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A Look into Advanced Molecular Tools Used by the CDC to Advance Public Health

“The short-term investigation of a tuberculosis outbreak can overwhelm state and local TB control program capacity; however, opportunities to interrupt ongoing transmission in vulnerable populations are important,” Benjamin Silk, PhD, said about his group’s work with molecular surveillance for recent TB transmission.
Since the LOTUS national surveillance program to detect large TB outbreaks in the US began as a pilot program in 2014, Dr. Silk and his colleagues have been stopping transmissions before they become outbreaks by using molecular surveillance and statistical methods that analyze the geospatial concentration of genotype-matched clusters.
While routine genotyping methods for outbreak control examine about 1% of the TB genome, Dr. Silk and his team are increasingly using whole genome sequencing (WGS), which analyzes around 90% of the genome and reveals how isolates are genetically related.
“Food production and distribution has really changed substantially over the last couple of decades in the United States. There are fewer food producers and they have wider distribution. So on average, the means our food is coming from farther away. There are also more ready-to-eat and industrially produced foods and we’re seeing more highly disseminated outbreaks where there are illnesses all over the country that may not be readily detectable at the local level and require national, state and federal coordination,” said Matthew Wise, PhD, MPH, in his talk about the impact of WGS on multistate enteric disease outbreak investigations.
The PulseNet national laboratory network that detects foodborne illness outbreaks uses pulsed-field gel electrophoresis (PFGE) DNA fingerprinting to identify bacteria that make people ill. But PFGE results, based on genetic information available at the cut sites of genome fragments, are not always correct, so PulseNet has begun testing organisms by WGS, which contains information from many more positions in the genome.
In one of several outbreaks Dr. Wise described, Listeria isolated from a sprout facility was closely related to five clinical isolates from listeriosis cases, and based on WGS with only limited epidemiologic data, the sprouts were removed from the market and the firm shut down.
“We’re detecting more clusters of listeriosis, we’re detecting them sooner; the number of outbreaks that have a food source identified has been going up; the median number of cases in this outbreak has actually been going down; and the number of cases that we are actually able to link to a specific food item is going up,” Dr. Wise said.

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