Droplet Digital PCR and PCR-free BIOSensors for the Detection of Resistance-associated SNPs in Pneumocystis Jirovecii

Pneumocystis Pneumonia Clinical Trial

— DDBIOS  

Official title:

Droplet Digital PCR and PCR-free BIOSensors for the Detection of Resistance-associated SNPs in Pneumocystis Jirovecii

Clinical Trial Details — Status: Not yet recruiting

Administrative data

• NCT number: NCT06431958
• Other study ID #: 29BRC24.0085 - DDBIOS
• Status: Not yet recruiting
• Start date: June 1, 2024
• Est. completion date: December 31, 2026

Study information

• Verified date: April 2024
• Source: University Hospital, Brest
• Contact: Gilles NEVEZ
• Phone: 0298345091
• Email: gilles.nevez[@]chu-brest.fr
• Is FDA regulated: No
• Study type: Observational

Clinical Trial Summary

The main objective of the proposed research is to identify Pneumocystis jirovecii mutant strains on 4 genes encoding therapeutic targets such as dihydropteroate synthase (DHPS), dihydrofolate reductase (DHFR), cytochrome b (CYB), inosine-5'-monophosphate dehydrogenase (IMPDH) and therefore to assess the prevalence of potentially resistant strains in patients infected with P. jirovecii.

Description:

Pneumocystis jirovecii (P. jirovecii) is an opportunistic pathogenic fungus responsible for pulmonary infection or Pneumocystis pneumonia (PCP) in immunocompromised patients. There is currently no system for its in vitro culture. The diagnostic methods used are mainly based on molecular biology techniques which also allow the detection and analysis of single nucleotide polymorphisms (SNPs), particularly at the level of genes coding for the targets of molecules widely used in the prevention and treatment of PCP. These SNPs may represent missense mutations potentially associated with treatment resistance. They may result from exposure of patients to these treatments before the development of P. jirovecii infection. However, data concerning the prevalence of these mutations remains scarce, particularly in France. Methods for detecting these mutations based on PCR followed by DNA sequencing have limitations in terms of sensitivity. The evaluation of new, more sensitive and rapid tools for the detection and characterization of pathogens in this context is necessary.

The main objective of the proposed research is to identify P. jirovecii mutant strains on 4 genes encoding therapeutic targets such as dihydropteroate synthase (DHPS), dihydrofolate reductase (DHFR), cytochrome b (CYB), inosine-5'-monophosphate dehydrogenase (IMPDH) and therefore to assess the prevalence of potentially resistant strains in patients infected with P. jirovecii.

The secondary objectives are:

• to determine the factors associated (e.g. exposure to treatments) with mutant P. jirovecii strains

• to determine the impact of mutations on the effectiveness of anti-Pneumocystis treatment (e.g. favorable vs. unfavorable evolution of the infection)

• to evaluate two methods - digital droplet PCR and biosensors without PCR - for the detection and characterization of mutations associated with resistance in Pneumocystis jirovecii

Recruitment information / eligibility

• Status: Not yet recruiting
• Enrollment: 300
• Est. completion date: December 31, 2026
• Est. primary completion date: December 31, 2026
• Accepts healthy volunteers: No
• Gender: All
• Age group: N/A and older

Eligibility

Inclusion Criteria:

• Patients in whom P. jirovecii was detected in a pulmonary sample (bronchoalveolar lavage, sputum, bronchial aspiration, oropharyngeal rinse, nasopharyngeal sample)

• No opposition

• Patient affiliated to a social security system

Exclusion Criteria:

• Patients under legal protection (guardianship, curatorship)

• Refusal to participate

Related Conditions & MeSH terms

• Pneumocystis Pneumonia
• Pneumonia, Pneumocystis

Locations

Country	Name	City	State
France	Chu Brest	Brest

Sponsors (1)

Lead Sponsor	Collaborator
University Hospital, Brest

Country where clinical trial is conducted

France, 

References & Publications (7)

Argy N, Le Gal S, Coppee R, Song Z, Vindrios W, Massias L, Kao WC, Hunte C, Yazdanpanah Y, Lucet JC, Houze S, Clain J, Nevez G. Pneumocystis Cytochrome b Mutants Associated With Atovaquone Prophylaxis Failure as the Cause of Pneumocystis Infection Outbrea — View Citation

Bonnet PL, Hoffmann CV, Le Nan N, Bellamy L, Hoarau G, Flori P, Demar M, Argy N, Morio F, Le Gal S, Nevez G. Atovaquone exposure and Pneumocystis jirovecii cytochrome b mutations: French data and review of the literature. Med Mycol. 2023 Sep 4;61(9):myad0 — View Citation

de la Horra C, Friaza V, Morilla R, Delgado J, Medrano FJ, Miller RF, de Armas Y, Calderon EJ. Update on Dihydropteroate Synthase (DHPS) Mutations in Pneumocystis jirovecii. J Fungi (Basel). 2021 Oct 13;7(10):856. doi: 10.3390/jof7100856. — View Citation

Hoffmann CV, Nevez G, Moal MC, Quinio D, Le Nan N, Papon N, Bouchara JP, Le Meur Y, Le Gal S. Selection of Pneumocystis jirovecii Inosine 5'-Monophosphate Dehydrogenase Mutants in Solid Organ Transplant Recipients: Implication of Mycophenolic Acid. J Fung — View Citation

Kojabad AA, Farzanehpour M, Galeh HEG, Dorostkar R, Jafarpour A, Bolandian M, Nodooshan MM. Droplet digital PCR of viral DNA/RNA, current progress, challenges, and future perspectives. J Med Virol. 2021 Jul;93(7):4182-4197. doi: 10.1002/jmv.26846. Epub 20 — View Citation

Nahimana A, Rabodonirina M, Bille J, Francioli P, Hauser PM. Mutations of Pneumocystis jirovecii dihydrofolate reductase associated with failure of prophylaxis. Antimicrob Agents Chemother. 2004 Nov;48(11):4301-5. doi: 10.1128/AAC.48.11.4301-4305.2004. — View Citation

Pla L, Avino A, Eritja R, Ruiz-Gaitan A, Peman J, Friaza V, Calderon EJ, Aznar E, Martinez-Manez R, Santiago-Felipe S. Triplex Hybridization-Based Nanosystem for the Rapid Screening of Pneumocystis Pneumonia in Clinical Samples. J Fungi (Basel). 2020 Nov — View Citation

Outcome

Type	Measure	Description	Time frame	Safety issue
Other	to determine the impact of mutations on the effectiveness of anti-Pneumocystis treatment (e.g. favorable vs. unfavorable evolution of the infection)		1 month and 3 month
Other	to evaluate two methods - digital droplet PCR and biosensors without PCR - for the detection and characterization of mutations associated with resistance in Pneumocystis jirovecii		at inclusion
Primary	Presence of specific strains of Pneumocystis jirovecii potentially resistant to treatments in patients infected with this fungus	Four genes encoding therapeutic targets such as dihydropteroate synthase (DHPS), dihydrofolate reductase (DHFR), cytochrome b (CYB), inosine-5'-monophosphate dehydrogenase (IMPDH) will be amplified and sequenced to detect single nucleotide polymorphisms (Single Nucleotide Polymorphism, SNP), in particular those potentially linked to resistance to anti-Pneumocystis treatments.	at inclusion
Secondary	to determine the factors associated (e.g. exposure to treatments) with P. jirovecii mutant strains		at inclusion