DNA sequencing trialled at US public health lab

The tests are around the feasibility of using the technology in real-time in a public health laboratory instead of other techniques such as pulsed-field gel electrophoresis (PFGE) which has limited discriminatory power.

Small and affordable benchtop whole genome sequencing (WGS) equipment has made it possible for clinical and public health labs to invest in the technology.

New York on the front line​

Wadsworth is one of the first public health labs to have the technology, which places New York on the front lines of detecting foodborne pathogen outbreaks.

"Having this technology at our disposal will greatly enhance our capacity for protecting the public from foodborne illnesses, which sicken thousands of Americans every year​," said Acting Commissioner Howard Zucker.

“Knowing the exact source of an outbreak can prevent illness from spreading and prevent many people from getting sick." ​

Scientists at Wadsworth have been working with the Cornell University Food Safety Lab, who helped analyze the data, to demonstrate the effectiveness of the technology.

Researchers at the lab are applying the technology to follow outbreaks in real time to further test its utility in a public health laboratory.

Method evaluation​

A study published in the Centers for Disease Control and Prevention journal Emerging Infectious Diseases​ ​demonstrated that whole-genome cluster analysis of S. enterica serovar Enteritidis results in improved detection of clusters of common PFGE types and outbreak resolution.

Analysis of a dataset showed that all isolates associated with a long-term care facility (LTCF) outbreak in 2010 belonged to a well-supported clade with an average <1.0 SNP distance between all the isolates in the clade.

This clade is 78 single nucleotide polymorphisms (SNPs) distant from the nearest neighboring sporadic isolates, said the researchers.

“Additional clinical isolates obtained during the time of the outbreak from patients in surrounding communities not previously associated with the outbreak also belonged to the clade, which expanded the number of possible outbreak cases from seven to 16. ​

“Identification of these additional 9 matching isolates suggests a common contaminated source outside the LTCF. ​

“Knowledge of these cases at the time of the outbreak might have improved the chances of finding the outbreak source, which was never identified.”​

It took eight days to sequence and analyze the samples for the case study, and the lab has since hastened the process.

As it accumulates genome data and if technologies improve as expected, it may be possible to link sequenced samples to historical data and shorten the turnaround time to four days.

Challenges to address​

Many challenges need to be addressed before a WGS–based surveillance system can be implemented but pilot studies are under way, said the researchers.

“In addition to standardization of protocols and analyses, several questions still need to be resolved. What constitutes an epidemiologically meaningful phylogenetic cluster? ​

“Do circulating persistent clones confound this analysis? How will this information be reported to epidemiologists?”​

WGS is gaining traction in other states through the GenomeTrakr initiative sponsored by the US Food and Drug Administration (FDA). The FDA is providing equipment, reagents, funds for personnel, and training on the equipment to seven State Public Health Laboratories including New York.

In return the public health labs upload raw sequence data to a centralized site for analysis and clusters that appear are reported back to local labs and epidemiologists, for a quick, coordinated response.