Successfully typing of bacteria at the species or strain level is not easy – fast, cost-effective methods like 16S ribosomal RNA gene sequencing lack accuracy, while technologies such as matrix-assisted laser desorption/ionization time-of-flight MS are more precise but remain expensive and laborious. Lukasz Krych and colleagues have developed an alternative: ON-rep-seq – an approach targeting specific fragments of the bacterial genome (1). “We’ve developed a system that assigns each bacterium a unique genetic barcode,” says Krych. “This allows us to run hundreds of samples simultaneously, drastically reducing the cost of analysis.”
While early results have proven promising, Krych urges caution. “More work is needed on algorithm development and the integration of a more user-friendly software package,” he says. “This technology is a true reflection of advances in biotechnology, computer science, and nanotechnology, all integrated into a single package.” Pressing ahead, the team is collaborating with a number of private companies and universities to provide real-world testing of their method.
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References
- L Krych et al., “DNA enrichment and tagmentation method for species-level identification and strain-level differentiation using ON-rep-seq”, Commun Biol, 2, 369 (2019). DOI: 10.1038/s42003-019-0617