Lab Matters Summer 2019 - Page 19

FROM THE BENCH With the Help of Automation, San Diego Rejoins PulseNet by Kim Krisberg, writer “Using PFGE, we could look at banding patterns, but with WGS we can do a full retina scan,” said Tracy Basler, a molecular scientist within the San Diego public health lab. “WGS is a total game-changer.” In 2012, San Diego’s local public health lab lost its funding for PulseNet testing, which meant suspected specimens had to be sent to the state lab instead. In a foodborne illness outbreak—when time is of the essence—it wasn’t an ideal situation. Last year, however, with whole genome sequencing (WGS) becoming the new gold standard for PulseNet, the lab saw a chance to get back in the game. In particular, staff saw a new opportunity to automate the testing process, allowing it to leverage its existing resources to generate even more foodborne illness data than before and without extra money or staff. The key? Welcoming the robot known as Biomek i-Series to the bench. “Onboarding automation has been a lot more complicated than we first realized, but the benefits are tremendous,” said Syreeta Steele, PhD, assistant laboratory director at the San Diego Health & Human Services Agency Public Health Laboratory. “It’s been extremely beneficial to our ability to participate in PulseNet.” A nationwide lab network for detecting, tracing and solving foodborne illness outbreaks, PulseNet is a central pillar in the county’s food safety system. For more than two decades, the network relied on pulsed-field gel electrophoresis (PFGE) to generate the DNA fingerprints that enable public health detectives to connect the dots between individual cases of illness to reveal and track larger outbreaks. But in 2012, the San Diego lab—a relatively small lab with a staff of about 30—lost its funding to continue PFGE testing for PulseNet, forcing it to turn to the California Department of Public Health Microbial Diseases Laboratory (MDL) to fill in the gap. But with the shift to WGS—which greatly amplifies the precision of testing results— the San Diego lab could automate part of the testing process and revive its PulseNet testing and participation. PublicHealthLabs @APHL With the new robot on board, the San Diego lab has been able to automate the process of preparing DNA fragments— typically known as library prep—for sequencing. The robot does all the prep work, Basler said, including converting DNA samples into smaller pieces and tagging them—a process that would have otherwise required dedicated lab staff and hours of hands-on work. Instead, the robot, which can process up to 96 specimens in a single run, works on its own over the course of a day, readying DNA samples for sequencing and eventual upload to PulseNet. “Our county is home to about 3 million people, so any time we had to refer isolates to MDL, it slowed things down,” Steele said. With the blessing and support of the staff at MDL and APHL, the PulseNet WGS protocols were validated and implemented. “Now we can test here in the (local) lab and get results much faster” Steele reported. Of course, automation isn’t as easy as ordering a robot and plugging it in. Basler said the lab’s new robot required an incredible amount of fine-tuning to make sure it could do the prep work as well as a trained laboratorian would. “It’s a pretty heavy learning curve,” she said. “Everything has to be exact— really perfect—and a lot goes into the verification phase. It’s quite time- consuming, but we kept at it. …It takes a lot of determination and a lot of repetition, but it’s been well worth it.” Molecular Scientist Tracy Basler checks samples in the Biomek-i-Series. Photo: San Diego County PHL integrating a robot into its WGS process; next, the lab has plans to expand its use to prepping Hepatitis C specimens for CDC’s Global Hepatitis Outbreak and Surveillance Testing (GHOST) program. Steele noted that while the San Diego lab isn’t the first to employ the help of a robot, the lab has added in enhancements that free up even more hands-on staff time. For example, the lab uses a specialized feeder—what Basler described as a “giant Pez dispenser”—to replenish the robot’s pipetting tips when needed. Such time-saving automation, Basler said, is the only reason the lab has been able to rejoin the PulseNet community. “We’re resource-strapped here and these are time-intensive processes, so automation is a huge help when it comes to efficiency,” Basler said. “Now, we can respond to and keep up with large foodborne outbreaks locally… It’s helped elevate the lab, even though our resources aren’t changing.” n DIGITAL EXTRA: Read more on the PulseNet transition to whole genome sequencing. The robot wasn’t purchased just for foodborne pathogen testing, but to eventually help automate all of the lab’s sequencing work, according to Basler. Re-booting the lab’s participation in PulseNet was only the lab’s first try at Summer 2019 LAB MATTERS 17