DoGsTAilS: Developing a nanopore-based diagnostic approach for the effective antibiotic treatment of canine infections
Antimicrobial resistance (AMR) is an urgent global health concern, and not just for humans. Recurrent urinary tract and skin infections are common in dogs, leading to repeated courses of antibiotic treatment. Current culture-based diagnostic and antibiotic susceptibility tests take at least 48 hours; in the meantime, inappropriate or broad-spectrum antimicrobials may be used. Natalie and her team developed a rapid method for identifying the responsible pathogen in canine skin (pyoderma) and urinary tract infections (UTIs) and predicting potential antimicrobial resistance using MinION.
Their current work aims to optimise this method to reduce both the time and cost-per-sample.
- MinION Mk1B will be replaced by the MinION Mk1C. The on-board data analysis (EPI2ME) steps, including species identification with WIMP and AMR prediction with ARMA, will enable 100% real-time results
- The 1D2 library preparation will be replaced with rapid PCR barcoding (SQK-RPB004), allowing for lower DNA input samples and multiplexing, reducing the cost-per-sample
- MinION flow cells may be replaced with Flongle flow cells, further reducing cost per sample
