Public Health Laboratory

The Contra Costa Public Health Laboratory is a California State and Federally certified facility that provides high complexity testing services in the areas of bacteriology, parasitology , mycobacteriology, mycology, immunology, and virology. Microbiological examinations of food and water are also provided in support of Environmental Health Programs. Reference services are an integral part of the laboratory program.

The Public Health Laboratory and its branches are under the direction of the Contra Costa County Health Officer and are regulated by the Laboratory Field Services of the California State Department of Health Services.

Ordering Laboratory Tests

Laboratory tests may be requested by an authorized person, in writing, using laboratory test request form which is provided by the laboratory. Oral or written instructions for appropriate specimen collection and specimen mailing containers will be provided upon request. Records of test requisitions are retained for at least 2 years. Patient specimens must be accurately labeled to assure that accurate test results are reported.

Laboratory Forms

• Laboratory Requisition Slip
• Unusual Disease Case History Form
• NonDiagnostic General Health Assessment Renewal Form

Orthopox/Monkeypox Specimen Collection Instructions

The Contra Costa County Public Health Laboratory is accepting and forwarding received Orthopox/Monkeypox specimens to the California Department of Public Health- Viral and Rickettsial Disease Laboratory (CDPH-VRDL) for screening. If sending specimens through the Public Health Department/Laboratory for screening, please contact CoCoCD@cchealth.org for additional guidance. Additionally, all high-priority cases will be directed to CDPH-VRDL for screening.

Commercial and university laboratory facilities (i.e. LabCorp, Quest, Aegis, Stanford, etc) are also currently available to provide Orthopoxvirus screening for providers that have active contracts or agreements.

See more information regarding Monkeypox.

• Specimen Collection Instruction
• Viral and Rickettsial Disease Laboratory General Purpose Specimen Submittal Form
• Monkeypox Screening Form

Essential Tests to be Submitted to Public Health Laboratory

Specimens should be submitted to the Public Health Laboratory on patients suspected of having botulism, plague, rabies, typhoid fever, diphtheria, or who have culture positive isolates of Mycobacterium tuberculosis, Salmonella sps. or positive malaria blood films.

• Reportable Diseases -- Title 17, California Code of Regulations, §2500 (March 2020)
• Reportable Conditions: Notifications by Laboratories -- Title 17. California Code of Regulations, §2500 (March 2020)
• Guidance for Laboratories on Reporting Select Agent Test Requests and Results (January 2014)

Please see the following website for additional guidance on California Reportable Diseases and Conditions:

• cdph.ca.gov

Whole Genome Sequencing for SARS-CoV-2 positive specimens

The currently available COVID-19 vaccines have high efficacy for prevention of symptomatic SARS-CoV-2 infection. However, breakthrough cases among fully vaccinated people are expected. The Contra Costa Public Health Department is seeking to investigate whether these cases and other high-risk scenarios may be caused by particular SARS-CoV-2 variants or current Variants of Concern (VOC). As such, the department is encouraging clinicians and clinical laboratories located within Contra Costa County to forward positive specimens (≥500uL) for WGS that meet criteria.

WGS is not currently a validated assay and you will not receive laboratory reports from the Contra Costa Public Health Laboratory or California Department of Public Health (CDPH). However, the Contra Costa Public Health Department may reach out for purposes of Contact Tracing to control the spread of SARS-CoV-2 and certain variants.

Notification about cases and questions please call 925-370-5775.

• Vaccine Breakthrough: Person who has SARS-CoV-2 RNA detected by a molecular test (e.g., PCR or NAAT) on a respiratory specimen collected ≥14 days after completing the primary vaccination series (i.e., ≥14 days following receipt of the second dose in a 2-dose series or ≥14 days following receipt of one dose of a single-dose FDA-authorized COVID-19 vaccine). Symptomatic breakthrough cases (also referred to as Vaccine Breakthrough cases of interest [VBCI]) will be prioritized for WGS, but asymptomatic vaccine breakthrough cases can be reviewed to see if potential follow up with WGS is appropriate;
• Hospitalized Patients (or ICU Patients);
• Outbreaks with high attack rate in a given outbreak or more cases than expected;
• Concerns for variants due to drop in diagnostic assay target (ex: N target, ORF target, S target) or any marked difference in real-time RT-PCR viral target(s) cycle threshold values (CT);
• Concern for variants due to other clinical history, such as, patient is immunocompromised, prolonged infection, failed to improve after receiving monoclonal antibody, death, etc.;
• Travel Associated: (1) case with recent travel or (2) case with contact to someone that had recent international travel;
• Reinfection: positive SARS-CoV-2 PCR or NAAT >90 days after first positive test. (please submit original specimens from both original infection and subsequent infection.

AND

Original positive respiratory specimen must be available for WGS and the Cycle threshold (Ct) value ≤30 (if Ct available) or RLU ≥1150. (e.g. nasal or NP swabs in viral transport medium (VTM), saline, or molecular transport medium, Hologic Aptima media, sputa. Please note that dry swabs, are not acceptable for WGS.)

Sample Storage and Shipment:

Include a requisition form OR CDPH Specimen Submittal Form

• Patient Demographics: Name, DOB, description of symptoms and onset, clinical information (hospitalization, death, etc).
• Test Information: collection date, Ct ≤30 or or RLU ≥1150, COVID-19 test type, lab that performed test.
• Reason WGS is being requested. If Vaccine Breakthrough, please provide dates of vaccination and manufacturer.

For both WGS, please request the lab store the original positive sample or a portion of the original positive sample ( ≥500 uL) frozen until shipment and shipped on dry ice to the CCPHL. Please ship using the following:

Attn: Stephanie Trammell or Kelly Riddle
Contra Costa County Public Health Laboratory
2500 Alhambra Ave, Rm. 209
Martinez, CA 94553
925-370-5775

For additional information please see: cchealth.org/covid19/providers/

For questions regarding Contra Costa County's other COVID-19 surveillance efforts for which you are a participant, please contact Stephanie Trammell at Contra Costa Public Health Laboratory, stephanie.trammell@cchealth.org.

• SARS-CoV-2 surveillance submission form

Influenza

Contra Costa County participates in national Hospitalized Influenza Surveillance Program (FluSurv-NET) and would like to thank you for your ongoing collaboration and participation. Clinical respiratory specimens submitted to the Public Health Laboratory for PCR testing have enabled the Centers for Disease Control and Prevention (CDC) to monitor the types and subtypes of circulating influenza viruses.

Contra Costa Public Health Laboratory along with the CDC California Emerging Infections Program (CEIP) continues to request that all clinical laboratories in Contra Costa County collect and submit influenza specimens from patients who meet the following criteria:

• Hospitalized within 14 days of positive influenza result AND
• Positive result for influenza by rapid test; OR
• Positive type A result for influenza by molecular test, and no definitive influenza A subtype result available

Botulism

In adults, diagnosis is established by the demonstration of the specific toxin in the patient's serum or stool. In infants, diagnosis is established by identification of Clostridium botulinum organisms and/or toxin in the patient's stool specimen. Call 925-370-5775 for specific instructions.

Plague

Diagnosis is confirmed by culture of the causative agent, Yersinia pestis, from the patient's blood, buboes, spinal fluid or sputum and by a significant rise in antibody titer.

Rabies Tests

The Public Health Laboratory examines and tests various animals at high risk for rabies after contact with humans, domestic animals, and for surveillance purposes. Arrangements for animal testing are made through Animal Control, 925-646-2995 (Martinez), or 510-374-3966 (Pinole), and/or Communicable Disease Control 925-313-6740. A fee is charges to persons requesting an animal for rabies which is not required for Public Health control.

Typhoid Fever

A culture of the organism from which the diagnosis of typhoid fever is established must be submitted to the Public Health Laboratory for definitive identification. Following treatment, stool and urine specimens submitted for Public Health release of typhoid cases are to be sent to the Public Health Laboratory for culture and clearance.

Salmonellosis

A culture on which the diagnosis of salmonellosis (other than typhoid fever) has been established must be submitted to the Public Health Laboratory for definitive identification. Following treatment, stool specimens from individuals incertain occupations must be submitted to the Public Health Laboratory for culture and Public Health clearance.

Tuberculosis

Isolation and identification of acid fast bacilli and antibiotic susceptibility tests on Mycobacterium tuberculosis are available at the Public Health Laboratory. A culture on which the diagnosis of tuberculosis has been established must be submitted to the Public Health Laboratory for definitive diagnosis and drug susceptibility testing (if required). The name, address, and date of birth of the person from whom the specimen was obtained, the date the specimen was obtained, and the name, address and telephone number of the health care provider of the patient must be provided (Title 17, California Code of Regulations, Section 1075).

Malaria

Blood films for the detection of malaria parasites may be submitted to the Public Health Laboratory. Blood films on which the diagnosis of malaria has been established must be sent to the Public Health Laboratory for confirmation (Title 17, California Code of Regulations, Section 1075).

Food Poisoning and Water Pollution

Food and water specimens suspected of causing illness must be submitted to the Public Health Laboratory through the Communicable Disease Program 925-313-6740 or the Environmental Health Program 925-692-2500.

Sexually Transmitted Diseases (General)

Diagnostic services for syphilis include darkfields, RPR/VDRL and TP-PA confirmatory testing are available. Other diagnostic services include detection of gonorrhea and chlamydia by highly sensitive molecular assays and microscopic detection of genital infections by protozoa, fungi, and Gardnerella vaginalis. Providers may wish to refer patients to Public Health STD clinics in Richmond, Pittsburg, and Concord (see information on STD Program.

Routine Diagnostic Services Available

The Public Health Laboratory can provide, on request, a complete list of routine diagnostic services available to health care providers and associated fees. There are no charges for required tests, reference or referral services and specimens tested to control an outbreak. All other services have cost-charge rates.

New Diagnostic Services Available

The Public Health Laboratory has recently added many new and unique testing services including molecular diagnostic tests that utilize polymerase chain reaction (PCR) detection methods. These include Blood Lead Screening (venous blood or capillary blood), Human Immunodeficiency Virus Quantitation, Hepatitis C antibody screening and confirmation, Hepatitis C virus detection, and genotyping, and direct detection of Mycobacterium tuberculosis in sputum.

Referral Services

A variety of referral services are available through the Public Health Laboratory. Unique serology and culture tests performed by the State Microbial Diseases Laboratory (MDL), the State Viral and Rickettsial Diseases Laboratory (VRDL), and the Centers for Disease Control (CDC) must be accessed through the local Public Health Laboratory. A complete history should be submitted with the specimen to avoid any delays in testing. When specimens are submitted with complete information, turn around times for MDL/VRDL serology testing is usually two weeks and for CDC four weeks. Turn around time for culture specimens will vary.