The elusive genes that make pathogens drug resistant can be easily detected at last,﻿ thanks to a test based on the CRISPR–Cas9 gene-editing tool.

Medical laboratories use DNA sequencing to detect some pathogens in samples from patients. But it is difficult to spot genes that confer resistance to antimicrobial compounds — such as those that make certain bacteria penicillin resistant — because of their low abundance.

To address this problem, Emily Crawford at the Chan Zuckerberg Biohub in San Francisco, California, and her colleagues developed a method called FLASH (finding low abundance sequences by hybridization). FLASH harnesses a set of RNA molecules to direct the Cas9 enzyme to antimicrobial-resistance genes. Cas9 then cuts the genes’ DNA into fragments that are copied many times before being sequenced.

The authors used the technique to detect antimicrobial-resistance genes in samples from four patients with lower-respiratory tract infections such as pneumonia. They were also able to detect such genes in samples from five people infected with the malaria parasite Plasmodium falciparum.

Clarification: The caption for the image in this story has been amended to clarify the type of sample used in the analysis.