## Protocol Section
### Identification Module
**NCT ID:** NCT06431958

**Acronym:** DDBIOS

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

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

#### Organization Study ID Info
**ID:** 29BRC24.0085 - DDBIOS
#### Organization
**Class:** OTHER
**Full Name:** University Hospital, Brest
### Status Module
#### Completion Date
**Date:** 2026-12-31

**Type:** ESTIMATED

#### Expanded Access Info
#### Last Update Post Date
**Date:** 2024-05-29

**Type:** ACTUAL

**Last Update Submit Date:** 2024-05-22

**Overall Status:** NOT_YET_RECRUITING

#### Primary Completion Date
**Date:** 2026-12-31

**Type:** ESTIMATED

#### Start Date
**Date:** 2024-06-01

**Type:** ESTIMATED

**Status Verified Date:** 2024-04

#### Study First Post Date
**Date:** 2024-05-29
**Type:** ACTUAL
**Study First Submit Date:** 2024-05-22
**Study First Submit QC Date:** 2024-05-22
### Sponsor Collaborators Module

#### Lead Sponsor

**Class:** OTHER

**Name:** University Hospital, Brest

#### Responsible Party

**Type:** SPONSOR

### Oversight Module

**Is FDA Regulated Device:** False

**Is FDA Regulated Drug:** False

**Oversight Has DMC:** False

### Description Module

**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

### Conditions Module

**Conditions:**

- Pneumocystis Pneumonia

**Keywords:**

- Pneumocystis jirovecii

- mutant

- anti-microbial resistance

- DHPS

- DHFR

- Cytochrome b

- IMPDH

### Design Module

#### Design Info

**Observational Model:** CASE_ONLY

**Time Perspective:** RETROSPECTIVE

#### Enrollment Info

**Count:** 300

**Type:** ESTIMATED

**Study Type:** OBSERVATIONAL

### Outcomes Module

#### Other Outcomes

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

**Time Frame:** 1 month and 3 month

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

**Time Frame:** at inclusion

#### Primary Outcomes

**Description:** 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.

**Measure:** Presence of specific strains of Pneumocystis jirovecii potentially resistant to treatments in patients infected with this fungus

**Time Frame:** at inclusion

#### Secondary Outcomes

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

**Time Frame:** at inclusion

### Eligibility Module

**Eligibility Criteria:** 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

**Sampling Method:** NON_PROBABILITY_SAMPLE

**Sex:** ALL

**Standard Ages:**

- CHILD

- ADULT

- OLDER_ADULT

**Study Population:** Patients in whom P. jirovecii was detected in a pulmonary sample (bronchoalveolar lavage, sputum, bronchial aspiration, oropharyngeal rinse, nasopharyngeal sample) can be included in the study

### Contacts Locations Module

#### Central Contacts

**Contact 1:**

**Email:** gilles.nevez@chu-brest.fr

**Name:** Gilles NEVEZ

**Phone:** 0298345091

**Role:** CONTACT

**Contact 2:**

**Email:** solene.legal@chu-brest.fr

**Name:** Solène LE GAL

**Phone:** 0298345094

**Role:** CONTACT

#### Locations

**Location 1:**

**City:** Brest

**Country:** France

**Facility:** Chu Brest

**Zip:** 29609

### IPD Sharing Statement Module

**Access Criteria:** Data access requests will be reviewed by the internal committee of Brest UH. Requestors will be required to sign and complete a data access agreement

**Description:** All collected data that underlie results in a publication

**Info Types:**

- STUDY_PROTOCOL

**IPD Sharing:** YES

**Time Frame:** Data will be available beginning three years and ending fifteen years following the final study report completion

### References Module

#### References

**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 Fungi (Basel). 2021 Oct 10;7(10):849. doi: 10.3390/jof7100849.

**PMID:** 34682270

**Citation:** 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 Outbreak Among Heart Transplant Recipients. Clin Infect Dis. 2018 Aug 31;67(6):913-919. doi: 10.1093/cid/ciy154. Erratum In: Clin Infect Dis. 2019 Jan 1;68(1):175.

**PMID:** 29514207

**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):myad095. doi: 10.1093/mmy/myad095.

**PMID:** 37656874

**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.

**PMID:** 34682277

**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.

**PMID:** 15504856

**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 2021 Mar 11. Erratum In: J Med Virol. 2024 May;96(5):e29632.

**PMID:** 33538349

**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 17;6(4):292. doi: 10.3390/jof6040292.

**PMID:** 33213011

## Derived Section

### Condition Browse Module - Ancestors

- ID: D000011014

- Term: Pneumonia

- ID: D000012141

- Term: Respiratory Tract Infections

- ID: D000007239

- Term: Infections

- ID: D000008171

- Term: Lung Diseases

- ID: D000012140

- Term: Respiratory Tract Diseases

- ID: D000008172

- Term: Lung Diseases, Fungal

- ID: D000009181

- Term: Mycoses

- ID: D000001423

- Term: Bacterial Infections and Mycoses

- ID: D000016720

- Term: Pneumocystis Infections

### Condition Browse Module - Browse Branches

- Abbrev: BC01

- Name: Infections

- Abbrev: BC08

- Name: Respiratory Tract (Lung and Bronchial) Diseases

- Abbrev: All

- Name: All Conditions

- Abbrev: BC23

- Name: Symptoms and General Pathology

- Abbrev: Rare

- Name: Rare Diseases

### Condition Browse Module - Browse Leaves

- ID: M13910

- Name: Pneumonia, Pneumocystis

- Relevance: HIGH

- As Found: Pneumocystis

- ID: M13904

- Name: Pneumonia

- Relevance: LOW

- As Found: Unknown

- ID: M10283

- Name: Infections

- Relevance: LOW

- As Found: Unknown

- ID: M6368

- Name: Communicable Diseases

- Relevance: LOW

- As Found: Unknown

- ID: M14978

- Name: Respiratory Tract Infections

- Relevance: LOW

- As Found: Unknown

- ID: M11168

- Name: Lung Diseases

- Relevance: LOW

- As Found: Unknown

- ID: M14977

- Name: Respiratory Tract Diseases

- Relevance: LOW

- As Found: Unknown

- ID: M11169

- Name: Lung Diseases, Fungal

- Relevance: LOW

- As Found: Unknown

- ID: M12136

- Name: Mycoses

- Relevance: LOW

- As Found: Unknown

- ID: M4722

- Name: Bacterial Infections

- Relevance: LOW

- As Found: Unknown

- ID: M4721

- Name: Bacterial Infections and Mycoses

- Relevance: LOW

- As Found: Unknown

- ID: M19082

- Name: Pneumocystis Infections

- Relevance: LOW

- As Found: Unknown

- ID: T4598

- Name: Pneumocystis Jirovecii Pneumonia

- Relevance: HIGH

- As Found: Pneumocystis

- ID: T4599

- Name: Pneumocystosis

- Relevance: HIGH

- As Found: Pneumocystis

### Condition Browse Module - Meshes

- ID: D000011020

- Term: Pneumonia, Pneumocystis

### Intervention Browse Module - Browse Branches

- Abbrev: Infe

- Name: Anti-Infective Agents

- Abbrev: All

- Name: All Drugs and Chemicals

### Intervention Browse Module - Browse Leaves

- ID: M4222

- Name: Anti-Bacterial Agents

- Relevance: LOW

- As Found: Unknown

- ID: M4214

- Name: Anti-Infective Agents

- Relevance: LOW

- As Found: Unknown

### Misc Info Module

- Version Holder: 2024-05-31
