Clinical trial NCT06442345: Pneumocystis Jirovecii Genotyping
Official title: Real-time Pneumocystis Jirovecii Genotyping to Support Clinical Decision Making in the Management of Nosocomial Outbreaks
Study type: OBSERVATIONAL
Overall status: NOT_YET_RECRUITING
Conditions: Pneumocystis Pneumonia
Keywords: PCP
Genotyping
Lead sponsor: Nottingham University Hospitals NHS Trust
Sponsor class: OTHER
First posted: 2024-06-04
Enrollment: 70
Sex: ALL
Minimum age (years): 18
Standard ages: ADULT
OLDER_ADULT
Observational model: CASE_ONLY
Time perspective: RETROSPECTIVE
Sampling method: NON_PROBABILITY_SAMPLE
Study population: Adults PCP positive patients over the age of 18 years.

Brief summary: We share our lives with microorganisms, and these generally do not pose a problem if an individual is healthy with a normal immune system. However, if the immune system was not functioning properly (e.g., cancer patients), they are at risk of infection. One microorganism, a fungus called Pneumocystis jirovecii (PCP), can cause severe chest infections in patients without properly functioning immune systems, leading to hospitalisation and death if untreated. If patients remain without a functioning immune system, they have a greater chance of repeated infection.

PCP spreads through air from person-to-person and can survive on environmental surfaces. Patients can be infected after contact with these surfaces. Hospitals have a responsibility to ensure PCP infected patients do not pass it on to other unwell patients. In cases where PCP has infected multiple patients, knowing if the same fungi has been passed along (or transmitted) from patient-to-patient is vital in understanding if there is an outbreak in the hospital. Understanding how similar (the relatedness) the PCP strain is allows healthcare workers to detect any transmission between patients or the environment.

To understand how related each patient's PCP infection is we will utilise a laboratory test called multilocus sequence typing (MLST). This test looks at sections of the fungi's genetic code using deoxyribonucleic acid (DNA) sequencing to create a code (genotype) which tells us how related one PCP is to others tested, allowing comparison between patients and ultimately spotting transmission.

Our aim is to develop this sequencing test using PCP positive patient samples and ensure it performs to high-quality standards. Surplus material from seventy known PCP positive patient samples will be tested. Each sample will be analysed to see if the DNA genotype matches or is similar to other patient samples we have tested, helping to understand how PCP may spread between patients.

Detailed description: We share our lives with microorganisms, and these generally do not pose a problem if an individual is healthy with a normal immune system. However, if the immune system was not functioning properly (e.g., cancer patients), they are at risk of infection. One microorganism, a fungus called Pneumocystis jirovecii (PCP), can cause severe chest infections in patients without properly functioning immune systems, leading to hospitalisation and death if untreated. If patients remain without a functioning immune system, they have a greater chance of repeated infection.

PCP spreads through air from person-to-person and can survive on environmental surfaces. Patients can be infected after contact with these surfaces. Hospitals have a responsibility to ensure PCP infected patients do not pass it on to other unwell patients. In cases where PCP has infected multiple patients, knowing if the same fungi has been passed along (or transmitted) from patient-to-patient is vital in understanding if there is an outbreak in the hospital. Understanding how similar (the relatedness) the PCP strain is allows healthcare workers to detect any transmission between patients or the environment.

To understand how related each patient's PCP infection is we will utilise a laboratory test called multilocus sequence typing (MLST). This test looks at sections of the fungi's genetic code using deoxyribonucleic acid (DNA) sequencing to create a code (genotype) which tells us how related one PCP is to others tested, allowing comparison between patients and ultimately spotting transmission.

Our aim is to develop this sequencing test using PCP positive patient samples and ensure it performs to high-quality standards. Surplus material from seventy known PCP positive patient samples will be tested. Each sample will be analysed to see if the DNA genotype matches or is similar to other patient samples we have tested, helping to understand how PCP may spread between patients.

Eligibility criteria: Inclusion Criteria:

* Total nucleic acid extracts from adult patients (over 18 years old) with a positive PCP diagnosis (\& detected at \> 50 copies/10ul) from routine respiratory panel testing.

Exclusion Criteria:

* Total nucleic acid extracts from patients with a negative PCP diagnosis from routine respiratory panel testing
* Total nucleic acid extracts from non-adult patients (under 18 years old).
* PCP positive total nucleic extract samples with \< 50 copies/10ul.
* Patients included on the UK National Opt-Out register

Primary outcomes:
measure: Objective 1: Development of a MLST PCP genotyping assay within NUH.
timeFrame: 18 months
Secondary outcomes:
measure: Objective 2: Analyse PCP positive patient samples and identify the PCP genotype, assessing links between patient metadata and genotype
timeFrame: 18 months
Other outcomes:
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