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Whole-Genome Sequencing Detects Outbreaks Faster

Bench-top whole-genome sequencing platforms provided accurate detection of gram-negative bacteria at speeds faster than traditional identification, researchers found.

Whole-gene sequencing accurately discriminated between outbreak and non-outbreak isolates of Enterococcus faecium and Enterobacter cloacae when compared with conventional gene typing, and the results took less than a day, according to Sharon Peacock, PhD, of the University of Cambridge in England.

The platform also showed it was able to determine whether resistance of the bacteria was attributable to the presence of carbapenemases or other resistance mechanisms, they wrote online in JAMA Internal Medicine.

Rapid detection and effective treatment of gram-negative bacteria are paramount in controlling the emergence and spread of such threats, though the data required to fight these bugs are usually collected retrospectively and can fail to impact disease control, they noted.

They added that the most recent generation of bench-top DNA sequencing platforms "can provide an accurate whole-genome sequence for a broad range of bacteria in less than a day."

The authors compared whole-genome sequencing with current standard clinical microbiology investigation practices for nosocomial outbreaks due to multidrug-resistant bacteria in one outbreak of vancomycin-resistant E. faecium and in one outbreak of carbapenem-resistant E. cloacae.

The researchers collected clinical specimens and tested them for antimicrobial susceptibility through disk diffusion techniques and received additional testing through a reference laboratory, where needed.

In the E. cloacae outbreak, three patients at Cambridge University Hospitals NHS Foundation Trust tested positive for the bug. Isolates were sequenced along with four carbapenem-susceptible E. cloacae samples from patients in other wards as a control.

A single-nucleotide polymorphism-generated phylogenetic tree showed isolates from the outbreak were more closely related to each other than those from the control samples. Further analysis showed that the first two patients in the outbreak likely spread the bug between each other or from a third patient. The third patient infected with the drug-resistant strain was shown to likely not have received the same bug as the first two patients.

The study of the E. faecium outbreak included three children with hematologic malignancies at the same hospital. The authors sequenced seven isolates from the three patients and another vancomycin-resistant isolate from a fourth, unrelated patient from 7 weeks prior to the outbreak.

The phylogenetic tree of these samples showed two of the samples were related, while one sample from the three children and the control sample were unrelated to the others, "despite an overlap in time and place" in the third child.

Additional sampling of the related cases showed "that these isolates represented sampling from a larger underlying population," which they noted "was not possible to determine whether the second episode of vancomycin-resistant E. faecium bacteremia in one patient was due to relapse by the same isolate, or re-infection from the other."

An accompanying editorial by Garth Ehrlich, PhD, and J. Christopher Post, MD, PhD, both from the Allegheny-Singer Research Institute in Pittsburgh, noted that current methods are inadequate and that use of genome sequencing platforms will "revolutionize data acquisition for theranostics and tracking of outbreaks."

"Whole genome sequencing is critical as a diagnostic tool because the vast majority of bacterial pathogens possess a supragenome that is much larger than the genome of any individual strain," they wrote, adding that whole-genome sequencing will improve understanding of "rates and breadth of horizontal gene flow within and between species, the evolution of new virulence trails, and the role of host genetics in host-pathogen interactions."

The authors also said that the adoption of this technology can provide an outlet for sequencing to regional and local laboratories that provides higher-quality output at a rate faster than current techniques.

They also cautioned that future prospective studies are needed to show a cost-benefit analysis of using these techniques for individual patients and in public health.

Reference: Peacock SJ, et al "Rapid bacterial whole-genome sequencing to enhance diagnostic and public health microbiology" JAMA Intern Med 2013; DOI: 10.1001/jamainternmed.2013.7734.


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