Study examines practicality of genome sequencing for salmonella surveillance

A recent study demonstrated the practicality of using rapid whole-genome sequencing for the surveillance of salmonella in a state public health laboratory.

The results of the study were published in the Center for Disease Control and Prevention's Emerging Infectious Diseases journal.

The study was conducted to determine whether genome sequencing could be used in real time in a public health laboratory to improve discrimination of outbreak clusters of salmonella. Sequencing was previously found to work in improving discrimination although its effectiveness in a real world situation was unknown.

A retrospective analysis investigated isolates from an outbreak of salmonella and found that additional cases could be attributed to the outbreak strain through the use of genome sequencing.

Another prospective analysis included 58 isolates obtained in 2012, including from an epidemiologically defined outbreak. Whole-genome sequencing identified additional isolates attributable to the outbreak but that differed from the outbreak-associated pulsed-field gel electrophoresis (PFGE) type.

Additional putative outbreak clusters were detected in both the prospective and retrospective analyses using genome sequencing.

Approximately 85 percent of salmonella isolates can be classified into five PFGE types. The method has limited discriminatory power, however, when it comes to outbreak detection.

Henk den Bakker, who led the study, is a research associate with Cornell University in New York.