Skip to main content
Article thumbnail
Location of Repository

Genomic diversity of ten Escherichia coli strains associated with bloodstream infections.

By Ali Salman Bin Thani


Escherichia coli are usually regarded as a harmless human colonic flora. However,\ud pathogenic strains of E. coli have been associated with infections that could range from infected mucosal surfaces by intestinal pathogenic E. coli to the more severe cases of disseminated infections throughout the body by the extraintestinal pathogroups. The main focus of this project was to investigate the genomic contents of pathogenic bloodstream infection (BSI)-associated E. coli strains. This is because the genome contents of the E. coli BSI-associated isolates have not been well studied, with only few reports indicating that the pathogenincity of these strains could be attributed to horizontally acquired DNAs known as genomic islands (GEIs).\ud The genomic contents of 10 clinical BSI-associated E. coli strains, isolated at the\ud Leicester Royal Infirmary were investigated in this study. The first approach used to\ud investigate the genomic contents of these strains was by interrogating the downstream\ud ends of tRNA genes for their GEI contents by the sequential PCR strategy tRIP-PCR\ud (tRNA interrogation for pathogenicity islands) followed by the SGSP-PCR (single\ud genome specific primer-PCR). In this approach the flanking regions of the tRNA sites were used to first screen the tRNA genes for their GEIs followed by amplifying the boundaries of the identified GEIs. In the second approach termed Microarray-Assisted mobilome Prospecting (MAmP), the physical genome size of the tested strains obtained by the pulsed-field gel electrophoresis (PFGE) is compared to the sum total of the bits of the genome detected or visualized by the array. The difference between the two measurements is used to estimate the size of the novel, non-microarray-represented mobile genome (mobilome) present in the tested strains.\ud Remarkably, despite only studying 10 E. coli strains, associated with a single disease\ud type the tRIP-PCR method has identified at least 3 GEIs that contain novel sequences,\ud and 46 GEIs, resembling uropathogenic E. coli CFT073-like entities. One particular\ud strain E105 had 13 tRNA sites occupied with GEIs. On the other hand, an average\ud novel, non-microarray-borne mobilome of (219 kb /strain) was obtained by the MAmP\ud which, corresponds with previous studies.\ud The strategies used in this study had proved successful in addressing and identifying\ud mobilome-rich strains. Therefore, using such approaches in combination with whole\ud genome sequencing progects could prioritize the strains and the genomic regions that\ud need to be sequenced. Such prioritization would avoid sequencing of hundreds of\ud isolates to identify their novel gene pool and would reduce the cost of genomic\ud sequencing. Moreover, applying such approaches for the identification of new virulence genes and/or pathogenic mechanisms could lead to significant improvements in the\ud treatment of E. coli infections

Publisher: University of Leicester
Year: 2008
OAI identifier:

Suggested articles


  1. (2003). A doi
  2. (2002). A A and Allan doi
  3. (1996). A minimal gene set for cellular life derived by comparison of complete bacterial genomes." doi
  4. (2001). A model for measurement error for gene expression arrays." doi
  5. (2005). A novel DNA modification by sulphur." doi
  6. (1988). A Novel suicide vector and its use in construction of insertion mutations: Osmoregulation of outer membrane proteins and virulence determinants in Vibrio cholerae requires toxR."
  7. (1989). A plasmid extraction procedure on a miniprep scale."
  8. (2000). A whole-genome microarray reveals genetic diversity among Helicobacter pylori strains." doi
  9. (2000). Achieving 100% typeability of Pseudomonas aeruginosa by pulsed-field gel electrophoresis."
  10. (1994). Actin accumulation associated with clustered and localized adherence in Escherichia coli isolated from patients with diarrhea."
  11. (1994). Adhesin regulatory genes within large, unstable DNA regions of pathogenic Escherichia coli - cross-talk between different adhesin gene clusters." doi
  12. (2001). afa-8 Gene cluster is carried by a pathogenicity island inserted into the tRNAPhe of human and bovine pathogenic Escherichia coli isolates." doi
  13. (1984). Alteration of apparent restriction endonuclease recognition specificities by DNA methylases." doi
  14. (1997). Amelioration of bacterial genomes: Rates of change and exchange." doi
  15. (1998). and Fasano A doi
  16. (2000). Andremont A doi
  17. (1985). Andremont A O doi
  18. (1993). Asymmetrical recognition and activity of the I-SceI endonuclease on its site and on intron-exon junctions."
  19. (2000). Bacteraemia and antibiotic resistance of its pathogens reported in England and Wales between
  20. (2001). Bacterial comparative genomic hybridization: A method for directly identifying lateral gene transfer." doi
  21. (2002). Bacterial pathogenesis, a molecular approach.
  22. (2003). Calculation for molecular biology and biotechnology, a guide to mathematics in the laboratory.
  23. (1999). Characterization of the integration site of Yersinia high-pathogenicity island in Escherichia coli." doi
  24. (1992). Chromosome transfer in Rhodobacter sphaeroides: Hfr formation and genetic-evidence for two unique circular chromosomes."
  25. (1990). Cleavage at the 12-base-pair sequence 5'-TCTAGATCTAGA-3' using M.XbaI (TCTAGm6A) methylation and DpnI (Gm6A/TC) cleavage."
  26. (1991). Cleavage of yeast and bacteriophage-T7 genomes at a single doi
  27. (1995). Clonal relationships among bloodstream isolates of Escherichia coli."
  28. (2005). Comparison of Escherichia coli isolates implicated in human urinary tract infection and avian colibacillosis." doi
  29. (2007). Defining genomic islands and uropathogen-specific genes in uropathogenic Escherichia coli." doi
  30. (1993). Effect of site-specific methylation on restriction endonucleases and DNA modification methyltransferases." doi
  31. (2004). Essential Role for the gtfA gene encoding a putative glycosyltransferase in the adherence of Porphyromonas gingivalis” doi
  32. (2002). Evidence for Lateral Transfer of Genes Encoding Ferredoxins, Nitroreductase, NADH oxidase, and alcohol dehydrogenase 3 from anaerobic prokaryotes to Giardia lamblia and Entamoeba histolytica” doi
  33. (2005). Extensive gene diversity in septicemic Escherichia coli strains." doi
  34. (2007). Extraintestinal pathogenic Escherichia coli strains of avian and human origin: Link between phylogenetic relationships and common virulence patterns." doi
  35. (1995). Genetics and regulation of heme iron transport in Shigella dysenteriae and detection of an analogous system in Escherichia coli O157-H7."
  36. (2001). Genome sequence of enterohaemorrhagic Escherichia coli O157: H7." doi
  37. (1995). Genomic cleavage map of Salmonella typhi ty2."
  38. (2004). Genomic subtraction for the identification of putative new virulence factors of an avian pathogenic Escherichia coli strain of O2 serogroup." doi
  39. (2005). Horizontal and vertical gene transfer: the life history of pathogens." doi
  40. (2002). Identification of a type III secretion system in uropathogenic Escherichia coli." doi
  41. (2004). Impact of the locus of enterocyte effacement pathogenicity island on the evolution of pathogenic Escherichia coli." doi
  42. (1993). In vivo regulatory responses of 4 Escherichia coli operons which encode leucyl-transfer RNAs."
  43. (2004). Instability of pathogenicity islands in uropathogenic Escherichia coli 536." doi
  44. (2000). Integrated genomic map from uropathogenic Escherichia coli J96." doi
  45. (2004). Islander: a database of integrative islands in prokaryotic genomes, the associated integrases and their DNA site specificities." doi
  46. (2003). IslandPath: aiding detection of genomic islands in prokaryotes." doi
  47. (2007). Laboratory strains of Escherichia coli: model citizens or deceitful delinquents growing old disgracefully?" doi
  48. (1981). Location of the tufB promoter of Escherichia coli - cotranscription of tufB with 4 transfer-RNA genes." doi
  49. (2001). Microarrays for microbiologists." doi
  50. (2002). Molecular genetics of methicillin-resistant Staphylococcus aureus." doi
  51. (1992). New tools for the physical and genetic-mapping of Lactococcus strains." doi
  52. (1990). Organization of the bacterial chromosome."
  53. (2007). pan-genome: towards a knowledge-based discovery of novel targets for vaccines and antibacterials” Drug Discovery Today 12(11/12):429-439. doi
  54. (2004). Pathogenicity islands in bacterial pathogenesis." doi
  55. (1993). physical map of the genome of Rhizobium meliloti 1021."
  56. (1991). Plasmids of Pseudomonas cepacia strains of diverse origins."
  57. (2005). Prevalence of pathogenicity island IICFT073 genes among extraintestinal clinical isolates of Escherichia coli." doi
  58. (1998). Prevalence Stacyphipps S,
  59. (2004). Pulsed-field gel electrophoresis study of Mycobacterium abscessus isolates previously affected by DNA degradation." doi
  60. (1990). Purification and characterization of the in vitro activity of I-Sce-I, a novel and highly specific endonuclease encoded by a group-I intron." doi
  61. (1990). Pyelonephritogenic Escherichia coli and killing of cultured human renal proximal tubular epithelial cells: Role of hemolysin in some strains."
  62. (1997). Rapid and effective method for preparation of fecal specimens for PCR assays." doi
  63. (1981). Rapid procedure for detection and isolation of Kothapalli
  64. (1987). Restriction endonucleases for pulsed field-mapping of bacterial genomes." doi
  65. Sensitivity and specificity of DNA probes with the stool blot technique for detection of Escherichia coli enterotoxins." doi
  66. (2002). Sepsis: current concepts in intracellular signaling." doi
  67. (1984). Site-specific cleavage of DNA at 8-base-pair and 10-base-pair sequences." doi
  68. (2004). Streptomyces coelicolor A3(2) lacks a genomic island present in the chromosome of Streptomyces lividans 66." doi
  69. (1995). Study of the organization of the genomes of Escherichia coli, Brucella melitensis and Agrobacterium tumefaciens by insertion of a unique restriction site." doi
  70. (1994). The I-CeuI endonuclease -purification and potential role in the evolution of Chlamydomonas group-I introns." doi
  71. (1992). The I-CeuI endonuclease recognizes a sequence of 19 base-pairs and preferentially cleaves the coding strand of the Chlamydomonas moewusii chloroplast large subunit ribosomalRNA gene." doi
  72. (2005). The microbial pan-genome." doi
  73. (1997). The Pai-associated leuX specific tRNALeu5 affects type 1 fimbriation in pathogenic Escherichia coli by control of FimB recombinase expression." doi
  74. (1991). Tn5cos: a transposon for restriction mapping of large plasmids using phage lambda terminase." doi
  75. (1994). Tn5Map, a transposon for the rapid mapping of restriction sites in plasmids." doi
  76. (2005). Transcriptional adaptation of Shigella flexneri during infection of macrophages and epithelial cells: Insights into the strategies of a cytosolic bacterial pathogen." doi
  77. (1989). Transfer RNA genes frequently serve as integration sites for prokaryotic genetic elements." doi
  78. (1999). Transfer RNAs and pathogenicity islands." doi
  79. (1996). TreeView: An application to display phylogenetic trees on personal computers." doi
  80. (1992). Tris-dependent site-specific cleavage of Streptomyces lividans DNA." doi
  81. (2004). Two Periplasmic disulfide oxidoreductase, DsbA and SrgA, target outer membrane protein SpiA, a component of the Salmonella pathogenicity island 2 type III secretion system” doi
  82. (1999). Typespecific contributions to chromosome size differences in Escherichia coli."
  83. (2002). Yersinia high-pathogenicity island contributes to virulence in Escherichia coli causing extraintestinal infections." doi

To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.