ADAPT-AST (Adaptive Antimicrobial Susceptibility Testing)

The aim of this study is to develop and evaluate an adaptive informatics approach for laboratory antimicrobial susceptibility testing (AST) for urinary tract infection (UTI) pathogens compared with current practice to improve patient outcomes, reduce AMR risks and reduce waste of laboratory resources.

UTI is a leading cause of community and hospital acquired infection and a major driver of antimicrobial prescribing in primary and secondary care. The continued proliferation of AMR also increasingly limits treatment choices for many UTIs. Despite the importance of UTI, antimicrobial susceptibility testing (AST) of urine specimens is based on inflexible 'one-size-fits' all standard operating procedures (SOPs). Either a very large unfocused panel of antimicrobials is immediately tested (leading to wasted resources), or more commonly, and particularly in low or middle income (LMIC) settings, a selected subset of antimicrobials is tested at day one prior to a second or even third panel of antimicrobials. Such an approach does not adapt to prior information such as previous resistance patterns, antimicrobial prescribing, or demographic information, despite these factors being powerful (strong) predictors of resistance. This results in imprecise, inefficient, and inequitable provision of antimicrobial susceptibility information, which provides suboptimal support of decisions for treatment of UTI.

This project will use statistical techniques based on Bayesian causal inference to predict urine AST results and prioritise testing using patient demographics, prescribing, admission, and microbiology laboratory care data. The clinical utility of resulting algorithms will be evaluated in terms of their ability to increase the number, timeliness and appropriateness of usable AST results available to clinicians, and their ability to reduce laboratory resource costs through better test prioritisation. The anticipated benefits of a successfully developed, evaluated, and implemented system are faster and more precise treatments of UTI in patients with drug-resistant organisms and more efficient resource management, particularly in laboratory and pharmacy workflows.

Inclusion criteria

• o The specimens for which AST predictions & recommendations will be made are urine specimens processed by LCL Microbiology laboratory taken from patients ≥ 18 years old in LUHFT and/or GP locations that grew organisms within the period of the study dataset; these are the only specimens for which AST results will be available to train and test ADAPT-AST. Predictions will be made for all urine specimen types, including mid-stream urines, catheter specimens of urine and nephrostomy urine.

Exclusion criteria

• Urine specimens processed by LCL that did not grow organisms within the period of the study dataset
• Urine specimens taken from patients < 18 years old
• Predictions will be made for asymptomatic bacteriuria screening specimens in pregnant women who have had specimens sent from a GP, but not those which have been sent from Liverpool Womens' NHS Foundation Trust (LWfT) Predictions for non-bacterial organisms grown in urine (i.e., fungi) will not be made.