• DNA microarrays and global gene expression patterns
• Genomic indexing of Salmonella and E.coli
• Salmonella virulence gene expression during infectionLag Phase
• Salmonella Infection of Chicken oviduct (SafeHouse)
• Influence of Commensal flora, immune response and behaviour on Salmonella infection (VTRI104)
• Environmental regulation of the invasion and intracellular virulence gene programmes of Salmonella: a ppGpp dependent switch

• Regulation of Salmonella SPI1 & SPI2
• Bacterial nitrate metabolism in colonisation of the mammalian gastrointestinal tract
• Analysis of factors affecting Salmonella contamination of meat during the slaughter process (Biotracer)

• "Non genetic variation" gene expression within bacterial populations (Finished)

• Nucleoid associated proteins: DNA topology and gene expression.
• Acambis project on enterotoxigenic E.coli (Finished)

Genomic indexing of Salmonella and E.coli

Main researcher: Sacha Lucchini

Phylogenetic classification based on rRNA/rDNA sequences is usually able to provide an accurate classification of microorganisms above the species level (Gupta, 2000).

However, it has become evident that lateral gene transfer is an important mechanism for the adaptation of bacteria to new ecological niches, complicating phylogenetic analysis that relies upon a small number of genes.

One example is the Salmonella pathogenicity islands which encode virulence factors that were acquired at different times(Groisman & Ochman, 1997). Whole-genome based methods are thus required to determine the repertoire of virulence genes found in bacterial pathogens. Gene-specific microarrays have been used to compare the entire genome of Salmonella Typhimurium (Porwollick et al., 2002), Helicobacter pylori (Salama et al., 2000) or Staphylococcus aureus.

Genomic Indexing

We have performed genomic indexing of a number of pathogenic E. coli strains in collaboration with Prof. Martin Woodward and Dr. Muna Anjum of the Veterinary Laboratories Agency.

Genomic index of Salmonella Typhimurium - SL1344 ΔSPI1 compared with LT2a. Genes absent in SL1344 ΔSPI1 were determined with microarrays and are indicated in red and yellow.

• Groisman, E. A. & Ochman, H. (1997). Trends Microbiol 5, 343-349.
• Gupta, R. S. (2000). FEMS Microbiol Rev 24, 367-402.
• Porwollik, (2002). Proc Natl Acad Sci U S A 99, 8956-8961.
• Salama, N., Guillemin, K., McDaniel, T. K., Sherlock, G., Tompkins, L. & Falkow, S. (2000). Proc Natl Acad Sci U S A 97, 14668-14673.