Biology and Diversity of Emerging Eukaryotic Pathogens



Introduction: The team “Biology and Diversity of Emerging Eukaryotic Pathogens” (BDEEP) targets eukaryotic pathogens responsible for emergent or re-emergent diseases with growing impact for the last years, currently constituting major public health issues. These agents are responsible for severe nosocomial diseases, like opportunistic micromycetal fungi such as Pneumocystis, or frequent community infections, like the protists Blastocystis or Cryptosporidium. However, although these pathogens are among the most frequently encountered by humans worldwide, the diseases they cause are usually neglected or considered “rare” by health authorities and research organizations. Consequently, basic biology research on these eukaryotic microorganisms is urgently required to understand their circulation in ecosystems, mechanisms of proliferation and infection, pathophysiology, to clarify their real biodiversity, and to define cost-effective, field-adapted, rational prevention and control strategies.

Collaborations are developed with numerous French laboratories and hospitals and groups established in Europe, Asia, Africa, North and South America, and Australia. Research projects are supported by University of Lille 2, Institute Pasteur of Lille, CNRS, Inserm, French Ministry of Health, (3 National Clinical Research Hospital Programs funded), National Research Agencies (6 programs funded by ANR), Region Nord Pas de Calais (2 programs), and Research Grants from private companies, platforms and associations like Genediffusion/Pegase, Genoscreen, Pfizer, and “Vaincre la mucoviscidose”


Parasitic protozoa: Blastocystis, Cryptosporidium and eukaryotic microbiota analysis: BDEEP will focus its research activities on the intestinal parasitic protozoa Blastocystis and Cryptosporidium for which the team has a recognized international expertise. Both parasites are responsible for gastrointestinal infections which can be severe, sometimes fatal in immunocompromised patients, and currently constitute major socioeconomic and public health issues. Since these parasites remain neglected by health authorities, basic knowledge on their biodiversity, circulation, and pathophysiology is urgently required especially because few or no efficient treatments are available against these infections. Moreover, as they exhibit a large genetic diversity and can be found in numerous hosts, these protozoa also represent invaluable models to address a major biological question in the field of Ecology of Parasitism which roughly summarizes the main research goal of BDEEP: what is the nature of the genetic diversity of these parasites and its impact on the circulation and pathogenicity of different species, strains, or subtypes? The project will be focused on three specific aims: 1) Determining the prevalence and biodiversity of these parasites in human populations, 2) Tracking risk factors of transmission to humans and 3) Clarifying the pathogenicity of different species, strains or subtypes and identifying virulence factors. To achieve our goals, large-scale epidemiological studies including human, animal and environmental samples will be performed in different countries. Reproducible animal models of blastocystosis and cryptosporidiosis are developed in our group. In addition, variations in the composition of intestinal prokaryotic and eukaryotic microbiota of different hosts will be followed by metagenomics during infection. By revealing the presence of cultivable or uncultivable pro- and eukaryotic microorganisms, metagenomics makes-it-possible a high-throughput exploring of multiple coinfection in colonized or infected hosts. This research domain is also providing data and ideas of high practical interest, especially in the field of prevention strategy, and/or prophylaxis. It could contribute to understand, for instance, whether changes in microbiome hosts can influence clinical outcome. Comparative genomics and transcriptomics studies will also be performed to identify species, strains or subtype-specific genes involved in virulence which may lead to the design of inhibitors. In parallel, functional genetics will also be developed for both parasites to study proteins of interest.


Pneumocystis intimate host-parasite interaction and pulmonary colonization

Introduction - Pneumocystis organisms are atypical opportunistic fungi that are aerially-transmitted from host-to-host. They form a group of host-species-specific microorganisms colonizing or infecting a vast diversity of mammalian hosts in various ecosystems. In human, Pneumocystis can cause severe pneumonia (PcP) in immunosupppressed hosts. Clinical and experimental data also support an increased prevalence of Pneumocystis colonization, acting as a co-morbidity factor in chronic pulmonary diseases.Interestingly, the concept of colonization by Pneumocystis organisms is not separable from the concept of very narrow host-specificity of Pneumocystis organisms. Consequently, our research covers two major domains that interact reciprocally: (i) Pneumocystis host-species specificity to clarify molecular basis of this unique trait among pulmonary fungal pathogens, and (ii) Pneumocystis transmission and colonization in immunocompromised or immunocompetent hosts to assess colonization-to-disease shift in relation with the immune status of the host as well as the impact of colonization on human chronic pulmonary diseases. This translational project brings together several fields of expertise such as basic mycology, comparative genomics, transcriptomics, metagenomics, phylogenomics, and clinical research.

Pneumocystis host-specificity – Unraveling the molecular basis of the Pneumocystis host-specificity is a real challenge if one considers the absence of a continuous in vitro culture method and the lack of a complete and annotated genome sequence for these fungi. To overcome these obstacles, we use reproducible PcP experimental models and highly-efficient cell-sorting methods, which were developed by our team and allow separating both Pneumocystis cells from lung tissue and Pneumocystis cysts from trophic forms. We are also developing an integrated initiative combining cutting-edge genomic and transcriptomic approaches that consist in performing: (i) a de novo genome sequencing of two closely-related Pneumocystis species (i.e. P. carinii and P. murina) and comparative genomics to characterize candidate genes that may be involved in host specificity; (ii) dual-RNAseq to simultaneously decode the cellular and molecular bases of mammalian-host-lung/Pneumocystis interactions from both the host and pathogen viewpoints. We anticipate that understanding the molecular and cellular bases of the Pneumocystis-host specificity is critical (i) to understand the long-term and specific adaptation of Pneumocystis to the lung environment, (ii) to identify the metabolic strategies used by these fungi to grow and survive in the alveolar space.

Pneumocystis transmission and colonization in immunocompromised or immunocompetent hosts - To better delineate the shift from Pneumocystis colonization to PcP in immunocompromised patients, we propose to relate the degree of host immunodepression and the risk of infection by Pneumocystis using an experimental model of transmission mimicking natural airborne contamination. The relative-risk of contracting Pneumocystis infection according to the host immune status will be established. Furthermore, as P. jirovecii has been recognized to contribute to the aggravation of chronic obstructive respiratory diseases, our group will aim at assessing the circulation and impact of the colonization by P. jirovecii and other fungal pathogens on pulmonary impairment and inflammation in patients with COPD during clinical ongoing follow-up at the Lille University Hospital Center in the “FungiCOPD” prospective clinical study, that we coordinate. Clinical data combined with results from experiments conducted in animal models of COPD will allow us to decrypt biological mechanisms likely involved in the fungal colonization-to-infection shift potentially responsible for the alteration of lung function in such chronic pulmonary conditions.


Conclusions: The BDEEP team tries to address key issues common to these two groups of organisms regarding i) prevalence, molecular diversity, and circulation in human and animal populations, ii) characterization of genetic diversity and its impact on pathogenic power and on transmission of the identified species and variants, iii) the molecules and mechanisms involved in pathogenesis and proliferation and iv) interactions with host cells.

BDEEP expertise in Protistology, Parasitology, and Mycology will be promoted in our activities as it is commonly requested by public laboratories, regional and governmental agencies, and private companies as part of the identification and taxonomy of microorganisms of medical or environmental interest.

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