Crop Biotech Update

Global Consortium of Scientists Develop Affordable Sequencing Method for Pathogen Analysis to Help Tackle Global Epidemics

January 5, 2022

A global consortium of scientists led by Earlham Institute and the University of Liverpool in the United Kingdom marked a significant milestone by developing cheap and accessible methods for sequencing large collections of bacterial pathogens that low- and middle-income countries (LMICs) can use at a cost of less than US$10 per genome.

During the coronavirus pandemic, genomic surveillance has been in the spotlight and the ability of countries to contribute through low-cost and rapid whole genome sequencing (WGS) has become increasingly important. The methods developed by the consortium can be applied to large collections of pathogens and will strengthen global research collaborations to tackle future pandemics.

Focusing on the pathogen Salmonella enterica, this large-scale genomic sequencing initiative was led by the worldwide 10,000 Salmonella genomes research consortium (10KSG) with scientists from 16 countries. 10KSG aims to make genomic data more accessible to LMICs and the project has sequenced and analyzed 10,000 Salmonella genomes from Africa and Latin America. The researcher's innovative WGS approach aimed to streamline the large-scale collection and genome sequencing of bacterial isolates and collected more than 10,400 clinical and environmental bacterial isolates from LMICs in under a year.

The sample logistics pipeline, developed by the University of Liverpool, was optimized by shipping the heat-inactivated bacterial isolates as ‘thermolysates' in ambient conditions from different countries to the UK. The isolates were sequenced at the Earlham Institute using the unique LITE protocol - a low-cost, low input automated method for rapid genome sequencing. In total, the gene library construction and DNA sequencing bioinformatic analysis were done with a total reagent cost of less than US$10 (around £7.50GBP) per genome.

For more details, read the article in the Earlham Institute Newsroom.

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