OneAMRdx: real-time, sequencing-based diagnostics for the detection and prevention of antimicrobial resistance (AMR)

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Antimicrobial resistance (AMR) is a serious threat to public health with a recent study finding that 1.3M deaths were attributable to AMR globally in 2019[1]. This would increase to 10M deaths in 2050 on the current trajectory. AMR is a global problem that has been accelerated by the overuse of antibiotics, if not brought under control it will leave us without any effective drugs to treat infections and putting patients at risk of infection even with minor procedures. One bacterial species, Klebsiella pneumoniae, is frequently resistant to all antibiotics and is a major cause of hospital-acquired infections such as sepsis and pneumonia. Resistant infections are associated with longer hospital stays, increased costs of treatment and worse outcomes for patients when compared with non-resistant strains of the same species. In order to treat an infection a doctor needs to know what organism it is caused by and what antibiotics will be effective against it. The gold standard antimicrobial susceptibility testing involves growing or culturing the organism to find the lowest concentration of antibiotic that will stop it growing, a value known as the MIC. This process is often automated in large hospital laboratories but can still take between two days and several weeks to complete. Doctors will prescribe a broad-spectrum antibiotic and wait to see if the treatment is effective. This means a certain percentage of patients receive antibiotics that are ineffective which actually increases resistance. If technology was available that could rapidly identify resistance it would improve the effectiveness of the early therapy leading to better outcomes, reduced hospital stays and less resistance in the clinical environment.One such technology is nanopore sequencing in which individual DNA molecules are read as they pass through a tiny protein pore. The sequence read-off can be used to determine what is causing an infection and which antibiotics would be the best to treat it. This process is known as clinical metagenomic sequencing which means sequencing without the need for isolation or culture. Metagenomics is powerful for discovery but sometimes a targeted approach i.e. looking for something specific, is more sensitive as there is less background noise to sift through and it is cheaper. Another technology is single-cell sequencing which is a way to trap single-cells inside tiny droplets. This is done using a microfluidics device, a small piece of plastic with channels running through it, in which cells suspended in water and oil travelling through the channels meet junctions. Because oil and water don't mix the result is an emulsion with millions of tiny droplets containing individual cells which can be analysed separately.In this project I will develop targeted methods for detecting antibiotic resistance using nanopore sequencing and single-cell methods. The droplets act as a bag to make sure nothing from the cell e.g. plasmids which are small rings of DNA often containing resistance genes, gets separated from the rest of the cells' contents which is important for accurate resistance prediction. The use of nanopore sequencing allows the read-out to be performed in minutes rather than days like for existing culture methods. This project is developing the technology so that rapid, cheap tests will be available in future, tests that can be performed in a GP surgery or hospital allowing the doctor to make confident prescribing decisions that don't lead to resistance. Better prescribing coupled with newly developed drugs and non-pharmaceutical interventions will protect the effectiveness of antibiotics and avoid an antibiotic apocalypse where people die of untreatable infections and even routine operations are impossible to perform.Antimicrobial Resistance Collaborators. Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. Lancet. 2022 Feb 12;399(10325):629-655.