Phase 3 trials of antimicrobial compounds generally include microbiological analyses of samples taken from participants. These samples may be analysed at laboratories associated with a clinical trial site or at a central microbiological facility.
The aim is to identify and characterize the pathogens responsible for infections in trial participants. In some cases, identification is a trial inclusion/exclusion criterion, if an investigational drug is targeting a specific pathogen or group of pathogens, or if patients with known resistant infections are excluded.
As well as identifying the causative pathogen, microbiological analyses will often also aim to characterize the specific strain involved, as different strains may have markedly different susceptibility to antibiotics. Some or all clinical isolates may undergo more intensive analysis, such as whole genome sequencing, which can reveal known or novel resistance mechanisms. Trials typically also assess the susceptibility of isolates to different antibiotics.
The microbiological analyses are integrated with clinical data to provide insights into how treatment responses are affected by the nature of the pathogen causing an infection.
Guidance on required microbiological studies has been provided by the FDA and the EMA.