Google Scholar 

  • Hayashi K, Morooka N, Yamamoto Y, Fujita K, Isono K, Choi S, Ohtsubo E, Baba T, Wanner BL, Mori H et al (2006) Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110. Mol Syst Biol 2:2006.0007

    Article  Google Scholar 

  • Ho TD, Davis BM, Ritchie JM, Waldor MK (2008) Type 2 secretion promotes enterohemorrhagic Escherichia coli adherence and intestinal colonization. Infect Immun 76:1858–1865

    Article  CAS  Google Scholar 

  • Iguchi A, Iyoda S, Terajima J, Watanabe H, Osawa R (2006) Spontaneous recombination between homologous prophage regions causes large-scale inversions within the Escherichia coli O157:H7 chromosome. Gene 372:199–207

    Article  CAS  Google Scholar 

  • Iguchi A, Thomson NR, Ogura Y, Saunders D, Ooka T, Henderson IR, Harris D, Asadulghani M, Kurokawa K, Dean P et al (2009) Complete genome sequence and comparative genome analysis of enteropathogenic Escherichia coli O127:H6 strain E2348/69. J Bacteriol 191:347–354

    Article  CAS  Google Scholar 

  • Jeong H, Barbe V, Lee CH, Vallenet D, Yu DS, Choi SH, Couloux A, Lee SW, Yoon SH, Cattolico L et al (2009) Genome sequences of Escherichia coli B strains REL606 and BL21(DE3). J Mol Biol 394:644–652

    Article  CAS  Google Scholar 

  • Jin Q, Yuan Z, Xu J, Wang Y, Shen Y, Lu W, Wang J, Liu H, Yang J, Yang F et al (2002) Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157. Nucleic Acids Res 30:4432–4441

    Article  CAS  Google Scholar 

  • Johnson TJ, Johnson SJ, Nolan LK (2006a) Complete DNA sequence of a ColBM plasmid from avian pathogenic Escherichia coli suggests that it evolved from closely related ColV virulence plasmids. J Bacteriol 188:5975–5983

    Article  CAS  Google Scholar 

  • Johnson TJ, Kariyawasam S, Wannemuehler Y, Mangiamele P, Johnson SJ, Doetkott C, Skyberg JA, Lynne AM, Johnson JR, Nolan LK (2007) The genome sequence of avian pathogenic Escherichia coli strain O1:K1:H7 shares strong similarities with human extraintestinal pathogenic E. coli genomes. J Bacteriol 189:3228–3236

    Article  CAS  Google Scholar 

  • Johnson TJ, Wannemeuhler YM, Scaccianoce JA, Johnson SJ, Nolan LK (2006b) Complete DNA sequence, comparative genomics, and prevalence of an IncHI2 plasmid occurring among extraintestinal pathogenic Escherichia coli isolates. Antimicrob Agents Chemother 50:3929–3933

    Article  CAS  Google Scholar 

  • Karch H, Bohm H, Schmidt H, Gunzer F, Aleksic S, Heesemann J (1993) Clonal structure and pathogenicity of Shiga-like toxin-producing, sorbitol-fermenting Escherichia coli O157:H. J Clin Microbiol 31:1200–1205

    CAS  Google Scholar 

  • Kulasekara BR, Jacobs M, Zhou Y, Wu Z, Sims E, Saenphimmachak C, Rohmer L, Ritchie JM, Radey M, McKevitt M et al (2009) Analysis of the genome of the Escherichia coli O157:H7 2006 spinach-associated outbreak isolate indicates candidate genes that may enhance virulence. Infect Immun 77:3713–3721

    Article  CAS  Google Scholar 

  • Lawrence JG, Ochman H (1997) Amelioration of bacterial genomes: rates of change and exchange. J Mol Evol 44:383–397

    Article  CAS  Google Scholar 

  • Le Gall T, Clermont O, Gouriou S, Picard B, Nassif X, Denamur E, Tenaillon O (2007) Extraintestinal virulence is a coincidental by-product of commensalism in B2 phylogenetic group Escherichia coli strains. Mol Biol Evol 24:2373–2384

    Article  Google Scholar 

  • Leopold SR, Magrini V, Holt NJ, Shaikh N, Mardis ER, Cagno J, Ogura Y, Iguchi A, Hayashi T, Mellmann A et al (2009) A precise reconstruction of the emergence and constrained radiations of Escherichia coli O157 portrayed by backbone concatenomic analysis. Proc Natl Acad Sci USA 106:8713–8718

    CAS  Google Scholar 

  • Makino K, Ishii K, Yasunaga T, Hattori M, Yokoyama K, Yutsudo CH, Kubota Y, Yamaichi Y, Iida T, Yamamoto K et al (1998) Complete nucleotide sequences of 93-kb and 3.3-kb plasmids of an enterohemorrhagic Escherichia coli O157:H7 derived from Sakai outbreak. DNA Res 5:1–9

    Article  CAS  Google Scholar 

  • Manning SD, Motiwala AS, Springman AC, Qi W, Lacher DW, Ouellette LM, Mladonicky JM, Somsel P, Rudrik JT, Dietrich SE et al (2008) Variation in virulence among clades of Escherichia coli O157:H7 associated with disease outbreaks. Proc Natl Acad Sci USA 105:4868–4873

    Article  CAS  Google Scholar 

  • Mau B, Glasner JD, Darling AE, Perna NT (2006) Genome-wide detection and analysis of homologous recombination among sequenced strains of Escherichia coli. Genome Biol 7:R44

    Article  Google Scholar 

  • Medigue C, Rouxel T, Vigier P, Henaut A, Danchin A (1991) Evidence for horizontal gene transfer in Escherichia coli speciation. J Mol Biol 222:851–856

    Article  CAS  Google Scholar 

  • Milkman R, Bridges MM (1993) Molecular evolution of the Escherichia coli chromosome. IV. Sequence comparisons. Genetics 133:455–468

    CAS  Google Scholar 

  • Miller JR, Delcher AL, Koren S, Venter E, Walenz BP, Brownley A, Johnson J, Li K, Mobarry C, Sutton G (2008) Aggressive assembly of pyrosequencing reads with mates. Bioinformatics 24:2818–2824

    Article  CAS  Google Scholar 

  • Moriel DG, Bertoldi I, Spagnuolo A, Marchi S, Rosini R, Nesta B, Pastorello I, Corea VA, Torricelli G, Cartocci E et al (2010) Identification of protective and broadly conserved vaccine antigens from the genome of extraintestinal pathogenic Escherichia coli. Proc Natl Acad Sci USA 107:9072–9077

    Google Scholar 

  • Nie H, Yang F, Zhang X, Yang J, Chen L, Wang J, Xiong Z, Peng J, Sun L, Dong J et al (2006) Complete genome sequence of Shigella flexneri 5b and comparison with Shigella flexneri 2a. BMC Genomics 7:173

    Article  Google Scholar 

  • Ochman H, Selander RK (1984a) Evidence for clonal population structure in Escherichia coli. Proc Natl Acad Sci USA 81:198–201

    Article  CAS  Google Scholar 

  • Ochman H, Selander RK (1984b) Standard reference strains of Escherichia coli from natural populations. J Bacteriol 157:690–693

    CAS  Google Scholar 

  • Ochman H, Whittam TS, Caugant DA, Selander RK (1983) Enzyme polymorphism and genetic population structure in Escherichia coli and Shigella. J Gen Microbiol 129:2715–2726

    CAS  Google Scholar 

  • Ogura Y, Ooka T, Iguchi A, Toh H, Asadulghani M, Oshima K, Kodama T, Abe H, Nakayama K, Kurokawa K et al (2009) Comparative genomics reveal the mechanism of the parallel evolution of O157 and non-O157 enterohemorrhagic Escherichia coli. Proc Natl Acad Sci USA 106:17939–17944

    Article  CAS  Google Scholar 

  • Oshima K, Toh H, Ogura Y, Sasamoto H, Morita H, Park SH, Ooka T, Iyoda S, Taylor TD, Hayashi T et al (2008) Complete genome sequence and comparative analysis of the wild-type commensal Escherichia coli strain SE11 isolated from a healthy adult. DNA Res 15:375–386

    Article  CAS  Google Scholar 

  • Peng J, Zhang X, Yang J, Wang J, Yang E, Bin W, Wei C, Sun M, Jin Q (2006) The use of comparative genomic hybridization to characterize genome dynamics and diversity among the serotypes of Shigella. BMC Genomics 7:218

    Article  Google Scholar 

  • Perna NT, Plunkett G 3rd, Burland V, Mau B, Glasner JD, Rose DJ, Mayhew GF, Evans PS, Gregor J, Kirkpatrick HA et al (2001) Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 409:529–533

    Article  CAS  Google Scholar 

  • Plunkett G 3rd, Burland V, Daniels DL, Blattner FR (1993) Analysis of the Escherichia coli genome. III. DNA sequence of the region from 87.2 to 89.2 minutes. Nucleic Acids Res 21:3391–3398

    Article  CAS  Google Scholar 

  • Pupo GM, Lan R, Reeves PR (2000) Multiple independent origins of Shigella clones of Escherichia coli and convergent evolution of many of their characteristics. Proc Natl Acad Sci USA 97:10567–10572

    Article  CAS  Google Scholar 

  • Rasko DA, Rosovitz MJ, Myers GS, Mongodin EF, Fricke WF, Gajer P, Crabtree J, Sebaihia M, Thomson NR, Chaudhuri R et al (2008) The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates. J Bacteriol 190:6881–6893

    Article  CAS  Google Scholar 

  • Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T et al (2006) Escherichia coli K-12: a cooperatively developed annotation snapshot – 2005. Nucleic Acids Res 34:1–9

    Article  CAS  Google Scholar 

  • Sofia HJ, Burland V, Daniels DL, Plunkett G 3rd, Blattner FR (1994) Analysis of the Escherichia coli genome. V. DNA sequence of the region from 76.0 to 81.5 minutes. Nucleic Acids Res 22:2576–2586

    Article  CAS  Google Scholar 

  • Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL, Angiuoli SV, Crabtree J, Jones AL, Durkin AS et al (2005) Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial “pan-genome”. Proc Natl Acad Sci USA 102:13950–13955

    Article  CAS  Google Scholar 

  • Toh H, Oshima K, Toyoda A, Ogura Y, Ooka T, Sasamoto H, Park SH, Iyoda S, Kurokawa K, Morita H et al (2010) Complete genome sequence of the wild-type commensal Escherichia coli strain SE15, belonging to phylogenetic group B2. J Bacteriol 192:1165–1166

    Google Scholar 

  • Touchon M, Hoede C, Tenaillon O, Barbe V, Baeriswyl S, Bidet P, Bingen E, Bonacorsi S, Bouchier C, Bouvet O et al (2009) Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet 5:e1000344

    Article  Google Scholar 

  • Wei J, Goldberg MB, Burland V, Venkatesan MM, Deng W, Fournier G, Mayhew GF, Plunkett G 3rd, Rose DJ, Darling A et al (2003) Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T. Infect Immun 71:2775–2786

    Article  CAS  Google Scholar 

  • Welch RA, Burland V, Plunkett G 3rd, Redford P, Roesch P, Rasko D, Buckles EL, Liou SR, Boutin A, Hackett J et al (2002) Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc Natl Acad Sci USA 99:17020–17024

    Article  CAS  Google Scholar 

  • Whittam TS, Ochman H, Selander RK (1983) Geographic components of linkage disequilibrium in natural populations of Escherichia coli. Mol Biol Evol 1:67–83

    CAS  Google Scholar 

  • Whittam TS, Wachsmuth IK, Wilson RA (1988) Genetic evidence of clonal descent of Escherichia coli O157:H7 associated with hemorrhagic colitis and hemolytic uremic syndrome. J Infect Dis 157:1124–1133

    CAS  Google Scholar 

  • Whittam TS, Wilson RA (1988) Genetic relationships among pathogenic Escherichia coli of serogroup O157. Infect Immun 56:2467–2473

    CAS  Google Scholar 

  • Whittam TS, Wolfe ML, Wachsmuth IK, Orskov F, Orskov I, Wilson RA (1993) Clonal relationships among Escherichia coli strains that cause hemorrhagic colitis and infantile diarrhea. Infect Immun 61:1619–1629

    CAS  Google Scholar 

  • Yang J, Nie H, Chen L, Zhang X, Yang F, Xu X, Zhu Y, Yu J, Jin Q (2007) Revisiting the molecular evolutionary history of Shigella spp. J Mol Evol 64:71–79

    Article  CAS  Google Scholar 

  • Yang F, Yang J, Zhang X, Chen L, Jiang Y, Yan Y, Tang X, Wang J, Xiong Z, Dong J et al (2005) Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery. Nucleic Acids Res 33:6445–6458

    Article  Google Scholar 

  • Ye C, Lan R, Xia S, Zhang J, Sun Q, Zhang S, Jing H, Wang L, Li Z, Zhou Z et al (2010) Emergence of a new multidrug-resistant serotype X variant in an epidemic clone of Shigella flexneri. J Clin Microbiol 48:419–426

    Google Scholar 

  • Zhou Z, Li X, Liu B, Beutin L, Xu J, Ren Y, Feng L, Lan R, Reeves PR, Wang L (2010) Derivation of Escherichia coli O157:H7 from its O55:H7 precursor. PLoS One 5:e8700

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Genetics and the Genome Center of Wisconsin, University of Wisconsin, Madison, WI, 53706, USA

    Nicole T. Perna

Authors
  1. Nicole T. Perna
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Nicole T. Perna .

Editor information

Editors and Affiliations

  1. Dept. Food Science, Cornell University, Stocking Hall 116, Ithaca, 14853, New York, USA

    Martin Wiedmann

  2. National Center for Food Safety &, Technology, Illinois Institute of Technology, S. Archer Rd. 6502, Summit, 60501, Illinois, USA

    Wei Zhang

Rights and permissions

Reprints and permissions

Copyright information

© 2011 Springer New York

About this chapter

Cite this chapter

Perna, N.T. (2011). Genomics of Escherichia and Shigella . 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_5

Download citation

Publish with us

Policies and ethics

Search

Navigation