Studying antibiotic-resistant bacteria from patient samples in Basel

AI summary

From the trial's eligibility criteria. Machine-read from the registry text on this page, so it can be wrong. The registry text below and the trial team decide who can take part.

The trial is looking for adults with a urinary tract infection, pneumonia or a deep-seated infection caused by E. coli, Klebsiella species, S. aureus or P. aeruginosa. Control participants without infection can also join.

Age

18 years and older

Sex

All sexes

Disease stage

Confirmed urinary tract infection, pneumonia (including after lung transplantation or with cystic fibrosis) or deep-seated infection caused by one of the four named bacteria. Controls have no detectable bacteria and no other infection.

Biomarker or test result

Infection with E. coli, Klebsiella species, S. aureus or P. aeruginosa found in the routine microbiology lab.

Main reasons for not taking part

• Refused research use and reuse of their data or samples (general consent)
• Bacteria other than the four named bacteria found in the routine microbiology lab
• Younger than 18 years
• Controls without a signed general consent

The registry criteria, word for word

What the trial wants to find out

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.

The 6 groups in the trial

• A) Urinary tract infection

  Processing of residual urine for proteomic, metabolomic and transcriptomic analysis, immunocytochemical or fluorescence in-situ hybridisation (FISH) analysis, flow cytometry analysis (FACS), immunophenotyping. If positive for target bacteria: sample stored at biobank. If previous antibiotic treatment: plasma sample storage. Exploration of bacterial properties (Highly sensitive mass spectrometry, whole genome sequencing), expression of virulence factors, genomic alterations of bacterial species, metabolism, surface molecule expression, gene expression levels, cytokine levels, immune cell biology, antibiotic concentration (chromatography/mass spectrometry). Demographical, clinical, microbiological, laboratory, epidemiological and hospital-associated data will be analysed. 500 samples per target bacteria (S. aureus, P. aeruginosa, E. coli, Klebsiella species) included. First, a pilot study from randomly selected patients within each bacterial species group (n=50, each) is done.

  Treatment: analysis of antimicrobial resistance

• B) Pneumonia

  Processing of residual samples (tracheal secretion, bronchioalveolar lavage (BAL)) for proteomic, metabolomic, transcriptomic and cytological analysis. If positive for target bacteria: sample stored at biobank. If previous antibiotic treatment: plasma sample storage. Exploration of bacterial properties. Demographical, clinical, microbiological, laboratory, epidemiological and hospital-associated data will be analysed. 500 samples per target bacteria (S. aureus, P. aeruginosa, E. coli, Klebsiella species) included.

  Treatment: analysis of antimicrobial resistance

• C) Deep-seated infections

  Processing of intraoperative material residual samples for proteomic, metabolomic, transcriptomic and cytological analysis. If positive for target bacteria: sample stored at biobank. Exploration of bacterial properties. Demographical, clinical, microbiological, laboratory, epidemiological and hospital-associated data will be analysed. 500 samples per target bacteria (S. aureus, P. aeruginosa, E. coli, Klebsiella species) included.

  Treatment: analysis of antimicrobial resistance

• D) Controls for A), B) and C)

  Control samples result from patients with a suspected infection (infection sites A), B) or C), in which no microbiological confirmed infection has been diagnosed. Storage at biobank

  Treatment: analysis of antimicrobial resistance

• E) Clinical controls for A), B) and C) without obtained samples

  For clinical controls, clinical characteristics of patients with detection of target pathogens in their routine samples (but which could not be included for sample analysis in this study) will be assessed.

  Treatment: analysis of antimicrobial resistance

• F) Cohort with analysis whether the application of Article (Art) 34 HFV can avoid a bias

  Since part of the data and samples in this study are collected with the representative consent of the ethics committees, it is investigated whether the application of Art. 34 HFV prevents selection bias with respect to the study population. For this purpose, differences between the actual study population using Art. 34 HFV and the study population with provided research consent will be descriptively investigated in terms of the prevalence of multi-resistant germs and other available population characteristics.

  Treatment: analysis of antimicrobial resistance