New technique identifies pathogens in patient samples faster and in greater detail

Dec. 9, 2013

In research published online ahead of print in the Journal of Clinical Microbiology, Danish investigators have shown how to identify pathogens faster, directly from clinical samples. The investigators used whole genome sequencing to identify and completely characterize bacteria causing urinary tract infections. They identified the microorganisms in just 18 hours, characterized the pathogens' patterns of antibiotic susceptibility, and identified specific strains. Their work may help patients heal more quickly and avoid unnecessarily prolonged illness or death. It may also help prevent outbreaks of hospital-acquired disease and identify emerging infections.

The investigators also identified bacteria in the patient samples that they did not detect using conventional techniques. “Lactobacillus iners, Gardnerella vaginalis, Prevotella, and A. urinae have all been implicated in [urinary tract infections], even though their precise roles as pathogens and normal colonizers of the genital tract have not been firmly established,” they write. They note that by conventional methods A. urinae is rarely identified and frequently misclassified.

The ability to identify strains in patients with repeated infections enables clinicians to know whether the patient's infection is new or recurrent. The typing of bacterial strains enables rapid comparison of bacteria from different patients, so that doctors can detect the spread of infections within the hospital and identify emerging infections.

Researchers predict that rapidly falling prices and automation will make whole genome sequencing a standard technology for infection detection and control, in and out of the hospital. Read the article in manuscript.