(Bloomberg) — After salmonella poisoned people in Minnesota in 2014, state germ sleuths already had a suspicion of what the culprit might be: raw, stuffed chicken that had caused close to half a dozen earlier outbreaks.
The question was, where had it come from, and who still had it in their freezers? Detailed DNA analysis showed six people were infected with an identical salmonella germ found on meat labeled chicken Kiev. Using a technology called whole genome sequencing, Minnesota health officials were able to determine precisely which cases were linked to the outbreak and track the infections back to a manufacturer. A health alert was issued, product was pulled from shelves, tested and recalled. The outbreak was halted with only one hospitalization for salmonellosis.
Now state health labs want to use the same technology to identify even more dangerous and insidious bacterial strains: those with drug resistance.
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Computer analysis of complete genomes of bacteria is enabling disease-trackers to match strains collected from patients, food, animals and the environment, and identify outbreaks, as well as their likely source and mode of transmission. It’s giving scientists an earlier jump on emerging pathogens, especially those not stopped by life-saving antibiotics. Failure to act on drug-resistant infections will lead to 10 million extra deaths a year and cost the global economy $100 trillion by 2050, a report released by the U.K. government in February found.
“I don’t think you can overstate the severity of the risk of antibiotic resistance,” Tom Frieden, director of the Centers for Disease Control and Prevention, said in a telephone interview. “It is not just about the infections that people may get that are hard to treat — pneumonias, urinary tract infections, skin infections — it’s actually about the fabric of modern medicine, because we assume we can treat infections that come along with transplants, cancer chemotherapy and arthritis treatments, but that assumption is increasingly incorrect.”
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With antibiotic-resistant bacteria causing 2 million illnesses and about 23,000 deaths a year in the United States, the government is beefing up surveillance in public health labs across the country.
By 2018, it wants all states to have the sequencing capacity, with funds appropriated by Congress to support the purchase of next-generation devices, including platforms from San Diego-based Illumina Inc. and Thermo Fisher Scientific Inc.’s Carlsbad, Calif.-based Life Technologies unit. It’s a vital public health need, said Carlota Medus, an epidemiologist with the Minnesota Department of Health, who worked on the 2014 chicken Kiev case.
“Whole genome sequencing cuts out all the noise,” she said in a telephone interview. “It helps us know that what we’re seeing is real.”
Infections from stuffed chicken recurred twice in 2015, and one of them showed signs of drug resistance. Medus wants to use the power of whole genome sequencing to quickly identify which cases are connected — and the most virulent.
Researchers at the Washington-based Walter Reed Institute of Research last month reported using whole genome sequencing to find the first U.S. case of a bacterial infection harboring the so-called mcr-1 gene that renders powerless the last-resort drug colistin. The same gene also turned up in gut bacteria from a pig. The finding was made on a RS II unit, a so-called long-read sequencer from Menlo Park, Calif.-based Pacific Biosciences of California Inc., and a MiSeq benchtop sequencer from Illumina.
The new bioinformatics tools are replacing a less-precise technique for comparing DNA called pulsed-field gel electrophoresis, said Alfred DeMaria, Massachusetts’ state epidemiologist. The method uses an electrical field to push DNA fragments of different sizes into groups, so that different organisms create “fingerprint” patterns in the gel.
The technique is “becoming obsolete,” DeMaria said. “Everyone is using whole genome sequencing. We can recognize more subtle relationships between organisms. We can not only tell that two salmonella came from the same source, we can tell which of them has been around longer.”
CDC and its partner agencies demonstrated the utility of whole genome sequencing with a project that began in September 2013 in which gene-sequence data was coupled with epidemiological information from fresh cases of listeria, another bacterium that causes foodborne disease, to identify clusters and solve outbreaks.