Rapid diagnosis of key aetiologies of sepsis and associated infections in LMICs using CRISPR-based assays

Invasive bacterial infections are a major cause of mortality and morbidity globally, with the highest disease burden in low-and-middle-income-countries (LMICs). Rise of infections from antimicrobial resistant (AMR) bacteria is disproportionately affecting public health in these countries, given their wider dissemination in the populations of LMICs compared with richer countries. Rapid, accurate and affordable diagnostics are often lacking in the resource-poor settings, which hampers empirical therapy and attempts to improve antibiotic stewardship. To circumvent these obstacles, we have assembled an international team of clinical microbiologists, clinicians, bioinformaticians and modelers across four sites: Angkor Hospital for Children (Cambodia), Mahosot Hospital (Laos), Mahidol-Oxford Research Unit (Thailand), University of Oslo (Norway) and we will devise rapid clustered regularly interspaced short palindromic repeats (CRISPR)-based assays for identification of pathogen and/or antimicrobial resistance (AMR) for regionally and globally dominant causes of morbidity and mortality by bacterial infections. CRISPR technology enables the development of molecular assays that have performance characteristics similar to other molecular tests (e.g. PCR) in terms of sensitivity and specificity, but which are more rapid to perform and can be in lateral flow dipstick format to remove the need for expensive equipment. This is ideal for use in resource-limited settings typical to many LMIC clinics. Our project has considerable potential to improve future public health in LMICs by improving therapy choices and reducing the mortality and morbidity from bacterial infections.

Invasive bacterial infections are a major cause of mortality and morbidity globally, with the highest disease burden in low-and-middle-income-countries (LMICs). Rise of infections from antimicrobial resistant (AMR) bacteria is disproportionately affecting public health in these countries, given their wider dissemination in the populations of LMICs compared with richer countries. Rapid, accurate and affordable diagnostics are often lacking in the resource-poor settings, which hampers empirical therapy and attempts to improve antibiotic stewardship. To circumvent these obstacles, we will devise rapid clustered regularly interspaced short palindromic repeats (CRISPR)-based assays for identification of pathogen and/or antimicrobial resistance (AMR) for regionally and globally dominant causes of morbidity and mortality by bacterial infections. CRISPR technology enables the development of molecular assays that have performance characteristics similar to other molecular tests (e.g. PCR) in terms of sensitivity and specificity, but which are more rapid to perform and can be in lateral flow dipstick format to remove the need for expensive equipment. This is ideal for use in resource-limited settings typical to many LMIC clinics. We have assembled a multidisciplinary team to maximize our potential by including expertise on all aspects of the problem: 1. clinical practice in LMICs, 2. first-hand experience in CRISPR-based and other molecular methods for test development and evaluation, 3. population genomics and bioinformatics for target selection and optimization. We will focus on multiple major bacterial pathogens: Burkholderia pseudomallei, Staphylococcus aureus, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Salmonella enterica serovar Typhi and Streptococcus pneumoniae. The RADICAL project has considerable potential to improve future public health in LMICs by improving therapy choices and reducing the mortality and morbidity from bacterial infections.