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NCT Number: NCT05017766

NCCR AntiResist:: New Approaches to Combat Antibiotic-resistant Bacteria

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.

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Key information

Age range

18 year and older

Sex eligibility

All sexes

Study type

Observational

Primary location

University Hospital Basel

Basel, 4031, Switzerland

Location status: Recruiting

Location contact

Adrian Egli, Prof.

SUB_INVESTIGATOR

Bram Stieltjes, Dr.

SUB_INVESTIGATOR

Christoph Dehio, Prof.

SUB_INVESTIGATOR

Daiana Stolz, Prof.

SUB_INVESTIGATOR

Dirk Buman, Prof.

SUB_INVESTIGATOR

Mario Morgenstern, PD

SUB_INVESTIGATOR

Martin Siegemund, Prof.

SUB_INVESTIGATOR

Nina Khanna, Prof.

PRINCIPAL_INVESTIGATOR

Nina Khanna, Prof. Dr. med.

CONTACT

[email protected]

+41 61 328 73 25

Richard Kühl, Dr.

SUB_INVESTIGATOR

Richard Kühl, Dr. med.

CONTACT

[email protected]

+41 61 328 65 45

Sarah Tschudin Sutter, Prof.

SUB_INVESTIGATOR

Urs Jenal, Prof.

SUB_INVESTIGATOR

About this study

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.

Who can participate

Healthy volunteers accepted: Yes

Only the study team can determine whether someone qualifies for participation.

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

Treatment and study plan

analysis of antimicrobial resistance

Other

In samples from patients infected with one of the focus pathogens (E. coli, Klebsiella species, S. aureus, P. aeruginosa) will be:

(i) isolated and pathogenic bacteria characterized; (ii) pathogen in-situ properties at single-cell and bulk average determined; (iii) human metabolites, proteins and cells determined (iv) antibiotic concentration determined (v) bacterial growth monitored

Deducted from the data will be:

  • relevant human components and pathogen properties that are common to most patients with similar indication
  • underlying regulatory networks and triggers in pathogen cells and human tissues.

Clinical outcomes (survival/mortality) and treatment response (response or failure) will be correlated to the in vitro retrieved host and bacterial data.

Primary outcomes

  1. Clinical outcome: survival rate

    Time frame: one time assessment at baseline

    Survival rate (correlated to the in vitro retrieved host and bacterial data. In vitro retrieved host and bacterial data include: Proteomics, Metabolomics, FISH, Histology, PCR/Microbial genome sequencing, Microbial transcriptome, Antibiotic concentration, Timelapse studies, phenotypic characterisations, molecular typing, innate immune response characterization, Antibiotic tolerance testing, Microfluidic systems, 3-D models, Transcriptomics, Flow cytometry (FACS))

  2. Clinical outcome: mortality rate

    Time frame: one time assessment at baseline

    Mortality rate (correlated to the in vitro retrieved host and bacterial data. In vitro retrieved host and bacterial data include: Proteomics, Metabolomics, FISH, Histology, PCR/Microbial genome sequencing, Microbial transcriptome, Antibiotic concentration, Timelapse studies, phenotypic characterisations, molecular typing, innate immune response characterization, Antibiotic tolerance testing, Microfluidic systems, 3-D models, Transcriptomics, Flow cytometry (FACS))

  3. Treatment response (binary: yes/ no)

    Time frame: one time assessment at baseline

    Treatment response (correlated to the in vitro retrieved host and bacterial data. In vitro retrieved host and bacterial data include: Proteomics, Metabolomics, FISH, Histology, PCR/Microbial genome sequencing, Microbial transcriptome, Antibiotic concentration, Timelapse studies, phenotypic characterisations, molecular typing, innate immune response characterization, Antibiotic tolerance testing, Microfluidic systems, 3-D models, Transcriptomics, Flow cytometry (FACS))

Study contacts

Contact information is provided by the study sponsor or research team.

Christoph Dehio, Prof.

CONTACT

Nina Khanna, Prof.

CONTACT

[email protected]

+41 61 328 73 25

Sponsors and collaborators

Lead sponsor

University Hospital, Basel, Switzerland

Other

Collaborators

  • Swiss National Science Foundation

Registry information

Official study title

NCCR AntiResist: Mono-center Study to Identify New Approaches to Combat Antibiotic-resistant Bacteria.

Acronym: AntiResist

Important dates

Study start
2020
Primary completion
2028
Study completion
2028
First posted
Aug 24, 2021
Registry last updated
Mar 4, 2025

OpenTrials presents study information sourced from ClinicalTrials.gov. The official registry record should be consulted for the latest information.

View the official ClinicalTrials.gov record (opens in a new tab)

This listing is for discovery and informational purposes only. It is not medical advice, does not guarantee that a study is recruiting, and does not determine eligibility. Contact the study team and a qualified healthcare professional when considering participation.

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