A novel field-based surveillance approach for antimicrobial resistance for pandemic preparedness

Cheng, Zhenyu | $237,970

Nova Scotia Dalhousie University 2021 SSHRC

Overview: Infectious diseases cause some of the most pressing challenges faced by humanity today. Along with the social and economic turbulence, it highlights the importance of pandemic preparedness, including the development of new ways of doing research in a pandemic context. The 20th century was marked by major achievements in quelling infectious disease via sanitation, vaccines and antibiotics. Unfortunately, many of these achievements have been undermined by antimicrobial resistance (AMR) mechanisms that facilitate the emergence of drug-resistant microbes. This proposal will address an outstanding need for rapid tests to detect AMR infections. We will harness the power of CRISPR genome editing to create consortia of bacteriophages with barcoded genomes that will be used to monitor the emergence of AMR infections. Following validation, we will use this approach as the basis for a new point-of-care AMR detection tool.

There are two specific aims for this proposal.

Aim 1. To create a consortium of phages for multiplexing detection of drug-resistant bacterial pathogens. We will first isolate wild bacteriophage that infect high-priority AMR bacteria and sequence their complete genomes by high-throughput sequencing (HTS). Once we modify these phages with unique genetic barcodes via CRISPR genome editing, pilot experiments will be performed to identify phage that only infect and kill a microbe once it has required AMR. Once these phage biosensors have been established, they will be used in combination to allow AMR monitoring of complex microbial communities like those found in vivo.

Aim 2. To create a “portable” HTS surveillance system for early detection of AMR infections. We will establish low-cost detection suite consisting of an equipment-free DNA extraction and amplification protocol and a miniature version of the HTS platform, the nanopore minion. The efficiency and sensitivity of detecting AMR pathogens from clinical samples will be examined and optimized.

Impacts: this pandemic-inspired emergency solution project holds the potential to revolutionize AMR surveillance by creating a novel point-of-care detection tool and enabling this community-based system to function under pandemic restrictions. The detection platform developed in this project is low cost, making it an ideal tool in resource-limited regions in the world.

With funding from the Government of Canada

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