Portable Sequencer Identifies Drug-Resistant Bacteria

Klebsiella pneumoniae bacteria (CDC.gov)

18 Jan. 2019. Researchers using a hand-held genomic sequencing device were able to identify targets for combating drug-resistant bacteria much faster than current methods. A team from Johns Hopkins University in Baltimore describes their techniques in the January 2019 issue of Antimicrobial Agents and Chemotherapy (paid subscription required).

The problem of infections from microbes becoming more resistant to current antibiotics is a global and growing public health issue. In the U.S., according to Centers for Disease Control and Prevention, at least 2 million people get an infection resistant to antibiotics each year, leading to some 23,000 deaths. World Health Organization says the kinds of infections becoming resistant to antibiotics is growing to include those from pneumonia, tuberculosis, blood poisoning, gonorrhea, and foodborne diseases.

A team from the lab of Johns Hopkins pathologist and microbiologist Patricia Simner is seeking faster ways of identifying the precise nature of infections, to provide patients with the best available treatments as soon as possible, since delays increase the chance for poor outcomes. “The current standard process of identifying appropriate treatment options for highly drug-resistant bacteria,” says pediatrics professor and first author Pranita Tamma in a university statement, “can take up to 96 hours from the time the lab receives samples, but our findings suggest that with the use of a rapid whole genome sequencing method, we might reduce that time to about one day less.”

The rapid whole genome sequencing method used by the researchers is a portable device called the Minion made by Oxford Nanopore Technologies in the U.K. The MinIon is a portable disease surveillance system that analyzes DNA from blood samples, returning results in as little as an hour, and operates as a plug-in peripheral on a laptop computer. The MinIon technology forces single strands of DNA through nanoscale pores, which makes it possible to analyze samples in real time.

The Johns Hopkins team sought to test the feasibility of a nanopore device to quickly spot genes that expose vulnerabilities in bacteria, thus offering targets for the right kind of antibiotics. To prove the concept, the researchers analyzed the whole genomes of Klebsiella pneumoniae, a gram-negative bacteria associated with pneumonia, bloodstream infections, wound or surgical site infections, and meningitis, particularly in health care settings. “Gram” refers to a classification for bacteria where the microbes either retain (gram-positive) or shed (gram-negative) a test stain on their protective cell coatings.

The team drew samples of Klebsiella pneumoniae bacteria from 40 patients at Johns Hopkins medical center. After establishing reference measures as baselines, the researchers analyzed the samples using 2 different methods: (1) genomic analysis of samples in real time, where the team could make judgements about susceptible genes while the analysis was underway, or (2) assembling the genome, then identifying target genes and mutations. The real-time method identified vulnerabilities in the genome in about 8 hours, but with an accuracy rate of 77 percent. The assembly method took a little longer — 14 hours — and with 92 percent accuracy. Both methods are faster than current techniques, by about an entire day.

“While we still need to wait 24 hours to get the culture to grow,” adds Simner, “we were able to cut time to identifying effective antibiotic therapy by at least 20 hours, compared to our current standard of care.” The researchers say more use of automation could reduce the analytical time even further.

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