December 15, 2014
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Whole-genome sequencing may prevent, control hospital outbreaks

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Whole-genome sequencing may be a cost-effective means of preventing and controlling nosocomial infections in a timely manner, according to recent findings.

“Whole-genome sequencing of bacterial isolates provides a promising new method for investigating the epidemiology of outbreaks, particularly when coupled to clinical locational and temporal data,” researchers wrote in Genome Medicine.

The researchers investigated a 2011 outbreak of Acinetobacter baumannii at Queen Elizabeth Hospital in Birmingham, England. The outbreak, which lasted 80 weeks, occurred after the hospitalization of a military patient from Afghanistan who was carrying a novel strain of the bacterium.

During the outbreak, the researchers switched midway from using traditional methods of infection prevention and control to whole-genome sequencing. Using the Vitek 2 (bioMérieux) system, the researchers identified 114 multidrug-resistant Acinetobacter isolates from routine clinical samples. The isolates were tested for bacterial identification and antibiotic susceptibility, with multidrug resistance defined as resistance to three or more classes of antibiotics. The researchers determined that 74 isolates acquired from 49 patients and 10 environmental isolates were genomically similar enough to the reference outbreak strain — pulsotype 27 — to be considered part of the outbreak.

The new method also was able to effectively rule out 18 isolates from the outbreak. Of the isolates revealed to be part of the pulsotype 27 strain, the researchers identified 31 single nucleotide variants and seven genotypic clusters. Within-host diversity was documented in two patients, and this included combinations of related and unrelated strains.

The researchers were able to use a combination of whole-genome sequencing and epidemiological data to recreate potential transmission events that connected all but 10 of the patients, and established links between the clinical and environmental isolates. Improvements in environmental decontamination protocols were implemented after a contaminated bed and a burn unit were identified as vehicles of transmission.

The investigation suggests whole-genome sequencing may play a valuable role in preventing and controlling nosocomial infections, according to the researchers.

“[Whole-genome sequencing] is now poised to make an impact on hospital infection prevention and control, delivering cost-effective identification of routes of infection within a clinically relevant time frame and allowing infection control teams to track, and even prevent, the spread of drug-resistant hospital pathogens,” the researchers wrote.

Disclosure: The researchers report no relevant financial disclosures.