Coloured scanning electron micrograph of methicillin-resistant Staphylococcus aureus bacteria

When applied to respiratory fluid, a CRISPR-based method identified a gene that confers antibiotic resistance on the bacterium Staphylococcus aureus (yellow). Credit: Cdc/Phanie/Shutterstock

Medical research

CRISPR zeroes in on antibiotic-resistance genes

Surveillance system sweeps human samples for microbial genes that pathogens rely on to dodge drug treatment.

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.