Center for Pediatric Genomics
A Rational Design of a New Diagnostic Method for Pediatric Pneumocystis Pneumonia

A Rational Design of a New Diagnostic Method for Pediatric Pneumocystis Pneumonia

Principle Investigator: Alexey Porollo, PhD, Center for Autoimmune Genomics & Etiology

A photo of Alexey Porollo.Pneumocystis pneumonia (PCP) may become lethal if left untreated underscoring the need for a sensitive diagnostic method, especially in children. Pneumocystis pneumonia (PCP) is an opportunistic fungal respiratory infection, frequently associated with HIV/AIDS patients, and is an emerging threat to the immunocompromised patients without HIV. It is estimated that there are more than 400,000 new cases of PCP worldwide annually. Importantly, PCP has been recognized as a disease in children with primary cell-mediated immunodeficiency -- pediatric patients receiving chemotherapy for hematological malignancies, solid organ and bone marrow transplant recipients, and those requiring immunosuppressants. The pathogen is not susceptible to azole-based antifungals, and a wide prophylaxis of the infection is problematic. Clinical manifestation of PCP is non-specific. The current gold standard diagnostic approach is a microscopic study of the stained bronchoalveolar lavage specimens. However, being an invasive procedure, it is impractical for all suspected patients to undergo such testing, especially those with respiratory failure. Since pneumocystosis is an airborne infection, we hypothesize that it will be possible to identify a set of abundant fungal gene transcripts in the upper respiratory tract that will enable the quantification of infection burden and discriminate it from colonization. Also, since pneumocystis spp. are obligate parasitic organisms and have different metabolic strategies compared to other free living (pathogenic) fungi, we hypothesize that it will be possible to identify the PCP signature metabolites by comparing the metabolomics profiles of pneumocystosis with other respiratory fungal infections and bacterial pneumonia.

We are collecting biological specimens from the four groups of pediatric patients: (i) diagnosed with PCP; (ii) diagnosed with other fungal infections; (iii) diagnosed with bacterial pneumonia; and (iv) with no symptoms of pneumonia nor fungal infection. Specimens will include nasal swabs and oral washes (all from URT). In addition, we are identifying biomarkers unique to PCP. For the collected samples, we are conducting meta-transcriptomic sequencing (RNA-seq) and LC-MS/MS-based metabolomics analysis. Finally, we are designing prototype tests for candidate biomarkers derived from the instrumental analysis. For the identified candidates, we are assigning tailored molecular biological assays to assess their sensitivity, specificity, and amenability to quantification. We are evaluating predictive models based on both individual and combined biomarkers.

The overarching goal of this project is to improve pediatric healthcare for PCP-infected patients through the discovery of biomarkers and design of new, rapid, noninvasive, molecular tests for PCP based on the biomedical analysis of the transcriptomics and metabolomics data. This project will lay out a foundation for a minimally invasive, rapid, molecular clinical test at the point-of-care for PCP in pediatric patients, thereby improving child healthcare.

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