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Whole-Genome Sequencing Accurately identifies Bacteria in Clinical Specimens

Researchers in Denmark have found that using whole-genome sequencing directly on clinical samples identified the bacteria causing urinary tract infections in 18 hours.

“Using conventional methodologies, this would have taken several days to weeks, and even using whole-genome sequencing on cultured bacteria would have taken an extra day,” Frank M. Aarestrup, DVM, PhD, of the Technical University of Denmark, said in a press release.

In the study, the researchers examined 35 random urine samples from patients with suspected UTIs using conventional microbiology, whole-genome sequencing of isolated bacteria and directly sequencing the clinical samples. Using conventional identification, they found 19 different isolates for species identification and antimicrobial susceptibility testing.

When they performed whole-genome sequencing on the 17 isolates made in pure culture, the results confirmed the conventional identification in the cases. In addition, there was agreement between the predicted antimicrobial susceptibility. The researchers also performed whole-genome sequencing on 23 of the urine samples, including the 19 positive samples. In the 17 isolates made in pure culture, the sequencing on the urine samples yielded the same species identification.

“Rapid identification of the causative agent, and of any antibiotic resistance, is crucial to choosing the correct treatment for individual patients,” Aarestrup said. “Choosing the wrong antibiotic will lead to longer infections and, in the worst case, deaths.

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