Lab Matters Spring 2017 - Page 35

member spotlight Testing 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 individuals. Success Stories • 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 microbiology position. Goals 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 immunosuppressed individuals. 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 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.” • 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. PublicHealthLabs @APHL Spring 2017 LAB MATTERS 33