Evolution of microbial pathogens

The whole meeting was quintessentially ‘Cold Spring Harbor’, comprising broad-ranging presentations that were interspersed by animated and lively discussions. In particular, the session on Microbial Evolution and Genomics led to considerable discussion about the direction of post-genomic research in dissecting the host–pathogen interactions.One of the surprises from microbial genome sequencing projects was the extent of lateral gene transfer between different microbes, often indicated by islands of DNA with a different GC content and/or codon preference than the rest of the genome. Many of these islands contain sequences similar to known phage genes. In the pre-genomic era, the bacterial chromosome was thought to be a graveyard for dead phage – many lysogenic phages were thought to be cryptic remnants of ancestral viruses. Three talks emphasized that, in contrast with this pre-genomic perspective, ‘bacteria act as hotels for phage that may be sleeping but are very much alive’ and play important roles in the mechanism and evolution of bacterial virulence.Matthew Waldor (Tufts University, Boston, MA, USA) briefly reviewed the role of filamentous phage in the transfer of cholera toxin between Vibrio cholerae strains, and then focused on the role of phage in virulence of the enteric pathogen Escherichia coli O157:H7, the genome of which has recently been sequenced (see http://www.genetics.wisc.edu/). This particular E. coli strain is responsible for several worldwide outbreaks of serious food-related illnesses. Genomic sequence analysis has revealed at least 13 phage on the chromosome of this E. coli strain. One lambdoid prophage contains a principal virulence factor, the shiga-like toxin (Stx), which causes severe clinical conditions such as the hemolytic uremic syndrome. Expression of Stx is induced by the late genes of the phage, thus induction of lytic growth of the phage enhances the virulence of E. coli O157:H7. This leads to a practical paradox: because the phage itself produces the toxin, treatment of infected patients with antibiotics that kill the bacteria and induce the phage could exacerbate clinical symptoms.Lionello Bossi (CNRS, Gif-sur-Yvette, France) described two lysogenic phage on the chromosome of Salmonella enterica serovar Typhimurium (S. enterica Typhimurium). These phage, Gifsy-1 and Gifsy-2, both transfer virulence genes between several Salmonella serovars****The genomes of several Salmonellae are being sequenced (see http://www.salmonella.org, http://genome.wustl.edu/gsc/bacterial/salmonella.shtml and http://www.sanger.ac.uk/Projects/S_typhi/).. Gifsy-2 contains the sodC gene, an essential virulence determinant. Both Gifsy phage are functional and, under appropriate conditions, will excise from the chromosome, lyse their host, and form visible plaques on recipient strains. Theresa Ho (University of Illinois, Urbana, IL, USA) discussed another gene on the Gifsy-2 genome, grvA, which has an avirulence phenotype – mutations in grvA increase virulence relative to the wild-type strain. This is the first true avirulence gene described in Salmonella, and emphasizes the unique role of the phage in optimizing Salmonella virulence. Together these talks emphasized the pivotal role of phage in the simultaneous acquisition of multiple virulence determinants. Given the number of ‘phage-like’ genes that have been identified in searches for virulence genes, additional genome sequences are likely to reveal other novel virulence factors associated with phage. The integral role of phage in the virulence of many bacteria, and the ability to transfer virulence genes between bacteria within the host, emphasizes that phage are major factors in the evolution of bacterial virulence.Pathogenicity islands are contiguous clusters of genes that are required for virulence and are not found in closely related bacteria. S. enterica Typhimurium has at least five large pathogenicity islands not present in the closely related E. coli that are critical for its virulence. Two presentations focused on how the acquisition of pathogenicity islands allowed the evolutionary adaptation of pathogens to new niches. Robert Kingsley (Texas A&M University, TX, USA) described a pathogenicity island that affects the transmissibility of Salmonella, and that might have contributed to the adaptation of Salmonella from cold-blooded to warm-blooded hosts. Howard Shuman (Columbia University, NY, USA) summarized the work of several laboratories, including his own, on the origin and function of genes from Legionella pneumophilia that are required for intracellular multiplication. Legionella can grow within human alveolar macrophages and kill them, causing Legionnaires’ disease. In the environment, Legionella can grow in a similar way in free-living protozoa, and it appears that many of the genes involved in the human disease are also required for growth in protozoa. A cluster of Legionella genes, called either icm or dot, facilitate the transfer of effector molecules to the host cell, and are required for intracellular growth in humans and in protozoa. These genes are not required for growth in vitro and encode a secretion apparatus that is similar to the type IV systems used by enteric bacteria to transfer effector molecules into host cells. Intriguing differences between the icm/dot system and other type IV secretory systems suggest that the Legionella system has unique functions. Based upon genetic and genomic comparisons with related bacteria, acquisition of the icm genes probably led to an evolutionary leap for Legionella to an intracellular niche.Thus, microbial genome sequences are providing new insights into the evolution of microbial virulence and into virulence determinants and their acquisition. Progress in this direction has resulted from intellectual exchanges between the fields of genomics, genetics, biochemistry and cell biology. The insights from these studies will probably lead to practical applications in disease management and treatment that would have been inconceivable less than a decade ago.