Public Health Update

San Joaquin County Public Health Laboratory: Reinventing the Public Health Laboratory in a Post-Pandemic World

San Joaquin County Public Health Laboratory (SJCPHL) is a state and federal certified CLIA diagnostic and ELAP accredited high complexity laboratory. The SJCPHL is an essential bridge between the local community and public health, providing testing for our health department programs, local hospitals, correctional facilities, county clinics, health departments from other counties, and more. With so many PH laboratories closing, and regionalization becoming the new norm, how does a PH Laboratory remain viable in the current economic climate? The SJCPHL in Stockton has managed to embrace the traditional role of a Public Health Lab while still looking ahead by incorporating new technologies and “lab friendly” instrumentation.

New facility: Room to grow

In November 2022, the laboratory transitioned to a new state of the art facility with approximately 4,800 square feet on the same campus at 1601 E. Hazelton.

Diverse testing menu: Keeping the testing local

In 2022 SJCPHL performed approximately 30,000 tests from a diversified test menu including:

• Special Bacteriology: Reference level testing to isolate and identify organisms responsible for: Botulism, Plague, Cholera and Typhoid, and for Campylobacter, Shigella, E. coli 0157:H7 and Salmonella. Clearance testing for Salmonella, Shigella and Shiga Toxin producing organisms. Clearance testing allows Health Departments to determine when it is safe for the ill individuals to return to a daycare, school, or workplace.

• Examinations for sexually transmitted diseases including Chlamydia, Gonorrhea, Trichomonas, HIV, Herpes, and Syphilis

• HIV viral load testing to monitor the level of HIV virus in a patient’s blood.

• HCV viral Load testing to monitor the level of Hepatitis C virus (HCV) in a patient’s blood.

• Full Mycology Laboratory.

• Parasite testing for suspected blood parasites that cause diseases like Malaria, Babesiosis and others. Performing testing for intestinal parasites like Giardia, Entamoeba histolytica, Cryptosporidium and others.

• TB isolation and identification using DNA probes and rapid methods for Mycobacterium tuberculosis. We also perform susceptibility testing for Mycobacterium tuberculosis with results that aid physicians in determining the most efficient drug regimen for the patient. SJCPHL can offer our Quantiferon Assay to detect latent Mycobacterium tuberculosis infections.

• Molecular tests for Norovirus, Enterovirus, Flavivirus, Influenza, Herpes, Measles, Mumps, Gonorrhea, Chlamydia, Shiga toxin, Bordetella pertussis as well as a molecular assay for respiratory viruses with multiple organism targets.

• Comprehensive COVID-19 (SARS-CoV-2) testing including high-throughput PCR, serology, and surveillance on the suspect variants using Whole Genome Sequencing (WGS).

• Testing animals for Rabies. Unlike a Clinical Laboratory, one unique aspect of a Public Health Laboratory is the ability to perform Rabies testing. Timely testing of animals suspected of having Rabies is important for quick administration of prophylaxis, if needed, to save a person from unnecessary treatment and to provide them peace of mind.

• Food poisoning examinations looking for organisms such as Staphylococcus, Salmonella, Listeria, and other organisms that contaminate food products.

• Environmental Testing including microbiological analysis of drinking water (also available to the public), labor camp water and dairy water.

Laboratory Response Network:

SJPHL serves as the Laboratory Response Network (LRN) Reference Laboratory for San Joaquin as well as the counties of Alpine, Amador, Calaveras, Mariposa, Mono, Stanislaus, and Tuolumne. The LRN B is an integrated network of public health laboratories that can respond to bioterrorism threats, emerging/re-emerging infectious diseases, antibiotic resistant agents, and other public health emergencies. SJCPHL has a dedicated BSL3 suite equipped with specialized equipment and highly trained staff to rule-out suspect Bioterrorism agents such as Anthrax, Plague, Mpox, Tularemia, Brucella, Burkholderia, and Ricin. The BSL3 lab provides high-level containment and enhanced safety features. During the COVID-19 pandemic and Mpox outbreaks, SJCPHL was one of the diagnostic labs providing localized testing and provided guidance to the local sentinel laboratories and health departments within the catchment area.

Ease of Access:

SJCPHL has recently expanded the laboratory information feature by adding a user-friendly web portal application free of charge to clients. This modernization allows for faster turnaround times, reduces manual data entry errors and improves efficiency. The portal does require a brief training session so please contact the Lab for details. Phone: 209-4683460 or email: phlcopiaoutreach@sjcphs.org

Building partnerships: Sharing our expertise

SJCPHL works with groups within Public Health Services (PHS), our other health partners in San Joaquin County, and our health partners in the other counties we proudly serve. This includes:

• Working closely with physicians, nurses, and Environmental Health specialists to facilitate the diagnosis and control of infectious disease. We offer technical consultation for specimen collection, shipping and packaging, microbiological techniques and procedures, laboratory safety, quality assurance and epidemiology.

• Providing packaging and shipping training for both

Category A, Infectious Substances and Category B, Biological Substances to the sentinel laboratories in our catchment area.

• Hosting the Public Health Microbiologist Training Program, the LabAspire Assistant director fellowship and a Public Health rotation for the future Clinical Laboratory Scientists trainees from our local hospitals.

Surveillance:

A powerful tool for public health

SJCPHL participates in several surveillance programs such as the National Respiratory and Enteric Virus Surveillance System (NREVSS). With timely collection of data, we can monitor disease circulation patterns and changes in disease occurrence (outbreaks), and can guide public health action.

New technologies: Competing through innovation

Whole Genome Sequencing: Our COVID-19 (SARS-CoV-2) as well as bacterial WGS testing will expand with a high throughput instrument from Clear Lab Dx. This new user friendly instrument will allow us to analyze cases with quick turnaround time and generate a genetic fingerprint of the bacteria or virus from the patient. This will enable the health department to find clusters of disease that represent unrecognized outbreaks.

MALDI-TOF: Identification of bacteria and fungi by traditional methods can be a time consuming and complex task. Emerging technology like the Matrix-Assisted Laser Desorption/ionization TimeOf-Flight (MALDI-TOF) found on our new Bruker MALDI Biotyper system will allow our laboratory to identify organisms more quickly and efficiently, especially Mycobacteria species, therefore guiding treatment options.

Carbapenem-resistant Enterobacterales: Carbapenem-resistant (CRE) are strains of bacteria that are resistant to an antibiotic class (carpabenem) used to treat severe infections. SJCPHL will soon bring on the Cepheid Carbapenemase Resistance Molecular Test (Xpert Carba-R) to our Cepheid instrument. Performing this assay in house will reduce result turn-around time, direct patient treatment and help prevent the spread of these drug-resistant organisms in our community.

Contributors:

H. Kaur, Public Health Laboratory Director

S. Stewart, Supervising Public Microbiologist

S. Hazari, Supervising Public Microbiologist

M. Paniagua Alexander, Senior Public Health Microbiologist

R. Patel, Senior Public Health Microbiologist

J. Bernal, Senior Public Health Microbiologist