Sequencing Access for All

Though the first bacterial genome was sequenced over two decades ago, the technology has largely been limited to high-income countries – creating a disparity between the need for bacterial sequencing and its accessibility. Now, a worldwide consortium of scientists has developed an inexpensive pipeline for collecting and sequencing bacterial pathogens – for less than US$10 per genome (1).

The consortium used Salmonella enterica to test their method. “The number of publicly available sequenced Salmonella genomes reached 350,000 in 2021,” said study author Neil Hall (2). “However, limited genome-based surveillance of Salmonella infections has been done in [low- and middle-income] countries and the existing dataset did not accurately represent the Salmonella pathogens that are currently causing disease across the world.”

The LITE (Low Input, Transposase Enabled) pipeline has a low DNA requirement – reporting that, for Salmonella, 1 ng is equal to over 150,000 copies of the genome. With a diverse collection of 10,419 bacterial isolates, the researchers successfully generated 6,117 high-quality Salmonella genomes that have already been used in published studies. “Our pipeline represents a cost-effective and robust tool for generating bacterial genomic data […] to allow investigation of the epidemiology, drug resistance, and virulence factors of isolates,” said Darren Heavens, who developed the whole-genome sequencing pipeline.

Overall, the work represents the value of global collaboration to tackle future epidemics and pandemics. Going forward, the authors suggest that “early investment in the development of a shared, protected, and version-controlled database for the storage of epidemiological information” is needed to implement approaches like theirs worldwide.