Rapid 'bacterial fingerprinting' might cut antibiotic overuse

Urine test tubes
Urine test tubes

BaltzarDK / iStock

A new "bacterial fingerprinting" precision test that identifies bacteria at the subspecies level rather than by species could one day help physicians identify pathogenic bacteria faster and reduce antibiotic overprescribing, researchers from the University of Washington and the maker of the test reported.

In a study this week in PLoS One, the investigators used a novel polymerase chain reaction–based clonotyping assay made by Seattle-based ID Genomics on Escherichia coli isolates. The test can differentiate pathogens on the clonal, or subspecies level, instead of just distinguishing among species, producing a "bacterial fingerprint."

This fingerprint is then matched against the company's reference database of pathogen strains and their antibiotic profiles. With information about a particular clonotype's potential resistance, a patient can be prescribed the antibiotic best suited to his or her infection.

The test, called CloNet, is also very fast. It identified E coli clonotypes directly in patients' urine within 25 to 35 minutes, with high specificity and sensitivity compared with culture tests, the authors reported. Conventional lab results typically take hours to days.

Depending on E coli concentration, CloNet achieved a sensitivity of 87.7% to 98.4%, specificity of 98.4% to 96.5%, positive-predictive value of 93.8% to 97.5%, and negative-predictive value of 91.8% to 99.6%.

Guiding empiric therapy

The researchers assessed how well CloNet could guide empiric antibiotic therapy in 220 patients with urinary tract infections (UTIs) who had E coli in their urine samples. They matched resistance profiles to the most effective antibiotic treatment.

In looking at what antibiotics the test would allow for any given clonotype, the researchers discovered an antibiotic-pathogen mismatch of only 4.6% for fluoroquinolones, 7.9% for trimethoprim-sulfamethoxazole, 4.3% for cefazolin, and 0.3% for nitrofurantoin.

By comparing treatment options based on CloNet results with the current standard treatment for UTIs, they reported that using the test could reduce the relative likelihood of antibiotic-pathogen mismatch by almost 67%.

"Precision technology is a critical tool for preventing the overuse of broad-spectrum antibiotics by encouraging the use of first-line antibiotics, as recommended by current guidelines," Evgeni Sokurenko, MD, PhD, co-founder of ID Genomics and professor of microbiology at the University of Washington, said in an ID Genomics news release.

"The results in this article show how ID Genomics' system may improve patient outcomes. We are looking forward to applying the technique to a broad range of infectious diseases."

"Results from this study provide proof-of-concept that a clonal diagnostic approach to bacterial identification can be more accurate than empiric therapy decisions alone, and faster than traditional culture approaches," said Thomas Fritsche, MD, PhD, who was not involved in the study. He is a clinical microbiologist and medical director of laboratory medicine at the Marshfield Clinic in Wisconsin.

The authors summarize the technology thus: "The clonal diagnostics approach merges epidemiologic surveillance, antimicrobial stewardship, and molecular diagnostics to bring evidence-based medicine directly to the point of care."

See also:

Mar 28 PLoS One study

Mar 29 ID Genomics news release

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