Scientists at the Sacramento County Public Health (SCPH) Laboratory have successfully introduced Deeplex, an advanced tuberculosis (TB) testing method, to Sacramento County and surrounding jurisdictions. The new DNA sequencing test can identify drug-resistant tuberculosis in as little as two days. Traditional tuberculosis drug susceptibility testing often takes several weeks.
“Tuberculosis is alive and well,” said Mark Pandori, director of the SCPH Laboratory. “It’s extremely serious. You can die of tuberculosis if it’s not treated properly, and we’re seeing increasing resistance to the medications used to treat it.”
Tuberculosis, commonly known as TB, spreads through the air and primarily affects the lungs. Public health experts consider rapid detection and treatment critical because untreated or improperly treated infections can continue spreading within communities.
“Due to the seriousness of TB, clinicians have had to initiate treatment right away without final drug test results,” said Pandori. “Now we can provide a definitive diagnosis and information about what drugs will work and what drugs will not within a few days, and the faster we can get a correct treatment onto someone, the less likely it’s going to spread.”
Clinicians have often begun tuberculosis treatment without complete laboratory confirmation because waiting weeks for final results can delay care. Providers had to make early treatment decisions without a full drug resistance profile. Some patients then later required major treatment changes after additional laboratory results became available.
“With this new test, we can take a sputum sample (mucus that comes up from the lungs when someone coughs deeply) and provide results for 13 drugs in about two days,” said Christopher Holden-Counts, assistant laboratory director for the SCPH Laboratory.
Inside the SCPH laboratory, scientists prepare every day for infectious disease threats most residents never see. They test for tuberculosis, HIV, measles and other infectious diseases. They support outbreak investigations across the region. They provide testing for community clinics who serve residents directly. They also maintain the capability to respond quickly when rare or dangerous pathogens emerge in Northern California.
“If you want to think about it in terms of government service, you have police trained torespond to emergencies and firefighters trained to respond to fires,” said Pandori. “We are trained and ready to respond to rare and highly specialized pathogens that come into the community. There are infectious disease organisms, not uncommonly seen in the geographical regions just east of the Sacramento area, that are very dangerous. Things such as plague, or hantavirus for example.”
Pandori has worked in laboratory science for more than three decades. He started in virology research focused primarily on HIV before moving into public health laboratory leadership roles in San Francisco, Alameda County and the State of Nevada. He joined Sacramento County after relocating with his wife and looking for a new opportunity in California.
Working alongside him is Holden-Counts, who began working in laboratories in 2016 and joined Sacramento County four years ago after completing graduate school during the COVID-19 pandemic. As a Northern California native who grew up in Vacaville, he said working in SCPH Laboratory feels personal.
Tuberculosis testing has traditionally posed major challenges for clinicians and laboratories. Confirming an infection and determining which drugs will successfully treat it requires growing the bacteria in a laboratory, a process that can take weeks. Drug susceptibility testing adds even more time before clinicians know whether a patient’s treatment plan is effective.
Scientists in France originally developed the Deeplex test, which has already seen use in parts of Europe and India. Public health laboratories in the United States adopted the technology more slowly because the testing requires specialized equipment, advanced DNA sequencing capability and extensive validation work.
The SCPH Laboratory expanded its DNA sequencing capabilities during the COVID-19 pandemic while helping track viral variants and emerging infectious disease threats. The laboratory used that investment to validate Deeplex locally and bring the test online in Sacramento County.
The laboratory team spent nearly a year validating the test and evaluating its accuracy, sensitivity and reliability before implementation.
“We were able to get it to work reliably,” said Holden-Counts. “It is the most sensitive thing we’ve ever seen.”
Pandori credited the laboratory staff for continuing to refine the process until they achieved the level of sensitivity needed to confidently run the test in Sacramento County.
“We’re really fortunate to have staff that wouldn’t let it go,” said Pandori.
The SCPH Laboratory already serves as a regional testing hub for several Northern California counties that do not operate their own public health laboratories, including Nevada, El Dorado and Placer counties. The laboratory currently performs measles testing for Shasta County and supports surrounding public health systems during staffing shortages and outbreak response efforts.
“Most people never see the work happening inside a public health laboratory but innovations like this directly protect the health and safety of our communities,” said Sacramento County Public Health Officer Dr. Phuong Luu. “This advancement helps patients receive the right treatment faster and strengthens our region’s ability to respond to serious infectious diseases.
Few laboratories in California currently offer advanced tuberculosis sequencing at this level, including many larger metropolitan regions. The addition of Deeplex testing could further expand Sacramento County’s role as a regional public health laboratory leader.
“If this continues to be successful, it’s possible we’ll be asked to offer this service well beyond Sacramento County’s borders,” said Pandori.
The SCPH laboratory team also sees broader potential for the sequencing technology beyond tuberculosis. Scientists are already exploring ways to apply similar DNA sequencing methods to other bacterial infections and future emerging disease threats.