Genomic enumeration of antibiotic resistance in space through whole genome nanopore sequencing
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The growing antibiotic resistance crisis is significantly costly both financially and in terms of human life. Unfortunately, resistance to antibiotics is becoming more widespread and cannot be contained by the bounds of Earth. Previous research has revealed that isolates from the International Space Station (ISS) demonstrate antibiotic resistance1. Through the use of culture- and molecular-based capabilities that are well- established onboard the ISS, the Genomic Enumeration of Antibiotic Resistance in Space (GEARS) payload will characterize the frequency and genomic identity of antibiotic resistant organisms. While selective media aims to define resistance
frequency on ISS surfaces, full genome characterization is required to identify antibiotic resistance genes, as well as their frequency and relatedness across genomes. Nanopore sequencing has been continually performed onboard since 2016 but has not included sample preparation and sequencing of an organism's full genome2. 3. 4. The work described here details a spaceflight-compatible method for in situ whole genome nanopore sequencing of culture isolates. Specifically, optimizations toward DNA extraction, library preparation, and the implementation of new sequencing chemistries beyond those of current ISS protocols have been validated with antibiotic-resistant organisms returned from the ISS. Beyond advancing spaceflight sequencing, establishing antibiotic-resistance profiles of ISS organisms will enhance NASA's crew health risk assessments.