Our lab has used a combination of genetic, molecular, biochemical, and genomic approaches to understand general biological processes and the evolution of pathogens, and to design new therapeutic approaches to thwart infections.

Evolution of emerging infectious diseases. Genes that encode exotoxins are often carried on phage. Metagenomic studies by the Rohwer lab demonstrated that phage in the environment are an abundant source of exotoxin genes, including Diptheria toxin, Cholerae toxin, Shiga toxin, and many others. To gain insight into the evolution of new infectious diseases, we are studying exotoxin genes in the Tijuana River Estuary, a vulnerable natural habitat that is impacted by upstream human activities. We have identified novel reservoirs of exotoxin genes in the environment, providing a mechanism for the rapid evolution of new pathogens by the transfer of these virulence factors to new bacteria, potentially converting avirulent bacteria into pathogens.

Host specificity of Salmonella. The genus Salmonella enterica includes over 2500 distinct serovars that are a major cause of food poisoning. These Salmonella serovars infect different types of animals. Strains with new virulence properties may arise by changes in host-specificity that allow them to infect a new animal host. Until recently, little was known about the genetic determinants of host-specificity in bacteria. To identify genes responsible for host-specific virulence traits, we developed methods to construct genetic hybrids between broad host-range Salmonella sv. Typhimurium and the host-specific sv. Typhi. It was not possible to alter the host-specificity of Typhi by genetic exchange with any single region of the Typhimurium chromosome, indicating that host-specificity is determined by multiple, unlinked genetic loci. Coupling these results with comparative genomics, results from our lab and other research groups indicates that pseudogenes limit the host-range of bacterial pathogens.

Chromosome rearrangements. In contrast to most well studied bacteria including Salmonella sv. Typhimurium and E. coli, inversions between the seven rrn operons on the chromosome of host-specific Salmonella serovar Typhi occur at a high frequency. We have used genetic and molecular tools to determine why inversions occur so much more readily in host-specific pathogens. Our studies indicate that the abundance of inversions (and pseudogenes) is a result of the host-restricted lifestyle.

Designer antimicrobials. Traditional broad-spectrum antibiotics suffer from high levels of resistance, and disruption of the host microbiome that can result in chronic secondary sequelae. Nevertheless, because it is often difficult to differentiate the cause of an infection based upon symptoms alone, broad spectrum antibiotics continue to be widely used. New diagnostic methods allow rapid, precise identification of pathogens responsible for an infection, allowing the rationale use of narrow-spectrum antimicrobials. It is possible to design genome based antisense nucleotides that disrupt a critical genetic target that is present in a particular pathogen, but lacking in the microbiome or host genomes. In addition, antisense nucleotides can be rapidly redesigned for new target specificity in response to development of resistance. Genetic analysis of mutants resistant to antisense nucleotides has identified secondary targets that can be simultaneously inhibited to enhance effectiveness of this approach. Engineered bacterial genetic exchange mechanisms allow efficient delivery of the antisense nucleotides in vivo.