Clinical trial NCT05017766: NCCR AntiResist:: New Approaches to Combat Antibiotic-resistant Bacteria
Official title: NCCR AntiResist: Mono-center Study to Identify New Approaches to Combat Antibiotic-resistant Bacteria.
Study type: OBSERVATIONAL
Overall status: RECRUITING
Conditions: Antimicrobial Resistance (AMR)
Keywords: National Center of Competence in Research (NCCR)
Urinary tract infection (UTI)
Pneumonia
Deep-seated infections
E. coli
Klebsiella species
S. aureus
P. aeruginosa
bacterial properties
Community-acquired pneumonia (CAP)
Hospital-acquired pneumonia (HAP)
Ventilator-associated pneumonia (VAP)
cystic fibrosis (CF)
Lead sponsor: University Hospital, Basel, Switzerland
Sponsor class: OTHER
Collaborators: name: Swiss National Science Foundation
First posted: 2021-08-24
Enrollment: 8000
Sex: ALL
Minimum age (years): 18
Standard ages: ADULT
OLDER_ADULT
Accepts healthy volunteers: yes
Observational model: COHORT
Time perspective: PROSPECTIVE
Sampling method: NON_PROBABILITY_SAMPLE
Study population: Patient samples during routine collection at the University Hospital of Basel from November 2020 to approximately December 2024.

Brief summary: This is an explorative, mono-center study including prospectively collected patient samples from the University Hospital of Basel. It is to investigate antimicrobial resistance (AMR) including three clinical manifestations of infectious diseases: urinary tract infection, pneumonia and deep-seated infections. The focus is on four bacteria (E. coli, Klebsiella species, S. aureus, P. aeruginosa) that are part of the high priority list of World Health Organization (WHO). Residual patient samples are analysed for proteomic, metabolomic and transcriptomic analysis, immunocytochemical or fluorescence in-situ hybridisation (FISH) analysis, flow cytometry analysis (FACS) and immunophenotyping and exploration of bacterial properties.

Detailed description: The National Center of Competence in Research (NCCR) AntiResist aims at utilizing patient samples in order to investigate the physiology of bacterial pathogens in human patients and establishing a unique multidisciplinary network of clinicians, biologists, engineers, chemists, computational scientists and drug developers.

The goal of this project is to elucidate the physiological properties of bacterial pathogens in infected human patients in order to provide new ways of combatting superbugs. These clinical data will be used to guide and benchmark development of patient-mimicking and in-vitro models, accelerate the search for novel bacterial targets, antibacterial compounds and non-conventional strategies.

In detail, the focus will be on three clinical manifestations of infectious diseases caused by four critical bacterial pathogens belonging to WHO "priority pathogens" list: E. coli, Klebsiella species, S. aureus and P. aeruginosa :

A) Urinary tract infection B) Pneumonia C) Deep-seated infections D) Controls for A), B) and C) E) Clinical controls for A), B) and C) without obtained samples F) Analysis whether the application of Art. 34 HFV (Weiterverwendung biologischen Materials und/oder gesundheitsbezogener Personendaten für die Forschung bei fehlender Einwilligung und Information) can avoid a bias.

Eligibility criteria: Inclusion Criteria:

* Patients with confirmed (i) urinary tract infection, (ii) pneumonia (including patients after lung transplantation, cystic fibrosis) or (iii) deep-seated infection with focus pathogen:

  * E. coli
  * Klebsiella species
  * S. aureus
  * P. aeruginosa
* Controls: no detectable bacteria in routine microbiology lab and no other infection site at inclusion of the sample and follow up for 10 days, signed general consent
* Clinical controls without obtained samples, but with confirmed (i) urinary tract infection, (ii) pneumonia (including patients after lung transplantation, cystic fibrosis) or (iii) deep-seated infection with focus pathogen:

  * E. coli
  * Klebsiella species
  * S. aureus
  * P. aeruginosa

Exclusion Criteria:

* Patients who have refused research and reuse of their data/samples (e.g. general consent) or any other decline (e.g. Patientenverfügung).
* other than one of the focus bacteria in routine microbiology lab
* Age: \<18 years
* Controls without signed general consent

Primary outcomes:
measure: Clinical outcome: survival rate
timeFrame: one time assessment at baseline
measure: Clinical outcome: mortality rate
timeFrame: one time assessment at baseline
measure: Treatment response (binary: yes/ no)
timeFrame: one time assessment at baseline
Secondary outcomes:
Other outcomes:
Locations:
city: Basel
country: Switzerland
facility: University Hospital Basel
Study officials:
affiliation: University Hospital Basel, Division of Infectiology
name: Nina Khanna, Prof.
role: PRINCIPAL_INVESTIGATOR
References: