January 26, 2016
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Novel clonotyping test predicts E. coli susceptibility

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A novel method of clonotyping extraintestinal pathogenic Escherichia coli could enable clinicians and epidemiologists to predict antimicrobial susceptibility from urine samples, according to recent research.

“Extraintestinal pathogenic E. coli (ExPEC), a subset of E. coli, is the major cause of urinary tract infections, newborn meningitis and bacterial sepsis,” Veronika Tchesnokova, MD, PhD, research scientist at the University of Washington, and colleagues wrote. “ExPEC strains are highly clonal, with certain closely related clonal groups associated with characteristic antimicrobial resistance profiles. Therefore, subspecies delineation of ExPEC clonal groups has significant potential for improving the diagnostics of antimicrobial resistance, especially if it can be performed directly from the clinical specimen and quickly.”

Unlike the current standard for clonal typing, which involves sequencing approximately seven genes and splitting E. coli into sequence types, Tchesnokova and colleagues’ method relied on clonotype-specific combinations of seven single-nucleotide polymorphisms (SNPs) selected from the fumC and fimH genes. By identifying the binary combinations of these SNPs, the researchers wrote, it is possible to quickly profile and predict an ExPEC sample’s distinct antibiotic resistances.

Tchesnokova and colleagues developed and tested this method using a reference set of 2,559 clinical E. coli isolates of primarily urinary origin recovered from patients between October 2010 and June 2013 at eight laboratories. Using genetic data obtained through the standard clonal typing method, the researchers employed an algorithm to select the seven SNPs necessary to predict clonotype group resistance. The method’s performance was tested using 582 isolates from this group containing relevant polymorphisms, as well as in 160 random urine samples obtained from a clinical microbiology laboratory.

Analysis of the seven SNPs identified 54 unique combinations that could be used to predict resistance. When tested, the novel process predicted sequence type identity in 72% of isolates with a mean 97% accuracy, which Tchesnokova and colleagues wrote was similar to the slower method currently used. The test could be conducted with high sensitivity and specificity, and was successfully performed within 45 minutes in the urine samples included in the analysis.

“The novel seven SNP typing test described here should be a useful tool for both epidemiological analysis and clinical diagnostics, particularly for the prediction of antimicrobial susceptibility,” the researchers wrote. “It is highly reliable, inexpensive, easy to perform, robust and can potentially be adapted for high-throughput automation.” – by Dave Muoio

Disclosure: Tchesnokova reports submission of patent applications pertaining to tests for specific E. coli strains. Please see the full study for a list of all other authors’ relevant financial disclosures.