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

Status

Active, not recruiting

Phases

Unknown

Study type

Observational

Source

ClinicalTrials.gov

Registry ID

NCT06431958

Acronym

DDBIOS

Enrollment

300

Registered

2024-05-29

Start date

2024-06-01

Completion date

2026-12-31

Last updated

2024-08-09

For informational purposes only — not medical advice. Sourced from public registries and may not reflect the latest updates. Terms

Conditions

Pneumocystis Pneumonia

Keywords

Pneumocystis jirovecii, mutant, anti-microbial resistance, DHPS, DHFR, Cytochrome b, IMPDH

Brief 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.

Detailed 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

Interventions

None listed

Study design

Observational model

CASE_ONLY

Time perspective

RETROSPECTIVE

Eligibility

Sex/Gender

ALL

Healthy volunteers

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

Design outcomes

Primary

Measure	Time frame	Description
Presence of specific strains of Pneumocystis jirovecii potentially resistant to treatments in patients infected with this fungus	at inclusion	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.

Secondary

Measure	Time frame
to determine the factors associated (e.g. exposure to treatments) with P. jirovecii mutant strains	at inclusion

Other

Measure	Time frame
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
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

Countries

France

Outcome results