The focus of our research centers on the complex nature of the interaction between a pathogen and its host. From both perspectives, the organism must sense the presence of the other, respond accordingly, and adapt to the many changes throughout the interaction. We leverage the fields of microbiology, immunology, genetics, genomics, and transcriptomics to understand various aspects of pathogens, their virulence mechanisms, and the response elicited by the host when challenged with these pathogens.

Circular representations and comparison of the Y. pseudotuberculosis IP32953 and Y. pestis CO92 genomes.
Circular representations and comparison of the Y. pseudotuberculosis IP32953 and Y. pestis CO92 genomes.

Science in Support of National Objectives

Our research is primarily focused in the Laboratory’s mission of biodefense by studying key pathogens and how they cause disease in humans and animals. Increased understanding of the diversity and nature of pathogens will provide insightful details into what genetic markers may be used for detection, identification, and forensics. The ability to distinguish and discriminate between virulent and non- or less virulent pathogens is another area of active research. Our goal is to better understand what genetic factors are involved in the virulence process and thus help to identify potential methods to block or treat disease. Similarly, understanding how the host responds to invasion by the pathogen and how the pathogen evades or uses the immune response to better subvert the host, will help in the development of vaccines and prophylaxes.

Major Accomplishments

Through genome sequencing and comparative genomics, we identified markers that are specific to select bacterial pathogens and may thus be used for their detection and identification. We studied the global expression profile of several pathogens as a function of growth, temperature, and pH, and have related the expression of virulence factors to specific conditions. We performed comparative genomic analyses to better understand the differences between closely related pathogens of the Yersinia, Francisella and Brucella groups, information that can now be used to explore the impact of specific key genes on virulence and host-adaptation.

In addition, we have studied the initiation of host innate immune responses to Francisella tularensis as well as understanding bacterial factors important for environmental persistence. Using commercial and custom microarray technologies, we identified genes and gene pathways important in both the host and pathogen during infections of both human and mouse macrophages. This approach has generated a global understanding of factors involved in the initial infection process and has revealed marked differences in the host response to two strains of F. tularensis, both fully virulent in mouse models. Such distinctions underscore the importance of comparative studies in understanding host response, immunity and virulence. We are also performing similar studies with the fully virulent strain of F. tularensis subspecies tularensis. 

Circular representations and comparison of the Y. pseudotuberculosis IP32953 and Y. pestis CO92 genomes.
Whole genome linear comparison of both chromosomes of B. abortus 2308, B. melitensis 16M, and B. suis 1330 (from Chain et al. 2006).

Currently, the primary reservoir for F. tularensis in nature is unknown, although the bacterium has one of the largest host ranges described to date. Interestingly, F. tularensis can often be isolated from water sources and has been shown to survive inside amoeba species. Our studies are aimed at understanding the interaction between the bacterium and Acanthamoeba castellanii, a potential model for its natural reservoir. To date, we have shown that F. tularensis subspecies novicida and F. tularensis LVS both survive inside encysted amoeba. Further, unlike LVS, novicida appears to cause rapid encystment of the amoeba suggesting the bacterium may secrete factors involved in amoeba encystment, thus ensuring its own persistence.  We are also assessing the ability of the fully virulent strain of F. tularensis to induce amoeba encystment in an attempt to understand long-term survival within the environment.

Scientific Impact

We have identified those regions of the genome of Yersinia pestis that are unique to this highly virulent pathogen and that distinguish it from less virulent and/or avirulent members of this group. These regions are being examined by animal studies on specific knockout mutants to determine the possible role they play in the virulence process. Again, through comparative genomics, we have identified a unique pattern of inactivation of flagellar associated genes within the various Brucella human pathogens that may play a role in host-specificity. For Francisella, we are making progress in understanding how highly pathogenic and less pathogenic strains interact with amoeba.

Related Publications

Contact: Patrick Chain [bio], 925-424-5492,

Circular representation of the F. tularensis SchuS4 genome. (from Larsson et al. 2005)

New Frontiers

We are using microarray and sequencing technologies to better understand how the host and pathogen interact with one another, what genes are preferentially being expressed upon invasion, and what genes are required for virulence and onset of disease. Through a variety of methods, we are exploring subsets of genes that may be required for a pathogen’s disease-causing ability. We are interested in supporting initial evidence with targeted mutants and test our hypotheses in an in vivo model of infection.

Further, we intend to leverage whole genome comparisons of the pathogenic Brucella species performed in our laboratory and the availability of immune sera from infected patients and animals obtained from the Republic of Kazakhstan (a foci of Brucella infection), to identify and generate diagnostic protein reagents for the early diagnosis of Brucellosis in humans and animals as well as potential vaccine targets. Targeted unique genes encoding proteins likely to be surface exposed within the Brucella can be overexpressed and screened with immune sera from animals and humans in order to generate a set of diagnostic reagents and vaccine targets which will be independent of bacterial lipopolysaccharide (LPS) and thus, of much greater specificity since LPS is a molecule found in the cell wall of all gram negative organisms.