The focus of our laboratory for many years has been to understand why certain bacteria are pathogenic, how they became pathogenic, and how they interact with their animal host.  We study several model systems:


1.    Salmonella typhimurium infection of the mouse.


Our research on Salmonella infection first concentrated on the bacterial genes that were essential for bacterial entry into cultured cells.  Increasingly, we have shifted our attention away from cell culture to examine the interaction of these bacteria with the Peyer’s patch. The Peyer’s patch contains specialized terminally differentiated epithelial cells called M cells, which appear to be the primary entry point of Salmonella typhimurium to penetrate the intestinal mucosal barrier to cause infection. Several labs, including our own, have characterized the bacterial genes important for this act of cellular penetration.  A few years ago our laboratory reported that when Salmonella entered the Peyer’s patch, they often interacted with resident macrophages and killed them by a process that was similar to programmed cell death or apoptosis. In collaboration with Arturo Zychlinsky’s laboratory at NYU, we showed that a particular Salmonella virulence gene, SipB, targets caspase 1 in macrophages and that this interaction leads to macrophage cell death as well as the induction of the cytokines IL-1b and IL-18. More recently, we showed that caspase-1 knockout mice are resistant to oral challenge by Salmonella. It appears that in the absence of this host factor, there is no inflammatory response by the host. We currently are trying to understand why the absence of the caspase-1-induced inflammatory response by the host leads to host resistance to infection and disease. Also, we are examining the sequence of events that occur in infected animals following invasion of the Peyer’s patch to understand how the bacteria eventually enter the mesenteric lymph nodes and enter the spleen and liver to cause a systemic infection and subsequent death of the host animal.


Other facets of Salmonella research in the laboratory include looking at specific Salmonella genes that are expressed exclusively when these bacteria enter cells. Salmonella are facultative intracellular parasites, so they grow in ordinary culture in the laboratory, but in the animal host, they reside and replicate within host cells. We know that a major cellular target of Salmonella growth and replication is within macrophages, but more recent data suggests there are other cellular targets as well.


Recent studies from our laboratory that illustrate our research on Salmonella include:


  1. Monack, D. M., B. Raupach, A. E. Hromockyj, and S. Falkow 1996. Salmonella typhimurium invasion induces apoptosis in infected macrophages Proc Natl Acad Sci U S A. 93:9833-8.
  2. Valdivia, R. H., and S. Falkow 1997. Fluorescence-based isolation of bacterial genes expressed within host cells Science. 277:2007-11.
  3. Valdivia, R. H., and S. Falkow 1997. Probing bacterial gene expression within host cells Trends Microbiol. 5:360-3.
  4. Lee, A. K., and S. Falkow 1998. Constitutive and inducible green fluorescent protein expression in Bartonella henselae Infect Immun. 66:3964-7.
  5. Valdivia, R. H., D. M. Cirillo, A. K. Lee, D. M. Bouley, and S. Falkow 2000. mig-14 is a horizontally acquired, host-induced gene required for salmonella enterica lethal infection in the murine model of typhoid fever [In Process Citation] Infect Immun. 68:7126-31.
  6. Lee, A. K., C. S. Detweiler, and S. Falkow 2000. OmpR regulates the two-component system  SsrA-ssrB in Salmonella pathogenicity island 2 J Bacteriol. 182:771-81.
  7. Monack, D., and S. Falkow 2000. Apoptosis as a common bacterial virulence strategy. Int J Med Microbiol. 290:7-13.
  8. Monack, D. M., D. Hersh, N. Ghori, D. Bouley, A. Zychlinsky, and S. Falkow 2000. Salmonella exploits caspase-1 to colonize Peyer's patches in a murine typhoid model J Exp Med. 192:249-58.


Currently, we have expanded our research tools with Salmonella to include a spotted DNA microarray in which we can examine the expression of all the known chromosomal and plasmid genes of both Salmonella typhi and S. typhimurium during infection of cultured host cells and in infected animals. We also employ both human and murine DNA microarrays so that we can simultaneously examine the response of host genes to Salmonella infection.


2. Helicobacter pylori


Helicobacter pylori colonize the stomach of half of the world's population, causing a wide spectrum of disease ranging from asymptomatic gastritis to ulcers to gastric cancer. Although the basis for these diverse clinical outcomes is not understood, more severe disease is associated with strains harboring a pathogenicity island. To characterize the genetic diversity of more and less virulent strains, we examined the genomic content of 15 H. pylori clinical isolates by using a whole genome H. pylori DNA microarray. We found that a full 22% of H. pylori genes are dispensable in one or more strains, thus defining a minimal functional core of 1281 H. pylori genes. While the core genes encode most metabolic and cellular processes, the strain- specific genes include genes unique to H. pylori (restriction modification genes, transposases, and genes encoding cell surface proteins), which may aid the bacteria under specific circumstances during their long-term infection of genetically diverse hosts. We observed distinct patterns of the strain-specific gene distribution along the chromosome, which may result from different mechanisms of gene acquisition and loss. Among the strain-specific genes, we have found a class of candidate virulence genes identified by their coinheritance with the pathogenicity island. 


In parallel, we also have examined the response of 26000 human gene sequences found in cultured gastric epithelial cells to H. pylori infection. These results show that a number of gene families are up regulated in response to infection. One set of human genes up regulated are involved with a generalized inflammatory response. Perhaps the most striking human gene response involves gene families involved with the cytoskeleton, extracellular matrix, host cell motility, and tight-junctions. At least early in the infectious process, it appears that the host cell genes involved with averting apoptosis are brought into play. Some human genes appear to be down-regulated with respect to H. pylori infection and these appear to be involved with the host cell replication cycle. That is, infected epithelial cells appear to enter cell cycle arrest.


A number of individual research projects are ongoing as well. In particular we are investigating animal models of H. pylori infection using well-defined mutant strains of bacteria. A major collaborative project with several laboratories involves examining epidemiological well-defined clinical isolates obtained from patients with gastric cancer. We wish to see if there is a particular bacterial phenotype associated with the eventual development of cancer subsequent to H. pylori infection.


Recent studies that illustrate our research into H. pylori pathogenesis include:


  1. Segal, E. D., S. Falkow, and L. S. Tompkins 1996. Helicobacter pylori attachment to gastric cells induces cytoskeletal rearrangements and tyrosine phosphorylation of host cell proteins Proc Natl Acad Sci U S A. 93:1259-64.
  2. Segal, E. D., C. Lange, A. Covacci, L. S. Tompkins, and S. Falkow 1997. Induction of host signal transduction pathways by Helicobacter pylori Proc Natl Acad Sci U S A. 94:7595-9.
  3. Segal, E. D., J. Cha, J. Lo, S. Falkow, and L. S. Tompkins 1999. Altered states: involvement of phosphorylated CagA in the induction of host cellular growth changes by Helicobacter pylori Proc Natl Acad Sci U S A. 96:14559-64.
  4. Salama, N., K. Guillemin, T. K. McDaniel, G. Sherlock, L. Tompkins, and S. Falkow 2000. A whole-genome microarray reveals genetic diversity among Helicobacter pylori strains Proc Natl Acad Sci U S A. 97:14668-14673.
  5. Salama, N.R., G. Otto, and S. Falkow. 2001. Vacuolating cytotoxin of Helicobacter pylori plays a role during colonization in a mouse model of infection.  Infect Immun 69:0000, in press.