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Alameda County, CA, like many communities in The Golden State, has
been inhabited by an evolving mix of peoples through the centuries.
First came the Ohlone Native Americans, who hunted on the lands
surrounding modern-day San Francisco Bay. They were followed, in turn, by
Spanish colonists, Mexican ranchers and a motley mix of American and Asian
portions of adjacent Contra Costa and Santa Clara Counties.
From the beginning, the county has had a symbiotic relationship with its
neighbor on the other side of San Francisco Bay. In the late 18th and early
19th centuries, Alameda County was a ferry and trolley car suburb of “Fog
City.” Since 1933, after the San Francisco–Oakland Bay Bridge linked the two
jurisdictions, commuters can travel back and forth entirely by car or bus (or
by underwater tube since 1967). Today, said Mark Pandori, PhD, HCLD(ABB),
director of the Alameda County Public Health Laboratory, the county has its
own, multi-faceted identity, although it remains linked to San Francisco.
Realizing a Technological Vision in Alameda
County, California
by Nancy Maddox, MPH, writer
Sky high housing prices, for example, are driving many San Franciscans into
East Bay, as the urban area immediately east of San Francisco Bay is known.
Rents in Oakland—Alameda County’s county seat and the largest East Bay
city—are rising faster than anywhere else in the country. Yet even with the
rising cost of living, Alameda County’s population is “perhaps more diverse
than any other Bay Area county,” said Pandori, with large African-American,
Asian, Latino and LGBTQ communities. The presence of the University of
adds to the mix.
Pandori said this diverse and peripatetic population of about 1.5 million
makes TB, HIV and sexually transmitted disease (STD) testing priorities for the
public health laboratory. “But what’s interesting,” he said, “is that beyond the
heavily urbanized zone, we have a huge rural zone east of the Oakland Hills.
There’s quite a lot of rabies out there—recently, all in bats—and some Lyme-
containing ticks in the southern end of the county.” The laboratory tests for
the rabies and speciates the ticks. The rural zone—easily over half of Alameda
County’s 821-square-mile area—is also home to a budding wine industry and,
importantly, a number of aquifers, wells, lakes and streams. Testing these local
waters, plus swimming pool water, supplies a major portion of the laboratory’s
business.
When Pandori assumed the directorship of the county’s public health
laboratory, he came with a “technological vision” that skewed toward advanced
molecular testing. Almost three years later, much of that vision has been
realized, with a heavy laboratory emphasis on PCR testing and whole genome
sequencing (WGS).
Facility
The Alameda County Public Health Laboratory occupies one of the most
distinctive laboratory facilities in the country—a three-story concrete, steel
“gigantic shock absorbers,” which encircle the building. The unusual structure
is the most visible sign of the subterranean Hayward Fault line that lies a mere
500 yards from the laboratory.
The building was erected in 2014 in a “pretty wooded glade” at the base of the
Oakland Hills, just “a stone’s throw away” from the acclaimed Oakland Zoo and
even nearer to Interstate 580, a major freeway traversing northern California.
lab, said Pandori, the security is “absolutely through the roof,” requiring entry
through four separate cardkey-locked doors just to reach the public health
has all the bells and whistles a modern public health laboratory demands,
Pandori, is “gorgeous.”
Director
Pandori was born in Philadelphia, but raised mostly in San Jose, CA. He earned
a BS in genetics from UC–Berkeley, and then decamped to Boston University,
where he developed HIV assays for a year. After that stint, Pandori returned
to the West Coast, earning a PhD in biomedical sciences from UC-San Diego
under the tutelage of John Guatelli, MD, and Douglas Richman, MD, two stars
of the HIV research community. A post-doctoral fellowship with Harvard
Medical School took him back to the East Coast, where he conducted viral
engineering for gene therapy at the Beth Israel Deaconess Medical Center, a
teaching hospital for the medical school. Pandori then worked as a post-doc
and instructor of medicine at Harvard Medical School for six years, before
another cross-country trip to California, where, in 2005, he became chief
microbiologist for the San Francisco Department of Public Health, working
under the direction of Sally Liska, DrPH. In 2009, he gained a joint position as
associate clinical professor of laboratory medicine at UC-San Francisco. And in
2010, after Liska’s retirement, he assumed the position of laboratory director.
The twin lures of a brand new laboratory and the opportunity to work with
an esteemed colleague, Erica Pan, MD, drew him to his current post in the
Alameda County Department of Public Health Laboratory in mid-2014.
Staff
time microbiologists (one at the PhD level), a laboratory supervisor (who is also
a DVM), two laboratory technicians and two administrators. Altogether, seven
currently one open microbiology position.
Revenue
The laboratory’s revenue comes from a mix of county general funds, grants
and billed laboratory tests.
What’s interesting is beyond the heavily urbanized zone,
we have a huge rural zone east of the Oakland Hills.
Alameda County Public Health Laboratory
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Testing
Overall, the laboratory’s highest-volume service is latent TB testing, followed
by oral uid HIV testing and testing of recreational and drinking water. Also
on the service menu is active TB testing, HIV RNA testing, STD testing (by PCR
and syphilis serology) and testing for in uenza and other respiratory agents
(by PCR). Thanks to the presence of a highly experienced mycologist on staff,
Steve Killian, the lab is a major center for mycology in Alameda County, often
dealing with identi cation of nosocomial infections in immunosuppressed
individuals.
Success Stories
• The laboratory is one of two facilities examining nucleic acid ampli cation
technologies for their ability to detect chlamydia and gonorrhea in rectal
and throat specimens, as part of a study led by the Duke Clinical Research
Institute and funded by the National Institutes of Health.
The lab is a major center for mycology in Alameda County,
often dealing with identification of nosocomial infections in
immunosuppressed individuals.
• In September 2016, the laboratory completed a large validation study on the
use of next-generation WGS for bacteriologic identi cation. Now, instead of
using traditional biochemical methods, it performs WGS on every sample
submitted for bacteriologic testing. Working in collaboration with David
Hess, PhD, of Santa Clara University, the laboratory developed a software
tool that rapidly identi es and characterizes bacterial species based on
whole genomic information. Said Pandori, “The bene ts of that are logistical
and informational. We have fewer biochemists on staff and less media to
maintain and do quality assurance on. We also have a massive amount of
data on organisms in our county. What does that mean? When we identify an
organism by WGS, we rapidly, automatically obtain information on subtype,
virulence factors (e.g., the presence or absence of Shiga toxin markers),
drug resistance markers and the relatedness of organisms.” One interesting
nding, so far, was the identi cation of a novel Neisseria meningitides that
presented as a sexually transmitted infection on a patient’s penis. As it
turned out, the N. meningitides contained gonococcal DNA.
• Last year, the laboratory served as a clinical trial site for a novel Treponema
pallidum serology assay—the automated rapid plasma reagin test, which will
soon be available commercially.
• Last December, the laboratory successfully used WGS to characterize the
microbe at the center of a Streptococcus pneumoniae outbreak in Alameda
County. Laboratory ndings informed the epidemiological investigation that
quickly resolved the outbreak.
Challenge
Pandori’s major challenge of the moment is nding quali ed (i.e., state-
certi ed) and motivated employees to ll vacancies, such as a currently open
microbiology position.
Goals
Pandori has three major goals for the laboratory.
• WGS: “The vision now is to see how far we can take our WGS efforts.
We want to follow in Wadsworth’s footsteps and see if we can use this
technology for TB drug susceptibility testing. That would give us a detailed
analysis of all TB organisms, including all of the drug-susceptibility data at
once at the time of culture and simultaneous with molecular epidemiology
data.”
• Establishing electronic ordering and results reporting via direct interfaces
with customers, including a user-friendly web interface where customers can
log in to review the status of a specimen.
• Neisseria: “It seems there might be genetic interplay amongst the organisms
in that genus. For example, N. gonorrhoeae seems to have gained some drug
resistance by mixing with other Neisseria in the throat. We want to study the
emergence of this potentially new public health threat.”
• Funding: “I’d like to expand our billing capabilities so we can bill additional
insurers.”
Alameda County Laboratory group
Microbiologist Thanh Tran reviews testing data in the Mycobacteriology Lab Laboratory assistant Rene Gonzalez in the Mycobacteriology lab