Pathogen Populations - Projects

Project Principal Investigator
Evolution of Eukaryotic Parasites Joana Carneiro Da Silva PhD
Impact of parasite diversity on vaccine efficacy and vaccine design Joana Carneiro Da Silva PhD
Impact of ongoing Schistosoma infection on malaria susceptibility Joana Carneiro Da Silva PhD
Parasite genomics resources Joana Carneiro Da Silva PhD
Lyme disease and comparative genomics of the Lyme agent, Borrelia Claire M. Fraser PhD,
NIAID-funded Genome Center for Infectious Diseases Integrated Genomics Research in Parasitic Tropical Diseases — Lymphatic Filariasis Subproject Julie Dunning Hotopp PhD
NIAID-funded Genome Center for Infectious Diseases Core Leader – Tech Core Julie Dunning Hotopp PhD
Genital Microbiome-Pathogen Interactions in a Sexual Transmission Network Jacques Ravel PhD
Evolution of Diversity in Microbial Pathogen Populations Jacques Ravel PhD
Genome Evolution and Pan-Genome Structure in Bacillus Jacques Ravel PhD
Genomic analysis of the biocontrol agent Lysobacter enzymogenes Jacques Ravel PhD
Regulation of Plasmodium vivax Parasites David Serre PhD
Host/pathogen Interactions and the Acquisition of Immunity to Malaria Parasites David Serre PhD
Characterization of Eukaryotic Parasites Causing Diarrhea David Serre PhD
Genome evolution during bacterial persistence in the human airways in COPD Herve S.G. Tettelin PhD
Identification of Virulence-Associated Properties by Comparative Genome Analysis of Streptococci Herve S.G. Tettelin PhD

Evolution of Eukaryotic Parasites

The phylum Apicomplexa comprises a diverse group of unicellular, eukaryotic parasites, many of which infect humans, or mammalian species on which human livelihood greatly depends. This phylum includes the causative agents of malaria, babesiosis, cryptosporidiosis, and toxoplasmosis in humans, as well as theileriosis and East Coast fever in cattle. The genome sequence for over a dozen apicomplexan species is available in either complete of draft form, including those of eight Plasmodium species, and three species of each in the Theileria, Babesia and Cryptosporidium genera.

Comparative genomic analyses of these genomes enables scientists to study the genetic correlates of pathogenicity and disease. In addition, several characteristics of these genomes, such as their small size, high gene density and lack of transposable genetic elements, make apicomplexasan ideal system to study the evolution of eukaryotic genomes.

Impact of parasite diversity on vaccine efficacy and vaccine design

One key contributor to the low efficacy of malaria vaccines in field trials has been the tremendous genetic variation in antigenic loci in Plasmodium falciparum, which has resulted in vaccine escape, whereupon a vaccine induces an allele-specific immune response that is most effective against epitopes similar to those in the vaccine, but has reduced efficacy against antigenically different parasites. We are characterizing the genetic diversity in a variety of P. falciparum antigenic loci that are vaccine candidates, for which we develop new algorithms, such as ETHA(link to bioinformatics project above) and ISCA(link to bioinformatics project above).

We collaborate actively with Sanaria, a biotechnology company in Maryland developing vaccines against malaria, on their PfSPZ Vaccine program, with the primary goals of (i) understanding the outcome of vaccine efficacy trials (e.g., Epstein et al, 2017, Moser et al.), and (ii) and to identify parasite targets of PfSPZ Vaccine-induced protection.

Impact of ongoing Schistosoma infection on malaria susceptibility

Despite significant progress in recent decades, parasitic diseases remain among the principal causes of mortality and morbidity worldwide. Malaria parasites and helminths alone are responsible for more than half a billion clinical infections every year, with half of the world’s population at risk. Using a combination of genomics and transcriptomics methods, we are characterizing the effect of ongoing Schistosoma haematobium infection on the host immune response to malaria infection in children and investigating if the immunomodulation exerted by schistosomiasis is long-lasting. This and multi-disciplinary studies carried on under the same award represent an initial step in the quantitative characterization of the role of co-infection on the outcome of parasitic infections, and in the investigation of host sex biases in parasitic infection studies. These two topics are critically understudied and yet impact millions of people worldwide. The implications of these findings could be wide-ranging and include novel approaches to study parasitic infection and co-infections in human and animal models, as well as public health insights into immunization and treatment approaches in high-priority parasitic diseases.

Parasite genomics resources

As part of these and previous parasite-focused projects, we have generated online genomics resources for Theileria parva , a parasite that causes East Coast Fever in cattle, and the human parasite Cryptosporidium hominis. These resources allow the user to search each parasite genome for proteins that satisfy several criteria important in the selection of viable vaccine candidates.

Lyme disease and comparative genomics of the Lyme agent, Borrelia

Lyme disease is the fifth most common Nationally Notifiable disease and the most commonly reported vector-borne illness in the United States. It is caused by spirochetes of the bacterial species group Borrelia burgdorferi sensu lato that is obligatorily transmitted by hard-bodied ticks (e.g., Ixodes scapularis in the US). Whereas incidence of Lyme disease in the USA is currently concentrated in the Northeast, Upper Midwest, and West Coast, the disease prevalence continues to rise and the geographic range of pathogen and tick populations continue to expand, with climate changes and declining biodiversity across the global as likely driving factors. Three specific public-health risks have emerged as results of the ongoing geographic expansion of Lyme disease pathogens and vectors. The first risk is the growth of previously rare and isolated pathogen populations ("spill-over"). For example, a new, highly human-virulent species B. mayonii has recently been discovered in the Upper Midwest. The second risk is the colonization of new areas by well-established pathogen populations elsewhere (“invasion”). For example, at least four different types of B. burgdorferi sensu stricto, the main pathogenic species in the U.S., are found in both Europe and North America, likely due to recent cross-Atlantic migration. The third risk is the increasing hybridization between previously segregated species or strains due to recombination (“mixing”). For example, Borrelia populations consists of recombinant genomes in North America and cross-species recombinants in Europe.

Given these heightening Lyme disease risks, there is a pressing need to characterize the full extent of genetic variations of Lyme disease pathogens by whole-genome sequencing. IGS scientists have previously sequenced and published complete genome sequences of over twenty Borrelia bacteria and performed extensive comparative analysis of these genomes. High-quality genome sequences of additional Borrelia strains that span the world-wide range of genetic and epidemiological diversity, including newly discovered Borrelia species and emerging strains of this clinically important bacteria, are currently in the works. Whole-genome sequencing are essential for deducing mechanisms of pathogenesis through comparative analyses, as well as for identifying genetic targets for vaccines, diagnostics, and therapeutics. In addition, high-quality reference genomes representing national and global Borrelia diversity have to potential to provide unprecedented resolution for epidemiological tracking, prediction, and control of the spread of Lyme pathogens.

[PI's: Dr. Sherwood Casjens, U. Of Utah, Dr. Benjamin Luft, Stonybrook U., Dr. Weigang Qiu, Hunter College of U. Of New York, Dr. Steven Schutzer, Rutgers U.]


NIAID-funded Genome Center for Infectious Diseases Integrated Genomics Research in Parasitic Tropical Diseases — Lymphatic Filariasis Subproject

Parasitic diseases impose a tremendous toll on the global public health. Malaria causes up to 1.24 million deaths every year, while human filariasis is a neglected tropical disease that remains a major cause of disability in the developing world. This subproject focuses on the filarial nematode Brugia malayi, which causes lymphatic filariasis. Population genomics, multi-species transcriptomics, and whole genome sequencing are used to improve our understanding of the organisms responsible for this important neglected tropical disease.


NIAID-funded Genome Center for Infectious Diseases Core Leader – Tech Core

Genomics has revolutionized research into infectious diseases and is poised to revolutionize the clinic. Through the activities in this technology core, we provide high-throughput genome sequencing and analysis focused on understanding host, pathogen, and microbiome interactions as determinants of disease outcome. We provide state-of-the-art, large-scale, high-throughput sequencing data for analysis of genomes, transcriptomes, metagenomes, metatranscriptomes, and microRNAs using the best methodologies and technologies available.


Genital Microbiome-Pathogen Interactions in a Sexual Transmission Network

Abundant lactobacilli in the human vagina are thought to protect against invasion by non-indigenous bacteria, including sexually transmitted infections caused by Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (GC). The means by which this happens are not well understood. It could be that these exclusionary mechanisms are properties of the vaginal microbiome, features of the host immune system and physiology, or some combination of both. The goal of this project is to employ a systems biology approach to identify biomarkers of the vaginal and penile microbiome, the host and the pathogens that are associated with increased or decreased risks of infection by CT, GC or both. Project 3 of this research program will rely on samples collected by the Clinical Core C from STING networks of sex partners who have been exposed to and possibly infected by CT, GC, or both. In these networks we expect that about 20-40% of the participants will have been exposed to, but not infected by these pathogens. This will give us the unique opportunity to assess the role of the microbiome in preventing or facilitating infections by CT and GC. Our overarching hypothesis is that when pathogen transmission does not occur the genetic traits of the infecting pathogen(s) may be insufficient to overcome the host response or the exclusionary mechanisms of the microbiome environment; or that features of the microbiome are protective or induce a protective mucosal environment. In this project, we will build on these findings and use modern ‘omic technologies to identify specific functional features of the vaginal and penile microbiota associated with susceptibility and resistance to infection and co-infection and the importance of host and pathogen genetic variation in this infection process, which will be done in collaboration with Projects 1 & 2. We will achieve these goals by addressing three integrated specific aims: Aim 1. Characterize the genomic variations in CT/GC in participants of the STING networks of sex partners; Aim 2. Use ‘omic approaches and system biology analysis characterize the molecular interactions between the host, the pathogens and the genital microbiota in discordant and concordant couples for CT/GC infections; Aim 3. Validate and explore mechanistic explanations for how the microbiota prevent or facilitate infection by CT/GC using an in vitro three-dimensional model of endocervical epithelial cells. Our long-term goal is to leverage the information generated in this project to develop improved diagnostic methods, identify novel targets for new drug development and develop targeted and effective curative or preventive therapies, and ultimately, promote health, reduce risk to unintended adverse sequelae of STI and improve the quality of life for men and women who are at risk of STIs.


Evolution of Diversity in Microbial Pathogen Populations

The use of sequencing or chip-based genomic approaches makes it possible to gain insights into the genetic diversity and genome dynamics of bacterial pathogen populations. We study Yersinia pestis, Escherichia coli O157:H7 and diverse Bacillus and Chlamydia species as model systems, all of which have several representative in-house sequenced genome sequences available. A comparative analysis of these populations allows to analyze the types of host variation, selection and adaptation occurring during the time course of a single or multiple outbreaks of human disease and further to elucidate common and unique traits in genome evolution and speciation. To study these subtle but important genetic variations, we have developed a bioinformatics pipeline that facilitates the discovery and validation of rare polymorphisms taking into account the respective genome sequence read coverage and quality. Applying single nucleotide polymorphism (SNP)-based genotyping and re-sequencing methodologies, we are able to reconstitute a detailed evolutionary history of these microbial pathogens and resolve their genetically highly homogenous population structures. Studying the pan-genome, the global gene reservoir of the species, led to an estimate of the degree of reductive evolution and the extent of influx of genetic material via horizontal gene transfer, which aids in the definition of more accurate genetic species borders. The discovery of such genetic alterations in these dynamic bacterial pathogen populations can therefore provide insights into the genome evolution as well as the individual pathogenic potential critical for future forensic, diagnostic and epidemiological studies.


Genome Evolution and Pan-Genome Structure in Bacillus

Most of the aerobic Gram-positive spore-forming bacteria were originally placed in the genus Bacillus. As a result, it is a very diverse genus consisting of at least six clades and GC-content ranging from 33-64%. The sequencing of several Bacillus genomes has been completed in the last few years, but has mainly covered genomes of the pathogenic Bacillus thuringiensis-anthracis-cereus group or those closely related to B. subtilis. The ancient nature of B. megaterium makes it of particular importance in understanding the genome evolution, genome dynamics and speciation in Bacillus. The aim of this genomic study is to catalogue the genomic inventory of B. megaterium strain QMB1551 that carries an array of seven plasmids, and the naturally plasmidless isolate DSM319, to study the Bacillus biology through in-depth comparative genomics. The simultaneous sequencing of two prominent B. megaterium strains, deeply rooted in the phylogeny, presents an unique opportunity to study the genomic plasticity and genome evolution of the Bacillus group of organisms and can help to identify unique genetic traits not previously seen in Bacillus. Using the whole genome data of both genomes will allow to predict the species pan-genome and the extent of exchange of genetic material. The potential dissemination of genetic information between chromosomes and plasmids and to other members of the Bacillus group leads to a generation of unique genotype and phenotypes that might be relevant for species-specific niche adaptations.


Genomic analysis of the biocontrol agent Lysobacter enzymogenes

Genomic analysis of the biocontrol agent Lysobacter enzymogenes. The genomic analysis of Lysobacter enzymogenes is a collaborative effort with Donald Kobayashi, Ph.D., from Rutgers University. This rapidly emerging bacterium is of major ecological and agricultural relevance. Known primarily as a prolific producer of enzymes and antibiotics, such as ß-lactams containing substituted side chains, macrocyclic lactams and macrocyclic peptide antibiotics, the species is gaining recognition for a number of novel features stemming from its ecological diversity, industrial applications, and most notably, unique biotic interactions. Lysobacter spp. genomes consist of relatively high G+C content typically ranging between the 65-72%. The group is regarded as a rich source for production of novel antibiotics. The feature of gliding motility alone has piqued the interest of many, since the role of gliding bacteria in soil ecology is poorly understood. In addition, while a number of different mechanisms have been proposed for gliding motility among a wide range of bacterial species, the genetic mechanism in Lysobacter remains unknown. Recent studies indicate L. enzymogenes is capable of establishing unique pathogenic interactions with a broad range of hosts that include lower plants and microbial eukaryotic hosts. This promiscuous behavior provides a unique opportunity to establish L. enzymogenes as a model organism for pathogenic interaction studies with lower organisms. Availability of the genome sequence of L. enzymogenes will provide insights into the general biology, parasitic lifestyle and biological control capacity of the organism. This project is funded under the U.S. Department of Agriculture Microbial Genome Sequencing Program (USDA-CRESS).


Regulation of Plasmodium vivax Parasites

Plasmodium vivax is a unicellular parasite responsible for the majority of the cases of human malaria outside sub-Saharan Africa. While on-going malaria elimination efforts are reducing the burden of falciparum malaria worldwide, the situation is much less promising for P. vivax, which displays very different features than P. falciparum. Unfortunately, our understanding of the biology of P. vivax parasites dramatically lags behind that of P. falciparum, primarily due to our inability to propagate these parasites in vitro. We are using a combination of genomic approaches, including single cell gene expression profiling, to better understand these parasites and how they are regulated throughout their life cycle in patients as well as during their development in mosquitoes.


Host/pathogen Interactions and the Acquisition of Immunity to Malaria Parasites

Plasmodium falciparum causes more than 200 million cases of clinical malaria and half a million deaths every year. Falciparum malaria disproportionally affects young children as individuals living in endemic areas gradually acquire immunity against the disease. We are interested in understanding the role of the host and parasite gene expression in this acquisition of immunity against falciparum malaria and are conducting a study of infected Malian children followed for four years to better characterize the molecular changes accompanying the gradual acquisition of resistance to malaria parasites.


Characterization of Eukaryotic Parasites Causing Diarrhea

Diarrheal diseases are responsible for more than two billion cases every year and constitute one of the main global health challenges. The disease is particularly common in developing countries, where it disproportionally affects young children who, on average, get diarrhea three times a year. Diarrhea results from an infection in the intestinal tract, which can be caused by a variety of bacteria, viruses and eukaryotic parasites. In most studies, less than half of the diarrhea cases can be attributed to a known pathogen. We have developed new tools to comprehensively characterize all eukaryotic parasites present in a sample and are screening 3,600 stool samples collected by the GEMS study in four countries from infants with diarrhea and matched controls to identify novel pathogens and assess their contributions to the disease etiology.


Genome evolution during bacterial persistence in the human airways in COPD

I have conducted in-depth comparative genomics analyses of isolates of nontypeable Haemophilus influenzae (NTHi) that are critical to the pathogenesis of chronic obstructive pulmonary disease (COPD). We conducted whole-genome sequencing of 269 longitudinally collected cleared and persistent NTHi from a 15-y prospective study of adults with COPD (d). We elucidated the phylogeny of NTHi isolates, identified genomic changes that occur with persistence in the human airways, and evaluated the effect of selective pressure on candidate vaccine antigens. Slipped-strand mispairing, mediated by changes in simple sequence repeats in multiple genes during persistence, was found to regulate expression of critical virulence functions and to be a major mechanism for survival in the hostile environment of the human airways. Our results advanced our understanding of how a bacterial pathogen that plays a critical role in COPD adapts to survival in the human respiratory tract. We are now studying host-pathogen interactions in COPD focusing on NTHi as well as Moraxella catarrhalis (Mcat). Guided by dynamic changes in genomes and transcriptomes in human airways, we will elucidate mechanisms that mediate persistence of NTHi and Mcat using relevant model systems.

[PI: Tim Murphy, U. at Buffalo]


Identification of Virulence-Associated Properties by Comparative Genome Analysis of Streptococci

From a common ancestor, Streptococcus pneumoniae and Streptococcus mitis evolved in parallel into one of the most important pathogens and a mutualistic colonizer of humans, respectively. This evolutionary scenario provides a unique basis for studies of both infection-associated properties and properties important for harmonious coexistence with the host. We performed detailed comparisons of 60 genomes of S. pneumoniae, S. mitis, Streptococcus pseudopneumoniae, the three Streptococcus oralis subspecies oralis, tigurinus, and dentisani, and Streptococcus infantis. Nonfunctional remnants of ancestral genes in both S. pneumoniae and in S. mitis support the evolutionary model and the concept that evolutionary changes on both sides were required to reach their present relationship to the host. We used in-depth comparative genomics approaches to identify 224 genes associated with virulence. The striking difference to commensal streptococci was the diversity of regulatory mechanisms, including regulation of capsule production, a significantly larger arsenal of enzymes involved in carbohydrate hydrolysis, and proteins known to interfere with innate immune factors. The exclusive presence of the virulence factors in S. pneumoniae enhances their potential as vaccine components, as a direct impact on beneficial members of the commensal microbiota can be excluded. In addition to loss of these virulence-associated genes, adaptation of S. mitis to a mutualistic relationship with the host apparently required preservation or acquisition of 25 genes lost or absent from S. pneumoniae.

[Not funded, collaborator: Mogens Kilian, Denmark]