Germ sleuths go high-tech in battle against drug resistance

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.

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 lifesaving 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."

With antibiotic-resistant bacteria causing 2 million illnesses and about 23,000 deaths a year in the U.S., 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 Illumina Inc. and Thermo Fisher Scientific Inc.'s 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 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 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 cannot 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.

"If you look at listeria, it's a real success story," CDC's Frieden said. "There are people alive today in America who would be dead if it was not for the advanced molecular detection program that we've had that's allowed us to quickly identify outbreaks and get contaminated products off the market."

"It's a new world out there," Frieden said. "We're really doing things which were almost unimaginable just a few years ago."

The program was so successful that the government decided to expand it to cover other foodborne pathogens, such as salmonella.

Data gathered from human, food and environmental sources can be shared among CDC's research partners on a cloud-based platform, he said.

"We are very excited about this and think it's going to teach us a lot," said Robert Tauxe, director of the CDC's division of foodborne, waterborne and environmental diseases in Atlanta. Last year, nine listeria outbreaks were detected, whereas only two to three were previously uncovered annually. "We are finding more outbreaks than we were before and we are finding them when they're smaller," he said.

The cost of the technology has fallen, making it more affordable for routine public health applications, Tauxe said. The MiSeq unit from Illumina costs about $100,000, much less than the more meticulous long-read devices from PacBio, which the CDC and Food and Drug Administration use to generate "gold-standard" references for outbreak detection and surveillance analyses. These can go for as much as $750,000.

Over the past four years, microbe sequencing has become an increasingly important business for San Diego-based Illumina, the biggest maker of machines that decode DNA. Work that began principally in research laboratories has frequently been applied more in state and U.S. health laboratories, said Dawn Barry, vice president for applied genomics.

"In about 2012, we started to see more appetite for genome subtyping and testing," she said in a telephone interview. "From there, it's really started to take off."

Jonas Korlach, Pacific Biosciences' chief scientific officer, said he's also seen a big increase in the use of whole-genome sequencing in foodborne diseases outbreaks.

"FDA sequences with PacBio to get a complete understanding of what they're dealing with," Korlach said. "That's a paradigm shift."