Overall, the laboratory’s highest-volume service is latent TB testing, followed
by oral fluid 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 influenza 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 identification of nosocomial infections in immunosuppressed
• The laboratory is one of two facilities examining nucleic acid amplification
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.
Alameda County Laboratory group
Microbiologist Thanh Tran reviews testing data in the Mycobacteriology Lab Laboratory assistant Rene Gonzalez in the Mycobacteriology lab
• In September 2016, the laboratory completed a large validation study on the
use of next-generation WGS for bacteriologic identification. 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 identifies and characterizes bacterial species based on
whole genomic information. Said Pandori, “The benefits of that are logistical Challenge
Pandori’s major challenge of the moment is finding qualified (i.e., state-
certified) and motivated employees to fill vacancies, such as a currently open
Pandori has three major goals for the laboratory.
T he lab is a major center for mycology in Alameda County,
often dealing with identification of nosocomial infections in
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
finding, so far, was the identification 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.
• 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
• 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
• Last December, the laboratory successfully used WGS to characterize the
microbe at the center of a Streptococcus pneumoniae outbreak in Alameda
County. Laboratory findings informed the epidemiological investigation that
quickly resolved the outbreak.
Spring 2017 LAB MATTERS